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annotate tomo.py @ 46:d73e715e975b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit baa3866a541a552710bec26ae5d37a8c624563ac"
author rv43
date Thu, 21 Apr 2022 18:10:17 +0000
parents f7c75e9643f2
children c693117d01e9
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1 #!/usr/bin/env python3
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2
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3 # -*- coding: utf-8 -*-
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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
1
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21 import argparse
0
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22 import numpy as np
41
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23 try:
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24 import numexpr as ne
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25 except:
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26 pass
0
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27 import multiprocessing as mp
41
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28 try:
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29 import scipy.ndimage as spi
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30 except:
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31 pass
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32 try:
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33 import tomopy
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34 except:
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35 pass
0
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36 from time import time
41
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37 try:
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38 from skimage.transform import iradon
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39 except:
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40 pass
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41 try:
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42 from skimage.restoration import denoise_tv_chambolle
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43 except:
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44 pass
0
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45
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46 import msnc_tools as msnc
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47
41
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48 # the following tomopy routines don't run with more than 24 cores on Galaxy-Dev
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49 # - tomopy.find_center_vo
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50 # - tomopy.prep.stripe.remove_stripe_fw
46
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51 #RV the same problem reappeared once I started testing with the tenstom_1304r-1 case
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52 # not resolved yet
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53 num_core_tomopy_limit = 24
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54
0
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55 class set_numexpr_threads:
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56
1
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57 def __init__(self, num_core):
0
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58 cpu_count = mp.cpu_count()
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59 logging.debug(f'start: num_core={num_core} cpu_count={cpu_count}')
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60 if num_core is None or num_core < 1 or num_core > cpu_count:
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61 self.num_core = cpu_count
0
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62 else:
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63 self.num_core = num_core
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64 logging.debug(f'self.num_core={self.num_core}')
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65
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66 def __enter__(self):
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67 self.num_core_org = ne.set_num_threads(self.num_core)
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68 logging.debug(f'self.num_core={self.num_core}')
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69
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70 def __exit__(self, exc_type, exc_value, traceback):
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71 ne.set_num_threads(self.num_core_org)
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72
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73 class ConfigTomo(msnc.Config):
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74 """Class for processing a config file.
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75 """
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76
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77 def __init__(self, config_file=None, config_dict=None):
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78 super().__init__(config_file, config_dict)
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79
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80 def _validate_txt(self):
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81 """Returns False if any required config parameter is illegal or missing.
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82 """
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83 is_valid = True
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84
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85 # Check for required first-level keys
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86 pars_required = ['tdf_data_path', 'tbf_data_path', 'detector_id']
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87 pars_missing = []
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88 is_valid = super().validate(pars_required, pars_missing)
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89 if len(pars_missing) > 0:
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90 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')
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91 self.detector_id = self.config.get('detector_id')
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92
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93 # Find tomography dark field images file/folder
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94 self.tdf_data_path = self.config.get('tdf_data_path')
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95
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96 # Find tomography bright field images file/folder
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97 self.tbf_data_path = self.config.get('tbf_data_path')
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98
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99 # Check number of tomography image stacks
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100 self.num_tomo_stacks = self.config.get('num_tomo_stacks', 1)
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101 if not msnc.is_int(self.num_tomo_stacks, 1):
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102 self.num_tomo_stacks = None
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103 msnc.illegal_value('num_tomo_stacks', self.num_tomo_stacks, 'config file')
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104 return False
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105 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')
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106
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107 # Find tomography images file/folders and stack parameters
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108 tomo_data_paths_indices = sorted({key:value for key,value in self.config.items()
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109 if 'tomo_data_path' in key}.items())
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110 if len(tomo_data_paths_indices) != self.num_tomo_stacks:
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111 logging.error(f'Incorrect number of tomography data path names in config file')
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112 is_valid = False
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113 self.tomo_data_paths = [tomo_data_paths_indices[i][1] for i in range(self.num_tomo_stacks)]
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114 self.tomo_data_indices = [msnc.get_trailing_int(tomo_data_paths_indices[i][0])
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115 if msnc.get_trailing_int(tomo_data_paths_indices[i][0]) else None
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116 for i in range(self.num_tomo_stacks)]
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117 tomo_ref_height_indices = sorted({key:value for key,value in self.config.items()
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118 if 'z_pos' in key}.items())
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119 if self.num_tomo_stacks > 1 and len(tomo_ref_height_indices) != self.num_tomo_stacks:
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120 logging.error(f'Incorrect number of tomography reference heights in config file')
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121 is_valid = False
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122 if len(tomo_ref_height_indices):
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123 self.tomo_ref_heights = [
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124 tomo_ref_height_indices[i][1] for i in range(self.num_tomo_stacks)]
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125 else:
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126 self.tomo_ref_heights = [0.0]*self.num_tomo_stacks
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127
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128 # Check tomo angle (theta) range
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129 self.start_theta = self.config.get('start_theta', 0.)
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130 if not msnc.is_num(self.start_theta, 0.):
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131 msnc.illegal_value('start_theta', self.start_theta, 'config file')
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132 is_valid = False
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133 logging.debug(f'start_theta = {self.start_theta}')
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134 self.end_theta = self.config.get('end_theta', 180.)
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135 if not msnc.is_num(self.end_theta, self.start_theta):
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136 msnc.illegal_value('end_theta', self.end_theta, 'config file')
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137 is_valid = False
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138 logging.debug(f'end_theta = {self.end_theta}')
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139 self.num_thetas = self.config.get('num_thetas')
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140 if not (self.num_thetas is None or msnc.is_int(self.num_thetas, 1)):
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141 msnc.illegal_value('num_thetas', self.num_thetas, 'config file')
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142 self.num_thetas = None
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143 is_valid = False
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144 logging.debug(f'num_thetas = {self.num_thetas}')
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145
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146 return is_valid
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147
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148 def _validate_yaml(self):
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149 """Returns False if any required config parameter is illegal or missing.
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150 """
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151 is_valid = True
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152
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153 # Check for required first-level keys
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154 pars_required = ['dark_field', 'bright_field', 'stack_info', 'detector']
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155 pars_missing = []
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156 is_valid = super().validate(pars_required, pars_missing)
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157 if len(pars_missing) > 0:
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158 logging.error(f'Missing item(s) in config file: {", ".join(pars_missing)}')
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159 self.detector_id = self.config['detector'].get('id')
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160
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161 # Find tomography dark field images file/folder
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162 self.tdf_data_path = self.config['dark_field'].get('data_path')
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163
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164 # Find tomography bright field images file/folder
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165 self.tbf_data_path = self.config['bright_field'].get('data_path')
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166
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167 # Check number of tomography image stacks
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168 stack_info = self.config['stack_info']
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169 self.num_tomo_stacks = stack_info.get('num', 1)
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170 if not msnc.is_int(self.num_tomo_stacks, 1):
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171 self.num_tomo_stacks = None
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172 msnc.illegal_value('stack_info:num', self.num_tomo_stacks, 'config file')
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173 return False
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174 logging.info(f'num_tomo_stacks = {self.num_tomo_stacks}')
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175
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176 # Find tomography images file/folders and stack parameters
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177 stacks = stack_info.get('stacks')
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178 if stacks is None or len(stacks) is not self.num_tomo_stacks:
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179 msnc.illegal_value('stack_info:stacks', stacks, 'config file')
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180 return False
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181 self.tomo_data_paths = []
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182 self.tomo_data_indices = []
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183 self.tomo_ref_heights = []
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184 for stack in stacks:
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185 self.tomo_data_paths.append(stack.get('data_path'))
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186 self.tomo_data_indices.append(stack.get('index'))
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187 self.tomo_ref_heights.append(stack.get('ref_height'))
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188
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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189 # Check tomo angle (theta) range
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190 theta_range = self.config.get('theta_range')
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191 if theta_range is None:
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192 self.start_theta = 0.
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193 self.end_theta = 180.
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194 self.num_thetas = None
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195 else:
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196 self.start_theta = theta_range.get('start', 0.)
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197 if not msnc.is_num(self.start_theta, 0.):
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198 msnc.illegal_value('theta_range:start', self.start_theta, 'config file')
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199 is_valid = False
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200 logging.debug(f'start_theta = {self.start_theta}')
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201 self.end_theta = theta_range.get('end', 180.)
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202 if not msnc.is_num(self.end_theta, self.start_theta):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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203 msnc.illegal_value('theta_range:end', self.end_theta, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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204 is_valid = False
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205 logging.debug(f'end_theta = {self.end_theta}')
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206 self.num_thetas = theta_range.get('num')
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207 if self.num_thetas and not msnc.is_int(self.num_thetas, 1):
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208 msnc.illegal_value('theta_range:num', self.num_thetas, 'config file')
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209 self.num_thetas = None
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210 is_valid = False
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211 logging.debug(f'num_thetas = {self.num_thetas}')
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212
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213 return is_valid
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214
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215 def validate(self):
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216 """Returns False if any required config parameter is illegal or missing.
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217 """
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218 is_valid = True
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219
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220 # Check work_folder (shared by both file formats)
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221 work_folder = os.path.abspath(self.config.get('work_folder', ''))
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222 if not os.path.isdir(work_folder):
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223 msnc.illegal_value('work_folder', work_folder, 'config file')
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224 is_valid = False
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225 logging.info(f'work_folder: {work_folder}')
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226
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227 # Check data filetype (shared by both file formats)
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228 self.data_filetype = self.config.get('data_filetype', 'tif')
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229 if not isinstance(self.data_filetype, str) or (self.data_filetype != 'tif' and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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230 self.data_filetype != 'h5'):
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231 msnc.illegal_value('data_filetype', self.data_filetype, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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232
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233 if self.suffix == '.yml' or self.suffix == '.yaml':
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234 is_valid = self._validate_yaml()
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235 elif self.suffix == '.txt':
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236 is_valid = self._validate_txt()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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237 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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238 logging.error(f'Undefined or illegal config file extension: {self.suffix}')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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diff changeset
239 is_valid = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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240
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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241 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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242 if self.tdf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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243 if self.data_filetype == 'h5':
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244 if isinstance(self.tdf_data_path, str):
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245 if not os.path.isabs(self.tdf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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246 self.tdf_data_path = os.path.abspath(
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247 f'{work_folder}/{self.tdf_data_path}')
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248 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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249 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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250 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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251 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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252 if isinstance(self.tdf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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253 self.tdf_data_path = os.path.abspath(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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254 f'{work_folder}/{self.tdf_data_path}/nf')
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255 elif isinstance(self.tdf_data_path, str):
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256 if not os.path.isabs(self.tdf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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257 self.tdf_data_path = os.path.abspath(
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258 f'{work_folder}/{self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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259 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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260 msnc.illegal_value('tdf_data_path', self.tdf_data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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261 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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262 logging.info(f'dark field images path = {self.tdf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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263
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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264 # Find tomography bright field images file/folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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265 if self.tbf_data_path:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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266 if self.data_filetype == 'h5':
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267 if isinstance(self.tbf_data_path, str):
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268 if not os.path.isabs(self.tbf_data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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269 self.tbf_data_path = os.path.abspath(
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270 f'{work_folder}/{self.tbf_data_path}')
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271 else:
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272 msnc.illegal_value('tbf_data_path', tbf_data_fil, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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273 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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274 else:
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275 if isinstance(self.tbf_data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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276 self.tbf_data_path = os.path.abspath(
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277 f'{work_folder}/{self.tbf_data_path}/nf')
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278 elif isinstance(self.tbf_data_path, str):
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279 if not os.path.isabs(self.tbf_data_path):
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280 self.tbf_data_path = os.path.abspath(
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diff changeset
281 f'{work_folder}/{self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
282 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
283 msnc.illegal_value('tbf_data_path', self.tbf_data_path, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
284 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
285 logging.info(f'bright field images path = {self.tbf_data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
286
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
287 # Find tomography images file/folders and stack parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
288 tomo_data_paths = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
289 tomo_data_indices = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
290 tomo_ref_heights = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
291 for data_path, index, ref_height in zip(self.tomo_data_paths, self.tomo_data_indices,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
292 self.tomo_ref_heights):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
293 if self.data_filetype == 'h5':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
294 if isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
295 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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296 data_path = os.path.abspath(f'{work_folder}/{data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
297 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
298 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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diff changeset
299 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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300 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
301 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
302 if isinstance(data_path, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
303 data_path = os.path.abspath(f'{work_folder}/{data_path}/nf')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
304 elif isinstance(data_path, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
305 if not os.path.isabs(data_path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
306 data_path = os.path.abspath(f'{work_folder}/{data_path}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
307 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
308 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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parents:
diff changeset
309 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
310 data_path = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
311 tomo_data_paths.append(data_path)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
312 if index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
313 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
314 logging.error('Missing stack_info:stacks:index in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
315 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
316 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
317 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
318 index = 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
319 elif not isinstance(index, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
320 msnc.illegal_value(f'stack_info:stacks:index', index, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
321 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
322 index = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
323 tomo_data_indices.append(index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
324 if ref_height is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
325 if self.num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
326 logging.error('Missing stack_info:stacks:ref_height in config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
327 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
328 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
329 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
330 ref_height = 0.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
331 elif not msnc.is_num(ref_height):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
332 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"
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parents:
diff changeset
333 is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
334 ref_height = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
335 # Set reference heights relative to first stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
336 if (len(tomo_ref_heights) and msnc.is_num(ref_height) and
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
337 msnc.is_num(tomo_ref_heights[0])):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
338 ref_height = (round(ref_height-tomo_ref_heights[0], 3))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
339 tomo_ref_heights.append(ref_height)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
340 tomo_ref_heights[0] = 0.0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
341 logging.info('tomography data paths:')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
342 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
343 logging.info(f' {tomo_data_paths[i]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
344 logging.info(f'tomography data path indices: {tomo_data_indices}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
345 logging.info(f'tomography reference heights: {tomo_ref_heights}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
346
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
347 # Update config in memory
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
348 if self.suffix == '.txt':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
349 self.config = {}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
350 dark_field = self.config.get('dark_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
351 if dark_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
352 self.config['dark_field'] = {'data_path' : self.tdf_data_path}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
353 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
354 self.config['dark_field']['data_path'] = self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
355 bright_field = self.config.get('bright_field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
356 if bright_field is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
357 self.config['bright_field'] = {'data_path' : self.tbf_data_path}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
358 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
359 self.config['bright_field']['data_path'] = self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
360 detector = self.config.get('detector')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
361 if detector is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
362 self.config['detector'] = {'id' : self.detector_id}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
363 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
364 detector['id'] = self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
365 self.config['work_folder'] = work_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
366 self.config['data_filetype'] = self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
367 stack_info = self.config.get('stack_info')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
368 if stack_info is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
369 stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
370 for i in range(self.num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
371 stacks.append({'data_path' : tomo_data_paths[i], 'index' : tomo_data_indices[i],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
372 'ref_height' : tomo_ref_heights[i]})
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
373 self.config['stack_info'] = {'num' : self.num_tomo_stacks, 'stacks' : stacks}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
374 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
375 stack_info['num'] = self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
376 stacks = stack_info.get('stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
377 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
378 stack['data_path'] = tomo_data_paths[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
379 stack['index'] = tomo_data_indices[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
380 stack['ref_height'] = tomo_ref_heights[i]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
381 if self.num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
382 theta_range = {'start' : self.start_theta, 'end' : self.end_theta,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
383 'num' : self.num_thetas}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
384 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
385 theta_range = {'start' : self.start_theta, 'end' : self.end_theta}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
386 self.config['theta_range'] = theta_range
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
387
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
388 # Cleanup temporary validation variables
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
389 del self.tdf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
390 del self.tbf_data_path
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
391 del self.detector_id
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
392 del self.data_filetype
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
393 del self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
394 del self.tomo_data_paths
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
395 del self.tomo_data_indices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
396 del self.tomo_ref_heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
397 del self.start_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
398 del self.end_theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
399 del self.num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
400
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
401 return is_valid
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
402
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
403 class Tomo:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
404 """Processing tomography data with misalignment.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
405 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
406
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
407 def __init__(self, config_file=None, config_dict=None, config_out=None, output_folder='.',
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
408 log_level='INFO', log_stream='tomo.log', galaxy_flag=False, test_mode=False,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
409 num_core=-1):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
410 """Initialize with optional config input file or dictionary
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
411 """
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
412 self.num_core = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
413 self.config_out = config_out
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
414 self.output_folder = output_folder
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
415 self.galaxy_flag = galaxy_flag
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
416 self.test_mode = test_mode
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
417 self.save_plots = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
418 self.save_plots_only = True # Make input argument?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
419 self.cf = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
420 self.config = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
421 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
422 self.tdf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
423 self.tbf = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
424 self.tomo_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
425 self.tomo_recon_stacks = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
426
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
427 # Validate input parameters
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
428 if config_file is not None and not os.path.isfile(config_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
429 raise OSError(f'Invalid config_file input {config_file} {type(config_file)}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
430 if config_dict is not None and not isinstance(config_dict, dict):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
431 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
432 if config_out is not None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
433 if isinstance(config_out, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
434 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
435 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
436 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
437 raise OSError(f'Invalid log_stream path')
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 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
440 if not os.path.isdir(output_folder):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
441 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
442 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
443 path = os.path.split(log_stream)[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
444 if path and not os.path.isdir(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
445 raise OSError(f'Invalid log_stream path')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
446 if not os.path.isabs(path):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
447 log_stream = f'{output_folder}/{log_stream}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
448 if not isinstance(galaxy_flag, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
449 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
450 if not isinstance(test_mode, bool):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
451 raise ValueError(f'Invalid test_mode input {test_mode} {type(test_mode)}')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
452 if not isinstance(num_core, int) or num_core < -1 or num_core == 0:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
453 raise ValueError(f'Invalid num_core input {num_core} {type(num_core)}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
454 if num_core == -1:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
455 self.num_core = mp.cpu_count()
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
456 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
457 self.num_core = num_core
0
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"
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parents:
diff changeset
459 # Set log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
460 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
461 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
462 self.save_plots_only = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
463 if isinstance(log_stream, str):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
464 logging.basicConfig(filename=f'{log_stream}', filemode='w',
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
465 format=logging_format, level=logging.INFO, force=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
466 #format=logging_format, level=logging.WARNING, force=True)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
467 elif isinstance(log_stream, io.TextIOWrapper):
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
468 #logging.basicConfig(filemode='w', format=logging_format, level=logging.WARNING,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
469 logging.basicConfig(filemode='w', format=logging_format, level=logging.INFO,
0
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470 stream=log_stream, force=True)
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471 else:
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472 raise ValueError(f'Invalid log_stream: {log_stream}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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473 logging.warning('Ignoring log_level argument in test mode')
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474 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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475 level = getattr(logging, log_level.upper(), None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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476 if not isinstance(level, int):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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477 raise ValueError(f'Invalid log_level: {log_level}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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478 if log_stream is sys.stdout:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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479 logging.basicConfig(format=logging_format, level=level, force=True,
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480 handlers=[logging.StreamHandler()])
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481 else:
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482 if isinstance(log_stream, str):
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483 logging.basicConfig(filename=f'{log_stream}', filemode='w',
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484 format=logging_format, level=level, force=True)
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485 elif isinstance(log_stream, io.TextIOWrapper):
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486 logging.basicConfig(filemode='w', format=logging_format, level=level,
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487 stream=log_stream, force=True)
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488 else:
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489 raise ValueError(f'Invalid log_stream: {log_stream}')
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490 stream_handler = logging.StreamHandler()
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491 logging.getLogger().addHandler(stream_handler)
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492 stream_handler.setLevel(logging.WARNING)
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493 stream_handler.setFormatter(logging.Formatter(logging_format))
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diff changeset
494
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495 # Check/set output config file name
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496 if self.config_out is None:
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497 self.config_out = f'{self.output_folder}/config.yaml'
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498 elif (self.config_out is os.path.basename(self.config_out) and
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diff changeset
499 not os.path.isabs(self.config_out)):
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500 self.config_out = f'{self.output_folder}/{self.config_out}'
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diff changeset
501
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
502 # Create config object and load config file
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503 self.cf = ConfigTomo(config_file, config_dict)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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504 if not self.cf.load_flag:
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505 self.is_valid = False
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diff changeset
506 return
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diff changeset
507
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
508 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
509 assert(self.output_folder == '.')
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diff changeset
510 assert(self.test_mode is False)
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diff changeset
511 self.save_plots = True
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diff changeset
512 self.save_plots_only = True
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diff changeset
513 else:
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diff changeset
514 # Input validation is already performed during link_data_to_galaxy
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diff changeset
515
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
516 # Check config file parameters
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diff changeset
517 self.is_valid = self.cf.validate()
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diff changeset
518
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
519 # Load detector info file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
520 df = msnc.Detector(self.cf.config['detector']['id'])
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diff changeset
521
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
522 # Check detector info file parameters
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diff changeset
523 if df.validate():
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diff changeset
524 pixel_size = df.getPixelSize()
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diff changeset
525 num_rows, num_columns = df.getDimensions()
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diff changeset
526 if not pixel_size or not num_rows or not num_columns:
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diff changeset
527 self.is_valid = False
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diff changeset
528 else:
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diff changeset
529 pixel_size = None
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diff changeset
530 num_rows = None
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diff changeset
531 num_columns = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
532 self.is_valid = False
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diff changeset
533
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
534 # Update config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
535 self.cf.config['detector']['pixel_size'] = pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
536 self.cf.config['detector']['rows'] = num_rows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
537 self.cf.config['detector']['columns'] = num_columns
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
538 logging.debug(f'pixel_size = self.cf.config["detector"]["pixel_size"]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
539 logging.debug(f'num_rows: {self.cf.config["detector"]["rows"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
540 logging.debug(f'num_columns: {self.cf.config["detector"]["columns"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
541
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
542 # Safe config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
543 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
544 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
545
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
546 # Initialize shortcut to config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
547 self.config = self.cf.config
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
548
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
549 # Initialize tomography stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
550 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
551 if num_tomo_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
552 self.tomo_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
553 self.tomo_recon_stacks = [np.array([]) for _ in range(num_tomo_stacks)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
554
2
b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e"
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diff changeset
555 logging.debug(f'num_core = {self.num_core}')
1
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diff changeset
556 logging.debug(f'config_file = {config_file}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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diff changeset
557 logging.debug(f'config_dict = {config_dict}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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diff changeset
558 logging.debug(f'config_out = {self.config_out}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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diff changeset
559 logging.debug(f'output_folder = {self.output_folder}')
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parents: 0
diff changeset
560 logging.debug(f'log_stream = {log_stream}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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diff changeset
561 logging.debug(f'log_level = {log_level}')
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diff changeset
562 logging.debug(f'galaxy_flag = {self.galaxy_flag}')
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diff changeset
563 logging.debug(f'test_mode = {self.test_mode}')
0
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parents:
diff changeset
564 logging.debug(f'save_plots = {self.save_plots}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
565 logging.debug(f'save_plots_only = {self.save_plots_only}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
566
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
567 def _selectImageRanges(self, available_stacks=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
568 """Select image files to be included in analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
569 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
570 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
571 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
572 if available_stacks is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
573 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
574 elif len(available_stacks) != stack_info['num']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
575 logging.warning('Illegal dimension of available_stacks in getImageFiles '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
576 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
577 available_stacks = [False]*stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
578
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
579 # Check number of tomography angles/thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
580 num_thetas = self.config['theta_range'].get('num')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
581 if num_thetas is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
582 num_thetas = pyip.inputInt('\nEnter the number of thetas (>0): ', greaterThan=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
583 elif not msnc.is_int(num_thetas, 0):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
584 msnc.illegal_value('num_thetas', num_thetas, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
585 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
586 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
587 self.config['theta_range']['num'] = num_thetas
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
588 logging.debug(f'num_thetas = {self.config["theta_range"]["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
589
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
590 # Find tomography dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
591 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
592 img_start = dark_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
593 img_offset = dark_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
594 num_imgs = dark_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
595 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
596 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
597 num_imgs, 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
598 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
599 logging.error('Unable to find suitable dark field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
600 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
601 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
602 dark_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
603 dark_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
604 dark_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
605 logging.debug(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
606 logging.debug(f'Dark field image offset: {dark_field["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
607 logging.debug(f'Number of dark field images: {dark_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
608
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
609 # Find tomography bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
610 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
611 img_start = bright_field.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
612 img_offset = bright_field.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
613 num_imgs = bright_field.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
614 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
615 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
616 num_imgs, 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
617 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
618 logging.error('Unable to find suitable bright field images')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
619 self.is_valid = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
620 bright_field['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
621 bright_field['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
622 bright_field['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
623 logging.debug(f'Bright field image start index: {bright_field["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
624 logging.debug(f'Bright field image offset: {bright_field["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
625 logging.debug(f'Number of bright field images: {bright_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
626
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
627 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
628 for i,stack in enumerate(stack_info['stacks']):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
629 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
630 if self.tomo_stacks[i].size or available_stacks[i]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
631 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
632 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
633 img_start = stack.get('img_start', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
634 img_offset = stack.get('img_offset', -1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
635 num_imgs = stack.get('num', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
636 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
637 img_start, img_offset, num_imgs = msnc.selectImageRange(img_start, img_offset,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
638 num_imgs, f'tomography stack {index}', num_thetas)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
639 if img_start < 0 or num_imgs != num_thetas:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
640 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
641 self.is_valid = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
642 stack['img_start'] = img_start
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
643 stack['img_offset'] = img_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
644 stack['num'] = num_imgs
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
645 logging.debug(f'Tomography stack {index} image start index: {stack["img_start"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
646 logging.debug(f'Tomography stack {index} image offset: {stack["img_offset"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
647 logging.debug(f'Number of tomography images for stack {index}: {stack["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
648
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
649 # Safe updated config to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
650 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
651 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
652
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
653 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
654
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
655 def _genDark(self, tdf_files):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
656 """Generate dark field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
657 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
658 # Load the dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
659 logging.debug('Loading dark field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
660 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
661 tdf_stack = msnc.loadImageStack(tdf_files, self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
662 dark_field['img_offset'], dark_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
663
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
664 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
665 self.tdf = np.median(tdf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
666 del tdf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
667
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
668 # RV make input of some kind (not always needed)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
669 tdf_cutoff = 21
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
670 self.tdf[self.tdf > tdf_cutoff] = np.nan
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
671 tdf_mean = np.nanmean(self.tdf)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
672 logging.debug(f'tdf_cutoff = {tdf_cutoff}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
673 logging.debug(f'tdf_mean = {tdf_mean}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
674 np.nan_to_num(self.tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
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parents: 2
diff changeset
675 if self.galaxy_flag:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
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parents: 40
diff changeset
676 msnc.quickImshow(self.tdf, title='dark field', path='setup_pngs',
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
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parents: 2
diff changeset
677 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
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diff changeset
678 elif not self.test_mode:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
679 msnc.quickImshow(self.tdf, title='dark field', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
680 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
681
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
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parents: 40
diff changeset
682 def _genBright(self, tbf_files):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
683 """Generate bright field.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
684 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
685 # Load the bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
686 logging.debug('Loading bright field...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
687 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
688 tbf_stack = msnc.loadImageStack(tbf_files, self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
689 bright_field['img_offset'], bright_field['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
690
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
691 # Take median
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
692 """Median or mean: It may be best to try the median because of some image
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
693 artifacts that arise due to crinkles in the upstream kapton tape windows
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
694 causing some phase contrast images to appear on the detector.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
695 One thing that also may be useful in a future implementation is to do a
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
696 brightfield adjustment on EACH frame of the tomo based on a ROI in the
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
697 corner of the frame where there is no sample but there is the direct X-ray
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
698 beam because there is frame to frame fluctuations from the incoming beam.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
699 We don’t typically account for them but potentially could.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
700 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
701 self.tbf = np.median(tbf_stack, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
702 del tbf_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
703
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
704 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
705 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
706 self.tbf -= self.tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
707 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
708 logging.warning('Dark field unavailable')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
709 if self.galaxy_flag:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
710 msnc.quickImshow(self.tbf, title='bright field', path='setup_pngs',
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
711 save_fig=True, save_only=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
712 elif not self.test_mode:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
713 msnc.quickImshow(self.tbf, title='bright field', path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
714 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
715
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
716 def _setDetectorBounds(self, tomo_stack_files):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
717 """Set vertical detector bounds for image stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
718 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
719 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
720 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
721 img_x_bounds = [None, None]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
722 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
723 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
724 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
725 if img_x_bounds[0] < 0:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
726 msnc.illegal_value('img_x_bounds[0]', img_x_bounds[0], 'config file')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
727 img_x_bounds[0] = 0
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
728 if not msnc.is_index_range(img_x_bounds, 0, self.tbf.shape[0]):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
729 msnc.illegal_value('img_x_bounds[1]', img_x_bounds[1], 'config file')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
730 img_x_bounds[1] = self.tbf.shape[0]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
731 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
732 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
733 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
734 self.cf.config['preprocess'] = {'img_x_bounds' : [0, self.tbf.shape[0]]}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
735 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
736 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
737 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
738 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
739
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
740 # Check reference heights
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
741 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
742 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
743 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
744 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
745 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
746 num_x_min = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
747 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
748 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
749 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
750 delta_z = stacks[1]['ref_height']-stacks[0]['ref_height']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
751 for i in range(2, num_tomo_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
752 delta_z = min(delta_z, stacks[i]['ref_height']-stacks[i-1]['ref_height'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
753 logging.debug(f'delta_z = {delta_z}')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
754 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
755 logging.debug(f'num_x_min = {num_x_min}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
756 if num_x_min > self.tbf.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
757 logging.warning('Image bounds and pixel size prevent seamless stacking')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
758 num_x_min = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
759
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
760 # Select image bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
761 if self.galaxy_flag:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
762 x_sum = np.sum(self.tbf, 1)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
763 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
764 x_sum_max = x_sum.max()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
765 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
766 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
767 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
768 fit = msnc.fitStep(y=x_sum, model='rectangle', form='atan')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
769 x_low = fit.get('center1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
770 x_upp = fit.get('center2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
771 sig_low = fit.get('sigma1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
772 sig_upp = fit.get('sigma2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
773 if (x_low is not None and x_upp is not None and sig_low is not None and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
774 sig_upp is not None and 0 <= x_low < x_upp <= x_sum.size and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
775 (sig_low+sig_upp)/(x_upp-x_low) < 0.1):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
776 if num_tomo_stacks == 1 or num_x_min is None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
777 x_low = int(x_low-(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
778 x_upp = int(x_upp+(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
779 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
780 x_low = int((x_low+x_upp)/2-num_x_min/2)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
781 x_upp = x_low+num_x_min
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
782 if x_low < 0:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
783 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
784 if x_upp > x_sum.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
785 x_upp = x_sum.size
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
786 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
787 x_low = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
788 x_upp = x_sum.size
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
789 msnc.quickPlot((range(x_sum.size), x_sum),
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
790 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
791 ([x_upp-1, x_upp-1], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
792 title=f'sum bright field over theta/y (row bounds: [{x_low}, {x_upp}])',
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
793 path='setup_pngs', name='detectorbounds.png', save_fig=True, save_only=True,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
794 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
795 for i,stack in enumerate(stacks):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
796 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
797 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
798 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
799 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
800 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
801 tomo_stack[x_low,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
802 tomo_stack[x_upp-1,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
803 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
804 msnc.quickImshow(tomo_stack, title=title, path='setup_pngs',
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
805 name=f'tomo_{stack["index"]}.png', save_fig=True, save_only=True,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
806 show_grid=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
807 del tomo_stack
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
808
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
809 # Update config and save to file
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
810 img_x_bounds = [x_low, x_upp]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
811 logging.debug(f'img_x_bounds: {img_x_bounds}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
812 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
813 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
814 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
815 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
816 self.cf.saveFile(self.config_out)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
817 del x_sum
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
818 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
819
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
820 # For one tomography stack only: load the first image
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
821 title = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
822 msnc.quickImshow(self.tbf, title='bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
823 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
824 tomo_stack = msnc.loadImageStack(tomo_stack_files[0], self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
825 stacks[0]['img_offset'], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
826 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
827 msnc.quickImshow(tomo_stack[0,:,:], title=title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
828 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
829 '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
830 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
831 print('\nSelect image bounds from bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
832 tomo_or_bright = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
833 if tomo_or_bright:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
834 x_sum = np.sum(tomo_stack[0,:,:], 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
835 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
836 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
837 tmp = np.copy(tomo_stack[0,:,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
838 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
839 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
840 tmp[img_x_bounds[1]-1,:] = tmp_max
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
841 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
842 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
843 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
844 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
845 x_sum_max = x_sum.max()
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
846 msnc.quickPlot((range(x_sum.size), x_sum),
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
847 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
848 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum_min, x_sum_max], 'r-'),
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
849 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
850 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
851 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
852 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
853 if use_bounds == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
854 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
855 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
856 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
857 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
858 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
859 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
860 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
861 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
862 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
863 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
864 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
865 save_fig=self.save_plots, save_only=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
866 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
867 x_sum = np.sum(self.tbf, 1)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
868 x_sum_min = x_sum.min()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
869 x_sum_max = x_sum.max()
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
870 use_bounds = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
871 if img_x_bounds[0] is not None and img_x_bounds[1] is not None:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
872 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
873 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
874 tmp[img_x_bounds[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
875 tmp[img_x_bounds[1]-1,:] = tmp_max
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
876 title = 'bright field'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
877 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
878 del tmp
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
879 msnc.quickPlot((range(x_sum.size), x_sum),
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
880 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
881 ([img_x_bounds[1]-1, img_x_bounds[1]-1], [x_sum_min, x_sum_max], 'r-'),
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
882 title='sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
883 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
884 f'upper bound = {img_x_bounds[1]} (exclusive)]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
885 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
886 if use_bounds == 'no':
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
887 use_fit = 'no'
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
888 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
889 x_low = fit.get('center1', None)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
890 x_upp = fit.get('center2', None)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
891 sig_low = fit.get('sigma1', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
892 sig_upp = fit.get('sigma2', None)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
893 if (x_low is not None and x_upp is not None and sig_low is not None and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
894 sig_upp is not None and 0 <= x_low < x_upp <= x_sum.size and
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
895 (sig_low+sig_upp)/(x_upp-x_low) < 0.1):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
896 if num_tomo_stacks == 1 or num_x_min is None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
897 x_low = int(x_low-(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
898 x_upp = int(x_upp+(x_upp-x_low)/10)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
899 else:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
900 x_low = int((x_low+x_upp)/2-num_x_min/2)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
901 x_upp = x_low+num_x_min
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
902 if x_low < 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
903 x_low = 0
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
904 if x_upp > x_sum.size:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
905 x_upp = x_sum.size
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
906 tmp = np.copy(self.tbf)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
907 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
908 tmp[x_low,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
909 tmp[x_upp-1,:] = tmp_max
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
910 title = 'bright field'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
911 msnc.quickImshow(tmp, title=title)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
912 del tmp
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
913 msnc.quickPlot((range(x_sum.size), x_sum),
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
914 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
915 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
916 title='sum over theta and y')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
917 print(f'lower bound = {x_low} (inclusive)')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
918 print(f'upper bound = {x_upp} (exclusive)]')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
919 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
920 if use_fit == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
921 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
922 num_x_min, 'sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
923 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
924 img_x_bounds = [x_low, x_upp]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
925 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
926 logging.warning('Image bounds and pixel size prevent seamless stacking')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
927 #msnc.quickPlot(range(img_x_bounds[0], img_x_bounds[1]),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
928 # x_sum[img_x_bounds[0]:img_x_bounds[1]],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
929 # title='sum over theta and y', path=self.output_folder,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
930 # save_fig=self.save_plots, save_only=True)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
931 msnc.quickPlot((range(x_sum.size), x_sum),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
932 ([img_x_bounds[0], img_x_bounds[0]], [x_sum_min, x_sum_max], 'r-'),
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
933 ([img_x_bounds[1], img_x_bounds[1]], [x_sum_min, x_sum_max], 'r-'),
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
934 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
935 save_fig=self.save_plots, save_only=True)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
936 del x_sum
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
937 for i,stack in enumerate(stacks):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
938 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
939 stack['img_offset'], 1)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
940 tomo_stack = tomo_stack[0,:,:]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
941 if num_x_min is not None:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
942 tomo_stack_max = tomo_stack.max()
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
943 tomo_stack[img_x_bounds[0],:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
944 tomo_stack[img_x_bounds[1]-1,:] = tomo_stack_max
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
945 title = f'tomography image at theta={self.config["theta_range"]["start"]}'
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
946 if self.galaxy_flag:
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
947 msnc.quickImshow(tomo_stack, title=title, path='setup_pngs',
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
948 name=f'tomo_{stack["index"]}.png', save_fig=True, save_only=True,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
949 show_grid=True)
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
950 else:
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
951 msnc.quickImshow(tomo_stack, title=title, path=self.output_folder,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
952 name=f'tomo_{stack["index"]}.png', save_fig=self.save_plots,
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
953 save_only=True, show_grid=True)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
954 del tomo_stack
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
955 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
956
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
957 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
958 msnc.clearFig('bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
959 msnc.clearFig('sum over theta and y')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
960 if title:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
961 msnc.clearFig(title)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
962
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
963 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
964 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
965 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
966 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
967 preprocess['img_x_bounds'] = img_x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
968 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
969
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
970 def _setZoomOrSkip(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
971 """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
972 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
973 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
974 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
975 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
976 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
977 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
978 '\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
979 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
980 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
981 min=1, max=100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
982 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
983 zoom_perc = preprocess['zoom_perc']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
984 if msnc.is_num(zoom_perc, 1., 100.):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
985 zoom_perc = int(zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
986 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
987 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
988 zoom_perc = 100
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
989 num_theta_skip = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
990 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
991 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
992 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
993 '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
994 blank=True) == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
995 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
996 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
997 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
998 num_theta_skip = preprocess['num_theta_skip']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
999 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
1000 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
1001 num_theta_skip = 0
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1002 logging.debug(f'zoom_perc = {zoom_perc}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1003 logging.debug(f'num_theta_skip = {num_theta_skip}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1004
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1005 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1006 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1007 self.cf.config['preprocess'] = {'zoom_perc' : zoom_perc,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1008 'num_theta_skip' : num_theta_skip}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1009 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1010 preprocess['zoom_perc'] = zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1011 preprocess['num_theta_skip'] = num_theta_skip
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1012 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1013
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1014 def _loadTomo(self, base_name, index, required=False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1015 """Load a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1016 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1017 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1018 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1019 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1020 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1021 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1022 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
1023 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1024 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1025 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1026 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1027 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
1028 load_flag = 'no'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1029 available = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1030 if os.path.isfile(tomo_file):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1031 available = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1032 if required:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1033 load_flag = 'yes'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1034 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1035 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
1036 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1037 if load_flag == 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1038 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1039 logging.info(f'Loading {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1040 try:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1041 stack = np.load(tomo_file)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1042 except IOError or ValueError:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1043 stack = np.array([])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1044 logging.error(f'Error loading {tomo_file}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1045 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1046 if stack.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1047 msnc.quickImshow(stack[:,0,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1048 save_fig=self.save_plots, save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1049 return stack, available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1050
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1051 def _saveTomo(self, base_name, stack, index=None):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1052 """Save a tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1053 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1054 zoom_perc = None
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1055 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1056 if preprocess:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1057 zoom_perc = preprocess.get('zoom_perc')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1058 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
1059 title = f'{base_name} fullres'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1060 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1061 title = f'{base_name} {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1062 if index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1063 title += f'_{index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1064 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
1065 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1066 logging.info(f'Saving {tomo_file} ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1067 np.save(tomo_file, stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1068 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1069
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1070 def _genTomo(self, tomo_stack_files, available_stacks, num_core=None):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1071 """Generate tomography fields.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1072 """
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1073 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1074 num_core = self.num_core
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1075 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1076 assert(len(self.tomo_stacks) == self.config['stack_info']['num'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1077 assert(len(self.tomo_stacks) == len(stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1078 if len(available_stacks) != len(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1079 logging.warning('Illegal dimension of available_stacks in _genTomo'+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1080 f'({len(available_stacks)}');
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1081 available_stacks = [False]*self.num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1082
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1083 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1084 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1085 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1086 img_y_bounds = [0, self.tbf.shape[1]]
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1087 zoom_perc = 100
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1088 num_theta_skip = 0
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1089 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1090 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1091 img_y_bounds = preprocess.get('img_y_bounds', [0, self.tbf.shape[1]])
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1092 zoom_perc = preprocess.get('zoom_perc', 100)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1093 num_theta_skip = preprocess.get('num_theta_skip', 0)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1094
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1095 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1096 tdf = self.tdf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1097 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1098 logging.warning('Dark field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1099 if not self.tbf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1100 raise ValueError('Bright field unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1101 tbf = self.tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1102
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1103 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1104 # Check if stack is already loaded or available
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1105 if self.tomo_stacks[i].size or available_stacks[i]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1106 continue
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1107
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1108 # Load a stack of tomography images
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1109 index = stack['index']
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1110 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1111 tomo_stack = msnc.loadImageStack(tomo_stack_files[i], self.config['data_filetype'],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1112 stack['img_offset'], self.config['theta_range']['num'], num_theta_skip,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1113 img_x_bounds, img_y_bounds)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1114 tomo_stack = tomo_stack.astype('float64')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1115 logging.debug(f'loading stack {index} took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1116
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1117 # Subtract dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1118 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1119 t0 = time()
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1120 with set_numexpr_threads(self.num_core):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1121 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1122 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
1123
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1124 # Normalize
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1125 t0 = time()
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1126 with set_numexpr_threads(self.num_core):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1127 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
1128 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
1129
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1130 # 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
1131 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1132 cutoff = 1.e-6
1
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diff changeset
1133 with set_numexpr_threads(self.num_core):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1134 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1135 with set_numexpr_threads(self.num_core):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1136 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1137 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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parents:
diff changeset
1138 f'{time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1139
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1140 # Get rid of nans/infs that may be introduced by normalization
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1141 t0 = time()
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parents:
diff changeset
1142 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1143 logging.debug(f'remove nans/infs took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1144
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1145 # Downsize tomography stack to smaller size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1146 tomo_stack = tomo_stack.astype('float32')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1147 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1148 title = f'red stack fullres {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1149 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1150 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1151 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
1152 if zoom_perc != 100:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1153 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1154 logging.info(f'Zooming in ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1155 tomo_zoom_list = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1156 for j in range(tomo_stack.shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1157 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1158 tomo_zoom_list.append(tomo_zoom)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1159 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1160 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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parents:
diff changeset
1161 del tomo_zoom_list
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1162 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1163 title = f'red stack {zoom_perc}p {index}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1164 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1165 msnc.quickImshow(tomo_stack[0,:,:], title=title, path=self.output_folder,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1166 save_fig=self.save_plots, save_only=self.save_plots_only)
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1167
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1168 # Convert tomography stack from theta,row,column to row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1169 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1170
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1171 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1172 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1173 if not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1174 self._saveTomo('red stack', tomo_stack, index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1175 else:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1176 np.savetxt(f'{self.output_folder}/red_stack_{index}.txt',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1177 tomo_stack[0,:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1178
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1179 # Combine stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1180 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1181 self.tomo_stacks[i] = tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1182 logging.debug(f'combining nstack took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1183
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1184 # 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
1185 stack['preprocessed'] = True
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1186 stack.pop('reconstructed', 'reconstructed not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1187 find_center = self.config.get('find_center')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1188 if find_center:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
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parents: 2
diff changeset
1189 find_center.pop('completed', 'completed not found')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1190 if self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1191 find_center.pop('lower_center_offset', 'lower_center_offset not found')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
1192 find_center.pop('upper_center_offset', 'upper_center_offset not found')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1193 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
1194
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1195 if self.tdf.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1196 del tdf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1197 del tbf
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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diff changeset
1198
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1199 def _reconstructOnePlane(self, tomo_plane_T, center, thetas_deg, eff_pixel_size,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
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parents: 2
diff changeset
1200 cross_sectional_dim, plot_sinogram=True, num_core=1):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1201 """Invert the sinogram for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1202 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1203 # tomo_plane_T index order: column,theta
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1204 assert(0 <= center < tomo_plane_T.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1205 center_offset = center-tomo_plane_T.shape[0]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1206 two_offset = 2*int(np.round(center_offset))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
1207 two_offset_abs = np.abs(two_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1208 max_rad = int(0.5*(cross_sectional_dim/eff_pixel_size)*1.1) # 10% slack to avoid edge effects
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1209 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1210 if two_offset >= 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1211 logging.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1212 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1213 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1214 logging.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1215 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1216 if plot_sinogram and not self.test_mode:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1217 msnc.quickImshow(sinogram.T, f'sinogram center offset{center_offset:.2f}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1218 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1219 save_only=self.save_plots_only, aspect='auto')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1220
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1221 # Inverting sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1222 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1223 recon_sinogram = iradon(sinogram, theta=thetas_deg, circle=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1224 logging.debug(f'inverting sinogram took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1225 del sinogram
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1226
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1227 # Removing ring artifacts
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1228 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1229 t0 = time()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1230 # recon_sinogram = filters.gaussian(recon_sinogram, 3.0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1231 recon_sinogram = spi.gaussian_filter(recon_sinogram, 0.5)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1232 recon_clean = np.expand_dims(recon_sinogram, axis=0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1233 del recon_sinogram
38
c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa"
rv43
parents: 37
diff changeset
1234 t1 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1235 logging.debug(f'running remove_ring on {num_core} cores ...')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1236 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=17, ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1237 logging.debug(f'... remove_ring took {time()-t1:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1238 logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1239 return recon_clean
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1240
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1241 def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1242 # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1243 edges = denoise_tv_chambolle(recon_plane, weight = weight)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1244 vmax = np.max(edges[0,:,:])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1245 vmin = -vmax
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1246 if self.galaxy_flag:
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1247 msnc.quickImshow(edges[0,:,:], title, path=path, save_fig=True, save_only=True,
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1248 cmap='gray', vmin=vmin, vmax=vmax)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1249 else:
11
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1250 if path is None:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1251 path=self.output_folder
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1252 msnc.quickImshow(edges[0,:,:], f'{title} coolwarm', path=path,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1253 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')
11
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1254 msnc.quickImshow(edges[0,:,:], f'{title} gray', path=path,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1255 save_fig=self.save_plots, save_only=self.save_plots_only, cmap='gray',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1256 vmin=vmin, vmax=vmax)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1257 del edges
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1258
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1259 def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim,
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1260 tol=0.1, num_core=1, galaxy_param=None):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1261 """Find center for a single tomography plane.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1262 """
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1263 if self.galaxy_flag:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1264 assert(isinstance(galaxy_param, dict))
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1265 if not os.path.exists('find_center_pngs'):
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1266 os.mkdir('find_center_pngs')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1267 # sinogram index order: theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1268 # need index order column,theta for iradon, so take transpose
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1269 sinogram_T = sinogram.T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1270 center = sinogram.shape[1]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1271
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1272 # try automatic center finding routines for initial value
38
c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa"
rv43
parents: 37
diff changeset
1273 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1274 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1275 logging.debug(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1276 print(f'running find_center_vo on {num_core_tomopy_limit} cores ...')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1277 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
37
51dc93d0806a "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 87acf8a257d5d51cf249de085e555bb11d1dbd88"
rv43
parents: 36
diff changeset
1278 else:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1279 logging.debug(f'running find_center_vo on {num_core} cores ...')
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1280 print(f'running find_center_vo on {num_core} cores ...')
37
51dc93d0806a "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 87acf8a257d5d51cf249de085e555bb11d1dbd88"
rv43
parents: 36
diff changeset
1281 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1282 logging.debug(f'... find_center_vo took {time()-t0:.2f} seconds!')
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1283 print(f'... find_center_vo took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1284 center_offset_vo = tomo_center-center
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1285 if self.test_mode:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1286 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1287 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1288 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1289 elif self.galaxy_flag:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1290 logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
38
c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa"
rv43
parents: 37
diff changeset
1291 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1292 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1293 print('OK AA')
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1294 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1295 eff_pixel_size, cross_sectional_dim, False, num_core)
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1296 print('OK BB')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1297 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1298 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1299 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1300 print('OK CC')
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1301 del recon_plane
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1302 if not galaxy_param['center_type_selector']:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1303 del sinogram_T
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1304 return float(center_offset_vo)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1305 else:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1306 print(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1307 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1308 eff_pixel_size, cross_sectional_dim, False, num_core)
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1309 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1310 self._plotEdgesOnePlane(recon_plane, title)
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1311 if not self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1312 if (pyip.inputYesNo('Try finding center using phase correlation '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1313 '(y/[n])? ', blank=True) == 'yes'):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1314 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1315 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1316 error = 1.
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1317 while error > tol:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1318 prev = tomo_center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1319 tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1320 rotc_guess=tomo_center)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1321 error = np.abs(tomo_center-prev)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1322 center_offset = tomo_center-center
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1323 print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1324 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1325 eff_pixel_size, cross_sectional_dim, False, num_core)
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1326 title = f'edges row{row} center_offset{center_offset:.2f} PC'
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1327 self._plotEdgesOnePlane(recon_plane, title)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1328 if (pyip.inputYesNo('Accept a center location ([y]) or continue '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1329 'search (n)? ', blank=True) != 'no'):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1330 center_offset = pyip.inputNum(
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1331 f' Enter chosen center offset [{-int(center)}, {int(center)}] '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1332 f'([{center_offset_vo:.2f}])): ', blank=True)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1333 if center_offset == '':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1334 center_offset = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1335 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1336 del recon_plane
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1337 return float(center_offset)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1338
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1339 # perform center finding search
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1340 print('OK DD')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1341 while True:
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1342 if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1343 set_center = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1344 if galaxy_param['center_type_selector'] == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1345 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1346 set_range = galaxy_param['set_range']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1347 center_offset_step = galaxy_param['set_step']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1348 if (not msnc.is_num(set_range, 0) or not msnc.is_num(center_offset_step) or
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1349 center_offset_step <= 0):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1350 logging.warning('Illegal center finding search parameter, skip search')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1351 del sinogram_T
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1352 return float(center_offset_vo)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1353 set_range = center_offset_step*max(1, int(set_range/center_offset_step))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1354 center_offset_low = set_center-set_range
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1355 center_offset_upp = set_center+set_range
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1356 else:
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1357 center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1358 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1359 center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1360 f'[{center_offset_low}, {int(center)}]: ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1361 min=center_offset_low, max=int(center))
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1362 if center_offset_upp == center_offset_low:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1363 center_offset_step = 1
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1364 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1365 center_offset_step = pyip.inputInt('Enter step size for center offset search '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1366 f'[1, {center_offset_upp-center_offset_low}]: ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1367 min=1, max=center_offset_upp-center_offset_low)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1368 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1369 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1370 for center_offset in center_offsets:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1371 if center_offset == center_offset_vo:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1372 continue
38
c09b8ee8f68f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 62ea2c5a3629c5e4b5b59fadc282214326f093aa"
rv43
parents: 37
diff changeset
1373 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1374 logging.debug(f'running _reconstructOnePlane on {num_core} cores ...')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1375 recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1376 thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1377 logging.debug(f'... _reconstructOnePlane took {time()-t0:.2f} seconds!')
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1378 title = f'edges row{row} center_offset{center_offset:.2f}'
11
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1379 if self.galaxy_flag:
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1380 self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
11
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1381 else:
ec7c3e84d611 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
rv43
parents: 7
diff changeset
1382 self._plotEdgesOnePlane(recon_plane, title)
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1383 if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1384 min=0, max=1):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1385 break
44
0ac719053d6f "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ffffe9eee44b5fb4f5fcdf34b06de5a9bd1eff74"
rv43
parents: 43
diff changeset
1386 print('OK EE')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1387
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1388 del sinogram_T
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1389 del recon_plane
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1390 if self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1391 center_offset = center_offset_vo
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1392 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1393 center_offset = pyip.inputNum(f' Enter chosen center offset '+
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1394 f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1395 return float(center_offset)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1396
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1397 def _reconstructOneTomoStack(self, tomo_stack, thetas, row_bounds=None,
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1398 center_offsets=[], sigma=0.1, rwidth=30, num_core=1, algorithm='gridrec',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1399 run_secondary_sirt=False, secondary_iter=100):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1400 """reconstruct a single tomography stack.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1401 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1402 # stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1403 # thetas must be in radians
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1404 # centers_offset: tomography axis shift in pixels relative to column center
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1405 # RV should we remove stripes?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1406 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1407 # RV should we remove rings?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1408 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1409 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1410 if row_bounds is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1411 row_bounds = [0, tomo_stack.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1412 else:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1413 if not msnc.is_index_range(row_bounds, 0, tomo_stack.shape[0]):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1414 raise ValueError('Illegal row bounds in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1415 if thetas.size != tomo_stack.shape[1]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1416 raise ValueError('theta dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1417 if not len(center_offsets):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1418 centers = np.zeros((row_bounds[1]-row_bounds[0]))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1419 elif len(center_offsets) == 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1420 centers = np.linspace(center_offsets[0], center_offsets[1],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1421 row_bounds[1]-row_bounds[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1422 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1423 if center_offsets.size != row_bounds[1]-row_bounds[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1424 raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1425 centers = center_offsets
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1426 centers += tomo_stack.shape[2]/2
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1427 if True:
39
8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8"
rv43
parents: 38
diff changeset
1428 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1429 if num_core > num_core_tomopy_limit:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1430 logging.debug('running remove_stripe_fw on {num_core_tomopy_limit} cores ...')
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1431 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1432 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1433 ncore=num_core_tomopy_limit)
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1434 else:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1435 logging.debug(f'running remove_stripe_fw on {num_core} cores ...')
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1436 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1437 tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1438 logging.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1439 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1440 tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]]
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1441 logging.debug('performing initial reconstruction')
39
8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8"
rv43
parents: 38
diff changeset
1442 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1443 logging.debug(f'running recon on {num_core} cores ...')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1444 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True,
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1445 algorithm=algorithm, ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1446 logging.debug(f'... recon took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1447 if run_secondary_sirt and secondary_iter > 0:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1448 logging.debug(f'running {secondary_iter} secondary iterations')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1449 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1450 #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver /
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1451 # cuda driver combination."
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1452 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iter}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1453 #SIRT did not finish while running overnight
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1454 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iter}
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1455 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1456 'num_iter':secondary_iter}
39
8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8"
rv43
parents: 38
diff changeset
1457 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1458 logging.debug(f'running recon on {num_core} cores ...')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1459 tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1460 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1461 algorithm=tomopy.astra, ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1462 logging.debug(f'... recon took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1463 if True:
39
8a3036b0a34c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit ebd998fc223b35670269b851ff6d12178ced3ee8"
rv43
parents: 38
diff changeset
1464 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1465 logging.debug(f'running remove_ring on {num_core} cores ...')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1466 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1467 ncore=num_core)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1468 logging.debug(f'... remove_ring took {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1469 return tomo_recon_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1470
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1471 def findImageFiles(self, tiff_to_h5_flag = False):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1472 """Find all available image files.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1473 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1474 self.is_valid = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1475
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1476 # Find dark field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1477 dark_field = self.config['dark_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1478 img_start, num_imgs, dark_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1479 dark_field['data_path'], self.config['data_filetype'], 'dark field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1480 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1481 logging.error('Unable to find suitable dark field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1482 if dark_field['data_path']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1483 self.is_valid = False
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1484 img_start_old = dark_field.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1485 num_imgs_old = dark_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1486 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1487 dark_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1488 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1489 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1490 logging.error('Inconsistent number of availaible dark field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1491 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1492 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1493 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1494 dark_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1495 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1496 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1497 logging.error('Inconsistent image start index for dark field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1498 if dark_field['data_path']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1499 self.is_valid = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1500 logging.info(f'Number of dark field images = {dark_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1501 logging.info(f'Dark field image start index = {dark_field["img_start"]}')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1502 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1503 dark_files = msnc.combine_tiffs_in_h5(dark_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1504 f'{self.config["work_folder"]}/dark_field.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1505 dark_field['data_path'] = dark_files[0]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1506
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1507 # Find bright field images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1508 bright_field = self.config['bright_field']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1509 img_start, num_imgs, bright_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1510 bright_field['data_path'], self.config['data_filetype'], 'bright field')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1511 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1512 logging.error('Unable to find suitable bright field images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1513 self.is_valid = False
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1514 img_start_old = bright_field.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1515 num_imgs_old = bright_field.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1516 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1517 bright_field['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1518 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1519 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1520 logging.error('Inconsistent number of availaible bright field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1521 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1522 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1523 bright_field['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1524 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1525 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1526 logging.warning('Inconsistent image start index for bright field images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1527 self.is_valid = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1528 logging.info(f'Number of bright field images = {bright_field["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1529 logging.info(f'Bright field image start index = {bright_field["img_start"]}')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1530 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1531 bright_files = msnc.combine_tiffs_in_h5(bright_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1532 f'{self.config["work_folder"]}/bright_field.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1533 bright_field['data_path'] = bright_files[0]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1534
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1535 # Find tomography images
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1536 tomo_stack_files = []
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1537 for stack in self.config['stack_info']['stacks']:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1538 index = stack['index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1539 img_start, num_imgs, tomo_files = msnc.findImageFiles(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1540 stack['data_path'], self.config['data_filetype'], f'tomography set {index}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1541 if img_start < 0 or num_imgs < 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1542 logging.error('Unable to find suitable tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1543 self.is_valid = False
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1544 img_start_old = stack.get('img_start')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1545 num_imgs_old = stack.get('num')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1546 if num_imgs_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1547 stack['num'] = num_imgs
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1548 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1549 if num_imgs_old > num_imgs:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1550 logging.error('Inconsistent number of availaible tomography images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1551 self.is_valid = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1552 if img_start_old is None:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1553 stack['img_start'] = img_start
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1554 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1555 if img_start_old < img_start:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1556 logging.warning('Inconsistent image start index for tomography images')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1557 self.is_valid = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1558 logging.info(f'Number of tomography images for set {index} = {stack["num"]}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1559 logging.info(f'Tomography set {index} image start index = {stack["img_start"]}')
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1560 if num_imgs and tiff_to_h5_flag and self.config['data_filetype'] == 'tif':
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1561 tomo_files = msnc.combine_tiffs_in_h5(tomo_files, num_imgs,
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1562 f'{self.config["work_folder"]}/tomo_field_{index}.h5')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1563 stack['data_path'] = tomo_files[0]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1564 tomo_stack_files.append(tomo_files)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1565 del tomo_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1566
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1567 # Safe updated config
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1568 if tiff_to_h5_flag:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1569 self.config['data_filetype'] == 'h5'
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1570 if self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1571 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1572
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1573 return dark_files, bright_files, tomo_stack_files
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1574
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1575 def loadTomoStacks(self, input_name):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1576 """Load tomography stacks (only for Galaxy).
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1577 """
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1578 assert(self.galaxy_flag)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1579 t0 = time()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1580 logging.info(f'Loading preprocessed tomography stack from {input_name} ...')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1581 stack_info = self.config['stack_info']
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1582 stacks = stack_info.get('stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1583 assert(len(self.tomo_stacks) == stack_info['num'])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1584 with np.load(input_name) as f:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1585 for i,stack in enumerate(stacks):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1586 self.tomo_stacks[i] = f[f'set_{stack["index"]}']
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1587 logging.info(f'loaded stack {i}: index = {stack["index"]}, shape = '+
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1588 f'{self.tomo_stacks[i].shape}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1589 logging.info(f'... done in {time()-t0:.2f} seconds!')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1590
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1591 def genTomoStacks(self, galaxy_param=None, num_core=None):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1592 """Preprocess tomography images.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1593 """
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1594 if num_core is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1595 num_core = self.num_core
33
afb612b64f26 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit c566c32f7c1506ab271ae08eb14a2982ee511938"
rv43
parents: 32
diff changeset
1596 logging.info(f'num_core = {num_core}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1597 # Try loading any already preprocessed stacks (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1598 # preprocessed stack order for each one in stack: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1599 stack_info = self.config['stack_info']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1600 stacks = stack_info['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1601 num_tomo_stacks = stack_info['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1602 assert(num_tomo_stacks == len(self.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1603 available_stacks = [False]*num_tomo_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1604 if self.galaxy_flag:
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1605 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1606 tdf_files = galaxy_param['tdf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1607 tbf_files = galaxy_param['tbf_files']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1608 tomo_stack_files = galaxy_param['tomo_stack_files']
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1609 assert(num_tomo_stacks == len(tomo_stack_files))
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1610 if not os.path.exists('setup_pngs'):
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1611 os.mkdir('setup_pngs')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1612 else:
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1613 if galaxy_param:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1614 logging.warning('Ignoring galaxy_param in genTomoStacks (only for Galaxy)')
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1615 galaxy_param = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1616 tdf_files, tbf_files, tomo_stack_files = self.findImageFiles()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1617 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1618 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1619 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1620 if not self.tomo_stacks[i].size and stack.get('preprocessed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1621 self.tomo_stacks[i], available_stacks[i] = \
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1622 self._loadTomo('red stack', stack['index'])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1623
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1624 # Preprocess any unloaded stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1625 if False in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1626 logging.debug('Preprocessing tomography images')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1627
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1628 # Check required image files (skip in Galaxy)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1629 if not self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1630 self._selectImageRanges(available_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1631 if not self.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1632 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1633
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1634 # Generate dark field
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1635 if tdf_files:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1636 self._genDark(tdf_files)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1637
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1638 # Generate bright field
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1639 self._genBright(tbf_files)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1640
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1641 # Set vertical detector bounds for image stack
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1642 self._setDetectorBounds(tomo_stack_files)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1643
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1644 # Set zoom and/or theta skip to reduce memory the requirement
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1645 self._setZoomOrSkip()
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1646
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1647 # Generate tomography fields
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1648 self._genTomo(tomo_stack_files, available_stacks, num_core)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1649
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1650 # Save tomography stack to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1651 if self.galaxy_flag:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1652 t0 = time()
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
1653 output_name = galaxy_param['output_name']
2
b8977c98800b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e"
rv43
parents: 1
diff changeset
1654 logging.info(f'Saving preprocessed tomography stack to {output_name} ...')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1655 save_stacks = {f'set_{stack["index"]}':tomo_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1656 for stack,tomo_stack in zip(stacks,self.tomo_stacks)}
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1657 np.savez(output_name, **save_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1658 logging.info(f'... done in {time()-t0:.2f} seconds!')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1659
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1660 del available_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1661
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1662 # Adjust sample reference height, update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1663 preprocess = self.config.get('preprocess')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1664 if preprocess is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1665 img_x_bounds = [0, self.tbf.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1666 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1667 img_x_bounds = preprocess.get('img_x_bounds', [0, self.tbf.shape[0]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1668 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1669 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1670 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1671 pixel_size *= img_x_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1672 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1673 stack['ref_height'] = stack['ref_height']+pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1674 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1675
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1676 def findCenters(self, galaxy_param=None, num_core=None):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1677 """Find rotation axis centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1678 """
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1679 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1680 num_core = self.num_core
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1681 logging.info(f'num_core = {num_core}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1682 logging.debug('Find centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1683 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1684 available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)]
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1685 logging.debug('Available stacks: {available_stacks}')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1686 if self.galaxy_flag:
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1687 row_bounds = galaxy_param['row_bounds']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1688 center_rows = galaxy_param['center_rows']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1689 center_type_selector = galaxy_param['center_type_selector']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1690 if center_type_selector:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1691 if center_type_selector == 'vo':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1692 set_center = None
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1693 elif center_type_selector == 'user':
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1694 set_center = galaxy_param['set_center']
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1695 else:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1696 logging.error('Illegal center_type_selector entry in galaxy_param '+
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1697 f'({center_type_selector})')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1698 galaxy_param['center_type_selector'] = None
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1699 logging.debug(f'row_bounds = {row_bounds}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1700 logging.debug(f'center_rows = {center_rows}')
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1701 logging.debug(f'center_type_selector = {center_type_selector}')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1702 else:
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1703 if galaxy_param:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1704 logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1705 galaxy_param = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1706
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1707 # Check for valid available center stack index
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1708 find_center = self.config.get('find_center')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1709 center_stack_index = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1710 if find_center and 'center_stack_index' in find_center:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1711 center_stack_index = find_center['center_stack_index']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1712 if (not isinstance(center_stack_index, int) or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1713 center_stack_index not in available_stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1714 msnc.illegal_value('center_stack_index', center_stack_index, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1715 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1716 if self.test_mode:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1717 assert(find_center.get('completed', False) == False)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1718 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1719 print('\nFound calibration center offset info for stack '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1720 f'{center_stack_index}')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1721 if (pyip.inputYesNo('Do you want to use this again ([y]/n)? ',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1722 blank=True) != 'no' and find_center.get('completed', False) == True):
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1723 return
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1724
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1725 # Load the required preprocessed stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1726 # preprocessed stack order: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1727 num_tomo_stacks = self.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1728 assert(len(stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1729 assert(len(self.tomo_stacks) == num_tomo_stacks)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1730 if num_tomo_stacks == 1:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1731 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1732 center_stack_index = stacks[0]['index']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1733 elif center_stack_index != stacks[0]['index']:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1734 raise ValueError(f'Inconsistent center_stack_index {center_stack_index}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1735 if not self.tomo_stacks[0].size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1736 self.tomo_stacks[0], available = self._loadTomo('red stack', center_stack_index,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1737 required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1738 center_stack = self.tomo_stacks[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1739 if not center_stack.size:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1740 stacks[0]['preprocessed'] = False
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1741 raise OSError('Unable to load the required preprocessed tomography stack')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1742 assert(stacks[0].get('preprocessed', False) == True)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1743 elif self.galaxy_flag:
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1744 center_stack_index = stacks[int(num_tomo_stacks/2)]['index']
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1745 tomo_stack_index = available_stacks.index(center_stack_index)
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1746 center_stack = self.tomo_stacks[tomo_stack_index]
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1747 if not center_stack.size:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1748 stacks[tomo_stack_index]['preprocessed'] = False
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1749 raise OSError('Unable to load the required preprocessed tomography stack')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1750 assert(stacks[tomo_stack_index].get('preprocessed', False) == True)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1751 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1752 while True:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1753 if not center_stack_index:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1754 center_stack_index = pyip.inputInt('\nEnter tomography stack index to get '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1755 f'rotation axis centers {available_stacks}: ')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1756 while center_stack_index not in available_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1757 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
1758 f'rotation axis centers {available_stacks}: ')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1759 tomo_stack_index = available_stacks.index(center_stack_index)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1760 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
1761 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
1762 'red stack', center_stack_index, required=True)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1763 center_stack = self.tomo_stacks[tomo_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1764 if not center_stack.size:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1765 stacks[tomo_stack_index]['preprocessed'] = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1766 logging.error(f'Unable to load the {center_stack_index}th '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1767 'preprocessed tomography stack, pick another one')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1768 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1769 break
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1770 assert(stacks[tomo_stack_index].get('preprocessed', False) == True)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1771 if find_center is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1772 self.config['find_center'] = {'center_stack_index' : center_stack_index}
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1773 find_center = self.config['find_center']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1774 else:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1775 find_center['center_stack_index'] = center_stack_index
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1776 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1777 row_bounds = find_center.get('row_bounds', None)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1778 center_rows = [find_center.get('lower_row', None),
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1779 find_center.get('upper_row', None)]
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1780 if row_bounds is None:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1781 row_bounds = [0, center_stack.shape[0]]
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1782 if row_bounds[0] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1783 row_bounds[0] = 0
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1784 if row_bounds[1] == -1:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1785 row_bounds[1] = center_stack.shape[0]
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1786 if center_rows[0] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1787 center_rows[0] = 0
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1788 if center_rows[1] == -1:
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
1789 center_rows[1] = center_stack.shape[0]-1
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1790 if not msnc.is_index_range(row_bounds, 0, center_stack.shape[0]):
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1791 msnc.illegal_value('row_bounds', row_bounds)
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1792 return
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1793
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1794 # Set thetas (in degrees)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1795 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1796 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1797 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1798 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1799 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1800 thetas_deg = np.linspace(theta_start, theta_end, int(num_theta/(num_theta_skip+1)),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1801 endpoint=False)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1802
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1803 # Get non-overlapping sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1804 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1805 pixel_size = self.config['detector']['pixel_size']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1806 if pixel_size is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1807 raise ValueError('Detector pixel size unavailable')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1808 eff_pixel_size = 100.*pixel_size/zoom_perc
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1809 logging.debug(f'eff_pixel_size = {eff_pixel_size}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1810 if num_tomo_stacks == 1:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1811 accept = 'yes'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1812 if not self.test_mode and not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1813 accept = 'no'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1814 print('\nSelect bounds for image reconstruction')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1815 if msnc.is_index_range(row_bounds, 0, center_stack.shape[0]):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1816 a_tmp = np.copy(center_stack[:,0,:])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1817 a_tmp_max = a_tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1818 a_tmp[row_bounds[0],:] = a_tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1819 a_tmp[row_bounds[1]-1,:] = a_tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1820 print(f'lower bound = {row_bounds[0]} (inclusive)')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1821 print(f'upper bound = {row_bounds[1]} (exclusive)')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1822 msnc.quickImshow(a_tmp, title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1823 aspect='auto')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1824 del a_tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1825 accept = pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1826 if accept == 'no':
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1827 (n1, n2) = msnc.selectImageBounds(center_stack[:,0,:], 0,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1828 title=f'center stack theta={theta_start}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1829 else:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1830 n1 = row_bounds[0]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1831 n2 = row_bounds[1]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1832 else:
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1833 tomo_ref_heights = [stack['ref_height'] for stack in stacks]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1834 n1 = int((1.+(tomo_ref_heights[0]+center_stack.shape[0]*eff_pixel_size-
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1835 tomo_ref_heights[1])/eff_pixel_size)/2)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1836 n2 = center_stack.shape[0]-n1
40
fa94fe25ca46 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9978af8877d8e9722d252ab9bee4cbd4654aa100"
rv43
parents: 39
diff changeset
1837 logging.debug(f'n1 = {n1}, n2 = {n2} (n2-n1) = {(n2-n1)*eff_pixel_size:.3f} mm')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1838 if not self.test_mode and not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1839 tmp = center_stack[:,0,:]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1840 tmp_max = tmp.max()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1841 tmp[n1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1842 tmp[n2-1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1843 if msnc.is_index_range(center_rows, 0, tmp.shape[0]):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1844 tmp[center_rows[0],:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1845 tmp[center_rows[1]-1,:] = tmp_max
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1846 extent = [0, tmp.shape[1], tmp.shape[0], 0]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1847 msnc.quickImshow(tmp, title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1848 path=self.output_folder, extent=extent, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1849 save_only=self.save_plots_only, aspect='auto')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1850 del tmp
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1851 #extent = [0, center_stack.shape[2], n2, n1]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1852 #msnc.quickImshow(center_stack[n1:n2,0,:], title=f'center stack theta={theta_start}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1853 # path=self.output_folder, extent=extent, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1854 # save_only=self.save_plots_only, show_grid=True, aspect='auto')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1855
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1856 # Get cross sectional diameter in mm
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1857 cross_sectional_dim = center_stack.shape[2]*eff_pixel_size
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1858 logging.debug(f'cross_sectional_dim = {cross_sectional_dim}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1859
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1860 # Determine center offset at sample row boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1861 logging.info('Determine center offset at sample row boundaries')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1862
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1863 # Lower row center
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1864 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1865 use_center = 'no'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1866 row = center_rows[0]
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1867 print('Ok1')
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1868 if self.test_mode or self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1869 assert(msnc.is_int(row, n1, n2-2))
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1870 print('Ok2')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1871 if msnc.is_int(row, n1, n2-2):
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1872 if self.test_mode or self.galaxy_flag:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1873 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1874 else:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1875 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1876 use_row = pyip.inputYesNo('\nCurrent row index for lower center = '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1877 f'{row}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1878 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1879 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1880 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1881 center_offset = find_center.get('lower_center_offset')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1882 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1883 use_center = pyip.inputYesNo('Current lower center offset = '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1884 f'{center_offset}, use this value ([y]/n)? ', blank=True)
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1885 print(f'Ok3 {use_center} {use_row}')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1886 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1887 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1888 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1889 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1890 aspect='auto')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1891 row = pyip.inputInt('\nEnter row index to find lower center '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1892 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
1893 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1894 row = n1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1895 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1896 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1897 # center_stack order: row,theta,column
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1898 print('Ok4')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1899 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1900 eff_pixel_size, cross_sectional_dim, num_core=num_core,
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1901 galaxy_param=galaxy_param)
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1902 print('Ok5')
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1903 logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}')
43
0b9ce9489ecc "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 006ce85b82c2f8eb386cb1648803d7768016c067"
rv43
parents: 41
diff changeset
1904 print('Ok6')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1905
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1906 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1907 find_center['row_bounds'] = [n1, n2]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1908 find_center['lower_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1909 find_center['lower_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1910 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1911 lower_row = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1912
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1913 # Upper row center
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1914 use_row = 'no'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1915 use_center = 'no'
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1916 row = center_rows[1]
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1917 if self.test_mode or self.galaxy_flag:
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1918 assert(msnc.is_int(row, lower_row+1, n2-1))
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1919 if msnc.is_int(row, lower_row+1, n2-1):
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1920 if self.test_mode or self.galaxy_flag:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1921 use_row = 'yes'
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1922 else:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1923 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1924 use_row = pyip.inputYesNo('\nCurrent row index for upper center = '
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1925 f'{row}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1926 if self.save_plots_only:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1927 msnc.clearFig(f'theta={theta_start}')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1928 if use_row != 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1929 center_offset = find_center.get('upper_center_offset')
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1930 if msnc.is_num(center_offset):
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1931 use_center = pyip.inputYesNo('Current upper center offset = '+
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1932 f'{center_offset}, use this value ([y]/n)? ', blank=True)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1933 if use_center == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1934 if use_row == 'no':
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1935 if not self.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1936 msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}',
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
1937 aspect='auto')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1938 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
1939 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
1940 if row == '':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1941 row = n2-1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1942 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1943 msnc.clearFig(f'theta={theta_start}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1944 # center_stack order: row,theta,column
24
817a8101d2e4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3d7910473008ec94bc0b4580d62e61310e69917d"
rv43
parents: 23
diff changeset
1945 center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
1946 eff_pixel_size, cross_sectional_dim, num_core=num_core,
13
40395e60d2be "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
rv43
parents: 11
diff changeset
1947 galaxy_param=galaxy_param)
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
1948 logging.info(f'upper_center_offset = {center_offset:.2f}')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1949 del center_stack
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1950
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1951 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1952 find_center['upper_row'] = row
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1953 find_center['upper_center_offset'] = center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1954 find_center['completed'] = True
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1955 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1956
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1957 def checkCenters(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1958 """Check centers for the tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1959 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1960 #RV TODO load all stacks and check at all stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1961 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1962 logging.debug('Check centers for tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1963 center_stack_index = self.config.get('center_stack_index')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1964 if center_stack_index is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1965 raise ValueError('Unable to read center_stack_index from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1966 center_stack_index = self.tomo_stacks[self.tomo_data_indices.index(center_stack_index)]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1967 lower_row = self.config.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1968 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1969 raise ValueError('Unable to read lower_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1970 lower_center_offset = self.config.get('lower_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1971 if lower_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1972 raise ValueError('Unable to read lower_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1973 upper_row = self.config.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1974 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1975 raise ValueError('Unable to read upper_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1976 upper_center_offset = self.config.get('upper_center_offset')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1977 if upper_center_offset is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1978 raise ValueError('Unable to read upper_center_offset from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1979 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1980 shift = upper_center_offset-lower_center_offset
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1981 if lower_row == 0:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1982 logging.warning(f'lower_row == 0: one row offset between both planes')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1983 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1984 lower_row -= 1
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1985 lower_center_offset -= center_slope
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1986
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1987 # stack order: stack,row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1988 if center_stack_index:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1989 stack1 = self.tomo_stacks[center_stack_index-1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1990 stack2 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1991 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1992 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1993 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1994 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1995 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1996 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1997 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1998 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
1999 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2000 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2001 shift_i = shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2002 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2003 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2004 title=f'stacks {stack1} {stack2} shifted {2*i} theta={self.start_theta}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2005 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2006 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2007 if center_stack_index < self.num_tomo_stacks-1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2008 stack1 = self.tomo_stacks[center_stack_index]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2009 stack2 = self.tomo_stacks[center_stack_index+1]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2010 if not stack1.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2011 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2012 elif not stack2.size:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2013 logging.error(f'Unable to load required tomography stack {stack1}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2014 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2015 assert(0 <= lower_row < stack2.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2016 assert(0 <= upper_row < stack1.shape[0])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2017 plane1 = stack1[upper_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2018 plane2 = stack2[lower_row,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2019 for i in range(-2, 3):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2020 shift_i = -shift+2*i
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2021 plane1_shifted = spi.shift(plane2, [0, shift_i])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2022 msnc.quickPlot((plane1[0,:],), (plane1_shifted[0,:],),
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2023 title=f'stacks {stack1} {stack2} shifted {2*i} theta={start_theta}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2024 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2025 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2026 del plane1, plane2, plane1_shifted
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2027
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2028 # Update config file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2029 self.config = msnc.update('config.txt', 'check_centers', True, 'find_centers')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2030
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2031 def reconstructTomoStacks(self, galaxy_param=None, num_core=None):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2032 """Reconstruct tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2033 """
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2034 if num_core is None:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2035 num_core = self.num_core
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
2036 logging.info(f'num_core = {num_core}')
21
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2037 if self.galaxy_flag:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2038 assert(galaxy_param)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2039 if not os.path.exists('center_slice_pngs'):
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2040 os.mkdir('center_slice_pngs')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2041 logging.debug('Reconstruct tomography stacks')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2042 stacks = self.config['stack_info']['stacks']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2043 assert(len(self.tomo_stacks) == self.config['stack_info']['num'])
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2044 assert(len(self.tomo_stacks) == len(stacks))
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2045 assert(len(self.tomo_recon_stacks) == len(stacks))
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2046 if self.galaxy_flag:
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2047 assert(isinstance(galaxy_param, dict))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2048 # Get rotation axis centers
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2049 center_offsets = galaxy_param['center_offsets']
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2050 assert(isinstance(center_offsets, list) and len(center_offsets) == 2)
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2051 lower_center_offset = center_offsets[0]
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2052 assert(msnc.is_num(lower_center_offset))
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2053 upper_center_offset = center_offsets[1]
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2054 assert(msnc.is_num(upper_center_offset))
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2055 else:
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2056 if galaxy_param:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2057 logging.warning('Ignoring galaxy_param in reconstructTomoStacks (only for Galaxy)')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2058 galaxy_param = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2059 lower_center_offset = None
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2060 upper_center_offset = None
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2061
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2062 # Get rotation axis rows and centers
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2063 find_center = self.config['find_center']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2064 lower_row = find_center.get('lower_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2065 if lower_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2066 logging.error('Unable to read lower_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2067 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2068 upper_row = find_center.get('upper_row')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2069 if upper_row is None:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2070 logging.error('Unable to read upper_row from config')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2071 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2072 logging.debug(f'lower_row = {lower_row} upper_row = {upper_row}')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2073 assert(lower_row < upper_row)
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2074 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2075 lower_center_offset = find_center.get('lower_center_offset')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2076 if lower_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2077 logging.error('Unable to read lower_center_offset from config')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2078 return
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2079 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2080 upper_center_offset = find_center.get('upper_center_offset')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2081 if upper_center_offset is None:
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2082 logging.error('Unable to read upper_center_offset from config')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2083 return
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2084 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2085
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2086 # Set thetas (in radians)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2087 theta_range = self.config['theta_range']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2088 theta_start = theta_range['start']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2089 theta_end = theta_range['end']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2090 num_theta = theta_range['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2091 num_theta_skip = self.config['preprocess'].get('num_theta_skip', 0)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2092 thetas = np.radians(np.linspace(theta_start, theta_end,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2093 int(num_theta/(num_theta_skip+1)), endpoint=False))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2094
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2095 # Reconstruct tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2096 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2097 if zoom_perc == 100:
21
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2098 basetitle = 'recon stack fullres'
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2099 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2100 basetitle = f'recon stack {zoom_perc}p'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2101 load_error = False
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2102 stacks = self.config['stack_info']['stacks']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2103 for i,stack in enumerate(stacks):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2104 # Check if stack can be loaded
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2105 # reconstructed stack order for each one in stack : row/z,x,y
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2106 # preprocessed stack order for each one in stack: row,theta,column
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2107 index = stack['index']
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2108 if not self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2109 available = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2110 if stack.get('reconstructed', False):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2111 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack', index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2112 if self.tomo_recon_stacks[i].size or available:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2113 if self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2114 self.tomo_stacks[i] = np.array([])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2115 assert(stack.get('preprocessed', False) == True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2116 assert(stack.get('reconstructed', False) == True)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2117 continue
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2118 stack['reconstructed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2119 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2120 self.tomo_stacks[i], available = self._loadTomo('red stack', index,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2121 required=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2122 if not self.tomo_stacks[i].size:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2123 logging.error(f'Unable to load tomography stack {index} for reconstruction')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2124 stack[i]['preprocessed'] = False
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2125 load_error = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2126 continue
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2127 assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2128 center_offsets = [lower_center_offset-lower_row*center_slope,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2129 upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope]
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2130 t0 = time()
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
2131 logging.debug(f'running _reconstructOneTomoStack on {num_core} cores ...')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2132 self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i],
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2133 thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2134 algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25)
41
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
2135 logging.debug(f'... _reconstructOneTomoStack took {time()-t0:.2f} seconds!')
ef5c2f7b49ec "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
rv43
parents: 40
diff changeset
2136 logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!')
21
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2137 if self.galaxy_flag:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2138 x_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2139 title = f'{basetitle} {index} xslice{x_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2140 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2141 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2142 y_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2143 title = f'{basetitle} {index} yslice{y_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2144 msnc.quickImshow(self.tomo_recon_stacks[i][:,y_slice,:], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2145 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2146 z_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2147 title = f'{basetitle} {index} zslice{z_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2148 msnc.quickImshow(self.tomo_recon_stacks[i][:,:,z_slice], title=title,
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2149 path='center_slice_pngs', save_fig=True, save_only=True)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2150 elif not self.test_mode:
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2151 x_slice = int(self.tomo_stacks[i].shape[0]/2)
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2152 title = f'{basetitle} {index} xslice{x_slice}'
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2153 msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title,
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2154 path=self.output_folder, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2155 save_only=self.save_plots_only)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2156 msnc.quickPlot(self.tomo_recon_stacks[i]
21
3caba2116858 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
rv43
parents: 20
diff changeset
2157 [x_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:],
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2158 title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[2]/2)}',
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2159 path=self.output_folder, save_fig=self.save_plots,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2160 save_only=self.save_plots_only)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2161 self._saveTomo('recon stack', self.tomo_recon_stacks[i], index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2162 self.tomo_stacks[i] = np.array([])
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2163
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2164 # Update config and save to file
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2165 stack['reconstructed'] = True
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2166 combine_stacks = self.config.get('combine_stacks')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2167 if combine_stacks and index in combine_stacks.get('stacks', []):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2168 combine_stacks['stacks'].remove(index)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2169 self.cf.saveFile(self.config_out)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2170
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2171 # Save reconstructed tomography stack to file
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2172 if self.galaxy_flag:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2173 t0 = time()
15
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
rv43
parents: 13
diff changeset
2174 output_name = galaxy_param['output_name']
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2175 logging.info(f'Saving reconstructed tomography stack to {output_name} ...')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2176 save_stacks = {f'set_{stack["index"]}':tomo_stack
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2177 for stack,tomo_stack in zip(stacks,self.tomo_recon_stacks)}
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2178 np.savez(output_name, **save_stacks)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents: 2
diff changeset
2179 logging.info(f'... done in {time()-t0:.2f} seconds!')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2180
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2181 def combineTomoStacks(self):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2182 """Combine the reconstructed tomography stacks.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2183 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2184 # stack order: stack,row(z),x,y
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2185 logging.debug('Combine reconstructed tomography stacks')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2186 # Load any unloaded reconstructed stacks
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2187 stack_info = self.config['stack_info']
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2188 stacks = stack_info['stacks']
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2189 for i,stack in enumerate(stacks):
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2190 available = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2191 if not self.tomo_recon_stacks[i].size and stack.get('reconstructed', False):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2192 self.tomo_recon_stacks[i], available = self._loadTomo('recon stack',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2193 stack['index'], required=True)
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2194 if not self.tomo_recon_stacks[i].size:
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2195 logging.error(f'Unable to load reconstructed stack {stack["index"]}')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2196 stack['reconstructed'] = False
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2197 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2198 if i:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2199 if (self.tomo_recon_stacks[i].shape[1] != self.tomo_recon_stacks[0].shape[1] or
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2200 self.tomo_recon_stacks[i].shape[1] != self.tomo_recon_stacks[0].shape[1]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2201 logging.error('Incompatible reconstructed tomography stack dimensions')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2202 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2203
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2204 # Get center stack boundaries
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2205 row_bounds = self.config['find_center']['row_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2206 if not msnc.is_index_range(row_bounds, 0, self.tomo_recon_stacks[0].shape[0]):
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2207 msnc.illegal_value('row_bounds', row_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2208 return
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2209
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2210 # Selecting x bounds (in yz-plane)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2211 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2212 #RV FIX :=
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2213 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,2)) for tomo_recon_stack in
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2214 self.tomo_recon_stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2215 combine_stacks = self.config.get('combine_stacks')
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2216 if combine_stacks and 'x_bounds' in combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2217 x_bounds = combine_stacks['x_bounds']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2218 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
2219 msnc.illegal_value('x_bounds', x_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2220 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2221 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2222 if pyip.inputYesNo('\nCurrent image x-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2223 f'[{x_bounds[0]}, {x_bounds[1]}], use these values ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2224 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2225 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2226 'Do you want to change the image x-bounds ([y]/n)? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2227 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2228 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
2229 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2230 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
2231 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2232 msnc.quickPlot(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2233 if pyip.inputYesNo('\nDo you want to change the image x-bounds (y/n)? ') == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2234 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
2235 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2236 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
2237 if False and self.test_mode:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2238 np.savetxt(f'{self.output_folder}/recon_stack_sum_yz.txt',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2239 tomosum[x_bounds[0]:x_bounds[1]], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2240 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2241 msnc.clearFig('recon stack sum yz')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2242
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2243 # Selecting y bounds (in xz-plane)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2244 tomosum = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2245 #RV FIX :=
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2246 [tomosum := tomosum+np.sum(tomo_recon_stack, axis=(0,1)) for tomo_recon_stack in
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2247 self.tomo_recon_stacks]
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2248 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
2249 y_bounds = combine_stacks['y_bounds']
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2250 if not msnc.is_index_range(y_bounds, 0, self.tomo_recon_stacks[0].shape[1]):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2251 msnc.illegal_value('y_bounds', y_bounds, 'config file')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2252 elif not self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2253 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2254 if pyip.inputYesNo('\nCurrent image y-bounds: '+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2255 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
2256 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2257 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2258 '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
2259 blank=True) == 'no':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2260 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
2261 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2262 y_bounds = msnc.selectArrayBounds(tomosum, title='recon stack sum yz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2263 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2264 msnc.quickPlot(tomosum, title='recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2265 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
2266 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
2267 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2268 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
2269 if False and self.test_mode:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2270 np.savetxt(f'{self.output_folder}/recon_stack_sum_xz.txt',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2271 tomosum[y_bounds[0]:y_bounds[1]], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2272 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2273 msnc.clearFig('recon stack sum xz')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2274
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2275 # Combine reconstructed tomography stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2276 logging.info(f'Combining reconstructed stacks ...')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2277 t0 = time()
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2278 num_tomo_stacks = stack_info['num']
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2279 if num_tomo_stacks == 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2280 low_bound = row_bounds[0]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2281 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2282 low_bound = 0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2283 tomo_recon_combined = self.tomo_recon_stacks[0][low_bound:row_bounds[1]:,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2284 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2285 if num_tomo_stacks > 2:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2286 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2287 [self.tomo_recon_stacks[i][row_bounds[0]:row_bounds[1],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2288 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2289 for i in range(1, num_tomo_stacks-1)])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2290 if num_tomo_stacks > 1:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2291 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2292 [self.tomo_recon_stacks[num_tomo_stacks-1][row_bounds[0]:,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2293 x_bounds[0]:x_bounds[1],y_bounds[0]:y_bounds[1]]])
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2294 logging.info(f'... done in {time()-t0:.2f} seconds!')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2295 combined_stacks = [stack['index'] for stack in stacks]
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2296
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2297 # Wrap up if in test_mode
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2298 tomosum = np.sum(tomo_recon_combined, axis=(1,2))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2299 if self.test_mode:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2300 zoom_perc = self.config['preprocess'].get('zoom_perc', 100)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2301 filename = 'recon combined sum xy'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2302 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
2303 filename += ' fullres.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2304 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2305 filename += f' {zoom_perc}p.dat'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2306 msnc.quickPlot(tomosum, title='recon combined sum xy',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2307 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2308 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2309 if False:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2310 np.savetxt(f'{self.output_folder}/recon_combined_sum_xy.txt',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2311 tomosum, fmt='%.6e')
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2312 np.savetxt(f'{self.output_folder}/recon_combined.txt',
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2313 tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:], fmt='%.6e')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2314
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2315 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2316 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2317 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2318 combine_stacks['y_bounds'] = y_bounds
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2319 combine_stacks['stacks'] = combined_stacks
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2320 else:
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2321 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds,
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2322 'stacks' : combined_stacks}
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2323 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2324 return
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2325
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2326 # Selecting z bounds (in xy-plane)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2327 msnc.quickPlot(tomosum, title='recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2328 if pyip.inputYesNo(
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2329 '\nDo you want to change the image z-bounds (y/[n])? ',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2330 blank=True) != 'yes':
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2331 z_bounds = [0, tomo_recon_combined.shape[0]]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2332 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2333 z_bounds = msnc.selectArrayBounds(tomosum, title='recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2334 if z_bounds[0] != 0 or z_bounds[1] != tomo_recon_combined.shape[0]:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2335 tomo_recon_combined = tomo_recon_combined[z_bounds[0]:z_bounds[1],:,:]
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2336 if self.save_plots_only:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2337 msnc.clearFig('recon combined sum xy')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2338
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2339 # Plot center slices
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2340 msnc.quickImshow(tomo_recon_combined[int(tomo_recon_combined.shape[0]/2),:,:],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2341 title=f'recon combined xslice{int(tomo_recon_combined.shape[0]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2342 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2343 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2344 msnc.quickImshow(tomo_recon_combined[:,int(tomo_recon_combined.shape[1]/2),:],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2345 title=f'recon combined yslice{int(tomo_recon_combined.shape[1]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2346 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2347 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2348 msnc.quickImshow(tomo_recon_combined[:,:,int(tomo_recon_combined.shape[2]/2)],
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2349 title=f'recon combined zslice{int(tomo_recon_combined.shape[2]/2)}',
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2350 path=self.output_folder, save_fig=self.save_plots,
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2351 save_only=self.save_plots_only)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2352
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2353 # Save combined reconstructed tomo stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2354 base_name = 'recon combined'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2355 for stack in stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2356 base_name += f' {stack["index"]}'
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2357 self._saveTomo(base_name, tomo_recon_combined)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2358
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2359 # Update config and save to file
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2360 if combine_stacks:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2361 combine_stacks['x_bounds'] = x_bounds
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2362 combine_stacks['y_bounds'] = y_bounds
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2363 combine_stacks['z_bounds'] = z_bounds
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2364 combine_stacks['stacks'] = combined_stacks
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2365 else:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2366 self.config['combine_stacks'] = {'x_bounds' : x_bounds, 'y_bounds' : y_bounds,
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2367 'z_bounds' : z_bounds, 'stacks' : combined_stacks}
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2368 self.cf.saveFile(self.config_out)
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2369
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2370 def runTomo(config_file=None, config_dict=None, output_folder='.', log_level='INFO',
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2371 test_mode=False, num_core=-1):
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2372 """Run a tomography analysis.
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2373 """
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2374 # Instantiate Tomo object
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2375 tomo = Tomo(config_file=config_file, output_folder=output_folder, log_level=log_level,
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2376 test_mode=test_mode, num_core=num_core)
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2377 if not tomo.is_valid:
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2378 raise ValueError('Invalid config and/or detector file provided.')
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2379
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2380 # Preprocess the image files
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2381 assert(tomo.config['stack_info'])
0
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2382 num_tomo_stacks = tomo.config['stack_info']['num']
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2383 assert(num_tomo_stacks == len(tomo.tomo_stacks))
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
rv43
parents:
diff changeset
2384 preprocessed_stacks = []
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2385 if not tomo.test_mode:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2386 preprocess = tomo.config.get('preprocess', None)
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2387 if preprocess:
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
rv43
parents: 0
diff changeset
2388 preprocessed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
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diff changeset
2389 if stack.get('preprocessed', False)]
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diff changeset
2390 if len(preprocessed_stacks) != num_tomo_stacks:
0
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diff changeset
2391 tomo.genTomoStacks()
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diff changeset
2392 if not tomo.is_valid:
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diff changeset
2393 IOError('Unable to load all required image files.')
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diff changeset
2394 tomo.cf.saveFile(tomo.config_out)
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diff changeset
2395
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2396 # Find centers
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parents:
diff changeset
2397 find_center = tomo.config.get('find_center')
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diff changeset
2398 if find_center is None or not find_center.get('completed', False):
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parents:
diff changeset
2399 tomo.findCenters()
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diff changeset
2400
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2401 # Check centers
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parents:
diff changeset
2402 #if num_tomo_stacks > 1 and not tomo.config.get('check_centers', False):
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parents:
diff changeset
2403 # tomo.checkCenters()
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diff changeset
2404
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2405 # Reconstruct tomography stacks
1
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diff changeset
2406 assert(tomo.config['stack_info']['stacks'])
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diff changeset
2407 reconstructed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
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diff changeset
2408 if stack.get('reconstructed', False)]
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diff changeset
2409 if len(reconstructed_stacks) != num_tomo_stacks:
0
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diff changeset
2410 tomo.reconstructTomoStacks()
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diff changeset
2411
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diff changeset
2412 # Combine reconstructed tomography stacks
1
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diff changeset
2413 reconstructed_stacks = [stack['index'] for stack in tomo.config['stack_info']['stacks']
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diff changeset
2414 if stack.get('reconstructed', False)]
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diff changeset
2415 combine_stacks = tomo.config.get('combine_stacks')
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diff changeset
2416 if len(reconstructed_stacks) and (combine_stacks is None or
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diff changeset
2417 combine_stacks.get('stacks') != reconstructed_stacks):
0
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diff changeset
2418 tomo.combineTomoStacks()
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diff changeset
2419
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parents:
diff changeset
2420 #%%============================================================================
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diff changeset
2421 if __name__ == '__main__':
1
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diff changeset
2422
0
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parents:
diff changeset
2423 # Parse command line arguments
1
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parents: 0
diff changeset
2424 parser = argparse.ArgumentParser(
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diff changeset
2425 description='Tomography reconstruction')
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diff changeset
2426 parser.add_argument('-c', '--config',
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diff changeset
2427 default=None,
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diff changeset
2428 help='Input config')
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diff changeset
2429 parser.add_argument('-o', '--output_folder',
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diff changeset
2430 default='.',
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diff changeset
2431 help='Output folder')
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diff changeset
2432 parser.add_argument('-l', '--log_level',
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diff changeset
2433 default='INFO',
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parents: 0
diff changeset
2434 help='Log level')
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diff changeset
2435 parser.add_argument('-t', '--test_mode',
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diff changeset
2436 action='store_true',
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diff changeset
2437 default=False,
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diff changeset
2438 help='Test mode flag')
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diff changeset
2439 parser.add_argument('--num_core',
3
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diff changeset
2440 type=int,
1
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diff changeset
2441 default=-1,
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parents: 0
diff changeset
2442 help='Number of cores')
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diff changeset
2443 args = parser.parse_args()
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diff changeset
2444
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parents: 0
diff changeset
2445 if args.config is None:
0
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diff changeset
2446 if os.path.isfile('config.yaml'):
1
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diff changeset
2447 args.config = 'config.yaml'
0
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diff changeset
2448 else:
1
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diff changeset
2449 args.config = 'config.txt'
0
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parents:
diff changeset
2450
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2451 # Set basic log configuration
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2452 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
1
e4778148df6b "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7bc44bd6a5a7d503fc4d6f6fb67b3a04a631430b"
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parents: 0
diff changeset
2453 if not args.test_mode:
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diff changeset
2454 level = getattr(logging, args.log_level.upper(), None)
0
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diff changeset
2455 if not isinstance(level, int):
1
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parents: 0
diff changeset
2456 raise ValueError(f'Invalid log_level: {args.log_level}')
0
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diff changeset
2457 logging.basicConfig(format=logging_format, level=level, force=True,
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diff changeset
2458 handlers=[logging.StreamHandler()])
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diff changeset
2459
1
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diff changeset
2460 logging.debug(f'config = {args.config}')
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diff changeset
2461 logging.debug(f'output_folder = {args.output_folder}')
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diff changeset
2462 logging.debug(f'log_level = {args.log_level}')
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diff changeset
2463 logging.debug(f'test_mode = {args.test_mode}')
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diff changeset
2464 logging.debug(f'num_core = {args.num_core}')
0
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diff changeset
2465
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parents:
diff changeset
2466 # Run tomography analysis
1
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diff changeset
2467 runTomo(config_file=args.config, output_folder=args.output_folder, log_level=args.log_level,
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diff changeset
2468 test_mode=args.test_mode, num_core=args.num_core)
0
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diff changeset
2469
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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parents:
diff changeset
2470 #%%============================================================================
1
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diff changeset
2471 # input('Press any key to continue')
0
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diff changeset
2472 #%%============================================================================