tomo: tomo.py annotate

annotate tomo.py @ 1:e4778148df6b draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"

author	rv43
date	Thu, 31 Mar 2022 18:24:16 +0000
parents	cb1b0d757704
children	b8977c98800b

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
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	23 import numexpr as ne
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	24 import multiprocessing as mp
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	25 import scipy.ndimage as spi
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	26 import tomopy
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	27 from time import time
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	28 from skimage.transform import iradon
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	29 from skimage.restoration import denoise_tv_chambolle
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	30
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	31 import msnc_tools as msnc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	32
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	33 class set_numexpr_threads:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	34
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	35 def __init__(self, num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	36 cpu_count = mp.cpu_count()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	37 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	38 self.num_core = cpu_count
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	39 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	40 self.num_core = num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	41
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	42 def __enter__(self):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	43 self.num_core_org = ne.set_num_threads(self.num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	44
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	45 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	46 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	47
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	48 class ConfigTomo(msnc.Config):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	49 """Class for processing a config file.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	50 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	51
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	52 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	53 super().__init__(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	54
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	55 def _validate_txt(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	56 """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	57 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	58 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	59
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	60 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	61 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	62 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	63 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	64 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	65 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	66 self.detector_id = self.config.get('detector_id')
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 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	69 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	70
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	71 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	72 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	73
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	74 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	75 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	76 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	77 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	78 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	79 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	80 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	81
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	82 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	83 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	84 if 'tomo_data_path' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	85 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	86 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	87 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	88 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	89 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	90 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	91 for i in range(self.num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	92 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	93 if 'z_pos' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	94 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	95 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	96 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	97 if len(tomo_ref_height_indices):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	98 self.tomo_ref_heights = [
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	99 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	100 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	101 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	102
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	103 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	104 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	105 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	106 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	107 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	108 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	109 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	110 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	111 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	112 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	113 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	114 self.num_thetas = self.config.get('num_thetas')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	115 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	116 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	117 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	118 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	119 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	120
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	121 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	122
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	123 def _validate_yaml(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	124 """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	125 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	126 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	127
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	128 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	129 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	130 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	131 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	132 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	133 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	134 self.detector_id = self.config['detector'].get('id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	135
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	136 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	137 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	138
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	139 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	140 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	141
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	142 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	143 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	144 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	145 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	146 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	147 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	148 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	149 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	150
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	151 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	152 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	153 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	154 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	155 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	156 self.tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	157 self.tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	158 self.tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	159 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	160 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	161 self.tomo_data_indices.append(stack.get('index'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	162 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	163
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	164 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	165 theta_range = self.config.get('theta_range')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	166 if theta_range is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	167 self.start_theta = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	168 self.end_theta = 180.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	169 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	170 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	171 self.start_theta = theta_range.get('start', 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	172 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	173 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	174 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	175 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	176 self.end_theta = theta_range.get('end', 180.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	177 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	178 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	179 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	180 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	181 self.num_thetas = theta_range.get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	182 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	183 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	184 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	185 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	186 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	187
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	188 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	189
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	190 def validate(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	191 """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	192 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	193 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	194
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	195 # Check work_folder (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	196 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	197 if not os.path.isdir(work_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	198 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	199 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	200 logging.info(f'work_folder: {work_folder}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	201
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	202 # Check data filetype (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	203 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	204 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	205 self.data_filetype != 'h5'):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	206 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	207
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	208 if self.suffix == '.yml' or self.suffix == '.yaml':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	209 is_valid = self._validate_yaml()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	210 elif self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	211 is_valid = self._validate_txt()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	212 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	213 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	214 is_valid = False
0 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 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	217 if self.tdf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	218 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	219 if isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	220 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	221 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	222 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	223 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	224 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	225 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	226 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	227 if isinstance(self.tdf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	228 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	229 f'{work_folder}/{self.tdf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	230 elif isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	231 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	232 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	233 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	234 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	235 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	236 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	237 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	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.tbf_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.tbf_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.tbf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	244 self.tbf_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.tbf_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('tbf_data_path', tbf_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.tbf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	251 self.tbf_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.tbf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	253 elif isinstance(self.tbf_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.tbf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	255 self.tbf_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.tbf_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('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	259 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	260 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	261
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	262 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	263 tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	264 tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	265 tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	266 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	267 self.tomo_ref_heights):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	268 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	269 if isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	270 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	271 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	272 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	273 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	274 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	275 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	276 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	277 if isinstance(data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	278 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	279 elif isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	280 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	281 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	282 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	283 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	284 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	285 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	286 tomo_data_paths.append(data_path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	287 if index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	288 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	289 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	290 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	291 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	292 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	293 index = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	294 elif not isinstance(index, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	295 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	296 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	297 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	298 tomo_data_indices.append(index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	299 if ref_height is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	300 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	301 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	302 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	303 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	304 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	305 ref_height = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	306 elif not msnc.is_num(ref_height):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	307 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	308 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	309 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	310 # Set reference heights relative to first stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	311 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	312 msnc.is_num(tomo_ref_heights[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	313 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	314 tomo_ref_heights.append(ref_height)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	315 tomo_ref_heights[0] = 0.0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	316 logging.info('tomography data paths:')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	317 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	318 logging.info(f' {tomo_data_paths[i]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	319 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	320 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	321
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	322 # Update config in memory
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	323 if self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	324 self.config = {}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	325 dark_field = self.config.get('dark_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	326 if dark_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	327 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	328 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	329 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	330 bright_field = self.config.get('bright_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	331 if bright_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	332 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	333 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	334 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	335 detector = self.config.get('detector')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	336 if detector is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	337 self.config['detector'] = {'id' : self.detector_id}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	338 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	339 detector['id'] = self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	340 self.config['work_folder'] = work_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	341 self.config['data_filetype'] = self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	342 stack_info = self.config.get('stack_info')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	343 if stack_info is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	344 stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	345 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	346 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	347 'ref_height' : tomo_ref_heights[i]})
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	348 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	349 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	350 stack_info['num'] = self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	351 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	352 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	353 stack['data_path'] = tomo_data_paths[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	354 stack['index'] = tomo_data_indices[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	355 stack['ref_height'] = tomo_ref_heights[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	356 if self.num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	357 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	358 'num' : self.num_thetas}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	359 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	360 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	361 self.config['theta_range'] = theta_range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	362
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	363 # Cleanup temporary validation variables
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	364 del self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	365 del self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	366 del self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	367 del self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	368 del self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	369 del self.tomo_data_paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	370 del self.tomo_data_indices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	371 del self.tomo_ref_heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	372 del self.start_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	373 del self.end_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	374 del self.num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	375
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	376 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	377
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	378 class Tomo:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	379 """Processing tomography data with misalignment.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	380 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	381
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	382 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	383 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	384 num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	385 """Initialize with optional config input file or dictionary
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	386 """
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	387 self.num_core = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	388 self.config_out = config_out
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	389 self.output_folder = output_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	390 self.galaxy_flag = galaxy_flag
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	391 self.test_mode = test_mode
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	392 self.save_plots = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	393 self.save_plots_only = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	394 self.cf = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	395 self.config = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	396 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	397 self.tdf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	398 self.tbf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	399 self.tomo_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	400 self.tomo_recon_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	401
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	402 # Validate input parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	403 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	404 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	405 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	406 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	407 if config_out is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	408 if isinstance(config_out, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	409 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	410 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	411 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	412 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	413 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	414 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	415 if not os.path.isdir(output_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	416 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	417 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	418 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	419 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	420 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	421 if not os.path.isabs(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	422 log_stream = f'{output_folder}/{log_stream}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	423 if not isinstance(galaxy_flag, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	424 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	425 if not isinstance(test_mode, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	426 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	427 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	428 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	429 if num_core == -1:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	430 self.num_core = mp.cpu_count()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	431 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	432 self.num_core = num_core
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	433
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	434 # Set log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	435 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	436 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	437 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	438 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	439 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	440 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	441 #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	442 elif isinstance(log_stream, io.TextIOWrapper):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	443 #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	444 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	445 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	446 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	447 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	448 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	449 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	450 level = getattr(logging, log_level.upper(), None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	451 if not isinstance(level, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	452 raise ValueError(f'Invalid log_level: {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	453 if log_stream is sys.stdout:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	454 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	455 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	456 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	457 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	458 logging.basicConfig(filename=f'{log_stream}', filemode='w',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	459 format=logging_format, level=level, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	460 elif isinstance(log_stream, io.TextIOWrapper):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	461 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	462 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	463 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	464 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	465 stream_handler = logging.StreamHandler()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	466 logging.getLogger().addHandler(stream_handler)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	467 stream_handler.setLevel(logging.WARNING)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	468 stream_handler.setFormatter(logging.Formatter(logging_format))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	469
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	470 # Check/set output config file name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	471 if self.config_out is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	472 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	473 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	474 not os.path.isabs(self.config_out)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	475 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	476
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	477 # Create config object and load config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	478 self.cf = ConfigTomo(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	479 if not self.cf.load_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	480 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	481 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	482
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	483 if self.galaxy_flag:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	484 self.num_core = 1 #RV can I set this? mp.cpu_count()
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	485 assert(self.output_folder == '.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	486 assert(self.test_mode is False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	487 self.save_plots = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	488 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	489 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	490 # 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	491
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	492 # Check config file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	493 self.is_valid = self.cf.validate()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	494
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	495 # Load detector info file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	496 df = msnc.Detector(self.cf.config['detector']['id'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	497
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	498 # Check detector info file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	499 if df.validate():
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	500 pixel_size = df.getPixelSize()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	501 num_rows, num_columns = df.getDimensions()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	502 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	503 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	504 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	505 pixel_size = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	506 num_rows = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	507 num_columns = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	508 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	509
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	510 # Update config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	511 self.cf.config['detector']['pixel_size'] = pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	512 self.cf.config['detector']['rows'] = num_rows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	513 self.cf.config['detector']['columns'] = num_columns
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	514 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	515 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	516 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	517
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	518 # Safe config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	519 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	520 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	521
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	522 # Initialize shortcut to config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	523 self.config = self.cf.config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	524
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	525 # Initialize tomography stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	526 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	527 if num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	528 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	529 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	530
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	531 logging.info(f'num_core = {self.num_core}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	532 logging.debug(f'config_file = {config_file}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	533 logging.debug(f'config_dict = {config_dict}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	534 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	535 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	536 logging.debug(f'log_stream = {log_stream}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	537 logging.debug(f'log_level = {log_level}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	538 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	539 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	540 logging.debug(f'save_plots = {self.save_plots}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	541 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	542
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	543 def _selectImageRanges(self, available_stacks=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	544 """Select image files to be included in analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	545 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	546 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	547 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	548 if available_stacks is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	549 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	550 elif len(available_stacks) != stack_info['num']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	551 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	552 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	553 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	554
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	555 # Check number of tomography angles/thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	556 num_thetas = self.config['theta_range'].get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	557 if num_thetas is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	558 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	559 elif not msnc.is_int(num_thetas, 0):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	560 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	561 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	562 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	563 self.config['theta_range']['num'] = num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	564 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	565
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	566 # Find tomography dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	567 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	568 img_start = dark_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	569 img_offset = dark_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	570 num_imgs = dark_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	571 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	572 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	573 num_imgs, 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	574 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	575 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	576 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	577 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	578 dark_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	579 dark_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	580 dark_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	581 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	582 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	583 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	584
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	585 # Find tomography bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	586 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	587 img_start = bright_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	588 img_offset = bright_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	589 num_imgs = bright_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	590 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	591 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	592 num_imgs, 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	593 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	594 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	595 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	596 bright_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	597 bright_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	598 bright_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	599 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	600 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	601 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	602
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	603 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	604 for i,stack in enumerate(stack_info['stacks']):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	605 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	606 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	607 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	608 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	609 img_start = stack.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	610 img_offset = stack.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	611 num_imgs = stack.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, f'tomography stack {index}', num_thetas)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	615 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	616 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	617 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	618 stack['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	619 stack['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	620 stack['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	621 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	622 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	623 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	624
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	625 # Safe updated config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	626 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	627 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	628
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	629 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	630
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	631 def _genDark(self, tdf_files, dark_field_pngname):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	632 """Generate dark field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	633 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	634 # Load the dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	635 logging.debug('Loading dark field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	636 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	637 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	638 dark_field['img_offset'], dark_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	639
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	640 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	641 self.tdf = np.median(tdf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	642 del tdf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	643
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	644 # 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	645 tdf_cutoff = 21
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	646 self.tdf[self.tdf > tdf_cutoff] = np.nan
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	647 tdf_mean = np.nanmean(self.tdf)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	648 logging.debug(f'tdf_cutoff = {tdf_cutoff}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	649 logging.debug(f'tdf_mean = {tdf_mean}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	650 np.nan_to_num(self.tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	651 if not self.test_mode and not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	652 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	653 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	654 elif self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	655 msnc.quickImshow(self.tdf, title='dark field', name=dark_field_pngname,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	656 save_fig=True, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	657
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	658 def _genBright(self, tbf_files, bright_field_pngname):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	659 """Generate bright field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	660 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	661 # Load the bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	662 logging.debug('Loading bright field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	663 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	664 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	665 bright_field['img_offset'], bright_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	666
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	667 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	668 """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	669 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	670 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	671 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	672 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	673 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	674 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	675 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	676 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	677 self.tbf = np.median(tbf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	678 del tbf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	679
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	680 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	681 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	682 self.tbf -= self.tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	683 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	684 logging.warning('Dark field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	685 if not self.test_mode and not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	686 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	687 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	688 elif self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	689 msnc.quickImshow(self.tbf, title='bright field', name=bright_field_pngname,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	690 save_fig=True, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	691
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	692 def _setDetectorBounds(self, tomo_stack_files, tomo_field_pngname, detectorbounds_pngname):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	693 """Set vertical detector bounds for image stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	694 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	695 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	696 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	697 img_x_bounds = [None, None]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	698 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	699 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	700 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	701 if img_x_bounds[0] < 0:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	702 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	703 img_x_bounds[0] = 0
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	704 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	705 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	706 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	707 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	708 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	709 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	710 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	711 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	712 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	713 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	714 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	715
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	716 # Check reference heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	717 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	718 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	719 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	720 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	721 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	722 num_x_min = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	723 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	724 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	725 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	726 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	727 for i in range(2, num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	728 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	729 logging.debug(f'delta_z = {delta_z}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	730 num_x_min = int(delta_z/pixel_size)+1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	731 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	732 if num_x_min > self.tbf.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	733 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	734 num_x_min = self.tbf.shape[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	735
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	736 # Select image bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	737 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	738 if num_x_min is None or num_x_min >= self.tbf.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	739 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	740 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	741 margin = int(num_x_min/10)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	742 offset = min(0, int((self.tbf.shape[0]-num_x_min)/2-margin))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	743 img_x_bounds = [offset, num_x_min+offset+2*margin]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	744 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	745 stacks[0]['img_offset'], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	746 x_sum = np.sum(tomo_stack[0,:,:], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	747 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	748 msnc.quickImshow(tomo_stack[0,:,:], title=title, name=tomo_field_pngname,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	749 save_fig=True, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	750 msnc.quickPlot((range(x_sum.size), x_sum),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	751 ([img_x_bounds[0], img_x_bounds[0]], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	752 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	753 title='sum over theta and y', name=detectorbounds_pngname,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	754 save_fig=True, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	755
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	756 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	757 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	758 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	759 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	760 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	761 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	762 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	763
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	764 # 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	765 title = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	766 msnc.quickImshow(self.tbf, title='bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	767 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	768 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	769 stacks[0]['img_offset'], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	770 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	771 msnc.quickImshow(tomo_stack[0,:,:], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	772 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	773 '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	774 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	775 print('\nSelect image bounds from bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	776 tomo_or_bright = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	777 if tomo_or_bright:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	778 x_sum = np.sum(tomo_stack[0,:,:], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	779 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	780 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	781 msnc.quickPlot((range(x_sum.size), x_sum),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	782 ([img_x_bounds[0], img_x_bounds[0]], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	783 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	784 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	785 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	786 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	787 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	788 if use_bounds == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	789 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	790 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	791 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	792 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	793 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	794 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	795 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	796 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	797 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	798 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	799 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	800 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	801 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	802 x_sum = np.sum(self.tbf, 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	803 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	804 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	805 msnc.quickPlot((range(x_sum.size), x_sum),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	806 ([img_x_bounds[0], img_x_bounds[0]], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	807 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	808 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	809 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	810 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	811 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	812 if use_bounds == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	813 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	814 x_low = fit.get('center1', None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	815 x_upp = fit.get('center2', None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	816 if (x_low is not None and x_low >= 0 and x_upp is not None and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	817 x_low < x_upp < x_sum.size):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	818 x_low = int(x_low-(x_upp-x_low)/10)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	819 if x_low < 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	820 x_low = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	821 x_upp = int(x_upp+(x_upp-x_low)/10)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	822 if x_upp >= x_sum.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	823 x_upp = x_sum.size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	824 msnc.quickPlot((range(x_sum.size), x_sum),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	825 ([x_low, x_low], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	826 ([x_upp, x_upp], [x_sum.min(), x_sum.max()], 'r-'),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	827 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	828 print(f'lower bound = {x_low} (inclusive)\nupper bound = {x_upp} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	829 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	830 if use_fit == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	831 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	832 num_x_min, 'sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	833 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	834 img_x_bounds = [x_low, x_upp]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	835 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	836 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	837 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	838 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	839 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	840 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	841 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	842
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	843 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	844 msnc.clearFig('bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	845 msnc.clearFig('sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	846 if title:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	847 msnc.clearFig(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	848
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	849 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	850 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	851 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	852 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	853 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	854 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	855
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	856 def _setZoomOrSkip(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	857 """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	858 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	859 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	860 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	861 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	862 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	863 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	864 '\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	865 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	866 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	867 min=1, max=100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	868 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	869 zoom_perc = preprocess['zoom_perc']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	870 if msnc.is_num(zoom_perc, 1., 100.):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	871 zoom_perc = int(zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	872 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	873 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	874 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	875 num_theta_skip = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	876 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	877 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	878 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	879 '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	880 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	881 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	882 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	883 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	884 num_theta_skip = preprocess['num_theta_skip']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	885 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	886 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	887 num_theta_skip = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	888 logging.info(f'zoom_perc = {zoom_perc}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	889 logging.info(f'num_theta_skip = {num_theta_skip}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	890
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	891 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	892 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	893 self.cf.config['preprocess'] = {'zoom_perc' : zoom_perc,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	894 'num_theta_skip' : num_theta_skip}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	895 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	896 preprocess['zoom_perc'] = zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	897 preprocess['num_theta_skip'] = num_theta_skip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	898 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	899
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	900 def _loadTomo(self, base_name, index, required=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	901 """Load a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	902 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	903 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	904 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	905 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	906 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	907 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	908 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	909 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	910 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	911 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	912 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	913 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	914 load_flag = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	915 available = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	916 if os.path.isfile(tomo_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	917 available = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	918 if required:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	919 load_flag = 'yes'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	920 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	921 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	922 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	923 if load_flag == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	924 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	925 logging.info(f'Loading {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	926 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	927 stack = np.load(tomo_file)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	928 except IOError or ValueError:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	929 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	930 logging.error(f'Error loading {tomo_file}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	931 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	932 if stack.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	933 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	934 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	935 return stack, available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	936
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	937 def _saveTomo(self, base_name, stack, index=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	938 """Save a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	939 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	940 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	941 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	942 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	943 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	944 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	945 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	946 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	947 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	948 if index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	949 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	950 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	951 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	952 logging.info(f'Saving {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	953 np.save(tomo_file, stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	954 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	955
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	956 def _genTomo(self, tomo_stack_files, available_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	957 """Generate tomography fields.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	958 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	959 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	960 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	961 assert(len(self.tomo_stacks) == len(stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	962 if len(available_stacks) != len(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	963 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	964 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	965 available_stacks = [False]*self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	966
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	967 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	968 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	969 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	970 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	971 zoom_perc = 100
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	972 num_theta_skip = 0
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	973 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	974 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	975 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	976 zoom_perc = preprocess.get('zoom_perc', 100)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	977 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	978
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	979 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	980 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	981 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	982 logging.warning('Dark field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	983 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	984 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	985 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	986
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	987 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	988 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	989 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	990 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	991
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	992 # Load a stack of tomography images
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	993 index = stack['index']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	994 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	995 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	996 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	997 img_x_bounds, img_y_bounds)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	998 tomo_stack = tomo_stack.astype('float64')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	999 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	1000
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1001 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1002 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1003 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1004 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1005 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1006 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	1007
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1008 # Normalize
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1009 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1010 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1011 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	1012 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	1013
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1014 # Remove non-positive values and linearize data
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1015 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1016 cutoff = 1.e-6
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1017 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1018 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	1019 with set_numexpr_threads(self.num_core):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1020 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1021 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	1022 f'{time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1023
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1024 # 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	1025 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1026 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	1027 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	1028
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1029 # Downsize tomography stack to smaller size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1030 tomo_stack = tomo_stack.astype('float32')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1031 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1032 title = f'red stack fullres {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1033 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1034 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	1035 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	1036 if zoom_perc != 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1037 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1038 logging.info(f'Zooming in ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1039 tomo_zoom_list = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1040 for j in range(tomo_stack.shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1041 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	1042 tomo_zoom_list.append(tomo_zoom)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1043 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	1044 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	1045 del tomo_zoom_list
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1046 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1047 title = f'red stack {zoom_perc}p {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1048 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1049 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	1050 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	1051
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1052 # 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	1053 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1054
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1055 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1056 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1057 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1058 self._saveTomo('red stack', tomo_stack, index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1059 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1060 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	1061 tomo_stack[0,:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1062
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1063 # Combine stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1064 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1065 self.tomo_stacks[i] = tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1066 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	1067
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1068 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1069 stack['preprocessed'] = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1070 stack.pop('reconstructed', 'reconstructed not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1071 find_center = self.config.get('find_center')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1072 if find_center:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1073 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1074 find_center.pop('completed', 'completed not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1075 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	1076 find_center.pop('upper_center_offset', 'upper_center_offset not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1077 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1078 if find_center.get('center_stack_index', -1) == index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1079 self.config.pop('find_center')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1080 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1081
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1082 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1083 del tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1084 del tbf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1085
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1086 def _reconstructOnePlane(self, tomo_plane_T, center, thetas_deg, eff_pixel_size,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1087 cross_sectional_dim, plot_sinogram=True):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1088 """Invert the sinogram for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1089 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1090 # tomo_plane_T index order: column,theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1091 assert(0 <= center < tomo_plane_T.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1092 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	1093 two_offset = 2*int(np.round(center_offset))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1094 two_offset_abs = np.abs(two_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1095 max_rad = int(0.5(cross_sectional_dim/eff_pixel_size)1.1) # 10% slack to avoid edge effects
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1096 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	1097 if two_offset >= 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1098 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	1099 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	1100 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1101 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	1102 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	1103 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	1104 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	1105 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	1106 save_only=self.save_plots_only, aspect='auto')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1107
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1108 # Inverting sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1109 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1110 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	1111 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	1112 del sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1113
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1114 # Removing ring artifacts
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1115 # 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	1116 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1117 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1118 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	1119 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	1120 del recon_sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1121 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1122 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	1123 return recon_clean
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1124
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1125 def _plotEdgesOnePlane(self, recon_plane, base_name, weight=0.001):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1126 # 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	1127 edges = denoise_tv_chambolle(recon_plane, weight = weight)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1128 vmax = np.max(edges[0,:,:])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1129 vmin = -vmax
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1130 msnc.quickImshow(edges[0,:,:], f'{base_name} coolwarm', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1131 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1132 msnc.quickImshow(edges[0,:,:], f'{base_name} gray', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1133 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='gray',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1134 vmin=vmin, vmax=vmax)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1135 del edges
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1136
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1137 def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1138 tol=0.1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1139 """Find center for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1140 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1141 # sinogram index order: theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1142 # 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	1143 sinogram_T = sinogram.T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1144 center = sinogram.shape[1]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1145
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1146 # try automatic center finding routines for initial value
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1147 tomo_center = tomopy.find_center_vo(sinogram)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1148 center_offset_vo = tomo_center-center
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1149 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1150 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	1151 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1152 eff_pixel_size, cross_sectional_dim, False)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1153 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1154 base_name=f'edges row{row} center_offset_vo{center_offset_vo:.2f}'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1155 self._plotEdgesOnePlane(recon_plane, base_name)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1156 use_phase_corr = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1157 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1158 use_phase_corr = pyip.inputYesNo('Try finding center using phase correlation '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1159 '(y/[n])? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1160 if use_phase_corr == 'yes':
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1161 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1162 rotc_guess=tomo_center)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1163 error = 1.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1164 while error > tol:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1165 prev = tomo_center
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1166 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1167 rotc_guess=tomo_center)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1168 error = np.abs(tomo_center-prev)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1169 center_offset = tomo_center-center
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1170 print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1171 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1172 eff_pixel_size, cross_sectional_dim, False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1173 base_name=f'edges row{row} center_offset{center_offset:.2f}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1174 self._plotEdgesOnePlane(recon_plane, base_name)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1175 accept_center = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1176 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1177 accept_center = pyip.inputYesNo('Accept a center location ([y]) or continue '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1178 'search (n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1179 if accept_center != 'no':
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1180 del sinogram_T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1181 del recon_plane
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1182 if self.test_mode:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1183 center_offset = center_offset_vo
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1184 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1185 center_offset = pyip.inputNum(
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1186 f' Enter chosen center offset [{-int(center)}, {int(center)}] '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1187 f'([{center_offset_vo}])): ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1188 if center_offset == '':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1189 center_offset = center_offset_vo
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1190 return float(center_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1191
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1192 while True:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1193 center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1194 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	1195 center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1196 f'[{center_offset_low}, {int(center)}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1197 min=center_offset_low, max=int(center))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1198 if center_offset_upp == center_offset_low:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1199 center_offset_step = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1200 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1201 center_offset_step = pyip.inputInt('Enter step size for center offset search '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1202 f'[1, {center_offset_upp-center_offset_low}]: ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1203 min=1, max=center_offset_upp-center_offset_low)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1204 for center_offset in range(center_offset_low, center_offset_upp+center_offset_step,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1205 center_offset_step):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1206 logging.info(f'center_offset = {center_offset}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1207 recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1208 thetas_deg, eff_pixel_size, cross_sectional_dim, False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1209 base_name=f'edges row{row} center_offset{center_offset}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1210 self._plotEdgesOnePlane(recon_plane, base_name)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1211 if pyip.inputInt('\nContinue (0) or end the search (1): ', min=0, max=1):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1212 break
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1213
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1214 del sinogram_T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1215 del recon_plane
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1216 center_offset = pyip.inputNum(f' Enter chosen center offset '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1217 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	1218 return float(center_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1219
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1220 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	1221 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	1222 run_secondary_sirt=False, secondary_iter=100):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1223 """reconstruct a single tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1224 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1225 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1226 # thetas must be in radians
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1227 # 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	1228 # RV should we remove stripes?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1229 # 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	1230 # RV should we remove rings?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1231 # 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	1232 # 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	1233 if row_bounds is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1234 row_bounds = [0, tomo_stack.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1235 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1236 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	1237 raise ValueError('Illegal row bounds in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1238 if thetas.size != tomo_stack.shape[1]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1239 raise ValueError('theta dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1240 if not len(center_offsets):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1241 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	1242 elif len(center_offsets) == 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1243 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	1244 row_bounds[1]-row_bounds[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1245 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1246 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	1247 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1248 centers = center_offsets
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1249 centers += tomo_stack.shape[2]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1250 if True:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1251 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1252 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1253 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1254 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1255 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	1256 algorithm=algorithm, ncore=num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1257 if run_secondary_sirt and secondary_iter > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1258 #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	1259 #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	1260 # cuda driver combination."
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1261 #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	1262 #SIRT did not finish while running overnight
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1263 #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	1264 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	1265 'num_iter':secondary_iter}
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1266 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	1267 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	1268 algorithm=tomopy.astra, ncore=num_core)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1269 if True:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1270 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1271 return tomo_recon_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1272
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1273 def findImageFiles(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1274 """Find all available image files.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1275 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1276 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1277
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1278 # Find dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1279 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1280 img_start, num_imgs, dark_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1281 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	1282 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1283 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	1284 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1285 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1286 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	1287 num_imgs_old = dark_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1288 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1289 dark_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1290 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1291 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1292 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	1293 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1294 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1295 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1296 dark_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1297 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1298 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1299 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	1300 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1301 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1302 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	1303 logging.info(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	1304
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1305 # Find bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1306 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1307 img_start, num_imgs, bright_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1308 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	1309 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1310 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	1311 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1312 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	1313 num_imgs_old = bright_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1314 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1315 bright_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1316 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1317 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1318 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	1319 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1320 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1321 bright_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1322 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1323 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1324 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	1325 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1326 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	1327 logging.info(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	1328
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1329 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1330 tomo_stack_files = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1331 for stack in self.config['stack_info']['stacks']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1332 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1333 img_start, num_imgs, tomo_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1334 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	1335 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1336 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1337 self.is_valid = False
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1338 img_start_old = stack.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1339 num_imgs_old = stack.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1340 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1341 stack['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1342 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1343 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1344 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	1345 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1346 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1347 stack['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1348 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1349 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1350 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	1351 self.is_valid = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1352 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	1353 logging.info(f'Tomography set {index} image start index = {stack["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1354 tomo_stack_files.append(tomo_files)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1355 del tomo_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1356
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1357 # Safe updated config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1358 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1359 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1360
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1361 return dark_files, bright_files, tomo_stack_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1362
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1363 def genTomoStacks(self, tdf_files=None, tbf_files=None, tomo_stack_files=None,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1364 dark_field_pngname=None, bright_field_pngname=None, tomo_field_pngname=None,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1365 detectorbounds_pngname=None, output_name=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1366 """Preprocess tomography images.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1367 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1368 # 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	1369 # 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	1370 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1371 stacks = stack_info['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1372 num_tomo_stacks = stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1373 assert(num_tomo_stacks == len(self.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1374 available_stacks = [False]*num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1375 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1376 assert(tdf_files is None or isinstance(tdf_files, list))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1377 assert(isinstance(tbf_files, list))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1378 assert(isinstance(tomo_stack_files, list))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1379 assert(num_tomo_stacks == len(tomo_stack_files))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1380 assert(isinstance(dark_field_pngname, str))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1381 assert(isinstance(bright_field_pngname, str))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1382 assert(isinstance(tomo_field_pngname, str))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1383 assert(isinstance(detectorbounds_pngname, str))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1384 assert(isinstance(output_name, str))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1385 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1386 if tdf_files:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1387 logging.warning('Ignoring tdf_files in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1388 if tbf_files:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1389 logging.warning('Ignoring tbf_files in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1390 if tomo_stack_files:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1391 logging.warning('Ignoring tomo_stack_files in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1392 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	1393 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1394 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1395 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1396 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	1397 self.tomo_stacks[i], available_stacks[i] = \
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1398 self._loadTomo('red stack', stack['index'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1399 if dark_field_pngname:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1400 logging.warning('Ignoring dark_field_pngname in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1401 if bright_field_pngname:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1402 logging.warning('Ignoring bright_field_pngname in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1403 if tomo_field_pngname:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1404 logging.warning('Ignoring tomo_field_pngname in genTomoStacks (only for Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1405 if detectorbounds_pngname:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1406 logging.warning('Ignoring detectorbounds_pngname in genTomoStacks '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1407 '(only used in Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1408 if output_name:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1409 logging.warning('Ignoring output_name in genTomoStacks '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1410 '(only used in Galaxy)')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1411
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1412 # Preprocess any unloaded stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1413 if False in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1414 logging.debug('Preprocessing tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1415
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1416 # Check required image files (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1417 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1418 self._selectImageRanges(available_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1419 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1420 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1421
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1422 # Generate dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1423 if tdf_files:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1424 self._genDark(tdf_files, dark_field_pngname)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1425
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1426 # Generate bright field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1427 self._genBright(tbf_files, bright_field_pngname)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1428
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1429 # Set vertical detector bounds for image stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1430 self._setDetectorBounds(tomo_stack_files, tomo_field_pngname, detectorbounds_pngname)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1431
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1432 # 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	1433 self._setZoomOrSkip()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1434
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1435 # Generate tomography fields
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1436 self._genTomo(tomo_stack_files, available_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1437
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1438 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1439 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1440 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1441 logging.info(f'Saving preprocessed tomography stack to file ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1442 save_stacks = {f'set_{stack["index"]}':tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1443 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	1444 np.savez(output_name, **save_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1445 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	1446
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1447 del available_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1448
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1449 # 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	1450 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1451 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1452 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1453 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1454 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	1455 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1456 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1457 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1458 pixel_size *= img_x_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1459 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1460 stack['ref_height'] = stack['ref_height']+pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1461 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1462
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1463 def findCenters(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1464 """Find rotation axis centers for the tomography stacks.
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 logging.debug('Find centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1467 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1468 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	1469 logging.debug('Available stacks: {available_stacks}')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1470
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1471 # Check for valid available center stack index
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1472 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	1473 center_stack_index = None
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1474 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	1475 center_stack_index = find_center['center_stack_index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1476 if (not isinstance(center_stack_index, int) or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1477 center_stack_index not in available_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1478 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	1479 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1480 if self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1481 assert(find_center.get('completed', False) == False)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1482 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1483 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	1484 f'{center_stack_index}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1485 if (pyip.inputYesNo('Do you want to use this again (y/n)? ') == 'yes' and
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1486 find_center.get('completed', False) == True):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1487 return
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1488
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1489 # Load the required preprocessed stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1490 # preprocessed stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1491 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1492 assert(len(stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1493 assert(len(self.tomo_stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1494 if num_tomo_stacks == 1:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1495 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1496 center_stack_index = stacks[0]['index']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1497 elif center_stack_index != stacks[0]['index']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1498 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	1499 if not self.tomo_stacks[0].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1500 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	1501 required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1502 center_stack = self.tomo_stacks[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1503 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1504 stacks[0]['preprocessed'] = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1505 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	1506 assert(stacks[0].get('preprocessed', False) == True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1507 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1508 while True:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1509 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1510 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	1511 f'rotation axis centers {available_stacks}: ')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1512 while center_stack_index not in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1513 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	1514 f'rotation axis centers {available_stacks}: ')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1515 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	1516 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	1517 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	1518 'red stack', center_stack_index, required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1519 center_stack = self.tomo_stacks[tomo_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1520 if not center_stack.size:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1521 stacks[tomo_stack_index]['preprocessed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1522 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	1523 'preprocessed tomography stack, pick another one')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1524 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1525 break
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1526 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	1527 if find_center is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1528 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	1529 find_center = self.config['find_center']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1530 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1531 find_center['center_stack_index'] = center_stack_index
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1532
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1533 # Set thetas (in degrees)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1534 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1535 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1536 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1537 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1538 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	1539 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	1540 endpoint=False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1541
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1542 # Get non-overlapping sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1543 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	1544 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1545 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1546 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1547 eff_pixel_size = 100.*pixel_size/zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1548 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	1549 tomo_ref_heights = [stack['ref_height'] for stack in stacks]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1550 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1551 n1 = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1552 height = center_stack.shape[0]*eff_pixel_size
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1553 if not self.test_mode and pyip.inputYesNo('\nDo you want to reconstruct the full '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1554 f'sample height ({height:.3f} mm) (y/n)? ') == 'no':
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1555 height = pyip.inputNum('\nEnter the desired reconstructed sample height '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1556 f'in mm [0, {height:.3f}]: ', min=0, max=height)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1557 n1 = int(0.5*(center_stack.shape[0]-height/eff_pixel_size))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1558 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1559 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	1560 tomo_ref_heights[1])/eff_pixel_size)/2)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1561 n2 = center_stack.shape[0]-n1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1562 logging.info(f'n1 = {n1}, n2 = {n2} (n2-n1) = {(n2-n1)*eff_pixel_size:.3f} mm')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1563 if not center_stack.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1564 RuntimeError('Center stack not loaded')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1565 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1566 msnc.quickImshow(center_stack[:,0,:], title=f'center stack theta={theta_start}',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1567 path=self.output_folder, save_fig=self.save_plots,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1568 save_only=self.save_plots_only)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1569
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1570 # Get cross sectional diameter in mm
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1571 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	1572 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	1573
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1574 # Determine center offset at sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1575 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	1576
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1577 # Lower row center
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1578 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1579 use_center = 'no'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1580 row = find_center.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1581 if msnc.is_int(row, n1, n2-2):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1582 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1583 assert(row is not None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1584 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1585 else:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1586 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	1587 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	1588 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	1589 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1590 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1591 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1592 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	1593 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1594 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	1595 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	1596 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1597 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1598 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1599 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	1600 aspect='auto')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1601 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	1602 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	1603 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1604 row = n1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1605 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1606 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1607 # center_stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1608 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1609 eff_pixel_size, cross_sectional_dim)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1610 logging.info(f'Lower center offset = {center_offset}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1611
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1612 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1613 find_center['row_bounds'] = [n1, n2]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1614 find_center['lower_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1615 find_center['lower_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1616 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1617 lower_row = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1618
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1619 # Upper row center
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1620 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1621 use_center = 'no'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1622 row = find_center.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1623 if msnc.is_int(row, lower_row+1, n2-1):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1624 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1625 assert(row is not None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1626 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1627 else:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1628 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	1629 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	1630 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	1631 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1632 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1633 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1634 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	1635 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1636 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	1637 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	1638 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1639 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1640 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1641 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	1642 aspect='auto')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1643 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	1644 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	1645 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1646 row = n2-1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1647 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1648 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1649 # center_stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1650 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1651 eff_pixel_size, cross_sectional_dim)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1652 logging.info(f'upper_center_offset = {center_offset}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1653 del center_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1654
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1655 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1656 find_center['upper_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1657 find_center['upper_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1658 find_center['completed'] = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1659 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1660
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1661 def checkCenters(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1662 """Check centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1663 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1664 #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	1665 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1666 logging.debug('Check centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1667 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	1668 if center_stack_index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1669 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	1670 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	1671 lower_row = self.config.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1672 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1673 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	1674 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	1675 if lower_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1676 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	1677 upper_row = self.config.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1678 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1679 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	1680 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	1681 if upper_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1682 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	1683 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	1684 shift = upper_center_offset-lower_center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1685 if lower_row == 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1686 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	1687 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1688 lower_row -= 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1689 lower_center_offset -= center_slope
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1690
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1691 # stack order: stack,row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1692 if center_stack_index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1693 stack1 = self.tomo_stacks[center_stack_index-1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1694 stack2 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1695 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1696 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	1697 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1698 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	1699 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1700 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1701 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1702 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1703 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1704 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1705 shift_i = shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1706 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1707 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1708 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	1709 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	1710 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1711 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	1712 stack1 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1713 stack2 = self.tomo_stacks[center_stack_index+1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1714 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1715 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	1716 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1717 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	1718 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1719 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1720 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1721 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1722 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1723 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1724 shift_i = -shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1725 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1726 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1727 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	1728 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	1729 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1730 del plane1, plane2, plane1_shifted
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1731
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1732 # Update config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1733 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	1734
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1735 def reconstructTomoStacks(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1736 """Reconstruct tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1737 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1738 logging.debug('Reconstruct tomography stacks')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1739 stacks = self.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1740 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	1741 assert(len(self.tomo_stacks) == len(stacks))
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1742 assert(len(self.tomo_recon_stacks) == len(stacks))
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1743
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1744 # Get rotation axis rows and centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1745 find_center = self.config['find_center']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1746 lower_row = find_center.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1747 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1748 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	1749 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1750 lower_center_offset = find_center.get('lower_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1751 if lower_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1752 logging.error('Unable to read lower_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1753 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1754 upper_row = find_center.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1755 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1756 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	1757 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1758 upper_center_offset = find_center.get('upper_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1759 if upper_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1760 logging.error('Unable to read upper_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1761 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1762 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	1763 assert(lower_row < upper_row)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1764 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	1765
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1766 # Set thetas (in radians)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1767 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1768 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1769 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1770 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1771 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	1772 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	1773 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	1774
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1775 # Reconstruct tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1776 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	1777 if zoom_perc == 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1778 basetitle = 'recon stack full'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1779 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1780 basetitle = f'recon stack {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1781 load_error = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1782 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1783 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1784 # Check if stack can be loaded
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1785 # 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	1786 # 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	1787 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1788 available = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1789 if stack.get('reconstructed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1790 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack', index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1791 if self.tomo_recon_stacks[i].size or available:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1792 if self.tomo_stacks[i].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1793 self.tomo_stacks[i] = np.array([])
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1794 assert(stack.get('preprocessed', False) == True)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1795 assert(stack.get('reconstructed', False) == True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1796 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1797 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1798 stack['reconstructed'] = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1799 if not self.tomo_stacks[i].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1800 self.tomo_stacks[i], available = self._loadTomo('red stack', index,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1801 required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1802 if not self.tomo_stacks[i].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1803 logging.error(f'Unable to load tomography stack {index} for reconstruction')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1804 stack[i]['preprocessed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1805 load_error = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1806 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1807 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1808 center_offsets = [lower_center_offset-lower_row*center_slope,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1809 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1810 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1811 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1812 thetas, center_offsets=center_offsets, sigma=0.1, num_core=self.num_core,
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1813 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1814 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1815 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1816 row_slice = int(self.tomo_stacks[i].shape[0]/2)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1817 title = f'{basetitle} {index} slice{row_slice}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1818 msnc.quickImshow(self.tomo_recon_stacks[i][row_slice,:,:], title=title,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1819 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	1820 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1821 msnc.quickPlot(self.tomo_recon_stacks[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1822 [row_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1823 title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[2]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1824 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	1825 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1826 self._saveTomo('recon stack', self.tomo_recon_stacks[i], index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1827 # else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1828 # np.savetxt(self.output_folder+f'recon_stack_{index}.txt',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1829 # self.tomo_recon_stacks[i][row_slice,:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1830 self.tomo_stacks[i] = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1831
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1832 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1833 stack['reconstructed'] = True
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1834 combine_stacks = self.config.get('combine_stacks')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1835 if combine_stacks and index in combine_stacks.get('stacks', []):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1836 combine_stacks['stacks'].remove(index)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1837 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1838
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1839 def combineTomoStacks(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1840 """Combine the reconstructed tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1841 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1842 # stack order: stack,row(z),x,y
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1843 logging.debug('Combine reconstructed tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1844 # Load any unloaded reconstructed stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1845 stack_info = self.config['stack_info']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1846 stacks = stack_info['stacks']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1847 for i,stack in enumerate(stacks):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1848 available = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1849 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	1850 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	1851 stack['index'], required=True)
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1852 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	1853 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	1854 stack['reconstructed'] = False
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1855 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1856 if i:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1857 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	1858 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	1859 logging.error('Incompatible reconstructed tomography stack dimensions')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1860 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1861
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1862 # Get center stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1863 row_bounds = self.config['find_center']['row_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1864 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	1865 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	1866 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1867
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1868 # Selecting x bounds (in yz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1869 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1870 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1871 [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	1872 self.tomo_recon_stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1873 combine_stacks = self.config.get('combine_stacks')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1874 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	1875 x_bounds = combine_stacks['x_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1876 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	1877 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	1878 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1879 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1880 if pyip.inputYesNo('\nCurrent image x-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1881 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	1882 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1883 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1884 '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	1885 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1886 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	1887 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1888 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	1889 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1890 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1891 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	1892 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	1893 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1894 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	1895 if False and self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1896 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	1897 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	1898 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1899 msnc.clearFig('recon stack sum yz')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1900
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1901 # Selecting y bounds (in xz-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1902 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1903 #RV FIX :=
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1904 [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	1905 self.tomo_recon_stacks]
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1906 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	1907 y_bounds = combine_stacks['y_bounds']
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1908 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	1909 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	1910 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1911 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1912 if pyip.inputYesNo('\nCurrent image y-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1913 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	1914 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1915 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1916 '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	1917 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1918 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	1919 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1920 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	1921 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1922 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1923 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	1924 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	1925 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1926 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	1927 if False and self.test_mode:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1928 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	1929 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	1930 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1931 msnc.clearFig('recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1932
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1933 # Combine reconstructed tomography stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1934 logging.info(f'Combining reconstructed stacks ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1935 t0 = time()
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1936 num_tomo_stacks = stack_info['num']
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1937 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1938 low_bound = row_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1939 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1940 low_bound = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1941 tomo_recon_combined = self.tomo_recon_stacks[0][low_bound:row_bounds[1]:,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1942 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	1943 if num_tomo_stacks > 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1944 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1945 [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	1946 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	1947 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	1948 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1949 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1950 [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	1951 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	1952 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	1953 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	1954
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1955 # Wrap up if in test_mode
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1956 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	1957 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1958 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	1959 filename = 'recon combined sum xy'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1960 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	1961 filename += ' fullres.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1962 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1963 filename += f' {zoom_perc}p.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1964 msnc.quickPlot(tomosum, title='recon combined sum xy',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1965 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	1966 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1967 if False:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1968 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	1969 tomosum, fmt='%.6e')
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1970 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	1971 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	1972
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1973 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1974 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1975 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1976 combine_stacks['y_bounds'] = y_bounds
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1977 combine_stacks['stacks'] = combined_stacks
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1978 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1979 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	1980 'stacks' : combined_stacks}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1981 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1982 return
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1983
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	1984 # Selecting z bounds (in xy-plane)
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1985 msnc.quickPlot(tomosum, title='recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1986 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1987 '\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	1988 blank=True) != 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1989 z_bounds = [0, tomo_recon_combined.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1990 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1991 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	1992 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	1993 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	1994 logging.info(f'tomo_recon_combined.shape = {tomo_recon_combined.shape}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1995 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1996 msnc.clearFig('recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1997
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1998 # Plot center slices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	1999 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	2000 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	2001 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	2002 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2003 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	2004 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	2005 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	2006 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2007 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	2008 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	2009 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	2010 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2011
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2012 # Save combined reconstructed tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2013 base_name = 'recon combined'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2014 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2015 base_name += f' {stack["index"]}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2016 self._saveTomo(base_name, tomo_recon_combined)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2017
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2018 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2019 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2020 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2021 combine_stacks['y_bounds'] = y_bounds
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2022 combine_stacks['z_bounds'] = z_bounds
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2023 combine_stacks['stacks'] = combined_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2024 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2025 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	2026 'z_bounds' : z_bounds, 'stacks' : combined_stacks}
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2027 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2028
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2029 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	2030 test_mode=False, num_core=-1):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2031 """Run a tomography analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2032 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2033 # Instantiate Tomo object
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2034 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	2035 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	2036 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2037 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	2038
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2039 # Preprocess the image files
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2040 assert(tomo.config['stack_info'])
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2041 num_tomo_stacks = tomo.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2042 assert(num_tomo_stacks == len(tomo.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2043 preprocessed_stacks = []
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2044 if not tomo.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2045 preprocess = tomo.config.get('preprocess', None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2046 if preprocess:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2047 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	2048 if stack.get('preprocessed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2049 if len(preprocessed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2050 tomo.genTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2051 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2052 IOError('Unable to load all required image files.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2053 tomo.cf.saveFile(tomo.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2054
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2055 # Find centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2056 find_center = tomo.config.get('find_center')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2057 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	2058 tomo.findCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2059
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2060 # Check centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2061 #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	2062 # tomo.checkCenters()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2063
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2064 # Reconstruct tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2065 assert(tomo.config['stack_info']['stacks'])
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2066 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	2067 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2068 if len(reconstructed_stacks) != num_tomo_stacks:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2069 tomo.reconstructTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2070
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2071 # Combine reconstructed tomography stacks
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2072 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	2073 if stack.get('reconstructed', False)]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2074 combine_stacks = tomo.config.get('combine_stacks')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2075 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	2076 combine_stacks.get('stacks') != reconstructed_stacks):
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2077 tomo.combineTomoStacks()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2078
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2079 #%%============================================================================
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2080 if __name__ == '__main__':
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2081
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2082 # Parse command line arguments
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2083 parser = argparse.ArgumentParser(
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2084 description='Tomography reconstruction')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2085 parser.add_argument('-c', '--config',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2086 default=None,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2087 help='Input config')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2088 parser.add_argument('-o', '--output_folder',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2089 default='.',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2090 help='Output folder')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2091 parser.add_argument('-l', '--log_level',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2092 default='INFO',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2093 help='Log level')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2094 parser.add_argument('-t', '--test_mode',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2095 action='store_true',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2096 default=False,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2097 help='Test mode flag')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2098 parser.add_argument('--num_core',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2099 default=-1,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2100 help='Number of cores')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2101 args = parser.parse_args()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2102
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2103 if args.config is None:
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2104 if os.path.isfile('config.yaml'):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2105 args.config = 'config.yaml'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2106 else:
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2107 args.config = 'config.txt'
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2108
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2109 # Set basic log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2110 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	2111 if not args.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2112 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	2113 if not isinstance(level, int):
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2114 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	2115 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	2116 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2117
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2118 logging.debug(f'config = {args.config}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2119 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	2120 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	2121 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	2122 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	2123
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2124 # Run tomography analysis
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2125 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	2126 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	2127
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2128 #%%============================================================================
1 e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b" rv43 parents: 0 diff changeset	2129 # input('Press any key to continue')
0 cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	2130 #%%============================================================================

Mercurial > repos > rv43 > tomo

annotate tomo.py @ 1:e4778148df6b draft