tomo: tomo.py annotate

annotate tomo.py @ 61:75dd6e15f628 draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55"

author	rv43
date	Wed, 17 Aug 2022 12:11:20 +0000
parents	26f99fdd8d61
children	98a83f03d91b

rev	line source
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1 #!/usr/bin/env python3
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	3 # -- coding: utf-8 --
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	4 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	5 Created on Fri Dec 10 09:54:37 2021
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	6
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	7 @author: rv43
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	8 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	9
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	10 import logging
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	11
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	12 import os
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	13 import sys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	14 import getopt
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	15 import re
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	16 import io
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	17 import argparse
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	18 import numpy as np
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	19 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	20 import numexpr as ne
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	21 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	22 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	23 import multiprocessing as mp
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	24 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	25 import scipy.ndimage as spi
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	26 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	27 pass
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	28 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	29 import tomopy
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	30 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	31 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	32 from time import time
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	33 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	34 from skimage.transform import iradon
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	35 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	36 pass
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	37 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	38 from skimage.restoration import denoise_tv_chambolle
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	39 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	40 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	41
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	42 from detector import TomoDetectorConfig
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	43 from fit import Fit
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	44 #from msnctools.general import illegal_value, is_int, is_num, is_index_range, get_trailing_int, \
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	45 from general import illegal_value, is_int, is_num, is_index_range, get_trailing_int, \
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	46 input_int, input_num, input_yesno, input_menu, findImageFiles, loadImageStack, clearPlot, \
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	47 draw_mask_1d, quickPlot, clearImshow, quickImshow, combine_tiffs_in_h5, Config
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	48 from general import selectImageRange, selectImageBounds
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	49
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	50 # the following tomopy routines don't run with more than 24 cores on Galaxy-Dev
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	51 # - tomopy.find_center_vo
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	52 # - tomopy.prep.stripe.remove_stripe_fw
46 d73e715e975b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac" rv43 parents: 45 diff changeset	53 num_core_tomopy_limit = 24
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	54
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	55 class set_numexpr_threads:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	56
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	57 def __init__(self, num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	58 cpu_count = mp.cpu_count()
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	59 logging.debug(f'start: num_core={num_core} cpu_count={cpu_count}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	60 if num_core is None or num_core < 1 or num_core > cpu_count:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	61 self.num_core = cpu_count
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	62 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	63 self.num_core = num_core
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	64 logging.debug(f'self.num_core={self.num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	65
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	66 def __enter__(self):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	67 self.num_core_org = ne.set_num_threads(self.num_core)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	68 logging.debug(f'self.num_core={self.num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	69
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	70 def __exit__(self, exc_type, exc_value, traceback):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	71 ne.set_num_threads(self.num_core_org)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	72
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	73 class ConfigTomo(Config):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	74 """Class for processing a config file.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	75 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	76
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	77 def __init__(self, config_file=None, config_dict=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	78 super().__init__(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	79
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	80 def _validate_txt(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	81 """Returns False if any required config parameter is illegal or missing.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	82 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	83 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	84
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	85 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	86 pars_required = ['tdf_data_path', 'tbf_data_path', 'detector_id']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	87 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	88 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	89 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	90 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	91 self.detector_id = self.config.get('detector_id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	92
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	93 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	94 self.tdf_data_path = self.config.get('tdf_data_path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	95
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	96 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	97 self.tbf_data_path = self.config.get('tbf_data_path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	98
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	99 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	100 self.num_tomo_stacks = self.config.get('num_tomo_stacks', 1)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	101 if not is_int(self.num_tomo_stacks, 1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	102 self.num_tomo_stacks = None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	103 illegal_value(self.num_tomo_stacks, 'num_tomo_stacks', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	104 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	105 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	106
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	107 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	108 tomo_data_paths_indices = sorted({key:value for key,value in self.config.items()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	109 if 'tomo_data_path' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	110 if len(tomo_data_paths_indices) != self.num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	111 logging.error(f'Incorrect number of tomography data path names in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	112 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	113 self.tomo_data_paths = [tomo_data_paths_indices[i][1] for i in range(self.num_tomo_stacks)]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	114 self.tomo_data_indices = [get_trailing_int(tomo_data_paths_indices[i][0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	115 if get_trailing_int(tomo_data_paths_indices[i][0]) else None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	116 for i in range(self.num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	117 tomo_ref_height_indices = sorted({key:value for key,value in self.config.items()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	118 if 'z_pos' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	119 if self.num_tomo_stacks > 1 and len(tomo_ref_height_indices) != self.num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	120 logging.error(f'Incorrect number of tomography reference heights in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	121 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	122 if len(tomo_ref_height_indices):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	123 self.tomo_ref_heights = [
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	124 tomo_ref_height_indices[i][1] for i in range(self.num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	125 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	126 self.tomo_ref_heights = [0.0]*self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	127
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	128 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	129 self.start_theta = self.config.get('start_theta', 0.)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	130 if not is_num(self.start_theta, 0.):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	131 illegal_value(self.start_theta, 'start_theta', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	132 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	133 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	134 self.end_theta = self.config.get('end_theta', 180.)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	135 if not is_num(self.end_theta, self.start_theta):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	136 illegal_value(self.end_theta, 'end_theta', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	137 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	138 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	139 self.num_thetas = self.config.get('num_thetas')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	140 if not (self.num_thetas is None or is_int(self.num_thetas, 1)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	141 illegal_value(self.num_thetas, 'num_thetas', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	142 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	143 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	144 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	145
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	146 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	147
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	148 def _validate_yaml(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	149 """Returns False if any required config parameter is illegal or missing.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	150 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	151 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	152
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	153 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	154 pars_required = ['dark_field', 'bright_field', 'stack_info', 'detector']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	155 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	156 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	157 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	158 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	159 self.detector_id = self.config['detector'].get('id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	160
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	161 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	162 self.tdf_data_path = self.config['dark_field'].get('data_path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	163
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	164 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	165 self.tbf_data_path = self.config['bright_field'].get('data_path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	166
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	167 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	168 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	169 self.num_tomo_stacks = stack_info.get('num', 1)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	170 if not is_int(self.num_tomo_stacks, 1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	171 self.num_tomo_stacks = None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	172 illegal_value(self.num_tomo_stacks, 'num_tomo_stacks', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	173 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	174 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	175
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	176 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	177 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	178 if stacks is None or len(stacks) is not self.num_tomo_stacks:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	179 illegal_value(stacks, 'stacks', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	180 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	181 self.tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	182 self.tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	183 self.tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	184 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	185 self.tomo_data_paths.append(stack.get('data_path'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	186 self.tomo_data_indices.append(stack.get('index'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	187 self.tomo_ref_heights.append(stack.get('ref_height'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	188
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	189 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	190 theta_range = self.config.get('theta_range')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	191 if theta_range is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	192 self.start_theta = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	193 self.end_theta = 180.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	194 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	195 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	196 self.start_theta = theta_range.get('start', 0.)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	197 if not is_num(self.start_theta, 0.):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	198 illegal_value(self.start_theta, 'theta_range:start', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	199 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	200 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	201 self.end_theta = theta_range.get('end', 180.)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	202 if not is_num(self.end_theta, self.start_theta):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	203 illegal_value(self.end_theta, 'theta_range:end', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	204 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	205 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	206 self.num_thetas = theta_range.get('num')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	207 if self.num_thetas and not is_int(self.num_thetas, 1):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	208 illegal_value(self.num_thetas, 'theta_range:num', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	209 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	210 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	211 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	212
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	213 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	214
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	215 def validate(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	216 """Returns False if any required config parameter is illegal or missing.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	217 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	218 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	219
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	220 # Check work_folder (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	221 work_folder = os.path.abspath(self.config.get('work_folder', ''))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	222 if not os.path.isdir(work_folder):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	223 illegal_value(work_folder, 'work_folder', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	224 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	225 logging.info(f'work_folder: {work_folder}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	226
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	227 # Check data filetype (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	228 self.data_filetype = self.config.get('data_filetype', 'tif')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	229 if not isinstance(self.data_filetype, str) or (self.data_filetype != 'tif' and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	230 self.data_filetype != 'h5'):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	231 illegal_value(self.data_filetype, 'data_filetype', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	232
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	233 if self.suffix == '.yml' or self.suffix == '.yaml':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	234 is_valid = self._validate_yaml()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	235 elif self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	236 is_valid = self._validate_txt()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	237 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	238 logging.error(f'Undefined or illegal config file extension: {self.suffix}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	239 is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	240
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	241 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	242 if self.tdf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	243 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	244 if isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	245 if not os.path.isabs(self.tdf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	246 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	247 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	248 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	249 illegal_value(tdf_data_fil, 'tdf_data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	250 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	251 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	252 if isinstance(self.tdf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	253 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	254 f'{work_folder}/{self.tdf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	255 elif isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	256 if not os.path.isabs(self.tdf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	257 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	258 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	259 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	260 illegal_value(self.tdf_data_path, 'tdf_data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	261 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	262 logging.info(f'dark field images path = {self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	263
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	264 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	265 if self.tbf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	266 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	267 if isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	268 if not os.path.isabs(self.tbf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	269 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	270 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	271 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	272 illegal_value(tbf_data_fil, 'tbf_data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	273 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	274 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	275 if isinstance(self.tbf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	276 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	277 f'{work_folder}/{self.tbf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	278 elif isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	279 if not os.path.isabs(self.tbf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	280 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	281 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	282 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	283 illegal_value(self.tbf_data_path, 'tbf_data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	284 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	285 logging.info(f'bright field images path = {self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	286
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	287 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	288 tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	289 tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	290 tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	291 for data_path, index, ref_height in zip(self.tomo_data_paths, self.tomo_data_indices,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	292 self.tomo_ref_heights):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	293 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	294 if isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	295 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	296 data_path = os.path.abspath(f'{work_folder}/{data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	297 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	298 illegal_value(data_path, 'stack_info:stacks:data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	299 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	300 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	301 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	302 if isinstance(data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	303 data_path = os.path.abspath(f'{work_folder}/{data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	304 elif isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	305 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	306 data_path = os.path.abspath(f'{work_folder}/{data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	307 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	308 illegal_value(data_path, 'stack_info:stacks:data_path', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	309 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	310 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	311 tomo_data_paths.append(data_path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	312 if index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	313 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	314 logging.error('Missing stack_info:stacks:index in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	315 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	316 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	317 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	318 index = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	319 elif not isinstance(index, int):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	320 illegal_value(index, 'stack_info:stacks:index', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	321 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	322 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	323 tomo_data_indices.append(index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	324 if ref_height is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	325 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	326 logging.error('Missing stack_info:stacks:ref_height in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	327 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	328 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	329 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	330 ref_height = 0.
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	331 elif not is_num(ref_height):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	332 illegal_value(ref_height, 'stack_info:stacks:ref_height', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	333 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	334 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	335 # Set reference heights relative to first stack
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	336 if (len(tomo_ref_heights) and is_num(ref_height) and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	337 is_num(tomo_ref_heights[0])):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	338 ref_height = (round(ref_height-tomo_ref_heights[0], 3))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	339 tomo_ref_heights.append(ref_height)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	340 tomo_ref_heights[0] = 0.0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	341 logging.info('tomography data paths:')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	342 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	343 logging.info(f' {tomo_data_paths[i]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	344 logging.info(f'tomography data path indices: {tomo_data_indices}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	345 logging.info(f'tomography reference heights: {tomo_ref_heights}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	346
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	347 # Update config in memory
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	348 if self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	349 self.config = {}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	350 dark_field = self.config.get('dark_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	351 if dark_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	352 self.config['dark_field'] = {'data_path' : self.tdf_data_path}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	353 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	354 self.config['dark_field']['data_path'] = self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	355 bright_field = self.config.get('bright_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	356 if bright_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	357 self.config['bright_field'] = {'data_path' : self.tbf_data_path}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	358 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	359 self.config['bright_field']['data_path'] = self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	360 detector = self.config.get('detector')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	361 if detector is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	362 self.config['detector'] = {'id' : self.detector_id}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	363 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	364 detector['id'] = self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	365 self.config['work_folder'] = work_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	366 self.config['data_filetype'] = self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	367 stack_info = self.config.get('stack_info')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	368 if stack_info is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	369 stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	370 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	371 stacks.append({'data_path' : tomo_data_paths[i], 'index' : tomo_data_indices[i],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	372 'ref_height' : tomo_ref_heights[i]})
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	373 self.config['stack_info'] = {'num' : self.num_tomo_stacks, 'stacks' : stacks}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	374 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	375 stack_info['num'] = self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	376 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	377 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	378 stack['data_path'] = tomo_data_paths[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	379 stack['index'] = tomo_data_indices[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	380 stack['ref_height'] = tomo_ref_heights[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	381 if self.num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	382 theta_range = {'start' : self.start_theta, 'end' : self.end_theta,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	383 'num' : self.num_thetas}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	384 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	385 theta_range = {'start' : self.start_theta, 'end' : self.end_theta}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	386 self.config['theta_range'] = theta_range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	387
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	388 # Cleanup temporary validation variables
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	389 del self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	390 del self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	391 del self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	392 del self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	393 del self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	394 del self.tomo_data_paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	395 del self.tomo_data_indices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	396 del self.tomo_ref_heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	397 del self.start_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	398 del self.end_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	399 del self.num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	400
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	401 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	402
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	403 class Tomo:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	404 """Processing tomography data with misalignment.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	405 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	406
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	407 def __init__(self, config_file=None, config_dict=None, config_out=None, output_folder='.',
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	408 log_level='INFO', log_stream='tomo.log', galaxy_flag=False, test_mode=False,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	409 num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	410 """Initialize with optional config input file or dictionary
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	411 """
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	412 self.num_core = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	413 self.config_out = config_out
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	414 self.output_folder = output_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	415 self.galaxy_flag = galaxy_flag
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	416 self.test_mode = test_mode
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	417 self.save_plots = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	418 self.save_plots_only = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	419 self.cf = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	420 self.config = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	421 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	422 self.tdf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	423 self.tbf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	424 self.tomo_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	425 self.tomo_recon_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	426
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	427 # Validate input parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	428 if config_file is not None and not os.path.isfile(config_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	429 raise OSError(f'Invalid config_file input {config_file} {type(config_file)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	430 if config_dict is not None and not isinstance(config_dict, dict):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	431 raise ValueError(f'Invalid config_dict input {config_dict} {type(config_dict)}')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	432 if self.config_out is not None and not isinstance(self.config_out, str):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	433 raise OSError(f'Invalid config_out input {self.config_out} {type(self.config_out)}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	434 if not os.path.isdir(output_folder):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	435 os.mkdir(os.path.abspath(output_folder))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	436 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	437 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	438 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	439 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	440 if not os.path.isabs(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	441 log_stream = f'{output_folder}/{log_stream}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	442 if not isinstance(galaxy_flag, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	443 raise ValueError(f'Invalid galaxy_flag input {galaxy_flag} {type(galaxy_flag)}')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	444 if not isinstance(self.test_mode, bool):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	445 raise ValueError(f'Invalid test_mode input {self.test_mode} {type(self.test_mode)}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	446 if not isinstance(num_core, int) or num_core < -1 or num_core == 0:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	447 raise ValueError(f'Invalid num_core input {num_core} {type(num_core)}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	448 if num_core == -1:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	449 self.num_core = mp.cpu_count()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	450 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	451 self.num_core = num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	452
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	453 # Set log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	454 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	455 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	456 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	457 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	458 logging.basicConfig(filename=f'{log_stream}', filemode='w',
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	459 format=logging_format, level=logging.INFO, force=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	460 #format=logging_format, level=logging.WARNING, force=True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	461 elif isinstance(log_stream, io.TextIOWrapper):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	462 #logging.basicConfig(filemode='w', format=logging_format, level=logging.WARNING,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	463 logging.basicConfig(filemode='w', format=logging_format, level=logging.INFO,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	464 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	465 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	466 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	467 logging.warning('Ignoring log_level argument in test mode')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	468 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	469 level = getattr(logging, log_level.upper(), None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	470 if not isinstance(level, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	471 raise ValueError(f'Invalid log_level: {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	472 if log_stream is sys.stdout:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	473 logging.basicConfig(format=logging_format, level=level, force=True,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	474 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	475 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	476 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	477 logging.basicConfig(filename=f'{log_stream}', filemode='w',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	478 format=logging_format, level=level, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	479 elif isinstance(log_stream, io.TextIOWrapper):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	480 logging.basicConfig(filemode='w', format=logging_format, level=level,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	481 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	482 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	483 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	484 stream_handler = logging.StreamHandler()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	485 logging.getLogger().addHandler(stream_handler)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	486 stream_handler.setLevel(logging.WARNING)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	487 stream_handler.setFormatter(logging.Formatter(logging_format))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	488
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	489 # Check/set output config file name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	490 if self.config_out is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	491 self.config_out = f'{self.output_folder}/config.yaml'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	492 elif (self.config_out is os.path.basename(self.config_out) and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	493 not os.path.isabs(self.config_out)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	494 self.config_out = f'{self.output_folder}/{self.config_out}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	495
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	496 # Create config object and load config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	497 self.cf = ConfigTomo(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	498 if not self.cf.load_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	499 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	500 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	501
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	502 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	503 assert(self.output_folder == '.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	504 assert(self.test_mode is False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	505 self.save_plots = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	506 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	507 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	508 # Input validation is already performed during link_data_to_galaxy
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	509
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	510 # Check config file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	511 self.is_valid = self.cf.validate()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	512
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	513 # Load detector info file
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	514 df = TomoDetectorConfig(self.cf.config['detector']['id'])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	515
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	516 # Check detector info file parameters
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	517 if df.valid:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	518 pixel_size = df.pixel_size
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	519 num_rows, num_columns = df.dimensions
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	520 if not pixel_size or not num_rows or not num_columns:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	521 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	522 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	523 pixel_size = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	524 num_rows = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	525 num_columns = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	526 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	527
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	528 # Update config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	529 self.cf.config['detector']['pixel_size'] = pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	530 self.cf.config['detector']['rows'] = num_rows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	531 self.cf.config['detector']['columns'] = num_columns
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	532 logging.debug(f'pixel_size = self.cf.config["detector"]["pixel_size"]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	533 logging.debug(f'num_rows: {self.cf.config["detector"]["rows"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	534 logging.debug(f'num_columns: {self.cf.config["detector"]["columns"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	535
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	536 # Safe config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	537 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	538 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	539
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	540 # Initialize shortcut to config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	541 self.config = self.cf.config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	542
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	543 # Initialize tomography stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	544 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	545 if num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	546 self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	547 self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	548
2 b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e" rv43 parents: 1 diff changeset	549 logging.debug(f'num_core = {self.num_core}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	550 logging.debug(f'config_file = {config_file}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	551 logging.debug(f'config_dict = {config_dict}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	552 logging.debug(f'config_out = {self.config_out}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	553 logging.debug(f'output_folder = {self.output_folder}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	554 logging.debug(f'log_stream = {log_stream}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	555 logging.debug(f'log_level = {log_level}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	556 logging.debug(f'galaxy_flag = {self.galaxy_flag}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	557 logging.debug(f'test_mode = {self.test_mode}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	558 logging.debug(f'save_plots = {self.save_plots}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	559 logging.debug(f'save_plots_only = {self.save_plots_only}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	560
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	561 def _selectImageRanges(self, available_stacks=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	562 """Select image files to be included in analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	563 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	564 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	565 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	566 if available_stacks is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	567 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	568 elif len(available_stacks) != stack_info['num']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	569 logging.warning('Illegal dimension of available_stacks in getImageFiles '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	570 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	571 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	572
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	573 # Check number of tomography angles/thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	574 num_thetas = self.config['theta_range'].get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	575 if num_thetas is None:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	576 num_thetas = input_int('\nEnter the number of thetas', 1)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	577 elif not is_int(num_thetas, 0):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	578 illegal_value(num_thetas, 'num_thetas', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	579 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	580 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	581 self.config['theta_range']['num'] = num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	582 logging.debug(f'num_thetas = {self.config["theta_range"]["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	583
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	584 # Find tomography dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	585 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	586 img_start = dark_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	587 img_offset = dark_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	588 num_imgs = dark_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	589 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	590 img_start, img_offset, num_imgs = selectImageRange(img_start, img_offset,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	591 num_imgs, 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	592 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	593 logging.error('Unable to find suitable dark field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	594 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	595 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	596 dark_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	597 dark_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	598 dark_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	599 logging.debug(f'Dark field image start index: {dark_field["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	600 logging.debug(f'Dark field image offset: {dark_field["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	601 logging.debug(f'Number of dark field images: {dark_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	602
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	603 # Find tomography bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	604 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	605 img_start = bright_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	606 img_offset = bright_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	607 num_imgs = bright_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	608 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	609 img_start, img_offset, num_imgs = selectImageRange(img_start, img_offset,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	610 num_imgs, 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	611 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	612 logging.error('Unable to find suitable bright field images')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	613 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	614 bright_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	615 bright_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	616 bright_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	617 logging.debug(f'Bright field image start index: {bright_field["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	618 logging.debug(f'Bright field image offset: {bright_field["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	619 logging.debug(f'Number of bright field images: {bright_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	620
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	621 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	622 for i,stack in enumerate(stack_info['stacks']):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	623 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	624 if self.tomo_stacks[i].size or available_stacks[i]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	625 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	626 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	627 img_start = stack.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	628 img_offset = stack.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	629 num_imgs = stack.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	630 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	631 img_start, img_offset, num_imgs = selectImageRange(img_start, img_offset,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	632 num_imgs, f'tomography stack {index}', num_thetas)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	633 if img_start < 0 or num_imgs != num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	634 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	635 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	636 stack['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	637 stack['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	638 stack['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	639 logging.debug(f'Tomography stack {index} image start index: {stack["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	640 logging.debug(f'Tomography stack {index} image offset: {stack["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	641 logging.debug(f'Number of tomography images for stack {index}: {stack["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	642
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	643 # Safe updated config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	644 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	645 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	646
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	647 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	648
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	649 def _genDark(self, tdf_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	650 """Generate dark field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	651 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	652 # Load the dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	653 logging.debug('Loading dark field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	654 dark_field = self.config['dark_field']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	655 tdf_stack = loadImageStack(tdf_files, self.config['data_filetype'],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	656 dark_field['img_offset'], dark_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	657
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	658 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	659 self.tdf = np.median(tdf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	660 del tdf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	661
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	662 # Remove dark field intensities above the cutoff
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	663 tdf_cutoff = dark_field.get('cutoff')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	664 if tdf_cutoff is not None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	665 if not is_num(tdf_cutoff, 0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	666 logging.warning(f'Ignoring illegal value of tdf_cutoff {tdf_cutoff}')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	667 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	668 self.tdf[self.tdf > tdf_cutoff] = np.nan
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	669 logging.debug(f'tdf_cutoff = {tdf_cutoff}')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	670
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	671 tdf_mean = np.nanmean(self.tdf)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	672 logging.debug(f'tdf_mean = {tdf_mean}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	673 np.nan_to_num(self.tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	674 if self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	675 quickImshow(self.tdf, title='dark field', path='setup_pngs',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	676 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	677 elif not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	678 quickImshow(self.tdf, title='dark field', path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	679 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	680
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	681 def _genBright(self, tbf_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	682 """Generate bright field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	683 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	684 # Load the bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	685 logging.debug('Loading bright field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	686 bright_field = self.config['bright_field']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	687 tbf_stack = loadImageStack(tbf_files, self.config['data_filetype'],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	688 bright_field['img_offset'], bright_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	689
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	690 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	691 """Median or mean: It may be best to try the median because of some image
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	692 artifacts that arise due to crinkles in the upstream kapton tape windows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	693 causing some phase contrast images to appear on the detector.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	694 One thing that also may be useful in a future implementation is to do a
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	695 brightfield adjustment on EACH frame of the tomo based on a ROI in the
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	696 corner of the frame where there is no sample but there is the direct X-ray
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	697 beam because there is frame to frame fluctuations from the incoming beam.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	698 We don’t typically account for them but potentially could.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	699 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	700 self.tbf = np.median(tbf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	701 del tbf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	702
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	703 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	704 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	705 self.tbf -= self.tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	706 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	707 logging.warning('Dark field unavailable')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	708 if self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	709 quickImshow(self.tbf, title='bright field', path='setup_pngs',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	710 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	711 elif not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	712 quickImshow(self.tbf, title='bright field', path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	713 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	714
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	715 def _setDetectorBounds(self, tomo_stack_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	716 """Set vertical detector bounds for image stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	717 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	718 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	719 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	720 img_x_bounds = [None, None]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	721 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	722 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	723 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	724 if img_x_bounds[0] < 0:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	725 illegal_value(img_x_bounds[0], 'preprocess:img_x_bounds[0]', 'config file')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	726 img_x_bounds[0] = 0
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	727 if not is_index_range(img_x_bounds, 0, self.tbf.shape[0]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	728 illegal_value(img_x_bounds[1], 'preprocess:img_x_bounds[1]', 'config file')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	729 img_x_bounds[1] = self.tbf.shape[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	730 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	731 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	732 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	733 self.cf.config['preprocess'] = {'img_x_bounds' : [0, self.tbf.shape[0]]}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	734 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	735 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	736 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	737 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	738
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	739 # Check reference heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	740 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	741 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	742 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	743 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	744 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	745 num_x_min = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	746 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	747 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	748 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	749 delta_z = stacks[1]['ref_height']-stacks[0]['ref_height']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	750 for i in range(2, num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	751 delta_z = min(delta_z, stacks[i]['ref_height']-stacks[i-1]['ref_height'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	752 logging.debug(f'delta_z = {delta_z}')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	753 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	754 logging.debug(f'num_x_min = {num_x_min}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	755 if num_x_min > self.tbf.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	756 logging.warning('Image bounds and pixel size prevent seamless stacking')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	757 num_x_min = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	758
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	759 # Select image bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	760 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	761 x_sum = np.sum(self.tbf, 1)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	762 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	763 x_sum_max = x_sum.max()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	764 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	765 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	766 if num_x_min is not None:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	767 fit = Fit.fit_data(np.array(range(len(x_sum))), x_sum, models='rectangle',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	768 form='atan', guess=True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	769 parameters = fit.best_values
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	770 x_low = parameters.get('center1', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	771 x_upp = parameters.get('center2', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	772 sig_low = parameters.get('sigma1', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	773 sig_upp = parameters.get('sigma2', None)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	774 if (x_low is not None and x_upp is not None and sig_low is not None and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	775 sig_upp is not None and 0 <= x_low < x_upp <= x_sum.size and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	776 (sig_low+sig_upp)/(x_upp-x_low) < 0.1):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	777 if num_tomo_stacks == 1 or num_x_min is None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	778 x_low = int(x_low-(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	779 x_upp = int(x_upp+(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	780 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	781 x_low = int((x_low+x_upp)/2-num_x_min/2)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	782 x_upp = x_low+num_x_min
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	783 if x_low < 0:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	784 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	785 if x_upp > x_sum.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	786 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	787 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	788 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	789 x_upp = x_sum.size
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	790 quickPlot((range(x_sum.size), x_sum),
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	791 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	792 ([x_upp-1, x_upp-1], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	793 title=f'sum bright field over theta/y (row bounds: [{x_low}, {x_upp}])',
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	794 path='setup_pngs', name='detectorbounds.png', save_fig=True, save_only=True,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	795 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	796 for i,stack in enumerate(stacks):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	797 tomo_stack = loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	798 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	799 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	800 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	801 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	802 tomo_stack[x_low,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	803 tomo_stack[x_upp-1,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	804 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	805 quickImshow(tomo_stack, title=title, path='setup_pngs',
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	806 name=f'tomo_{stack["index"]}.png', save_fig=True, save_only=True,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	807 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	808 del tomo_stack
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	809
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	810 # Update config and save to file
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	811 img_x_bounds = [x_low, x_upp]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	812 logging.debug(f'img_x_bounds: {img_x_bounds}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	813 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	814 self.cf.config['preprocess'] = {'img_x_bounds' : img_x_bounds}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	815 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	816 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	817 self.cf.saveFile(self.config_out)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	818 del x_sum
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	819 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	820
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	821 # For one tomography stack only: load the first image
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	822 title = None
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	823 quickImshow(self.tbf, title='bright field')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	824 if num_tomo_stacks == 1:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	825 tomo_stack = loadImageStack(tomo_stack_files[0], self.config['data_filetype'],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	826 stacks[0]['img_offset'], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	827 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	828 quickImshow(tomo_stack[0,:,:], title=title)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	829 tomo_or_bright = input_menu(['bright field', 'first tomography image'],
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	830 header='\nSelect image bounds from')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	831 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	832 print('\nSelect image bounds from bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	833 tomo_or_bright = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	834 if tomo_or_bright:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	835 x_sum = np.sum(tomo_stack[0,:,:], 1)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	836 use_bounds = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	837 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	838 tmp = np.copy(tomo_stack[0,:,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	839 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	840 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	841 tmp[img_x_bounds[1]-1,:] = tmp_max
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	842 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	843 quickImshow(tmp, title=title)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	844 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	845 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	846 x_sum_max = x_sum.max()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	847 quickPlot((range(x_sum.size), x_sum),
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	848 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	849 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum_min, x_sum_max], 'r-'),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	850 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	851 print(f'lower bound = {img_x_bounds[0]} (inclusive)\n'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	852 f'upper bound = {img_x_bounds[1]} (exclusive)]')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	853 use_bounds = input_yesno('Accept these bounds (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	854 if not use_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	855 img_x_bounds = list(selectImageBounds(tomo_stack[0,:,:], 0,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	856 img_x_bounds[0], img_x_bounds[1], num_x_min,
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	857 f'tomography image at theta={self.config["theta_range"]["start"]}'))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	858 if num_x_min is not None and img_x_bounds[1]-img_x_bounds[0]+1 < num_x_min:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	859 logging.warning('Image bounds and pixel size prevent seamless stacking')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	860 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	861 quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	862 save_fig=self.save_plots, save_only=True)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	863 quickPlot(range(img_x_bounds[0], img_x_bounds[1]),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	864 x_sum[img_x_bounds[0]:img_x_bounds[1]],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	865 title='sum over theta and y', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	866 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	867 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	868 x_sum = np.sum(self.tbf, 1)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	869 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	870 x_sum_max = x_sum.max()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	871 use_bounds = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	872 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	873 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	874 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	875 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	876 tmp[img_x_bounds[1]-1,:] = tmp_max
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	877 title = 'bright field'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	878 quickImshow(tmp, title=title)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	879 del tmp
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	880 quickPlot((range(x_sum.size), x_sum),
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	881 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	882 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum_min, x_sum_max], 'r-'),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	883 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	884 print(f'lower bound = {img_x_bounds[0]} (inclusive)\n'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	885 f'upper bound = {img_x_bounds[1]} (exclusive)]')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	886 use_bounds = input_yesno('Accept these bounds (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	887 if not use_bounds:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	888 use_fit = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	889 fit = Fit.fit_data(np.array(range(len(x_sum))), x_sum, models='rectangle',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	890 form='atan', guess=True)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	891 parameters = fit.best_values
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	892 x_low = parameters.get('center1', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	893 x_upp = parameters.get('center2', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	894 sig_low = parameters.get('sigma1', None)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	895 sig_upp = parameters.get('sigma2', None)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	896 if (x_low is not None and x_upp is not None and sig_low is not None and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	897 sig_upp is not None and 0 <= x_low < x_upp <= x_sum.size and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	898 (sig_low+sig_upp)/(x_upp-x_low) < 0.1):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	899 if num_tomo_stacks == 1 or num_x_min is None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	900 x_low = int(x_low-(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	901 x_upp = int(x_upp+(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	902 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	903 x_low = int((x_low+x_upp)/2-num_x_min/2)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	904 x_upp = x_low+num_x_min
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	905 if x_low < 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	906 x_low = 0
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	907 if x_upp > x_sum.size:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	908 x_upp = x_sum.size
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	909 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	910 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	911 tmp[x_low,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	912 tmp[x_upp-1,:] = tmp_max
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	913 title = 'bright field'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	914 quickImshow(tmp, title=title)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	915 del tmp
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	916 quickPlot((range(x_sum.size), x_sum),
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	917 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	918 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	919 title='sum over theta and y')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	920 print(f'lower bound = {x_low} (inclusive)')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	921 print(f'upper bound = {x_upp} (exclusive)]')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	922 use_fit = input_yesno('Accept these bounds (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	923 if use_fit:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	924 img_x_bounds = [x_low, x_upp]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	925 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	926 accept = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	927 while not accept:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	928 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	929 legend='sum over theta and y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	930 print(f'img_x_bounds = {img_x_bounds}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	931 while (len(img_x_bounds) != 1 or (len(x_sum) >= num_x_min and
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	932 img_x_bounds[0][1]-img_x_bounds[0][0]+1 < num_x_min)):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	933 exit('Should not be here')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	934 print('Please select exactly one continuous range')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	935 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	936 legend='sum over theta and y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	937 img_x_bounds = list(img_x_bounds[0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	938 quickPlot(x_sum, vlines=img_x_bounds, title='sum over theta and y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	939 print(f'img_x_bounds = {img_x_bounds} (lower bound inclusive, upper bound '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	940 'exclusive)')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	941 accept = input_yesno('Accept these bounds (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	942 if not accept:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	943 img_x_bounds = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	944 if num_x_min is not None and img_x_bounds[1]-img_x_bounds[0]+1 < num_x_min:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	945 logging.warning('Image bounds and pixel size prevent seamless stacking')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	946 #quickPlot(range(img_x_bounds[0], img_x_bounds[1]),
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	947 # x_sum[img_x_bounds[0]:img_x_bounds[1]],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	948 # title='sum over theta and y', path=self.output_folder,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	949 # save_fig=self.save_plots, save_only=True)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	950 quickPlot((range(x_sum.size), x_sum),
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	951 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	952 ([img_x_bounds[1], img_x_bounds[1]], [x_sum_min, x_sum_max], 'r-'),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	953 title='sum over theta and y', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	954 save_fig=self.save_plots, save_only=True)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	955 del x_sum
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	956 for i,stack in enumerate(stacks):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	957 tomo_stack = loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	958 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	959 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	960 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	961 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	962 tomo_stack[img_x_bounds[0],:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	963 tomo_stack[img_x_bounds[1]-1,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	964 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	965 if self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	966 quickImshow(tomo_stack, title=title, path='setup_pngs',
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	967 name=f'tomo_{stack["index"]}.png', save_fig=True, save_only=True,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	968 show_grid=True)
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	969 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	970 quickImshow(tomo_stack, title=title, path=self.output_folder,
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	971 name=f'tomo_{stack["index"]}.png', save_fig=self.save_plots,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	972 save_only=True, show_grid=True)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	973 del tomo_stack
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	974 logging.debug(f'img_x_bounds: {img_x_bounds}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	975
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	976 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	977 clearImshow('bright field')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	978 clearPlot('sum over theta and y')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	979 if title:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	980 clearPlot(title)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	981
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	982 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	983 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	984 self.cf.config['preprocess'] = {'img_x_bounds' : img_x_bounds}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	985 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	986 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	987 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	988
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	989 def _setZoomOrSkip(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	990 """Set zoom and/or theta skip to reduce memory the requirement for the analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	991 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	992 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	993 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	994 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	995 if preprocess is None or 'zoom_perc' not in preprocess:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	996 if input_yesno('\nDo you want to zoom in to reduce memory requirement (y/n)?', 'n'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	997 zoom_perc = input_int(' Enter zoom percentage', 1, 100)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	998 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	999 zoom_perc = preprocess['zoom_perc']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1000 if is_num(zoom_perc, 1., 100.):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1001 zoom_perc = int(zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1002 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1003 illegal_value(zoom_perc, 'preprocess:zoom_perc', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1004 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1005 num_theta_skip = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1006 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1007 if preprocess is None or 'num_theta_skip' not in preprocess:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1008 if input_yesno('Do you want to skip thetas to reduce memory requirement (y/n)?',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1009 'n'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1010 num_theta_skip = input_int(' Enter the number skip theta interval', 0,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1011 self.num_thetas-1)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1012 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1013 num_theta_skip = preprocess['num_theta_skip']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1014 if not is_int(num_theta_skip, 0):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1015 illegal_value(num_theta_skip, 'preprocess:num_theta_skip', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1016 num_theta_skip = 0
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1017 logging.debug(f'zoom_perc = {zoom_perc}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1018 logging.debug(f'num_theta_skip = {num_theta_skip}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1019
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1020 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1021 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1022 self.cf.config['preprocess'] = {'zoom_perc' : zoom_perc,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1023 'num_theta_skip' : num_theta_skip}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1024 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1025 preprocess['zoom_perc'] = zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1026 preprocess['num_theta_skip'] = num_theta_skip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1027 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1028
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1029 def _loadTomo(self, base_name, index, required=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1030 """Load a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1031 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1032 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1033 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1034 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1035 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1036 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1037 if zoom_perc is None or zoom_perc == 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1038 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1039 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1040 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1041 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1042 tomo_file = re.sub(r"\s+", '_', f'{self.output_folder}/{title}.npy')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1043 load_flag = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1044 available = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1045 if os.path.isfile(tomo_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1046 available = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1047 if required:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1048 load_flag = True
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1049 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1050 load_flag = input_yesno(f'\nDo you want to load {tomo_file} (y/n)?')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1051 stack = np.array([])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1052 if load_flag:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1053 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1054 logging.info(f'Loading {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1055 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1056 stack = np.load(tomo_file)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1057 except IOError or ValueError:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1058 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1059 logging.error(f'Error loading {tomo_file}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1060 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1061 if stack.size:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1062 quickImshow(stack[:,0,:], title=title, path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1063 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1064 return stack, available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1065
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1066 def _saveTomo(self, base_name, stack, index=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1067 """Save a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1068 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1069 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1070 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1071 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1072 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1073 if zoom_perc is None or zoom_perc == 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1074 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1075 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1076 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1077 if index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1078 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1079 tomo_file = re.sub(r"\s+", '_', f'{self.output_folder}/{title}.npy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1080 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1081 logging.info(f'Saving {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1082 np.save(tomo_file, stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1083 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1084
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1085 def _genTomo(self, tomo_stack_files, available_stacks, num_core=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1086 """Generate tomography fields.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1087 """
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1088 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1089 num_core = self.num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1090 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1091 assert(len(self.tomo_stacks) == self.config['stack_info']['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1092 assert(len(self.tomo_stacks) == len(stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1093 if len(available_stacks) != len(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1094 logging.warning('Illegal dimension of available_stacks in _genTomo'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1095 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1096 available_stacks = [False]*self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1097
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1098 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1099 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1100 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1101 img_y_bounds = [0, self.tbf.shape[1]]
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1102 zoom_perc = 100
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1103 num_theta_skip = 0
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1104 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1105 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1106 img_y_bounds = preprocess.get('img_y_bounds', [0, self.tbf.shape[1]])
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1107 zoom_perc = preprocess.get('zoom_perc', 100)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1108 num_theta_skip = preprocess.get('num_theta_skip', 0)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1109
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1110 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1111 tdf = self.tdf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1112 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1113 logging.warning('Dark field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1114 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1115 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1116 tbf = self.tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1117
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1118 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1119 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1120 if self.tomo_stacks[i].size or available_stacks[i]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1121 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1122
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1123 # Load a stack of tomography images
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1124 index = stack['index']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1125 t0 = time()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1126 tomo_stack = loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1127 stack['img_offset'], self.config['theta_range']['num'], num_theta_skip,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1128 img_x_bounds, img_y_bounds)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1129 tomo_stack = tomo_stack.astype('float64')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1130 logging.debug(f'loading stack {index} took {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1131
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1132 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1133 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1134 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1135 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1136 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1137 logging.debug(f'subtracting dark field took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1138
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1139 # Normalize
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1140 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1141 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1142 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1143 logging.debug(f'normalizing took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1144
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1145 # Remove non-positive values and linearize data
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1146 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1147 cutoff = 1.e-6
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1148 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1149 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1150 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1151 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1152 logging.debug('removing non-positive values and linearizing data took '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1153 f'{time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1154
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1155 # Get rid of nans/infs that may be introduced by normalization
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1156 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1157 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1158 logging.debug(f'remove nans/infs took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1159
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1160 # Downsize tomography stack to smaller size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1161 tomo_stack = tomo_stack.astype('float32')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1162 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1163 title = f'red stack fullres {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1164 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1165 quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1166 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1167 if zoom_perc != 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1168 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1169 logging.info(f'Zooming in ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1170 tomo_zoom_list = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1171 for j in range(tomo_stack.shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1172 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1173 tomo_zoom_list.append(tomo_zoom)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1174 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1175 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1176 del tomo_zoom_list
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1177 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1178 title = f'red stack {zoom_perc}p {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1179 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1180 quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1181 save_fig=self.save_plots, save_only=self.save_plots_only)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1182
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1183 # Convert tomography stack from theta,row,column to row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1184 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1185
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1186 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1187 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1188 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1189 self._saveTomo('red stack', tomo_stack, index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1190 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1191 np.savetxt(f'{self.output_folder}/red_stack_{index}.txt',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1192 tomo_stack[0,:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1193
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1194 # Combine stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1195 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1196 self.tomo_stacks[i] = tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1197 logging.debug(f'combining nstack took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1198
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1199 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1200 stack['preprocessed'] = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1201 stack.pop('reconstructed', 'reconstructed not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1202 find_center = self.config.get('find_center')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1203 if find_center:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1204 find_center.pop('completed', 'completed not found')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1205 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1206 find_center.pop('lower_center_offset', 'lower_center_offset not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1207 find_center.pop('upper_center_offset', 'upper_center_offset not found')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1208 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1209
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1210 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1211 del tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1212 del tbf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1213
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1214 def _reconstructOnePlane(self, tomo_plane_T, center, thetas_deg, eff_pixel_size,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1215 cross_sectional_dim, plot_sinogram=True, num_core=1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1216 """Invert the sinogram for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1217 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1218 # tomo_plane_T index order: column,theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1219 assert(0 <= center < tomo_plane_T.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1220 center_offset = center-tomo_plane_T.shape[0]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1221 two_offset = 2*int(np.round(center_offset))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1222 two_offset_abs = np.abs(two_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1223 max_rad = int(0.5(cross_sectional_dim/eff_pixel_size)1.1) # 10% slack to avoid edge effects
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	1224 if max_rad > 0.5*tomo_plane_T.shape[0]:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	1225 max_rad = 0.5*tomo_plane_T.shape[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1226 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1227 if two_offset >= 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1228 logging.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1229 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1230 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1231 logging.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1232 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1233 if plot_sinogram and not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1234 quickImshow(sinogram.T, f'sinogram center offset{center_offset:.2f}',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1235 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1236 save_only=self.save_plots_only, aspect='auto')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1237
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1238 # Inverting sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1239 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1240 recon_sinogram = iradon(sinogram, theta=thetas_deg, circle=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1241 logging.debug(f'inverting sinogram took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1242 del sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1243
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1244 # Performing Gaussian filtering and removing ring artifacts
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1245 recon_parameters = self.config.get('recon_parameters')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1246 if recon_parameters is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1247 sigma = 1.0
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1248 ring_width = 15
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1249 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1250 sigma = recon_parameters.get('gaussian_sigma', 1.0)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1251 if not is_num(sigma, 0.0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1252 logging.warning(f'Illegal gaussian_sigma ({sigma}) in _reconstructOnePlane, '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1253 'set to a default value of 1.0')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1254 sigma = 1.0
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1255 ring_width = recon_parameters.get('ring_width', 15)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1256 if not is_int(ring_width, 0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1257 logging.warning(f'Illegal ring_width ({ring_width}) in _reconstructOnePlane, '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1258 'set to a default value of 15')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1259 ring_width = 15
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1260 t0 = time()
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1261 recon_sinogram = spi.gaussian_filter(recon_sinogram, sigma, mode='nearest')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1262 recon_clean = np.expand_dims(recon_sinogram, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1263 del recon_sinogram
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1264 t1 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1265 logging.debug(f'running remove_ring on {num_core} cores ...')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1266 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=ring_width, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1267 logging.debug(f'... remove_ring took {time()-t1:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1268 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1269 return recon_clean
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1270
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1271 def _plotEdgesOnePlane(self, recon_plane, title, path=None):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1272 vis_parameters = self.config.get('vis_parameters')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1273 if vis_parameters is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1274 weight = 0.1
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1275 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1276 weight = vis_parameters.get('denoise_weight', 0.1)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1277 if not is_num(weight, 0.0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1278 logging.warning(f'Illegal weight ({weight}) in _plotEdgesOnePlane, '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1279 'set to a default value of 0.1')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1280 weight = 0.1
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1281 edges = denoise_tv_chambolle(recon_plane, weight=weight)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1282 vmax = np.max(edges[0,:,:])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1283 vmin = -vmax
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1284 if self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1285 quickImshow(edges[0,:,:], title, path=path, save_fig=True, save_only=True,
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1286 cmap='gray', vmin=vmin, vmax=vmax)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1287 else:
11 ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1288 if path is None:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1289 path=self.output_folder
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1290 quickImshow(edges[0,:,:], f'{title} coolwarm', path=path,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1291 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1292 quickImshow(edges[0,:,:], f'{title} gray', path=path,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1293 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='gray',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1294 vmin=vmin, vmax=vmax)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1295 del edges
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1296
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1297 def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim,
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1298 tol=0.1, num_core=1, galaxy_param=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1299 """Find center for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1300 """
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1301 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1302 assert(isinstance(galaxy_param, dict))
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1303 if not os.path.exists('find_center_pngs'):
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1304 os.mkdir('find_center_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1305 # sinogram index order: theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1306 # need index order column,theta for iradon, so take transpose
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1307 sinogram_T = sinogram.T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1308 center = sinogram.shape[1]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1309
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1310 # try automatic center finding routines for initial value
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1311 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1312 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1313 logging.debug(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1314 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
37 51dc93d0806a "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 87acf8a257d5d51cf249de085e555bb11d1dbd88" rv43 parents: 36 diff changeset	1315 else:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1316 logging.debug(f'running find_center_vo on {num_core} cores ...')
37 51dc93d0806a "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 87acf8a257d5d51cf249de085e555bb11d1dbd88" rv43 parents: 36 diff changeset	1317 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1318 logging.debug(f'... find_center_vo took {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1319 center_offset_vo = tomo_center-center
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1320 if self.test_mode:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1321 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1322 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1323 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1324 elif self.galaxy_flag:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1325 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1326 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1327 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1328 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1329 eff_pixel_size, cross_sectional_dim, False, num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1330 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1331 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1332 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1333 del recon_plane
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1334 if not galaxy_param['center_type_selector']:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1335 del sinogram_T
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1336 return float(center_offset_vo)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1337 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1338 print(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1339 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1340 eff_pixel_size, cross_sectional_dim, False, num_core)
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1341 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1342 self._plotEdgesOnePlane(recon_plane, title)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1343 if not self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1344 if input_yesno('Try finding center using phase correlation (y/n)?', 'n'):
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1345 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1346 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1347 error = 1.
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1348 while error > tol:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1349 prev = tomo_center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1350 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1351 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1352 error = np.abs(tomo_center-prev)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1353 center_offset = tomo_center-center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1354 print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1355 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1356 eff_pixel_size, cross_sectional_dim, False, num_core)
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1357 title = f'edges row{row} center_offset{center_offset:.2f} PC'
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1358 self._plotEdgesOnePlane(recon_plane, title)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1359 if input_yesno('Accept a center location (y) or continue search (n)?', 'y'):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1360 center_offset = input_num(' Enter chosen center offset', -center, center,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1361 center_offset_vo)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1362 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1363 del recon_plane
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1364 return float(center_offset)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1365
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1366 # perform center finding search
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1367 while True:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1368 if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1369 set_center = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1370 if galaxy_param['center_type_selector'] == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1371 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1372 set_range = galaxy_param['set_range']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1373 center_offset_step = galaxy_param['set_step']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1374 if (not is_num(set_range, 0) or not is_num(center_offset_step) or
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1375 center_offset_step <= 0):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1376 logging.warning('Illegal center finding search parameter, skip search')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1377 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1378 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1379 set_range = center_offset_step*max(1, int(set_range/center_offset_step))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1380 center_offset_low = set_center-set_range
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1381 center_offset_upp = set_center+set_range
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1382 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1383 center_offset_low = input_int('\nEnter lower bound for center offset',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1384 -center, center)
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1385 center_offset_upp = input_int('Enter upper bound for center offset',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1386 center_offset_low, center)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1387 if center_offset_upp == center_offset_low:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1388 center_offset_step = 1
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1389 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1390 center_offset_step = input_int('Enter step size for center offset search',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1391 1, center_offset_upp-center_offset_low)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1392 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1393 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1394 for center_offset in center_offsets:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1395 if center_offset == center_offset_vo:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1396 continue
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1397 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1398 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1399 recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1400 thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1401 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1402 title = f'edges row{row} center_offset{center_offset:.2f}'
11 ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1403 if self.galaxy_flag:
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1404 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
11 ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1405 else:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1406 self._plotEdgesOnePlane(recon_plane, title)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1407 if self.galaxy_flag or input_int('\nContinue (0) or end the search (1)', 0, 1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1408 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1409
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1410 del sinogram_T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1411 del recon_plane
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1412 if self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1413 center_offset = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1414 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1415 center_offset = input_num(' Enter chosen center offset', -center, center)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1416 return float(center_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1417
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1418 def _reconstructOneTomoStack(self, tomo_stack, thetas, row_bounds=None, center_offsets=[],
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1419 num_core=1, algorithm='gridrec'):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1420 """reconstruct a single tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1421 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1422 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1423 # thetas must be in radians
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1424 # centers_offset: tomography axis shift in pixels relative to column center
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1425 # RV should we remove stripes?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1426 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1427 # RV should we remove rings?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1428 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1429 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1430 if row_bounds is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1431 row_bounds = [0, tomo_stack.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1432 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1433 if not is_index_range(row_bounds, 0, tomo_stack.shape[0]):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1434 raise ValueError('Illegal row bounds in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1435 if thetas.size != tomo_stack.shape[1]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1436 raise ValueError('theta dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1437 if not len(center_offsets):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1438 centers = np.zeros((row_bounds[1]-row_bounds[0]))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1439 elif len(center_offsets) == 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1440 centers = np.linspace(center_offsets[0], center_offsets[1],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1441 row_bounds[1]-row_bounds[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1442 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1443 if center_offsets.size != row_bounds[1]-row_bounds[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1444 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1445 centers = center_offsets
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1446 centers += tomo_stack.shape[2]/2
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1447
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1448 # Removing horizontal stripe and ring artifacts and perform secondary iterations
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1449 recon_parameters = self.config.get('recon_parameters')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1450 if recon_parameters is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1451 sigma = 2.0
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1452 secondary_iters = 0
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1453 ring_width = 15
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1454 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1455 sigma = recon_parameters.get('stripe_fw_sigma', 2.0)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1456 if not is_num(sigma, 0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1457 logging.warning(f'Illegal stripe_fw_sigma ({sigma}) in '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1458 '_reconstructOneTomoStack, set to a default value of 2.0')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1459 ring_width = 15
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1460 secondary_iters = recon_parameters.get('secondary_iters', 0)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1461 if not is_int(secondary_iters, 0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1462 logging.warning(f'Illegal secondary_iters ({secondary_iters}) in '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1463 '_reconstructOneTomoStack, set to a default value of 0 (skip them)')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1464 ring_width = 0
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1465 ring_width = recon_parameters.get('ring_width', 15)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1466 if not is_int(ring_width, 0):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1467 logging.warning(f'Illegal ring_width ({ring_width}) in _reconstructOnePlane, '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1468 'set to a default value of 15')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1469 ring_width = 15
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1470 if True:
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1471 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1472 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1473 logging.debug('running remove_stripe_fw on {num_core_tomopy_limit} cores ...')
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1474 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1475 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1476 ncore=num_core_tomopy_limit)
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1477 else:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1478 logging.debug(f'running remove_stripe_fw on {num_core} cores ...')
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1479 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1480 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1481 logging.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1482 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1483 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1484 logging.debug('performing initial reconstruction')
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1485 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1486 logging.debug(f'running recon on {num_core} cores ...')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1487 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1488 algorithm=algorithm, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1489 logging.debug(f'... recon took {time()-t0:.2f} seconds!')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1490 if secondary_iters > 0:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1491 logging.debug(f'running {secondary_iters} secondary iterations')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1492 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iters}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1493 #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver /
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1494 # cuda driver combination."
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1495 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iters}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1496 #SIRT did not finish while running overnight
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1497 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iters}
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1498 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1499 'num_iter':secondary_iters}
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1500 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1501 logging.debug(f'running recon on {num_core} cores ...')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1502 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1503 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1504 algorithm=tomopy.astra, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1505 logging.debug(f'... recon took {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1506 if True:
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1507 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1508 logging.debug(f'running remove_ring on {num_core} cores ...')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1509 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=ring_width, out=tomo_recon_stack,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1510 ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1511 logging.debug(f'... remove_ring took {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1512 return tomo_recon_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1513
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1514 def findImageFiles(self, tiff_to_h5_flag = False):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1515 """Find all available image files.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1516 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1517 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1518
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1519 # Find dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1520 dark_field = self.config['dark_field']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1521 img_start, num_imgs, dark_files = findImageFiles(
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1522 dark_field['data_path'], self.config['data_filetype'], 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1523 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1524 logging.error('Unable to find suitable dark field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1525 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1526 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1527 img_start_old = dark_field.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1528 num_imgs_old = dark_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1529 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1530 dark_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1531 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1532 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1533 logging.error('Inconsistent number of availaible dark field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1534 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1535 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1536 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1537 dark_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1538 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1539 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1540 logging.error('Inconsistent image start index for dark field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1541 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1542 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1543 logging.info(f'Number of dark field images = {dark_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1544 logging.info(f'Dark field image start index = {dark_field["img_start"]}')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1545 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1546 dark_files = combine_tiffs_in_h5(dark_files, num_imgs,
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1547 f'{self.config["work_folder"]}/dark_field.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1548 dark_field['data_path'] = dark_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1549
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1550 # Find bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1551 bright_field = self.config['bright_field']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1552 img_start, num_imgs, bright_files = findImageFiles(
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1553 bright_field['data_path'], self.config['data_filetype'], 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1554 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1555 logging.error('Unable to find suitable bright field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1556 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1557 img_start_old = bright_field.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1558 num_imgs_old = bright_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1559 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1560 bright_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1561 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1562 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1563 logging.error('Inconsistent number of availaible bright field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1564 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1565 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1566 bright_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1567 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1568 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1569 logging.warning('Inconsistent image start index for bright field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1570 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1571 logging.info(f'Number of bright field images = {bright_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1572 logging.info(f'Bright field image start index = {bright_field["img_start"]}')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1573 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1574 bright_files = combine_tiffs_in_h5(bright_files, num_imgs,
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1575 f'{self.config["work_folder"]}/bright_field.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1576 bright_field['data_path'] = bright_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1577
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1578 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1579 tomo_stack_files = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1580 for stack in self.config['stack_info']['stacks']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1581 index = stack['index']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1582 img_start, num_imgs, tomo_files = findImageFiles(
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1583 stack['data_path'], self.config['data_filetype'], f'tomography set {index}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1584 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1585 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1586 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1587 img_start_old = stack.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1588 num_imgs_old = stack.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1589 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1590 stack['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1591 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1592 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1593 logging.error('Inconsistent number of availaible tomography images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1594 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1595 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1596 stack['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1597 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1598 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1599 logging.warning('Inconsistent image start index for tomography images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1600 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1601 logging.info(f'Number of tomography images for set {index} = {stack["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1602 logging.info(f'Tomography set {index} image start index = {stack["img_start"]}')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1603 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1604 tomo_files = combine_tiffs_in_h5(tomo_files, num_imgs,
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1605 f'{self.config["work_folder"]}/tomo_field_{index}.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1606 stack['data_path'] = tomo_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1607 tomo_stack_files.append(tomo_files)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1608 del tomo_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1609
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1610 # Safe updated config
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1611 if tiff_to_h5_flag:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1612 self.config['data_filetype'] == 'h5'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1613 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1614 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1615
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1616 return dark_files, bright_files, tomo_stack_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1617
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1618 def loadTomoStacks(self, input_name, recon_flag=False):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1619 """Load tomography stacks (only for Galaxy).
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1620 """
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1621 assert(self.galaxy_flag)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1622 t0 = time()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1623 logging.info(f'Loading preprocessed tomography stack from {input_name} ...')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1624 stack_info = self.config['stack_info']
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1625 stacks = stack_info.get('stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1626 assert(len(self.tomo_stacks) == stack_info['num'])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1627 with np.load(input_name) as f:
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1628 if recon_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1629 for i,stack in enumerate(stacks):
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1630 self.tomo_recon_stacks[i] = f[f'set_{stack["index"]}']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1631 logging.info(f'loaded stack {i}: index = {stack["index"]}, shape = '+
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1632 f'{self.tomo_recon_stacks[i].shape}')
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1633 else:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1634 for i,stack in enumerate(stacks):
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1635 self.tomo_stacks[i] = f[f'set_{stack["index"]}']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1636 logging.info(f'loaded stack {i}: index = {stack["index"]}, shape = '+
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	1637 f'{self.tomo_stacks[i].shape}')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1638 logging.info(f'... done in {time()-t0:.2f} seconds!')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1639
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1640 def genTomoStacks(self, galaxy_param=None, num_core=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1641 """Preprocess tomography images.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1642 """
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1643 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1644 num_core = self.num_core
33 afb612b64f26 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit c566c32f7c1506ab271ae08eb14a2982ee511938" rv43 parents: 32 diff changeset	1645 logging.info(f'num_core = {num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1646 # Try loading any already preprocessed stacks (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1647 # preprocessed stack order for each one in stack: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1648 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1649 stacks = stack_info['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1650 num_tomo_stacks = stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1651 assert(num_tomo_stacks == len(self.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1652 available_stacks = [False]*num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1653 if self.galaxy_flag:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1654 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1655 tdf_files = galaxy_param['tdf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1656 tbf_files = galaxy_param['tbf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1657 tomo_stack_files = galaxy_param['tomo_stack_files']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1658 assert(num_tomo_stacks == len(tomo_stack_files))
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1659 if not os.path.exists('setup_pngs'):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1660 os.mkdir('setup_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1661 else:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1662 if galaxy_param:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1663 logging.warning('Ignoring galaxy_param in genTomoStacks (only for Galaxy)')
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1664 galaxy_param = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1665 tdf_files, tbf_files, tomo_stack_files = self.findImageFiles()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1666 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1667 return
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1668 if self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1669 required = True
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1670 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1671 required = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1672 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1673 if not self.tomo_stacks[i].size and stack.get('preprocessed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1674 self.tomo_stacks[i], available_stacks[i] = \
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1675 self._loadTomo('red stack', stack['index'], required=required)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1676
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1677 # Preprocess any unloaded stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1678 if False in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1679 logging.debug('Preprocessing tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1680
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1681 # Check required image files (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1682 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1683 self._selectImageRanges(available_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1684 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1685 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1686
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1687 # Generate dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1688 if tdf_files:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1689 self._genDark(tdf_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1690
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1691 # Generate bright field
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1692 self._genBright(tbf_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1693
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1694 # Set vertical detector bounds for image stack
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1695 self._setDetectorBounds(tomo_stack_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1696
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1697 # Set zoom and/or theta skip to reduce memory the requirement
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1698 self._setZoomOrSkip()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1699
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1700 # Generate tomography fields
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1701 self._genTomo(tomo_stack_files, available_stacks, num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1702
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1703 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1704 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1705 t0 = time()
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1706 output_name = galaxy_param['output_name']
2 b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e" rv43 parents: 1 diff changeset	1707 logging.info(f'Saving preprocessed tomography stack to {output_name} ...')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1708 save_stacks = {f'set_{stack["index"]}':tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1709 for stack,tomo_stack in zip(stacks,self.tomo_stacks)}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1710 np.savez(output_name, **save_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1711 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1712
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1713 del available_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1714
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1715 # Adjust sample reference height, update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1716 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1717 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1718 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1719 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1720 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1721 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1722 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1723 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1724 pixel_size *= img_x_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1725 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1726 stack['ref_height'] = stack['ref_height']+pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1727 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1728
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1729 def findCenters(self, galaxy_param=None, num_core=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1730 """Find rotation axis centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1731 """
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1732 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1733 num_core = self.num_core
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1734 logging.info(f'num_core = {num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1735 logging.debug('Find centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1736 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1737 available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)]
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1738 logging.debug('Available stacks: {available_stacks}')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1739 if self.galaxy_flag:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1740 row_bounds = galaxy_param['row_bounds']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1741 center_rows = galaxy_param['center_rows']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1742 center_type_selector = galaxy_param['center_type_selector']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1743 if center_type_selector:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1744 if center_type_selector == 'vo':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1745 set_center = None
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1746 elif center_type_selector == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1747 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1748 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1749 logging.error('Illegal center_type_selector entry in galaxy_param '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1750 f'({center_type_selector})')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1751 galaxy_param['center_type_selector'] = None
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1752 logging.debug(f'row_bounds = {row_bounds}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1753 logging.debug(f'center_rows = {center_rows}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1754 logging.debug(f'center_type_selector = {center_type_selector}')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1755 else:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1756 if galaxy_param:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1757 logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1758 galaxy_param = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1759
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1760 # Check for valid available center stack index
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1761 find_center = self.config.get('find_center')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1762 center_stack_index = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1763 if find_center and 'center_stack_index' in find_center:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1764 center_stack_index = find_center['center_stack_index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1765 if (not isinstance(center_stack_index, int) or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1766 center_stack_index not in available_stacks):
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1767 illegal_value(center_stack_index, 'find_center:center_stack_index', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1768 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1769 if self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1770 assert(find_center.get('completed', False) == False)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1771 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1772 print('\nFound calibration center offset info for stack '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1773 f'{center_stack_index}')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1774 if (input_yesno('Do you want to use this again (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1775 and find_center.get('completed', False) == True):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1776 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1777
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1778 # Load the required preprocessed stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1779 # preprocessed stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1780 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1781 assert(len(stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1782 assert(len(self.tomo_stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1783 if num_tomo_stacks == 1:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1784 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1785 center_stack_index = stacks[0]['index']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1786 elif center_stack_index != stacks[0]['index']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1787 raise ValueError(f'Inconsistent center_stack_index {center_stack_index}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1788 if not self.tomo_stacks[0].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1789 self.tomo_stacks[0], available = self._loadTomo('red stack', center_stack_index,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1790 required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1791 center_stack = self.tomo_stacks[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1792 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1793 stacks[0]['preprocessed'] = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1794 raise OSError('Unable to load the required preprocessed tomography stack')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1795 assert(stacks[0].get('preprocessed', False) == True)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1796 elif self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1797 center_stack_index = stacks[int(num_tomo_stacks/2)]['index']
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1798 tomo_stack_index = available_stacks.index(center_stack_index)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1799 center_stack = self.tomo_stacks[tomo_stack_index]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1800 if not center_stack.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1801 stacks[tomo_stack_index]['preprocessed'] = False
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1802 raise OSError('Unable to load the required preprocessed tomography stack')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1803 assert(stacks[tomo_stack_index].get('preprocessed', False) == True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1804 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1805 while True:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1806 if not center_stack_index:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1807 center_stack_index = input_int('\nEnter tomography stack index to get '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1808 f'rotation axis centers ({available_stacks})', inset=available_stacks)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1809 while center_stack_index not in available_stacks:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1810 center_stack_index = input_int('\nEnter tomography stack index to get '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1811 f'rotation axis centers ({available_stacks})', inset=available_stacks)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1812 tomo_stack_index = available_stacks.index(center_stack_index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1813 if not self.tomo_stacks[tomo_stack_index].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1814 self.tomo_stacks[tomo_stack_index], available = self._loadTomo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1815 'red stack', center_stack_index, required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1816 center_stack = self.tomo_stacks[tomo_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1817 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1818 stacks[tomo_stack_index]['preprocessed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1819 logging.error(f'Unable to load the {center_stack_index}th '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1820 'preprocessed tomography stack, pick another one')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1821 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1822 break
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1823 assert(stacks[tomo_stack_index].get('preprocessed', False) == True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1824 if find_center is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1825 self.config['find_center'] = {'center_stack_index' : center_stack_index}
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1826 find_center = self.config['find_center']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1827 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1828 find_center['center_stack_index'] = center_stack_index
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1829 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1830 row_bounds = find_center.get('row_bounds', None)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1831 center_rows = [find_center.get('lower_row', None),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1832 find_center.get('upper_row', None)]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1833 if row_bounds is None:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1834 row_bounds = [0, center_stack.shape[0]]
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1835 if row_bounds[0] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1836 row_bounds[0] = 0
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1837 if row_bounds[1] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1838 row_bounds[1] = center_stack.shape[0]
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1839 if center_rows[0] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1840 center_rows[0] = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1841 if center_rows[1] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1842 center_rows[1] = center_stack.shape[0]-1
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1843 if not is_index_range(row_bounds, 0, center_stack.shape[0]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1844 illegal_value(row_bounds, 'row_bounds', 'Tomo:findCenters')
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1845 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1846
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1847 # Set thetas (in degrees)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1848 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1849 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1850 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1851 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1852 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1853 thetas_deg = np.linspace(theta_start, theta_end, int(num_theta/(num_theta_skip+1)),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1854 endpoint=False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1855
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1856 # Get non-overlapping sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1857 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1858 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1859 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1860 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1861 eff_pixel_size = 100.*pixel_size/zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1862 logging.debug(f'eff_pixel_size = {eff_pixel_size}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1863 if num_tomo_stacks == 1:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1864 accept = True
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1865 if not self.test_mode and not self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1866 accept = False
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1867 print('\nSelect bounds for image reconstruction')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1868 if is_index_range(row_bounds, 0, center_stack.shape[0]):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1869 a_tmp = np.copy(center_stack[:,0,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1870 a_tmp_max = a_tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1871 a_tmp[row_bounds[0],:] = a_tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1872 a_tmp[row_bounds[1]-1,:] = a_tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1873 print(f'lower bound = {row_bounds[0]} (inclusive)')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1874 print(f'upper bound = {row_bounds[1]} (exclusive)')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1875 quickImshow(a_tmp, title=f'center stack theta={theta_start}',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1876 aspect='auto')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1877 del a_tmp
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1878 accept = input_yesno('Accept these bounds (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1879 if accept:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1880 n1 = row_bounds[0]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1881 n2 = row_bounds[1]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1882 else:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1883 n1, n2 = selectImageBounds(center_stack[:,0,:], 0,
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1884 title=f'center stack theta={theta_start}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1885 else:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1886 tomo_ref_heights = [stack['ref_height'] for stack in stacks]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1887 n1 = int((1.+(tomo_ref_heights[0]+center_stack.shape[0]*eff_pixel_size-
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1888 tomo_ref_heights[1])/eff_pixel_size)/2)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1889 n2 = center_stack.shape[0]-n1
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1890 logging.debug(f'n1 = {n1}, n2 = {n2} (n2-n1) = {(n2-n1)*eff_pixel_size:.3f} mm')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1891 if not self.test_mode and not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1892 tmp = center_stack[:,0,:]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1893 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1894 tmp[n1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1895 tmp[n2-1,:] = tmp_max
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1896 if is_index_range(center_rows, 0, tmp.shape[0]):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1897 tmp[center_rows[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1898 tmp[center_rows[1]-1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1899 extent = [0, tmp.shape[1], tmp.shape[0], 0]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1900 quickImshow(tmp, title=f'center stack theta={theta_start}',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1901 path=self.output_folder, extent=extent, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1902 save_only=self.save_plots_only, aspect='auto')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1903 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1904 #extent = [0, center_stack.shape[2], n2, n1]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1905 #quickImshow(center_stack[n1:n2,0,:], title=f'center stack theta={theta_start}',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1906 # path=self.output_folder, extent=extent, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1907 # save_only=self.save_plots_only, show_grid=True, aspect='auto')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1908
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1909 # Get cross sectional diameter in mm
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1910 cross_sectional_dim = center_stack.shape[2]*eff_pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1911 logging.debug(f'cross_sectional_dim = {cross_sectional_dim}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1912
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1913 # Determine center offset at sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1914 logging.info('Determine center offset at sample row boundaries')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1915
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1916 # Lower row center
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1917 use_row = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1918 use_center = False
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1919 row = center_rows[0]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1920 if self.test_mode or self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1921 assert(is_int(row, n1, n2-2))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1922 if is_int(row, n1, n2-2):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1923 if self.test_mode or self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1924 use_row = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1925 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1926 quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1927 use_row = input_yesno('\nCurrent row index for lower center = '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1928 f'{row}, use this value (y/n)?', 'y')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1929 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1930 clearImshow(f'theta={theta_start}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1931 if use_row:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1932 center_offset = find_center.get('lower_center_offset')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1933 if is_num(center_offset):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1934 use_center = input_yesno('Current lower center offset = '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1935 f'{center_offset}, use this value (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1936 if not use_center:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1937 if not use_row:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1938 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1939 quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1940 aspect='auto')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1941 row = input_int('\nEnter row index to find lower center', n1, n2-2, n1)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1942 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1943 row = n1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1944 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1945 clearImshow(f'theta={theta_start}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1946 # center_stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1947 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1948 eff_pixel_size, cross_sectional_dim, num_core=num_core,
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1949 galaxy_param=galaxy_param)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1950 logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1951
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1952 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1953 find_center['row_bounds'] = [n1, n2]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1954 find_center['lower_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1955 find_center['lower_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1956 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1957 lower_row = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1958
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1959 # Upper row center
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1960 use_row = False
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1961 use_center = False
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1962 row = center_rows[1]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1963 if self.test_mode or self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1964 assert(is_int(row, lower_row+1, n2-1))
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1965 if is_int(row, lower_row+1, n2-1):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1966 if self.test_mode or self.galaxy_flag:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1967 use_row = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1968 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1969 quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1970 use_row = input_yesno('\nCurrent row index for upper center = '
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1971 f'{row}, use this value (y/n)?', 'y')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1972 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1973 clearImshow(f'theta={theta_start}')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1974 if use_row:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1975 center_offset = find_center.get('upper_center_offset')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1976 if is_num(center_offset):
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	1977 use_center = input_yesno('Current upper center offset = '+
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1978 f'{center_offset}, use this value (y/n)?', 'y')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1979 if not use_center:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1980 if not use_row:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1981 if not self.test_mode:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1982 quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1983 aspect='auto')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1984 row = input_int('\nEnter row index to find upper center', lower_row+1, n2-1, n2-1)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1985 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1986 row = n2-1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1987 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	1988 clearImshow(f'theta={theta_start}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1989 # center_stack order: row,theta,column
24 817a8101d2e4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3d7910473008ec94bc0b4580d62e61310e69917d" rv43 parents: 23 diff changeset	1990 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1991 eff_pixel_size, cross_sectional_dim, num_core=num_core,
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1992 galaxy_param=galaxy_param)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1993 logging.info(f'upper_center_offset = {center_offset:.2f}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1994 del center_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1995
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1996 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1997 find_center['upper_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1998 find_center['upper_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1999 find_center['completed'] = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2000 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2001
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2002 def checkCenters(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2003 """Check centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2004 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2005 #RV TODO load all stacks and check at all stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2006 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2007 logging.debug('Check centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2008 center_stack_index = self.config.get('center_stack_index')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2009 if center_stack_index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2010 raise ValueError('Unable to read center_stack_index from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2011 center_stack_index = self.tomo_stacks[self.tomo_data_indices.index(center_stack_index)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2012 lower_row = self.config.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2013 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2014 raise ValueError('Unable to read lower_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2015 lower_center_offset = self.config.get('lower_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2016 if lower_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2017 raise ValueError('Unable to read lower_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2018 upper_row = self.config.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2019 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2020 raise ValueError('Unable to read upper_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2021 upper_center_offset = self.config.get('upper_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2022 if upper_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2023 raise ValueError('Unable to read upper_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2024 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2025 shift = upper_center_offset-lower_center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2026 if lower_row == 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2027 logging.warning(f'lower_row == 0: one row offset between both planes')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2028 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2029 lower_row -= 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2030 lower_center_offset -= center_slope
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2031
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2032 # stack order: stack,row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2033 if center_stack_index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2034 stack1 = self.tomo_stacks[center_stack_index-1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2035 stack2 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2036 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2037 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2038 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2039 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2040 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2041 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2042 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2043 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2044 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2045 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2046 shift_i = shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2047 plane1_shifted = spi.shift(plane2, [0, shift_i])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2048 quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2049 title=f'stacks {stack1} {stack2} shifted {2*i} theta={self.start_theta}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2050 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2051 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2052 if center_stack_index < self.num_tomo_stacks-1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2053 stack1 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2054 stack2 = self.tomo_stacks[center_stack_index+1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2055 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2056 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2057 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2058 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2059 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2060 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2061 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2062 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2063 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2064 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2065 shift_i = -shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2066 plane1_shifted = spi.shift(plane2, [0, shift_i])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2067 quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2068 title=f'stacks {stack1} {stack2} shifted {2*i} theta={start_theta}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2069 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2070 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2071 del plane1, plane2, plane1_shifted
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2072
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2073 # Update config file
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2074 self.config = update('config.txt', 'check_centers', True, 'find_centers')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2075
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2076 def reconstructTomoStacks(self, galaxy_param=None, num_core=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2077 """Reconstruct tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2078 """
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2079 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2080 num_core = self.num_core
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2081 logging.info(f'num_core = {num_core}')
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2082 if self.galaxy_flag:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2083 assert(galaxy_param)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2084 if not os.path.exists('center_slice_pngs'):
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2085 os.mkdir('center_slice_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2086 logging.debug('Reconstruct tomography stacks')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2087 stacks = self.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2088 assert(len(self.tomo_stacks) == self.config['stack_info']['num'])
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2089 assert(len(self.tomo_stacks) == len(stacks))
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2090 assert(len(self.tomo_recon_stacks) == len(stacks))
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2091 if self.galaxy_flag:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2092 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2093 # Get rotation axis centers
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2094 center_offsets = galaxy_param['center_offsets']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2095 assert(isinstance(center_offsets, list) and len(center_offsets) == 2)
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2096 lower_center_offset = center_offsets[0]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2097 assert(is_num(lower_center_offset))
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2098 upper_center_offset = center_offsets[1]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2099 assert(is_num(upper_center_offset))
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2100 else:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2101 if galaxy_param:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2102 logging.warning('Ignoring galaxy_param in reconstructTomoStacks (only for Galaxy)')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2103 galaxy_param = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2104 lower_center_offset = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2105 upper_center_offset = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2106
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2107 # Get rotation axis rows and centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2108 find_center = self.config['find_center']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2109 lower_row = find_center.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2110 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2111 logging.error('Unable to read lower_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2112 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2113 upper_row = find_center.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2114 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2115 logging.error('Unable to read upper_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2116 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2117 logging.debug(f'lower_row = {lower_row} upper_row = {upper_row}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2118 assert(lower_row < upper_row)
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2119 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2120 lower_center_offset = find_center.get('lower_center_offset')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2121 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2122 logging.error('Unable to read lower_center_offset from config')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2123 return
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2124 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2125 upper_center_offset = find_center.get('upper_center_offset')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2126 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2127 logging.error('Unable to read upper_center_offset from config')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2128 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2129 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2130
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2131 # Set thetas (in radians)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2132 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2133 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2134 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2135 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2136 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2137 thetas = np.radians(np.linspace(theta_start, theta_end,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2138 int(num_theta/(num_theta_skip+1)), endpoint=False))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2139
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2140 # Reconstruct tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2141 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2142 if zoom_perc == 100:
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2143 basetitle = 'recon stack fullres'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2144 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2145 basetitle = f'recon stack {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2146 load_error = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2147 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2148 # Check if stack can be loaded
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2149 # reconstructed stack order for each one in stack : row/z,x,y
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2150 # preprocessed stack order for each one in stack: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2151 index = stack['index']
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2152 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2153 available = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2154 if stack.get('reconstructed', False):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2155 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack', index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2156 if self.tomo_recon_stacks[i].size or available:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2157 if self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2158 self.tomo_stacks[i] = np.array([])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2159 assert(stack.get('preprocessed', False) == True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2160 assert(stack.get('reconstructed', False) == True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2161 continue
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2162 stack['reconstructed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2163 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2164 self.tomo_stacks[i], available = self._loadTomo('red stack', index,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2165 required=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2166 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2167 logging.error(f'Unable to load tomography stack {index} for reconstruction')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2168 stack[i]['preprocessed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2169 load_error = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2170 continue
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2171 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2172 center_offsets = [lower_center_offset-lower_row*center_slope,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2173 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2174 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2175 logging.debug(f'running _reconstructOneTomoStack on {num_core} cores ...')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2176 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2177 thetas, center_offsets=center_offsets, num_core=num_core,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2178 algorithm='gridrec')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2179 logging.debug(f'... _reconstructOneTomoStack took {time()-t0:.2f} seconds!')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2180 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2181 if self.galaxy_flag:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2182 x_slice = int(self.tomo_recon_stacks[i].shape[0]/2)
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2183 title = f'{basetitle} {index} xslice{x_slice}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2184 quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2185 path='center_slice_pngs', save_fig=True, save_only=True)
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2186 y_slice = int(self.tomo_recon_stacks[i].shape[1]/2)
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2187 title = f'{basetitle} {index} yslice{y_slice}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2188 quickImshow(self.tomo_recon_stacks[i][:,y_slice,:], title=title,
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2189 path='center_slice_pngs', save_fig=True, save_only=True)
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2190 z_slice = int(self.tomo_recon_stacks[i].shape[2]/2)
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2191 title = f'{basetitle} {index} zslice{z_slice}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2192 quickImshow(self.tomo_recon_stacks[i][:,:,z_slice], title=title,
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2193 path='center_slice_pngs', save_fig=True, save_only=True)
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2194 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2195 x_slice = int(self.tomo_recon_stacks[i].shape[0]/2)
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2196 title = f'{basetitle} {index} xslice{x_slice}'
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2197 quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2198 path=self.output_folder, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2199 save_only=self.save_plots_only)
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2200 y_slice = int(self.tomo_recon_stacks[i].shape[1]/2)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2201 title = f'{basetitle} {index} yslice{y_slice}'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2202 quickImshow(self.tomo_recon_stacks[i][:,y_slice,:], title=title,
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2203 path=self.output_folder, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2204 save_only=self.save_plots_only)
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2205 z_slice = int(self.tomo_recon_stacks[i].shape[2]/2)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2206 title = f'{basetitle} {index} zslice{z_slice}'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2207 quickImshow(self.tomo_recon_stacks[i][:,:,z_slice], title=title,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2208 path=self.output_folder, save_fig=self.save_plots,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2209 save_only=self.save_plots_only)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2210 # quickPlot(self.tomo_recon_stacks[i]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2211 # [x_slice,int(self.tomo_recon_stacks[i].shape[1]/2),:],
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2212 # title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[1]/2)}',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2213 # path=self.output_folder, save_fig=self.save_plots,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2214 # save_only=self.save_plots_only)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2215 if not self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2216 self._saveTomo('recon stack', self.tomo_recon_stacks[i], index)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2217 self.tomo_stacks[i] = np.array([])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2218
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2219 # Update config and save to file
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2220 stack['reconstructed'] = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2221 combine_stacks = self.config.get('combine_stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2222 if combine_stacks and index in combine_stacks.get('stacks', []):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2223 combine_stacks['stacks'].remove(index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2224 self.cf.saveFile(self.config_out)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2225
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2226 if self.galaxy_flag:
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2227 # Save reconstructed tomography stack to file
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2228 t0 = time()
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2229 output_name = galaxy_param['output_name']
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2230 logging.info(f'Saving reconstructed tomography stack to {output_name} ...')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2231 save_stacks = {f'set_{stack["index"]}':tomo_stack
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2232 for stack,tomo_stack in zip(stacks,self.tomo_recon_stacks)}
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2233 np.savez(output_name, **save_stacks)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2234 logging.info(f'... done in {time()-t0:.2f} seconds!')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2235
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2236 # Create cross section profile in yz-plane
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2237 tomosum = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2238 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,2)) for tomo_recon_stack in
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2239 self.tomo_recon_stacks]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2240 quickPlot(tomosum, title='recon stack sum yz', path='center_slice_pngs',
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2241 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2242
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2243 # Create cross section profile in xz-plane
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2244 tomosum = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2245 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,1)) for tomo_recon_stack in
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2246 self.tomo_recon_stacks]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2247 quickPlot(tomosum, title='recon stack sum xz', path='center_slice_pngs',
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2248 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2249
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2250 # Create cross section profile in xy-plane
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2251 num_tomo_stacks = len(stacks)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2252 row_bounds = self.config['find_center']['row_bounds']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2253 if not is_index_range(row_bounds, 0, self.tomo_recon_stacks[0].shape[0]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2254 illegal_value(row_bounds, 'find_center:row_bounds', 'config file')
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2255 return
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2256 if num_tomo_stacks == 1:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2257 low_bound = row_bounds[0]
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2258 else:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2259 low_bound = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2260 tomosum = np.sum(self.tomo_recon_stacks[0][low_bound:row_bounds[1],:,:], axis=(1,2))
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2261 if num_tomo_stacks > 2:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2262 tomosum = np.concatenate([tomosum]+
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2263 [np.sum(self.tomo_recon_stacks[i][row_bounds[0]:row_bounds[1],:,:],
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2264 axis=(1,2)) for i in range(1, num_tomo_stacks-1)])
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2265 if num_tomo_stacks > 1:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2266 tomosum = np.concatenate([tomosum,
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2267 np.sum(self.tomo_recon_stacks[num_tomo_stacks-1][row_bounds[0]:,:,:],
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2268 axis=(1,2))])
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2269 quickPlot(tomosum, title='recon stack sum xy', path='center_slice_pngs',
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2270 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2271
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2272 def combineTomoStacks(self, galaxy_param=None):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2273 """Combine the reconstructed tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2274 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2275 # stack order: stack,row(z),x,y
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2276 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2277 assert(galaxy_param)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2278 if not os.path.exists('combine_pngs'):
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2279 os.mkdir('combine_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2280 logging.debug('Combine reconstructed tomography stacks')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2281 stack_info = self.config['stack_info']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2282 stacks = stack_info['stacks']
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2283 assert(len(self.tomo_recon_stacks) == stack_info['num'])
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2284 assert(len(self.tomo_recon_stacks) == len(stacks))
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2285 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2286 assert(isinstance(galaxy_param, dict))
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2287 # Get image bounds
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2288 x_bounds = galaxy_param['x_bounds']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2289 assert(isinstance(x_bounds, list) and len(x_bounds) == 2)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2290 y_bounds = galaxy_param['y_bounds']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2291 assert(isinstance(y_bounds, list) and len(y_bounds) == 2)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2292 z_bounds = galaxy_param['z_bounds']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2293 assert(isinstance(z_bounds, list) and len(z_bounds) == 2)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2294 else:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2295 if galaxy_param:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2296 logging.warning('Ignoring galaxy_param in reconstructTomoStacks (only for Galaxy)')
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2297 galaxy_param = None
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2298
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2299 # Load any unloaded reconstructed stacks
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2300 for i,stack in enumerate(stacks):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2301 available = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2302 if not self.tomo_recon_stacks[i].size and stack.get('reconstructed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2303 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2304 stack['index'], required=True)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2305 if not self.tomo_recon_stacks[i].size:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2306 logging.error(f'Unable to load reconstructed stack {stack["index"]}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2307 stack['reconstructed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2308 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2309 if i:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2310 if (self.tomo_recon_stacks[i].shape[1] != self.tomo_recon_stacks[0].shape[1] or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2311 self.tomo_recon_stacks[i].shape[1] != self.tomo_recon_stacks[0].shape[1]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2312 logging.error('Incompatible reconstructed tomography stack dimensions')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2313 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2314
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2315 # Get center stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2316 row_bounds = self.config['find_center']['row_bounds']
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2317 if not is_index_range(row_bounds, 0, self.tomo_recon_stacks[0].shape[0]):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2318 illegal_value(row_bounds, 'find_center:row_bounds', 'config file')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2319 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2320
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2321 # Selecting x bounds (in yz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2322 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2323 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2324 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,2)) for tomo_recon_stack in
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2325 self.tomo_recon_stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2326 combine_stacks = self.config.get('combine_stacks')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2327 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2328 if x_bounds[0] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2329 x_bounds[0] = 0
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2330 if x_bounds[1] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2331 x_bounds[1] = tomosum.size
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2332 if not is_index_range(x_bounds, 0, tomosum.size):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2333 illegal_value(x_bounds, 'x_bounds', 'galaxy input')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2334 tomosum_min = tomosum.min()
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2335 tomosum_max = tomosum.max()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2336 quickPlot((range(tomosum.size), tomosum),
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2337 ([x_bounds[0], x_bounds[0]], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2338 ([x_bounds[1]-1, x_bounds[1]-1], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2339 title=f'recon stack sum yz', path='combine_pngs', save_fig=True, save_only=True)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2340 else:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2341 x_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2342 change_x_bounds = 'y'
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2343 if combine_stacks and 'x_bounds' in combine_stacks:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2344 x_bounds = combine_stacks['x_bounds']
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2345 if is_index_range(x_bounds, 0, tomosum.size):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2346 if not self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2347 quickPlot(tomosum, vlines=x_bounds, title='recon stack sum yz')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2348 print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2349 'exclusive)')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2350 change_x_bounds = 'n'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2351 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2352 illegal_value(x_bounds, 'combine_stacks:x_bounds', 'config file')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2353 x_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2354 if self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2355 if x_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2356 x_bounds = [0, tomosum.size]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2357 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2358 if not input_yesno('\nDo you want to change the image x-bounds (y/n)?',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2359 change_x_bounds):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2360 if x_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2361 x_bounds = [0, tomosum.size]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2362 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2363 accept = False
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2364 if x_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2365 index_ranges = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2366 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2367 index_ranges = [x_bounds]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2368 while not accept:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2369 mask, x_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2370 title='select x data range', legend='recon stack sum yz')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2371 while len(x_bounds) != 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2372 print('Please select exactly one continuous range')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2373 mask, x_bounds = draw_mask_1d(tomosum, title='select x data range',
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2374 legend='recon stack sum yz')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2375 x_bounds = list(x_bounds[0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2376 quickPlot(tomosum, vlines=x_bounds, title='recon stack sum yz')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2377 print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2378 'exclusive)')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2379 accept = input_yesno('Accept these bounds (y/n)?', 'y')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2380 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2381 clearPlot('recon stack sum yz')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2382 logging.info(f'x_bounds = {x_bounds}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2383
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2384 # Selecting y bounds (in xz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2385 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2386 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2387 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,1)) for tomo_recon_stack in
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2388 self.tomo_recon_stacks]
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2389 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2390 if y_bounds[0] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2391 y_bounds[0] = 0
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2392 if y_bounds[1] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2393 y_bounds[1] = tomosum.size
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2394 if not is_index_range(y_bounds, 0, tomosum.size):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2395 illegal_value(y_bounds, 'y_bounds', 'galaxy input')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2396 tomosum_min = tomosum.min()
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2397 tomosum_max = tomosum.max()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2398 quickPlot((range(tomosum.size), tomosum),
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2399 ([y_bounds[0], y_bounds[0]], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2400 ([y_bounds[1]-1, y_bounds[1]-1], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2401 title=f'recon stack sum xz', path='combine_pngs', save_fig=True, save_only=True)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2402 else:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2403 y_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2404 change_y_bounds = 'y'
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2405 if combine_stacks and 'y_bounds' in combine_stacks:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2406 y_bounds = combine_stacks['y_bounds']
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2407 if is_index_range(y_bounds, 0, tomosum.size):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2408 if not self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2409 quickPlot(tomosum, vlines=y_bounds, title='recon stack sum xz')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2410 print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2411 'exclusive)')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2412 change_y_bounds = 'n'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2413 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2414 illegal_value(y_bounds, 'combine_stacks:y_bounds', 'config file')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2415 y_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2416 if self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2417 if y_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2418 y_bounds = [0, tomosum.size]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2419 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2420 if not input_yesno('\nDo you want to change the image y-bounds (y/n)?',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2421 change_y_bounds):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2422 if y_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2423 y_bounds = [0, tomosum.size]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2424 else:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2425 accept = False
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2426 if y_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2427 index_ranges = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2428 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2429 index_ranges = [y_bounds]
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2430 while not accept:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2431 mask, y_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2432 title='select x data range', legend='recon stack sum xz')
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2433 while len(y_bounds) != 1:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2434 print('Please select exactly one continuous range')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2435 mask, y_bounds = draw_mask_1d(tomosum, title='select x data range',
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2436 legend='recon stack sum xz')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2437 y_bounds = list(y_bounds[0])
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2438 quickPlot(tomosum, vlines=y_bounds, title='recon stack sum xz')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2439 print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2440 'exclusive)')
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2441 accept = input_yesno('Accept these bounds (y/n)?', 'y')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2442 if self.save_plots_only:
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2443 clearPlot('recon stack sum xz')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2444 logging.info(f'y_bounds = {y_bounds}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2445
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2446 # Combine reconstructed tomography stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2447 logging.info(f'Combining reconstructed stacks ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2448 t0 = time()
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2449 num_tomo_stacks = len(stacks)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2450 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2451 low_bound = row_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2452 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2453 low_bound = 0
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2454 tomo_recon_combined = self.tomo_recon_stacks[0][low_bound:row_bounds[1],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2455 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2456 if num_tomo_stacks > 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2457 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2458 [self.tomo_recon_stacks[i][row_bounds[0]:row_bounds[1],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2459 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2460 for i in range(1, num_tomo_stacks-1)])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2461 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2462 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2463 [self.tomo_recon_stacks[num_tomo_stacks-1][row_bounds[0]:,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2464 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2465 logging.info(f'... done in {time()-t0:.2f} seconds!')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2466 combined_stacks = [stack['index'] for stack in stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2467
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2468 # Selecting z bounds (in xy-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2469 tomosum = np.sum(tomo_recon_combined, axis=(1,2))
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2470 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2471 if z_bounds[0] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2472 z_bounds[0] = 0
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2473 if z_bounds[1] == -1:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2474 z_bounds[1] = tomosum.size
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2475 if not is_index_range(z_bounds, 0, tomosum.size):
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2476 illegal_value(z_bounds, 'z_bounds', 'galaxy input')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2477 tomosum_min = tomosum.min()
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2478 tomosum_max = tomosum.max()
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2479 quickPlot((range(tomosum.size), tomosum),
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2480 ([z_bounds[0], z_bounds[0]], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2481 ([z_bounds[1]-1, z_bounds[1]-1], [tomosum_min, tomosum_max], 'r-'),
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2482 title=f'recon stack sum xy', path='combine_pngs', save_fig=True, save_only=True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2483 else:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2484 z_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2485 if combine_stacks and 'z_bounds' in combine_stacks:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2486 z_bounds = combine_stacks['z_bounds']
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2487 if is_index_range(z_bounds, 0, tomosum.size):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2488 if not self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2489 quickPlot(tomosum, vlines=z_bounds, title='recon stack sum xy')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2490 print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2491 'exclusive)')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2492 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2493 illegal_value(z_bounds, 'combine_stacks:z_bounds', 'config file')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2494 z_bounds = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2495 if self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2496 if z_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2497 z_bounds = [0, tomosum.size]
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2498 else:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2499 if not input_yesno('\nDo you want to change the image z-bounds (y/n)?', 'n'):
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2500 if z_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2501 z_bounds = [0, tomosum.size]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2502 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2503 accept = False
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2504 if z_bounds is None:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2505 index_ranges = None
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2506 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2507 index_ranges = [z_bounds]
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2508 while not accept:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2509 mask, z_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2510 title='select x data range', legend='recon stack sum xy')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2511 while len(z_bounds) != 1:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2512 print('Please select exactly one continuous range')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2513 mask, z_bounds = draw_mask_1d(tomosum, title='select x data range',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2514 legend='recon stack sum xy')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2515 z_bounds = list(z_bounds[0])
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2516 quickPlot(tomosum, vlines=z_bounds, title='recon stack sum xy')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2517 print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2518 'exclusive)')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2519 accept = input_yesno('Accept these bounds (y/n)?', 'y')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2520 if self.save_plots_only:
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2521 clearPlot('recon stack sum xy')
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2522 logging.info(f'z_bounds = {z_bounds}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2523
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2524 # Plot center slices
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2525 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2526 path = 'combine_pngs'
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2527 save_fig = True
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2528 save_only = True
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2529 else:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2530 path = self.output_folder
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2531 save_fig = self.save_plots
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2532 save_only = self.save_plots_only
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2533 quickImshow(tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2534 title=f'recon combined xslice{int(tomo_recon_combined.shape[0]/2)}',
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2535 path=path, save_fig=save_fig, save_only=save_only)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2536 quickImshow(tomo_recon_combined[:,int(tomo_recon_combined.shape[1]/2),:],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2537 title=f'recon combined yslice{int(tomo_recon_combined.shape[1]/2)}',
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2538 path=path, save_fig=save_fig, save_only=save_only)
49 26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12" rv43 parents: 48 diff changeset	2539 quickImshow(tomo_recon_combined[:,:,int(tomo_recon_combined.shape[2]/2)],
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2540 title=f'recon combined zslice{int(tomo_recon_combined.shape[2]/2)}',
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2541 path=path, save_fig=save_fig, save_only=save_only)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2542
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2543 # Save combined reconstructed tomography stack or test mode data to file
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2544 if self.galaxy_flag:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2545 t0 = time()
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2546 output_name = galaxy_param['output_name']
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2547 logging.info(f'Saving combined reconstructed tomography stack to {output_name} ...')
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2548 np.save(output_name, tomo_recon_combined)
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2549 logging.info(f'... done in {time()-t0:.2f} seconds!')
61 75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2550 elif self.test_mode:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2551 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2552 filename = 'recon combined sum xy'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2553 if zoom_perc is None or zoom_perc == 100:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2554 filename += ' fullres.dat'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2555 else:
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2556 filename += f' {zoom_perc}p.dat'
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2557 quickPlot(tomosum, title='recon combined sum xy',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2558 path=self.output_folder, save_fig=self.save_plots,
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2559 save_only=self.save_plots_only)
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2560 np.savetxt(f'{self.output_folder}/recon_combined.txt',
75dd6e15f628 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 47b7bc203de6eac4d3e081b1fae8acb352f54b55" rv43 parents: 49 diff changeset	2561 tomo_recon_combined[int(tomosum.size/2),:,:], fmt='%.6e')
48 059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2562 else:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2563 base_name = 'recon combined'
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2564 for stack in stacks:
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2565 base_name += f' {stack["index"]}'
059819ea1f0e "planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d" rv43 parents: 47 diff changeset	2566 self._saveTomo(base_name, tomo_recon_combined)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2567
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2568 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2569 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2570 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2571 combine_stacks['y_bounds'] = y_bounds
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2572 combine_stacks['z_bounds'] = z_bounds
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2573 combine_stacks['stacks'] = combined_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2574 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2575 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2576 'z_bounds' : z_bounds, 'stacks' : combined_stacks}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2577 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2578
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2579 def runTomo(config_file=None, config_dict=None, output_folder='.', log_level='INFO',
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2580 test_mode=False, num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2581 """Run a tomography analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2582 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2583 # Instantiate Tomo object
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2584 tomo = Tomo(config_file=config_file, output_folder=output_folder, log_level=log_level,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2585 test_mode=test_mode, num_core=num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2586 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2587 raise ValueError('Invalid config and/or detector file provided.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2588
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2589 # Preprocess the image files
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2590 assert(tomo.config['stack_info'])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2591 num_tomo_stacks = tomo.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2592 assert(num_tomo_stacks == len(tomo.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2593 preprocessed_stacks = []
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2594 if not tomo.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2595 preprocess = tomo.config.get('preprocess', None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2596 if preprocess:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2597 preprocessed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2598 if stack.get('preprocessed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2599 if len(preprocessed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2600 tomo.genTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2601 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2602 IOError('Unable to load all required image files.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2603 tomo.cf.saveFile(tomo.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2604
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2605 # Find centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2606 find_center = tomo.config.get('find_center')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2607 if find_center is None or not find_center.get('completed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2608 tomo.findCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2609
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2610 # Check centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2611 #if num_tomo_stacks > 1 and not tomo.config.get('check_centers', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2612 # tomo.checkCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2613
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2614 # Reconstruct tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2615 assert(tomo.config['stack_info']['stacks'])
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2616 reconstructed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2617 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2618 if len(reconstructed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2619 tomo.reconstructTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2620
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2621 # Combine reconstructed tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2622 reconstructed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2623 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2624 combine_stacks = tomo.config.get('combine_stacks')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2625 if len(reconstructed_stacks) and (combine_stacks is None or
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2626 combine_stacks.get('stacks') != reconstructed_stacks):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2627 tomo.combineTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2628
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2629 #%%============================================================================
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2630 if __name__ == '__main__':
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2631
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2632 # Parse command line arguments
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2633 parser = argparse.ArgumentParser(
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2634 description='Tomography reconstruction')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2635 parser.add_argument('-c', '--config',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2636 default=None,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2637 help='Input config')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2638 parser.add_argument('-o', '--output_folder',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2639 default='.',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2640 help='Output folder')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2641 parser.add_argument('-l', '--log_level',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2642 default='INFO',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2643 help='Log level')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2644 parser.add_argument('-t', '--test_mode',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2645 action='store_true',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2646 default=False,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2647 help='Test mode flag')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2648 parser.add_argument('--num_core',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2649 type=int,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2650 default=-1,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2651 help='Number of cores')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2652 args = parser.parse_args()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2653
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2654 if args.config is None:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2655 if os.path.isfile('config.yaml'):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2656 args.config = 'config.yaml'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2657 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2658 args.config = 'config.txt'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2659
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2660 # Set basic log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2661 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2662 if not args.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2663 level = getattr(logging, args.log_level.upper(), None)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2664 if not isinstance(level, int):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2665 raise ValueError(f'Invalid log_level: {args.log_level}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2666 logging.basicConfig(format=logging_format, level=level, force=True,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2667 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2668
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2669 logging.debug(f'config = {args.config}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2670 logging.debug(f'output_folder = {args.output_folder}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2671 logging.debug(f'log_level = {args.log_level}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2672 logging.debug(f'test_mode = {args.test_mode}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2673 logging.debug(f'num_core = {args.num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2674
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2675 # Run tomography analysis
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2676 runTomo(config_file=args.config, output_folder=args.output_folder, log_level=args.log_level,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2677 test_mode=args.test_mode, num_core=args.num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2678
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2679 #%%============================================================================
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2680 # input('Press any key to continue')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2681 #%%============================================================================

Mercurial > repos > rv43 > tomo

annotate tomo.py @ 61:75dd6e15f628 draft