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annotate workflow/models.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
parents
children 1cf15b61cd83
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69
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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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 logging
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7
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8 import numpy as np
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9 import os
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10 import yaml
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11
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12 from functools import cache
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13 from pathlib import PosixPath
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14 from pydantic import validator, ValidationError, conint, confloat, constr, \
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15 conlist, FilePath, PrivateAttr
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16 from pydantic import BaseModel as PydanticBaseModel
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17 from nexusformat.nexus import *
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18 from time import time
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19 from typing import Optional, Literal
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20 from typing_extensions import TypedDict
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21 try:
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22 from pyspec.file.spec import FileSpec
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23 except:
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24 pass
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25
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26 from msnctools.general import is_int, is_num, input_int, input_int_list, input_num, input_yesno, \
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27 input_menu, index_nearest, string_to_list, file_exists_and_readable
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29
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30 def import_scanparser(station):
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31 if station in ('id1a3', 'id3a'):
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32 from msnctools.scanparsers import SMBRotationScanParser
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33 globals()['ScanParser'] = SMBRotationScanParser
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34 elif station in ('id3b'):
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35 from msnctools.scanparsers import FMBRotationScanParser
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36 globals()['ScanParser'] = FMBRotationScanParser
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37 else:
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38 raise RuntimeError(f'Invalid station: {station}')
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39
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40 @cache
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41 def get_available_scan_numbers(spec_file:str):
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42 scans = FileSpec(spec_file).scans
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43 scan_numbers = list(scans.keys())
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44 for scan_number in scan_numbers.copy():
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45 try:
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46 parser = ScanParser(spec_file, scan_number)
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47 try:
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48 scan_type = parser.get_scan_type()
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49 except:
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50 scan_type = None
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51 pass
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52 except:
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53 scan_numbers.remove(scan_number)
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54 return(scan_numbers)
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55
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56 @cache
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57 def get_scanparser(spec_file:str, scan_number:int):
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58 if scan_number not in get_available_scan_numbers(spec_file):
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59 return(None)
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60 else:
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61 return(ScanParser(spec_file, scan_number))
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62
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63
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64 class BaseModel(PydanticBaseModel):
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65 class Config:
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66 validate_assignment = True
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67 arbitrary_types_allowed = True
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68
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69 @classmethod
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70 def construct_from_cli(cls):
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71 obj = cls.construct()
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72 obj.cli()
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73 return(obj)
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74
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75 @classmethod
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76 def construct_from_yaml(cls, filename):
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77 try:
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78 with open(filename, 'r') as infile:
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79 indict = yaml.load(infile, Loader=yaml.CLoader)
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80 except:
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81 raise ValueError(f'Could not load a dictionary from {filename}')
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82 else:
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83 obj = cls(**indict)
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84 return(obj)
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85
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86 @classmethod
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87 def construct_from_file(cls, filename):
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88 file_exists_and_readable(filename)
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89 filename = os.path.abspath(filename)
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90 fileformat = os.path.splitext(filename)[1]
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91 yaml_extensions = ('.yaml','.yml')
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92 nexus_extensions = ('.nxs','.nx5','.h5','.hdf5')
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93 t0 = time()
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94 if fileformat.lower() in yaml_extensions:
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95 obj = cls.construct_from_yaml(filename)
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96 logger.info(f'Constructed a model from {filename} in {time()-t0:.2f} seconds.')
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97 return(obj)
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98 elif fileformat.lower() in nexus_extensions:
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99 obj = cls.construct_from_nexus(filename)
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100 logger.info(f'Constructed a model from {filename} in {time()-t0:.2f} seconds.')
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101 return(obj)
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102 else:
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103 logger.error(f'Unsupported file extension for constructing a model: {fileformat}')
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104 raise TypeError(f'Unrecognized file extension: {fileformat}')
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105
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106 def dict_for_yaml(self, exclude_fields=[]):
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107 yaml_dict = {}
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108 for field_name in self.__fields__:
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109 if field_name in exclude_fields:
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110 continue
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111 else:
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112 field_value = getattr(self, field_name, None)
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113 if field_value is not None:
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114 if isinstance(field_value, BaseModel):
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115 yaml_dict[field_name] = field_value.dict_for_yaml()
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116 elif isinstance(field_value,list) and all(isinstance(item,BaseModel)
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117 for item in field_value):
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118 yaml_dict[field_name] = [item.dict_for_yaml() for item in field_value]
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119 elif isinstance(field_value, PosixPath):
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120 yaml_dict[field_name] = str(field_value)
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121 else:
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122 yaml_dict[field_name] = field_value
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123 else:
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124 continue
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125 return(yaml_dict)
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126
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127 def write_to_yaml(self, filename=None):
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128 yaml_dict = self.dict_for_yaml()
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129 if filename is None:
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130 logger.info('Printing yaml representation here:\n'+
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131 f'{yaml.dump(yaml_dict, sort_keys=False)}')
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132 else:
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133 try:
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134 with open(filename, 'w') as outfile:
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135 yaml.dump(yaml_dict, outfile, sort_keys=False)
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136 logger.info(f'Successfully wrote this model to {filename}')
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137 except:
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138 logger.error(f'Unknown error -- could not write to {filename} in yaml format.')
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139 logger.info('Printing yaml representation here:\n'+
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140 f'{yaml.dump(yaml_dict, sort_keys=False)}')
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141
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142 def write_to_file(self, filename, force_overwrite=False):
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143 file_writeable, fileformat = self.output_file_valid(filename,
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144 force_overwrite=force_overwrite)
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145 if fileformat == 'yaml':
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146 if file_writeable:
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147 self.write_to_yaml(filename=filename)
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148 else:
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149 self.write_to_yaml()
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150 elif fileformat == 'nexus':
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151 if file_writeable:
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152 self.write_to_nexus(filename=filename)
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153
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154 def output_file_valid(self, filename, force_overwrite=False):
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155 filename = os.path.abspath(filename)
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156 fileformat = os.path.splitext(filename)[1]
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157 yaml_extensions = ('.yaml','.yml')
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158 nexus_extensions = ('.nxs','.nx5','.h5','.hdf5')
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159 if fileformat.lower() not in (*yaml_extensions, *nexus_extensions):
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160 return(False, None) # Only yaml and NeXus files allowed for output now.
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161 elif fileformat.lower() in yaml_extensions:
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162 fileformat = 'yaml'
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163 elif fileformat.lower() in nexus_extensions:
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164 fileformat = 'nexus'
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165 if os.path.isfile(filename):
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166 if os.access(filename, os.W_OK):
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167 if not force_overwrite:
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168 logger.error(f'{filename} will not be overwritten.')
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169 return(False, fileformat)
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170 else:
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171 logger.error(f'Cannot access {filename} for writing.')
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172 return(False, fileformat)
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173 if os.path.isdir(os.path.dirname(filename)):
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174 if os.access(os.path.dirname(filename), os.W_OK):
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175 return(True, fileformat)
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176 else:
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177 logger.error(f'Cannot access {os.path.dirname(filename)} for writing.')
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178 return(False, fileformat)
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179 else:
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180 try:
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181 os.makedirs(os.path.dirname(filename))
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182 return(True, fileformat)
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183 except:
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184 logger.error(f'Cannot create {os.path.dirname(filename)} for output.')
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185 return(False, fileformat)
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186
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187 def set_single_attr_cli(self, attr_name, attr_desc='unknown attribute', list_flag=False,
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188 **cli_kwargs):
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189 if cli_kwargs.get('chain_attr_desc', False):
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190 cli_kwargs['attr_desc'] = attr_desc
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191 try:
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192 attr = getattr(self, attr_name, None)
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193 if attr is None:
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194 attr = self.__fields__[attr_name].type_.construct()
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195 if cli_kwargs.get('chain_attr_desc', False):
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196 cli_kwargs['attr_desc'] = attr_desc
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197 input_accepted = False
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198 while not input_accepted:
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199 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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200 attr.cli(**cli_kwargs)
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201 except ValidationError as e:
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parents:
diff changeset
202 print(e)
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203 print(f'Removing {attr_desc} configuration')
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204 attr = self.__fields__[attr_name].type_.construct()
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diff changeset
205 continue
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diff changeset
206 except KeyboardInterrupt as e:
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diff changeset
207 raise e
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diff changeset
208 except BaseException as e:
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209 print(f'{type(e).__name__}: {e}')
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210 print(f'Removing {attr_desc} configuration')
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211 attr = self.__fields__[attr_name].type_.construct()
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diff changeset
212 continue
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diff changeset
213 try:
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214 setattr(self, attr_name, attr)
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215 except ValidationError as e:
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216 print(e)
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217 except KeyboardInterrupt as e:
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218 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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219 except BaseException as e:
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220 print(f'{type(e).__name__}: {e}')
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diff changeset
221 else:
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222 input_accepted = True
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diff changeset
223 except:
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224 input_accepted = False
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225 while not input_accepted:
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226 attr = getattr(self, attr_name, None)
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227 if attr is None:
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228 input_value = input(f'Type and enter a value for {attr_desc}: ')
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229 else:
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230 input_value = input(f'Type and enter a new value for {attr_desc} or press '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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231 f'enter to keep the current one ({attr}): ')
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232 if list_flag:
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233 input_value = string_to_list(input_value, remove_duplicates=False, sort=False)
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234 if len(input_value) == 0:
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235 input_value = getattr(self, attr_name, None)
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diff changeset
236 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
237 setattr(self, attr_name, input_value)
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diff changeset
238 except ValidationError as e:
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239 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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240 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
241 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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242 except BaseException as e:
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243 print(f'Unexpected {type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
244 else:
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245 input_accepted = True
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246
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247 def set_list_attr_cli(self, attr_name, attr_desc='unknown attribute', **cli_kwargs):
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248 if cli_kwargs.get('chain_attr_desc', False):
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249 cli_kwargs['attr_desc'] = attr_desc
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250 attr = getattr(self, attr_name, None)
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251 if attr is not None:
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252 # Check existing items
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253 for item in attr:
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254 item_accepted = False
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255 while not item_accepted:
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256 item.cli(**cli_kwargs)
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257 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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258 setattr(self, attr_name, attr)
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259 except ValidationError as e:
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260 print(e)
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diff changeset
261 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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262 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
263 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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264 print(f'{type(e).__name__}: {e}')
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diff changeset
265 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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266 item_accepted = True
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diff changeset
267 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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268 # Initialize list for new attribute & starting item
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269 attr = []
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270 item = self.__fields__[attr_name].type_.construct()
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271 # Append (optional) additional items
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272 append = input_yesno(f'Add a {attr_desc} configuration? (y/n)', 'n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
273 while append:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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274 attr.append(item.__class__.construct_from_cli())
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diff changeset
275 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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276 setattr(self, attr_name, attr)
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277 except ValidationError as e:
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diff changeset
278 print(e)
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279 print(f'Removing last {attr_desc} configuration from the list')
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diff changeset
280 attr.pop()
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diff changeset
281 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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282 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
283 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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284 print(f'{type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
285 print(f'Removing last {attr_desc} configuration from the list')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
286 attr.pop()
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diff changeset
287 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
288 append = input_yesno(f'Add another {attr_desc} configuration? (y/n)', 'n')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
289
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diff changeset
290
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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291 class Detector(BaseModel):
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292 prefix: constr(strip_whitespace=True, min_length=1)
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293 rows: conint(gt=0)
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diff changeset
294 columns: conint(gt=0)
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295 pixel_size: conlist(item_type=confloat(gt=0), min_items=1, max_items=2)
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296 lens_magnification: confloat(gt=0) = 1.0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
297
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
298 @property
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299 def get_pixel_size(self):
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300 return(list(np.asarray(self.pixel_size)/self.lens_magnification))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
301
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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302 def construct_from_yaml(self, filename):
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parents:
diff changeset
303 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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304 with open(filename, 'r') as infile:
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305 indict = yaml.load(infile, Loader=yaml.CLoader)
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306 detector = indict['detector']
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307 self.prefix = detector['id']
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308 pixels = detector['pixels']
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309 self.rows = pixels['rows']
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310 self.columns = pixels['columns']
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311 self.pixel_size = pixels['size']
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312 self.lens_magnification = indict['lens_magnification']
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313 except:
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314 logging.warning(f'Could not load a dictionary from {filename}')
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315 return(False)
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316 else:
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317 return(True)
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318
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319 def cli(self):
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320 print('\n -- Configure the detector -- ')
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321 self.set_single_attr_cli('prefix', 'detector ID')
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322 self.set_single_attr_cli('rows', 'number of pixel rows')
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323 self.set_single_attr_cli('columns', 'number of pixel columns')
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324 self.set_single_attr_cli('pixel_size', 'pixel size in mm (enter either a single value for '+
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325 'square pixels or a pair of values for the size in the respective row and column '+
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326 'directions)', list_flag=True)
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327 self.set_single_attr_cli('lens_magnification', 'lens magnification')
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328
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329 def construct_nxdetector(self):
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330 nxdetector = NXdetector()
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331 nxdetector.local_name = self.prefix
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332 pixel_size = self.get_pixel_size
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333 if len(pixel_size) == 1:
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334 nxdetector.x_pixel_size = pixel_size[0]
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335 nxdetector.y_pixel_size = pixel_size[0]
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336 else:
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337 nxdetector.x_pixel_size = pixel_size[0]
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338 nxdetector.y_pixel_size = pixel_size[1]
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339 nxdetector.x_pixel_size.attrs['units'] = 'mm'
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340 nxdetector.y_pixel_size.attrs['units'] = 'mm'
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341 return(nxdetector)
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342
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343
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344 class ScanInfo(TypedDict):
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345 scan_number: int
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346 starting_image_offset: conint(ge=0)
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347 num_image: conint(gt=0)
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348 ref_x: float
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349 ref_z: float
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350
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351 class SpecScans(BaseModel):
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352 spec_file: FilePath
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353 scan_numbers: conlist(item_type=conint(gt=0), min_items=1)
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354 stack_info: conlist(item_type=ScanInfo, min_items=1) = []
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355
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356 @validator('spec_file')
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357 def validate_spec_file(cls, spec_file):
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358 try:
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359 spec_file = os.path.abspath(spec_file)
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360 sspec_file = FileSpec(spec_file)
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361 except:
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362 raise ValueError(f'Invalid SPEC file {spec_file}')
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363 else:
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diff changeset
364 return(spec_file)
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diff changeset
365
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366 @validator('scan_numbers')
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367 def validate_scan_numbers(cls, scan_numbers, values):
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368 spec_file = values.get('spec_file')
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369 if spec_file is not None:
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370 spec_scans = FileSpec(spec_file)
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371 for scan_number in scan_numbers:
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372 scan = spec_scans.get_scan_by_number(scan_number)
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373 if scan is None:
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374 raise ValueError(f'There is no scan number {scan_number} in {spec_file}')
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375 return(scan_numbers)
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376
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377 @validator('stack_info')
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378 def validate_stack_info(cls, stack_info, values):
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379 scan_numbers = values.get('scan_numbers')
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380 assert(len(scan_numbers) == len(stack_info))
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381 for scan_info in stack_info:
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382 assert(scan_info['scan_number'] in scan_numbers)
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383 is_int(scan_info['starting_image_offset'], ge=0, lt=scan_info['num_image'],
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384 raise_error=True)
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385 return(stack_info)
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386
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387 @classmethod
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388 def construct_from_nxcollection(cls, nxcollection:NXcollection):
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389 config = {}
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390 config['spec_file'] = nxcollection.attrs['spec_file']
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391 scan_numbers = []
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392 stack_info = []
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393 for nxsubentry_name, nxsubentry in nxcollection.items():
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394 scan_number = int(nxsubentry_name.split('_')[-1])
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395 scan_numbers.append(scan_number)
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396 stack_info.append({'scan_number': scan_number,
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397 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
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398 'num_image': len(nxsubentry.sample.rotation_angle),
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399 'ref_x': float(nxsubentry.sample.x_translation),
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400 'ref_z': float(nxsubentry.sample.z_translation)})
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401 config['scan_numbers'] = sorted(scan_numbers)
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402 config['stack_info'] = stack_info
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403 return(cls(**config))
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diff changeset
404
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diff changeset
405 @property
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406 def available_scan_numbers(self):
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407 return(get_available_scan_numbers(self.spec_file))
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408
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409 def set_from_nxcollection(self, nxcollection:NXcollection):
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410 self.spec_file = nxcollection.attrs['spec_file']
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411 scan_numbers = []
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412 stack_info = []
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413 for nxsubentry_name, nxsubentry in nxcollection.items():
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414 scan_number = int(nxsubentry_name.split('_')[-1])
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415 scan_numbers.append(scan_number)
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416 stack_info.append({'scan_number': scan_number,
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417 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
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418 'num_image': len(nxsubentry.sample.rotation_angle),
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419 'ref_x': float(nxsubentry.sample.x_translation),
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420 'ref_z': float(nxsubentry.sample.z_translation)})
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421 self.scan_numbers = sorted(scan_numbers)
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422 self.stack_info = stack_info
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423
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424 def get_scan_index(self, scan_number):
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425 scan_index = [scan_index for scan_index, scan_info in enumerate(self.stack_info)
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426 if scan_info['scan_number'] == scan_number]
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427 if len(scan_index) > 1:
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428 raise ValueError('Duplicate scan_numbers in image stack')
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429 elif len(scan_index) == 1:
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430 return(scan_index[0])
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431 else:
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432 return(None)
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433
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434 def get_scanparser(self, scan_number):
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435 return(get_scanparser(self.spec_file, scan_number))
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436
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437 # def get_detector_data(self, detector_prefix, scan_number=None, scan_step_index=None):
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438 # if scan_number is None:
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439 # scan_number = self.scan_numbers[0]
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440 # if scan_step_index is None:
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441 # scan_info = self.stack_info[self.get_scan_index(scan_number)]
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442 # scan_step_index = scan_info['starting_image_offset']
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443 # parser = self.get_scanparser(scan_number)
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444 # return(parser.get_detector_data(detector_prefix, scan_step_index))
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445
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446 def get_detector_data(self, detector_prefix, scan_number=None, scan_step_index=None):
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447 image_stacks = []
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448 if scan_number is None:
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449 scan_numbers = self.scan_numbers
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450 else:
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451 scan_numbers = [scan_number]
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452 for scan_number in scan_numbers:
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453 parser = self.get_scanparser(scan_number)
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454 scan_info = self.stack_info[self.get_scan_index(scan_number)]
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455 image_offset = scan_info['starting_image_offset']
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456 if scan_step_index is None:
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457 num_image = scan_info['num_image']
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458 image_stacks.append(parser.get_detector_data(detector_prefix,
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459 (image_offset, image_offset+num_image)))
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diff changeset
460 else:
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461 image_stacks.append(parser.get_detector_data(detector_prefix,
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diff changeset
462 image_offset+scan_step_index))
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463 if len(image_stacks) == 1:
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464 return(image_stacks[0])
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465 else:
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466 return(image_stacks)
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467
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468 def scan_numbers_cli(self, attr_desc, **kwargs):
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469 available_scan_numbers = self.available_scan_numbers
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470 station = kwargs.get('station')
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471 if (station is not None and station in ('id1a3', 'id3a') and
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472 'scan_type' in kwargs):
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473 scan_type = kwargs['scan_type']
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474 if scan_type == 'ts1':
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475 available_scan_numbers = []
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476 for scan_number in self.available_scan_numbers:
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477 parser = self.get_scanparser(scan_number)
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478 if parser.scan_type == scan_type:
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479 available_scan_numbers.append(scan_number)
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480 elif scan_type == 'df1':
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481 tomo_scan_numbers = kwargs['tomo_scan_numbers']
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diff changeset
482 available_scan_numbers = []
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diff changeset
483 for scan_number in tomo_scan_numbers:
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484 parser = self.get_scanparser(scan_number-2)
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diff changeset
485 assert(parser.scan_type == scan_type)
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486 available_scan_numbers.append(scan_number-2)
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487 elif scan_type == 'bf1':
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488 tomo_scan_numbers = kwargs['tomo_scan_numbers']
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diff changeset
489 available_scan_numbers = []
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490 for scan_number in tomo_scan_numbers:
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491 parser = self.get_scanparser(scan_number-1)
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492 assert(parser.scan_type == scan_type)
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493 available_scan_numbers.append(scan_number-1)
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494 if len(available_scan_numbers) == 1:
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495 input_mode = 1
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496 else:
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497 if hasattr(self, 'scan_numbers'):
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498 print(f'Currently selected {attr_desc}scan numbers are: {self.scan_numbers}')
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499 menu_options = [f'Select a subset of the available {attr_desc}scan numbers',
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500 f'Use all available {attr_desc}scan numbers in {self.spec_file}',
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501 f'Keep the currently selected {attr_desc}scan numbers']
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diff changeset
502 else:
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parents:
diff changeset
503 menu_options = [f'Select a subset of the available {attr_desc}scan numbers',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
504 f'Use all available {attr_desc}scan numbers in {self.spec_file}']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
505 print(f'Available scan numbers in {self.spec_file} are: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
506 f'{available_scan_numbers}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
507 input_mode = input_menu(menu_options, header='Choose one of the following options '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
508 'for selecting scan numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
509 if input_mode == 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
510 accept_scan_numbers = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
511 while not accept_scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
512 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
513 self.scan_numbers = \
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
514 input_int_list(f'Enter a series of {attr_desc}scan numbers')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
515 except ValidationError as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
516 print(e)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
517 except KeyboardInterrupt as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
518 raise e
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
519 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
520 print(f'Unexpected {type(e).__name__}: {e}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
521 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
522 accept_scan_numbers = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
523 elif input_mode == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
524 self.scan_numbers = available_scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
525 elif input_mode == 2:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
526 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
527
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
528 def cli(self, **cli_kwargs):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
529 if cli_kwargs.get('attr_desc') is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
530 attr_desc = f'{cli_kwargs["attr_desc"]} '
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
531 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
532 attr_desc = ''
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
533 print(f'\n -- Configure which scans to use from a single {attr_desc}SPEC file')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
534 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
535 self.scan_numbers_cli(attr_desc)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
536
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
537 def construct_nxcollection(self, image_key, thetas, detector):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
538 nxcollection = NXcollection()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
539 nxcollection.attrs['spec_file'] = str(self.spec_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
540 parser = self.get_scanparser(self.scan_numbers[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
541 nxcollection.attrs['date'] = parser.spec_scan.file_date
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
542 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
543 # Get scan info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
544 scan_info = self.stack_info[self.get_scan_index(scan_number)]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
545 # Add an NXsubentry to the NXcollection for each scan
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
546 entry_name = f'scan_{scan_number}'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
547 nxsubentry = NXsubentry()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
548 nxcollection[entry_name] = nxsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
549 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
550 nxsubentry.start_time = parser.spec_scan.date
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
551 nxsubentry.spec_command = parser.spec_command
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
552 # Add an NXdata for independent dimensions to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
553 num_image = scan_info['num_image']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
554 if thetas is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
555 thetas = num_image*[0.0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
556 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
557 assert(num_image == len(thetas))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
558 # nxsubentry.independent_dimensions = NXdata()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
559 # nxsubentry.independent_dimensions.rotation_angle = thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
560 # nxsubentry.independent_dimensions.rotation_angle.units = 'degrees'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
561 # Add an NXinstrument to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
562 nxsubentry.instrument = NXinstrument()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
563 # Add an NXdetector to the NXinstrument to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
564 nxsubentry.instrument.detector = detector.construct_nxdetector()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
565 nxsubentry.instrument.detector.frame_start_number = scan_info['starting_image_offset']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
566 nxsubentry.instrument.detector.image_key = image_key
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
567 # Add an NXsample to the scan's NXsubentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
568 nxsubentry.sample = NXsample()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
569 nxsubentry.sample.rotation_angle = thetas
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
570 nxsubentry.sample.rotation_angle.units = 'degrees'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
571 nxsubentry.sample.x_translation = scan_info['ref_x']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
572 nxsubentry.sample.x_translation.units = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
573 nxsubentry.sample.z_translation = scan_info['ref_z']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
574 nxsubentry.sample.z_translation.units = 'mm'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
575 return(nxcollection)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
576
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
577
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
578 class FlatField(SpecScans):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
579
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
580 def image_range_cli(self, attr_desc, detector_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
581 stack_info = self.stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
582 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
583 # Parse the available image range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
584 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
585 image_offset = parser.starting_image_offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
586 num_image = parser.get_num_image(detector_prefix.upper())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
587 scan_index = self.get_scan_index(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
588
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
589 # Select the image set
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
590 last_image_index = image_offset+num_image-1
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
591 print(f'Available good image set index range: [{image_offset}, {last_image_index}]')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
592 image_set_approved = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
593 if scan_index is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
594 scan_info = stack_info[scan_index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
595 print(f'Current starting image offset and number of images: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
596 f'{scan_info["starting_image_offset"]} and {scan_info["num_image"]}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
597 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
598 if not image_set_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
599 print(f'Default starting image offset and number of images: '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
600 f'{image_offset} and {last_image_index-image_offset}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
601 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
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602 if image_set_approved:
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603 offset = image_offset
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604 num = last_image_index-offset
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diff changeset
605 while not image_set_approved:
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606 offset = input_int(f'Enter the starting image offset', ge=image_offset,
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607 le=last_image_index-1)#, default=image_offset)
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diff changeset
608 num = input_int(f'Enter the number of images', ge=1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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609 le=last_image_index-offset+1)#, default=last_image_index-offset+1)
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610 print(f'Current starting image offset and number of images: {offset} and {num}')
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611 image_set_approved = input_yesno(f'Accept these values (y/n)?', 'y')
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612 if scan_index is not None:
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diff changeset
613 scan_info['starting_image_offset'] = offset
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diff changeset
614 scan_info['num_image'] = num
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diff changeset
615 scan_info['ref_x'] = parser.horizontal_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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616 scan_info['ref_z'] = parser.vertical_shift
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diff changeset
617 else:
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618 stack_info.append({'scan_number': scan_number, 'starting_image_offset': offset,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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619 'num_image': num, 'ref_x': parser.horizontal_shift,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
620 'ref_z': parser.vertical_shift})
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621 self.stack_info = stack_info
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622
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diff changeset
623 def cli(self, **cli_kwargs):
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624 if cli_kwargs.get('attr_desc') is not None:
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625 attr_desc = f'{cli_kwargs["attr_desc"]} '
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diff changeset
626 else:
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627 attr_desc = ''
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628 station = cli_kwargs.get('station')
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diff changeset
629 detector = cli_kwargs.get('detector')
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630 print(f'\n -- Configure the location of the {attr_desc}scan data -- ')
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diff changeset
631 if station in ('id1a3', 'id3a'):
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632 self.spec_file = cli_kwargs['spec_file']
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diff changeset
633 tomo_scan_numbers = cli_kwargs['tomo_scan_numbers']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
634 scan_type = cli_kwargs['scan_type']
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diff changeset
635 self.scan_numbers_cli(attr_desc, station=station, tomo_scan_numbers=tomo_scan_numbers,
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diff changeset
636 scan_type=scan_type)
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diff changeset
637 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
638 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
639 self.scan_numbers_cli(attr_desc)
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diff changeset
640 self.image_range_cli(attr_desc, detector.prefix)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
641
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diff changeset
642
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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643 class TomoField(SpecScans):
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644 theta_range: dict = {}
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diff changeset
645
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diff changeset
646 @validator('theta_range')
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diff changeset
647 def validate_theta_range(cls, theta_range):
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648 if len(theta_range) != 3 and len(theta_range) != 4:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
649 raise ValueError(f'Invalid theta range {theta_range}')
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diff changeset
650 is_num(theta_range['start'], raise_error=True)
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diff changeset
651 is_num(theta_range['end'], raise_error=True)
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diff changeset
652 is_int(theta_range['num'], gt=1, raise_error=True)
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diff changeset
653 if theta_range['end'] <= theta_range['start']:
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diff changeset
654 raise ValueError(f'Invalid theta range {theta_range}')
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diff changeset
655 if 'start_index' in theta_range:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
656 is_int(theta_range['start_index'], ge=0, raise_error=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
657 return(theta_range)
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parents:
diff changeset
658
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
659 @classmethod
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diff changeset
660 def construct_from_nxcollection(cls, nxcollection:NXcollection):
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diff changeset
661 #RV Can I derive this from the same classfunction for SpecScans by adding theta_range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
662 config = {}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
663 config['spec_file'] = nxcollection.attrs['spec_file']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
664 scan_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
665 stack_info = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
666 for nxsubentry_name, nxsubentry in nxcollection.items():
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
667 scan_number = int(nxsubentry_name.split('_')[-1])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
668 scan_numbers.append(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
669 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
670 'starting_image_offset': int(nxsubentry.instrument.detector.frame_start_number),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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671 'num_image': len(nxsubentry.sample.rotation_angle),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
672 'ref_x': float(nxsubentry.sample.x_translation),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
673 'ref_z': float(nxsubentry.sample.z_translation)})
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
674 config['scan_numbers'] = sorted(scan_numbers)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
675 config['stack_info'] = stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
676 for name in nxcollection.entries:
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diff changeset
677 if 'scan_' in name:
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diff changeset
678 thetas = np.asarray(nxcollection[name].sample.rotation_angle)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
679 config['theta_range'] = {'start': thetas[0], 'end': thetas[-1], 'num': thetas.size}
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
680 break
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
681 return(cls(**config))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
682
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
683 def get_horizontal_shifts(self, scan_number=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
684 horizontal_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
685 if scan_number is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
686 scan_numbers = self.scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
687 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
688 scan_numbers = [scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
689 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
690 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
691 horizontal_shifts.append(parser.get_horizontal_shift())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
692 if len(horizontal_shifts) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
693 return(horizontal_shifts[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
694 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
695 return(horizontal_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
696
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
697 def get_vertical_shifts(self, scan_number=None):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
698 vertical_shifts = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
699 if scan_number is None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
700 scan_numbers = self.scan_numbers
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
701 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
702 scan_numbers = [scan_number]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
703 for scan_number in scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
704 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
705 vertical_shifts.append(parser.get_vertical_shift())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
706 if len(vertical_shifts) == 1:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
707 return(vertical_shifts[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
708 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
709 return(vertical_shifts)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
710
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
711 def theta_range_cli(self, scan_number, attr_desc, station):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
712 # Parse the available theta range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
713 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
714 theta_vals = parser.theta_vals
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
715 spec_theta_start = theta_vals.get('start')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
716 spec_theta_end = theta_vals.get('end')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
717 spec_num_theta = theta_vals.get('num')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
718
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
719 # Check for consistency of theta ranges between scans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
720 if scan_number != self.scan_numbers[0]:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
721 parser = self.get_scanparser(self.scan_numbers[0])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
722 if (parser.theta_vals.get('start') != spec_theta_start or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
723 parser.theta_vals.get('end') != spec_theta_end or
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
724 parser.theta_vals.get('num') != spec_num_theta):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
725 raise ValueError(f'Incompatible theta ranges between {attr_desc}scans:'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
726 f'\n\tScan {scan_number}: {theta_vals}'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
727 f'\n\tScan {self.scan_numbers[0]}: {parser.theta_vals}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
728 return
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
729
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
730 # Select the theta range for the tomo reconstruction from the first scan
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
731 thetas = np.linspace(spec_theta_start, spec_theta_end, spec_num_theta)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
732 delta_theta = thetas[1]-thetas[0]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
733 theta_range_approved = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
734 print(f'Theta range obtained from SPEC data: [{spec_theta_start}, {spec_theta_end})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
735 print(f'Theta step size = {delta_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
736 print(f'Number of theta values: {spec_num_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
737 exit('Done')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
738 default_start = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
739 default_end = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
740 if station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
741 theta_range_approved = input_yesno(f'Accept this theta range (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
742 if theta_range_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
743 theta_start = spec_theta_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
744 theta_end = spec_theta_end
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
745 num_theta = spec_num_theta
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
746 theta_index_start = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
747 elif station in ('id3b'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
748 if spec_theta_start <= 0.0 and spec_theta_end >= 180.0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
749 default_start = 0
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
750 default_end = 180
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
751 elif spec_theta_end-spec_theta_start == 180:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
752 default_start = spec_theta_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
753 default_end = spec_theta_end
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
754 while not theta_range_approved:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
755 theta_start = input_num(f'Enter the first theta (included)', ge=spec_theta_start,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
756 lt=spec_theta_end, default=default_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
757 theta_index_start = index_nearest(thetas, theta_start)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
758 theta_start = thetas[theta_index_start]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
759 theta_end = input_num(f'Enter the last theta (excluded)',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
760 ge=theta_start+delta_theta, le=spec_theta_end, default=default_end)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
761 theta_index_end = index_nearest(thetas, theta_end)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
762 theta_end = thetas[theta_index_end]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
763 num_theta = theta_index_end-theta_index_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
764 print(f'Selected theta range: [{theta_start}, {theta_start+delta_theta}, ..., '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
765 f'{theta_end})')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
766 print(f'Number of theta values: {num_theta}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
767 theta_range_approved = input_yesno(f'Accept this theta range (y/n)?', 'y')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
768 self.thetas = np.linspace(theta_start, theta_end, num_theta)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
769
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
770 def image_range_cli(self, attr_desc, detector_prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
771 stack_info = self.stack_info
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
772 for scan_number in self.scan_numbers:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
773 # Parse the available image range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
774 parser = self.get_scanparser(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
775 image_offset = parser.starting_image_offset
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
776 num_image = parser.get_num_image(detector_prefix.upper())
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
777 scan_index = self.get_scan_index(scan_number)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
778
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
779 # Select the image set matching the theta range
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
780 num_theta = self.theta_range['num']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
781 theta_index_start = self.theta_range['start_index']
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
782 if num_theta > num_image-theta_index_start:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
783 raise ValueError(f'Available {attr_desc}image indices incompatible with thetas:'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
784 f'\n\tNumber of thetas and offset = {num_theta} and {theta_index_start}'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
785 f'\n\tNumber of available images {num_image}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
786 if scan_index is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
787 scan_info = stack_info[scan_index]
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
788 scan_info['starting_image_offset'] = image_offset+theta_index_start
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
789 scan_info['num_image'] = num_theta
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
790 scan_info['ref_x'] = parser.horizontal_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
791 scan_info['ref_z'] = parser.vertical_shift
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
792 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
793 stack_info.append({'scan_number': scan_number,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
794 'starting_image_offset': image_offset+theta_index_start,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
795 'num_image': num_theta, 'ref_x': parser.horizontal_shift,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
796 'ref_z': parser.vertical_shift})
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797 self.stack_info = stack_info
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798
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799 def cli(self, **cli_kwargs):
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800 if cli_kwargs.get('attr_desc') is not None:
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801 attr_desc = f'{cli_kwargs["attr_desc"]} '
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802 else:
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803 attr_desc = ''
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804 cycle = cli_kwargs.get('cycle')
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805 btr = cli_kwargs.get('btr')
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806 station = cli_kwargs.get('station')
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807 detector = cli_kwargs.get('detector')
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808 print(f'\n -- Configure the location of the {attr_desc}scan data -- ')
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809 if station in ('id1a3', 'id3a'):
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810 basedir = f'/nfs/chess/{station}/{cycle}/{btr}'
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811 runs = [d for d in os.listdir(basedir) if os.path.isdir(os.path.join(basedir, d))]
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812 #RV index = 15-1
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813 #RV index = 7-1
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814 index = input_menu(runs, header='Choose a sample directory')
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815 self.spec_file = f'{basedir}/{runs[index]}/spec.log'
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816 self.scan_numbers_cli(attr_desc, station=station, scan_type='ts1')
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817 else:
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818 self.set_single_attr_cli('spec_file', attr_desc+'SPEC file path')
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819 self.scan_numbers_cli(attr_desc)
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820 for scan_number in self.scan_numbers:
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821 self.theta_range_cli(scan_number, attr_desc, station)
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822 self.image_range_cli(attr_desc, detector.prefix)
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823
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824
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825 class Sample(BaseModel):
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826 name: constr(min_length=1)
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827 description: Optional[str]
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828 rotation_angles: Optional[list]
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829 x_translations: Optional[list]
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830 z_translations: Optional[list]
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831
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diff changeset
832 @classmethod
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833 def construct_from_nxsample(cls, nxsample:NXsample):
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834 config = {}
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835 config['name'] = nxsample.name.nxdata
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836 if 'description' in nxsample:
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837 config['description'] = nxsample.description.nxdata
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838 if 'rotation_angle' in nxsample:
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839 config['rotation_angle'] = nxsample.rotation_angle.nxdata
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840 if 'x_translation' in nxsample:
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841 config['x_translation'] = nxsample.x_translation.nxdata
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842 if 'z_translation' in nxsample:
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843 config['z_translation'] = nxsample.z_translation.nxdata
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diff changeset
844 return(cls(**config))
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diff changeset
845
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diff changeset
846 def cli(self):
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847 print('\n -- Configure the sample metadata -- ')
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848 #RV self.name = 'test'
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849 #RV self.name = 'sobhani-3249-A'
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850 self.set_single_attr_cli('name', 'the sample name')
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851 #RV self.description = 'test sample'
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852 self.set_single_attr_cli('description', 'a description of the sample (optional)')
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853
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diff changeset
854
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855 class MapConfig(BaseModel):
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856 cycle: constr(strip_whitespace=True, min_length=1)
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857 btr: constr(strip_whitespace=True, min_length=1)
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858 title: constr(strip_whitespace=True, min_length=1)
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859 station: Literal['id1a3', 'id3a', 'id3b'] = None
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860 sample: Sample
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861 detector: Detector = Detector.construct()
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862 tomo_fields: TomoField
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863 dark_field: Optional[FlatField]
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864 bright_field: FlatField
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865 _thetas: list[float] = PrivateAttr()
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866 _field_types = ({'name': 'dark_field', 'image_key': 2}, {'name': 'bright_field',
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867 'image_key': 1}, {'name': 'tomo_fields', 'image_key': 0})
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868
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diff changeset
869 @classmethod
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870 def construct_from_nxentry(cls, nxentry:NXentry):
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871 config = {}
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872 config['cycle'] = nxentry.instrument.source.attrs['cycle']
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873 config['btr'] = nxentry.instrument.source.attrs['btr']
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874 config['title'] = nxentry.nxname
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875 config['station'] = nxentry.instrument.source.attrs['station']
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876 config['sample'] = Sample.construct_from_nxsample(nxentry['sample'])
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877 for nxobject_name, nxobject in nxentry.spec_scans.items():
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878 if isinstance(nxobject, NXcollection):
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879 config[nxobject_name] = SpecScans.construct_from_nxcollection(nxobject)
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diff changeset
880 return(cls(**config))
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881
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diff changeset
882 #FIX cache?
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diff changeset
883 @property
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diff changeset
884 def thetas(self):
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885 try:
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886 return(self._thetas)
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diff changeset
887 except:
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888 theta_range = self.tomo_fields.theta_range
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889 self._thetas = list(np.linspace(theta_range['start'], theta_range['end'],
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890 theta_range['num']))
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diff changeset
891 return(self._thetas)
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diff changeset
892
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diff changeset
893 def cli(self):
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894 print('\n -- Configure a map from a set of SPEC scans (dark, bright, and tomo), '+
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parents:
diff changeset
895 'and / or detector data -- ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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diff changeset
896 #RV self.cycle = '2021-3'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
897 #RV self.cycle = '2022-2'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
898 #RV self.cycle = '2023-1'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
899 self.set_single_attr_cli('cycle', 'beam cycle')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
900 #RV self.btr = 'z-3234-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
901 #RV self.btr = 'sobhani-3249-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
902 #RV self.btr = 'przybyla-3606-a'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
903 self.set_single_attr_cli('btr', 'BTR')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
904 #RV self.title = 'z-3234-A'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
905 #RV self.title = 'tomo7C'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
906 #RV self.title = 'cmc-test-dwell-1'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
907 self.set_single_attr_cli('title', 'title for the map entry')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
908 #RV self.station = 'id3a'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
909 #RV self.station = 'id3b'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
910 #RV self.station = 'id1a3'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
911 self.set_single_attr_cli('station', 'name of the station at which scans were collected '+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
912 '(currently choose from: id1a3, id3a, id3b)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
913 import_scanparser(self.station)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
914 self.set_single_attr_cli('sample')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
915 use_detector_config = False
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
916 if hasattr(self.detector, 'prefix') and len(self.detector.prefix):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
917 use_detector_config = input_yesno(f'Current detector settings:\n{self.detector}\n'+
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
918 f'Keep these settings? (y/n)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
919 if not use_detector_config:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
920 #RV have_detector_config = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
921 have_detector_config = input_yesno(f'Is a detector configuration file available? (y/n)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
922 if have_detector_config:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
923 #RV detector_config_file = 'retiga.yaml'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
924 #RV detector_config_file = 'andor2.yaml'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
925 detector_config_file = input(f'Enter detector configuration file name: ')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
926 have_detector_config = self.detector.construct_from_yaml(detector_config_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
927 if not have_detector_config:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
928 self.set_single_attr_cli('detector', 'detector')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
929 self.set_single_attr_cli('tomo_fields', 'Tomo field', chain_attr_desc=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
930 cycle=self.cycle, btr=self.btr, station=self.station, detector=self.detector)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
931 if self.station in ('id1a3', 'id3a'):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
932 have_dark_field = True
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
933 tomo_spec_file = self.tomo_fields.spec_file
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
934 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
935 have_dark_field = input_yesno(f'Are Dark field images available? (y/n)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
936 tomo_spec_file = None
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
937 if have_dark_field:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
938 self.set_single_attr_cli('dark_field', 'Dark field', chain_attr_desc=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
939 station=self.station, detector=self.detector, spec_file=tomo_spec_file,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
940 tomo_scan_numbers=self.tomo_fields.scan_numbers, scan_type='df1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
941 self.set_single_attr_cli('bright_field', 'Bright field', chain_attr_desc=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
942 station=self.station, detector=self.detector, spec_file=tomo_spec_file,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
943 tomo_scan_numbers=self.tomo_fields.scan_numbers, scan_type='bf1')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
944
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
945 def construct_nxentry(self, nxroot, include_raw_data=True):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
946 # Construct base NXentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
947 nxentry = NXentry()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
948
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
949 # Add an NXentry to the NXroot
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
950 nxroot[self.title] = nxentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
951 nxroot.attrs['default'] = self.title
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
952 nxentry.definition = 'NXtomo'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
953 # nxentry.attrs['default'] = 'data'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
954
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
955 # Add an NXinstrument to the NXentry
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
956 nxinstrument = NXinstrument()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
957 nxentry.instrument = nxinstrument
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
958
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
959 # Add an NXsource to the NXinstrument
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
960 nxsource = NXsource()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
961 nxinstrument.source = nxsource
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
962 nxsource.type = 'Synchrotron X-ray Source'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
963 nxsource.name = 'CHESS'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
964 nxsource.probe = 'x-ray'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
965
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
966 # Tag the NXsource with the runinfo (as an attribute)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
967 nxsource.attrs['cycle'] = self.cycle
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
968 nxsource.attrs['btr'] = self.btr
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
969 nxsource.attrs['station'] = self.station
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
970
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
971 # Add an NXdetector to the NXinstrument (don't fill in data fields yet)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
972 nxinstrument.detector = self.detector.construct_nxdetector()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
973
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
974 # Add an NXsample to NXentry (don't fill in data fields yet)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
975 nxsample = NXsample()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
976 nxentry.sample = nxsample
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
977 nxsample.name = self.sample.name
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
978 nxsample.description = self.sample.description
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
979
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
980 # Add an NXcollection to the base NXentry to hold metadata about the spec scans in the map
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
981 # Also obtain the data fields in NXsample and NXdetector
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
982 nxspec_scans = NXcollection()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
983 nxentry.spec_scans = nxspec_scans
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
984 image_keys = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
985 sequence_numbers = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
986 image_stacks = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
987 rotation_angles = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
988 x_translations = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
989 z_translations = []
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
diff changeset
990 for field_type in self._field_types:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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parents:
diff changeset
991 field_name = field_type['name']
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992 field = getattr(self, field_name)
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993 if field is None:
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994 continue
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995 image_key = field_type['image_key']
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996 if field_type['name'] == 'tomo_fields':
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997 thetas = self.thetas
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998 else:
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999 thetas = None
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1000 # Add the scans in a single spec file
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1001 nxspec_scans[field_name] = field.construct_nxcollection(image_key, thetas,
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1002 self.detector)
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1003 if include_raw_data:
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1004 image_stacks.append(field.get_detector_data(self.detector.prefix))
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1005 for scan_number in field.scan_numbers:
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1006 parser = field.get_scanparser(scan_number)
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1007 scan_info = field.stack_info[field.get_scan_index(scan_number)]
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1008 num_image = scan_info['num_image']
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1009 image_keys += num_image*[image_key]
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1010 sequence_numbers += [i for i in range(num_image)]
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1011 if thetas is None:
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1012 rotation_angles += scan_info['num_image']*[0.0]
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1013 else:
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1014 assert(num_image == len(thetas))
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1015 rotation_angles += thetas
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1016 x_translations += scan_info['num_image']*[scan_info['ref_x']]
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1017 z_translations += scan_info['num_image']*[scan_info['ref_z']]
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1018
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1019 if include_raw_data:
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1020 # Add image data to NXdetector
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1021 nxinstrument.detector.image_key = image_keys
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1022 nxinstrument.detector.sequence_number = sequence_numbers
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1023 nxinstrument.detector.data = np.concatenate([image for image in image_stacks])
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1024
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1025 # Add image data to NXsample
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1026 nxsample.rotation_angle = rotation_angles
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1027 nxsample.rotation_angle.attrs['units'] = 'degrees'
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1028 nxsample.x_translation = x_translations
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1029 nxsample.x_translation.attrs['units'] = 'mm'
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1030 nxsample.z_translation = z_translations
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1031 nxsample.z_translation.attrs['units'] = 'mm'
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1032
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1033 # Add an NXdata to NXentry
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1034 nxdata = NXdata()
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1035 nxentry.data = nxdata
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1036 nxdata.makelink(nxentry.instrument.detector.data, name='data')
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1037 nxdata.makelink(nxentry.instrument.detector.image_key)
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1038 nxdata.makelink(nxentry.sample.rotation_angle)
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1039 nxdata.makelink(nxentry.sample.x_translation)
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1040 nxdata.makelink(nxentry.sample.z_translation)
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1041 # nxdata.attrs['axes'] = ['field', 'row', 'column']
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1042 # nxdata.attrs['field_indices'] = 0
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1043 # nxdata.attrs['row_indices'] = 1
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1044 # nxdata.attrs['column_indices'] = 2
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1045
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1046
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1047 class TomoWorkflow(BaseModel):
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1048 sample_maps: conlist(item_type=MapConfig, min_items=1) = [MapConfig.construct()]
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1049
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1050 @classmethod
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1051 def construct_from_nexus(cls, filename):
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1052 nxroot = nxload(filename)
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1053 sample_maps = []
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1054 config = {'sample_maps': sample_maps}
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1055 for nxentry_name, nxentry in nxroot.items():
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1056 sample_maps.append(MapConfig.construct_from_nxentry(nxentry))
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1057 return(cls(**config))
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1058
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1059 def cli(self):
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1060 print('\n -- Configure a map -- ')
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1061 self.set_list_attr_cli('sample_maps', 'sample map')
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1062
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diff changeset
1063 def construct_nxfile(self, filename, mode='w-'):
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1064 nxroot = NXroot()
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1065 t0 = time()
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1066 for sample_map in self.sample_maps:
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1067 logger.info(f'Start constructing the {sample_map.title} map.')
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1068 import_scanparser(sample_map.station)
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1069 sample_map.construct_nxentry(nxroot)
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1070 logger.info(f'Constructed all sample maps in {time()-t0:.2f} seconds.')
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1071 logger.info(f'Start saving all sample maps to {filename}.')
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1072 nxroot.save(filename, mode=mode)
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1073
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1074 def write_to_nexus(self, filename):
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1075 t0 = time()
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1076 self.construct_nxfile(filename, mode='w')
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1077 logger.info(f'Saved all sample maps to {filename} in {time()-t0:.2f} seconds.')