Mercurial > repos > rv43 > test_tomo_reconstruct

annotate workflow/run_tomo.py @ 0:98e23dff1de2 draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 16:22:42 +0000
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1 #!/usr/bin/env python3
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2
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3 import logging
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4 logger = logging.getLogger(__name__)
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5
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6 import numpy as np
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7 try:
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8 import numexpr as ne
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9 except:
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10 pass
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12 import scipy.ndimage as spi
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13 except:
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14 pass
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15
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16 from multiprocessing import cpu_count
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17 from nexusformat.nexus import *
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18 from os import mkdir
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19 from os import path as os_path
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20 try:
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21 from skimage.transform import iradon
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22 except:
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23 pass
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25 from skimage.restoration import denoise_tv_chambolle
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26 except:
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27 pass
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28 from time import time
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30 import tomopy
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31 except:
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32 pass
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33 from yaml import safe_load, safe_dump
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34
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36 from msnctools.fit import Fit
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37 except:
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38 from fit import Fit
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39 try:
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40 from msnctools.general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \
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41 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \
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42 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot
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43 except:
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44 from general import illegal_value, is_int, is_int_pair, is_num, is_index_range, \
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45 input_int, input_num, input_yesno, input_menu, draw_mask_1d, select_image_bounds, \
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46 select_one_image_bound, clear_imshow, quick_imshow, clear_plot, quick_plot
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47
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48 try:
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49 from workflow.models import import_scanparser, FlatField, TomoField, TomoWorkflow
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50 from workflow.__version__ import __version__
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51 except:
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52 pass
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53
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54 num_core_tomopy_limit = 24
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55
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56 def nxcopy(nxobject:NXobject, exclude_nxpaths:list[str]=[], nxpath_prefix:str='') -> NXobject:
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57 '''Function that returns a copy of a nexus object, optionally exluding certain child items.
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58
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59 :param nxobject: the original nexus object to return a "copy" of
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60 :type nxobject: nexusformat.nexus.NXobject
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61 :param exlude_nxpaths: a list of paths to child nexus objects that
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62 should be exluded from the returned "copy", defaults to `[]`
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63 :type exclude_nxpaths: list[str], optional
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64 :param nxpath_prefix: For use in recursive calls from inside this
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65 function only!
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66 :type nxpath_prefix: str
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67 :return: a copy of `nxobject` with some children optionally exluded.
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68 :rtype: NXobject
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69 '''
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70
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71 nxobject_copy = nxobject.__class__()
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72 if not len(nxpath_prefix):
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73 if 'default' in nxobject.attrs:
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74 nxobject_copy.attrs['default'] = nxobject.attrs['default']
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75 else:
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76 for k, v in nxobject.attrs.items():
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77 nxobject_copy.attrs[k] = v
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78
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79 for k, v in nxobject.items():
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80 nxpath = os_path.join(nxpath_prefix, k)
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81
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82 if nxpath in exclude_nxpaths:
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83 continue
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84
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85 if isinstance(v, NXgroup):
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86 nxobject_copy[k] = nxcopy(v, exclude_nxpaths=exclude_nxpaths,
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87 nxpath_prefix=os_path.join(nxpath_prefix, k))
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88 else:
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89 nxobject_copy[k] = v
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90
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91 return(nxobject_copy)
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92
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93 class set_numexpr_threads:
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94
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95 def __init__(self, num_core):
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96 if num_core is None or num_core < 1 or num_core > cpu_count():
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97 self.num_core = cpu_count()
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98 else:
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99 self.num_core = num_core
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100
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101 def __enter__(self):
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102 self.num_core_org = ne.set_num_threads(self.num_core)
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103
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104 def __exit__(self, exc_type, exc_value, traceback):
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105 ne.set_num_threads(self.num_core_org)
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106
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107 class Tomo:
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108 """Processing tomography data with misalignment.
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109 """
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110 def __init__(self, galaxy_flag=False, num_core=-1, output_folder='.', save_figs=None,
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111 test_mode=False):
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112 """Initialize with optional config input file or dictionary
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113 """
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114 if not isinstance(galaxy_flag, bool):
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115 raise ValueError(f'Invalid parameter galaxy_flag ({galaxy_flag})')
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116 self.galaxy_flag = galaxy_flag
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117 self.num_core = num_core
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118 if self.galaxy_flag:
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119 if output_folder != '.':
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120 logger.warning('Ignoring output_folder in galaxy mode')
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121 self.output_folder = '.'
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122 if test_mode != False:
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123 logger.warning('Ignoring test_mode in galaxy mode')
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124 self.test_mode = False
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125 if save_figs is not None:
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126 logger.warning('Ignoring save_figs in galaxy mode')
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127 save_figs = 'only'
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128 else:
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129 self.output_folder = os_path.abspath(output_folder)
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130 if not os_path.isdir(output_folder):
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131 mkdir(os_path.abspath(output_folder))
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132 if not isinstance(test_mode, bool):
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133 raise ValueError(f'Invalid parameter test_mode ({test_mode})')
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134 self.test_mode = test_mode
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135 if save_figs is None:
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136 save_figs = 'no'
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137 self.test_config = {}
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138 if self.test_mode:
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139 if save_figs != 'only':
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140 logger.warning('Ignoring save_figs in test mode')
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141 save_figs = 'only'
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142 if save_figs == 'only':
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143 self.save_only = True
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144 self.save_figs = True
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145 elif save_figs == 'yes':
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146 self.save_only = False
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147 self.save_figs = True
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148 elif save_figs == 'no':
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149 self.save_only = False
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150 self.save_figs = False
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151 else:
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152 raise ValueError(f'Invalid parameter save_figs ({save_figs})')
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153 if self.save_only:
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154 self.block = False
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155 else:
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156 self.block = True
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157 if self.num_core == -1:
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158 self.num_core = cpu_count()
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159 if not is_int(self.num_core, gt=0, log=False):
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160 raise ValueError(f'Invalid parameter num_core ({num_core})')
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161 if self.num_core > cpu_count():
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162 logger.warning(f'num_core = {self.num_core} is larger than the number of available '
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163 f'processors and reduced to {cpu_count()}')
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164 self.num_core= cpu_count()
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165
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166 def read(self, filename):
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167 logger.info(f'looking for {filename}')
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168 if self.galaxy_flag:
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169 try:
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170 with open(filename, 'r') as f:
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171 config = safe_load(f)
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172 return(config)
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173 except:
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174 try:
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175 with NXFile(filename, mode='r') as nxfile:
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176 nxroot = nxfile.readfile()
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177 return(nxroot)
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178 except:
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179 raise ValueError(f'Unable to open ({filename})')
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180 else:
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181 extension = os_path.splitext(filename)[1]
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182 if extension == '.yml' or extension == '.yaml':
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183 with open(filename, 'r') as f:
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184 config = safe_load(f)
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185 # if len(config) > 1:
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186 # raise ValueError(f'Multiple root entries in {filename} not yet implemented')
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187 # if len(list(config.values())[0]) > 1:
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188 # raise ValueError(f'Multiple sample maps in {filename} not yet implemented')
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189 return(config)
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190 elif extension == '.nxs':
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191 with NXFile(filename, mode='r') as nxfile:
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192 nxroot = nxfile.readfile()
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193 return(nxroot)
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194 else:
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195 raise ValueError(f'Invalid filename extension ({extension})')
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196
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197 def write(self, data, filename):
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198 extension = os_path.splitext(filename)[1]
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199 if extension == '.yml' or extension == '.yaml':
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200 with open(filename, 'w') as f:
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201 safe_dump(data, f)
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202 elif extension == '.nxs' or extension == '.nex':
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203 data.save(filename, mode='w')
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204 elif extension == '.nc':
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205 data.to_netcdf(os_path=filename)
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206 else:
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207 raise ValueError(f'Invalid filename extension ({extension})')
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208
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209 def gen_reduced_data(self, data, img_x_bounds=None):
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210 """Generate the reduced tomography images.
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211 """
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212 logger.info('Generate the reduced tomography images')
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213
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214 # Create plot galaxy path directory if needed
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215 if self.galaxy_flag and not os_path.exists('tomo_reduce_plots'):
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216 mkdir('tomo_reduce_plots')
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217
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218 if isinstance(data, dict):
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219 # Create Nexus format object from input dictionary
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220 wf = TomoWorkflow(**data)
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221 if len(wf.sample_maps) > 1:
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222 raise ValueError(f'Multiple sample maps not yet implemented')
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223 # print(f'\nwf:\n{wf}\n')
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224 nxroot = NXroot()
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225 t0 = time()
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226 for sample_map in wf.sample_maps:
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227 logger.info(f'Start constructing the {sample_map.title} map.')
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228 import_scanparser(sample_map.station)
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229 sample_map.construct_nxentry(nxroot, include_raw_data=False)
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230 logger.info(f'Constructed all sample maps in {time()-t0:.2f} seconds.')
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231 nxentry = nxroot[nxroot.attrs['default']]
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232 # Get test mode configuration info
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233 if self.test_mode:
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234 self.test_config = data['sample_maps'][0]['test_mode']
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235 elif isinstance(data, NXroot):
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236 nxentry = data[data.attrs['default']]
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237 else:
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238 raise ValueError(f'Invalid parameter data ({data})')
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239
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240 # Create an NXprocess to store data reduction (meta)data
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241 reduced_data = NXprocess()
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242
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243 # Generate dark field
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244 if 'dark_field' in nxentry['spec_scans']:
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245 reduced_data = self._gen_dark(nxentry, reduced_data)
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246
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247 # Generate bright field
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248 reduced_data = self._gen_bright(nxentry, reduced_data)
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249
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250 # Set vertical detector bounds for image stack
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251 img_x_bounds = self._set_detector_bounds(nxentry, reduced_data, img_x_bounds=img_x_bounds)
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252 logger.info(f'img_x_bounds = {img_x_bounds}')
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253 reduced_data['img_x_bounds'] = img_x_bounds
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254
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255 # Set zoom and/or theta skip to reduce memory the requirement
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256 zoom_perc, num_theta_skip = self._set_zoom_or_skip()
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257 if zoom_perc is not None:
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258 reduced_data.attrs['zoom_perc'] = zoom_perc
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259 if num_theta_skip is not None:
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260 reduced_data.attrs['num_theta_skip'] = num_theta_skip
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261
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262 # Generate reduced tomography fields
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263 reduced_data = self._gen_tomo(nxentry, reduced_data)
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264
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265 # Create a copy of the input Nexus object and remove raw and any existing reduced data
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266 if isinstance(data, NXroot):
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267 exclude_items = [f'{nxentry._name}/reduced_data/data',
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268 f'{nxentry._name}/instrument/detector/data',
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269 f'{nxentry._name}/instrument/detector/image_key',
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270 f'{nxentry._name}/instrument/detector/sequence_number',
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271 f'{nxentry._name}/sample/rotation_angle',
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272 f'{nxentry._name}/sample/x_translation',
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273 f'{nxentry._name}/sample/z_translation',
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274 f'{nxentry._name}/data/data',
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275 f'{nxentry._name}/data/image_key',
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276 f'{nxentry._name}/data/rotation_angle',
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277 f'{nxentry._name}/data/x_translation',
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278 f'{nxentry._name}/data/z_translation']
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279 nxroot = nxcopy(data, exclude_nxpaths=exclude_items)
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280 nxentry = nxroot[nxroot.attrs['default']]
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281
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282 # Add the reduced data NXprocess
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283 nxentry.reduced_data = reduced_data
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284
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285 if 'data' not in nxentry:
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286 nxentry.data = NXdata()
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287 nxentry.attrs['default'] = 'data'
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288 nxentry.data.makelink(nxentry.reduced_data.data.tomo_fields, name='reduced_data')
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289 nxentry.data.makelink(nxentry.reduced_data.rotation_angle, name='rotation_angle')
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290 nxentry.data.attrs['signal'] = 'reduced_data'
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291
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292 return(nxroot)
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293
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294 def find_centers(self, nxroot, center_rows=None, center_stack_index=None):
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295 """Find the calibrated center axis info
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296 """
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297 logger.info('Find the calibrated center axis info')
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298
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299 if not isinstance(nxroot, NXroot):
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300 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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301 nxentry = nxroot[nxroot.attrs['default']]
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302 if not isinstance(nxentry, NXentry):
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303 raise ValueError(f'Invalid nxentry ({nxentry})')
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304 if self.galaxy_flag:
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305 if center_rows is not None:
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306 center_rows = tuple(center_rows)
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307 if not is_int_pair(center_rows):
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308 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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309 elif center_rows is not None:
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310 logger.warning(f'Ignoring parameter center_rows ({center_rows})')
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311 center_rows = None
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312 if self.galaxy_flag:
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313 if center_stack_index is not None and not is_int(center_stack_index, ge=0):
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314 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
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315 elif center_stack_index is not None:
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316 logger.warning(f'Ignoring parameter center_stack_index ({center_stack_index})')
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317 center_stack_index = None
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318
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319 # Create plot galaxy path directory and path if needed
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320 if self.galaxy_flag:
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321 if not os_path.exists('tomo_find_centers_plots'):
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322 mkdir('tomo_find_centers_plots')
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323 path = 'tomo_find_centers_plots'
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324 else:
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325 path = self.output_folder
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326
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327 # Check if reduced data is available
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328 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
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329 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
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330
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331 # Select the image stack to calibrate the center axis
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332 # reduced data axes order: stack,theta,row,column
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333 # Note: Nexus cannot follow a link if the data it points to is too big,
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334 # so get the data from the actual place, not from nxentry.data
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335 tomo_fields_shape = nxentry.reduced_data.data.tomo_fields.shape
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336 if len(tomo_fields_shape) != 4 or any(True for dim in tomo_fields_shape if not dim):
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337 raise KeyError('Unable to load the required reduced tomography stack')
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338 num_tomo_stacks = tomo_fields_shape[0]
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339 if num_tomo_stacks == 1:
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340 center_stack_index = 0
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341 default = 'n'
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342 else:
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343 if self.test_mode:
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344 center_stack_index = self.test_config['center_stack_index']-1 # make offset 0
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345 elif self.galaxy_flag:
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346 if center_stack_index is None:
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347 center_stack_index = int(num_tomo_stacks/2)
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348 if center_stack_index >= num_tomo_stacks:
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349 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
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350 else:
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351 center_stack_index = input_int('\nEnter tomography stack index to calibrate the '
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352 'center axis', ge=1, le=num_tomo_stacks, default=int(1+num_tomo_stacks/2))
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353 center_stack_index -= 1
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354 default = 'y'
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355
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356 # Get thetas (in degrees)
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357 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
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358
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359 # Get effective pixel_size
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360 if 'zoom_perc' in nxentry.reduced_data:
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361 eff_pixel_size = 100.*(nxentry.instrument.detector.x_pixel_size/
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362 nxentry.reduced_data.attrs['zoom_perc'])
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363 else:
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364 eff_pixel_size = nxentry.instrument.detector.x_pixel_size
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365
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366 # Get cross sectional diameter
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367 cross_sectional_dim = tomo_fields_shape[3]*eff_pixel_size
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368 logger.debug(f'cross_sectional_dim = {cross_sectional_dim}')
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369
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370 # Determine center offset at sample row boundaries
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371 logger.info('Determine center offset at sample row boundaries')
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372
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373 # Lower row center
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374 if self.test_mode:
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375 lower_row = self.test_config['lower_row']
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376 elif self.galaxy_flag:
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377 if center_rows is None or center_rows[0] == -1:
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378 lower_row = 0
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379 else:
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380 lower_row = min(center_rows)
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381 if not 0 <= lower_row < tomo_fields_shape[2]-1:
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382 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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383 else:
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384 lower_row = select_one_image_bound(
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385 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, bound=0,
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386 title=f'theta={round(thetas[0], 2)+0}',
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387 bound_name='row index to find lower center', default=default, raise_error=True)
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388 logger.debug('Finding center...')
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389 t0 = time()
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390 lower_center_offset = self._find_center_one_plane(
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391 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:]),
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392 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:],
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393 lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
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394 num_core=self.num_core)
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395 logger.debug(f'... done in {time()-t0:.2f} seconds')
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396 logger.debug(f'lower_row = {lower_row:.2f}')
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397 logger.debug(f'lower_center_offset = {lower_center_offset:.2f}')
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398
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399 # Upper row center
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400 if self.test_mode:
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401 upper_row = self.test_config['upper_row']
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402 elif self.galaxy_flag:
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403 if center_rows is None or center_rows[1] == -1:
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404 upper_row = tomo_fields_shape[2]-1
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405 else:
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406 upper_row = max(center_rows)
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407 if not lower_row < upper_row < tomo_fields_shape[2]:
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408 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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409 else:
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410 upper_row = select_one_image_bound(
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411 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0,
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412 bound=tomo_fields_shape[2]-1, title=f'theta={round(thetas[0], 2)+0}',
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413 bound_name='row index to find upper center', default=default, raise_error=True)
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414 logger.debug('Finding center...')
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415 t0 = time()
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416 upper_center_offset = self._find_center_one_plane(
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417 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:]),
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418 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:],
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419 upper_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
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420 num_core=self.num_core)
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421 logger.debug(f'... done in {time()-t0:.2f} seconds')
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422 logger.debug(f'upper_row = {upper_row:.2f}')
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423 logger.debug(f'upper_center_offset = {upper_center_offset:.2f}')
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424
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425 center_config = {'lower_row': lower_row, 'lower_center_offset': lower_center_offset,
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426 'upper_row': upper_row, 'upper_center_offset': upper_center_offset}
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427 if num_tomo_stacks > 1:
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428 center_config['center_stack_index'] = center_stack_index+1 # save as offset 1
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429
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430 # Save test data to file
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431 if self.test_mode:
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432 with open(f'{self.output_folder}/center_config.yaml', 'w') as f:
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433 safe_dump(center_config, f)
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434
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435 return(center_config)
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436
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437 def reconstruct_data(self, nxroot, center_info, x_bounds=None, y_bounds=None):
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438 """Reconstruct the tomography data.
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439 """
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440 logger.info('Reconstruct the tomography data')
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441
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442 if not isinstance(nxroot, NXroot):
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443 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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444 nxentry = nxroot[nxroot.attrs['default']]
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445 if not isinstance(nxentry, NXentry):
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446 raise ValueError(f'Invalid nxentry ({nxentry})')
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447 if not isinstance(center_info, dict):
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448 raise ValueError(f'Invalid parameter center_info ({center_info})')
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449
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450 # Create plot galaxy path directory and path if needed
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451 if self.galaxy_flag:
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452 if not os_path.exists('tomo_reconstruct_plots'):
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453 mkdir('tomo_reconstruct_plots')
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454 path = 'tomo_reconstruct_plots'
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455 else:
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456 path = self.output_folder
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457
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458 # Check if reduced data is available
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459 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
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460 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
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461
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462 # Create an NXprocess to store image reconstruction (meta)data
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463 nxprocess = NXprocess()
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464
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465 # Get rotation axis rows and centers
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466 lower_row = center_info.get('lower_row')
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467 lower_center_offset = center_info.get('lower_center_offset')
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468 upper_row = center_info.get('upper_row')
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469 upper_center_offset = center_info.get('upper_center_offset')
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470 if (lower_row is None or lower_center_offset is None or upper_row is None or
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471 upper_center_offset is None):
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472 raise KeyError(f'Unable to find valid calibrated center axis info in {center_info}.')
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473 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
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474
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475 # Get thetas (in degrees)
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476 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
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477
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478 # Reconstruct tomography data
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479 # reduced data axes order: stack,theta,row,column
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480 # reconstructed data order in each stack: row/z,x,y
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481 # Note: Nexus cannot follow a link if the data it points to is too big,
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482 # so get the data from the actual place, not from nxentry.data
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483 if 'zoom_perc' in nxentry.reduced_data:
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484 res_title = f'{nxentry.reduced_data.attrs["zoom_perc"]}p'
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diff changeset
485 else:
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486 res_title = 'fullres'
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487 load_error = False
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488 num_tomo_stacks = nxentry.reduced_data.data.tomo_fields.shape[0]
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489 tomo_recon_stacks = num_tomo_stacks*[np.array([])]
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490 for i in range(num_tomo_stacks):
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491 # Convert reduced data stack from theta,row,column to row,theta,column
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492 logger.debug(f'Reading reduced data stack {i+1}...')
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diff changeset
493 t0 = time()
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diff changeset
494 tomo_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[i])
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495 logger.debug(f'... done in {time()-t0:.2f} seconds')
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496 if len(tomo_stack.shape) != 3 or any(True for dim in tomo_stack.shape if not dim):
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497 raise ValueError(f'Unable to load tomography stack {i+1} for reconstruction')
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498 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
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499 assert(len(thetas) == tomo_stack.shape[1])
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500 assert(0 <= lower_row < upper_row < tomo_stack.shape[0])
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501 center_offsets = [lower_center_offset-lower_row*center_slope,
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502 upper_center_offset+(tomo_stack.shape[0]-1-upper_row)*center_slope]
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503 t0 = time()
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504 logger.debug(f'Running _reconstruct_one_tomo_stack on {self.num_core} cores ...')
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505 tomo_recon_stack = self._reconstruct_one_tomo_stack(tomo_stack, thetas,
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506 center_offsets=center_offsets, num_core=self.num_core, algorithm='gridrec')
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507 logger.debug(f'... done in {time()-t0:.2f} seconds')
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508 logger.info(f'Reconstruction of stack {i+1} took {time()-t0:.2f} seconds')
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509
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510 # Combine stacks
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511 tomo_recon_stacks[i] = tomo_recon_stack
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512
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513 # Resize the reconstructed tomography data
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514 # reconstructed data order in each stack: row/z,x,y
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515 if self.test_mode:
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516 x_bounds = self.test_config.get('x_bounds')
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517 y_bounds = self.test_config.get('y_bounds')
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518 z_bounds = None
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519 elif self.galaxy_flag:
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520 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
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diff changeset
521 lt=tomo_recon_stacks[0].shape[1]):
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522 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
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diff changeset
523 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
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diff changeset
524 lt=tomo_recon_stacks[0].shape[1]):
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525 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
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diff changeset
526 z_bounds = None
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diff changeset
527 else:
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diff changeset
528 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks)
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diff changeset
529 if x_bounds is None:
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diff changeset
530 x_range = (0, tomo_recon_stacks[0].shape[1])
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diff changeset
531 x_slice = int(x_range[1]/2)
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diff changeset
532 else:
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diff changeset
533 x_range = (min(x_bounds), max(x_bounds))
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diff changeset
534 x_slice = int((x_bounds[0]+x_bounds[1])/2)
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diff changeset
535 if y_bounds is None:
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diff changeset
536 y_range = (0, tomo_recon_stacks[0].shape[2])
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diff changeset
537 y_slice = int(y_range[1]/2)
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diff changeset
538 else:
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diff changeset
539 y_range = (min(y_bounds), max(y_bounds))
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diff changeset
540 y_slice = int((y_bounds[0]+y_bounds[1])/2)
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parents:
diff changeset
541 if z_bounds is None:
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diff changeset
542 z_range = (0, tomo_recon_stacks[0].shape[0])
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diff changeset
543 z_slice = int(z_range[1]/2)
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diff changeset
544 else:
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diff changeset
545 z_range = (min(z_bounds), max(z_bounds))
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diff changeset
546 z_slice = int((z_bounds[0]+z_bounds[1])/2)
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parents:
diff changeset
547
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diff changeset
548 # Plot a few reconstructed image slices
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diff changeset
549 if num_tomo_stacks == 1:
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diff changeset
550 basetitle = 'recon'
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diff changeset
551 else:
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diff changeset
552 basetitle = f'recon stack {i+1}'
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diff changeset
553 for i, stack in enumerate(tomo_recon_stacks):
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diff changeset
554 title = f'{basetitle} {res_title} xslice{x_slice}'
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parents:
diff changeset
555 quick_imshow(stack[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
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parents:
diff changeset
556 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
557 block=self.block)
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parents:
diff changeset
558 title = f'{basetitle} {res_title} yslice{y_slice}'
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diff changeset
559 quick_imshow(stack[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
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diff changeset
560 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
561 block=self.block)
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562 title = f'{basetitle} {res_title} zslice{z_slice}'
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diff changeset
563 quick_imshow(stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],
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diff changeset
564 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
565 block=self.block)
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diff changeset
566
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diff changeset
567 # Save test data to file
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diff changeset
568 # reconstructed data order in each stack: row/z,x,y
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diff changeset
569 if self.test_mode:
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diff changeset
570 for i, stack in enumerate(tomo_recon_stacks):
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571 np.savetxt(f'{self.output_folder}/recon_stack_{i+1}.txt',
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572 stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
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diff changeset
573
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diff changeset
574 # Add image reconstruction to reconstructed data NXprocess
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575 # reconstructed data order in each stack: row/z,x,y
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576 nxprocess.data = NXdata()
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577 nxprocess.attrs['default'] = 'data'
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578 for k, v in center_info.items():
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579 nxprocess[k] = v
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580 if x_bounds is not None:
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581 nxprocess.x_bounds = x_bounds
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582 if y_bounds is not None:
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583 nxprocess.y_bounds = y_bounds
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584 if z_bounds is not None:
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585 nxprocess.z_bounds = z_bounds
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586 nxprocess.data['reconstructed_data'] = np.asarray([stack[z_range[0]:z_range[1],
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587 x_range[0]:x_range[1],y_range[0]:y_range[1]] for stack in tomo_recon_stacks])
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588 nxprocess.data.attrs['signal'] = 'reconstructed_data'
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589
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diff changeset
590 # Create a copy of the input Nexus object and remove reduced data
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591 exclude_items = [f'{nxentry._name}/reduced_data/data', f'{nxentry._name}/data/reduced_data']
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592 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
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593
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diff changeset
594 # Add the reconstructed data NXprocess to the new Nexus object
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diff changeset
595 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
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596 nxentry_copy.reconstructed_data = nxprocess
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597 if 'data' not in nxentry_copy:
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diff changeset
598 nxentry_copy.data = NXdata()
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diff changeset
599 nxentry_copy.attrs['default'] = 'data'
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diff changeset
600 nxentry_copy.data.makelink(nxprocess.data.reconstructed_data, name='reconstructed_data')
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601 nxentry_copy.data.attrs['signal'] = 'reconstructed_data'
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602
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diff changeset
603 return(nxroot_copy)
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diff changeset
604
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605 def combine_data(self, nxroot, x_bounds=None, y_bounds=None):
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606 """Combine the reconstructed tomography stacks.
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607 """
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608 logger.info('Combine the reconstructed tomography stacks')
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609
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610 if not isinstance(nxroot, NXroot):
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611 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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612 nxentry = nxroot[nxroot.attrs['default']]
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diff changeset
613 if not isinstance(nxentry, NXentry):
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diff changeset
614 raise ValueError(f'Invalid nxentry ({nxentry})')
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diff changeset
615
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diff changeset
616 # Create plot galaxy path directory and path if needed
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617 if self.galaxy_flag:
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618 if not os_path.exists('tomo_combine_plots'):
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619 mkdir('tomo_combine_plots')
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620 path = 'tomo_combine_plots'
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diff changeset
621 else:
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diff changeset
622 path = self.output_folder
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diff changeset
623
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diff changeset
624 # Check if reconstructed image data is available
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diff changeset
625 if ('reconstructed_data' not in nxentry or 'reconstructed_data' not in nxentry.data):
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626 raise KeyError(f'Unable to find valid reconstructed image data in {nxentry}.')
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diff changeset
627
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diff changeset
628 # Create an NXprocess to store combined image reconstruction (meta)data
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diff changeset
629 nxprocess = NXprocess()
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diff changeset
630
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diff changeset
631 # Get the reconstructed data
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diff changeset
632 # reconstructed data order: stack,row(z),x,y
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633 # Note: Nexus cannot follow a link if the data it points to is too big,
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diff changeset
634 # so get the data from the actual place, not from nxentry.data
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diff changeset
635 num_tomo_stacks = nxentry.reconstructed_data.data.reconstructed_data.shape[0]
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636 if num_tomo_stacks == 1:
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diff changeset
637 logger.info('Only one stack available: leaving combine_data')
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diff changeset
638 return(None)
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diff changeset
639
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diff changeset
640 # Combine the reconstructed stacks
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diff changeset
641 # (load one stack at a time to reduce risk of hitting Nexus data access limit)
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diff changeset
642 t0 = time()
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diff changeset
643 logger.debug(f'Combining the reconstructed stacks ...')
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diff changeset
644 tomo_recon_combined = np.asarray(nxentry.reconstructed_data.data.reconstructed_data[0])
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diff changeset
645 if num_tomo_stacks > 2:
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diff changeset
646 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
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diff changeset
647 [nxentry.reconstructed_data.data.reconstructed_data[i]
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diff changeset
648 for i in range(1, num_tomo_stacks-1)])
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649 if num_tomo_stacks > 1:
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diff changeset
650 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
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diff changeset
651 [nxentry.reconstructed_data.data.reconstructed_data[num_tomo_stacks-1]])
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diff changeset
652 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
653 logger.info(f'Combining the reconstructed stacks took {time()-t0:.2f} seconds')
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diff changeset
654
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diff changeset
655 # Resize the combined tomography data stacks
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diff changeset
656 # combined data order: row/z,x,y
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657 if self.test_mode:
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658 x_bounds = None
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diff changeset
659 y_bounds = None
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660 z_bounds = self.test_config.get('z_bounds')
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661 elif self.galaxy_flag:
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662 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
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diff changeset
663 lt=tomo_recon_stacks[0].shape[1]):
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parents:
diff changeset
664 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
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diff changeset
665 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
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diff changeset
666 lt=tomo_recon_stacks[0].shape[1]):
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diff changeset
667 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
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diff changeset
668 z_bounds = None
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diff changeset
669 else:
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670 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_combined,
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diff changeset
671 z_only=True)
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parents:
diff changeset
672 if x_bounds is None:
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parents:
diff changeset
673 x_range = (0, tomo_recon_combined.shape[1])
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parents:
diff changeset
674 x_slice = int(x_range[1]/2)
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parents:
diff changeset
675 else:
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parents:
diff changeset
676 x_range = x_bounds
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diff changeset
677 x_slice = int((x_bounds[0]+x_bounds[1])/2)
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parents:
diff changeset
678 if y_bounds is None:
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diff changeset
679 y_range = (0, tomo_recon_combined.shape[2])
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diff changeset
680 y_slice = int(y_range[1]/2)
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parents:
diff changeset
681 else:
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diff changeset
682 y_range = y_bounds
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diff changeset
683 y_slice = int((y_bounds[0]+y_bounds[1])/2)
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diff changeset
684 if z_bounds is None:
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diff changeset
685 z_range = (0, tomo_recon_combined.shape[0])
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diff changeset
686 z_slice = int(z_range[1]/2)
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diff changeset
687 else:
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diff changeset
688 z_range = z_bounds
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689 z_slice = int((z_bounds[0]+z_bounds[1])/2)
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diff changeset
690
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parents:
diff changeset
691 # Plot a few combined image slices
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692 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
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diff changeset
693 title=f'recon combined xslice{x_slice}', path=path,
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diff changeset
694 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
695 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
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parents:
diff changeset
696 title=f'recon combined yslice{y_slice}', path=path,
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parents:
diff changeset
697 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
698 quick_imshow(tomo_recon_combined[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],
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parents:
diff changeset
699 title=f'recon combined zslice{z_slice}', path=path,
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diff changeset
700 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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parents:
diff changeset
701
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parents:
diff changeset
702 # Save test data to file
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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diff changeset
703 # combined data order: row/z,x,y
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parents:
diff changeset
704 if self.test_mode:
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parents:
diff changeset
705 np.savetxt(f'{self.output_folder}/recon_combined.txt', tomo_recon_combined[
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parents:
diff changeset
706 z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
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parents:
diff changeset
707
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parents:
diff changeset
708 # Add image reconstruction to reconstructed data NXprocess
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parents:
diff changeset
709 # combined data order: row/z,x,y
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parents:
diff changeset
710 nxprocess.data = NXdata()
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diff changeset
711 nxprocess.attrs['default'] = 'data'
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parents:
diff changeset
712 if x_bounds is not None:
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diff changeset
713 nxprocess.x_bounds = x_bounds
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parents:
diff changeset
714 if y_bounds is not None:
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parents:
diff changeset
715 nxprocess.y_bounds = y_bounds
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parents:
diff changeset
716 if z_bounds is not None:
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parents:
diff changeset
717 nxprocess.z_bounds = z_bounds
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parents:
diff changeset
718 nxprocess.data['combined_data'] = tomo_recon_combined
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parents:
diff changeset
719 nxprocess.data.attrs['signal'] = 'combined_data'
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parents:
diff changeset
720
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parents:
diff changeset
721 # Create a copy of the input Nexus object and remove reconstructed data
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parents:
diff changeset
722 exclude_items = [f'{nxentry._name}/reconstructed_data/data',
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diff changeset
723 f'{nxentry._name}/data/reconstructed_data']
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parents:
diff changeset
724 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
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parents:
diff changeset
725
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parents:
diff changeset
726 # Add the combined data NXprocess to the new Nexus object
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parents:
diff changeset
727 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
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parents:
diff changeset
728 nxentry_copy.combined_data = nxprocess
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parents:
diff changeset
729 if 'data' not in nxentry_copy:
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parents:
diff changeset
730 nxentry_copy.data = NXdata()
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parents:
diff changeset
731 nxentry_copy.attrs['default'] = 'data'
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parents:
diff changeset
732 nxentry_copy.data.makelink(nxprocess.data.combined_data, name='combined_data')
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parents:
diff changeset
733 nxentry_copy.data.attrs['signal'] = 'combined_data'
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parents:
diff changeset
734
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parents:
diff changeset
735 return(nxroot_copy)
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parents:
diff changeset
736
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parents:
diff changeset
737 def _gen_dark(self, nxentry, reduced_data):
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parents:
diff changeset
738 """Generate dark field.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
739 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
740 # Get the dark field images
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
741 image_key = nxentry.instrument.detector.get('image_key', None)
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parents:
diff changeset
742 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
743 field_indices = [index for index, key in enumerate(image_key) if key == 2]
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parents:
diff changeset
744 tdf_stack = nxentry.instrument.detector.data[field_indices,:,:]
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parents:
diff changeset
745 # RV the default NXtomo form does not accomodate bright or dark field stacks
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parents:
diff changeset
746 else:
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parents:
diff changeset
747 dark_field_scans = nxentry.spec_scans.dark_field
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parents:
diff changeset
748 dark_field = FlatField.construct_from_nxcollection(dark_field_scans)
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parents:
diff changeset
749 prefix = str(nxentry.instrument.detector.local_name)
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parents:
diff changeset
750 tdf_stack = dark_field.get_detector_data(prefix)
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parents:
diff changeset
751 if isinstance(tdf_stack, list):
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parents:
diff changeset
752 assert(len(tdf_stack) == 1) # TODO
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parents:
diff changeset
753 tdf_stack = tdf_stack[0]
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parents:
diff changeset
754
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parents:
diff changeset
755 # Take median
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parents:
diff changeset
756 if tdf_stack.ndim == 2:
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diff changeset
757 tdf = tdf_stack
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parents:
diff changeset
758 elif tdf_stack.ndim == 3:
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parents:
diff changeset
759 tdf = np.median(tdf_stack, axis=0)
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parents:
diff changeset
760 del tdf_stack
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parents:
diff changeset
761 else:
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diff changeset
762 raise ValueError(f'Invalid tdf_stack shape ({tdf_stack.shape})')
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parents:
diff changeset
763
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parents:
diff changeset
764 # Remove dark field intensities above the cutoff
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parents:
diff changeset
765 #RV tdf_cutoff = None
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parents:
diff changeset
766 tdf_cutoff = tdf.min()+2*(np.median(tdf)-tdf.min())
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parents:
diff changeset
767 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
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parents:
diff changeset
768 if tdf_cutoff is not None:
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parents:
diff changeset
769 if not is_num(tdf_cutoff, ge=0):
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diff changeset
770 logger.warning(f'Ignoring illegal value of tdf_cutoff {tdf_cutoff}')
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parents:
diff changeset
771 else:
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diff changeset
772 tdf[tdf > tdf_cutoff] = np.nan
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parents:
diff changeset
773 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
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parents:
diff changeset
774
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parents:
diff changeset
775 # Remove nans
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parents:
diff changeset
776 tdf_mean = np.nanmean(tdf)
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diff changeset
777 logger.debug(f'tdf_mean = {tdf_mean}')
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parents:
diff changeset
778 np.nan_to_num(tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
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parents:
diff changeset
779
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parents:
diff changeset
780 # Plot dark field
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781 if self.galaxy_flag:
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782 quick_imshow(tdf, title='dark field', path='tomo_reduce_plots', save_fig=self.save_figs,
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diff changeset
783 save_only=self.save_only)
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parents:
diff changeset
784 elif not self.test_mode:
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diff changeset
785 quick_imshow(tdf, title='dark field', path=self.output_folder, save_fig=self.save_figs,
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parents:
diff changeset
786 save_only=self.save_only)
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parents:
diff changeset
787 clear_imshow('dark field')
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parents:
diff changeset
788 # quick_imshow(tdf, title='dark field', block=True)
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parents:
diff changeset
789
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parents:
diff changeset
790 # Add dark field to reduced data NXprocess
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diff changeset
791 reduced_data.data = NXdata()
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diff changeset
792 reduced_data.data['dark_field'] = tdf
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parents:
diff changeset
793
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parents:
diff changeset
794 return(reduced_data)
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parents:
diff changeset
795
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parents:
diff changeset
796 def _gen_bright(self, nxentry, reduced_data):
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diff changeset
797 """Generate bright field.
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parents:
diff changeset
798 """
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parents:
diff changeset
799 # Get the bright field images
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parents:
diff changeset
800 image_key = nxentry.instrument.detector.get('image_key', None)
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parents:
diff changeset
801 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
802 field_indices = [index for index, key in enumerate(image_key) if key == 1]
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parents:
diff changeset
803 tbf_stack = nxentry.instrument.detector.data[field_indices,:,:]
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parents:
diff changeset
804 # RV the default NXtomo form does not accomodate bright or dark field stacks
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diff changeset
805 else:
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parents:
diff changeset
806 bright_field_scans = nxentry.spec_scans.bright_field
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diff changeset
807 bright_field = FlatField.construct_from_nxcollection(bright_field_scans)
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diff changeset
808 prefix = str(nxentry.instrument.detector.local_name)
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parents:
diff changeset
809 tbf_stack = bright_field.get_detector_data(prefix)
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diff changeset
810 if isinstance(tbf_stack, list):
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diff changeset
811 assert(len(tbf_stack) == 1) # TODO
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diff changeset
812 tbf_stack = tbf_stack[0]
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parents:
diff changeset
813
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parents:
diff changeset
814 # Take median if more than one image
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parents:
diff changeset
815 """Median or mean: It may be best to try the median because of some image
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parents:
diff changeset
816 artifacts that arise due to crinkles in the upstream kapton tape windows
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
817 causing some phase contrast images to appear on the detector.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
818 One thing that also may be useful in a future implementation is to do a
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parents:
diff changeset
819 brightfield adjustment on EACH frame of the tomo based on a ROI in the
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parents:
diff changeset
820 corner of the frame where there is no sample but there is the direct X-ray
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parents:
diff changeset
821 beam because there is frame to frame fluctuations from the incoming beam.
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parents:
diff changeset
822 We don’t typically account for them but potentially could.
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parents:
diff changeset
823 """
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parents:
diff changeset
824 if tbf_stack.ndim == 2:
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parents:
diff changeset
825 tbf = tbf_stack
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parents:
diff changeset
826 elif tbf_stack.ndim == 3:
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parents:
diff changeset
827 tbf = np.median(tbf_stack, axis=0)
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parents:
diff changeset
828 del tbf_stack
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parents:
diff changeset
829 else:
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parents:
diff changeset
830 raise ValueError(f'Invalid tbf_stack shape ({tbf_stacks.shape})')
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parents:
diff changeset
831
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parents:
diff changeset
832 # Subtract dark field
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parents:
diff changeset
833 if 'data' in reduced_data and 'dark_field' in reduced_data.data:
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parents:
diff changeset
834 tbf -= reduced_data.data.dark_field
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parents:
diff changeset
835 else:
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parents:
diff changeset
836 logger.warning('Dark field unavailable')
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parents:
diff changeset
837
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parents:
diff changeset
838 # Set any non-positive values to one
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
839 # (avoid negative bright field values for spikes in dark field)
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parents:
diff changeset
840 tbf[tbf < 1] = 1
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parents:
diff changeset
841
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
842 # Plot bright field
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
843 if self.galaxy_flag:
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parents:
diff changeset
844 quick_imshow(tbf, title='bright field', path='tomo_reduce_plots',
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parents:
diff changeset
845 save_fig=self.save_figs, save_only=self.save_only)
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parents:
diff changeset
846 elif not self.test_mode:
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parents:
diff changeset
847 quick_imshow(tbf, title='bright field', path=self.output_folder,
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parents:
diff changeset
848 save_fig=self.save_figs, save_only=self.save_only)
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parents:
diff changeset
849 clear_imshow('bright field')
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parents:
diff changeset
850 # quick_imshow(tbf, title='bright field', block=True)
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parents:
diff changeset
851
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diff changeset
852 # Add bright field to reduced data NXprocess
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diff changeset
853 if 'data' not in reduced_data:
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diff changeset
854 reduced_data.data = NXdata()
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diff changeset
855 reduced_data.data['bright_field'] = tbf
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parents:
diff changeset
856
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
857 return(reduced_data)
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parents:
diff changeset
858
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859 def _set_detector_bounds(self, nxentry, reduced_data, img_x_bounds=None):
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diff changeset
860 """Set vertical detector bounds for each image stack.
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diff changeset
861 Right now the range is the same for each set in the image stack.
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diff changeset
862 """
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diff changeset
863 if self.test_mode:
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864 return(tuple(self.test_config['img_x_bounds']))
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parents:
diff changeset
865
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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diff changeset
866 # Get the first tomography image and the reference heights
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diff changeset
867 image_key = nxentry.instrument.detector.get('image_key', None)
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diff changeset
868 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
869 field_indices = [index for index, key in enumerate(image_key) if key == 0]
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diff changeset
870 first_image = np.asarray(nxentry.instrument.detector.data[field_indices[0],:,:])
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871 theta = float(nxentry.sample.rotation_angle[field_indices[0]])
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872 z_translation_all = nxentry.sample.z_translation[field_indices]
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873 vertical_shifts = sorted(list(set(z_translation_all)))
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874 num_tomo_stacks = len(vertical_shifts)
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875 else:
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diff changeset
876 tomo_field_scans = nxentry.spec_scans.tomo_fields
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877 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
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parents:
diff changeset
878 vertical_shifts = tomo_fields.get_vertical_shifts()
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diff changeset
879 if not isinstance(vertical_shifts, list):
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parents:
diff changeset
880 vertical_shifts = [vertical_shifts]
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diff changeset
881 prefix = str(nxentry.instrument.detector.local_name)
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diff changeset
882 t0 = time()
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diff changeset
883 first_image = tomo_fields.get_detector_data(prefix, tomo_fields.scan_numbers[0], 0)
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parents:
diff changeset
884 logger.debug(f'Getting first image took {time()-t0:.2f} seconds')
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parents:
diff changeset
885 num_tomo_stacks = len(tomo_fields.scan_numbers)
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diff changeset
886 theta = tomo_fields.theta_range['start']
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parents:
diff changeset
887
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parents:
diff changeset
888 # Select image bounds
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parents:
diff changeset
889 title = f'tomography image at theta={round(theta, 2)+0}'
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parents:
diff changeset
890 if img_x_bounds is not None:
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parents:
diff changeset
891 if is_int_pair(img_x_bounds) and img_x_bounds[0] == -1 and img_x_bounds[1] == -1:
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parents:
diff changeset
892 img_x_bounds = None
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893 elif not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]):
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parents:
diff changeset
894 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
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parents:
diff changeset
895 if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):
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parents:
diff changeset
896 pixel_size = nxentry.instrument.detector.x_pixel_size
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parents:
diff changeset
897 # Try to get a fit from the bright field
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parents:
diff changeset
898 tbf = np.asarray(reduced_data.data.bright_field)
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parents:
diff changeset
899 tbf_shape = tbf.shape
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parents:
diff changeset
900 x_sum = np.sum(tbf, 1)
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parents:
diff changeset
901 x_sum_min = x_sum.min()
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parents:
diff changeset
902 x_sum_max = x_sum.max()
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parents:
diff changeset
903 fit = Fit.fit_data(x_sum, 'rectangle', x=np.array(range(len(x_sum))), form='atan',
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rv43
parents:
diff changeset
904 guess=True)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
905 parameters = fit.best_values
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parents:
diff changeset
906 x_low_fit = parameters.get('center1', None)
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parents:
diff changeset
907 x_upp_fit = parameters.get('center2', None)
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parents:
diff changeset
908 sig_low = parameters.get('sigma1', None)
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parents:
diff changeset
909 sig_upp = parameters.get('sigma2', None)
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parents:
diff changeset
910 have_fit = fit.success and x_low_fit is not None and x_upp_fit is not None and \
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parents:
diff changeset
911 sig_low is not None and sig_upp is not None and \
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parents:
diff changeset
912 0 <= x_low_fit < x_upp_fit <= x_sum.size and \
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parents:
diff changeset
913 (sig_low+sig_upp)/(x_upp_fit-x_low_fit) < 0.1
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parents:
diff changeset
914 if have_fit:
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parents:
diff changeset
915 # Set a 5% margin on each side
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
916 margin = 0.05*(x_upp_fit-x_low_fit)
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parents:
diff changeset
917 x_low_fit = max(0, x_low_fit-margin)
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parents:
diff changeset
918 x_upp_fit = min(tbf_shape[0], x_upp_fit+margin)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
919 if num_tomo_stacks == 1:
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rv43
parents:
diff changeset
920 if have_fit:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
921 # Set the default range to enclose the full fitted window
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
922 x_low = int(x_low_fit)
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rv43
parents:
diff changeset
923 x_upp = int(x_upp_fit)
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parents:
diff changeset
924 else:
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rv43
parents:
diff changeset
925 # Center a default range of 1 mm (RV: can we get this from the slits?)
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parents:
diff changeset
926 num_x_min = int((1.0-0.5*pixel_size)/pixel_size)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
927 x_low = int(0.5*(tbf_shape[0]-num_x_min))
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parents:
diff changeset
928 x_upp = x_low+num_x_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
929 else:
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parents:
diff changeset
930 # Get the default range from the reference heights
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
931 delta_z = vertical_shifts[1]-vertical_shifts[0]
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parents:
diff changeset
932 for i in range(2, num_tomo_stacks):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
933 delta_z = min(delta_z, vertical_shifts[i]-vertical_shifts[i-1])
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parents:
diff changeset
934 logger.debug(f'delta_z = {delta_z}')
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parents:
diff changeset
935 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)
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parents:
diff changeset
936 logger.debug(f'num_x_min = {num_x_min}')
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parents:
diff changeset
937 if num_x_min > tbf_shape[0]:
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parents:
diff changeset
938 logger.warning('Image bounds and pixel size prevent seamless stacking')
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parents:
diff changeset
939 if have_fit:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
940 # Center the default range relative to the fitted window
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
941 x_low = int(0.5*(x_low_fit+x_upp_fit-num_x_min))
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parents:
diff changeset
942 x_upp = x_low+num_x_min
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parents:
diff changeset
943 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
944 # Center the default range
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
945 x_low = int(0.5*(tbf_shape[0]-num_x_min))
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
946 x_upp = x_low+num_x_min
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
947 if self.galaxy_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
948 img_x_bounds = (x_low, x_upp)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
949 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
950 tmp = np.copy(tbf)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
951 tmp_max = tmp.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
952 tmp[x_low,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
953 tmp[x_upp-1,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
954 quick_imshow(tmp, title='bright field')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
955 tmp = np.copy(first_image)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
956 tmp_max = tmp.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
957 tmp[x_low,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
958 tmp[x_upp-1,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
959 quick_imshow(tmp, title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
960 del tmp
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
961 quick_plot((range(x_sum.size), x_sum),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
962 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
963 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
964 title='sum over theta and y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
965 print(f'lower bound = {x_low} (inclusive)')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
966 print(f'upper bound = {x_upp} (exclusive)]')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
967 accept = input_yesno('Accept these bounds (y/n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
968 clear_imshow('bright field')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
969 clear_imshow(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
970 clear_plot('sum over theta and y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
971 if accept:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
972 img_x_bounds = (x_low, x_upp)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
973 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
974 while True:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
975 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
976 legend='sum over theta and y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
977 if len(img_x_bounds) == 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
978 break
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
979 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
980 print(f'Choose a single connected data range')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
981 img_x_bounds = tuple(img_x_bounds[0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
982 if (num_tomo_stacks > 1 and img_x_bounds[1]-img_x_bounds[0]+1 <
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
983 int((delta_z-0.5*pixel_size)/pixel_size)):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
984 logger.warning('Image bounds and pixel size prevent seamless stacking')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
985 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
986 if num_tomo_stacks > 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
987 raise NotImplementedError('Selecting image bounds for multiple stacks on FMB')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
988 # For FMB: use the first tomography image to select range
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
989 # RV: revisit if they do tomography with multiple stacks
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
990 x_sum = np.sum(first_image, 1)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
991 x_sum_min = x_sum.min()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
992 x_sum_max = x_sum.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
993 if self.galaxy_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
994 if img_x_bounds is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
995 img_x_bounds = (0, first_image.shape[0])
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
996 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
997 quick_imshow(first_image, title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
998 print('Select vertical data reduction range from first tomography image')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
999 img_x_bounds = select_image_bounds(first_image, 0, title=title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1000 clear_imshow(title)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1001 if img_x_bounds is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1002 raise ValueError('Unable to select image bounds')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1003
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1004 # Plot results
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1005 if self.galaxy_flag:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1006 path = 'tomo_reduce_plots'
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1007 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1008 path = self.output_folder
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1009 x_low = img_x_bounds[0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1010 x_upp = img_x_bounds[1]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1011 tmp = np.copy(first_image)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1012 tmp_max = tmp.max()
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1013 tmp[x_low,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1014 tmp[x_upp-1,:] = tmp_max
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1015 quick_imshow(tmp, title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1016 block=self.block)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1017 del tmp
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1018 quick_plot((range(x_sum.size), x_sum),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1019 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1020 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1021 title='sum over theta and y', path=path, save_fig=self.save_figs,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1022 save_only=self.save_only, block=self.block)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1023
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1024 return(img_x_bounds)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1025
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1026 def _set_zoom_or_skip(self):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1027 """Set zoom and/or theta skip to reduce memory the requirement for the analysis.
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1028 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1029 # if input_yesno('\nDo you want to zoom in to reduce memory requirement (y/n)?', 'n'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1030 # zoom_perc = input_int(' Enter zoom percentage', ge=1, le=100)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1031 # else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1032 # zoom_perc = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1033 zoom_perc = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1034 # if input_yesno('Do you want to skip thetas to reduce memory requirement (y/n)?', 'n'):
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1035 # num_theta_skip = input_int(' Enter the number skip theta interval', ge=0,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1036 # lt=num_theta)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1037 # else:
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1038 # num_theta_skip = None
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1039 num_theta_skip = None
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1040 logger.debug(f'zoom_perc = {zoom_perc}')
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1041 logger.debug(f'num_theta_skip = {num_theta_skip}')
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1042
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1043 return(zoom_perc, num_theta_skip)
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1044
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1045 def _gen_tomo(self, nxentry, reduced_data):
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1046 """Generate tomography fields.
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1047 """
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1048 # Get full bright field
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1049 tbf = np.asarray(reduced_data.data.bright_field)
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1050 tbf_shape = tbf.shape
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1051
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1052 # Get image bounds
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1053 img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0])))
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1054 img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1])))
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1055
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1056 # Get resized dark field
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1057 # if 'dark_field' in data:
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1058 # tbf = np.asarray(reduced_data.data.dark_field[
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1059 # img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
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1060 # else:
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1061 # logger.warning('Dark field unavailable')
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1062 # tdf = None
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1063 tdf = None
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1064
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1065 # Resize bright field
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1066 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
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1067 tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
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1068
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1069 # Get the tomography images
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1070 image_key = nxentry.instrument.detector.get('image_key', None)
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1071 if image_key and 'data' in nxentry.instrument.detector:
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1072 field_indices_all = [index for index, key in enumerate(image_key) if key == 0]
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1073 z_translation_all = nxentry.sample.z_translation[field_indices_all]
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1074 z_translation_levels = sorted(list(set(z_translation_all)))
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1075 num_tomo_stacks = len(z_translation_levels)
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1076 tomo_stacks = num_tomo_stacks*[np.array([])]
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1077 horizontal_shifts = []
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1078 vertical_shifts = []
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1079 thetas = None
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1080 tomo_stacks = []
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1081 for i, z_translation in enumerate(z_translation_levels):
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1082 field_indices = [field_indices_all[index]
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1083 for index, z in enumerate(z_translation_all) if z == z_translation]
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1084 horizontal_shift = list(set(nxentry.sample.x_translation[field_indices]))
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1085 assert(len(horizontal_shift) == 1)
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1086 horizontal_shifts += horizontal_shift
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1087 vertical_shift = list(set(nxentry.sample.z_translation[field_indices]))
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1088 assert(len(vertical_shift) == 1)
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1089 vertical_shifts += vertical_shift
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1090 sequence_numbers = nxentry.instrument.detector.sequence_number[field_indices]
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1091 if thetas is None:
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1092 thetas = np.asarray(nxentry.sample.rotation_angle[field_indices]) \
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diff changeset
1093 [sequence_numbers]
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1094 else:
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1095 assert(all(thetas[i] == nxentry.sample.rotation_angle[field_indices[index]]
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1096 for i, index in enumerate(sequence_numbers)))
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1097 assert(list(set(sequence_numbers)) == [i for i in range(len(sequence_numbers))])
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1098 if list(sequence_numbers) == [i for i in range(len(sequence_numbers))]:
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1099 tomo_stack = np.asarray(nxentry.instrument.detector.data[field_indices])
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1100 else:
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1101 raise ValueError('Unable to load the tomography images')
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1102 tomo_stacks.append(tomo_stack)
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1103 else:
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1104 tomo_field_scans = nxentry.spec_scans.tomo_fields
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1105 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
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1106 horizontal_shifts = tomo_fields.get_horizontal_shifts()
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1107 vertical_shifts = tomo_fields.get_vertical_shifts()
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1108 prefix = str(nxentry.instrument.detector.local_name)
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1109 t0 = time()
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1110 tomo_stacks = tomo_fields.get_detector_data(prefix)
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1111 logger.debug(f'Getting tomography images took {time()-t0:.2f} seconds')
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1112 logger.debug(f'Getting all images took {time()-t0:.2f} seconds')
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1113 thetas = np.linspace(tomo_fields.theta_range['start'], tomo_fields.theta_range['end'],
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1114 tomo_fields.theta_range['num'])
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1115 if not isinstance(tomo_stacks, list):
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1116 horizontal_shifts = [horizontal_shifts]
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1117 vertical_shifts = [vertical_shifts]
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1118 tomo_stacks = [tomo_stacks]
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1119
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1120 reduced_tomo_stacks = []
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1121 if self.galaxy_flag:
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1122 path = 'tomo_reduce_plots'
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1123 else:
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1124 path = self.output_folder
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1125 for i, tomo_stack in enumerate(tomo_stacks):
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1126 # Resize the tomography images
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1127 # Right now the range is the same for each set in the image stack.
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1128 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
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1129 t0 = time()
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diff changeset
1130 tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1],
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1131 img_y_bounds[0]:img_y_bounds[1]].astype('float64')
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1132 logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds')
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1133
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1134 # Subtract dark field
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1135 if tdf is not None:
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1136 t0 = time()
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1137 with set_numexpr_threads(self.num_core):
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1138 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
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1139 logger.debug(f'Subtracting dark field took {time()-t0:.2f} seconds')
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1140
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1141 # Normalize
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1142 t0 = time()
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1143 with set_numexpr_threads(self.num_core):
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1144 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)
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1145 logger.debug(f'Normalizing took {time()-t0:.2f} seconds')
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1146
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1147 # Remove non-positive values and linearize data
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1148 t0 = time()
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1149 cutoff = 1.e-6
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1150 with set_numexpr_threads(self.num_core):
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1151 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)
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1152 with set_numexpr_threads(self.num_core):
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1153 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
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1154 logger.debug('Removing non-positive values and linearizing data took '+
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1155 f'{time()-t0:.2f} seconds')
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1156
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diff changeset
1157 # Get rid of nans/infs that may be introduced by normalization
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diff changeset
1158 t0 = time()
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1159 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)
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1160 logger.debug(f'Remove nans/infs took {time()-t0:.2f} seconds')
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1161
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diff changeset
1162 # Downsize tomography stack to smaller size
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1163 # TODO use theta_skip as well
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1164 tomo_stack = tomo_stack.astype('float32')
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1165 if not self.test_mode:
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1166 if len(tomo_stacks) == 1:
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diff changeset
1167 title = f'red fullres theta {round(thetas[0], 2)+0}'
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1168 else:
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diff changeset
1169 title = f'red stack {i+1} fullres theta {round(thetas[0], 2)+0}'
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diff changeset
1170 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
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1171 save_only=self.save_only, block=self.block)
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1172 # if not self.block:
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diff changeset
1173 # clear_imshow(title)
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1174 if False and zoom_perc != 100:
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1175 t0 = time()
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diff changeset
1176 logger.debug(f'Zooming in ...')
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1177 tomo_zoom_list = []
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1178 for j in range(tomo_stack.shape[0]):
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diff changeset
1179 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)
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1180 tomo_zoom_list.append(tomo_zoom)
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1181 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])
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diff changeset
1182 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1183 logger.info(f'Zooming in took {time()-t0:.2f} seconds')
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diff changeset
1184 del tomo_zoom_list
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diff changeset
1185 if not self.test_mode:
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diff changeset
1186 title = f'red stack {zoom_perc}p theta {round(thetas[0], 2)+0}'
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diff changeset
1187 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
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1188 save_only=self.save_only, block=self.block)
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1189 # if not self.block:
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1190 # clear_imshow(title)
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1191
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1192 # Save test data to file
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1193 if self.test_mode:
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1194 # row_index = int(tomo_stack.shape[0]/2)
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1195 # np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[row_index,:,:],
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1196 # fmt='%.6e')
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1197 row_index = int(tomo_stack.shape[1]/2)
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1198 np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[:,row_index,:],
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1199 fmt='%.6e')
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1200
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1201 # Combine resized stacks
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1202 reduced_tomo_stacks.append(tomo_stack)
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1203
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1204 # Add tomo field info to reduced data NXprocess
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1205 reduced_data['rotation_angle'] = thetas
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1206 reduced_data['x_translation'] = np.asarray(horizontal_shifts)
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1207 reduced_data['z_translation'] = np.asarray(vertical_shifts)
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1208 reduced_data.data['tomo_fields'] = np.asarray(reduced_tomo_stacks)
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1209
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1210 if tdf is not None:
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1211 del tdf
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diff changeset
1212 del tbf
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1213
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1214 return(reduced_data)
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1215
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1216 def _find_center_one_plane(self, sinogram, row, thetas, eff_pixel_size, cross_sectional_dim,
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1217 path=None, tol=0.1, num_core=1):
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1218 """Find center for a single tomography plane.
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1219 """
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diff changeset
1220 # Try automatic center finding routines for initial value
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1221 # sinogram index order: theta,column
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1222 # need column,theta for iradon, so take transpose
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1223 sinogram = np.asarray(sinogram)
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diff changeset
1224 sinogram_T = sinogram.T
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diff changeset
1225 center = sinogram.shape[1]/2
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diff changeset
1226
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diff changeset
1227 # Try using Nghia Vo’s method
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diff changeset
1228 t0 = time()
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diff changeset
1229 if num_core > num_core_tomopy_limit:
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parents:
diff changeset
1230 logger.debug(f'Running find_center_vo on {num_core_tomopy_limit} cores ...')
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diff changeset
1231 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
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diff changeset
1232 else:
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diff changeset
1233 logger.debug(f'Running find_center_vo on {num_core} cores ...')
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diff changeset
1234 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
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diff changeset
1235 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1236 logger.info(f'Finding the center using Nghia Vo’s method took {time()-t0:.2f} seconds')
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diff changeset
1237 center_offset_vo = tomo_center-center
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parents:
diff changeset
1238 logger.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
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parents:
diff changeset
1239 t0 = time()
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diff changeset
1240 logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
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diff changeset
1241 recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
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diff changeset
1242 eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1243 logger.debug(f'... done in {time()-t0:.2f} seconds')
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1244 logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
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diff changeset
1245
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diff changeset
1246 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
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diff changeset
1247 self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1248
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parents:
diff changeset
1249 # Try using phase correlation method
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1250 # if input_yesno('Try finding center using phase correlation (y/n)?', 'n'):
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diff changeset
1251 # t0 = time()
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diff changeset
1252 # logger.debug(f'Running find_center_pc ...')
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1253 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, rotc_guess=tomo_center)
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diff changeset
1254 # error = 1.
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diff changeset
1255 # while error > tol:
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parents:
diff changeset
1256 # prev = tomo_center
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diff changeset
1257 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
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diff changeset
1258 # rotc_guess=tomo_center)
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diff changeset
1259 # error = np.abs(tomo_center-prev)
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diff changeset
1260 # logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1261 # logger.info('Finding the center using the phase correlation method took '+
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parents:
diff changeset
1262 # f'{time()-t0:.2f} seconds')
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diff changeset
1263 # center_offset = tomo_center-center
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diff changeset
1264 # print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
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parents:
diff changeset
1265 # t0 = time()
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diff changeset
1266 # logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
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diff changeset
1267 # recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
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parents:
diff changeset
1268 # eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1269 # logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1270 # logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
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diff changeset
1271 #
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diff changeset
1272 # title = f'edges row{row} center_offset{center_offset:.2f} PC'
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diff changeset
1273 # self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1274
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diff changeset
1275 # Select center location
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diff changeset
1276 # if input_yesno('Accept a center location (y) or continue search (n)?', 'y'):
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diff changeset
1277 if True:
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diff changeset
1278 # center_offset = input_num(' Enter chosen center offset', ge=-center, le=center,
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diff changeset
1279 # default=center_offset_vo)
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diff changeset
1280 center_offset = center_offset_vo
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diff changeset
1281 del sinogram_T
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parents:
diff changeset
1282 del recon_plane
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diff changeset
1283 return float(center_offset)
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diff changeset
1284
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diff changeset
1285 # perform center finding search
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diff changeset
1286 while True:
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diff changeset
1287 center_offset_low = input_int('\nEnter lower bound for center offset', ge=-center,
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diff changeset
1288 le=center)
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diff changeset
1289 center_offset_upp = input_int('Enter upper bound for center offset',
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diff changeset
1290 ge=center_offset_low, le=center)
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1291 if center_offset_upp == center_offset_low:
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diff changeset
1292 center_offset_step = 1
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diff changeset
1293 else:
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diff changeset
1294 center_offset_step = input_int('Enter step size for center offset search', ge=1,
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diff changeset
1295 le=center_offset_upp-center_offset_low)
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diff changeset
1296 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)
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diff changeset
1297 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)
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1298 for center_offset in center_offsets:
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diff changeset
1299 if center_offset == center_offset_vo:
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diff changeset
1300 continue
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1301 t0 = time()
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1302 logger.debug(f'Running _reconstruct_one_plane on {num_core} cores ...')
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diff changeset
1303 recon_plane = self._reconstruct_one_plane(sinogram_T, center_offset+center, thetas,
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diff changeset
1304 eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1305 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1306 logger.info(f'Reconstructing center_offset {center_offset} took '+
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diff changeset
1307 f'{time()-t0:.2f} seconds')
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1308 title = f'edges row{row} center_offset{center_offset:.2f}'
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diff changeset
1309 self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1310 if input_int('\nContinue (0) or end the search (1)', ge=0, le=1):
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diff changeset
1311 break
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diff changeset
1312
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diff changeset
1313 del sinogram_T
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diff changeset
1314 del recon_plane
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diff changeset
1315 center_offset = input_num(' Enter chosen center offset', ge=-center, le=center)
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diff changeset
1316 return float(center_offset)
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diff changeset
1317
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diff changeset
1318 def _reconstruct_one_plane(self, tomo_plane_T, center, thetas, eff_pixel_size,
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diff changeset
1319 cross_sectional_dim, plot_sinogram=True, num_core=1):
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diff changeset
1320 """Invert the sinogram for a single tomography plane.
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1321 """
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diff changeset
1322 # tomo_plane_T index order: column,theta
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diff changeset
1323 assert(0 <= center < tomo_plane_T.shape[0])
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diff changeset
1324 center_offset = center-tomo_plane_T.shape[0]/2
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diff changeset
1325 two_offset = 2*int(np.round(center_offset))
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diff changeset
1326 two_offset_abs = np.abs(two_offset)
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diff changeset
1327 max_rad = int(0.55*(cross_sectional_dim/eff_pixel_size)) # 10% slack to avoid edge effects
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diff changeset
1328 if max_rad > 0.5*tomo_plane_T.shape[0]:
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diff changeset
1329 max_rad = 0.5*tomo_plane_T.shape[0]
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diff changeset
1330 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))
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diff changeset
1331 if two_offset >= 0:
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diff changeset
1332 logger.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')
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diff changeset
1333 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]
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diff changeset
1334 else:
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diff changeset
1335 logger.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')
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diff changeset
1336 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]
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diff changeset
1337 if not self.galaxy_flag and plot_sinogram:
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diff changeset
1338 quick_imshow(sinogram.T, f'sinogram center offset{center_offset:.2f}', aspect='auto',
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diff changeset
1339 path=self.output_folder, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
1340 block=self.block)
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diff changeset
1341
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diff changeset
1342 # Inverting sinogram
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diff changeset
1343 t0 = time()
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diff changeset
1344 recon_sinogram = iradon(sinogram, theta=thetas, circle=True)
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diff changeset
1345 logger.debug(f'Inverting sinogram took {time()-t0:.2f} seconds')
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diff changeset
1346 del sinogram
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diff changeset
1347
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diff changeset
1348 # Performing Gaussian filtering and removing ring artifacts
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diff changeset
1349 recon_parameters = None#self.config.get('recon_parameters')
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1350 if recon_parameters is None:
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diff changeset
1351 sigma = 1.0
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diff changeset
1352 ring_width = 15
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diff changeset
1353 else:
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diff changeset
1354 sigma = recon_parameters.get('gaussian_sigma', 1.0)
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1355 if not is_num(sigma, ge=0.0):
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diff changeset
1356 logger.warning(f'Invalid gaussian_sigma ({sigma}) in _reconstruct_one_plane, '+
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diff changeset
1357 'set to a default value of 1.0')
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diff changeset
1358 sigma = 1.0
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diff changeset
1359 ring_width = recon_parameters.get('ring_width', 15)
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diff changeset
1360 if not is_int(ring_width, ge=0):
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diff changeset
1361 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
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diff changeset
1362 'set to a default value of 15')
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diff changeset
1363 ring_width = 15
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diff changeset
1364 t0 = time()
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diff changeset
1365 recon_sinogram = spi.gaussian_filter(recon_sinogram, sigma, mode='nearest')
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diff changeset
1366 recon_clean = np.expand_dims(recon_sinogram, axis=0)
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parents:
diff changeset
1367 del recon_sinogram
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diff changeset
1368 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=ring_width, ncore=num_core)
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diff changeset
1369 logger.debug(f'Filtering and removing ring artifacts took {time()-t0:.2f} seconds')
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diff changeset
1370
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diff changeset
1371 return recon_clean
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diff changeset
1372
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diff changeset
1373 def _plot_edges_one_plane(self, recon_plane, title, path=None):
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diff changeset
1374 vis_parameters = None#self.config.get('vis_parameters')
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diff changeset
1375 if vis_parameters is None:
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diff changeset
1376 weight = 0.1
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diff changeset
1377 else:
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diff changeset
1378 weight = vis_parameters.get('denoise_weight', 0.1)
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diff changeset
1379 if not is_num(weight, ge=0.0):
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diff changeset
1380 logger.warning(f'Invalid weight ({weight}) in _plot_edges_one_plane, '+
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diff changeset
1381 'set to a default value of 0.1')
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diff changeset
1382 weight = 0.1
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diff changeset
1383 edges = denoise_tv_chambolle(recon_plane, weight=weight)
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diff changeset
1384 vmax = np.max(edges[0,:,:])
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diff changeset
1385 vmin = -vmax
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diff changeset
1386 if path is None:
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diff changeset
1387 path = self.output_folder
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diff changeset
1388 quick_imshow(edges[0,:,:], f'{title} coolwarm', path=path, cmap='coolwarm',
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diff changeset
1389 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
1390 quick_imshow(edges[0,:,:], f'{title} gray', path=path, cmap='gray', vmin=vmin, vmax=vmax,
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diff changeset
1391 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
1392 del edges
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diff changeset
1393
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diff changeset
1394 def _reconstruct_one_tomo_stack(self, tomo_stack, thetas, center_offsets=[], num_core=1,
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diff changeset
1395 algorithm='gridrec'):
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diff changeset
1396 """Reconstruct a single tomography stack.
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diff changeset
1397 """
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diff changeset
1398 # tomo_stack order: row,theta,column
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diff changeset
1399 # input thetas must be in degrees
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diff changeset
1400 # centers_offset: tomography axis shift in pixels relative to column center
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diff changeset
1401 # RV should we remove stripes?
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diff changeset
1402 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html
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diff changeset
1403 # RV should we remove rings?
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diff changeset
1404 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html
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diff changeset
1405 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?
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diff changeset
1406 if not len(center_offsets):
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parents:
diff changeset
1407 centers = np.zeros((tomo_stack.shape[0]))
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parents:
diff changeset
1408 elif len(center_offsets) == 2:
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parents:
diff changeset
1409 centers = np.linspace(center_offsets[0], center_offsets[1], tomo_stack.shape[0])
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diff changeset
1410 else:
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parents:
diff changeset
1411 if center_offsets.size != tomo_stack.shape[0]:
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parents:
diff changeset
1412 raise ValueError('center_offsets dimension mismatch in reconstruct_one_tomo_stack')
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parents:
diff changeset
1413 centers = center_offsets
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parents:
diff changeset
1414 centers += tomo_stack.shape[2]/2
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diff changeset
1415
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parents:
diff changeset
1416 # Get reconstruction parameters
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diff changeset
1417 recon_parameters = None#self.config.get('recon_parameters')
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diff changeset
1418 if recon_parameters is None:
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parents:
diff changeset
1419 sigma = 2.0
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parents:
diff changeset
1420 secondary_iters = 0
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parents:
diff changeset
1421 ring_width = 15
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1422 else:
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parents:
diff changeset
1423 sigma = recon_parameters.get('stripe_fw_sigma', 2.0)
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diff changeset
1424 if not is_num(sigma, ge=0):
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parents:
diff changeset
1425 logger.warning(f'Invalid stripe_fw_sigma ({sigma}) in '+
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parents:
diff changeset
1426 '_reconstruct_one_tomo_stack, set to a default value of 2.0')
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parents:
diff changeset
1427 ring_width = 15
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diff changeset
1428 secondary_iters = recon_parameters.get('secondary_iters', 0)
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diff changeset
1429 if not is_int(secondary_iters, ge=0):
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diff changeset
1430 logger.warning(f'Invalid secondary_iters ({secondary_iters}) in '+
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parents:
diff changeset
1431 '_reconstruct_one_tomo_stack, set to a default value of 0 (skip them)')
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parents:
diff changeset
1432 ring_width = 0
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parents:
diff changeset
1433 ring_width = recon_parameters.get('ring_width', 15)
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diff changeset
1434 if not is_int(ring_width, ge=0):
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parents:
diff changeset
1435 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
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parents:
diff changeset
1436 'set to a default value of 15')
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parents:
diff changeset
1437 ring_width = 15
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parents:
diff changeset
1438
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parents:
diff changeset
1439 # Remove horizontal stripe
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parents:
diff changeset
1440 t0 = time()
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diff changeset
1441 if num_core > num_core_tomopy_limit:
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parents:
diff changeset
1442 logger.debug('Running remove_stripe_fw on {num_core_tomopy_limit} cores ...')
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parents:
diff changeset
1443 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
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parents:
diff changeset
1444 ncore=num_core_tomopy_limit)
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diff changeset
1445 else:
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parents:
diff changeset
1446 logger.debug(f'Running remove_stripe_fw on {num_core} cores ...')
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parents:
diff changeset
1447 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
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parents:
diff changeset
1448 ncore=num_core)
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parents:
diff changeset
1449 logger.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds')
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parents:
diff changeset
1450
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parents:
diff changeset
1451 # Perform initial image reconstruction
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parents:
diff changeset
1452 logger.debug('Performing initial image reconstruction')
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parents:
diff changeset
1453 t0 = time()
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parents:
diff changeset
1454 logger.debug(f'Running recon on {num_core} cores ...')
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parents:
diff changeset
1455 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
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parents:
diff changeset
1456 sinogram_order=True, algorithm=algorithm, ncore=num_core)
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parents:
diff changeset
1457 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1458 logger.info(f'Performing initial image reconstruction took {time()-t0:.2f} seconds')
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parents:
diff changeset
1459
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parents:
diff changeset
1460 # Run optional secondary iterations
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diff changeset
1461 if secondary_iters > 0:
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parents:
diff changeset
1462 logger.debug(f'Running {secondary_iters} secondary iterations')
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parents:
diff changeset
1463 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iters}
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parents:
diff changeset
1464 #RV: doesn't work for me:
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parents:
diff changeset
1465 #"Error: CUDA error 803: system has unsupported display driver/cuda driver combination."
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parents:
diff changeset
1466 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iters}
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parents:
diff changeset
1467 #SIRT did not finish while running overnight
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parents:
diff changeset
1468 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iters}
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parents:
diff changeset
1469 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
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diff changeset
1470 'num_iter':secondary_iters}
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parents:
diff changeset
1471 t0 = time()
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parents:
diff changeset
1472 logger.debug(f'Running recon on {num_core} cores ...')
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parents:
diff changeset
1473 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
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parents:
diff changeset
1474 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
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parents:
diff changeset
1475 algorithm=tomopy.astra, ncore=num_core)
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parents:
diff changeset
1476 logger.debug(f'... done in {time()-t0:.2f} seconds')
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parents:
diff changeset
1477 logger.info(f'Performing secondary iterations took {time()-t0:.2f} seconds')
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parents:
diff changeset
1478
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1479 # Remove ring artifacts
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parents:
diff changeset
1480 t0 = time()
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parents:
diff changeset
1481 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=ring_width, out=tomo_recon_stack,
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diff changeset
1482 ncore=num_core)
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parents:
diff changeset
1483 logger.debug(f'Removing ring artifacts took {time()-t0:.2f} seconds')
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parents:
diff changeset
1484
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parents:
diff changeset
1485 return tomo_recon_stack
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parents:
diff changeset
1486
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parents:
diff changeset
1487 def _resize_reconstructed_data(self, data, z_only=False):
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diff changeset
1488 """Resize the reconstructed tomography data.
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parents:
diff changeset
1489 """
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1490 # Data order: row(z),x,y or stack,row(z),x,y
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diff changeset
1491 if isinstance(data, list):
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parents:
diff changeset
1492 for stack in data:
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parents:
diff changeset
1493 assert(stack.ndim == 3)
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parents:
diff changeset
1494 num_tomo_stacks = len(data)
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diff changeset
1495 tomo_recon_stacks = data
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diff changeset
1496 else:
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parents:
diff changeset
1497 assert(data.ndim == 3)
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diff changeset
1498 num_tomo_stacks = 1
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parents:
diff changeset
1499 tomo_recon_stacks = [data]
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rv43
parents:
diff changeset
1500
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parents:
diff changeset
1501 if z_only:
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parents:
diff changeset
1502 x_bounds = None
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rv43
parents:
diff changeset
1503 y_bounds = None
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parents:
diff changeset
1504 else:
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rv43
parents:
diff changeset
1505 # Selecting x bounds (in yz-plane)
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parents:
diff changeset
1506 tomosum = 0
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parents:
diff changeset
1507 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,2))
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parents:
diff changeset
1508 for i in range(num_tomo_stacks)]
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parents:
diff changeset
1509 select_x_bounds = input_yesno('\nDo you want to change the image x-bounds (y/n)?', 'y')
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parents:
diff changeset
1510 if not select_x_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1511 x_bounds = None
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parents:
diff changeset
1512 else:
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parents:
diff changeset
1513 accept = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1514 index_ranges = None
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parents:
diff changeset
1515 while not accept:
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parents:
diff changeset
1516 mask, x_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
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parents:
diff changeset
1517 title='select x data range', legend='recon stack sum yz')
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parents:
diff changeset
1518 while len(x_bounds) != 1:
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parents:
diff changeset
1519 print('Please select exactly one continuous range')
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parents:
diff changeset
1520 mask, x_bounds = draw_mask_1d(tomosum, title='select x data range',
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parents:
diff changeset
1521 legend='recon stack sum yz')
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parents:
diff changeset
1522 x_bounds = x_bounds[0]
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parents:
diff changeset
1523 # quick_plot(tomosum, vlines=x_bounds, title='recon stack sum yz')
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parents:
diff changeset
1524 # print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+
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parents:
diff changeset
1525 # 'exclusive)')
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parents:
diff changeset
1526 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
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parents:
diff changeset
1527 accept = True
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parents:
diff changeset
1528 logger.debug(f'x_bounds = {x_bounds}')
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parents:
diff changeset
1529
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1530 # Selecting y bounds (in xz-plane)
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parents:
diff changeset
1531 tomosum = 0
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parents:
diff changeset
1532 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,1))
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parents:
diff changeset
1533 for i in range(num_tomo_stacks)]
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parents:
diff changeset
1534 select_y_bounds = input_yesno('\nDo you want to change the image y-bounds (y/n)?', 'y')
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parents:
diff changeset
1535 if not select_y_bounds:
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parents:
diff changeset
1536 y_bounds = None
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parents:
diff changeset
1537 else:
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rv43
parents:
diff changeset
1538 accept = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1539 index_ranges = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1540 while not accept:
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parents:
diff changeset
1541 mask, y_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1542 title='select x data range', legend='recon stack sum xz')
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parents:
diff changeset
1543 while len(y_bounds) != 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1544 print('Please select exactly one continuous range')
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rv43
parents:
diff changeset
1545 mask, y_bounds = draw_mask_1d(tomosum, title='select x data range',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1546 legend='recon stack sum xz')
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parents:
diff changeset
1547 y_bounds = y_bounds[0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1548 # quick_plot(tomosum, vlines=y_bounds, title='recon stack sum xz')
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parents:
diff changeset
1549 # print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+
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parents:
diff changeset
1550 # 'exclusive)')
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parents:
diff changeset
1551 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1552 accept = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1553 logger.debug(f'y_bounds = {y_bounds}')
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parents:
diff changeset
1554
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1555 # Selecting z bounds (in xy-plane) (only valid for a single image stack)
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parents:
diff changeset
1556 if num_tomo_stacks != 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1557 z_bounds = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1558 else:
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rv43
parents:
diff changeset
1559 tomosum = 0
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1560 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(1,2))
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parents:
diff changeset
1561 for i in range(num_tomo_stacks)]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1562 select_z_bounds = input_yesno('Do you want to change the image z-bounds (y/n)?', 'n')
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parents:
diff changeset
1563 if not select_z_bounds:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1564 z_bounds = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1565 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1566 accept = False
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1567 index_ranges = None
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1568 while not accept:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1569 mask, z_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1570 title='select x data range', legend='recon stack sum xy')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1571 while len(z_bounds) != 1:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1572 print('Please select exactly one continuous range')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1573 mask, z_bounds = draw_mask_1d(tomosum, title='select x data range',
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1574 legend='recon stack sum xy')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1575 z_bounds = z_bounds[0]
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1576 # quick_plot(tomosum, vlines=z_bounds, title='recon stack sum xy')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1577 # print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1578 # 'exclusive)')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1579 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1580 accept = True
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1581 logger.debug(f'z_bounds = {z_bounds}')
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1582
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1583 return(x_bounds, y_bounds, z_bounds)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1584
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1585
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1586 def run_tomo(input_file:str, output_file:str, modes:list[str], center_file=None, num_core=-1,
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parents:
diff changeset
1587 output_folder='.', save_figs='no', test_mode=False) -> None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1588
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1589 if test_mode:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1590 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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1591 level = logging.getLevelName('INFO')
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1592 logging.basicConfig(filename=f'{output_folder}/tomo.log', filemode='w',
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1593 format=logging_format, level=level, force=True)
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1594 logger.info(f'input_file = {input_file}')
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1595 logger.info(f'center_file = {center_file}')
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1596 logger.info(f'output_file = {output_file}')
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1597 logger.debug(f'modes= {modes}')
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1598 logger.debug(f'num_core= {num_core}')
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1599 logger.info(f'output_folder = {output_folder}')
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1600 logger.info(f'save_figs = {save_figs}')
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1601 logger.info(f'test_mode = {test_mode}')
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1602
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1603 # Check for correction modes
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1604 legal_modes = ['reduce_data', 'find_center', 'reconstruct_data', 'combine_data', 'all']
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1605 if modes is None:
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1606 modes = ['all']
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1607 if not all(True if mode in legal_modes else False for mode in modes):
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1608 raise ValueError(f'Invalid parameter modes ({modes})')
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1609
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1610 # Instantiate Tomo object
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1611 tomo = Tomo(num_core=num_core, output_folder=output_folder, save_figs=save_figs,
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1612 test_mode=test_mode)
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1613
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1614 # Read input file
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diff changeset
1615 data = tomo.read(input_file)
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1616
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1617 # Generate reduced tomography images
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parents:
diff changeset
1618 if 'reduce_data' in modes or 'all' in modes:
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1619 data = tomo.gen_reduced_data(data)
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1620
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diff changeset
1621 # Find rotation axis centers for the tomography stacks.
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1622 center_data = None
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diff changeset
1623 if 'find_center' in modes or 'all' in modes:
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1624 center_data = tomo.find_centers(data)
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1625
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1626 # Reconstruct tomography stacks
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1627 if 'reconstruct_data' in modes or 'all' in modes:
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1628 if center_data is None:
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1629 # Read input file
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1630 center_data = tomo.read(center_file)
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1631 data = tomo.reconstruct_data(data, center_data)
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1632 center_data = None
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1633
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1634 # Combine reconstructed tomography stacks
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diff changeset
1635 if 'combine_data' in modes or 'all' in modes:
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1636 data = tomo.combine_data(data)
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1637
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1638 # Write output file
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diff changeset
1639 if data is not None and not test_mode:
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diff changeset
1640 if center_data is None:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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diff changeset
1641 data = tomo.write(data, output_file)
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diff changeset
1642 else:
98e23dff1de2 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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diff changeset
1643 data = tomo.write(center_data, output_file)
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1644
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1645 logger.info(f'Completed modes: {modes}')