tomo: tomo.py annotate

annotate tomo.py @ 47:c693117d01e9 draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty"

author	rv43
date	Mon, 25 Apr 2022 20:02:15 +0000
parents	d73e715e975b
children	059819ea1f0e

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
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	17 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	18 import pyinputplus as pyip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	19 except:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	20 pass
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	21 import argparse
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	22 import numpy as np
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	23 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	24 import numexpr as ne
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	25 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	26 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	27 import multiprocessing as mp
41 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 scipy.ndimage as spi
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
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	32 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	33 import tomopy
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	34 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	35 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	36 from time import time
41 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.transform import iradon
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
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	41 try:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	42 from skimage.restoration import denoise_tv_chambolle
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	43 except:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	44 pass
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	45
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	46 import msnc_tools as msnc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	47
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	48 # 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	49 # - tomopy.find_center_vo
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	50 # - tomopy.prep.stripe.remove_stripe_fw
46 d73e715e975b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac" rv43 parents: 45 diff changeset	51 num_core_tomopy_limit = 24
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	52
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	53 class set_numexpr_threads:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	54
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	55 def __init__(self, num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	56 cpu_count = mp.cpu_count()
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	57 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	58 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	59 self.num_core = cpu_count
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	60 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	61 self.num_core = num_core
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	62 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	63
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	64 def __enter__(self):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	65 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	66 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	67
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	68 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	69 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	70
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	71 class ConfigTomo(msnc.Config):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	72 """Class for processing a config file.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	73 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	74
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	75 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	76 super().__init__(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	77
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	78 def _validate_txt(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	79 """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	80 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	81 is_valid = True
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 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	84 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	85 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	86 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	87 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	88 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	89 self.detector_id = self.config.get('detector_id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	90
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	91 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	92 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	93
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	94 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	95 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	96
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	97 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	98 self.num_tomo_stacks = self.config.get('num_tomo_stacks', 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	99 if not msnc.is_int(self.num_tomo_stacks, 1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	100 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	101 msnc.illegal_value('num_tomo_stacks', self.num_tomo_stacks, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	102 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	103 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	104
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	105 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	106 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	107 if 'tomo_data_path' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	108 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	109 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	110 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	111 self.tomo_data_paths = [tomo_data_paths_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	112 self.tomo_data_indices = [msnc.get_trailing_int(tomo_data_paths_indices[i][0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	113 if msnc.get_trailing_int(tomo_data_paths_indices[i][0]) else None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	114 for i in range(self.num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	115 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	116 if 'z_pos' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	117 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	118 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	119 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	120 if len(tomo_ref_height_indices):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	121 self.tomo_ref_heights = [
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	122 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	123 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	124 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	125
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	126 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	127 self.start_theta = self.config.get('start_theta', 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	128 if not msnc.is_num(self.start_theta, 0.):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	129 msnc.illegal_value('start_theta', self.start_theta, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	130 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	131 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	132 self.end_theta = self.config.get('end_theta', 180.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	133 if not msnc.is_num(self.end_theta, self.start_theta):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	134 msnc.illegal_value('end_theta', self.end_theta, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	135 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	136 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	137 self.num_thetas = self.config.get('num_thetas')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	138 if not (self.num_thetas is None or msnc.is_int(self.num_thetas, 1)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	139 msnc.illegal_value('num_thetas', self.num_thetas, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	140 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	141 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	142 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	143
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	144 return is_valid
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 def _validate_yaml(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	147 """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	148 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	149 is_valid = True
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 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	152 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	153 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	154 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	155 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	156 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	157 self.detector_id = self.config['detector'].get('id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	158
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	159 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	160 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	161
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	162 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	163 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	164
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	165 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	166 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	167 self.num_tomo_stacks = stack_info.get('num', 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	168 if not msnc.is_int(self.num_tomo_stacks, 1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	169 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	170 msnc.illegal_value('stack_info:num', self.num_tomo_stacks, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	171 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	172 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	173
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	174 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	175 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	176 if stacks is None or len(stacks) is not self.num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	177 msnc.illegal_value('stack_info:stacks', stacks, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	178 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	179 self.tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	180 self.tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	181 self.tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	182 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	183 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	184 self.tomo_data_indices.append(stack.get('index'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	185 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	186
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	187 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	188 theta_range = self.config.get('theta_range')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	189 if theta_range is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	190 self.start_theta = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	191 self.end_theta = 180.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	192 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	193 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	194 self.start_theta = theta_range.get('start', 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	195 if not msnc.is_num(self.start_theta, 0.):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	196 msnc.illegal_value('theta_range:start', self.start_theta, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	197 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	198 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	199 self.end_theta = theta_range.get('end', 180.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	200 if not msnc.is_num(self.end_theta, self.start_theta):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	201 msnc.illegal_value('theta_range:end', self.end_theta, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	202 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	203 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	204 self.num_thetas = theta_range.get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	205 if self.num_thetas and not msnc.is_int(self.num_thetas, 1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	206 msnc.illegal_value('theta_range:num', self.num_thetas, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	207 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	208 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	209 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	210
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	211 return is_valid
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 def validate(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	214 """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	215 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	216 is_valid = True
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 # Check work_folder (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	219 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	220 if not os.path.isdir(work_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	221 msnc.illegal_value('work_folder', work_folder, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	222 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	223 logging.info(f'work_folder: {work_folder}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	224
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	225 # Check data filetype (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	226 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	227 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	228 self.data_filetype != 'h5'):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	229 msnc.illegal_value('data_filetype', self.data_filetype, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	230
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	231 if self.suffix == '.yml' or self.suffix == '.yaml':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	232 is_valid = self._validate_yaml()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	233 elif self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	234 is_valid = self._validate_txt()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	235 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	236 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	237 is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	238
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	239 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	240 if self.tdf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	241 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	242 if isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	243 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	244 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	245 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	246 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	247 msnc.illegal_value('tdf_data_path', tdf_data_fil, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	248 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	249 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	250 if isinstance(self.tdf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	251 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	252 f'{work_folder}/{self.tdf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	253 elif isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	254 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	255 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	256 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	257 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	258 msnc.illegal_value('tdf_data_path', self.tdf_data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	259 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	260 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	261
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	262 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	263 if self.tbf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	264 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	265 if isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	266 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	267 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	268 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	269 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	270 msnc.illegal_value('tbf_data_path', tbf_data_fil, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	271 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	272 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	273 if isinstance(self.tbf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	274 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	275 f'{work_folder}/{self.tbf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	276 elif isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	277 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	278 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	279 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	280 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	281 msnc.illegal_value('tbf_data_path', self.tbf_data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	282 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	283 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	284
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	285 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	286 tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	287 tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	288 tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	289 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	290 self.tomo_ref_heights):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	291 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	292 if isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	293 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	294 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	295 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	296 msnc.illegal_value(f'stack_info:stacks:data_path', data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	297 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	298 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	299 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	300 if isinstance(data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	301 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	302 elif isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	303 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	304 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	305 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	306 msnc.illegal_value(f'stack_info:stacks:data_path', data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	307 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	308 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	309 tomo_data_paths.append(data_path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	310 if index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	311 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	312 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	313 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	314 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	315 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	316 index = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	317 elif not isinstance(index, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	318 msnc.illegal_value(f'stack_info:stacks:index', index, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	319 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	320 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	321 tomo_data_indices.append(index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	322 if ref_height is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	323 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	324 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	325 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	326 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	327 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	328 ref_height = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	329 elif not msnc.is_num(ref_height):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	330 msnc.illegal_value(f'stack_info:stacks:ref_height', ref_height, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	331 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	332 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	333 # Set reference heights relative to first stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	334 if (len(tomo_ref_heights) and msnc.is_num(ref_height) and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	335 msnc.is_num(tomo_ref_heights[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	336 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	337 tomo_ref_heights.append(ref_height)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	338 tomo_ref_heights[0] = 0.0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	339 logging.info('tomography data paths:')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	340 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	341 logging.info(f' {tomo_data_paths[i]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	342 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	343 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	344
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	345 # Update config in memory
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	346 if self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	347 self.config = {}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	348 dark_field = self.config.get('dark_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	349 if dark_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	350 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	351 else:
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 bright_field = self.config.get('bright_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	354 if bright_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	355 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	356 else:
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 detector = self.config.get('detector')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	359 if detector is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	360 self.config['detector'] = {'id' : self.detector_id}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	361 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	362 detector['id'] = self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	363 self.config['work_folder'] = work_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	364 self.config['data_filetype'] = self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	365 stack_info = self.config.get('stack_info')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	366 if stack_info is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	367 stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	368 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	369 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	370 'ref_height' : tomo_ref_heights[i]})
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	371 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	372 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	373 stack_info['num'] = self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	374 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	375 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	376 stack['data_path'] = tomo_data_paths[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	377 stack['index'] = tomo_data_indices[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	378 stack['ref_height'] = tomo_ref_heights[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	379 if self.num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	380 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	381 'num' : self.num_thetas}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	382 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	383 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	384 self.config['theta_range'] = theta_range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	385
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	386 # Cleanup temporary validation variables
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	387 del self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	388 del self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	389 del self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	390 del self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	391 del self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	392 del self.tomo_data_paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	393 del self.tomo_data_indices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	394 del self.tomo_ref_heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	395 del self.start_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	396 del self.end_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	397 del self.num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	398
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	399 return is_valid
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 class Tomo:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	402 """Processing tomography data with misalignment.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	403 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	404
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	405 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	406 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	407 num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	408 """Initialize with optional config input file or dictionary
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	409 """
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	410 self.num_core = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	411 self.config_out = config_out
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	412 self.output_folder = output_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	413 self.galaxy_flag = galaxy_flag
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	414 self.test_mode = test_mode
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	415 self.save_plots = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	416 self.save_plots_only = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	417 self.cf = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	418 self.config = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	419 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	420 self.tdf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	421 self.tbf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	422 self.tomo_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	423 self.tomo_recon_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	424
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	425 # Validate input parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	426 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	427 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	428 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	429 raise ValueError(f'Invalid config_dict input {config_dict} {type(config_dict)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	430 if config_out is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	431 if isinstance(config_out, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	432 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	433 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	434 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	435 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	436 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	437 raise OSError(f'Invalid config_out input {config_out} {type(config_out)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	438 if not os.path.isdir(output_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	439 raise OSError(f'Invalid output_folder input {output_folder} {type(output_folder)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	440 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	441 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	442 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	443 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	444 if not os.path.isabs(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	445 log_stream = f'{output_folder}/{log_stream}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	446 if not isinstance(galaxy_flag, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	447 raise ValueError(f'Invalid galaxy_flag input {galaxy_flag} {type(galaxy_flag)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	448 if not isinstance(test_mode, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	449 raise ValueError(f'Invalid test_mode input {test_mode} {type(test_mode)}')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	450 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	451 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	452 if num_core == -1:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	453 self.num_core = mp.cpu_count()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	454 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	455 self.num_core = num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	456
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	457 # Set log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	458 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	459 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	460 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	461 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	462 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	463 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	464 #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	465 elif isinstance(log_stream, io.TextIOWrapper):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	466 #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	467 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	468 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	469 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	470 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	471 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	472 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	473 level = getattr(logging, log_level.upper(), None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	474 if not isinstance(level, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	475 raise ValueError(f'Invalid log_level: {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	476 if log_stream is sys.stdout:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	477 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	478 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	479 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	480 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	481 logging.basicConfig(filename=f'{log_stream}', filemode='w',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	482 format=logging_format, level=level, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	483 elif isinstance(log_stream, io.TextIOWrapper):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	484 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	485 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	486 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	487 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	488 stream_handler = logging.StreamHandler()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	489 logging.getLogger().addHandler(stream_handler)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	490 stream_handler.setLevel(logging.WARNING)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	491 stream_handler.setFormatter(logging.Formatter(logging_format))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	492
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	493 # Check/set output config file name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	494 if self.config_out is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	495 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	496 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	497 not os.path.isabs(self.config_out)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	498 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	499
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	500 # Create config object and load config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	501 self.cf = ConfigTomo(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	502 if not self.cf.load_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	503 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	504 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	505
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	506 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	507 assert(self.output_folder == '.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	508 assert(self.test_mode is False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	509 self.save_plots = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	510 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	511 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	512 # 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	513
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	514 # Check config file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	515 self.is_valid = self.cf.validate()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	516
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	517 # Load detector info file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	518 df = msnc.Detector(self.cf.config['detector']['id'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	519
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	520 # Check detector info file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	521 if df.validate():
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	522 pixel_size = df.getPixelSize()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	523 num_rows, num_columns = df.getDimensions()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	524 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	525 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	526 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	527 pixel_size = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	528 num_rows = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	529 num_columns = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	530 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	531
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	532 # Update config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	533 self.cf.config['detector']['pixel_size'] = pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	534 self.cf.config['detector']['rows'] = num_rows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	535 self.cf.config['detector']['columns'] = num_columns
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	536 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	537 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	538 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	539
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	540 # Safe config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	541 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	542 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	543
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	544 # Initialize shortcut to config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	545 self.config = self.cf.config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	546
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	547 # Initialize tomography stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	548 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	549 if num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	550 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	551 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	552
2 b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e" rv43 parents: 1 diff changeset	553 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	554 logging.debug(f'config_file = {config_file}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	555 logging.debug(f'config_dict = {config_dict}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	556 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	557 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	558 logging.debug(f'log_stream = {log_stream}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	559 logging.debug(f'log_level = {log_level}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	560 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	561 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	562 logging.debug(f'save_plots = {self.save_plots}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	563 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	564
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	565 def _selectImageRanges(self, available_stacks=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	566 """Select image files to be included in analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	567 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	568 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	569 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	570 if available_stacks is None:
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 elif len(available_stacks) != stack_info['num']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	573 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	574 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	575 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	576
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	577 # Check number of tomography angles/thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	578 num_thetas = self.config['theta_range'].get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	579 if num_thetas is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	580 num_thetas = pyip.inputInt('\nEnter the number of thetas (>0): ', greaterThan=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	581 elif not msnc.is_int(num_thetas, 0):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	582 msnc.illegal_value('num_thetas', num_thetas, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	583 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	584 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	585 self.config['theta_range']['num'] = num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	586 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	587
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	588 # Find tomography dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	589 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	590 img_start = dark_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	591 img_offset = dark_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	592 num_imgs = dark_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	593 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	594 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	595 num_imgs, 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	596 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	597 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	598 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	599 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	600 dark_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	601 dark_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	602 dark_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	603 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	604 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	605 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	606
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	607 # Find tomography bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	608 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	609 img_start = bright_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	610 img_offset = bright_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	611 num_imgs = bright_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	612 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	613 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	614 num_imgs, 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	615 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	616 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	617 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	618 bright_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	619 bright_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	620 bright_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	621 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	622 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	623 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	624
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	625 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	626 for i,stack in enumerate(stack_info['stacks']):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	627 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	628 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	629 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	630 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	631 img_start = stack.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	632 img_offset = stack.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	633 num_imgs = stack.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	634 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	635 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	636 num_imgs, f'tomography stack {index}', num_thetas)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	637 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	638 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	639 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	640 stack['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	641 stack['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	642 stack['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	643 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	644 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	645 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	646
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	647 # Safe updated config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	648 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	649 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	650
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	651 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	652
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	653 def _genDark(self, tdf_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	654 """Generate dark field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	655 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	656 # Load the dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	657 logging.debug('Loading dark field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	658 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	659 tdf_stack = msnc.loadImageStack(tdf_files, self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	660 dark_field['img_offset'], dark_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	661
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	662 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	663 self.tdf = np.median(tdf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	664 del tdf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	665
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	666 # RV make input of some kind (not always needed)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	667 tdf_cutoff = 21
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	668 self.tdf[self.tdf > tdf_cutoff] = np.nan
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	669 tdf_mean = np.nanmean(self.tdf)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	670 logging.debug(f'tdf_cutoff = {tdf_cutoff}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	671 logging.debug(f'tdf_mean = {tdf_mean}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	672 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	673 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	674 msnc.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	675 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	676 elif not self.test_mode:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	677 msnc.quickImshow(self.tdf, title='dark field', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	678 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	679
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	680 def _genBright(self, tbf_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	681 """Generate bright field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	682 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	683 # Load the bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	684 logging.debug('Loading bright field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	685 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	686 tbf_stack = msnc.loadImageStack(tbf_files, self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	687 bright_field['img_offset'], bright_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	688
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	689 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	690 """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	691 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	692 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	693 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	694 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	695 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	696 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	697 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	698 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	699 self.tbf = np.median(tbf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	700 del tbf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	701
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	702 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	703 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	704 self.tbf -= self.tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	705 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	706 logging.warning('Dark field unavailable')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	707 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	708 msnc.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	709 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	710 elif not self.test_mode:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	711 msnc.quickImshow(self.tbf, title='bright field', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	712 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	713
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	714 def _setDetectorBounds(self, tomo_stack_files):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	715 """Set vertical detector bounds for image stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	716 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	717 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	718 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	719 img_x_bounds = [None, None]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	720 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	721 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	722 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	723 if img_x_bounds[0] < 0:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	724 msnc.illegal_value('img_x_bounds[0]', img_x_bounds[0], 'config file')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	725 img_x_bounds[0] = 0
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	726 if not msnc.is_index_range(img_x_bounds, 0, self.tbf.shape[0]):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	727 msnc.illegal_value('img_x_bounds[1]', img_x_bounds[1], 'config file')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	728 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	729 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	730 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	731 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	732 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	733 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	734 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	735 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	736 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	737
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	738 # Check reference heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	739 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	740 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	741 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	742 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	743 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	744 num_x_min = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	745 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	746 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	747 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	748 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	749 for i in range(2, num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	750 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	751 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	752 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	753 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	754 if num_x_min > self.tbf.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	755 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	756 num_x_min = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	757
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	758 # Select image bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	759 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	760 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	761 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	762 x_sum_max = x_sum.max()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	763 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	764 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	765 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	766 fit = msnc.fitStep(y=x_sum, model='rectangle', form='atan')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	767 x_low = fit.get('center1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	768 x_upp = fit.get('center2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	769 sig_low = fit.get('sigma1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	770 sig_upp = fit.get('sigma2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	771 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	772 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	773 (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	774 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	775 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	776 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	777 else:
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)/2-num_x_min/2)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	779 x_upp = x_low+num_x_min
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	780 if x_low < 0:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	781 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	782 if x_upp > x_sum.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	783 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	784 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	785 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	786 x_upp = x_sum.size
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	787 msnc.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	788 ([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	789 ([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	790 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	791 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	792 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	793 for i,stack in enumerate(stacks):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	794 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	795 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	796 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	797 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	798 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	799 tomo_stack[x_low,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	800 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	801 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	802 msnc.quickImshow(tomo_stack, title=title, path='setup_pngs',
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	803 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	804 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	805 del tomo_stack
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	806
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	807 # Update config and save to file
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	808 img_x_bounds = [x_low, x_upp]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	809 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	810 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	811 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	812 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	813 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	814 self.cf.saveFile(self.config_out)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	815 del x_sum
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	816 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	817
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	818 # 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	819 title = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	820 msnc.quickImshow(self.tbf, title='bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	821 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	822 tomo_stack = msnc.loadImageStack(tomo_stack_files[0], self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	823 stacks[0]['img_offset'], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	824 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	825 msnc.quickImshow(tomo_stack[0,:,:], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	826 tomo_or_bright = pyip.inputNum('\nSelect image bounds from bright field (0) or '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	827 'from first tomography image (1): ', min=0, max=1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	828 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	829 print('\nSelect image bounds from bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	830 tomo_or_bright = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	831 if tomo_or_bright:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	832 x_sum = np.sum(tomo_stack[0,:,:], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	833 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	834 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	835 tmp = np.copy(tomo_stack[0,:,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	836 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	837 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	838 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	839 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	840 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	841 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	842 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	843 x_sum_max = x_sum.max()
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	844 msnc.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	845 ([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	846 ([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	847 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	848 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	849 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	850 use_bounds = pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	851 if use_bounds == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	852 img_x_bounds = msnc.selectImageBounds(tomo_stack[0,:,:], 0,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	853 img_x_bounds[0], img_x_bounds[1], num_x_min,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	854 f'tomography image at theta={self.config["theta_range"]["start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	855 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	856 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	857 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	858 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	859 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	860 msnc.quickPlot(range(img_x_bounds[0], img_x_bounds[1]),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	861 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	862 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	863 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	864 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	865 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	866 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	867 x_sum_max = x_sum.max()
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	868 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	869 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	870 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	871 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	872 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	873 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	874 title = 'bright field'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	875 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	876 del tmp
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	877 msnc.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	878 ([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	879 ([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	880 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	881 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	882 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	883 use_bounds = pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	884 if use_bounds == 'no':
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	885 use_fit = 'no'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	886 fit = msnc.fitStep(y=x_sum, model='rectangle', form='atan')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	887 x_low = fit.get('center1', None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	888 x_upp = fit.get('center2', None)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	889 sig_low = fit.get('sigma1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	890 sig_upp = fit.get('sigma2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	891 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	892 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	893 (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	894 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	895 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	896 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	897 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	898 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	899 x_upp = x_low+num_x_min
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	900 if x_low < 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	901 x_low = 0
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	902 if x_upp > x_sum.size:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	903 x_upp = x_sum.size
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	904 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	905 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	906 tmp[x_low,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	907 tmp[x_upp-1,:] = tmp_max
43 0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	908 title = 'bright field'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	909 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	910 del tmp
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	911 msnc.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	912 ([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	913 ([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	914 title='sum over theta and y')
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	915 print(f'lower bound = {x_low} (inclusive)')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	916 print(f'upper bound = {x_upp} (exclusive)]')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	917 use_fit = pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	918 if use_fit == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	919 img_x_bounds = msnc.selectArrayBounds(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	920 num_x_min, 'sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	921 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	922 img_x_bounds = [x_low, x_upp]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	923 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	924 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	925 #msnc.quickPlot(range(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	926 # 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	927 # 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	928 # save_fig=self.save_plots, save_only=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	929 msnc.quickPlot((range(x_sum.size), x_sum),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	930 ([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	931 ([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	932 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	933 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	934 del x_sum
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	935 for i,stack in enumerate(stacks):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	936 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	937 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	938 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	939 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	940 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	941 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	942 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	943 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	944 if self.galaxy_flag:
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	945 msnc.quickImshow(tomo_stack, title=title, path='setup_pngs',
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	946 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	947 show_grid=True)
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	948 else:
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	949 msnc.quickImshow(tomo_stack, title=title, path=self.output_folder,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067" rv43 parents: 41 diff changeset	950 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	951 save_only=True, show_grid=True)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	952 del tomo_stack
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	953 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	954
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	955 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	956 msnc.clearFig('bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	957 msnc.clearFig('sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	958 if title:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	959 msnc.clearFig(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	960
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	961 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	962 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	963 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	964 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	965 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	966 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	967
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	968 def _setZoomOrSkip(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	969 """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	970 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	971 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	972 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	973 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	974 if preprocess is None or 'zoom_perc' not in preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	975 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	976 '\nDo you want to zoom in to reduce memory requirement (y/[n])? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	977 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	978 zoom_perc = pyip.inputInt(' Enter zoom percentage [1, 100]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	979 min=1, max=100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	980 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	981 zoom_perc = preprocess['zoom_perc']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	982 if msnc.is_num(zoom_perc, 1., 100.):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	983 zoom_perc = int(zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	984 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	985 msnc.illegal_value('zoom_perc', zoom_perc, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	986 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	987 num_theta_skip = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	988 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	989 if preprocess is None or 'num_theta_skip' not in preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	990 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	991 'Do you want to skip thetas to reduce memory requirement (y/[n])? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	992 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	993 num_theta_skip = pyip.inputInt(' Enter the number skip theta interval'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	994 f' [0, {self.num_thetas-1}]: ', min=0, max=self.num_thetas-1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	995 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	996 num_theta_skip = preprocess['num_theta_skip']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	997 if not msnc.is_int(num_theta_skip, 0):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	998 msnc.illegal_value('num_theta_skip', num_theta_skip, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	999 num_theta_skip = 0
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1000 logging.debug(f'zoom_perc = {zoom_perc}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1001 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	1002
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1003 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1004 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1005 self.cf.config['preprocess'] = {'zoom_perc' : zoom_perc,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1006 'num_theta_skip' : num_theta_skip}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1007 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1008 preprocess['zoom_perc'] = zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1009 preprocess['num_theta_skip'] = num_theta_skip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1010 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1011
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1012 def _loadTomo(self, base_name, index, required=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1013 """Load a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1014 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1015 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1016 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1017 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1018 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1019 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1020 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	1021 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1022 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1023 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1024 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1025 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	1026 load_flag = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1027 available = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1028 if os.path.isfile(tomo_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1029 available = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1030 if required:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1031 load_flag = 'yes'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1032 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1033 load_flag = pyip.inputYesNo(f'\nDo you want to load {tomo_file} (y/n)? ')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1034 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1035 if load_flag == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1036 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1037 logging.info(f'Loading {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1038 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1039 stack = np.load(tomo_file)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1040 except IOError or ValueError:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1041 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1042 logging.error(f'Error loading {tomo_file}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1043 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	1044 if stack.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1045 msnc.quickImshow(stack[:,0,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1046 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	1047 return stack, available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1048
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1049 def _saveTomo(self, base_name, stack, index=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1050 """Save a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1051 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1052 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1053 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1054 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1055 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1056 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	1057 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1058 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1059 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1060 if index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1061 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1062 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	1063 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1064 logging.info(f'Saving {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1065 np.save(tomo_file, stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1066 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	1067
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1068 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	1069 """Generate tomography fields.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1070 """
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1071 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1072 num_core = self.num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1073 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1074 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	1075 assert(len(self.tomo_stacks) == len(stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1076 if len(available_stacks) != len(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1077 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	1078 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1079 available_stacks = [False]*self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1080
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1081 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1082 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1083 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1084 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	1085 zoom_perc = 100
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1086 num_theta_skip = 0
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1087 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1088 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	1089 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	1090 zoom_perc = preprocess.get('zoom_perc', 100)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1091 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	1092
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1093 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1094 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	1095 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1096 logging.warning('Dark field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1097 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1098 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1099 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	1100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1101 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1102 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1103 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	1104 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1105
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1106 # Load a stack of tomography images
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1107 index = stack['index']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1108 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1109 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1110 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	1111 img_x_bounds, img_y_bounds)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1112 tomo_stack = tomo_stack.astype('float64')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1113 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	1114
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1115 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1116 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1117 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1118 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1119 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1120 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	1121
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1122 # Normalize
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1123 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1124 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1125 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	1126 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	1127
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1128 # Remove non-positive values and linearize data
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1129 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1130 cutoff = 1.e-6
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1131 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1132 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	1133 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1134 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1135 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	1136 f'{time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1137
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1138 # 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	1139 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1140 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	1141 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	1142
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1143 # Downsize tomography stack to smaller size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1144 tomo_stack = tomo_stack.astype('float32')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1145 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1146 title = f'red stack fullres {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1147 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1148 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1149 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	1150 if zoom_perc != 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1151 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1152 logging.info(f'Zooming in ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1153 tomo_zoom_list = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1154 for j in range(tomo_stack.shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1155 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	1156 tomo_zoom_list.append(tomo_zoom)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1157 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	1158 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	1159 del tomo_zoom_list
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1160 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1161 title = f'red stack {zoom_perc}p {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1162 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1163 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1164 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	1165
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1166 # 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	1167 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1168
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1169 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1170 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1171 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1172 self._saveTomo('red stack', tomo_stack, index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1173 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1174 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	1175 tomo_stack[0,:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1176
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1177 # Combine stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1178 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1179 self.tomo_stacks[i] = tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1180 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	1181
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1182 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1183 stack['preprocessed'] = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1184 stack.pop('reconstructed', 'reconstructed not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1185 find_center = self.config.get('find_center')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1186 if find_center:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1187 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	1188 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1189 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	1190 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	1191 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1192
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1193 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1194 del tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1195 del tbf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1196
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1197 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	1198 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	1199 """Invert the sinogram for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1200 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1201 # tomo_plane_T index order: column,theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1202 assert(0 <= center < tomo_plane_T.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1203 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	1204 two_offset = 2*int(np.round(center_offset))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1205 two_offset_abs = np.abs(two_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1206 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	1207 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	1208 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	1209 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	1210 if two_offset >= 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1211 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	1212 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	1213 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1214 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	1215 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	1216 if plot_sinogram and not self.test_mode:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1217 msnc.quickImshow(sinogram.T, f'sinogram center offset{center_offset:.2f}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1218 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	1219 save_only=self.save_plots_only, aspect='auto')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1220
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1221 # Inverting sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1222 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1223 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	1224 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	1225 del sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1226
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1227 # Removing ring artifacts
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1228 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1229 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1230 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1231 recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1232 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	1233 del recon_sinogram
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1234 t1 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1235 logging.debug(f'running remove_ring on {num_core} cores ...')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1236 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1237 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	1238 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	1239 return recon_clean
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1240
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1241 def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1242 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1243 edges = denoise_tv_chambolle(recon_plane, weight = weight)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1244 vmax = np.max(edges[0,:,:])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1245 vmin = -vmax
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1246 if self.galaxy_flag:
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1247 msnc.quickImshow(edges[0,:,:], title, path=path, save_fig=True, save_only=True,
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1248 cmap='gray', vmin=vmin, vmax=vmax)
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1249 else:
11 ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1250 if path is None:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1251 path=self.output_folder
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1252 msnc.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	1253 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')
11 ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1254 msnc.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	1255 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	1256 vmin=vmin, vmax=vmax)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1257 del edges
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1258
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1259 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	1260 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	1261 """Find center for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1262 """
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1263 if self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1264 assert(isinstance(galaxy_param, dict))
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1265 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	1266 os.mkdir('find_center_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1267 # sinogram index order: theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1268 # 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	1269 sinogram_T = sinogram.T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1270 center = sinogram.shape[1]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1271
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1272 # 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	1273 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1274 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1275 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	1276 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	1277 else:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1278 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	1279 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	1280 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	1281 center_offset_vo = tomo_center-center
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1282 if self.test_mode:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1283 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	1284 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1285 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1286 elif self.galaxy_flag:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1287 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	1288 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1289 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	1290 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	1291 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	1292 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	1293 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	1294 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	1295 del recon_plane
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1296 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	1297 del sinogram_T
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1298 return float(center_offset_vo)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1299 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1300 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	1301 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	1302 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	1303 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	1304 self._plotEdgesOnePlane(recon_plane, title)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1305 if not self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1306 if (pyip.inputYesNo('Try finding center using phase correlation '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1307 '(y/[n])? ', blank=True) == 'yes'):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1308 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	1309 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1310 error = 1.
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1311 while error > tol:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1312 prev = tomo_center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1313 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	1314 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1315 error = np.abs(tomo_center-prev)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1316 center_offset = tomo_center-center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1317 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	1318 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	1319 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	1320 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	1321 self._plotEdgesOnePlane(recon_plane, title)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1322 if (pyip.inputYesNo('Accept a center location ([y]) or continue '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1323 'search (n)? ', blank=True) != 'no'):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1324 center_offset = pyip.inputNum(
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1325 f' Enter chosen center offset [{-int(center)}, {int(center)}] '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1326 f'([{center_offset_vo:.2f}])): ', blank=True)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1327 if center_offset == '':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1328 center_offset = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1329 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1330 del recon_plane
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1331 return float(center_offset)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1332
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1333 # perform center finding search
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1334 while True:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1335 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	1336 set_center = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1337 if galaxy_param['center_type_selector'] == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1338 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1339 set_range = galaxy_param['set_range']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1340 center_offset_step = galaxy_param['set_step']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1341 if (not msnc.is_num(set_range, 0) or not msnc.is_num(center_offset_step) or
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1342 center_offset_step <= 0):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1343 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	1344 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1345 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1346 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	1347 center_offset_low = set_center-set_range
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1348 center_offset_upp = set_center+set_range
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1349 else:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1350 center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1351 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1352 center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1353 f'[{center_offset_low}, {int(center)}]: ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1354 min=center_offset_low, max=int(center))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1355 if center_offset_upp == center_offset_low:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1356 center_offset_step = 1
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1357 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1358 center_offset_step = pyip.inputInt('Enter step size for center offset search '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1359 f'[1, {center_offset_upp-center_offset_low}]: ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1360 min=1, max=center_offset_upp-center_offset_low)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1361 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	1362 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	1363 for center_offset in center_offsets:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1364 if center_offset == center_offset_vo:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1365 continue
38 c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa" rv43 parents: 37 diff changeset	1366 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1367 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	1368 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	1369 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	1370 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	1371 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	1372 if self.galaxy_flag:
13 40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980" rv43 parents: 11 diff changeset	1373 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	1374 else:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7" rv43 parents: 7 diff changeset	1375 self._plotEdgesOnePlane(recon_plane, title)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1376 if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1377 min=0, max=1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1378 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1379
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1380 del sinogram_T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1381 del recon_plane
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1382 if self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1383 center_offset = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1384 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1385 center_offset = pyip.inputNum(f' Enter chosen center offset '+
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1386 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1387 return float(center_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1388
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1389 def _reconstructOneTomoStack(self, tomo_stack, thetas, row_bounds=None,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1390 center_offsets=[], sigma=0.1, rwidth=30, num_core=1, algorithm='gridrec',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1391 run_secondary_sirt=False, secondary_iter=100):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1392 """reconstruct a single tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1393 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1394 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1395 # thetas must be in radians
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1396 # 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	1397 # RV should we remove stripes?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1398 # 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	1399 # RV should we remove rings?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1400 # 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	1401 # 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	1402 if row_bounds is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1403 row_bounds = [0, tomo_stack.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1404 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1405 if not msnc.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	1406 raise ValueError('Illegal row bounds in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1407 if thetas.size != tomo_stack.shape[1]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1408 raise ValueError('theta dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1409 if not len(center_offsets):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1410 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	1411 elif len(center_offsets) == 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1412 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	1413 row_bounds[1]-row_bounds[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1414 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1415 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	1416 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1417 centers = center_offsets
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1418 centers += tomo_stack.shape[2]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1419 if True:
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1420 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1421 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1422 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	1423 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	1424 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	1425 ncore=num_core_tomopy_limit)
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1426 else:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1427 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	1428 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	1429 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	1430 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	1431 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1432 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	1433 logging.debug('performing initial reconstruction')
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1434 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1435 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	1436 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	1437 algorithm=algorithm, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1438 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	1439 if run_secondary_sirt and secondary_iter > 0:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1440 logging.debug(f'running {secondary_iter} secondary iterations')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1441 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1442 #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	1443 # cuda driver combination."
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1444 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1445 #SIRT did not finish while running overnight
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1446 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iter}
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1447 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1448 'num_iter':secondary_iter}
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1449 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1450 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	1451 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	1452 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	1453 algorithm=tomopy.astra, ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1454 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	1455 if True:
39 8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8" rv43 parents: 38 diff changeset	1456 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1457 logging.debug(f'running remove_ring on {num_core} cores ...')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1458 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1459 ncore=num_core)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1460 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	1461 return tomo_recon_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1462
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1463 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	1464 """Find all available image files.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1465 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1466 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1467
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1468 # Find dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1469 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1470 img_start, num_imgs, dark_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1471 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	1472 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1473 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	1474 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1475 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1476 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	1477 num_imgs_old = dark_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1478 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1479 dark_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1480 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1481 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1482 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	1483 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1484 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1485 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1486 dark_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1487 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1488 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1489 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	1490 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1491 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1492 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	1493 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	1494 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1495 dark_files = msnc.combine_tiffs_in_h5(dark_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1496 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	1497 dark_field['data_path'] = dark_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1498
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1499 # Find bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1500 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1501 img_start, num_imgs, bright_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1502 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	1503 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1504 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	1505 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1506 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	1507 num_imgs_old = bright_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1508 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1509 bright_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1510 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1511 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1512 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	1513 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1514 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1515 bright_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1516 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1517 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1518 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	1519 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1520 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	1521 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	1522 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1523 bright_files = msnc.combine_tiffs_in_h5(bright_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1524 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	1525 bright_field['data_path'] = bright_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1526
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1527 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1528 tomo_stack_files = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1529 for stack in self.config['stack_info']['stacks']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1530 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1531 img_start, num_imgs, tomo_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1532 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	1533 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1534 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1535 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1536 img_start_old = stack.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1537 num_imgs_old = stack.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1538 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1539 stack['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1540 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1541 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1542 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	1543 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1544 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1545 stack['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1546 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1547 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1548 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	1549 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1550 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	1551 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	1552 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1553 tomo_files = msnc.combine_tiffs_in_h5(tomo_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1554 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	1555 stack['data_path'] = tomo_files[0]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1556 tomo_stack_files.append(tomo_files)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1557 del tomo_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1558
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1559 # Safe updated config
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1560 if tiff_to_h5_flag:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1561 self.config['data_filetype'] == 'h5'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1562 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1563 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1564
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1565 return dark_files, bright_files, tomo_stack_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1566
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1567 def loadTomoStacks(self, input_name):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1568 """Load tomography stacks (only for Galaxy).
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1569 """
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1570 assert(self.galaxy_flag)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1571 t0 = time()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1572 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	1573 stack_info = self.config['stack_info']
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1574 stacks = stack_info.get('stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1575 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	1576 with np.load(input_name) as f:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1577 for i,stack in enumerate(stacks):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1578 self.tomo_stacks[i] = f[f'set_{stack["index"]}']
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1579 logging.info(f'loaded stack {i}: index = {stack["index"]}, shape = '+
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1580 f'{self.tomo_stacks[i].shape}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1581 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	1582
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1583 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	1584 """Preprocess tomography images.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1585 """
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1586 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1587 num_core = self.num_core
33 afb612b64f26 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit c566c32f7c1506ab271ae08eb14a2982ee511938" rv43 parents: 32 diff changeset	1588 logging.info(f'num_core = {num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1589 # 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	1590 # 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	1591 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1592 stacks = stack_info['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1593 num_tomo_stacks = stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1594 assert(num_tomo_stacks == len(self.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1595 available_stacks = [False]*num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1596 if self.galaxy_flag:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1597 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1598 tdf_files = galaxy_param['tdf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1599 tbf_files = galaxy_param['tbf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1600 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	1601 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	1602 if not os.path.exists('setup_pngs'):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1603 os.mkdir('setup_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1604 else:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1605 if galaxy_param:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1606 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	1607 galaxy_param = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1608 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	1609 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1610 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1611 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1612 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	1613 self.tomo_stacks[i], available_stacks[i] = \
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1614 self._loadTomo('red stack', stack['index'])
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 # Preprocess any unloaded stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1617 if False in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1618 logging.debug('Preprocessing tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1619
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1620 # Check required image files (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1621 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1622 self._selectImageRanges(available_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1623 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1624 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1625
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1626 # Generate dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1627 if tdf_files:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1628 self._genDark(tdf_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1629
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1630 # Generate bright field
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1631 self._genBright(tbf_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1632
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1633 # 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	1634 self._setDetectorBounds(tomo_stack_files)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1635
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1636 # 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	1637 self._setZoomOrSkip()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1638
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1639 # Generate tomography fields
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1640 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	1641
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1642 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1643 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1644 t0 = time()
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	1645 output_name = galaxy_param['output_name']
2 b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e" rv43 parents: 1 diff changeset	1646 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	1647 save_stacks = {f'set_{stack["index"]}':tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1648 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	1649 np.savez(output_name, **save_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1650 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	1651
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1652 del available_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1653
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1654 # 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	1655 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1656 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1657 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1658 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1659 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	1660 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1661 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1662 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1663 pixel_size *= img_x_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1664 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1665 stack['ref_height'] = stack['ref_height']+pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1666 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1667
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1668 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	1669 """Find rotation axis centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1670 """
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1671 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1672 num_core = self.num_core
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1673 logging.info(f'num_core = {num_core}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1674 logging.debug('Find centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1675 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1676 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	1677 logging.debug('Available stacks: {available_stacks}')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1678 if self.galaxy_flag:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1679 row_bounds = galaxy_param['row_bounds']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1680 center_rows = galaxy_param['center_rows']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1681 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	1682 if center_type_selector:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1683 if center_type_selector == 'vo':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1684 set_center = None
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1685 elif center_type_selector == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1686 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1687 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1688 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	1689 f'({center_type_selector})')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1690 galaxy_param['center_type_selector'] = None
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1691 logging.debug(f'row_bounds = {row_bounds}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1692 logging.debug(f'center_rows = {center_rows}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1693 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	1694 else:
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1695 if galaxy_param:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1696 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	1697 galaxy_param = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1698
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1699 # Check for valid available center stack index
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1700 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	1701 center_stack_index = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1702 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	1703 center_stack_index = find_center['center_stack_index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1704 if (not isinstance(center_stack_index, int) or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1705 center_stack_index not in available_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1706 msnc.illegal_value('center_stack_index', center_stack_index, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1707 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1708 if self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1709 assert(find_center.get('completed', False) == False)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1710 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1711 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	1712 f'{center_stack_index}')
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1713 if (pyip.inputYesNo('Do you want to use this again ([y]/n)? ',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1714 blank=True) != 'no' 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	1715 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1716
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1717 # Load the required preprocessed stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1718 # preprocessed stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1719 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1720 assert(len(stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1721 assert(len(self.tomo_stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1722 if num_tomo_stacks == 1:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1723 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1724 center_stack_index = stacks[0]['index']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1725 elif center_stack_index != stacks[0]['index']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1726 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	1727 if not self.tomo_stacks[0].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1728 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	1729 required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1730 center_stack = self.tomo_stacks[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1731 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1732 stacks[0]['preprocessed'] = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1733 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	1734 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	1735 elif self.galaxy_flag:
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1736 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	1737 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	1738 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	1739 if not center_stack.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1740 stacks[tomo_stack_index]['preprocessed'] = False
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1741 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	1742 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	1743 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1744 while True:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1745 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1746 center_stack_index = pyip.inputInt('\nEnter tomography stack index to get '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1747 f'rotation axis centers {available_stacks}: ')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1748 while center_stack_index not in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1749 center_stack_index = pyip.inputInt('\nEnter tomography stack index to get '
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1750 f'rotation axis centers {available_stacks}: ')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1751 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	1752 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	1753 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	1754 'red stack', center_stack_index, required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1755 center_stack = self.tomo_stacks[tomo_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1756 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1757 stacks[tomo_stack_index]['preprocessed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1758 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	1759 'preprocessed tomography stack, pick another one')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1760 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1761 break
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1762 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	1763 if find_center is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1764 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	1765 find_center = self.config['find_center']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1766 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1767 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	1768 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1769 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	1770 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	1771 find_center.get('upper_row', None)]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1772 if row_bounds is None:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1773 row_bounds = [0, center_stack.shape[0]]
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1774 if row_bounds[0] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1775 row_bounds[0] = 0
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1776 if row_bounds[1] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1777 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	1778 if center_rows[0] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1779 center_rows[0] = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1780 if center_rows[1] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	1781 center_rows[1] = center_stack.shape[0]-1
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1782 if not msnc.is_index_range(row_bounds, 0, center_stack.shape[0]):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1783 msnc.illegal_value('row_bounds', row_bounds)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1784 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1785
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1786 # Set thetas (in degrees)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1787 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1788 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1789 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1790 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1791 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	1792 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	1793 endpoint=False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1794
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1795 # Get non-overlapping sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1796 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	1797 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1798 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1799 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1800 eff_pixel_size = 100.*pixel_size/zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1801 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	1802 if num_tomo_stacks == 1:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1803 accept = 'yes'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1804 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	1805 accept = 'no'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1806 print('\nSelect bounds for image reconstruction')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1807 if msnc.is_index_range(row_bounds, 0, center_stack.shape[0]):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1808 a_tmp = np.copy(center_stack[:,0,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1809 a_tmp_max = a_tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1810 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	1811 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	1812 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	1813 print(f'upper bound = {row_bounds[1]} (exclusive)')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1814 msnc.quickImshow(a_tmp, title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1815 aspect='auto')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1816 del a_tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1817 accept = pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1818 if accept == 'no':
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1819 (n1, n2) = msnc.selectImageBounds(center_stack[:,0,:], 0,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1820 title=f'center stack theta={theta_start}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1821 else:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1822 n1 = row_bounds[0]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1823 n2 = row_bounds[1]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1824 else:
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1825 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	1826 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	1827 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	1828 n2 = center_stack.shape[0]-n1
40 fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100" rv43 parents: 39 diff changeset	1829 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	1830 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	1831 tmp = center_stack[:,0,:]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1832 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1833 tmp[n1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1834 tmp[n2-1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1835 if msnc.is_index_range(center_rows, 0, tmp.shape[0]):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1836 tmp[center_rows[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1837 tmp[center_rows[1]-1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1838 extent = [0, tmp.shape[1], tmp.shape[0], 0]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1839 msnc.quickImshow(tmp, title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1840 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	1841 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	1842 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1843 #extent = [0, center_stack.shape[2], n2, n1]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1844 #msnc.quickImshow(center_stack[n1:n2,0,:], title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1845 # 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	1846 # 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	1847
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1848 # Get cross sectional diameter in mm
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1849 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	1850 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	1851
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1852 # Determine center offset at sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1853 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	1854
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1855 # Lower row center
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1856 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1857 use_center = 'no'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1858 row = center_rows[0]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1859 if self.test_mode or self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1860 assert(msnc.is_int(row, n1, n2-2))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1861 if msnc.is_int(row, n1, n2-2):
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1862 if self.test_mode or self.galaxy_flag:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1863 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1864 else:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1865 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1866 use_row = pyip.inputYesNo('\nCurrent row index for lower center = '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1867 f'{row}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1868 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1869 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1870 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1871 center_offset = find_center.get('lower_center_offset')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1872 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1873 use_center = pyip.inputYesNo('Current lower center offset = '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1874 f'{center_offset}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1875 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1876 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1877 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1878 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1879 aspect='auto')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1880 row = pyip.inputInt('\nEnter row index to find lower center '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1881 f'[[{n1}], {n2-2}]: ', min=n1, max=n2-2, blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1882 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1883 row = n1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1884 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1885 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1886 # center_stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1887 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	1888 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	1889 galaxy_param=galaxy_param)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1890 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	1891
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1892 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1893 find_center['row_bounds'] = [n1, n2]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1894 find_center['lower_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1895 find_center['lower_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1896 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1897 lower_row = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1898
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1899 # Upper row center
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1900 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1901 use_center = 'no'
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	1902 row = center_rows[1]
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1903 if self.test_mode or self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1904 assert(msnc.is_int(row, lower_row+1, n2-1))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1905 if msnc.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	1906 if self.test_mode or self.galaxy_flag:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1907 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1908 else:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1909 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1910 use_row = pyip.inputYesNo('\nCurrent row index for upper center = '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1911 f'{row}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1912 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1913 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1914 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1915 center_offset = find_center.get('upper_center_offset')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1916 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1917 use_center = pyip.inputYesNo('Current upper center offset = '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1918 f'{center_offset}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1919 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1920 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1921 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1922 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1923 aspect='auto')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1924 row = pyip.inputInt('\nEnter row index to find upper center '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1925 f'[{lower_row+1}, [{n2-1}]]: ', min=lower_row+1, max=n2-1, blank=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1926 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1927 row = n2-1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1928 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1929 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1930 # center_stack order: row,theta,column
24 817a8101d2e4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3d7910473008ec94bc0b4580d62e61310e69917d" rv43 parents: 23 diff changeset	1931 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	1932 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	1933 galaxy_param=galaxy_param)
7 845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be" rv43 parents: 3 diff changeset	1934 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	1935 del center_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1936
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1937 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1938 find_center['upper_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1939 find_center['upper_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1940 find_center['completed'] = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1941 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1942
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1943 def checkCenters(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1944 """Check centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1945 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1946 #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	1947 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1948 logging.debug('Check centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1949 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	1950 if center_stack_index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1951 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	1952 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	1953 lower_row = self.config.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1954 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1955 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	1956 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	1957 if lower_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1958 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	1959 upper_row = self.config.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1960 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1961 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	1962 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	1963 if upper_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1964 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	1965 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	1966 shift = upper_center_offset-lower_center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1967 if lower_row == 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1968 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	1969 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1970 lower_row -= 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1971 lower_center_offset -= center_slope
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1972
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1973 # stack order: stack,row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1974 if center_stack_index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1975 stack1 = self.tomo_stacks[center_stack_index-1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1976 stack2 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1977 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1978 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	1979 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1980 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	1981 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1982 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1983 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1984 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1985 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1986 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1987 shift_i = shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1988 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1989 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1990 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	1991 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	1992 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1993 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	1994 stack1 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1995 stack2 = self.tomo_stacks[center_stack_index+1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1996 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1997 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	1998 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1999 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	2000 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2001 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2002 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2003 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2004 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2005 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2006 shift_i = -shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2007 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2008 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2009 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	2010 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	2011 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2012 del plane1, plane2, plane1_shifted
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2013
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2014 # Update config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2015 self.config = msnc.update('config.txt', 'check_centers', True, 'find_centers')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2016
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2017 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	2018 """Reconstruct tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2019 """
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2020 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2021 num_core = self.num_core
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2022 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	2023 if self.galaxy_flag:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2024 assert(galaxy_param)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2025 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	2026 os.mkdir('center_slice_pngs')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2027 logging.debug('Reconstruct tomography stacks')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2028 stacks = self.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2029 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	2030 assert(len(self.tomo_stacks) == len(stacks))
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2031 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	2032 if self.galaxy_flag:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2033 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2034 # Get rotation axis centers
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2035 center_offsets = galaxy_param['center_offsets']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2036 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	2037 lower_center_offset = center_offsets[0]
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2038 assert(msnc.is_num(lower_center_offset))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2039 upper_center_offset = center_offsets[1]
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2040 assert(msnc.is_num(upper_center_offset))
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2041 else:
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2042 if galaxy_param:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2043 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	2044 galaxy_param = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2045 lower_center_offset = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2046 upper_center_offset = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2047
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2048 # Get rotation axis rows and centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2049 find_center = self.config['find_center']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2050 lower_row = find_center.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2051 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2052 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	2053 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2054 upper_row = find_center.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2055 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2056 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	2057 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2058 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	2059 assert(lower_row < upper_row)
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2060 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2061 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	2062 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2063 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	2064 return
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2065 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2066 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	2067 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2068 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	2069 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2070 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	2071
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2072 # Set thetas (in radians)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2073 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2074 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2075 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2076 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2077 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	2078 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	2079 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	2080
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2081 # Reconstruct tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2082 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	2083 if zoom_perc == 100:
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2084 basetitle = 'recon stack fullres'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2085 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2086 basetitle = f'recon stack {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2087 load_error = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2088 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2089 # Check if stack can be loaded
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2090 # 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	2091 # 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	2092 index = stack['index']
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2093 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2094 available = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2095 if stack.get('reconstructed', False):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2096 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	2097 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	2098 if self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2099 self.tomo_stacks[i] = np.array([])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2100 assert(stack.get('preprocessed', False) == True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2101 assert(stack.get('reconstructed', False) == True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2102 continue
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2103 stack['reconstructed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2104 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2105 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	2106 required=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2107 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2108 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	2109 stack[i]['preprocessed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2110 load_error = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2111 continue
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2112 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	2113 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	2114 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	2115 t0 = time()
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2116 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	2117 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2118 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2119 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
41 ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7" rv43 parents: 40 diff changeset	2120 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	2121 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	2122 if self.galaxy_flag:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2123 x_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2124 title = f'{basetitle} {index} xslice{x_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2125 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2126 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2127 y_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2128 title = f'{basetitle} {index} yslice{y_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2129 msnc.quickImshow(self.tomo_recon_stacks[i][:,y_slice,:], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2130 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2131 z_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2132 title = f'{basetitle} {index} zslice{z_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2133 msnc.quickImshow(self.tomo_recon_stacks[i][:,:,z_slice], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2134 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2135 elif not self.test_mode:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2136 x_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2137 title = f'{basetitle} {index} xslice{x_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2138 msnc.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	2139 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	2140 save_only=self.save_plots_only)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2141 msnc.quickPlot(self.tomo_recon_stacks[i]
21 3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86" rv43 parents: 20 diff changeset	2142 [x_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:],
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2143 title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[2]/2)}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2144 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	2145 save_only=self.save_plots_only)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2146 self._saveTomo('recon stack', self.tomo_recon_stacks[i], index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2147 self.tomo_stacks[i] = np.array([])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2148
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2149 # Update config and save to file
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2150 stack['reconstructed'] = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2151 combine_stacks = self.config.get('combine_stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2152 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	2153 combine_stacks['stacks'].remove(index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2154 self.cf.saveFile(self.config_out)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2155
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2156 if self.galaxy_flag:
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2157 # Save reconstructed tomography stack to file
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2158 t0 = time()
15 1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691" rv43 parents: 13 diff changeset	2159 output_name = galaxy_param['output_name']
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2160 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	2161 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	2162 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	2163 np.savez(output_name, **save_stacks)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2164 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	2165
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2166 # 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	2167 tomosum = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2168 [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	2169 self.tomo_recon_stacks]
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2170 msnc.quickPlot(tomosum, title='recon stack sum yz', path='center_slice_pngs',
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2171 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2172
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2173 # 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	2174 tomosum = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2175 [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	2176 self.tomo_recon_stacks]
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2177 msnc.quickPlot(tomosum, title='recon stack sum xz', path='center_slice_pngs',
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2178 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2179
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2180 # 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	2181 num_tomo_stacks = len(stacks)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2182 row_bounds = self.config['find_center']['row_bounds']
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2183 if not msnc.is_index_range(row_bounds, 0, self.tomo_recon_stacks[0].shape[0]):
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2184 msnc.illegal_value('row_bounds', row_bounds, 'config file')
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2185 return
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2186 if num_tomo_stacks == 1:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2187 low_bound = row_bounds[0]
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2188 else:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2189 low_bound = 0
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2190 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	2191 if num_tomo_stacks > 2:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2192 tomosum = np.concatenate([tomosum]+
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2193 [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	2194 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	2195 print(f'tomosum.shape = {tomosum.shape}')
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2196 if num_tomo_stacks > 1:
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2197 tomosum = np.concatenate([tomosum,
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2198 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	2199 axis=(1,2))])
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2200 print(f'tomosum.shape = {tomosum.shape}')
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2201 msnc.quickPlot(tomosum, title='recon stack sum xy', path='center_slice_pngs',
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2202 save_fig=True, save_only=True)
c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2203
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2204 def combineTomoStacks(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2205 """Combine the reconstructed tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2206 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2207 # stack order: stack,row(z),x,y
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2208 logging.debug('Combine reconstructed tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2209 # Load any unloaded reconstructed stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2210 stack_info = self.config['stack_info']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2211 stacks = stack_info['stacks']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2212 for i,stack in enumerate(stacks):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2213 available = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2214 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	2215 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	2216 stack['index'], required=True)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2217 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	2218 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	2219 stack['reconstructed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2220 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2221 if i:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2222 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	2223 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	2224 logging.error('Incompatible reconstructed tomography stack dimensions')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2225 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2226
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2227 # Get center stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2228 row_bounds = self.config['find_center']['row_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2229 if not msnc.is_index_range(row_bounds, 0, self.tomo_recon_stacks[0].shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2230 msnc.illegal_value('row_bounds', row_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2231 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2232
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2233 # Selecting x bounds (in yz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2234 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2235 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2236 [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	2237 self.tomo_recon_stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2238 combine_stacks = self.config.get('combine_stacks')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2239 if combine_stacks and 'x_bounds' in combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2240 x_bounds = combine_stacks['x_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2241 if not msnc.is_index_range(x_bounds, 0, self.tomo_recon_stacks[0].shape[1]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2242 msnc.illegal_value('x_bounds', x_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2243 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2244 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2245 if pyip.inputYesNo('\nCurrent image x-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2246 f'[{x_bounds[0]}, {x_bounds[1]}], use these values ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2247 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2248 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2249 'Do you want to change the image x-bounds ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2250 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2251 x_bounds = [0, self.tomo_recon_stacks[0].shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2252 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2253 x_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2254 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2255 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2256 if pyip.inputYesNo('\nDo you want to change the image x-bounds (y/n)? ') == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2257 x_bounds = [0, self.tomo_recon_stacks[0].shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2258 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2259 x_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2260 if False and self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2261 np.savetxt(f'{self.output_folder}/recon_stack_sum_yz.txt',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2262 tomosum[x_bounds[0]:x_bounds[1]], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2263 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2264 msnc.clearFig('recon stack sum yz')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2265
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2266 # Selecting y bounds (in xz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2267 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2268 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2269 [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	2270 self.tomo_recon_stacks]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2271 if combine_stacks and 'y_bounds' in combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2272 y_bounds = combine_stacks['y_bounds']
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2273 if not msnc.is_index_range(y_bounds, 0, self.tomo_recon_stacks[0].shape[1]):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2274 msnc.illegal_value('y_bounds', y_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2275 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2276 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2277 if pyip.inputYesNo('\nCurrent image y-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2278 f'[{y_bounds[0]}, {y_bounds[1]}], use these values ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2279 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2280 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2281 'Do you want to change the image y-bounds ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2282 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2283 y_bounds = [0, self.tomo_recon_stacks[0].shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2284 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2285 y_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2286 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2287 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2288 if pyip.inputYesNo('\nDo you want to change the image y-bounds (y/n)? ') == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2289 y_bounds = [0, self.tomo_recon_stacks[0].shape[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2290 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2291 y_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2292 if False and self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2293 np.savetxt(f'{self.output_folder}/recon_stack_sum_xz.txt',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2294 tomosum[y_bounds[0]:y_bounds[1]], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2295 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2296 msnc.clearFig('recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2297
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2298 # Combine reconstructed tomography stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2299 logging.info(f'Combining reconstructed stacks ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2300 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2301 num_tomo_stacks = stack_info['num']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2302 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2303 low_bound = row_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2304 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2305 low_bound = 0
47 c693117d01e9 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac-dirty" rv43 parents: 46 diff changeset	2306 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	2307 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	2308 if num_tomo_stacks > 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2309 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2310 [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	2311 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	2312 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	2313 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2314 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2315 [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	2316 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	2317 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	2318 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	2319
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2320 # Wrap up if in test_mode
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2321 tomosum = np.sum(tomo_recon_combined, axis=(1,2))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2322 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2323 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	2324 filename = 'recon combined sum xy'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2325 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	2326 filename += ' fullres.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2327 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2328 filename += f' {zoom_perc}p.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2329 msnc.quickPlot(tomosum, title='recon combined sum xy',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2330 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	2331 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2332 if False:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2333 np.savetxt(f'{self.output_folder}/recon_combined_sum_xy.txt',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2334 tomosum, fmt='%.6e')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2335 np.savetxt(f'{self.output_folder}/recon_combined.txt',
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2336 tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2337
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2338 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2339 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2340 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2341 combine_stacks['y_bounds'] = y_bounds
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2342 combine_stacks['stacks'] = combined_stacks
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2343 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2344 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2345 'stacks' : combined_stacks}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2346 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2347 return
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2348
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2349 # Selecting z bounds (in xy-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2350 msnc.quickPlot(tomosum, title='recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2351 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2352 '\nDo you want to change the image z-bounds (y/[n])? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2353 blank=True) != 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2354 z_bounds = [0, tomo_recon_combined.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2355 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2356 z_bounds = msnc.selectArrayBounds(tomosum, title='recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2357 if z_bounds[0] != 0 or z_bounds[1] != tomo_recon_combined.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2358 tomo_recon_combined = tomo_recon_combined[z_bounds[0]:z_bounds[1],:,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2359 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2360 msnc.clearFig('recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2361
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2362 # Plot center slices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2363 msnc.quickImshow(tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2364 title=f'recon combined xslice{int(tomo_recon_combined.shape[0]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2365 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	2366 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2367 msnc.quickImshow(tomo_recon_combined[:,int(tomo_recon_combined.shape[1]/2),:],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2368 title=f'recon combined yslice{int(tomo_recon_combined.shape[1]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2369 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	2370 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2371 msnc.quickImshow(tomo_recon_combined[:,:,int(tomo_recon_combined.shape[2]/2)],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2372 title=f'recon combined zslice{int(tomo_recon_combined.shape[2]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2373 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	2374 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2375
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2376 # Save combined reconstructed tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2377 base_name = 'recon combined'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2378 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2379 base_name += f' {stack["index"]}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2380 self._saveTomo(base_name, tomo_recon_combined)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2381
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2382 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2383 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2384 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2385 combine_stacks['y_bounds'] = y_bounds
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2386 combine_stacks['z_bounds'] = z_bounds
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2387 combine_stacks['stacks'] = combined_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2388 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2389 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	2390 'z_bounds' : z_bounds, 'stacks' : combined_stacks}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2391 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2392
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2393 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	2394 test_mode=False, num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2395 """Run a tomography analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2396 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2397 # Instantiate Tomo object
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2398 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	2399 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	2400 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2401 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	2402
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2403 # Preprocess the image files
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2404 assert(tomo.config['stack_info'])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2405 num_tomo_stacks = tomo.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2406 assert(num_tomo_stacks == len(tomo.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2407 preprocessed_stacks = []
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2408 if not tomo.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2409 preprocess = tomo.config.get('preprocess', None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2410 if preprocess:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2411 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	2412 if stack.get('preprocessed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2413 if len(preprocessed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2414 tomo.genTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2415 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2416 IOError('Unable to load all required image files.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2417 tomo.cf.saveFile(tomo.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2418
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2419 # Find centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2420 find_center = tomo.config.get('find_center')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2421 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	2422 tomo.findCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2423
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2424 # Check centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2425 #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	2426 # tomo.checkCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2427
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2428 # Reconstruct tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2429 assert(tomo.config['stack_info']['stacks'])
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2430 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	2431 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2432 if len(reconstructed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2433 tomo.reconstructTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2434
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2435 # Combine reconstructed tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2436 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	2437 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2438 combine_stacks = tomo.config.get('combine_stacks')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2439 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	2440 combine_stacks.get('stacks') != reconstructed_stacks):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2441 tomo.combineTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2442
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2443 #%%============================================================================
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2444 if __name__ == '__main__':
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2445
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2446 # Parse command line arguments
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2447 parser = argparse.ArgumentParser(
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2448 description='Tomography reconstruction')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2449 parser.add_argument('-c', '--config',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2450 default=None,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2451 help='Input config')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2452 parser.add_argument('-o', '--output_folder',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2453 default='.',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2454 help='Output folder')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2455 parser.add_argument('-l', '--log_level',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2456 default='INFO',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2457 help='Log level')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2458 parser.add_argument('-t', '--test_mode',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2459 action='store_true',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2460 default=False,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2461 help='Test mode flag')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2462 parser.add_argument('--num_core',
3 f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6" rv43 parents: 2 diff changeset	2463 type=int,
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2464 default=-1,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2465 help='Number of cores')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2466 args = parser.parse_args()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2467
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2468 if args.config is None:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2469 if os.path.isfile('config.yaml'):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2470 args.config = 'config.yaml'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2471 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2472 args.config = 'config.txt'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2473
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2474 # Set basic log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2475 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	2476 if not args.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2477 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	2478 if not isinstance(level, int):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2479 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	2480 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	2481 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2482
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2483 logging.debug(f'config = {args.config}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2484 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	2485 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	2486 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	2487 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	2488
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2489 # Run tomography analysis
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2490 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	2491 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	2492
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2493 #%%============================================================================
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2494 # input('Press any key to continue')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2495 #%%============================================================================

Mercurial > repos > rv43 > tomo

annotate tomo.py @ 47:c693117d01e9 draft