tomo: tomo.py annotate

author	rv43
date	Tue, 29 Mar 2022 16:10:16 +0000
parents
children	e4778148df6b

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
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	21 import numpy as np
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	22 import numexpr as ne
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	23 import multiprocessing as mp
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	24 import scipy.ndimage as spi
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	25 import tomopy
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	26 from time import time
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	27 from skimage.transform import iradon
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	28 from skimage.restoration import denoise_tv_chambolle
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	29
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	30 import msnc_tools as msnc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	31
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	32 class set_numexpr_threads:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	33
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	34 def __init__(self, nthreads):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	35 cpu_count = mp.cpu_count()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	36 if nthreads is None or nthreads > cpu_count:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	37 self.n = cpu_count
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	38 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	39 self.n = nthreads
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	40
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	41 def __enter__(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	42 self.oldn = ne.set_num_threads(self.n)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	43
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	44 def __exit__(self, exc_type, exc_value, traceback):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	45 ne.set_num_threads(self.oldn)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	46
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	47 class ConfigTomo(msnc.Config):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	48 """Class for processing a config file.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	49 """
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 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	52 super().__init__(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	53
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	54 def _validate_txt(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	55 """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	56 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	57 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	58
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	59 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	60 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	61 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	62 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	63 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	64 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	65 self.detector_id = self.config.get('detector_id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	66
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	67 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	68 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	69
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	70 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	71 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	72
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	73 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	74 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	75 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	76 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	77 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	78 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	79 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	80
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	81 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	82 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	83 if 'tomo_data_path' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	84 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	85 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	86 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	87 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	88 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	89 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	90 for i in range(self.num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	91 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	92 if 'z_pos' in key}.items())
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	93 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	94 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	95 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	96 if len(tomo_ref_height_indices):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	97 self.tomo_ref_heights = [
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	98 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	99 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	100 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	101
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	102 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	103 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	104 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	105 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	106 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	107 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	108 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	109 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	110 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	111 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	112 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	113 self.num_thetas = self.config.get('num_thetas')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	114 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	115 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	116 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	117 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	118 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	119
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	120 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	121
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	122 def _validate_yaml(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	123 """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	124 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	125 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	126
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	127 # Check for required first-level keys
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	128 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	129 pars_missing = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	130 is_valid = super().validate(pars_required, pars_missing)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	131 if len(pars_missing) > 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	132 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	133 self.detector_id = self.config['detector'].get('id')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	134
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	135 # Find tomography dark field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	136 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	137
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	138 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	139 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	140
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	141 # Check number of tomography image stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	142 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	143 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	144 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	145 self.num_tomo_stacks = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	146 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	147 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	148 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	149
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	150 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	151 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	152 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	153 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	154 return False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	155 self.tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	156 self.tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	157 self.tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	158 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	159 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	160 self.tomo_data_indices.append(stack.get('index'))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	161 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	162
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	163 # Check tomo angle (theta) range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	164 theta_range = self.config.get('theta_range')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	165 if theta_range is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	166 self.start_theta = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	167 self.end_theta = 180.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	168 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	169 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	170 self.start_theta = theta_range.get('start', 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	171 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	172 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	173 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	174 logging.debug(f'start_theta = {self.start_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	175 self.end_theta = theta_range.get('end', 180.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	176 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	177 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	178 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	179 logging.debug(f'end_theta = {self.end_theta}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	180 self.num_thetas = theta_range.get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	181 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	182 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	183 self.num_thetas = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	184 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	185 logging.debug(f'num_thetas = {self.num_thetas}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	186
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	187 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	188
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	189 def validate(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	190 """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	191 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	192 is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	193
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	194 # Check work_folder (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	195 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	196 if not os.path.isdir(work_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	197 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	198 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	199 logging.info(f'work_folder: {work_folder}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	200
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	201 # Check data filetype (shared by both file formats)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	202 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	203 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	204 self.data_filetype != 'h5'):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	205 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	206
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	207 if self.suffix == '.yml' or self.suffix == '.yaml':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	208 is_valid = self._validate_yaml()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	209 elif self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	210 is_valid = self._validate_txt()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	211 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	212 logging.error(f'Undefined or illegal config file extension: {self.suffix}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	213
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	214 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	215 if self.tdf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	216 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	217 if isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	218 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	219 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	220 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	221 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	222 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	223 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	224 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	225 if isinstance(self.tdf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	226 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	227 f'{work_folder}/{self.tdf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	228 elif isinstance(self.tdf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	229 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	230 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	231 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	232 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	233 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	234 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	235 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	236
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	237 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	238 if self.tbf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	239 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	240 if isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	241 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	242 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	243 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	244 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	245 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	246 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	247 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	248 if isinstance(self.tbf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	249 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	250 f'{work_folder}/{self.tbf_data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	251 elif isinstance(self.tbf_data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	252 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	253 self.tbf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	254 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	255 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	256 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	257 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	258 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	259
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	260 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	261 tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	262 tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	263 tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	264 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	265 self.tomo_ref_heights):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	266 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	267 if isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	268 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	269 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	270 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	271 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	272 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	273 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	274 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	275 if isinstance(data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	276 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	277 elif isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	278 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	279 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	280 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	281 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	282 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	283 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	284 tomo_data_paths.append(data_path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	285 if index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	286 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	287 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	288 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	289 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	290 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	291 index = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	292 elif not isinstance(index, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	293 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	294 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	295 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	296 tomo_data_indices.append(index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	297 if ref_height is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	298 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	299 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	300 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	301 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	302 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	303 ref_height = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	304 elif not msnc.is_num(ref_height):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	305 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	306 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	307 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	308 # Set reference heights relative to first stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	309 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	310 msnc.is_num(tomo_ref_heights[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	311 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	312 tomo_ref_heights.append(ref_height)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	313 tomo_ref_heights[0] = 0.0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	314 logging.info('tomography data paths:')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	315 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	316 logging.info(f' {tomo_data_paths[i]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	317 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	318 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	319
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	320 # Update config in memory
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	321 if self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	322 self.config = {}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	323 dark_field = self.config.get('dark_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	324 if dark_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	325 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	326 else:
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 bright_field = self.config.get('bright_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	329 if bright_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	330 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	331 else:
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 detector = self.config.get('detector')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	334 if detector is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	335 self.config['detector'] = {'id' : self.detector_id}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	336 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	337 detector['id'] = self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	338 self.config['work_folder'] = work_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	339 self.config['data_filetype'] = self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	340 stack_info = self.config.get('stack_info')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	341 if stack_info is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	342 stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	343 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	344 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	345 'ref_height' : tomo_ref_heights[i]})
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	346 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	347 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	348 stack_info['num'] = self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	349 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	350 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	351 stack['data_path'] = tomo_data_paths[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	352 stack['index'] = tomo_data_indices[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	353 stack['ref_height'] = tomo_ref_heights[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	354 if self.num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	355 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	356 'num' : self.num_thetas}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	357 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	358 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	359 self.config['theta_range'] = theta_range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	360
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	361 # Cleanup temporary validation variables
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	362 del self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	363 del self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	364 del self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	365 del self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	366 del self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	367 del self.tomo_data_paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	368 del self.tomo_data_indices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	369 del self.tomo_ref_heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	370 del self.start_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	371 del self.end_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	372 del self.num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	373
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	374 return is_valid
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 class Tomo:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	377 """Processing tomography data with misalignment.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	378 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	379
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	380 def __init__(self, config_file=None, config_dict=None, config_out=None, output_folder='.',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	381 log_level='INFO', log_stream='tomo.log', galaxy_flag=False, test_mode=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	382 """Initialize with optional config input file or dictionary
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	383 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	384 self.ncore = mp.cpu_count()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	385 self.config_out = config_out
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	386 self.output_folder = output_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	387 self.galaxy_flag = galaxy_flag
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	388 self.test_mode = test_mode
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	389 self.save_plots = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	390 self.save_plots_only = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	391 self.cf = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	392 self.config = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	393 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	394 self.tdf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	395 self.tbf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	396 self.tomo_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	397 self.tomo_recon_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	398
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	399 # Validate input parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	400 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	401 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	402 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	403 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	404 if config_out is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	405 if isinstance(config_out, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	406 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	407 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	408 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	409 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	410 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	411 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	412 if not os.path.isdir(output_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	413 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	414 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	415 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	416 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	417 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	418 if not os.path.isabs(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	419 log_stream = f'{output_folder}/{log_stream}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	420 if not isinstance(galaxy_flag, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	421 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	422 if not isinstance(test_mode, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	423 raise ValueError(f'Invalid test_mode input {test_mode} {type(test_mode)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	424
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	425 # Set log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	426 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	427 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	428 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	429 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	430 logging.basicConfig(filename=f'{log_stream}', filemode='w',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	431 format=logging_format, level=logging.WARNING, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	432 elif isinstance(log_stream, io.TextIOWrapper):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	433 logging.basicConfig(filemode='w', format=logging_format, level=logging.WARNING,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	434 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	435 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	436 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	437 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	438 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	439 level = getattr(logging, log_level.upper(), None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	440 if not isinstance(level, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	441 raise ValueError(f'Invalid log_level: {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	442 if log_stream is sys.stdout:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	443 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	444 handlers=[logging.StreamHandler()])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	445 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	446 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	447 logging.basicConfig(filename=f'{log_stream}', filemode='w',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	448 format=logging_format, level=level, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	449 elif isinstance(log_stream, io.TextIOWrapper):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	450 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	451 stream=log_stream, force=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	452 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	453 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	454 stream_handler = logging.StreamHandler()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	455 logging.getLogger().addHandler(stream_handler)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	456 stream_handler.setLevel(logging.WARNING)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	457 stream_handler.setFormatter(logging.Formatter(logging_format))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	458
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	459 # Check/set output config file name
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	460 if self.config_out is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	461 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	462 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	463 not os.path.isabs(self.config_out)):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	464 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	465
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	466 logging.info(f'ncore = {self.ncore}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	467 logging.debug(f'config_file = {config_file}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	468 logging.debug(f'config_dict = {config_dict}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	469 logging.debug(f'config_out = {self.config_out}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	470 logging.debug(f'output_folder = {self.output_folder}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	471 logging.debug(f'log_stream = {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	472 logging.debug(f'log_level = {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	473 logging.debug(f'galaxy_flag = {self.galaxy_flag}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	474 logging.debug(f'test_mode = {self.test_mode}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	475
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	476 # Create config object and load config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	477 self.cf = ConfigTomo(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	478 if not self.cf.load_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	479 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	480 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	481
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	482 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	483 self.ncore = 1 #RV can I set this? mp.cpu_count()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	484 assert(self.output_folder == '.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	485 assert(self.test_mode is False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	486 self.save_plots = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	487 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	488 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	489 # 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	490
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	491 # Check config file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	492 self.is_valid = self.cf.validate()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	493
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	494 # Load detector info file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	495 df = msnc.Detector(self.cf.config['detector']['id'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	496
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	497 # Check detector info file parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	498 if df.validate():
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	499 pixel_size = df.getPixelSize()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e" rv43 parents: diff changeset	500 num_rows, num_columns = df.getDimensions()

0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1 #!/usr/bin/env python3

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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2

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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3 # -*- coding: utf-8 -*-

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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4 """

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5 Created on Fri Dec 10 09:54:37 2021

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6

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7 @author: rv43

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8 """

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9

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10 import logging

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11

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12 import os

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13 import sys

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14 import getopt

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15 import re

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16 import io

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17 try:

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18 import pyinputplus as pyip

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19 except:

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20 pass

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21 import numpy as np

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22 import numexpr as ne

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23 import multiprocessing as mp

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24 import scipy.ndimage as spi

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25 import tomopy

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26 from time import time

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27 from skimage.transform import iradon

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28 from skimage.restoration import denoise_tv_chambolle

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29

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30 import msnc_tools as msnc

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31

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32 class set_numexpr_threads:

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33

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34 def __init__(self, nthreads):

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35 cpu_count = mp.cpu_count()

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36 if nthreads is None or nthreads > cpu_count:

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37 self.n = cpu_count

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38 else:

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39 self.n = nthreads

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40

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41 def __enter__(self):

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42 self.oldn = ne.set_num_threads(self.n)

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43

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44 def __exit__(self, exc_type, exc_value, traceback):

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45 ne.set_num_threads(self.oldn)

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46

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47 class ConfigTomo(msnc.Config):

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48 """Class for processing a config file.

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49 """

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50

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51 def __init__(self, config_file=None, config_dict=None):

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52 super().__init__(config_file, config_dict)

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53

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54 def _validate_txt(self):

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55 """Returns False if any required config parameter is illegal or missing.

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56 """

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57 is_valid = True

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58

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59 # Check for required first-level keys

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60 pars_required = ['tdf_data_path', 'tbf_data_path', 'detector_id']

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61 pars_missing = []

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62 is_valid = super().validate(pars_required, pars_missing)

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63 if len(pars_missing) > 0:

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64 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')

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65 self.detector_id = self.config.get('detector_id')

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66

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67 # Find tomography dark field images file/folder

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68 self.tdf_data_path = self.config.get('tdf_data_path')

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69

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70 # Find tomography bright field images file/folder

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71 self.tbf_data_path = self.config.get('tbf_data_path')

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72

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73 # Check number of tomography image stacks

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74 self.num_tomo_stacks = self.config.get('num_tomo_stacks', 1)

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75 if not msnc.is_int(self.num_tomo_stacks, 1):

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76 self.num_tomo_stacks = None

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77 msnc.illegal_value('num_tomo_stacks', self.num_tomo_stacks, 'config file')

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78 return False

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79 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')

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80

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81 # Find tomography images file/folders and stack parameters

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82 tomo_data_paths_indices = sorted({key:value for key,value in self.config.items()

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83 if 'tomo_data_path' in key}.items())

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84 if len(tomo_data_paths_indices) != self.num_tomo_stacks:

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85 logging.error(f'Incorrect number of tomography data path names in config file')

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86 is_valid = False

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87 self.tomo_data_paths = [tomo_data_paths_indices[i][1] for i in range(self.num_tomo_stacks)]

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88 self.tomo_data_indices = [msnc.get_trailing_int(tomo_data_paths_indices[i][0])

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89 if msnc.get_trailing_int(tomo_data_paths_indices[i][0]) else None

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90 for i in range(self.num_tomo_stacks)]

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91 tomo_ref_height_indices = sorted({key:value for key,value in self.config.items()

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92 if 'z_pos' in key}.items())

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93 if self.num_tomo_stacks > 1 and len(tomo_ref_height_indices) != self.num_tomo_stacks:

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94 logging.error(f'Incorrect number of tomography reference heights in config file')

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95 is_valid = False

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96 if len(tomo_ref_height_indices):

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97 self.tomo_ref_heights = [

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98 tomo_ref_height_indices[i][1] for i in range(self.num_tomo_stacks)]

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99 else:

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100 self.tomo_ref_heights = [0.0]*self.num_tomo_stacks

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101

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102 # Check tomo angle (theta) range

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103 self.start_theta = self.config.get('start_theta', 0.)

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104 if not msnc.is_num(self.start_theta, 0.):

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105 msnc.illegal_value('start_theta', self.start_theta, 'config file')

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106 is_valid = False

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107 logging.debug(f'start_theta = {self.start_theta}')

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108 self.end_theta = self.config.get('end_theta', 180.)

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109 if not msnc.is_num(self.end_theta, self.start_theta):

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110 msnc.illegal_value('end_theta', self.end_theta, 'config file')

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111 is_valid = False

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112 logging.debug(f'end_theta = {self.end_theta}')

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113 self.num_thetas = self.config.get('num_thetas')

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114 if not (self.num_thetas is None or msnc.is_int(self.num_thetas, 1)):

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115 msnc.illegal_value('num_thetas', self.num_thetas, 'config file')

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116 self.num_thetas = None

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117 is_valid = False

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118 logging.debug(f'num_thetas = {self.num_thetas}')

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119

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120 return is_valid

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121

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122 def _validate_yaml(self):

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123 """Returns False if any required config parameter is illegal or missing.

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124 """

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125 is_valid = True

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126

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127 # Check for required first-level keys

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128 pars_required = ['dark_field', 'bright_field', 'stack_info', 'detector']

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129 pars_missing = []

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130 is_valid = super().validate(pars_required, pars_missing)

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131 if len(pars_missing) > 0:

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132 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')

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133 self.detector_id = self.config['detector'].get('id')

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134

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135 # Find tomography dark field images file/folder

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136 self.tdf_data_path = self.config['dark_field'].get('data_path')

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137

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138 # Find tomography bright field images file/folder

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139 self.tbf_data_path = self.config['bright_field'].get('data_path')

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140

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141 # Check number of tomography image stacks

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142 stack_info = self.config['stack_info']

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143 self.num_tomo_stacks = stack_info.get('num', 1)

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144 if not msnc.is_int(self.num_tomo_stacks, 1):

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145 self.num_tomo_stacks = None

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146 msnc.illegal_value('stack_info:num', self.num_tomo_stacks, 'config file')

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147 return False

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148 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')

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149

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150 # Find tomography images file/folders and stack parameters

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151 stacks = stack_info.get('stacks')

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152 if stacks is None or len(stacks) is not self.num_tomo_stacks:

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153 msnc.illegal_value('stack_info:stacks', stacks, 'config file')

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154 return False

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155 self.tomo_data_paths = []

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156 self.tomo_data_indices = []

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157 self.tomo_ref_heights = []

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158 for stack in stacks:

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159 self.tomo_data_paths.append(stack.get('data_path'))

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160 self.tomo_data_indices.append(stack.get('index'))

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161 self.tomo_ref_heights.append(stack.get('ref_height'))

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162

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163 # Check tomo angle (theta) range

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164 theta_range = self.config.get('theta_range')

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165 if theta_range is None:

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166 self.start_theta = 0.

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167 self.end_theta = 180.

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168 self.num_thetas = None

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169 else:

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170 self.start_theta = theta_range.get('start', 0.)

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171 if not msnc.is_num(self.start_theta, 0.):

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172 msnc.illegal_value('theta_range:start', self.start_theta, 'config file')

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173 is_valid = False

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174 logging.debug(f'start_theta = {self.start_theta}')

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175 self.end_theta = theta_range.get('end', 180.)

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176 if not msnc.is_num(self.end_theta, self.start_theta):

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177 msnc.illegal_value('theta_range:end', self.end_theta, 'config file')

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178 is_valid = False

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179 logging.debug(f'end_theta = {self.end_theta}')

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180 self.num_thetas = theta_range.get('num')

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181 if self.num_thetas and not msnc.is_int(self.num_thetas, 1):

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182 msnc.illegal_value('theta_range:num', self.num_thetas, 'config file')

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183 self.num_thetas = None

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184 is_valid = False

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185 logging.debug(f'num_thetas = {self.num_thetas}')

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186

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187 return is_valid

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188

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189 def validate(self):

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190 """Returns False if any required config parameter is illegal or missing.

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191 """

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192 is_valid = True

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193

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194 # Check work_folder (shared by both file formats)

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195 work_folder = os.path.abspath(self.config.get('work_folder', ''))

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196 if not os.path.isdir(work_folder):

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197 msnc.illegal_value('work_folder', work_folder, 'config file')

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198 is_valid = False

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199 logging.info(f'work_folder: {work_folder}')

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200

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201 # Check data filetype (shared by both file formats)

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202 self.data_filetype = self.config.get('data_filetype', 'tif')

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203 if not isinstance(self.data_filetype, str) or (self.data_filetype != 'tif' and

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204 self.data_filetype != 'h5'):

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205 msnc.illegal_value('data_filetype', self.data_filetype, 'config file')

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206

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207 if self.suffix == '.yml' or self.suffix == '.yaml':

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208 is_valid = self._validate_yaml()

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209 elif self.suffix == '.txt':

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210 is_valid = self._validate_txt()

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211 else:

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212 logging.error(f'Undefined or illegal config file extension: {self.suffix}')

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213

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214 # Find tomography bright field images file/folder

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215 if self.tdf_data_path:

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216 if self.data_filetype == 'h5':

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217 if isinstance(self.tdf_data_path, str):

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218 if not os.path.isabs(self.tdf_data_path):

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219 self.tdf_data_path = os.path.abspath(

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220 f'{work_folder}/{self.tdf_data_path}')

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221 else:

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222 msnc.illegal_value('tdf_data_path', tdf_data_fil, 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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223 is_valid = False

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224 else:

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225 if isinstance(self.tdf_data_path, int):

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226 self.tdf_data_path = os.path.abspath(

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227 f'{work_folder}/{self.tdf_data_path}/nf')

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228 elif isinstance(self.tdf_data_path, str):

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229 if not os.path.isabs(self.tdf_data_path):

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230 self.tdf_data_path = os.path.abspath(

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231 f'{work_folder}/{self.tdf_data_path}')

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232 else:

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233 msnc.illegal_value('tdf_data_path', self.tdf_data_path, 'config file')

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234 is_valid = False

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235 logging.info(f'dark field images path = {self.tdf_data_path}')

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236

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237 # Find tomography bright field images file/folder

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238 if self.tbf_data_path:

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239 if self.data_filetype == 'h5':

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240 if isinstance(self.tbf_data_path, str):

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241 if not os.path.isabs(self.tbf_data_path):

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242 self.tbf_data_path = os.path.abspath(

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243 f'{work_folder}/{self.tbf_data_path}')

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244 else:

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245 msnc.illegal_value('tbf_data_path', tbf_data_fil, 'config file')

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246 is_valid = False

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247 else:

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248 if isinstance(self.tbf_data_path, int):

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249 self.tbf_data_path = os.path.abspath(

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250 f'{work_folder}/{self.tbf_data_path}/nf')

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251 elif isinstance(self.tbf_data_path, str):

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252 if not os.path.isabs(self.tbf_data_path):

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253 self.tbf_data_path = os.path.abspath(

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254 f'{work_folder}/{self.tbf_data_path}')

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255 else:

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256 msnc.illegal_value('tbf_data_path', self.tbf_data_path, 'config file')

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257 is_valid = False

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258 logging.info(f'bright field images path = {self.tbf_data_path}')

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259

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260 # Find tomography images file/folders and stack parameters

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261 tomo_data_paths = []

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262 tomo_data_indices = []

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263 tomo_ref_heights = []

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264 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"

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265 self.tomo_ref_heights):

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266 if self.data_filetype == 'h5':

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267 if isinstance(data_path, str):

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268 if not os.path.isabs(data_path):

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269 data_path = os.path.abspath(f'{work_folder}/{data_path}')

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270 else:

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271 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"

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272 is_valid = False

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273 data_path = None

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274 else:

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275 if isinstance(data_path, int):

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276 data_path = os.path.abspath(f'{work_folder}/{data_path}/nf')

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277 elif isinstance(data_path, str):

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278 if not os.path.isabs(data_path):

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279 data_path = os.path.abspath(f'{work_folder}/{data_path}')

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280 else:

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281 msnc.illegal_value(f'stack_info:stacks:data_path', data_path, 'config file')

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282 is_valid = False

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283 data_path = None

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284 tomo_data_paths.append(data_path)

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285 if index is None:

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286 if self.num_tomo_stacks > 1:

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287 logging.error('Missing stack_info:stacks:index in config file')

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288 is_valid = False

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289 index = None

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290 else:

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291 index = 1

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292 elif not isinstance(index, int):

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293 msnc.illegal_value(f'stack_info:stacks:index', index, 'config file')

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294 is_valid = False

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295 index = None

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296 tomo_data_indices.append(index)

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297 if ref_height is None:

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298 if self.num_tomo_stacks > 1:

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299 logging.error('Missing stack_info:stacks:ref_height in config file')

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300 is_valid = False

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301 ref_height = None

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302 else:

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303 ref_height = 0.

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304 elif not msnc.is_num(ref_height):

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305 msnc.illegal_value(f'stack_info:stacks:ref_height', ref_height, 'config file')

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306 is_valid = False

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307 ref_height = None

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308 # Set reference heights relative to first stack

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309 if (len(tomo_ref_heights) and msnc.is_num(ref_height) and

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310 msnc.is_num(tomo_ref_heights[0])):

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311 ref_height = (round(ref_height-tomo_ref_heights[0], 3))

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312 tomo_ref_heights.append(ref_height)

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313 tomo_ref_heights[0] = 0.0

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314 logging.info('tomography data paths:')

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315 for i in range(self.num_tomo_stacks):

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316 logging.info(f' {tomo_data_paths[i]}')

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317 logging.info(f'tomography data path indices: {tomo_data_indices}')

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318 logging.info(f'tomography reference heights: {tomo_ref_heights}')

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319

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320 # Update config in memory

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321 if self.suffix == '.txt':

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322 self.config = {}

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323 dark_field = self.config.get('dark_field')

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324 if dark_field is None:

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325 self.config['dark_field'] = {'data_path' : self.tdf_data_path}

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326 else:

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327 self.config['dark_field']['data_path'] = self.tdf_data_path

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328 bright_field = self.config.get('bright_field')

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329 if bright_field is None:

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330 self.config['bright_field'] = {'data_path' : self.tbf_data_path}

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331 else:

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332 self.config['bright_field']['data_path'] = self.tbf_data_path

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333 detector = self.config.get('detector')

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334 if detector is None:

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335 self.config['detector'] = {'id' : self.detector_id}

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336 else:

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337 detector['id'] = self.detector_id

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338 self.config['work_folder'] = work_folder

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339 self.config['data_filetype'] = self.data_filetype

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340 stack_info = self.config.get('stack_info')

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341 if stack_info is None:

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342 stacks = []

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343 for i in range(self.num_tomo_stacks):

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344 stacks.append({'data_path' : tomo_data_paths[i], 'index' : tomo_data_indices[i],

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345 'ref_height' : tomo_ref_heights[i]})

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346 self.config['stack_info'] = {'num' : self.num_tomo_stacks, 'stacks' : stacks}

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347 else:

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348 stack_info['num'] = self.num_tomo_stacks

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349 stacks = stack_info.get('stacks')

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350 for i,stack in enumerate(stacks):

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351 stack['data_path'] = tomo_data_paths[i]

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352 stack['index'] = tomo_data_indices[i]

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353 stack['ref_height'] = tomo_ref_heights[i]

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354 if self.num_thetas:

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355 theta_range = {'start' : self.start_theta, 'end' : self.end_theta,

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356 'num' : self.num_thetas}

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357 else:

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358 theta_range = {'start' : self.start_theta, 'end' : self.end_theta}

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359 self.config['theta_range'] = theta_range

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360

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361 # Cleanup temporary validation variables

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362 del self.tdf_data_path

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363 del self.tbf_data_path

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364 del self.detector_id

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365 del self.data_filetype

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366 del self.num_tomo_stacks

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367 del self.tomo_data_paths

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368 del self.tomo_data_indices

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369 del self.tomo_ref_heights

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370 del self.start_theta

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371 del self.end_theta

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372 del self.num_thetas

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373

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374 return is_valid

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375

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376 class Tomo:

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377 """Processing tomography data with misalignment.

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378 """

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379

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380 def __init__(self, config_file=None, config_dict=None, config_out=None, output_folder='.',

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381 log_level='INFO', log_stream='tomo.log', galaxy_flag=False, test_mode=False):

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382 """Initialize with optional config input file or dictionary

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383 """

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384 self.ncore = mp.cpu_count()

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385 self.config_out = config_out

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386 self.output_folder = output_folder

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387 self.galaxy_flag = galaxy_flag

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388 self.test_mode = test_mode

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389 self.save_plots = True # Make input argument?

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390 self.save_plots_only = True # Make input argument?

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391 self.cf = None

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392 self.config = None

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393 self.is_valid = True

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394 self.tdf = np.array([])

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395 self.tbf = np.array([])

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396 self.tomo_stacks = []

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397 self.tomo_recon_stacks = []

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398

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399 # Validate input parameters

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400 if config_file is not None and not os.path.isfile(config_file):

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401 raise OSError(f'Invalid config_file input {config_file} {type(config_file)}')

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402 if config_dict is not None and not isinstance(config_dict, dict):

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403 raise ValueError(f'Invalid config_dict input {config_dict} {type(config_dict)}')

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404 if config_out is not None:

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405 if isinstance(config_out, str):

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406 if isinstance(log_stream, str):

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407 path = os.path.split(log_stream)[0]

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408 if path and not os.path.isdir(path):

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409 raise OSError(f'Invalid log_stream path')

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410 else:

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411 raise OSError(f'Invalid config_out input {config_out} {type(config_out)}')

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412 if not os.path.isdir(output_folder):

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413 raise OSError(f'Invalid output_folder input {output_folder} {type(output_folder)}')

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414 if isinstance(log_stream, str):

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415 path = os.path.split(log_stream)[0]

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416 if path and not os.path.isdir(path):

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417 raise OSError(f'Invalid log_stream path')

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418 if not os.path.isabs(path):

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419 log_stream = f'{output_folder}/{log_stream}'

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420 if not isinstance(galaxy_flag, bool):

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421 raise ValueError(f'Invalid galaxy_flag input {galaxy_flag} {type(galaxy_flag)}')

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422 if not isinstance(test_mode, bool):

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423 raise ValueError(f'Invalid test_mode input {test_mode} {type(test_mode)}')

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424

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425 # Set log configuration

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426 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'

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427 if self.test_mode:

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428 self.save_plots_only = True

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429 if isinstance(log_stream, str):

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430 logging.basicConfig(filename=f'{log_stream}', filemode='w',

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431 format=logging_format, level=logging.WARNING, force=True)

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432 elif isinstance(log_stream, io.TextIOWrapper):

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433 logging.basicConfig(filemode='w', format=logging_format, level=logging.WARNING,

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434 stream=log_stream, force=True)

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435 else:

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436 raise ValueError(f'Invalid log_stream: {log_stream}')

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437 logging.warning('Ignoring log_level argument in test mode')

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438 else:

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439 level = getattr(logging, log_level.upper(), None)

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440 if not isinstance(level, int):

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441 raise ValueError(f'Invalid log_level: {log_level}')

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442 if log_stream is sys.stdout:

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443 logging.basicConfig(format=logging_format, level=level, force=True,

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444 handlers=[logging.StreamHandler()])

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445 else:

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446 if isinstance(log_stream, str):

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447 logging.basicConfig(filename=f'{log_stream}', filemode='w',

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448 format=logging_format, level=level, force=True)

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449 elif isinstance(log_stream, io.TextIOWrapper):

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450 logging.basicConfig(filemode='w', format=logging_format, level=level,

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451 stream=log_stream, force=True)

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452 else:

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453 raise ValueError(f'Invalid log_stream: {log_stream}')

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454 stream_handler = logging.StreamHandler()

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455 logging.getLogger().addHandler(stream_handler)

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456 stream_handler.setLevel(logging.WARNING)

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457 stream_handler.setFormatter(logging.Formatter(logging_format))

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458

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459 # Check/set output config file name

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460 if self.config_out is None:

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461 self.config_out = f'{self.output_folder}/config.yaml'

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462 elif (self.config_out is os.path.basename(self.config_out) and

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463 not os.path.isabs(self.config_out)):

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464 self.config_out = f'{self.output_folder}/{self.config_out}'

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465

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466 logging.info(f'ncore = {self.ncore}')

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467 logging.debug(f'config_file = {config_file}')

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468 logging.debug(f'config_dict = {config_dict}')

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469 logging.debug(f'config_out = {self.config_out}')

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470 logging.debug(f'output_folder = {self.output_folder}')

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471 logging.debug(f'log_stream = {log_stream}')

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472 logging.debug(f'log_level = {log_level}')

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473 logging.debug(f'galaxy_flag = {self.galaxy_flag}')

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474 logging.debug(f'test_mode = {self.test_mode}')

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475

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476 # Create config object and load config file

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477 self.cf = ConfigTomo(config_file, config_dict)

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478 if not self.cf.load_flag:

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479 self.is_valid = False

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480 return

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481

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482 if self.galaxy_flag:

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483 self.ncore = 1 #RV can I set this? mp.cpu_count()

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484 assert(self.output_folder == '.')

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485 assert(self.test_mode is False)

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486 self.save_plots = True

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487 self.save_plots_only = True

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488 else:

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489 # Input validation is already performed during link_data_to_galaxy

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490

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491 # Check config file parameters

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492 self.is_valid = self.cf.validate()

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493

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494 # Load detector info file

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495 df = msnc.Detector(self.cf.config['detector']['id'])

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496

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497 # Check detector info file parameters

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498 if df.validate():

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499 pixel_size = df.getPixelSize()

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500 num_rows, num_columns = df.getDimensions()

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501 if not pixel_size or not num_rows or not num_columns:

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502 self.is_valid = False

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503 else:

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504 pixel_size = None

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505 num_rows = None

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506 num_columns = None

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507 self.is_valid = False

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508

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509 # Update config

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510 self.cf.config['detector']['pixel_size'] = pixel_size

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511 self.cf.config['detector']['rows'] = num_rows

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512 self.cf.config['detector']['columns'] = num_columns

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513 logging.debug(f'pixel_size = self.cf.config["detector"]["pixel_size"]')

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514 logging.debug(f'num_rows: {self.cf.config["detector"]["rows"]}')

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515 logging.debug(f'num_columns: {self.cf.config["detector"]["columns"]}')

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516

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517 # Safe config to file

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518 if self.is_valid:

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519 self.cf.saveFile(self.config_out)

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520

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521 # Initialize shortcut to config

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522 self.config = self.cf.config

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523

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524 # Initialize tomography stack

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525 num_tomo_stacks = self.config['stack_info']['num']

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526 if num_tomo_stacks:

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527 self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)]

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528 self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)]

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529

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530 logging.debug(f'save_plots = {self.save_plots}')

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531 logging.debug(f'save_plots_only = {self.save_plots_only}')

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532

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533 def _selectImageRanges(self, available_stacks=None):

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534 """Select image files to be included in analysis.

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535 """

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536 self.is_valid = True

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537 stack_info = self.config['stack_info']

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538 if available_stacks is None:

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539 available_stacks = [False]*stack_info['num']

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540 elif len(available_stacks) != stack_info['num']:

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diff changeset

541 logging.warning('Illegal dimension of available_stacks in getImageFiles '+

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542 f'({len(available_stacks)}');

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543 available_stacks = [False]*stack_info['num']

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diff changeset

544

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545 # Check number of tomography angles/thetas

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546 num_thetas = self.config['theta_range'].get('num')

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547 if num_thetas is None:

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548 num_thetas = pyip.inputInt('\nEnter the number of thetas (>0): ', greaterThan=0)

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549 elif not msnc.is_int(num_thetas, 0):

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550 msnc.illegal_value('num_thetas', num_thetas, 'config file')

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551 self.is_valid = False

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552 return

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553 self.config['theta_range']['num'] = num_thetas

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554 logging.debug(f'num_thetas = {self.config["theta_range"]["num"]}')

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555

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556 # Find tomography dark field images

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557 dark_field = self.config['dark_field']

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558 img_start = dark_field.get('img_start', -1)

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559 img_offset = dark_field.get('img_offset', -1)

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560 num_imgs = dark_field.get('num', 0)

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561 if not self.test_mode:

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562 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,

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563 num_imgs, 'dark field')

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564 if img_start < 0 or num_imgs < 1:

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565 logging.error('Unable to find suitable dark field images')

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566 if dark_field['data_path']:

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567 self.is_valid = False

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568 dark_field['img_start'] = img_start

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diff changeset

569 dark_field['img_offset'] = img_offset

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570 dark_field['num'] = num_imgs

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571 logging.debug(f'Dark field image start index: {dark_field["img_start"]}')

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572 logging.debug(f'Dark field image offset: {dark_field["img_offset"]}')

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573 logging.debug(f'Number of dark field images: {dark_field["num"]}')

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574

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575 # Find tomography bright field images

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576 bright_field = self.config['bright_field']

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577 img_start = bright_field.get('img_start', -1)

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578 img_offset = bright_field.get('img_offset', -1)

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579 num_imgs = bright_field.get('num', 0)

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580 if not self.test_mode:

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581 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,

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582 num_imgs, 'bright field')

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583 if img_start < 0 or num_imgs < 1:

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584 logging.error('Unable to find suitable bright field images')

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585 if bright_field['data_path']:

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586 self.is_valid = False

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587 bright_field['img_start'] = img_start

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588 bright_field['img_offset'] = img_offset

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589 bright_field['num'] = num_imgs

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590 logging.debug(f'Bright field image start index: {bright_field["img_start"]}')

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591 logging.debug(f'Bright field image offset: {bright_field["img_offset"]}')

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592 logging.debug(f'Number of bright field images: {bright_field["num"]}')

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593

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594 # Find tomography images

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595 for i,stack in enumerate(stack_info['stacks']):

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596 # Check if stack is already loaded or available

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597 if self.tomo_stacks[i].size or available_stacks[i]:

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598 continue

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599 index = stack['index']

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600 img_start = stack.get('img_start', -1)

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601 img_offset = stack.get('img_offset', -1)

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602 num_imgs = stack.get('num', 0)

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603 if not self.test_mode:

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604 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,

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605 num_imgs, f'tomography stack {index}', num_thetas)

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606 if img_start < 0 or num_imgs != num_thetas:

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607 logging.error('Unable to find suitable tomography images')

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608 self.is_valid = False

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609 stack['img_start'] = img_start

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610 stack['img_offset'] = img_offset

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611 stack['num'] = num_imgs

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612 logging.debug(f'Tomography stack {index} image start index: {stack["img_start"]}')

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613 logging.debug(f'Tomography stack {index} image offset: {stack["img_offset"]}')

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614 logging.debug(f'Number of tomography images for stack {index}: {stack["num"]}')

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615 available_stacks[i] = True

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616

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617 # Safe updated config to file

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618 if self.is_valid:

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619 self.cf.saveFile(self.config_out)

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620

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621 return

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622

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623 def _genDark(self, tdf_files, dark_field_pngname):

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624 """Generate dark field.

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625 """

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626 # Load the dark field images

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627 logging.debug('Loading dark field...')

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628 dark_field = self.config['dark_field']

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629 tdf_stack = msnc.loadImageStack(tdf_files, self.config['data_filetype'],

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630 dark_field['img_offset'], dark_field['num'])

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631

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632 # Take median

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633 self.tdf = np.median(tdf_stack, axis=0)

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634 del tdf_stack

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635

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636 # RV make input of some kind (not always needed)

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637 tdf_cutoff = 21

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638 self.tdf[self.tdf > tdf_cutoff] = np.nan

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639 tdf_mean = np.nanmean(self.tdf)

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640 logging.debug(f'tdf_cutoff = {tdf_cutoff}')

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641 logging.debug(f'tdf_mean = {tdf_mean}')

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642 np.nan_to_num(self.tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)

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643 if not self.test_mode and not self.galaxy_flag:

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644 msnc.quickImshow(self.tdf, title='dark field', path=self.output_folder,

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645 save_fig=self.save_plots, save_only=self.save_plots_only)

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646 elif self.galaxy_flag:

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647 msnc.quickImshow(self.tdf, title='dark field', name=dark_field_pngname,

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648 save_fig=True, save_only=True)

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649

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650 def _genBright(self, tbf_files, bright_field_pngname):

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651 """Generate bright field.

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652 """

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653 # Load the bright field images

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654 logging.debug('Loading bright field...')

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655 bright_field = self.config['bright_field']

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656 tbf_stack = msnc.loadImageStack(tbf_files, self.config['data_filetype'],

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657 bright_field['img_offset'], bright_field['num'])

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658

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659 # Take median

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660 """Median or mean: It may be best to try the median because of some image

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661 artifacts that arise due to crinkles in the upstream kapton tape windows

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diff changeset

662 causing some phase contrast images to appear on the detector.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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663 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"

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664 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"

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665 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"

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diff changeset

666 beam because there is frame to frame fluctuations from the incoming beam.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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667 We don’t typically account for them but potentially could.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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668 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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669 self.tbf = np.median(tbf_stack, axis=0)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

670 del tbf_stack

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

671

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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672 # Subtract dark field

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

673 if self.tdf.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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674 self.tbf -= self.tdf

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

675 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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676 logging.warning('Dark field unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

677 if not self.test_mode and not self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

678 msnc.quickImshow(self.tbf, title='bright field', path=self.output_folder,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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679 save_fig=self.save_plots, save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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680 elif self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

681 msnc.quickImshow(self.tbf, title='bright field', name=bright_field_pngname,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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682 save_fig=True, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

683

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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684 def _setDetectorBounds(self, tomo_stack_files, tomo_field_pngname, detectorbounds_pngname):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

685 """Set vertical detector bounds for image stack.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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686 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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687 preprocess = self.config.get('preprocess')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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688 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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689 img_x_bounds = [None, None]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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690 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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691 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"

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692 if self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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693 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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694 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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695 self.cf.config['preprocess'] = {'img_x_bounds' : [0, self.tbf.shape[0]]}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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696 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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697 preprocess['img_x_bounds'] = img_x_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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698 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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699 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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700

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

701 # Check reference heights

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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702 pixel_size = self.config['detector']['pixel_size']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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703 if pixel_size is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

704 raise ValueError('Detector pixel size unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

705 if not self.tbf.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

706 raise ValueError('Bright field unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

707 num_x_min = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

708 num_tomo_stacks = self.config['stack_info']['num']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

709 stacks = self.config['stack_info']['stacks']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

710 if num_tomo_stacks > 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

711 delta_z = stacks[1]['ref_height']-stacks[0]['ref_height']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

712 for i in range(2, num_tomo_stacks):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

713 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"

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diff changeset

714 logging.debug(f'delta_z = {delta_z}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

715 num_x_min = int(delta_z/pixel_size)+1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

716 logging.debug(f'num_x_min = {num_x_min}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

717 if num_x_min > self.tbf.shape[0]:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

718 logging.warning('Image bounds and pixel size prevent seamless stacking')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

719 num_x_min = self.tbf.shape[0]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

720

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

721 # Select image bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

722 if self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

723 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

724 img_x_bounds = [0, self.tbf.shape[0]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

725 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

726 margin = int(num_x_min/10)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

727 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"

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parents:

diff changeset

728 img_x_bounds = [offset, num_x_min+offset+2*margin]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

729 tomo_stack = msnc.loadImageStack(tomo_stack_files[0], self.config['data_filetype'],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

730 stacks[0]['img_offset'], 1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

731 x_sum = np.sum(tomo_stack[0,:,:], 1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

732 title = f'tomography image at theta={self.config["theta_range"]["start"]}'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

733 msnc.quickImshow(tomo_stack[0,:,:], title=title, name=tomo_field_pngname,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

734 save_fig=True, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

735 msnc.quickPlot((range(x_sum.size), x_sum),

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

736 ([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"

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parents:

diff changeset

737 ([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"

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parents:

diff changeset

738 title='sum over theta and y', name=detectorbounds_pngname,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

739 save_fig=True, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

740

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

741 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

742 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

743 self.cf.config['preprocess'] = {'img_x_bounds' : img_x_bounds}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

744 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

745 preprocess['img_x_bounds'] = img_x_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

746 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

747 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

748

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

749 # For one tomography stack only: load the first image

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

750 title = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

751 msnc.quickImshow(self.tbf, title='bright field')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

752 if num_tomo_stacks == 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

753 tomo_stack = msnc.loadImageStack(tomo_stack_files[0], self.config['data_filetype'],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

754 stacks[0]['img_offset'], 1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

755 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

756 msnc.quickImshow(tomo_stack[0,:,:], title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

757 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

758 '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

759 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

760 print('\nSelect image bounds from bright field')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

761 tomo_or_bright = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

762 if tomo_or_bright:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

763 x_sum = np.sum(tomo_stack[0,:,:], 1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

764 use_bounds = 'no'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

765 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

766 if img_x_bounds[0] < 0:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

767 msnc.illegal_value('img_x_bounds[0]', img_x_bounds[0], 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

768 img_x_bounds[0] = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

769 if not img_x_bounds[0] < img_x_bounds[1] <= x_sum.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

770 msnc.illegal_value('img_x_bounds[1]', img_x_bounds[1], 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

771 img_x_bounds[1] = x_sum.size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

772 tomo_tmp = tomo_stack[0,:,:]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

773 tomo_tmp[img_x_bounds[0],:] = tomo_stack[0,:,:].max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

774 tomo_tmp[img_x_bounds[1]-1,:] = tomo_stack[0,:,:].max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

775 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

776 msnc.quickImshow(tomo_stack[0,:,:], title=title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

777 msnc.quickPlot((range(x_sum.size), x_sum),

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

778 ([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

779 ([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

780 title='sum over theta and y')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

781 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

782 f'upper bound = {img_x_bounds[1]} (exclusive)]')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

783 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

784 if use_bounds == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

785 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

786 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

787 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

788 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

789 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

790 tomo_tmp = tomo_stack[0,:,:]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

791 tomo_tmp[img_x_bounds[0],:] = tomo_stack[0,:,:].max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

792 tomo_tmp[img_x_bounds[1]-1,:] = tomo_stack[0,:,:].max()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

793 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

794 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

795 save_fig=self.save_plots, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

796 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

797 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

798 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

799 save_fig=self.save_plots, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

800 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

801 x_sum = np.sum(self.tbf, 1)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

802 use_bounds = 'no'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

803 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

804 if img_x_bounds[0] < 0:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

805 msnc.illegal_value('img_x_bounds[0]', img_x_bounds[0], 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

806 img_x_bounds[0] = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

807 if not img_x_bounds[0] < img_x_bounds[1] <= x_sum.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

808 msnc.illegal_value('img_x_bounds[1]', img_x_bounds[1], 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

809 img_x_bounds[1] = x_sum.size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

810 msnc.quickPlot((range(x_sum.size), x_sum),

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

811 ([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

812 ([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

813 title='sum over theta and y')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

814 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

815 f'upper bound = {img_x_bounds[1]} (exclusive)]')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

816 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

817 if use_bounds == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

818 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

819 x_low = fit.get('center1', None)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

820 x_upp = fit.get('center2', None)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

821 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

822 x_low < x_upp < x_sum.size):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

823 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

824 if x_low < 0:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

825 x_low = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

826 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

827 if x_upp >= x_sum.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

828 x_upp = x_sum.size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

829 msnc.quickPlot((range(x_sum.size), x_sum),

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

830 ([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

831 ([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

832 title='sum over theta and y')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

833 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

834 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

835 if use_fit == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

836 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

837 num_x_min, 'sum over theta and y')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

838 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

839 img_x_bounds = [x_low, x_upp]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

840 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

841 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

842 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

843 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

844 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

845 save_fig=self.save_plots, save_only=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

846 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

847

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

848 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

849 msnc.clearFig('bright field')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

850 msnc.clearFig('sum over theta and y')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

851 if title:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

852 msnc.clearFig(title)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

853

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

854 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

855 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

856 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

857 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

858 preprocess['img_x_bounds'] = img_x_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

859 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

860

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

861 def _setZoomOrSkip(self):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

862 """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

863 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

864 preprocess = self.config.get('preprocess')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

865 zoom_perc = 100

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

866 if not self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

867 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

868 if pyip.inputYesNo(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

869 '\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

870 blank=True) == 'yes':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

871 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

872 min=1, max=100)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

873 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

874 zoom_perc = preprocess['zoom_perc']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

875 if msnc.is_num(zoom_perc, 1., 100.):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

876 zoom_perc = int(zoom_perc)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

877 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

878 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

879 zoom_perc = 100

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

880 num_theta_skip = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

881 if not self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

882 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

883 if pyip.inputYesNo(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

884 '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

885 blank=True) == 'yes':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

886 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

887 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

888 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

889 num_theta_skip = preprocess['num_theta_skip']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

890 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

891 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

892 num_theta_skip = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

893 logging.info(f'zoom_perc = {zoom_perc}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

894 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

895

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

896 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

897 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

898 self.cf.config['preprocess'] = {'zoom_perc' : zoom_perc,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

899 'num_theta_skip' : num_theta_skip}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

900 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

901 preprocess['zoom_perc'] = zoom_perc

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

902 preprocess['num_theta_skip'] = num_theta_skip

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

903 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

904

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

905 def _loadTomo(self, base_name, index, required=False):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

906 """Load a tomography stack.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

907 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

908 # stack order: row,theta,column

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

909 zoom_perc = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

910 preprocess = self.config.get('preprocess')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

911 if preprocess:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

912 zoom_perc = preprocess.get('zoom_perc')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

913 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

914 title = f'{base_name} fullres'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

915 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

916 title = f'{base_name} {zoom_perc}p'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

917 title += f'_{index}'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

918 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

919 load_flag = 'no'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

920 available = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

921 if os.path.isfile(tomo_file):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

922 available = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

923 if required:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

924 load_flag = 'yes'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

925 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

926 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

927 stack = np.array([])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

928 if load_flag == 'yes':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

929 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

930 logging.info(f'Loading {tomo_file} ...')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

931 try:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

932 stack = np.load(tomo_file)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

933 except IOError or ValueError:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

934 stack = np.array([])

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diff changeset

935 logging.error(f'Error loading {tomo_file}')

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diff changeset

936 logging.info(f'... done in {time()-t0:.2f} seconds!')

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diff changeset

937 if stack.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

938 msnc.quickImshow(stack[:,0,:], title=title, path=self.output_folder,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

939 save_fig=self.save_plots, save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

940 return stack, available

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

941

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

942 def _saveTomo(self, base_name, stack, index=None):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

943 """Save a tomography stack.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

944 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

945 zoom_perc = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

946 preprocess = self.config.get('preprocess')

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diff changeset

947 if preprocess:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

948 zoom_perc = preprocess.get('zoom_perc')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

949 if zoom_perc is None or zoom_perc == 100:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

950 title = f'{base_name} fullres'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

951 else:

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diff changeset

952 title = f'{base_name} {zoom_perc}p'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

953 if index:

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diff changeset

954 title += f'_{index}'

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diff changeset

955 tomo_file = re.sub(r"\s+", '_', f'{self.output_folder}/{title}.npy')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

956 t0 = time()

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957 logging.info(f'Saving {tomo_file} ...')

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diff changeset

958 np.save(tomo_file, stack)

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959 logging.info(f'... done in {time()-t0:.2f} seconds!')

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diff changeset

960

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diff changeset

961 def _genTomo(self, tomo_stack_files, available_stacks):

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diff changeset

962 """Generate tomography fields.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

963 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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964 stacks = self.config['stack_info']['stacks']

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diff changeset

965 assert(len(self.tomo_stacks) == self.config['stack_info']['num'])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

966 assert(len(self.tomo_stacks) == len(stacks))

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diff changeset

967 if len(available_stacks) != len(stacks):

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diff changeset

968 logging.warning('Illegal dimension of available_stacks in _genTomo'+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

969 f'({len(available_stacks)}');

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diff changeset

970 available_stacks = [False]*self.num_tomo_stacks

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971

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diff changeset

972 preprocess = self.config.get('preprocess')

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diff changeset

973 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

974 img_x_bounds = [0, self.tbf.shape[0]]

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diff changeset

975 img_y_bounds = [0, self.tbf.shape[1]]

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diff changeset

976 zoom_perc = preprocess['zoom_perc']

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diff changeset

977 num_theta_skip = preprocess['num_theta_skip']

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diff changeset

978 else:

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diff changeset

979 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"

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diff changeset

980 img_y_bounds = preprocess.get('img_y_bounds', [0, self.tbf.shape[1]])

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diff changeset

981 zoom_perc = 100

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diff changeset

982 num_theta_skip = 0

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diff changeset

983

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diff changeset

984 if self.tdf.size:

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diff changeset

985 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"

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diff changeset

986 else:

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diff changeset

987 logging.warning('Dark field unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

988 if not self.tbf.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

989 raise ValueError('Bright field unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

990 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"

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diff changeset

991

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

992 for i,stack in enumerate(stacks):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

993 # Check if stack is already loaded or available

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

994 if self.tomo_stacks[i].size or available_stacks[i]:

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diff changeset

995 continue

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diff changeset

996

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

997 # Load a stack of tomography images

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

998 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

999 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1000 stack['img_offset'], self.config['theta_range']['num'], num_theta_skip,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1001 img_x_bounds, img_y_bounds)

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diff changeset

1002 tomo_stack = tomo_stack.astype('float64')

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diff changeset

1003 logging.debug(f'loading took {time()-t0:.2f} seconds!')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1004

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1005 # Subtract dark field

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1006 if self.tdf.size:

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diff changeset

1007 t0 = time()

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diff changeset

1008 with set_numexpr_threads(self.ncore):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1009 ne.evaluate('tomo_stack-tdf', out=tomo_stack)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1010 logging.debug(f'subtracting dark field took {time()-t0:.2f} seconds!')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1011

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1012 # Normalize

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1013 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1014 with set_numexpr_threads(self.ncore):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1015 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1016 logging.debug(f'normalizing took {time()-t0:.2f} seconds!')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1017

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1018 # Remove non-positive values and linearize data

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1019 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1020 cutoff = 1.e-6

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1021 with set_numexpr_threads(self.ncore):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1022 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1023 with set_numexpr_threads(self.ncore):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1024 ne.evaluate('-log(tomo_stack)', out=tomo_stack)

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diff changeset

1025 logging.debug('removing non-positive values and linearizing data took '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1026 f'{time()-t0:.2f} seconds!')

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diff changeset

1027

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1028 # Get rid of nans/infs that may be introduced by normalization

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1029 t0 = time()

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1030 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)

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1031 logging.debug(f'remove nans/infs took {time()-t0:.2f} seconds!')

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1032

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1033 # Downsize tomography stack to smaller size

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1034 tomo_stack = tomo_stack.astype('float32')

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1035 if not self.galaxy_flag:

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1036 index = stack['index']

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1037 title = f'red stack fullres {index}'

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1038 if not self.test_mode:

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1039 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,

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1040 save_fig=self.save_plots, save_only=self.save_plots_only)

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1041 if zoom_perc != 100:

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1042 t0 = time()

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1043 logging.info(f'Zooming in ...')

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1044 tomo_zoom_list = []

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1045 for j in range(tomo_stack.shape[0]):

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1046 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)

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1047 tomo_zoom_list.append(tomo_zoom)

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1048 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])

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1049 logging.info(f'... done in {time()-t0:.2f} seconds!')

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1050 del tomo_zoom_list

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1051 if not self.galaxy_flag:

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1052 title = f'red stack {zoom_perc}p {index}'

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1053 if not self.test_mode:

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1054 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,

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1055 save_fig=self.save_plots, save_only=self.save_plots_only)

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1056

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1057 # Convert tomography stack from theta,row,column to row,theta,column

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1058 tomo_stack = np.swapaxes(tomo_stack, 0, 1)

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1059

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1060 # Save tomography stack to file

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1061 if not self.galaxy_flag:

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1062 if not self.test_mode:

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1063 self._saveTomo('red stack', tomo_stack, index)

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1064 else:

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1065 np.savetxt(self.output_folder+f'red_stack_{index}.txt',

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1066 tomo_stack[0,:,:], fmt='%.6e')

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1067

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1068 # Combine stacks

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1069 t0 = time()

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1070 self.tomo_stacks[i] = tomo_stack

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1071 logging.debug(f'combining nstack took {time()-t0:.2f} seconds!')

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1072

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1073 # Update config and save to file

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1074 stack['preprocessed'] = True

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1075 self.cf.saveFile(self.config_out)

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1076

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1077 if self.tdf.size:

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1078 del tdf

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1079 del tbf

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1080

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1081 def _reconstructOnePlane(self, tomo_plane_T, center, thetas_deg, eff_pixel_size,

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1082 cross_sectional_dim, plot_sinogram=True):

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1083 """Invert the sinogram for a single tomography plane.

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1084 """

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1085 # tomo_plane_T index order: column,theta

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1086 assert(0 <= center < tomo_plane_T.shape[0])

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1087 center_offset = center-tomo_plane_T.shape[0]/2

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1088 two_offset = 2*int(np.round(center_offset))

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1089 two_offset_abs = np.abs(two_offset)

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1090 max_rad = int(0.5*(cross_sectional_dim/eff_pixel_size)*1.1) # 10% slack to avoid edge effects

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1091 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))

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1092 if two_offset >= 0:

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1093 logging.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')

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1094 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]

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1095 else:

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1096 logging.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')

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1097 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]

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1098 if plot_sinogram:

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1099 msnc.quickImshow(sinogram.T, f'sinogram center offset{center_offset:.2f}',

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1100 path=self.output_folder, save_fig=self.save_plots,

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1101 save_only=self.save_plots_only, aspect='auto')

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1102

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1103 # Inverting sinogram

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1104 t0 = time()

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1105 recon_sinogram = iradon(sinogram, theta=thetas_deg, circle=True)

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1106 logging.debug(f'inverting sinogram took {time()-t0:.2f} seconds!')

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1107 del sinogram

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1108

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1109 # Removing ring artifacts

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1110 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes

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1111 t0 = time()

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1112 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0)

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1113 recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5)

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1114 recon_clean = np.expand_dims(recon_sinogram, axis=0)

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1115 del recon_sinogram

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1116 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17)

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1117 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')

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1118 return recon_clean

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1119

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1120 def _plotEdgesOnePlane(self, recon_plane, base_name, weight=0.001):

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1121 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes

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1122 edges = denoise_tv_chambolle(recon_plane, weight = weight)

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1123 vmax = np.max(edges[0,:,:])

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1124 vmin = -vmax

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1125 msnc.quickImshow(edges[0,:,:], f'{base_name} coolwarm', path=self.output_folder,

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1126 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')

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1127 msnc.quickImshow(edges[0,:,:], f'{base_name} gray', path=self.output_folder,

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1128 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='gray',

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1129 vmin=vmin, vmax=vmax)

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1130 del edges

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1131

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1132 def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim,

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1133 tol=0.1):

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1134 """Find center for a single tomography plane.

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1135 """

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1136 # sinogram index order: theta,column

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1137 # need index order column,theta for iradon, so take transpose

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1138 sinogram_T = sinogram.T

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1139 center = sinogram.shape[1]/2

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1140

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1141 # try automatic center finding routines for initial value

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1142 tomo_center = tomopy.find_center_vo(sinogram)

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1143 center_offset_vo = tomo_center-center

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1144 print(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')

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1145 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,

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1146 eff_pixel_size, cross_sectional_dim, False)

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1147 base_name=f'edges row{row} center_offset_vo{center_offset_vo:.2f}'

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1148 self._plotEdgesOnePlane(recon_plane, base_name)

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1149 if pyip.inputYesNo('Try finding center using phase correlation (y/[n])? ',

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1150 blank=True) == 'yes':

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1151 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1,

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1152 rotc_guess=tomo_center)

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1153 error = 1.

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1154 while error > tol:

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1155 prev = tomo_center

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1156 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,

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1157 rotc_guess=tomo_center)

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1158 error = np.abs(tomo_center-prev)

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1159 center_offset = tomo_center-center

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1160 print(f'Center at row {row} using phase correlation = {center_offset:.2f}')

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1161 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,

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1162 eff_pixel_size, cross_sectional_dim, False)

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1163 base_name=f'edges row{row} center_offset{center_offset:.2f}'

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1164 self._plotEdgesOnePlane(recon_plane, base_name)

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1165 if pyip.inputYesNo('Accept a center location ([y]) or continue search (n)? ',

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1166 blank=True) != 'no':

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1167 del sinogram_T

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1168 del recon_plane

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1169 center_offset = pyip.inputNum(

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1170 f' Enter chosen center offset [{-int(center)}, {int(center)}] '+

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1171 f'([{center_offset_vo}])): ', blank=True)

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1172 if center_offset == '':

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1173 center_offset = center_offset_vo

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1174 return float(center_offset)

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1175

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1176 while True:

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1177 center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+

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1178 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))

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1179 center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+

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1180 f'[{center_offset_low}, {int(center)}]: ',

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1181 min=center_offset_low, max=int(center))

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1182 if center_offset_upp == center_offset_low:

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1183 center_offset_step = 1

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1184 else:

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1185 center_offset_step = pyip.inputInt('Enter step size for center offset search '+

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1186 f'[1, {center_offset_upp-center_offset_low}]: ',

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1187 min=1, max=center_offset_upp-center_offset_low)

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1188 for center_offset in range(center_offset_low, center_offset_upp+center_offset_step,

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1189 center_offset_step):

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1190 logging.info(f'center_offset = {center_offset}')

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1191 recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,

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1192 thetas_deg, eff_pixel_size, cross_sectional_dim, False)

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1193 base_name=f'edges row{row} center_offset{center_offset}'

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1194 self._plotEdgesOnePlane(recon_plane, base_name)

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1195 if pyip.inputInt('\nContinue (0) or end the search (1): ', min=0, max=1):

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1196 break

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1197

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1198 del sinogram_T

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1199 del recon_plane

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1200 center_offset = pyip.inputNum(f' Enter chosen center offset '+

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1201 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))

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1202 return float(center_offset)

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1203

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1204 def _reconstructOneTomoStack(self, tomo_stack, thetas, row_bounds=None,

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1205 center_offsets=[], sigma=0.1, rwidth=30, ncore=1, algorithm='gridrec',

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1206 run_secondary_sirt=False, secondary_iter=100):

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1207 """reconstruct a single tomography stack.

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1208 """

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diff changeset

1209 # stack order: row,theta,column

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diff changeset

1210 # thetas must be in radians

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diff changeset

1211 # centers_offset: tomography axis shift in pixels relative to column center

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diff changeset

1212 # RV should we remove stripes?

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1213 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html

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diff changeset

1214 # RV should we remove rings?

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1215 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html

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diff changeset

1216 # 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"

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diff changeset

1217 if row_bounds is None:

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diff changeset

1218 row_bounds = [0, tomo_stack.shape[0]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1219 else:

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diff changeset

1220 if not (0 <= row_bounds[0] <= row_bounds[1] <= tomo_stack.shape[0]):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1221 raise ValueError('Illegal row bounds in reconstructOneTomoStack')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1222 if thetas.size != tomo_stack.shape[1]:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1223 raise ValueError('theta dimension mismatch in reconstructOneTomoStack')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1224 if not len(center_offsets):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1225 centers = np.zeros((row_bounds[1]-row_bounds[0]))

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diff changeset

1226 elif len(center_offsets) == 2:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1227 centers = np.linspace(center_offsets[0], center_offsets[1],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1228 row_bounds[1]-row_bounds[0])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1229 else:

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diff changeset

1230 if center_offsets.size != row_bounds[1]-row_bounds[0]:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1231 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1232 centers = center_offsets

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diff changeset

1233 centers += tomo_stack.shape[2]/2

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diff changeset

1234 if True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1235 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack[row_bounds[0]:row_bounds[1]],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1236 sigma=sigma, ncore=ncore)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1237 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1238 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1239 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1240 algorithm=algorithm, ncore=ncore)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1241 if run_secondary_sirt and secondary_iter > 0:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1242 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1243 #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"

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parents:

diff changeset

1244 # cuda driver combination."

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1245 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1246 #SIRT did not finish while running overnight

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1247 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iter}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1248 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1249 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, init_recon=tomo_recon_stack,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1250 options=options, sinogram_order=True, algorithm=tomopy.astra, ncore=ncore)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1251 if True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1252 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"

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parents:

diff changeset

1253 return tomo_recon_stack

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1254

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1255 def findImageFiles(self):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1256 """Find all available image files.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1257 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1258 self.is_valid = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1259

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1260 # Find dark field images

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1261 dark_field = self.config['dark_field']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1262 img_start, num_imgs, dark_files = msnc.findImageFiles(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1263 dark_field['data_path'], self.config['data_filetype'], 'dark field')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1264 if img_start < 0 or num_imgs < 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1265 logging.error('Unable to find suitable dark field images')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1266 if dark_field['data_path']:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1267 self.is_valid = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1268 dark_field['num'] = num_imgs

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1269 dark_field['img_start'] = img_start

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1270 logging.info(f'Number of dark field images = {dark_field["num"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1271 logging.info(f'Dark field image start index = {dark_field["img_start"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1272

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1273 # Find bright field images

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1274 bright_field = self.config['bright_field']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1275 img_start, num_imgs, bright_files = msnc.findImageFiles(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1276 bright_field['data_path'], self.config['data_filetype'], 'bright field')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1277 if img_start < 0 or num_imgs < 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1278 logging.error('Unable to find suitable bright field images')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1279 self.is_valid = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1280 bright_field['num'] = num_imgs

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1281 bright_field['img_start'] = img_start

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1282 logging.info(f'Number of bright field images = {bright_field["num"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1283 logging.info(f'Bright field image start index = {bright_field["img_start"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1284

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1285 # Find tomography images

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1286 tomo_stack_files = []

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1287 for stack in self.config['stack_info']['stacks']:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1288 index = stack['index']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1289 img_start, num_imgs, tomo_files = msnc.findImageFiles(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1290 stack['data_path'], self.config['data_filetype'], f'tomography set {index}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1291 if img_start < 0 or num_imgs < 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1292 logging.error('Unable to find suitable tomography images')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1293 self.is_valid = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1294 stack['num'] = num_imgs

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1295 stack['img_start'] = img_start

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1296 logging.info(f'Number of tomography images for set {index} = {stack["num"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1297 logging.info(f'Tomography set {index} image start index = {stack["img_start"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1298 tomo_stack_files.append(tomo_files)

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1299 del tomo_files

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1300

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1301 # Safe updated config

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1302 if self.is_valid:

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1303 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1304

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1305 return dark_files, bright_files, tomo_stack_files

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1306

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1307 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"

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1308 dark_field_pngname=None, bright_field_pngname=None, tomo_field_pngname=None,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1309 detectorbounds_pngname=None, output_name=None):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1310 """Preprocess tomography images.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1311 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1312 # Try loading any already preprocessed stacks (skip in Galaxy)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1313 # preprocessed stack order for each one in stack: row,theta,column

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1314 stack_info = self.config['stack_info']

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1315 stacks = stack_info['stacks']

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1316 num_tomo_stacks = stack_info['num']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1317 assert(num_tomo_stacks == len(self.tomo_stacks))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1318 available_stacks = [False]*num_tomo_stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1319 if self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1320 assert(tdf_files is None or isinstance(tdf_files, list))

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1321 assert(isinstance(tbf_files, list))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1322 assert(isinstance(tomo_stack_files, list))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1323 assert(num_tomo_stacks == len(tomo_stack_files))

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1324 assert(isinstance(dark_field_pngname, str))

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1325 assert(isinstance(bright_field_pngname, str))

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1326 assert(isinstance(tomo_field_pngname, str))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1327 assert(isinstance(detectorbounds_pngname, str))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1328 assert(isinstance(output_name, str))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1329 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1330 if tdf_files:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1331 logging.warning('Ignoring tdf_files in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1332 if tbf_files:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1333 logging.warning('Ignoring tbf_files in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1334 if tomo_stack_files:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1335 logging.warning('Ignoring tomo_stack_files in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1336 tdf_files, tbf_files, tomo_stack_files = self.findImageFiles()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1337 if not self.is_valid:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1338 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1339 for i,stack in enumerate(stacks):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1340 if not self.tomo_stacks[i].size and stack.get('preprocessed', False):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1341 self.tomo_stacks[i], available_stacks[i] = \

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1342 self._loadTomo('red stack', stack['index'])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1343 if dark_field_pngname:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1344 logging.warning('Ignoring dark_field_pngname in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1345 if bright_field_pngname:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1346 logging.warning('Ignoring bright_field_pngname in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1347 if tomo_field_pngname:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1348 logging.warning('Ignoring tomo_field_pngname in genTomoStacks (only for Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1349 if detectorbounds_pngname:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1350 logging.warning('Ignoring detectorbounds_pngname in genTomoStacks '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1351 '(only used in Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1352 if output_name:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1353 logging.warning('Ignoring output_name in genTomoStacks '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1354 '(only used in Galaxy)')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1355

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1356 # Preprocess any unloaded stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1357 if False in available_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1358 logging.debug('Preprocessing tomography images')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1359

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1360 # Check required image files (skip in Galaxy)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1361 if not self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1362 self._selectImageRanges(available_stacks)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1363 if not self.is_valid:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1364 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1365

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1366 # Generate dark field

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1367 if tdf_files:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1368 self._genDark(tdf_files, dark_field_pngname)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1369

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1370 # Generate bright field

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1371 self._genBright(tbf_files, bright_field_pngname)

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diff changeset

1372

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1373 # Set vertical detector bounds for image stack

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1374 self._setDetectorBounds(tomo_stack_files, tomo_field_pngname, detectorbounds_pngname)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1375

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1376 # Set zoom and/or theta skip to reduce memory the requirement

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1377 self._setZoomOrSkip()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1378

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1379 # Generate tomography fields

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1380 self._genTomo(tomo_stack_files, available_stacks)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1381

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1382 # Save tomography stack to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1383 if self.galaxy_flag:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1384 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1385 logging.info(f'Saving preprocessed tomography stack to file ...')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1386 save_stacks = {f'set_{stack["index"]}':tomo_stack

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1387 for stack,tomo_stack in zip(stacks,self.tomo_stacks)}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1388 np.savez(output_name, **save_stacks)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1389 logging.info(f'... done in {time()-t0:.2f} seconds!')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1390

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1391 del available_stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1392

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1393 # Adjust sample reference height, update config and save to file

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1394 preprocess = self.config.get('preprocess')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1395 if preprocess is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1396 img_x_bounds = [0, self.tbf.shape[0]]

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diff changeset

1397 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1398 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"

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1399 pixel_size = self.config['detector']['pixel_size']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1400 if pixel_size is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1401 raise ValueError('Detector pixel size unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1402 pixel_size *= img_x_bounds[0]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1403 for stack in stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1404 stack['ref_height'] = stack['ref_height']+pixel_size

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diff changeset

1405 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1406

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1407 def findCenters(self):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1408 """Find rotation axis centers for the tomography stacks.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1409 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1410 logging.debug('Find centers for tomography stacks')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1411 stacks = self.config['stack_info']['stacks']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1412 available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1413 logging.debug('Avaliable stacks: {available_stacks}')

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diff changeset

1414

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1415 # Check for valid available center stack index

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1416 find_center = self.config.get('find_center')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1417 if find_center and 'center_stack_index' in find_center:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1418 center_stack_index = find_center['center_stack_index']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1419 if (not isinstance(center_stack_index, int) or

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1420 center_stack_index not in available_stacks):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1421 msnc.illegal_value('center_stack_index', center_stack_index, 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1422 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1423 if self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1424 find_center['completed'] = True

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diff changeset

1425 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1426 return

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diff changeset

1427 print('\nFound calibration center offset info for stack '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1428 f'{center_stack_index}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1429 if pyip.inputYesNo('Do you want to use this again (y/n)? ') == 'yes':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1430 find_center['completed'] = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1431 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1432 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1433

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1434 # Load the required preprocessed stack

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1435 # preprocessed stack order: row,theta,column

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1436 num_tomo_stacks = self.config['stack_info']['num']

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diff changeset

1437 assert(len(stacks) == num_tomo_stacks)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1438 assert(len(self.tomo_stacks) == num_tomo_stacks)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1439 if num_tomo_stacks == 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1440 center_stack_index = stacks[0]['index']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1441 if not self.tomo_stacks[0].size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1442 self.tomo_stacks[0], available = self._loadTomo('red stack', center_stack_index,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1443 required=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1444 center_stack = self.tomo_stacks[0]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1445 if not center_stack.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1446 logging.error('Unable to load the required preprocessed tomography stack')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1447 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1448 assert(stacks[0].get('preprocessed', False) == True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1449 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1450 while True:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1451 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

1452 f'rotation axis centers {available_stacks}: ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1453 while center_stack_index not in available_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1454 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

1455 f'rotation axis centers {available_stacks}: ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1456 tomo_stack_index = available_stacks.index(center_stack_index)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1457 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

1458 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

1459 'red stack', center_stack_index, required=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1460 center_stack = self.tomo_stacks[tomo_stack_index]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1461 if not center_stack.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1462 logging.error(f'Unable to load the {center_stack_index}th '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1463 'preprocessed tomography stack, pick another one')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1464 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1465 break

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1466 assert(stacks[tomo_stack_index].get('preprocessed', False) == True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1467 if find_center is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1468 self.config['find_center'] = {'center_stack_index' : center_stack_index}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1469 find_center = self.config['find_center']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1470

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1471 # Set thetas (in degrees)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1472 theta_range = self.config['theta_range']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1473 theta_start = theta_range['start']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1474 theta_end = theta_range['end']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1475 num_theta = theta_range['num']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1476 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1477 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"

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parents:

diff changeset

1478 endpoint=False)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1479

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1480 # Get non-overlapping sample row boundaries

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1481 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1482 pixel_size = self.config['detector']['pixel_size']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1483 if pixel_size is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1484 raise ValueError('Detector pixel size unavailable')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1485 eff_pixel_size = 100.*pixel_size/zoom_perc

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1486 logging.debug(f'eff_pixel_size = {eff_pixel_size}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1487 tomo_ref_heights = [stack['ref_height'] for stack in stacks]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1488 if num_tomo_stacks == 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1489 n1 = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1490 height = center_stack.shape[0]*eff_pixel_size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1491 if pyip.inputYesNo('\nDo you want to reconstruct the full samply height '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1492 f'({height:.3f} mm) (y/n)? ') == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1493 height = pyip.inputNum('\nEnter the desired reconstructed sample height '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1494 f'in mm [0, {height:.3f}]: ', min=0, max=height)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1495 n1 = int(0.5*(center_stack.shape[0]-height/eff_pixel_size))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1496 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1497 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"

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parents:

diff changeset

1498 tomo_ref_heights[1])/eff_pixel_size)/2)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1499 n2 = center_stack.shape[0]-n1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1500 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"

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parents:

diff changeset

1501 if not center_stack.size:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1502 RuntimeError('Center stack not loaded')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1503 msnc.quickImshow(center_stack[:,0,:], title=f'center stack theta={theta_start}',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1504 path=self.output_folder, save_fig=self.save_plots, save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1505

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1506 # Get cross sectional diameter in mm

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1507 cross_sectional_dim = center_stack.shape[2]*eff_pixel_size

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1508 logging.debug(f'cross_sectional_dim = {cross_sectional_dim}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1509

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1510 # Determine center offset at sample row boundaries

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1511 logging.info('Determine center offset at sample row boundaries')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1512

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1513 # Lower row center

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1514 use_row = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1515 use_center = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1516 row = find_center.get('lower_row')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1517 if msnc.is_int(row, n1, n2-2):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1518 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1519 use_row = pyip.inputYesNo('\nCurrent row index for lower center = '

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1520 f'{row}, use this value (y/n)? ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1521 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1522 msnc.clearFig(f'theta={theta_start}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1523 if use_row:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1524 center_offset = find_center.get('lower_center_offset')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1525 if msnc.is_num(center_offset):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1526 use_center = pyip.inputYesNo('Current lower center offset = '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1527 f'{center_offset}, use this value (y/n)? ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1528 if not use_center:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1529 if not use_row:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1530 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1531 row = pyip.inputInt('\nEnter row index to find lower center '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1532 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

1533 if row == '':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1534 row = n1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1535 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1536 msnc.clearFig(f'theta={theta_start}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1537 # center_stack order: row,theta,column

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1538 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

1539 eff_pixel_size, cross_sectional_dim)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1540 logging.info(f'Lower center offset = {center_offset}')

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 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1543 find_center['row_bounds'] = [n1, n2]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1544 find_center['lower_row'] = row

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1545 find_center['lower_center_offset'] = center_offset

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1546 self.cf.saveFile(self.config_out)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1547 lower_row = row

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1548

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1549 # Upper row center

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1550 use_row = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1551 use_center = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1552 row = find_center.get('upper_row')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1553 if msnc.is_int(row, lower_row+1, n2-1):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1554 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1555 use_row = pyip.inputYesNo('\nCurrent row index for upper center = '

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1556 f'{row}, use this value (y/n)? ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1557 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1558 msnc.clearFig(f'theta={theta_start}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1559 if use_row:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1560 center_offset = find_center.get('upper_center_offset')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1561 if msnc.is_num(center_offset):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1562 use_center = pyip.inputYesNo('Current upper center offset = '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1563 f'{center_offset}, use this value (y/n)? ')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1564 if not use_center:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1565 if not use_row:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1566 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1567 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

1568 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

1569 if row == '':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1570 row = n2-1

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1571 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1572 msnc.clearFig(f'theta={theta_start}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1573 # center_stack order: row,theta,column

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1574 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

1575 eff_pixel_size, cross_sectional_dim)

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1576 logging.info(f'upper_center_offset = {center_offset}')

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1577 del center_stack

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1578

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1579 # Update config and save to file

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1580 find_center['upper_row'] = row

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1581 find_center['upper_center_offset'] = center_offset

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1582 find_center['completed'] = True

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1583 self.cf.saveFile(self.config_out)

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1584

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1585 def checkCenters(self):

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1586 """Check centers for the tomography stacks.

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1587 """

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1588 #RV TODO load all stacks and check at all stack boundaries

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1589 return

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1590 logging.debug('Check centers for tomography stacks')

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1591 center_stack_index = self.config.get('center_stack_index')

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1592 if center_stack_index is None:

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1593 raise ValueError('Unable to read center_stack_index from config')

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1594 center_stack_index = self.tomo_stacks[self.tomo_data_indices.index(center_stack_index)]

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1595 lower_row = self.config.get('lower_row')

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1596 if lower_row is None:

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1597 raise ValueError('Unable to read lower_row from config')

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1598 lower_center_offset = self.config.get('lower_center_offset')

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1599 if lower_center_offset is None:

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1600 raise ValueError('Unable to read lower_center_offset from config')

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1601 upper_row = self.config.get('upper_row')

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1602 if upper_row is None:

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1603 raise ValueError('Unable to read upper_row from config')

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1604 upper_center_offset = self.config.get('upper_center_offset')

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1605 if upper_center_offset is None:

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1606 raise ValueError('Unable to read upper_center_offset from config')

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1607 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)

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1608 shift = upper_center_offset-lower_center_offset

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1609 if lower_row == 0:

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1610 logging.warning(f'lower_row == 0: one row offset between both planes')

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1611 else:

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1612 lower_row -= 1

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1613 lower_center_offset -= center_slope

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1614

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1615 # stack order: stack,row,theta,column

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1616 if center_stack_index:

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1617 stack1 = self.tomo_stacks[center_stack_index-1]

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1618 stack2 = self.tomo_stacks[center_stack_index]

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1619 if not stack1.size:

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1620 logging.error(f'Unable to load required tomography stack {stack1}')

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1621 elif not stack2.size:

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1622 logging.error(f'Unable to load required tomography stack {stack1}')

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1623 else:

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1624 assert(0 <= lower_row < stack2.shape[0])

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1625 assert(0 <= upper_row < stack1.shape[0])

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1626 plane1 = stack1[upper_row,:]

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1627 plane2 = stack2[lower_row,:]

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1628 for i in range(-2, 3):

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1629 shift_i = shift+2*i

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1630 plane1_shifted = spi.shift(plane2, [0, shift_i])

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1631 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),

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1632 title=f'stacks {stack1} {stack2} shifted {2*i} theta={self.start_theta}',

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1633 path=self.output_folder, save_fig=self.save_plots,

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1634 save_only=self.save_plots_only)

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1635 if center_stack_index < self.num_tomo_stacks-1:

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1636 stack1 = self.tomo_stacks[center_stack_index]

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1637 stack2 = self.tomo_stacks[center_stack_index+1]

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1638 if not stack1.size:

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1639 logging.error(f'Unable to load required tomography stack {stack1}')

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1640 elif not stack2.size:

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1641 logging.error(f'Unable to load required tomography stack {stack1}')

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1642 else:

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1643 assert(0 <= lower_row < stack2.shape[0])

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1644 assert(0 <= upper_row < stack1.shape[0])

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1645 plane1 = stack1[upper_row,:]

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1646 plane2 = stack2[lower_row,:]

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1647 for i in range(-2, 3):

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1648 shift_i = -shift+2*i

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1649 plane1_shifted = spi.shift(plane2, [0, shift_i])

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1650 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),

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1651 title=f'stacks {stack1} {stack2} shifted {2*i} theta={start_theta}',

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1652 path=self.output_folder, save_fig=self.save_plots,

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1653 save_only=self.save_plots_only)

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1654 del plane1, plane2, plane1_shifted

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1655

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1656 # Update config file

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1657 self.config = msnc.update('config.txt', 'check_centers', True, 'find_centers')

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1658

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1659 def reconstructTomoStacks(self):

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1660 """Reconstruct tomography stacks.

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1661 """

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1662 logging.debug('Reconstruct tomography stacks')

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1663

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1664 # Get rotation axis rows and centers

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1665 find_center = self.config['find_center']

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1666 lower_row = find_center.get('lower_row')

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1667 if lower_row is None:

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diff changeset

1668 logging.error('Unable to read lower_row from config')

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1669 return

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diff changeset

1670 lower_center_offset = find_center.get('lower_center_offset')

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diff changeset

1671 if lower_center_offset is None:

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diff changeset

1672 logging.error('Unable to read lower_center_offset from config')

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diff changeset

1673 return

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diff changeset

1674 upper_row = find_center.get('upper_row')

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diff changeset

1675 if upper_row is None:

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diff changeset

1676 logging.error('Unable to read upper_row from config')

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diff changeset

1677 return

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diff changeset

1678 upper_center_offset = find_center.get('upper_center_offset')

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diff changeset

1679 if upper_center_offset is None:

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diff changeset

1680 logging.error('Unable to read upper_center_offset from config')

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diff changeset

1681 return

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diff changeset

1682 logging.debug(f'lower_row = {lower_row} upper_row = {upper_row}')

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diff changeset

1683 assert(lower_row < upper_row)

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1684 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)

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1685

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1686 # Set thetas (in radians)

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1687 theta_range = self.config['theta_range']

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1688 theta_start = theta_range['start']

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1689 theta_end = theta_range['end']

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1690 num_theta = theta_range['num']

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1691 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)

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1692 thetas = np.radians(np.linspace(theta_start, theta_end,

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1693 int(num_theta/(num_theta_skip+1)), endpoint=False))

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1694

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1695 # Reconstruct tomo stacks

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1696 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)

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1697 if zoom_perc == 100:

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1698 basetitle = 'recon stack full'

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1699 else:

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1700 basetitle = f'recon stack {zoom_perc}p'

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1701 load_error = False

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1702 stacks = self.config['stack_info']['stacks']

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diff changeset

1703 for i,stack in enumerate(stacks):

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1704 # Check if stack can be loaded

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1705 # reconstructed stack order for each one in stack : row/z,x,y

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diff changeset

1706 # preprocessed stack order for each one in stack: row,theta,column

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diff changeset

1707 index = stack['index']

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1708 available = False

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diff changeset

1709 if stack.get('reconstructed', False):

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diff changeset

1710 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack', index)

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diff changeset

1711 if self.tomo_recon_stacks[i].size or available:

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diff changeset

1712 if self.tomo_stacks[i].size:

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diff changeset

1713 self.tomo_stacks[i] = np.array([])

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1714 assert(stack.get('reconstructed', False) == True)

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1715 continue

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1716 else:

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diff changeset

1717 stack['reconstructed'] = False

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diff changeset

1718 if not self.tomo_stacks[i].size:

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diff changeset

1719 self.tomo_stacks[i], available = self._loadTomo('red stack', index,

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1720 required=True)

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diff changeset

1721 if not self.tomo_stacks[i].size:

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diff changeset

1722 logging.error(f'Unable to load tomography stack {index} for reconstruction')

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1723 load_error = True

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diff changeset

1724 continue

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diff changeset

1725 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])

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diff changeset

1726 center_offsets = [lower_center_offset-lower_row*center_slope,

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diff changeset

1727 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]

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diff changeset

1728 t0 = time()

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diff changeset

1729 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],

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diff changeset

1730 thetas, center_offsets=center_offsets, sigma=0.1, ncore=self.ncore,

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diff changeset

1731 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)

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diff changeset

1732 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')

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diff changeset

1733 if not self.test_mode:

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diff changeset

1734 row_slice = int(self.tomo_stacks[i].shape[0]/2)

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diff changeset

1735 title = f'{basetitle} {index} slice{row_slice}'

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diff changeset

1736 msnc.quickImshow(self.tomo_recon_stacks[i][row_slice,:,:], title=title,

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diff changeset

1737 path=self.output_folder, save_fig=self.save_plots,

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diff changeset

1738 save_only=self.save_plots_only)

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diff changeset

1739 msnc.quickPlot(self.tomo_recon_stacks[i]

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diff changeset

1740 [row_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:],

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diff changeset

1741 title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[2]/2)}',

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diff changeset

1742 path=self.output_folder, save_fig=self.save_plots,

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diff changeset

1743 save_only=self.save_plots_only)

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diff changeset

1744 self._saveTomo('recon stack', self.tomo_recon_stacks[i], index)

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diff changeset

1745 # else:

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diff changeset

1746 # np.savetxt(self.output_folder+f'recon_stack_{index}.txt',

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diff changeset

1747 # self.tomo_recon_stacks[i][row_slice,:,:], fmt='%.6e')

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diff changeset

1748 self.tomo_stacks[i] = np.array([])

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diff changeset

1749

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diff changeset

1750 # Update config and save to file

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diff changeset

1751 stack['reconstructed'] = True

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diff changeset

1752 self.cf.saveFile(self.config_out)

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diff changeset

1753

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diff changeset

1754 def combineTomoStacks(self):

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1755 """Combine the reconstructed tomography stacks.

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diff changeset

1756 """

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diff changeset

1757 # stack order: stack,row(z),x,y

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1758 logging.debug('Combine reconstructed tomography stacks')

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diff changeset

1759 # Load any unloaded reconstructed stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1760 stacks = self.config['stack_info']['stacks']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1761 for i,stack in enumerate(stacks):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1762 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"

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parents:

diff changeset

1763 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1764 stack['index'], required=True)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1765 if not self.tomo_recon_stacks[i].size or not available:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1766 logging.error(f'Unable to load reconstructed stack {stack["index"]}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1767 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1768 if i:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1769 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"

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parents:

diff changeset

1770 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"

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parents:

diff changeset

1771 logging.error('Incompatible reconstructed tomography stack dimensions')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1772 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1773

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1774 # Get center stack boundaries

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1775 row_bounds = self.config['find_center']['row_bounds']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1776 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"

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parents:

diff changeset

1777 msnc.illegal_value('row_bounds', row_bounds, 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1778 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1779

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1780 # Selecting xy bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1781 tomosum = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1782 #RV FIX :=

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1783 #[tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,2)) for tomo_recon_stack in

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1784 # self.tomo_recon_stacks]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1785 combine_stacks =self.config.get('combine_stacks')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1786 if combine_stacks and 'x_bounds' in combine_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1787 x_bounds = combine_stacks['x_bounds']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1788 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

1789 msnc.illegal_value('x_bounds', x_bounds, 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1790 elif not self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1791 msnc.quickPlot(tomosum, title='recon stack sum yz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1792 if pyip.inputYesNo('\nCurrent image x-bounds: '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1793 f'[{x_bounds[0]}, {x_bounds[1]}], use these values ([y]/n)? ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1794 blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1795 if pyip.inputYesNo(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1796 'Do you want to change the image x-bounds ([y]/n)? ',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1797 blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1798 x_bounds = [0, self.tomo_recon_stacks[0].shape[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1799 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1800 x_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1801 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1802 msnc.quickPlot(tomosum, title='recon stack sum yz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1803 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"

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parents:

diff changeset

1804 x_bounds = [0, self.tomo_recon_stacks[0].shape[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1805 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1806 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

1807 if False and self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1808 np.savetxt(self.output_folder+'recon_stack_sum_yz.txt',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1809 tomosum[x_bounds[0]:x_bounds[1]], fmt='%.6e')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1810 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1811 msnc.clearFig('recon stack sum yz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1812 tomosum = 0

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1813 #RV FIX :=

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1814 #[tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,1)) for tomo_recon_stack in

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1815 # self.tomo_recon_stacks]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1816 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

1817 y_bounds = combine_stacks['y_bounds']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1818 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"

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parents:

diff changeset

1819 msnc.illegal_value('y_bounds', y_bounds, 'config file')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1820 elif not self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1821 msnc.quickPlot(tomosum, title='recon stack sum xz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1822 if pyip.inputYesNo('\nCurrent image y-bounds: '+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1823 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

1824 blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1825 if pyip.inputYesNo(

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1826 '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

1827 blank=True) == 'no':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1828 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

1829 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1830 y_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1831 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1832 msnc.quickPlot(tomosum, title='recon stack sum xz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1833 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

1834 y_bounds = [0, self.tomo_recon_stacks[0].shape[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1835 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

1836 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

1837 if False and self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1838 np.savetxt(self.output_folder+'recon_stack_sum_xz.txt',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1839 tomosum[y_bounds[0]:y_bounds[1]], fmt='%.6e')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1840 if self.save_plots_only:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1841 msnc.clearFig('recon stack sum xz')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1842

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1843 # Combine reconstructed tomography stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1844 logging.info(f'Combining reconstructed stacks ...')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1845 t0 = time()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1846 num_tomo_stacks = self.config['stack_info']['num']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1847 if num_tomo_stacks == 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1848 low_bound = row_bounds[0]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1849 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1850 low_bound = 0

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diff changeset

1851 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"

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diff changeset

1852 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1853 if num_tomo_stacks > 2:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1854 tomo_recon_combined = np.concatenate([tomo_recon_combined]+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1855 [self.tomo_recon_stacks[i][row_bounds[0]:row_bounds[1],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1856 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1857 for i in range(1, num_tomo_stacks-1)])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1858 if num_tomo_stacks > 1:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1859 tomo_recon_combined = np.concatenate([tomo_recon_combined]+

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1860 [self.tomo_recon_stacks[num_tomo_stacks-1][row_bounds[0]:,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1861 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1862 logging.info(f'... done in {time()-t0:.2f} seconds!')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1863 tomosum = np.sum(tomo_recon_combined, axis=(1,2))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1864 if self.test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1865 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1866 filename = 'recon combined sum xy'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1867 if zoom_perc is None or zoom_perc == 100:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1868 filename += ' fullres.dat'

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1869 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1870 filename += f' {zoom_perc}p.dat'

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1871 msnc.quickPlot(tomosum, title='recon combined sum xy',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1872 path=self.output_folder, save_fig=self.save_plots,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1873 save_only=self.save_plots_only)

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parents:

diff changeset

1874 if False:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1875 np.savetxt(self.output_folder+'recon_combined_sum_xy.txt',

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diff changeset

1876 tomosum, fmt='%.6e')

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diff changeset

1877 np.savetxt(self.output_folder+'recon_combined.txt',

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diff changeset

1878 tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:], fmt='%.6e')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1879 combine_stacks =self.config.get('combine_stacks')

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diff changeset

1880

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1881 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1882 if combine_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1883 combine_stacks['x_bounds'] = x_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1884 combine_stacks['y_bounds'] = y_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1885 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1886 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds}

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1887 self.cf.saveFile(self.config_out)

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diff changeset

1888 return

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1889 msnc.quickPlot(tomosum, title='recon combined sum xy')

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diff changeset

1890 if pyip.inputYesNo(

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diff changeset

1891 '\nDo you want to change the image z-bounds (y/[n])? ',

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diff changeset

1892 blank=True) != 'yes':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1893 z_bounds = [0, tomo_recon_combined.shape[0]]

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diff changeset

1894 else:

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diff changeset

1895 z_bounds = msnc.selectArrayBounds(tomosum, title='recon combined sum xy')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1896 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"

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diff changeset

1897 tomo_recon_combined = tomo_recon_combined[z_bounds[0]:z_bounds[1],:,:]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1898 logging.info(f'tomo_recon_combined.shape = {tomo_recon_combined.shape}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1899 if self.save_plots_only:

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diff changeset

1900 msnc.clearFig('recon combined sum xy')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1901

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1902 # Plot center slices

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1903 msnc.quickImshow(tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1904 title=f'recon combined xslice{int(tomo_recon_combined.shape[0]/2)}',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1905 path=self.output_folder, save_fig=self.save_plots,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1906 save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

1907 msnc.quickImshow(tomo_recon_combined[:,int(tomo_recon_combined.shape[1]/2),:],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1908 title=f'recon combined yslice{int(tomo_recon_combined.shape[1]/2)}',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1909 path=self.output_folder, save_fig=self.save_plots,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1910 save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1911 msnc.quickImshow(tomo_recon_combined[:,:,int(tomo_recon_combined.shape[2]/2)],

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1912 title=f'recon combined zslice{int(tomo_recon_combined.shape[2]/2)}',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1913 path=self.output_folder, save_fig=self.save_plots,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1914 save_only=self.save_plots_only)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1915

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1916 # Save combined reconstructed tomo stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1917 base_name = 'recon combined'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1918 combined_stacks = []

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1919 for stack in stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1920 base_name += f' {stack["index"]}'

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diff changeset

1921 combined_stacks.append(stack['index'])

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diff changeset

1922 self._saveTomo(base_name, tomo_recon_combined)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1923

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1924 # Update config and save to file

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1925 if combine_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1926 combine_stacks['x_bounds'] = x_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1927 combine_stacks['y_bounds'] = y_bounds

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1928 combine_stacks['stacks'] = combined_stacks

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diff changeset

1929 else:

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diff changeset

1930 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds,

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diff changeset

1931 'stacks' : combined_stacks}

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diff changeset

1932 self.cf.saveFile(self.config_out)

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diff changeset

1933

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1934 def runTomo(config_file=None, config_dict=None, output_folder='.', log_level='INFO',

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1935 test_mode=False):

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diff changeset

1936 """Run a tomography analysis.

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1937 """

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1938 # Instantiate Tomo object

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diff changeset

1939 tomo = Tomo(config_file=config_file, output_folder=output_folder, log_level=log_level,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1940 test_mode=test_mode)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1941 if not tomo.is_valid:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1942 raise ValueError('Invalid config and/or detector file provided.')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1943

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1944 # Preprocess the image files

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1945 num_tomo_stacks = tomo.config['stack_info']['num']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1946 assert(num_tomo_stacks == len(tomo.tomo_stacks))

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1947 preprocess = tomo.config.get('preprocess', None)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1948 preprocessed_stacks = []

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1949 if preprocess:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1950 preprocessed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1951 if stack.get('preprocessed', False)]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1952 if not len(preprocessed_stacks):

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diff changeset

1953 tomo.genTomoStacks()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1954 if not tomo.is_valid:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1955 IOError('Unable to load all required image files.')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1956 find_center = tomo.config.get('find_center')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1957 if find_center and find_center.get('completed', False):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1958 center_stack_index = find_center['center_stack_index']

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1959 if not center_stack_index in preprocessed_stacks:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1960 find_center['completed'] = False

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diff changeset

1961 #RV FIX

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1962 # tomo.config.pop('check_center', 'check_center not found')

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1963 # combined_stacks = tomo.config.get('combined_stacks')

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1964 # if combined_stacks:

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1965 # combined_stacks['completed'] = False

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diff changeset

1966 tomo.cf.saveFile(tomo.config_out)

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1967

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1968 # Find centers

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diff changeset

1969 find_center = tomo.config.get('find_center')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1970 if find_center is None or not find_center.get('completed', False):

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diff changeset

1971 tomo.findCenters()

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diff changeset

1972

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1973 # Check centers

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1974 #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"

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diff changeset

1975 # tomo.checkCenters()

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1976

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1977 # Reconstruct tomography stacks

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diff changeset

1978 if len(tomo.config.get('reconstructed_stacks', [])) != tomo.config['stack_info']['num']:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1979 tomo.reconstructTomoStacks()

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diff changeset

1980

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1981 # Combine reconstructed tomography stacks

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1982 combined_stacks = tomo.config.get('combined_stacks')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1983 if combined_stacks is None or not combined_stacks.get('completed', False):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1984 tomo.combineTomoStacks()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1985

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1986 #%%============================================================================

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diff changeset

1987 if __name__ == '__main__':

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diff changeset

1988 # Parse command line arguments

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diff changeset

1989 arguments = sys.argv[1:]

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1990 config_file = None

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1991 output_folder = '.'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1992 log_level = 'INFO'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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1993 test_mode = False

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1994 try:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1995 opts, args = getopt.getopt(arguments,"hc:o:l:t")

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1996 except getopt.GetoptError:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1997 print('usage: tomo.py -c <config_file> -o <output_folder> -l <log_level> -t')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1998 sys.exit(2)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

1999 for opt, arg in opts:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2000 if opt == '-h':

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2001 print('usage: tomo.py -c <config_file> -o <output_folder> -l <log_level> -t')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2002 sys.exit()

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2003 elif opt in ("-c"):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2004 config_file = arg

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2005 elif opt in ("-o"):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2006 output_folder = arg

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2007 elif opt in ("-l"):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2008 log_level = arg

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2009 elif opt in ("-t"):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2010 test_mode = True

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2011 if config_file is None:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2012 if os.path.isfile('config.yaml'):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2013 config_file = 'config.yaml'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2014 else:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2015 config_file = 'config.txt'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2016

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2017 # Set basic log configuration

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2018 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2019 if not test_mode:

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2020 level = getattr(logging, log_level.upper(), None)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2021 if not isinstance(level, int):

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2022 raise ValueError(f'Invalid log_level: {log_level}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2023 logging.basicConfig(format=logging_format, level=level, force=True,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2024 handlers=[logging.StreamHandler()])

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2025

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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parents:

diff changeset

2026 logging.debug(f'config_file = {config_file}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2027 logging.debug(f'output_folder = {output_folder}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2028 logging.debug(f'log_level = {log_level}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2029 logging.debug(f'test_mode = {test_mode}')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2030

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2031 # Run tomography analysis

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2032 runTomo(config_file=config_file, output_folder=output_folder, log_level=log_level,

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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diff changeset

2033 test_mode=test_mode)

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

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2034

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

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2035 #%%============================================================================

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

diff changeset

2036 input('Press any key to continue')

cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"

rv43

parents:

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2037 #%%============================================================================

Mercurial > repos > rv43 > tomo

annotate tomo.py @ 0:cb1b0d757704 draft