Mercurial > repos > rv43 > chess_tomo

annotate workflow/run_tomo.py @ 10:0f553c8d7b98 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Mon, 20 Mar 2023 19:30:19 +0000
parents 1dbb29320ce8
children 9c48ef48c604
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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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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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28 from time import time
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30 import tomopy
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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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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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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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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):
9
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diff changeset
167 logger.info(f'looking for {filename}')
4
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168 extension = os_path.splitext(filename)[1]
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169 if extension == '.yml' or extension == '.yaml' or self.galaxy_flag and extension == '.dat':
4
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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 # if len(config) > 1:
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173 # raise ValueError(f'Multiple root entries in {filename} not yet implemented')
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174 # if len(list(config.values())[0]) > 1:
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175 # raise ValueError(f'Multiple sample maps in {filename} not yet implemented')
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176 return(config)
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177 elif extension == '.nxs':
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178 with NXFile(filename, mode='r') as nxfile:
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179 nxroot = nxfile.readfile()
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180 return(nxroot)
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181 else:
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182 raise ValueError(f'Invalid filename extension ({extension})')
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183
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184 def write(self, data, filename):
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185 extension = os_path.splitext(filename)[1]
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186 if extension == '.yml' or extension == '.yaml':
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187 with open(filename, 'w') as f:
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188 safe_dump(data, f)
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189 elif extension == '.nxs':
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190 data.save(filename, mode='w')
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191 elif extension == '.nc':
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192 data.to_netcdf(os_path=filename)
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193 else:
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194 raise ValueError(f'Invalid filename extension ({extension})')
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195
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196 def gen_reduced_data(self, data, img_x_bounds=None):
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197 """Generate the reduced tomography images.
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198 """
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199 logger.info('Generate the reduced tomography images')
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200
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201 # Create plot galaxy path directory if needed
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202 if self.galaxy_flag and not os_path.exists('tomo_reduce_plots'):
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203 mkdir('tomo_reduce_plots')
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204
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205 if isinstance(data, dict):
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206 # Create Nexus format object from input dictionary
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207 wf = TomoWorkflow(**data)
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208 if len(wf.sample_maps) > 1:
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209 raise ValueError(f'Multiple sample maps not yet implemented')
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210 # print(f'\nwf:\n{wf}\n')
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211 nxroot = NXroot()
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212 t0 = time()
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213 for sample_map in wf.sample_maps:
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214 logger.info(f'Start constructing the {sample_map.title} map.')
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215 import_scanparser(sample_map.station)
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216 sample_map.construct_nxentry(nxroot, include_raw_data=False)
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217 logger.info(f'Constructed all sample maps in {time()-t0:.2f} seconds.')
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218 nxentry = nxroot[nxroot.attrs['default']]
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219 # Get test mode configuration info
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220 if self.test_mode:
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221 self.test_config = data['sample_maps'][0]['test_mode']
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222 elif isinstance(data, NXroot):
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223 nxentry = data[data.attrs['default']]
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224 else:
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225 raise ValueError(f'Invalid parameter data ({data})')
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226
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227 # Create an NXprocess to store data reduction (meta)data
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228 reduced_data = NXprocess()
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229
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230 # Generate dark field
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231 if 'dark_field' in nxentry['spec_scans']:
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232 reduced_data = self._gen_dark(nxentry, reduced_data)
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233
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234 # Generate bright field
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235 reduced_data = self._gen_bright(nxentry, reduced_data)
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236
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237 # Set vertical detector bounds for image stack
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238 img_x_bounds = self._set_detector_bounds(nxentry, reduced_data, img_x_bounds=img_x_bounds)
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239 logger.info(f'img_x_bounds = {img_x_bounds}')
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240 reduced_data['img_x_bounds'] = img_x_bounds
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241
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242 # Set zoom and/or theta skip to reduce memory the requirement
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243 zoom_perc, num_theta_skip = self._set_zoom_or_skip()
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244 if zoom_perc is not None:
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245 reduced_data.attrs['zoom_perc'] = zoom_perc
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246 if num_theta_skip is not None:
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247 reduced_data.attrs['num_theta_skip'] = num_theta_skip
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248
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249 # Generate reduced tomography fields
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250 reduced_data = self._gen_tomo(nxentry, reduced_data)
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251
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252 # Create a copy of the input Nexus object and remove raw and any existing reduced data
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253 if isinstance(data, NXroot):
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254 exclude_items = [f'{nxentry._name}/reduced_data/data',
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255 f'{nxentry._name}/instrument/detector/data',
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256 f'{nxentry._name}/instrument/detector/image_key',
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257 f'{nxentry._name}/instrument/detector/sequence_number',
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258 f'{nxentry._name}/sample/rotation_angle',
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259 f'{nxentry._name}/sample/x_translation',
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260 f'{nxentry._name}/sample/z_translation',
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261 f'{nxentry._name}/data/data',
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262 f'{nxentry._name}/data/image_key',
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263 f'{nxentry._name}/data/rotation_angle',
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264 f'{nxentry._name}/data/x_translation',
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265 f'{nxentry._name}/data/z_translation']
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266 nxroot = nxcopy(data, exclude_nxpaths=exclude_items)
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267 nxentry = nxroot[nxroot.attrs['default']]
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268
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269 # Add the reduced data NXprocess
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270 nxentry.reduced_data = reduced_data
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271
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272 if 'data' not in nxentry:
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273 nxentry.data = NXdata()
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274 nxentry.attrs['default'] = 'data'
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275 nxentry.data.makelink(nxentry.reduced_data.data.tomo_fields, name='reduced_data')
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276 nxentry.data.makelink(nxentry.reduced_data.rotation_angle, name='rotation_angle')
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277 nxentry.data.attrs['signal'] = 'reduced_data'
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278
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279 return(nxroot)
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280
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281 def find_centers(self, nxroot, center_rows=None, center_stack_index=None):
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282 """Find the calibrated center axis info
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283 """
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284 logger.info('Find the calibrated center axis info')
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285
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286 if not isinstance(nxroot, NXroot):
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287 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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288 nxentry = nxroot[nxroot.attrs['default']]
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289 if not isinstance(nxentry, NXentry):
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290 raise ValueError(f'Invalid nxentry ({nxentry})')
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291 if self.galaxy_flag:
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292 if center_rows is not None:
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293 center_rows = tuple(center_rows)
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294 if not is_int_pair(center_rows):
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295 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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296 elif center_rows is not None:
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297 logger.warning(f'Ignoring parameter center_rows ({center_rows})')
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298 center_rows = None
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299 if self.galaxy_flag:
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300 if center_stack_index is not None and not is_int(center_stack_index, ge=0):
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301 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
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302 elif center_stack_index is not None:
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303 logger.warning(f'Ignoring parameter center_stack_index ({center_stack_index})')
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304 center_stack_index = None
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305
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306 # Create plot galaxy path directory and path if needed
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307 if self.galaxy_flag:
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308 if not os_path.exists('tomo_find_centers_plots'):
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309 mkdir('tomo_find_centers_plots')
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310 path = 'tomo_find_centers_plots'
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311 else:
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312 path = self.output_folder
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313
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314 # Check if reduced data is available
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315 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
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316 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
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317
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318 # Select the image stack to calibrate the center axis
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319 # reduced data axes order: stack,theta,row,column
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320 # Note: Nexus cannot follow a link if the data it points to is too big,
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321 # so get the data from the actual place, not from nxentry.data
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322 tomo_fields_shape = nxentry.reduced_data.data.tomo_fields.shape
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323 if len(tomo_fields_shape) != 4 or any(True for dim in tomo_fields_shape if not dim):
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324 raise KeyError('Unable to load the required reduced tomography stack')
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325 num_tomo_stacks = tomo_fields_shape[0]
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326 if num_tomo_stacks == 1:
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327 center_stack_index = 0
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328 default = 'n'
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329 else:
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330 if self.test_mode:
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331 center_stack_index = self.test_config['center_stack_index']-1 # make offset 0
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332 elif self.galaxy_flag:
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333 if center_stack_index is None:
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334 center_stack_index = int(num_tomo_stacks/2)
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335 if center_stack_index >= num_tomo_stacks:
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336 raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})')
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337 else:
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338 center_stack_index = input_int('\nEnter tomography stack index to calibrate the '
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339 'center axis', ge=1, le=num_tomo_stacks, default=int(1+num_tomo_stacks/2))
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340 center_stack_index -= 1
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341 default = 'y'
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342
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343 # Get thetas (in degrees)
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344 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
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345
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346 # Get effective pixel_size
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347 if 'zoom_perc' in nxentry.reduced_data:
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348 eff_pixel_size = 100.*(nxentry.instrument.detector.x_pixel_size/
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349 nxentry.reduced_data.attrs['zoom_perc'])
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350 else:
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351 eff_pixel_size = nxentry.instrument.detector.x_pixel_size
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diff changeset
352
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353 # Get cross sectional diameter
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354 cross_sectional_dim = tomo_fields_shape[3]*eff_pixel_size
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355 logger.debug(f'cross_sectional_dim = {cross_sectional_dim}')
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diff changeset
356
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357 # Determine center offset at sample row boundaries
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358 logger.info('Determine center offset at sample row boundaries')
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359
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360 # Lower row center
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361 if self.test_mode:
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362 lower_row = self.test_config['lower_row']
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363 elif self.galaxy_flag:
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364 if center_rows is None:
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365 lower_row = 0
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366 else:
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367 lower_row = min(center_rows)
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368 if not 0 <= lower_row < tomo_fields_shape[2]-1:
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369 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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370 else:
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diff changeset
371 lower_row = select_one_image_bound(
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diff changeset
372 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0, bound=0,
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373 title=f'theta={round(thetas[0], 2)+0}',
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374 bound_name='row index to find lower center', default=default, raise_error=True)
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375 logger.debug('Finding center...')
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376 t0 = time()
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377 lower_center_offset = self._find_center_one_plane(
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378 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:]),
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379 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:],
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380 lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
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381 num_core=self.num_core)
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382 logger.debug(f'... done in {time()-t0:.2f} seconds')
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383 logger.debug(f'lower_row = {lower_row:.2f}')
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384 logger.debug(f'lower_center_offset = {lower_center_offset:.2f}')
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385
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386 # Upper row center
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387 if self.test_mode:
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388 upper_row = self.test_config['upper_row']
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389 elif self.galaxy_flag:
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390 if center_rows is None:
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391 upper_row = tomo_fields_shape[2]-1
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392 else:
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393 upper_row = max(center_rows)
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394 if not lower_row < upper_row < tomo_fields_shape[2]:
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395 raise ValueError(f'Invalid parameter center_rows ({center_rows})')
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diff changeset
396 else:
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397 upper_row = select_one_image_bound(
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398 nxentry.reduced_data.data.tomo_fields[center_stack_index,0,:,:], 0,
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399 bound=tomo_fields_shape[2]-1, title=f'theta={round(thetas[0], 2)+0}',
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400 bound_name='row index to find upper center', default=default, raise_error=True)
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401 logger.debug('Finding center...')
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402 t0 = time()
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403 upper_center_offset = self._find_center_one_plane(
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404 #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:]),
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405 nxentry.reduced_data.data.tomo_fields[center_stack_index,:,upper_row,:],
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406 upper_row, thetas, eff_pixel_size, cross_sectional_dim, path=path,
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407 num_core=self.num_core)
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408 logger.debug(f'... done in {time()-t0:.2f} seconds')
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409 logger.debug(f'upper_row = {upper_row:.2f}')
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410 logger.debug(f'upper_center_offset = {upper_center_offset:.2f}')
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411
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412 center_config = {'lower_row': lower_row, 'lower_center_offset': lower_center_offset,
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413 'upper_row': upper_row, 'upper_center_offset': upper_center_offset}
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414 if num_tomo_stacks > 1:
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415 center_config['center_stack_index'] = center_stack_index+1 # save as offset 1
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416
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417 # Save test data to file
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418 if self.test_mode:
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419 with open(f'{self.output_folder}/center_config.yaml', 'w') as f:
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420 safe_dump(center_config, f)
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421
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422 return(center_config)
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423
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424 def reconstruct_data(self, nxroot, center_info, x_bounds=None, y_bounds=None):
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425 """Reconstruct the tomography data.
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426 """
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427 logger.info('Reconstruct the tomography data')
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428
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429 if not isinstance(nxroot, NXroot):
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430 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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431 nxentry = nxroot[nxroot.attrs['default']]
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432 if not isinstance(nxentry, NXentry):
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433 raise ValueError(f'Invalid nxentry ({nxentry})')
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diff changeset
434 if not isinstance(center_info, dict):
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435 raise ValueError(f'Invalid parameter center_info ({center_info})')
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diff changeset
436
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437 # Create plot galaxy path directory and path if needed
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438 if self.galaxy_flag:
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439 if not os_path.exists('tomo_reconstruct_plots'):
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440 mkdir('tomo_reconstruct_plots')
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diff changeset
441 path = 'tomo_reconstruct_plots'
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diff changeset
442 else:
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443 path = self.output_folder
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444
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diff changeset
445 # Check if reduced data is available
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446 if ('reduced_data' not in nxentry or 'reduced_data' not in nxentry.data):
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447 raise KeyError(f'Unable to find valid reduced data in {nxentry}.')
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diff changeset
448
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diff changeset
449 # Create an NXprocess to store image reconstruction (meta)data
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450 nxprocess = NXprocess()
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451
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452 # Get rotation axis rows and centers
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453 lower_row = center_info.get('lower_row')
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454 lower_center_offset = center_info.get('lower_center_offset')
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455 upper_row = center_info.get('upper_row')
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456 upper_center_offset = center_info.get('upper_center_offset')
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diff changeset
457 if (lower_row is None or lower_center_offset is None or upper_row is None or
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diff changeset
458 upper_center_offset is None):
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diff changeset
459 raise KeyError(f'Unable to find valid calibrated center axis info in {center_info}.')
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460 center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row)
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461
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diff changeset
462 # Get thetas (in degrees)
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463 thetas = np.asarray(nxentry.reduced_data.rotation_angle)
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464
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diff changeset
465 # Reconstruct tomography data
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466 # reduced data axes order: stack,theta,row,column
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467 # reconstructed data order in each stack: row/z,x,y
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diff changeset
468 # Note: Nexus cannot follow a link if the data it points to is too big,
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diff changeset
469 # so get the data from the actual place, not from nxentry.data
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diff changeset
470 if 'zoom_perc' in nxentry.reduced_data:
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471 res_title = f'{nxentry.reduced_data.attrs["zoom_perc"]}p'
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diff changeset
472 else:
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473 res_title = 'fullres'
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diff changeset
474 load_error = False
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diff changeset
475 num_tomo_stacks = nxentry.reduced_data.data.tomo_fields.shape[0]
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476 tomo_recon_stacks = num_tomo_stacks*[np.array([])]
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diff changeset
477 for i in range(num_tomo_stacks):
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diff changeset
478 # Convert reduced data stack from theta,row,column to row,theta,column
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479 logger.debug(f'Reading reduced data stack {i+1}...')
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diff changeset
480 t0 = time()
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diff changeset
481 tomo_stack = np.asarray(nxentry.reduced_data.data.tomo_fields[i])
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482 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
483 if len(tomo_stack.shape) != 3 or any(True for dim in tomo_stack.shape if not dim):
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diff changeset
484 raise ValueError(f'Unable to load tomography stack {i+1} for reconstruction')
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diff changeset
485 tomo_stack = np.swapaxes(tomo_stack, 0, 1)
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diff changeset
486 assert(len(thetas) == tomo_stack.shape[1])
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diff changeset
487 assert(0 <= lower_row < upper_row < tomo_stack.shape[0])
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diff changeset
488 center_offsets = [lower_center_offset-lower_row*center_slope,
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489 upper_center_offset+(tomo_stack.shape[0]-1-upper_row)*center_slope]
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diff changeset
490 t0 = time()
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diff changeset
491 logger.debug(f'Running _reconstruct_one_tomo_stack on {self.num_core} cores ...')
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diff changeset
492 tomo_recon_stack = self._reconstruct_one_tomo_stack(tomo_stack, thetas,
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493 center_offsets=center_offsets, num_core=self.num_core, algorithm='gridrec')
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diff changeset
494 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
495 logger.info(f'Reconstruction of stack {i+1} took {time()-t0:.2f} seconds')
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diff changeset
496
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diff changeset
497 # Combine stacks
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498 tomo_recon_stacks[i] = tomo_recon_stack
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diff changeset
499
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parents:
diff changeset
500 # Resize the reconstructed tomography data
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diff changeset
501 # reconstructed data order in each stack: row/z,x,y
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diff changeset
502 if self.test_mode:
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diff changeset
503 x_bounds = self.test_config.get('x_bounds')
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diff changeset
504 y_bounds = self.test_config.get('y_bounds')
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diff changeset
505 z_bounds = None
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parents:
diff changeset
506 elif self.galaxy_flag:
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diff changeset
507 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
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diff changeset
508 lt=tomo_recon_stacks[0].shape[1]):
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diff changeset
509 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
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diff changeset
510 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
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diff changeset
511 lt=tomo_recon_stacks[0].shape[1]):
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diff changeset
512 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
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diff changeset
513 z_bounds = None
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diff changeset
514 else:
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diff changeset
515 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_stacks)
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diff changeset
516 if x_bounds is None:
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diff changeset
517 x_range = (0, tomo_recon_stacks[0].shape[1])
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diff changeset
518 x_slice = int(x_range[1]/2)
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parents:
diff changeset
519 else:
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diff changeset
520 x_range = (min(x_bounds), max(x_bounds))
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parents:
diff changeset
521 x_slice = int((x_bounds[0]+x_bounds[1])/2)
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diff changeset
522 if y_bounds is None:
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diff changeset
523 y_range = (0, tomo_recon_stacks[0].shape[2])
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diff changeset
524 y_slice = int(y_range[1]/2)
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diff changeset
525 else:
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diff changeset
526 y_range = (min(y_bounds), max(y_bounds))
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diff changeset
527 y_slice = int((y_bounds[0]+y_bounds[1])/2)
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diff changeset
528 if z_bounds is None:
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diff changeset
529 z_range = (0, tomo_recon_stacks[0].shape[0])
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diff changeset
530 z_slice = int(z_range[1]/2)
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diff changeset
531 else:
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diff changeset
532 z_range = (min(z_bounds), max(z_bounds))
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diff changeset
533 z_slice = int((z_bounds[0]+z_bounds[1])/2)
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parents:
diff changeset
534
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
535 # Plot a few reconstructed image slices
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parents:
diff changeset
536 if num_tomo_stacks == 1:
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diff changeset
537 basetitle = 'recon'
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parents:
diff changeset
538 else:
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parents:
diff changeset
539 basetitle = f'recon stack {i+1}'
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parents:
diff changeset
540 for i, stack in enumerate(tomo_recon_stacks):
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parents:
diff changeset
541 title = f'{basetitle} {res_title} xslice{x_slice}'
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parents:
diff changeset
542 quick_imshow(stack[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
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diff changeset
543 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
544 block=self.block)
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parents:
diff changeset
545 title = f'{basetitle} {res_title} yslice{y_slice}'
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diff changeset
546 quick_imshow(stack[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
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diff changeset
547 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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parents:
diff changeset
548 block=self.block)
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parents:
diff changeset
549 title = f'{basetitle} {res_title} zslice{z_slice}'
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parents:
diff changeset
550 quick_imshow(stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]],
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diff changeset
551 title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
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parents:
diff changeset
552 block=self.block)
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parents:
diff changeset
553
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parents:
diff changeset
554 # Save test data to file
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parents:
diff changeset
555 # reconstructed data order in each stack: row/z,x,y
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parents:
diff changeset
556 if self.test_mode:
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diff changeset
557 for i, stack in enumerate(tomo_recon_stacks):
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diff changeset
558 np.savetxt(f'{self.output_folder}/recon_stack_{i+1}.txt',
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diff changeset
559 stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
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parents:
diff changeset
560
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parents:
diff changeset
561 # Add image reconstruction to reconstructed data NXprocess
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parents:
diff changeset
562 # reconstructed data order in each stack: row/z,x,y
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diff changeset
563 nxprocess.data = NXdata()
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diff changeset
564 nxprocess.attrs['default'] = 'data'
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diff changeset
565 for k, v in center_info.items():
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parents:
diff changeset
566 nxprocess[k] = v
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diff changeset
567 if x_bounds is not None:
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diff changeset
568 nxprocess.x_bounds = x_bounds
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diff changeset
569 if y_bounds is not None:
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parents:
diff changeset
570 nxprocess.y_bounds = y_bounds
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parents:
diff changeset
571 if z_bounds is not None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
572 nxprocess.z_bounds = z_bounds
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parents:
diff changeset
573 nxprocess.data['reconstructed_data'] = np.asarray([stack[z_range[0]:z_range[1],
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
574 x_range[0]:x_range[1],y_range[0]:y_range[1]] for stack in tomo_recon_stacks])
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parents:
diff changeset
575 nxprocess.data.attrs['signal'] = 'reconstructed_data'
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parents:
diff changeset
576
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
577 # Create a copy of the input Nexus object and remove reduced data
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diff changeset
578 exclude_items = [f'{nxentry._name}/reduced_data/data', f'{nxentry._name}/data/reduced_data']
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parents:
diff changeset
579 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
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parents:
diff changeset
580
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
581 # Add the reconstructed data NXprocess to the new Nexus object
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
582 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
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parents:
diff changeset
583 nxentry_copy.reconstructed_data = nxprocess
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
584 if 'data' not in nxentry_copy:
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parents:
diff changeset
585 nxentry_copy.data = NXdata()
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diff changeset
586 nxentry_copy.attrs['default'] = 'data'
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parents:
diff changeset
587 nxentry_copy.data.makelink(nxprocess.data.reconstructed_data, name='reconstructed_data')
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parents:
diff changeset
588 nxentry_copy.data.attrs['signal'] = 'reconstructed_data'
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parents:
diff changeset
589
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
590 return(nxroot_copy)
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parents:
diff changeset
591
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diff changeset
592 def combine_data(self, nxroot, x_bounds=None, y_bounds=None):
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parents:
diff changeset
593 """Combine the reconstructed tomography stacks.
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parents:
diff changeset
594 """
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diff changeset
595 logger.info('Combine the reconstructed tomography stacks')
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parents:
diff changeset
596
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parents:
diff changeset
597 if not isinstance(nxroot, NXroot):
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parents:
diff changeset
598 raise ValueError(f'Invalid parameter nxroot ({nxroot})')
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parents:
diff changeset
599 nxentry = nxroot[nxroot.attrs['default']]
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parents:
diff changeset
600 if not isinstance(nxentry, NXentry):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
601 raise ValueError(f'Invalid nxentry ({nxentry})')
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parents:
diff changeset
602
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
603 # Create plot galaxy path directory and path if needed
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parents:
diff changeset
604 if self.galaxy_flag:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
605 if not os_path.exists('tomo_combine_plots'):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
606 mkdir('tomo_combine_plots')
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parents:
diff changeset
607 path = 'tomo_combine_plots'
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parents:
diff changeset
608 else:
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parents:
diff changeset
609 path = self.output_folder
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parents:
diff changeset
610
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
611 # Check if reconstructed image data is available
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parents:
diff changeset
612 if ('reconstructed_data' not in nxentry or 'reconstructed_data' not in nxentry.data):
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parents:
diff changeset
613 raise KeyError(f'Unable to find valid reconstructed image data in {nxentry}.')
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parents:
diff changeset
614
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
615 # Create an NXprocess to store combined image reconstruction (meta)data
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parents:
diff changeset
616 nxprocess = NXprocess()
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parents:
diff changeset
617
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parents:
diff changeset
618 # Get the reconstructed data
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parents:
diff changeset
619 # reconstructed data order: stack,row(z),x,y
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parents:
diff changeset
620 # Note: Nexus cannot follow a link if the data it points to is too big,
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parents:
diff changeset
621 # so get the data from the actual place, not from nxentry.data
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diff changeset
622 num_tomo_stacks = nxentry.reconstructed_data.data.reconstructed_data.shape[0]
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parents:
diff changeset
623 if num_tomo_stacks == 1:
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parents:
diff changeset
624 logger.info('Only one stack available: leaving combine_data')
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parents:
diff changeset
625 return(None)
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parents:
diff changeset
626
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parents:
diff changeset
627 # Combine the reconstructed stacks
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parents:
diff changeset
628 # (load one stack at a time to reduce risk of hitting Nexus data access limit)
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parents:
diff changeset
629 t0 = time()
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parents:
diff changeset
630 logger.debug(f'Combining the reconstructed stacks ...')
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parents:
diff changeset
631 tomo_recon_combined = np.asarray(nxentry.reconstructed_data.data.reconstructed_data[0])
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parents:
diff changeset
632 if num_tomo_stacks > 2:
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parents:
diff changeset
633 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
634 [nxentry.reconstructed_data.data.reconstructed_data[i]
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parents:
diff changeset
635 for i in range(1, num_tomo_stacks-1)])
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parents:
diff changeset
636 if num_tomo_stacks > 1:
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parents:
diff changeset
637 tomo_recon_combined = np.concatenate([tomo_recon_combined]+
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
638 [nxentry.reconstructed_data.data.reconstructed_data[num_tomo_stacks-1]])
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parents:
diff changeset
639 logger.debug(f'... done in {time()-t0:.2f} seconds')
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parents:
diff changeset
640 logger.info(f'Combining the reconstructed stacks took {time()-t0:.2f} seconds')
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parents:
diff changeset
641
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
642 # Resize the combined tomography data stacks
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parents:
diff changeset
643 # combined data order: row/z,x,y
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parents:
diff changeset
644 if self.test_mode:
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parents:
diff changeset
645 x_bounds = None
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parents:
diff changeset
646 y_bounds = None
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parents:
diff changeset
647 z_bounds = self.test_config.get('z_bounds')
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parents:
diff changeset
648 elif self.galaxy_flag:
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parents:
diff changeset
649 if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
650 lt=tomo_recon_stacks[0].shape[1]):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
651 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
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parents:
diff changeset
652 if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
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parents:
diff changeset
653 lt=tomo_recon_stacks[0].shape[1]):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
654 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
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parents:
diff changeset
655 z_bounds = None
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parents:
diff changeset
656 else:
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parents:
diff changeset
657 x_bounds, y_bounds, z_bounds = self._resize_reconstructed_data(tomo_recon_combined,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
658 z_only=True)
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parents:
diff changeset
659 if x_bounds is None:
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parents:
diff changeset
660 x_range = (0, tomo_recon_combined.shape[1])
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parents:
diff changeset
661 x_slice = int(x_range[1]/2)
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parents:
diff changeset
662 else:
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parents:
diff changeset
663 x_range = x_bounds
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
664 x_slice = int((x_bounds[0]+x_bounds[1])/2)
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parents:
diff changeset
665 if y_bounds is None:
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parents:
diff changeset
666 y_range = (0, tomo_recon_combined.shape[2])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
667 y_slice = int(y_range[1]/2)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
668 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
669 y_range = y_bounds
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
670 y_slice = int((y_bounds[0]+y_bounds[1])/2)
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parents:
diff changeset
671 if z_bounds is None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
672 z_range = (0, tomo_recon_combined.shape[0])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
673 z_slice = int(z_range[1]/2)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
674 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
675 z_range = z_bounds
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
676 z_slice = int((z_bounds[0]+z_bounds[1])/2)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
677
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
678 # Plot a few combined image slices
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
679 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]],
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
680 title=f'recon combined xslice{x_slice}', path=path,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
681 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
682 quick_imshow(tomo_recon_combined[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice],
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
683 title=f'recon combined yslice{y_slice}', path=path,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
684 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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parents:
diff changeset
685 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
686 title=f'recon combined zslice{z_slice}', path=path,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
687 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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parents:
diff changeset
688
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
689 # Save test data to file
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
690 # combined data order: row/z,x,y
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parents:
diff changeset
691 if self.test_mode:
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parents:
diff changeset
692 np.savetxt(f'{self.output_folder}/recon_combined.txt', tomo_recon_combined[
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
693 z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], fmt='%.6e')
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parents:
diff changeset
694
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
695 # Add image reconstruction to reconstructed data NXprocess
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
696 # combined data order: row/z,x,y
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parents:
diff changeset
697 nxprocess.data = NXdata()
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parents:
diff changeset
698 nxprocess.attrs['default'] = 'data'
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parents:
diff changeset
699 if x_bounds is not None:
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parents:
diff changeset
700 nxprocess.x_bounds = x_bounds
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parents:
diff changeset
701 if y_bounds is not None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
702 nxprocess.y_bounds = y_bounds
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
703 if z_bounds is not None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
704 nxprocess.z_bounds = z_bounds
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
705 nxprocess.data['combined_data'] = tomo_recon_combined
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
706 nxprocess.data.attrs['signal'] = 'combined_data'
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parents:
diff changeset
707
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
708 # Create a copy of the input Nexus object and remove reconstructed data
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
709 exclude_items = [f'{nxentry._name}/reconstructed_data/data',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
710 f'{nxentry._name}/data/reconstructed_data']
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parents:
diff changeset
711 nxroot_copy = nxcopy(nxroot, exclude_nxpaths=exclude_items)
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parents:
diff changeset
712
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
713 # Add the combined data NXprocess to the new Nexus object
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parents:
diff changeset
714 nxentry_copy = nxroot_copy[nxroot_copy.attrs['default']]
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parents:
diff changeset
715 nxentry_copy.combined_data = nxprocess
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
716 if 'data' not in nxentry_copy:
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parents:
diff changeset
717 nxentry_copy.data = NXdata()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
718 nxentry_copy.attrs['default'] = 'data'
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
719 nxentry_copy.data.makelink(nxprocess.data.combined_data, name='combined_data')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
720 nxentry_copy.data.attrs['signal'] = 'combined_data'
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parents:
diff changeset
721
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
722 return(nxroot_copy)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
723
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
724 def _gen_dark(self, nxentry, reduced_data):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
725 """Generate dark field.
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
726 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
727 # Get the dark field images
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
728 image_key = nxentry.instrument.detector.get('image_key', None)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
729 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
730 field_indices = [index for index, key in enumerate(image_key) if key == 2]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
731 tdf_stack = nxentry.instrument.detector.data[field_indices,:,:]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
732 # RV the default NXtomo form does not accomodate bright or dark field stacks
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
733 else:
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parents:
diff changeset
734 dark_field_scans = nxentry.spec_scans.dark_field
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
735 dark_field = FlatField.construct_from_nxcollection(dark_field_scans)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
736 prefix = str(nxentry.instrument.detector.local_name)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
737 tdf_stack = dark_field.get_detector_data(prefix)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
738 if isinstance(tdf_stack, list):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
739 assert(len(tdf_stack) == 1) # TODO
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
740 tdf_stack = tdf_stack[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
741
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
742 # Take median
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
743 if tdf_stack.ndim == 2:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
744 tdf = tdf_stack
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
745 elif tdf_stack.ndim == 3:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
746 tdf = np.median(tdf_stack, axis=0)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
747 del tdf_stack
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
748 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
749 raise ValueError(f'Invalid tdf_stack shape ({tdf_stack.shape})')
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parents:
diff changeset
750
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
751 # Remove dark field intensities above the cutoff
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
752 #RV tdf_cutoff = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
753 tdf_cutoff = tdf.min()+2*(np.median(tdf)-tdf.min())
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parents:
diff changeset
754 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
755 if tdf_cutoff is not None:
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diff changeset
756 if not is_num(tdf_cutoff, ge=0):
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diff changeset
757 logger.warning(f'Ignoring illegal value of tdf_cutoff {tdf_cutoff}')
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parents:
diff changeset
758 else:
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parents:
diff changeset
759 tdf[tdf > tdf_cutoff] = np.nan
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parents:
diff changeset
760 logger.debug(f'tdf_cutoff = {tdf_cutoff}')
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parents:
diff changeset
761
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
762 # Remove nans
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parents:
diff changeset
763 tdf_mean = np.nanmean(tdf)
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parents:
diff changeset
764 logger.debug(f'tdf_mean = {tdf_mean}')
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parents:
diff changeset
765 np.nan_to_num(tdf, copy=False, nan=tdf_mean, posinf=tdf_mean, neginf=0.)
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parents:
diff changeset
766
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parents:
diff changeset
767 # Plot dark field
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parents:
diff changeset
768 if self.galaxy_flag:
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parents:
diff changeset
769 quick_imshow(tdf, title='dark field', path='tomo_reduce_plots', save_fig=self.save_figs,
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parents:
diff changeset
770 save_only=self.save_only)
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parents:
diff changeset
771 elif not self.test_mode:
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parents:
diff changeset
772 quick_imshow(tdf, title='dark field', path=self.output_folder, save_fig=self.save_figs,
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parents:
diff changeset
773 save_only=self.save_only)
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parents:
diff changeset
774 clear_imshow('dark field')
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parents:
diff changeset
775 # quick_imshow(tdf, title='dark field', block=True)
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parents:
diff changeset
776
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
777 # Add dark field to reduced data NXprocess
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parents:
diff changeset
778 reduced_data.data = NXdata()
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parents:
diff changeset
779 reduced_data.data['dark_field'] = tdf
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parents:
diff changeset
780
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parents:
diff changeset
781 return(reduced_data)
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parents:
diff changeset
782
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parents:
diff changeset
783 def _gen_bright(self, nxentry, reduced_data):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
784 """Generate bright field.
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parents:
diff changeset
785 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
786 # Get the bright field images
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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diff changeset
787 image_key = nxentry.instrument.detector.get('image_key', None)
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parents:
diff changeset
788 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
789 field_indices = [index for index, key in enumerate(image_key) if key == 1]
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parents:
diff changeset
790 tbf_stack = nxentry.instrument.detector.data[field_indices,:,:]
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parents:
diff changeset
791 # RV the default NXtomo form does not accomodate bright or dark field stacks
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parents:
diff changeset
792 else:
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parents:
diff changeset
793 bright_field_scans = nxentry.spec_scans.bright_field
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parents:
diff changeset
794 bright_field = FlatField.construct_from_nxcollection(bright_field_scans)
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parents:
diff changeset
795 prefix = str(nxentry.instrument.detector.local_name)
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parents:
diff changeset
796 tbf_stack = bright_field.get_detector_data(prefix)
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parents:
diff changeset
797 if isinstance(tbf_stack, list):
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parents:
diff changeset
798 assert(len(tbf_stack) == 1) # TODO
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parents:
diff changeset
799 tbf_stack = tbf_stack[0]
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parents:
diff changeset
800
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
801 # Take median if more than one image
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parents:
diff changeset
802 """Median or mean: It may be best to try the median because of some image
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parents:
diff changeset
803 artifacts that arise due to crinkles in the upstream kapton tape windows
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parents:
diff changeset
804 causing some phase contrast images to appear on the detector.
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
805 One thing that also may be useful in a future implementation is to do a
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
806 brightfield adjustment on EACH frame of the tomo based on a ROI in the
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parents:
diff changeset
807 corner of the frame where there is no sample but there is the direct X-ray
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
808 beam because there is frame to frame fluctuations from the incoming beam.
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parents:
diff changeset
809 We don’t typically account for them but potentially could.
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parents:
diff changeset
810 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
811 if tbf_stack.ndim == 2:
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parents:
diff changeset
812 tbf = tbf_stack
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parents:
diff changeset
813 elif tbf_stack.ndim == 3:
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parents:
diff changeset
814 tbf = np.median(tbf_stack, axis=0)
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parents:
diff changeset
815 del tbf_stack
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parents:
diff changeset
816 else:
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parents:
diff changeset
817 raise ValueError(f'Invalid tbf_stack shape ({tbf_stacks.shape})')
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parents:
diff changeset
818
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
819 # Subtract dark field
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parents:
diff changeset
820 if 'data' in reduced_data and 'dark_field' in reduced_data.data:
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parents:
diff changeset
821 tbf -= reduced_data.data.dark_field
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parents:
diff changeset
822 else:
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parents:
diff changeset
823 logger.warning('Dark field unavailable')
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parents:
diff changeset
824
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
825 # Set any non-positive values to one
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
826 # (avoid negative bright field values for spikes in dark field)
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parents:
diff changeset
827 tbf[tbf < 1] = 1
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parents:
diff changeset
828
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parents:
diff changeset
829 # Plot bright field
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diff changeset
830 if self.galaxy_flag:
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parents:
diff changeset
831 quick_imshow(tbf, title='bright field', path='tomo_reduce_plots',
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parents:
diff changeset
832 save_fig=self.save_figs, save_only=self.save_only)
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parents:
diff changeset
833 elif not self.test_mode:
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parents:
diff changeset
834 quick_imshow(tbf, title='bright field', path=self.output_folder,
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parents:
diff changeset
835 save_fig=self.save_figs, save_only=self.save_only)
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parents:
diff changeset
836 clear_imshow('bright field')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
837 # quick_imshow(tbf, title='bright field', block=True)
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parents:
diff changeset
838
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
839 # Add bright field to reduced data NXprocess
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parents:
diff changeset
840 if 'data' not in reduced_data:
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parents:
diff changeset
841 reduced_data.data = NXdata()
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parents:
diff changeset
842 reduced_data.data['bright_field'] = tbf
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parents:
diff changeset
843
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parents:
diff changeset
844 return(reduced_data)
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parents:
diff changeset
845
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parents:
diff changeset
846 def _set_detector_bounds(self, nxentry, reduced_data, img_x_bounds=None):
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diff changeset
847 """Set vertical detector bounds for each image stack.
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parents:
diff changeset
848 Right now the range is the same for each set in the image stack.
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parents:
diff changeset
849 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
850 if self.test_mode:
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parents:
diff changeset
851 return(tuple(self.test_config['img_x_bounds']))
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parents:
diff changeset
852
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
853 # Get the first tomography image and the reference heights
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parents:
diff changeset
854 image_key = nxentry.instrument.detector.get('image_key', None)
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parents:
diff changeset
855 if image_key and 'data' in nxentry.instrument.detector:
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parents:
diff changeset
856 field_indices = [index for index, key in enumerate(image_key) if key == 0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
857 first_image = np.asarray(nxentry.instrument.detector.data[field_indices[0],:,:])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
858 theta = float(nxentry.sample.rotation_angle[field_indices[0]])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
859 z_translation_all = nxentry.sample.z_translation[field_indices]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
860 vertical_shifts = sorted(list(set(z_translation_all)))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
861 num_tomo_stacks = len(vertical_shifts)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
862 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
863 tomo_field_scans = nxentry.spec_scans.tomo_fields
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
864 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
865 vertical_shifts = tomo_fields.get_vertical_shifts()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
866 if not isinstance(vertical_shifts, list):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
867 vertical_shifts = [vertical_shifts]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
868 prefix = str(nxentry.instrument.detector.local_name)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
869 t0 = time()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
870 first_image = tomo_fields.get_detector_data(prefix, tomo_fields.scan_numbers[0], 0)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
871 logger.debug(f'Getting first image took {time()-t0:.2f} seconds')
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parents:
diff changeset
872 num_tomo_stacks = len(tomo_fields.scan_numbers)
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parents:
diff changeset
873 theta = tomo_fields.theta_range['start']
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parents:
diff changeset
874
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
875 # Select image bounds
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parents:
diff changeset
876 title = f'tomography image at theta={round(theta, 2)+0}'
5
543dba81eb15 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents: 4
diff changeset
877 if img_x_bounds is not None:
6
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parents: 5
diff changeset
878 if is_int_pair(img_x_bounds) and img_x_bounds[0] == -1 and img_x_bounds[1] == -1:
5
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parents: 4
diff changeset
879 img_x_bounds = None
6
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parents: 5
diff changeset
880 elif not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]):
05335876d167 planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents: 5
diff changeset
881 raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
4
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
882 if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
883 pixel_size = nxentry.instrument.detector.x_pixel_size
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parents:
diff changeset
884 # Try to get a fit from the bright field
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
885 tbf = np.asarray(reduced_data.data.bright_field)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
886 tbf_shape = tbf.shape
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
887 x_sum = np.sum(tbf, 1)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
888 x_sum_min = x_sum.min()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
889 x_sum_max = x_sum.max()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
890 fit = Fit.fit_data(x_sum, 'rectangle', x=np.array(range(len(x_sum))), form='atan',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
891 guess=True)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
892 parameters = fit.best_values
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
893 x_low_fit = parameters.get('center1', None)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
894 x_upp_fit = parameters.get('center2', None)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
895 sig_low = parameters.get('sigma1', None)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
896 sig_upp = parameters.get('sigma2', None)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
897 have_fit = fit.success and x_low_fit is not None and x_upp_fit is not None and \
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
898 sig_low is not None and sig_upp is not None and \
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
899 0 <= x_low_fit < x_upp_fit <= x_sum.size and \
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
900 (sig_low+sig_upp)/(x_upp_fit-x_low_fit) < 0.1
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
901 if have_fit:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
902 # Set a 5% margin on each side
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
903 margin = 0.05*(x_upp_fit-x_low_fit)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
904 x_low_fit = max(0, x_low_fit-margin)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
905 x_upp_fit = min(tbf_shape[0], x_upp_fit+margin)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
906 if num_tomo_stacks == 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
907 if have_fit:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
908 # Set the default range to enclose the full fitted window
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
909 x_low = int(x_low_fit)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
910 x_upp = int(x_upp_fit)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
911 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
912 # Center a default range of 1 mm (RV: can we get this from the slits?)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
913 num_x_min = int((1.0-0.5*pixel_size)/pixel_size)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
914 x_low = int(0.5*(tbf_shape[0]-num_x_min))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
915 x_upp = x_low+num_x_min
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
916 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
917 # Get the default range from the reference heights
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
918 delta_z = vertical_shifts[1]-vertical_shifts[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
919 for i in range(2, num_tomo_stacks):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
920 delta_z = min(delta_z, vertical_shifts[i]-vertical_shifts[i-1])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
921 logger.debug(f'delta_z = {delta_z}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
922 num_x_min = int((delta_z-0.5*pixel_size)/pixel_size)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
923 logger.debug(f'num_x_min = {num_x_min}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
924 if num_x_min > tbf_shape[0]:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
925 logger.warning('Image bounds and pixel size prevent seamless stacking')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
926 if have_fit:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
927 # Center the default range relative to the fitted window
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
928 x_low = int(0.5*(x_low_fit+x_upp_fit-num_x_min))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
929 x_upp = x_low+num_x_min
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
930 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
931 # Center the default range
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
932 x_low = int(0.5*(tbf_shape[0]-num_x_min))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
933 x_upp = x_low+num_x_min
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
934 if self.galaxy_flag:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
935 img_x_bounds = (x_low, x_upp)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
936 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
937 tmp = np.copy(tbf)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
938 tmp_max = tmp.max()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
939 tmp[x_low,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
940 tmp[x_upp-1,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
941 quick_imshow(tmp, title='bright field')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
942 tmp = np.copy(first_image)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
943 tmp_max = tmp.max()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
944 tmp[x_low,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
945 tmp[x_upp-1,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
946 quick_imshow(tmp, title=title)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
947 del tmp
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
948 quick_plot((range(x_sum.size), x_sum),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
949 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
950 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
951 title='sum over theta and y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
952 print(f'lower bound = {x_low} (inclusive)')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
953 print(f'upper bound = {x_upp} (exclusive)]')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
954 accept = input_yesno('Accept these bounds (y/n)?', 'y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
955 clear_imshow('bright field')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
956 clear_imshow(title)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
957 clear_plot('sum over theta and y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
958 if accept:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
959 img_x_bounds = (x_low, x_upp)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
960 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
961 while True:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
962 mask, img_x_bounds = draw_mask_1d(x_sum, title='select x data range',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
963 legend='sum over theta and y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
964 if len(img_x_bounds) == 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
965 break
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
966 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
967 print(f'Choose a single connected data range')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
968 img_x_bounds = tuple(img_x_bounds[0])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
969 if (num_tomo_stacks > 1 and img_x_bounds[1]-img_x_bounds[0]+1 <
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
970 int((delta_z-0.5*pixel_size)/pixel_size)):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
971 logger.warning('Image bounds and pixel size prevent seamless stacking')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
972 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
973 if num_tomo_stacks > 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
974 raise NotImplementedError('Selecting image bounds for multiple stacks on FMB')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
975 # For FMB: use the first tomography image to select range
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
976 # RV: revisit if they do tomography with multiple stacks
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
977 x_sum = np.sum(first_image, 1)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
978 x_sum_min = x_sum.min()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
979 x_sum_max = x_sum.max()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
980 if self.galaxy_flag:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
981 if img_x_bounds is None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
982 img_x_bounds = (0, first_image.shape[0])
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
983 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
984 quick_imshow(first_image, title=title)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
985 print('Select vertical data reduction range from first tomography image')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
986 img_x_bounds = select_image_bounds(first_image, 0, title=title)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
987 clear_imshow(title)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
988 if img_x_bounds is None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
989 raise ValueError('Unable to select image bounds')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
990
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
991 # Plot results
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
992 if self.galaxy_flag:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
993 path = 'tomo_reduce_plots'
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
994 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
995 path = self.output_folder
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
996 x_low = img_x_bounds[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
997 x_upp = img_x_bounds[1]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
998 tmp = np.copy(first_image)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
999 tmp_max = tmp.max()
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1000 tmp[x_low,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1001 tmp[x_upp-1,:] = tmp_max
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1002 quick_imshow(tmp, title=title, path=path, save_fig=self.save_figs, save_only=self.save_only,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1003 block=self.block)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1004 del tmp
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1005 quick_plot((range(x_sum.size), x_sum),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1006 ([x_low, x_low], [x_sum_min, x_sum_max], 'r-'),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1007 ([x_upp, x_upp], [x_sum_min, x_sum_max], 'r-'),
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1008 title='sum over theta and y', path=path, save_fig=self.save_figs,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1009 save_only=self.save_only, block=self.block)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1010
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1011 return(img_x_bounds)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1012
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1013 def _set_zoom_or_skip(self):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1014 """Set zoom and/or theta skip to reduce memory the requirement for the analysis.
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1015 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1016 # if input_yesno('\nDo you want to zoom in to reduce memory requirement (y/n)?', 'n'):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1017 # zoom_perc = input_int(' Enter zoom percentage', ge=1, le=100)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1018 # else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1019 # zoom_perc = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1020 zoom_perc = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1021 # if input_yesno('Do you want to skip thetas to reduce memory requirement (y/n)?', 'n'):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1022 # num_theta_skip = input_int(' Enter the number skip theta interval', ge=0,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1023 # lt=num_theta)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1024 # else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1025 # num_theta_skip = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1026 num_theta_skip = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1027 logger.debug(f'zoom_perc = {zoom_perc}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1028 logger.debug(f'num_theta_skip = {num_theta_skip}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1029
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1030 return(zoom_perc, num_theta_skip)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1031
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1032 def _gen_tomo(self, nxentry, reduced_data):
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1033 """Generate tomography fields.
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1034 """
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1035 # Get full bright field
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1036 tbf = np.asarray(reduced_data.data.bright_field)
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diff changeset
1037 tbf_shape = tbf.shape
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1038
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parents:
diff changeset
1039 # Get image bounds
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diff changeset
1040 img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0])))
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diff changeset
1041 img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1])))
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diff changeset
1042
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parents:
diff changeset
1043 # Get resized dark field
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parents:
diff changeset
1044 # if 'dark_field' in data:
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diff changeset
1045 # tbf = np.asarray(reduced_data.data.dark_field[
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parents:
diff changeset
1046 # img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]])
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parents:
diff changeset
1047 # else:
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diff changeset
1048 # logger.warning('Dark field unavailable')
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diff changeset
1049 # tdf = None
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diff changeset
1050 tdf = None
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diff changeset
1051
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parents:
diff changeset
1052 # Resize bright field
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diff changeset
1053 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
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diff changeset
1054 tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]
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parents:
diff changeset
1055
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parents:
diff changeset
1056 # Get the tomography images
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diff changeset
1057 image_key = nxentry.instrument.detector.get('image_key', None)
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diff changeset
1058 if image_key and 'data' in nxentry.instrument.detector:
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diff changeset
1059 field_indices_all = [index for index, key in enumerate(image_key) if key == 0]
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diff changeset
1060 z_translation_all = nxentry.sample.z_translation[field_indices_all]
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diff changeset
1061 z_translation_levels = sorted(list(set(z_translation_all)))
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diff changeset
1062 num_tomo_stacks = len(z_translation_levels)
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diff changeset
1063 tomo_stacks = num_tomo_stacks*[np.array([])]
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1064 horizontal_shifts = []
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diff changeset
1065 vertical_shifts = []
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1066 thetas = None
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1067 tomo_stacks = []
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diff changeset
1068 for i, z_translation in enumerate(z_translation_levels):
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diff changeset
1069 field_indices = [field_indices_all[index]
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diff changeset
1070 for index, z in enumerate(z_translation_all) if z == z_translation]
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diff changeset
1071 horizontal_shift = list(set(nxentry.sample.x_translation[field_indices]))
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diff changeset
1072 assert(len(horizontal_shift) == 1)
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diff changeset
1073 horizontal_shifts += horizontal_shift
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diff changeset
1074 vertical_shift = list(set(nxentry.sample.z_translation[field_indices]))
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diff changeset
1075 assert(len(vertical_shift) == 1)
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diff changeset
1076 vertical_shifts += vertical_shift
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diff changeset
1077 sequence_numbers = nxentry.instrument.detector.sequence_number[field_indices]
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parents:
diff changeset
1078 if thetas is None:
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parents:
diff changeset
1079 thetas = np.asarray(nxentry.sample.rotation_angle[field_indices]) \
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parents:
diff changeset
1080 [sequence_numbers]
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diff changeset
1081 else:
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parents:
diff changeset
1082 assert(all(thetas[i] == nxentry.sample.rotation_angle[field_indices[index]]
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parents:
diff changeset
1083 for i, index in enumerate(sequence_numbers)))
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parents:
diff changeset
1084 assert(list(set(sequence_numbers)) == [i for i in range(len(sequence_numbers))])
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parents:
diff changeset
1085 if list(sequence_numbers) == [i for i in range(len(sequence_numbers))]:
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diff changeset
1086 tomo_stack = np.asarray(nxentry.instrument.detector.data[field_indices])
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diff changeset
1087 else:
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diff changeset
1088 raise ValueError('Unable to load the tomography images')
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diff changeset
1089 tomo_stacks.append(tomo_stack)
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diff changeset
1090 else:
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diff changeset
1091 tomo_field_scans = nxentry.spec_scans.tomo_fields
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parents:
diff changeset
1092 tomo_fields = TomoField.construct_from_nxcollection(tomo_field_scans)
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diff changeset
1093 horizontal_shifts = tomo_fields.get_horizontal_shifts()
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diff changeset
1094 vertical_shifts = tomo_fields.get_vertical_shifts()
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parents:
diff changeset
1095 prefix = str(nxentry.instrument.detector.local_name)
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parents:
diff changeset
1096 t0 = time()
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diff changeset
1097 tomo_stacks = tomo_fields.get_detector_data(prefix)
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diff changeset
1098 logger.debug(f'Getting tomography images took {time()-t0:.2f} seconds')
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parents:
diff changeset
1099 logger.debug(f'Getting all images took {time()-t0:.2f} seconds')
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diff changeset
1100 thetas = np.linspace(tomo_fields.theta_range['start'], tomo_fields.theta_range['end'],
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diff changeset
1101 tomo_fields.theta_range['num'])
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diff changeset
1102 if not isinstance(tomo_stacks, list):
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diff changeset
1103 horizontal_shifts = [horizontal_shifts]
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diff changeset
1104 vertical_shifts = [vertical_shifts]
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diff changeset
1105 tomo_stacks = [tomo_stacks]
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parents:
diff changeset
1106
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parents:
diff changeset
1107 reduced_tomo_stacks = []
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diff changeset
1108 if self.galaxy_flag:
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diff changeset
1109 path = 'tomo_reduce_plots'
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diff changeset
1110 else:
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parents:
diff changeset
1111 path = self.output_folder
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parents:
diff changeset
1112 for i, tomo_stack in enumerate(tomo_stacks):
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parents:
diff changeset
1113 # Resize the tomography images
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parents:
diff changeset
1114 # Right now the range is the same for each set in the image stack.
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parents:
diff changeset
1115 if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]):
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parents:
diff changeset
1116 t0 = time()
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parents:
diff changeset
1117 tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1],
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parents:
diff changeset
1118 img_y_bounds[0]:img_y_bounds[1]].astype('float64')
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diff changeset
1119 logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds')
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diff changeset
1120
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parents:
diff changeset
1121 # Subtract dark field
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diff changeset
1122 if tdf is not None:
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parents:
diff changeset
1123 t0 = time()
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diff changeset
1124 with set_numexpr_threads(self.num_core):
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parents:
diff changeset
1125 ne.evaluate('tomo_stack-tdf', out=tomo_stack)
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parents:
diff changeset
1126 logger.debug(f'Subtracting dark field took {time()-t0:.2f} seconds')
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parents:
diff changeset
1127
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parents:
diff changeset
1128 # Normalize
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1129 t0 = time()
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1130 with set_numexpr_threads(self.num_core):
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1131 ne.evaluate('tomo_stack/tbf', out=tomo_stack, truediv=True)
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1132 logger.debug(f'Normalizing took {time()-t0:.2f} seconds')
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1133
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1134 # Remove non-positive values and linearize data
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1135 t0 = time()
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1136 cutoff = 1.e-6
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1137 with set_numexpr_threads(self.num_core):
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1138 ne.evaluate('where(tomo_stack<cutoff, cutoff, tomo_stack)', out=tomo_stack)
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1139 with set_numexpr_threads(self.num_core):
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1140 ne.evaluate('-log(tomo_stack)', out=tomo_stack)
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1141 logger.debug('Removing non-positive values and linearizing data took '+
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1142 f'{time()-t0:.2f} seconds')
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1143
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1144 # Get rid of nans/infs that may be introduced by normalization
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1145 t0 = time()
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1146 np.where(np.isfinite(tomo_stack), tomo_stack, 0.)
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1147 logger.debug(f'Remove nans/infs took {time()-t0:.2f} seconds')
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1148
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1149 # Downsize tomography stack to smaller size
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1150 # TODO use theta_skip as well
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1151 tomo_stack = tomo_stack.astype('float32')
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1152 if not self.test_mode:
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1153 if len(tomo_stacks) == 1:
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1154 title = f'red fullres theta {round(thetas[0], 2)+0}'
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1155 else:
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diff changeset
1156 title = f'red stack {i+1} fullres theta {round(thetas[0], 2)+0}'
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1157 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
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1158 save_only=self.save_only, block=self.block)
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1159 # if not self.block:
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1160 # clear_imshow(title)
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1161 if False and zoom_perc != 100:
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1162 t0 = time()
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1163 logger.debug(f'Zooming in ...')
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1164 tomo_zoom_list = []
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1165 for j in range(tomo_stack.shape[0]):
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diff changeset
1166 tomo_zoom = spi.zoom(tomo_stack[j,:,:], 0.01*zoom_perc)
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1167 tomo_zoom_list.append(tomo_zoom)
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1168 tomo_stack = np.stack([tomo_zoom for tomo_zoom in tomo_zoom_list])
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1169 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1170 logger.info(f'Zooming in took {time()-t0:.2f} seconds')
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diff changeset
1171 del tomo_zoom_list
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diff changeset
1172 if not self.test_mode:
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diff changeset
1173 title = f'red stack {zoom_perc}p theta {round(thetas[0], 2)+0}'
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diff changeset
1174 quick_imshow(tomo_stack[0,:,:], title=title, path=path, save_fig=self.save_figs,
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diff changeset
1175 save_only=self.save_only, block=self.block)
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diff changeset
1176 # if not self.block:
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1177 # clear_imshow(title)
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1178
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diff changeset
1179 # Save test data to file
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diff changeset
1180 if self.test_mode:
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diff changeset
1181 # row_index = int(tomo_stack.shape[0]/2)
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diff changeset
1182 # np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[row_index,:,:],
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diff changeset
1183 # fmt='%.6e')
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diff changeset
1184 row_index = int(tomo_stack.shape[1]/2)
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diff changeset
1185 np.savetxt(f'{self.output_folder}/red_stack_{i+1}.txt', tomo_stack[:,row_index,:],
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diff changeset
1186 fmt='%.6e')
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1187
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diff changeset
1188 # Combine resized stacks
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1189 reduced_tomo_stacks.append(tomo_stack)
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1190
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1191 # Add tomo field info to reduced data NXprocess
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1192 reduced_data['rotation_angle'] = thetas
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1193 reduced_data['x_translation'] = np.asarray(horizontal_shifts)
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1194 reduced_data['z_translation'] = np.asarray(vertical_shifts)
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1195 reduced_data.data['tomo_fields'] = np.asarray(reduced_tomo_stacks)
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1196
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1197 if tdf is not None:
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1198 del tdf
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diff changeset
1199 del tbf
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1200
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diff changeset
1201 return(reduced_data)
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1202
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1203 def _find_center_one_plane(self, sinogram, row, thetas, eff_pixel_size, cross_sectional_dim,
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diff changeset
1204 path=None, tol=0.1, num_core=1):
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diff changeset
1205 """Find center for a single tomography plane.
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1206 """
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diff changeset
1207 # Try automatic center finding routines for initial value
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1208 # sinogram index order: theta,column
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1209 # need column,theta for iradon, so take transpose
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1210 sinogram = np.asarray(sinogram)
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1211 sinogram_T = sinogram.T
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1212 center = sinogram.shape[1]/2
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1213
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1214 # Try using Nghia Vo’s method
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1215 t0 = time()
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1216 if num_core > num_core_tomopy_limit:
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1217 logger.debug(f'Running find_center_vo on {num_core_tomopy_limit} cores ...')
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1218 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core_tomopy_limit)
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1219 else:
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1220 logger.debug(f'Running find_center_vo on {num_core} cores ...')
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1221 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core)
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1222 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1223 logger.info(f'Finding the center using Nghia Vo’s method took {time()-t0:.2f} seconds')
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diff changeset
1224 center_offset_vo = tomo_center-center
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diff changeset
1225 logger.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
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diff changeset
1226 t0 = time()
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diff changeset
1227 logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
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diff changeset
1228 recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
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diff changeset
1229 eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1230 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1231 logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
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diff changeset
1232
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diff changeset
1233 title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
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diff changeset
1234 self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1235
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parents:
diff changeset
1236 # Try using phase correlation method
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diff changeset
1237 # if input_yesno('Try finding center using phase correlation (y/n)?', 'n'):
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diff changeset
1238 # t0 = time()
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diff changeset
1239 # logger.debug(f'Running find_center_pc ...')
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1240 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, rotc_guess=tomo_center)
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diff changeset
1241 # error = 1.
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diff changeset
1242 # while error > tol:
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diff changeset
1243 # prev = tomo_center
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diff changeset
1244 # tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol,
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diff changeset
1245 # rotc_guess=tomo_center)
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diff changeset
1246 # error = np.abs(tomo_center-prev)
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diff changeset
1247 # logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1248 # logger.info('Finding the center using the phase correlation method took '+
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diff changeset
1249 # f'{time()-t0:.2f} seconds')
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diff changeset
1250 # center_offset = tomo_center-center
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diff changeset
1251 # print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
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parents:
diff changeset
1252 # t0 = time()
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diff changeset
1253 # logger.debug(f'Running _reconstruct_one_plane on {self.num_core} cores ...')
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diff changeset
1254 # recon_plane = self._reconstruct_one_plane(sinogram_T, tomo_center, thetas,
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diff changeset
1255 # eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1256 # logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1257 # logger.info(f'Reconstructing row {row} took {time()-t0:.2f} seconds')
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diff changeset
1258 #
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diff changeset
1259 # title = f'edges row{row} center_offset{center_offset:.2f} PC'
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diff changeset
1260 # self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1261
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diff changeset
1262 # Select center location
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diff changeset
1263 # if input_yesno('Accept a center location (y) or continue search (n)?', 'y'):
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diff changeset
1264 if True:
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diff changeset
1265 # center_offset = input_num(' Enter chosen center offset', ge=-center, le=center,
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diff changeset
1266 # default=center_offset_vo)
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diff changeset
1267 center_offset = center_offset_vo
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parents:
diff changeset
1268 del sinogram_T
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parents:
diff changeset
1269 del recon_plane
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diff changeset
1270 return float(center_offset)
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parents:
diff changeset
1271
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parents:
diff changeset
1272 # perform center finding search
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diff changeset
1273 while True:
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diff changeset
1274 center_offset_low = input_int('\nEnter lower bound for center offset', ge=-center,
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diff changeset
1275 le=center)
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diff changeset
1276 center_offset_upp = input_int('Enter upper bound for center offset',
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diff changeset
1277 ge=center_offset_low, le=center)
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diff changeset
1278 if center_offset_upp == center_offset_low:
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diff changeset
1279 center_offset_step = 1
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diff changeset
1280 else:
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diff changeset
1281 center_offset_step = input_int('Enter step size for center offset search', ge=1,
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diff changeset
1282 le=center_offset_upp-center_offset_low)
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diff changeset
1283 num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step)
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diff changeset
1284 center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset)
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diff changeset
1285 for center_offset in center_offsets:
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diff changeset
1286 if center_offset == center_offset_vo:
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diff changeset
1287 continue
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diff changeset
1288 t0 = time()
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diff changeset
1289 logger.debug(f'Running _reconstruct_one_plane on {num_core} cores ...')
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diff changeset
1290 recon_plane = self._reconstruct_one_plane(sinogram_T, center_offset+center, thetas,
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diff changeset
1291 eff_pixel_size, cross_sectional_dim, False, num_core)
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diff changeset
1292 logger.debug(f'... done in {time()-t0:.2f} seconds')
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diff changeset
1293 logger.info(f'Reconstructing center_offset {center_offset} took '+
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diff changeset
1294 f'{time()-t0:.2f} seconds')
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diff changeset
1295 title = f'edges row{row} center_offset{center_offset:.2f}'
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diff changeset
1296 self._plot_edges_one_plane(recon_plane, title, path=path)
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diff changeset
1297 if input_int('\nContinue (0) or end the search (1)', ge=0, le=1):
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diff changeset
1298 break
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diff changeset
1299
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diff changeset
1300 del sinogram_T
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diff changeset
1301 del recon_plane
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diff changeset
1302 center_offset = input_num(' Enter chosen center offset', ge=-center, le=center)
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diff changeset
1303 return float(center_offset)
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diff changeset
1304
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diff changeset
1305 def _reconstruct_one_plane(self, tomo_plane_T, center, thetas, eff_pixel_size,
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diff changeset
1306 cross_sectional_dim, plot_sinogram=True, num_core=1):
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diff changeset
1307 """Invert the sinogram for a single tomography plane.
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diff changeset
1308 """
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diff changeset
1309 # tomo_plane_T index order: column,theta
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diff changeset
1310 assert(0 <= center < tomo_plane_T.shape[0])
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diff changeset
1311 center_offset = center-tomo_plane_T.shape[0]/2
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diff changeset
1312 two_offset = 2*int(np.round(center_offset))
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diff changeset
1313 two_offset_abs = np.abs(two_offset)
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diff changeset
1314 max_rad = int(0.55*(cross_sectional_dim/eff_pixel_size)) # 10% slack to avoid edge effects
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diff changeset
1315 if max_rad > 0.5*tomo_plane_T.shape[0]:
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diff changeset
1316 max_rad = 0.5*tomo_plane_T.shape[0]
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diff changeset
1317 dist_from_edge = max(1, int(np.floor((tomo_plane_T.shape[0]-two_offset_abs)/2.)-max_rad))
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parents:
diff changeset
1318 if two_offset >= 0:
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diff changeset
1319 logger.debug(f'sinogram range = [{two_offset+dist_from_edge}, {-dist_from_edge}]')
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diff changeset
1320 sinogram = tomo_plane_T[two_offset+dist_from_edge:-dist_from_edge,:]
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diff changeset
1321 else:
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diff changeset
1322 logger.debug(f'sinogram range = [{dist_from_edge}, {two_offset-dist_from_edge}]')
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diff changeset
1323 sinogram = tomo_plane_T[dist_from_edge:two_offset-dist_from_edge,:]
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diff changeset
1324 if not self.galaxy_flag and plot_sinogram:
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diff changeset
1325 quick_imshow(sinogram.T, f'sinogram center offset{center_offset:.2f}', aspect='auto',
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diff changeset
1326 path=self.output_folder, save_fig=self.save_figs, save_only=self.save_only,
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diff changeset
1327 block=self.block)
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diff changeset
1328
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diff changeset
1329 # Inverting sinogram
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diff changeset
1330 t0 = time()
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diff changeset
1331 recon_sinogram = iradon(sinogram, theta=thetas, circle=True)
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diff changeset
1332 logger.debug(f'Inverting sinogram took {time()-t0:.2f} seconds')
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parents:
diff changeset
1333 del sinogram
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diff changeset
1334
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diff changeset
1335 # Performing Gaussian filtering and removing ring artifacts
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diff changeset
1336 recon_parameters = None#self.config.get('recon_parameters')
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diff changeset
1337 if recon_parameters is None:
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parents:
diff changeset
1338 sigma = 1.0
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parents:
diff changeset
1339 ring_width = 15
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diff changeset
1340 else:
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diff changeset
1341 sigma = recon_parameters.get('gaussian_sigma', 1.0)
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diff changeset
1342 if not is_num(sigma, ge=0.0):
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diff changeset
1343 logger.warning(f'Invalid gaussian_sigma ({sigma}) in _reconstruct_one_plane, '+
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diff changeset
1344 'set to a default value of 1.0')
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parents:
diff changeset
1345 sigma = 1.0
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diff changeset
1346 ring_width = recon_parameters.get('ring_width', 15)
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diff changeset
1347 if not is_int(ring_width, ge=0):
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diff changeset
1348 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
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parents:
diff changeset
1349 'set to a default value of 15')
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parents:
diff changeset
1350 ring_width = 15
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parents:
diff changeset
1351 t0 = time()
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diff changeset
1352 recon_sinogram = spi.gaussian_filter(recon_sinogram, sigma, mode='nearest')
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diff changeset
1353 recon_clean = np.expand_dims(recon_sinogram, axis=0)
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diff changeset
1354 del recon_sinogram
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diff changeset
1355 recon_clean = tomopy.misc.corr.remove_ring(recon_clean, rwidth=ring_width, ncore=num_core)
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diff changeset
1356 logger.debug(f'Filtering and removing ring artifacts took {time()-t0:.2f} seconds')
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diff changeset
1357
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diff changeset
1358 return recon_clean
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diff changeset
1359
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diff changeset
1360 def _plot_edges_one_plane(self, recon_plane, title, path=None):
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diff changeset
1361 vis_parameters = None#self.config.get('vis_parameters')
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diff changeset
1362 if vis_parameters is None:
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diff changeset
1363 weight = 0.1
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diff changeset
1364 else:
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diff changeset
1365 weight = vis_parameters.get('denoise_weight', 0.1)
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diff changeset
1366 if not is_num(weight, ge=0.0):
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diff changeset
1367 logger.warning(f'Invalid weight ({weight}) in _plot_edges_one_plane, '+
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diff changeset
1368 'set to a default value of 0.1')
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diff changeset
1369 weight = 0.1
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diff changeset
1370 edges = denoise_tv_chambolle(recon_plane, weight=weight)
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diff changeset
1371 vmax = np.max(edges[0,:,:])
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diff changeset
1372 vmin = -vmax
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diff changeset
1373 if path is None:
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diff changeset
1374 path = self.output_folder
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diff changeset
1375 quick_imshow(edges[0,:,:], f'{title} coolwarm', path=path, cmap='coolwarm',
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diff changeset
1376 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
1377 quick_imshow(edges[0,:,:], f'{title} gray', path=path, cmap='gray', vmin=vmin, vmax=vmax,
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diff changeset
1378 save_fig=self.save_figs, save_only=self.save_only, block=self.block)
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diff changeset
1379 del edges
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diff changeset
1380
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diff changeset
1381 def _reconstruct_one_tomo_stack(self, tomo_stack, thetas, center_offsets=[], num_core=1,
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diff changeset
1382 algorithm='gridrec'):
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diff changeset
1383 """Reconstruct a single tomography stack.
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diff changeset
1384 """
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diff changeset
1385 # tomo_stack order: row,theta,column
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diff changeset
1386 # input thetas must be in degrees
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diff changeset
1387 # centers_offset: tomography axis shift in pixels relative to column center
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diff changeset
1388 # RV should we remove stripes?
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diff changeset
1389 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html
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diff changeset
1390 # RV should we remove rings?
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diff changeset
1391 # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html
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diff changeset
1392 # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test?
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diff changeset
1393 if not len(center_offsets):
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diff changeset
1394 centers = np.zeros((tomo_stack.shape[0]))
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diff changeset
1395 elif len(center_offsets) == 2:
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diff changeset
1396 centers = np.linspace(center_offsets[0], center_offsets[1], tomo_stack.shape[0])
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diff changeset
1397 else:
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diff changeset
1398 if center_offsets.size != tomo_stack.shape[0]:
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diff changeset
1399 raise ValueError('center_offsets dimension mismatch in reconstruct_one_tomo_stack')
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diff changeset
1400 centers = center_offsets
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diff changeset
1401 centers += tomo_stack.shape[2]/2
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diff changeset
1402
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diff changeset
1403 # Get reconstruction parameters
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diff changeset
1404 recon_parameters = None#self.config.get('recon_parameters')
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parents:
diff changeset
1405 if recon_parameters is None:
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parents:
diff changeset
1406 sigma = 2.0
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parents:
diff changeset
1407 secondary_iters = 0
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parents:
diff changeset
1408 ring_width = 15
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diff changeset
1409 else:
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parents:
diff changeset
1410 sigma = recon_parameters.get('stripe_fw_sigma', 2.0)
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diff changeset
1411 if not is_num(sigma, ge=0):
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parents:
diff changeset
1412 logger.warning(f'Invalid stripe_fw_sigma ({sigma}) in '+
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parents:
diff changeset
1413 '_reconstruct_one_tomo_stack, set to a default value of 2.0')
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parents:
diff changeset
1414 ring_width = 15
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parents:
diff changeset
1415 secondary_iters = recon_parameters.get('secondary_iters', 0)
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parents:
diff changeset
1416 if not is_int(secondary_iters, ge=0):
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parents:
diff changeset
1417 logger.warning(f'Invalid secondary_iters ({secondary_iters}) in '+
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parents:
diff changeset
1418 '_reconstruct_one_tomo_stack, set to a default value of 0 (skip them)')
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parents:
diff changeset
1419 ring_width = 0
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parents:
diff changeset
1420 ring_width = recon_parameters.get('ring_width', 15)
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diff changeset
1421 if not is_int(ring_width, ge=0):
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parents:
diff changeset
1422 logger.warning(f'Invalid ring_width ({ring_width}) in _reconstruct_one_plane, '+
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parents:
diff changeset
1423 'set to a default value of 15')
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parents:
diff changeset
1424 ring_width = 15
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parents:
diff changeset
1425
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parents:
diff changeset
1426 # Remove horizontal stripe
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parents:
diff changeset
1427 t0 = time()
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diff changeset
1428 if num_core > num_core_tomopy_limit:
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parents:
diff changeset
1429 logger.debug('Running remove_stripe_fw on {num_core_tomopy_limit} cores ...')
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parents:
diff changeset
1430 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
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parents:
diff changeset
1431 ncore=num_core_tomopy_limit)
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diff changeset
1432 else:
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parents:
diff changeset
1433 logger.debug(f'Running remove_stripe_fw on {num_core} cores ...')
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parents:
diff changeset
1434 tomo_stack = tomopy.prep.stripe.remove_stripe_fw(tomo_stack, sigma=sigma,
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parents:
diff changeset
1435 ncore=num_core)
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parents:
diff changeset
1436 logger.debug(f'... tomopy.prep.stripe.remove_stripe_fw took {time()-t0:.2f} seconds')
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parents:
diff changeset
1437
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parents:
diff changeset
1438 # Perform initial image reconstruction
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parents:
diff changeset
1439 logger.debug('Performing initial image reconstruction')
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parents:
diff changeset
1440 t0 = time()
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parents:
diff changeset
1441 logger.debug(f'Running recon on {num_core} cores ...')
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parents:
diff changeset
1442 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
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parents:
diff changeset
1443 sinogram_order=True, algorithm=algorithm, ncore=num_core)
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parents:
diff changeset
1444 logger.debug(f'... done in {time()-t0:.2f} seconds')
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parents:
diff changeset
1445 logger.info(f'Performing initial image reconstruction took {time()-t0:.2f} seconds')
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parents:
diff changeset
1446
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parents:
diff changeset
1447 # Run optional secondary iterations
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parents:
diff changeset
1448 if secondary_iters > 0:
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parents:
diff changeset
1449 logger.debug(f'Running {secondary_iters} secondary iterations')
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parents:
diff changeset
1450 #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iters}
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parents:
diff changeset
1451 #RV: doesn't work for me:
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diff changeset
1452 #"Error: CUDA error 803: system has unsupported display driver/cuda driver combination."
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parents:
diff changeset
1453 #options = {'method':'SIRT', 'proj_type':'linear', 'MinConstraint': 0, 'num_iter':secondary_iters}
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parents:
diff changeset
1454 #SIRT did not finish while running overnight
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parents:
diff changeset
1455 #options = {'method':'SART', 'proj_type':'linear', 'num_iter':secondary_iters}
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parents:
diff changeset
1456 options = {'method':'SART', 'proj_type':'linear', 'MinConstraint': 0,
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parents:
diff changeset
1457 'num_iter':secondary_iters}
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parents:
diff changeset
1458 t0 = time()
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parents:
diff changeset
1459 logger.debug(f'Running recon on {num_core} cores ...')
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parents:
diff changeset
1460 tomo_recon_stack = tomopy.recon(tomo_stack, np.radians(thetas), centers,
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parents:
diff changeset
1461 init_recon=tomo_recon_stack, options=options, sinogram_order=True,
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parents:
diff changeset
1462 algorithm=tomopy.astra, ncore=num_core)
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parents:
diff changeset
1463 logger.debug(f'... done in {time()-t0:.2f} seconds')
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parents:
diff changeset
1464 logger.info(f'Performing secondary iterations took {time()-t0:.2f} seconds')
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parents:
diff changeset
1465
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parents:
diff changeset
1466 # Remove ring artifacts
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parents:
diff changeset
1467 t0 = time()
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parents:
diff changeset
1468 tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=ring_width, out=tomo_recon_stack,
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parents:
diff changeset
1469 ncore=num_core)
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parents:
diff changeset
1470 logger.debug(f'Removing ring artifacts took {time()-t0:.2f} seconds')
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parents:
diff changeset
1471
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parents:
diff changeset
1472 return tomo_recon_stack
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parents:
diff changeset
1473
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parents:
diff changeset
1474 def _resize_reconstructed_data(self, data, z_only=False):
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parents:
diff changeset
1475 """Resize the reconstructed tomography data.
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parents:
diff changeset
1476 """
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parents:
diff changeset
1477 # Data order: row(z),x,y or stack,row(z),x,y
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parents:
diff changeset
1478 if isinstance(data, list):
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parents:
diff changeset
1479 for stack in data:
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parents:
diff changeset
1480 assert(stack.ndim == 3)
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parents:
diff changeset
1481 num_tomo_stacks = len(data)
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parents:
diff changeset
1482 tomo_recon_stacks = data
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diff changeset
1483 else:
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parents:
diff changeset
1484 assert(data.ndim == 3)
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parents:
diff changeset
1485 num_tomo_stacks = 1
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parents:
diff changeset
1486 tomo_recon_stacks = [data]
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parents:
diff changeset
1487
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parents:
diff changeset
1488 if z_only:
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parents:
diff changeset
1489 x_bounds = None
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parents:
diff changeset
1490 y_bounds = None
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parents:
diff changeset
1491 else:
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parents:
diff changeset
1492 # Selecting x bounds (in yz-plane)
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parents:
diff changeset
1493 tomosum = 0
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parents:
diff changeset
1494 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,2))
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parents:
diff changeset
1495 for i in range(num_tomo_stacks)]
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parents:
diff changeset
1496 select_x_bounds = input_yesno('\nDo you want to change the image x-bounds (y/n)?', 'y')
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parents:
diff changeset
1497 if not select_x_bounds:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1498 x_bounds = None
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parents:
diff changeset
1499 else:
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parents:
diff changeset
1500 accept = False
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1501 index_ranges = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1502 while not accept:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1503 mask, x_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1504 title='select x data range', legend='recon stack sum yz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1505 while len(x_bounds) != 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1506 print('Please select exactly one continuous range')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1507 mask, x_bounds = draw_mask_1d(tomosum, title='select x data range',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1508 legend='recon stack sum yz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1509 x_bounds = x_bounds[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1510 # quick_plot(tomosum, vlines=x_bounds, title='recon stack sum yz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1511 # print(f'x_bounds = {x_bounds} (lower bound inclusive, upper bound '+
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1512 # 'exclusive)')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1513 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1514 accept = True
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1515 logger.debug(f'x_bounds = {x_bounds}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1516
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1517 # Selecting y bounds (in xz-plane)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1518 tomosum = 0
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1519 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(0,1))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1520 for i in range(num_tomo_stacks)]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1521 select_y_bounds = input_yesno('\nDo you want to change the image y-bounds (y/n)?', 'y')
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rv43
parents:
diff changeset
1522 if not select_y_bounds:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1523 y_bounds = None
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parents:
diff changeset
1524 else:
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rv43
parents:
diff changeset
1525 accept = False
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1526 index_ranges = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1527 while not accept:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1528 mask, y_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1529 title='select x data range', legend='recon stack sum xz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1530 while len(y_bounds) != 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1531 print('Please select exactly one continuous range')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1532 mask, y_bounds = draw_mask_1d(tomosum, title='select x data range',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1533 legend='recon stack sum xz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1534 y_bounds = y_bounds[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1535 # quick_plot(tomosum, vlines=y_bounds, title='recon stack sum xz')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
diff changeset
1536 # print(f'y_bounds = {y_bounds} (lower bound inclusive, upper bound '+
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1537 # 'exclusive)')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1538 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1539 accept = True
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1540 logger.debug(f'y_bounds = {y_bounds}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1541
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1542 # Selecting z bounds (in xy-plane) (only valid for a single image stack)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1543 if num_tomo_stacks != 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1544 z_bounds = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1545 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1546 tomosum = 0
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1547 [tomosum := tomosum+np.sum(tomo_recon_stacks[i], axis=(1,2))
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1548 for i in range(num_tomo_stacks)]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1549 select_z_bounds = input_yesno('Do you want to change the image z-bounds (y/n)?', 'n')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1550 if not select_z_bounds:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1551 z_bounds = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1552 else:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1553 accept = False
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1554 index_ranges = None
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1555 while not accept:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1556 mask, z_bounds = draw_mask_1d(tomosum, current_index_ranges=index_ranges,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1557 title='select x data range', legend='recon stack sum xy')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1558 while len(z_bounds) != 1:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1559 print('Please select exactly one continuous range')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1560 mask, z_bounds = draw_mask_1d(tomosum, title='select x data range',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1561 legend='recon stack sum xy')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1562 z_bounds = z_bounds[0]
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1563 # quick_plot(tomosum, vlines=z_bounds, title='recon stack sum xy')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1564 # print(f'z_bounds = {z_bounds} (lower bound inclusive, upper bound '+
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1565 # 'exclusive)')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1566 # accept = input_yesno('Accept these bounds (y/n)?', 'y')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1567 accept = True
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1568 logger.debug(f'z_bounds = {z_bounds}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1569
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1570 return(x_bounds, y_bounds, z_bounds)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1571
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1572
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1573 def run_tomo(input_file:str, output_file:str, modes:list[str], center_file=None, num_core=-1,
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1574 output_folder='.', save_figs='no', test_mode=False) -> None:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1575
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1576 if test_mode:
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1577 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1578 level = logging.getLevelName('INFO')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1579 logging.basicConfig(filename=f'{output_folder}/tomo.log', filemode='w',
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1580 format=logging_format, level=level, force=True)
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1581 logger.info(f'input_file = {input_file}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1582 logger.info(f'center_file = {center_file}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1583 logger.info(f'output_file = {output_file}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1584 logger.debug(f'modes= {modes}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1585 logger.debug(f'num_core= {num_core}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1586 logger.info(f'output_folder = {output_folder}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1587 logger.info(f'save_figs = {save_figs}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
diff changeset
1588 logger.info(f'test_mode = {test_mode}')
9aa288729b9a planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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1589
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1590 # Check for correction modes
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1591 legal_modes = ['reduce_data', 'find_center', 'reconstruct_data', 'combine_data', 'all']
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1592 if modes is None:
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1593 modes = ['all']
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1594 if not all(True if mode in legal_modes else False for mode in modes):
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1595 raise ValueError(f'Invalid parameter modes ({modes})')
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1596
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1597 # Instantiate Tomo object
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1598 tomo = Tomo(num_core=num_core, output_folder=output_folder, save_figs=save_figs,
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1599 test_mode=test_mode)
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1600
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1601 # Read input file
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1602 data = tomo.read(input_file)
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1603
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1604 # Generate reduced tomography images
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1605 if 'reduce_data' in modes or 'all' in modes:
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1606 data = tomo.gen_reduced_data(data)
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1607
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1608 # Find rotation axis centers for the tomography stacks.
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1609 center_data = None
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1610 if 'find_center' in modes or 'all' in modes:
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1611 center_data = tomo.find_centers(data)
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1612
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1613 # Reconstruct tomography stacks
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1614 if 'reconstruct_data' in modes or 'all' in modes:
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1615 if center_data is None:
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1616 # Read input file
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1617 center_data = tomo.read(center_file)
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1618 data = tomo.reconstruct_data(data, center_data)
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1619 center_data = None
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1620
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1621 # Combine reconstructed tomography stacks
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1622 if 'combine_data' in modes or 'all' in modes:
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1623 data = tomo.combine_data(data)
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1624
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1625 # Write output file
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1626 if data is not None and not test_mode:
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1627 if center_data is None:
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1628 data = tomo.write(data, output_file)
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1629 else:
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1630 data = tomo.write(center_data, output_file)
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1631
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1632 logger.info(f'Completed modes: {modes}')