Mercurial > repos > kls286 > chap_test_20230328

annotate build/lib/CHAP/processor.py @ 0:cbbe42422d56 draft

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author kls286
date Tue, 28 Mar 2023 15:07:30 +0000
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1 #!/usr/bin/env python
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2 #-*- coding: utf-8 -*-
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3 #pylint: disable=
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4 """
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5 File : processor.py
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6 Author : Valentin Kuznetsov <vkuznet AT gmail dot com>
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7 Description: Processor module
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8 """
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9
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10 # system modules
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11 import argparse
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12 import json
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13 import logging
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14 import sys
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15 from time import time
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16
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17 # local modules
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18 # from pipeline import PipelineObject
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19
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20 class Processor():
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21 """
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22 Processor represent generic processor
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23 """
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24 def __init__(self):
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25 """
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26 Processor constructor
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27 """
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28 self.__name__ = self.__class__.__name__
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29 self.logger = logging.getLogger(self.__name__)
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30 self.logger.propagate = False
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31
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32 def process(self, data):
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33 """
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34 process data API
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35 """
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36
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37 t0 = time()
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38 self.logger.info(f'Executing "process" with type(data)={type(data)}')
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39
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40 data = self._process(data)
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41
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42 self.logger.info(f'Finished "process" in {time()-t0:.3f} seconds\n')
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43
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44 return(data)
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45
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46 def _process(self, data):
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47 # If needed, extract data from a returned value of Reader.read
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48 if isinstance(data, list):
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49 if all([isinstance(d,dict) for d in data]):
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50 data = data[0]['data']
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51 # process operation is a simple print function
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52 data += "process part\n"
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53 # and we return data back to pipeline
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54 return data
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55
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56
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57 class TFaaSImageProcessor(Processor):
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58 '''
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59 A Processor to get predictions from TFaaS inference server.
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60 '''
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61 def process(self, data, url, model, verbose=False):
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62 """
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63 process data API
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64 """
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65
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66 t0 = time()
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67 self.logger.info(f'Executing "process" with url {url} model {model}')
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68
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69 data = self._process(data, url, model, verbose)
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70
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71 self.logger.info(f'Finished "process" in {time()-t0:.3f} seconds\n')
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72
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73 return(data)
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74
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75 def _process(self, data, url, model, verbose):
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76 '''Print and return the input data.
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77
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78 :param data: Input image data, either file name or actual image data
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79 :type data: object
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80 :return: `data`
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81 :rtype: object
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82 '''
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83 from MLaaS.tfaas_client import predictImage
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84 from pathlib import Path
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85 self.logger.info(f"input data {type(data)}")
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86 if isinstance(data, str) and Path(data).is_file():
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87 imgFile = data
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88 data = predictImage(url, imgFile, model, verbose)
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89 else:
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90 rdict = data[0]
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91 import requests
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92 img = rdict['data']
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93 session = requests.Session()
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94 rurl = url + '/predict/image'
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95 payload = dict(model=model)
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96 files = dict(image=img)
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97 self.logger.info(f"HTTP request {rurl} with image file and {payload} payload")
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98 req = session.post(rurl, files=files, data=payload )
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99 data = req.content
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100 data = data.decode("utf-8").replace('\n', '')
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101 self.logger.info(f"HTTP response {data}")
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102
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103 return(data)
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104
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105 class URLResponseProcessor(Processor):
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106 def _process(self, data):
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107 '''Take data returned from URLReader.read and return a decoded version of
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108 the content.
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109
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110 :param data: input data (output of URLReader.read)
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111 :type data: list[dict]
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112 :return: decoded data contents
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113 :rtype: object
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114 '''
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115
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116 data = data[0]
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117
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118 content = data['data']
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119 encoding = data['encoding']
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120
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121 self.logger.debug(f'Decoding content of type {type(content)} with {encoding}')
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122
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123 try:
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124 content = content.decode(encoding)
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125 except:
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126 self.logger.warning(f'Failed to decode content of type {type(content)} with {encoding}')
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127
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128 return(content)
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129
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130 class PrintProcessor(Processor):
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131 '''A Processor to simply print the input data to stdout and return the
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132 original input data, unchanged in any way.
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133 '''
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134
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135 def _process(self, data):
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136 '''Print and return the input data.
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137
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138 :param data: Input data
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139 :type data: object
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140 :return: `data`
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141 :rtype: object
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142 '''
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143
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144 print(f'{self.__name__} data :')
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145
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146 if callable(getattr(data, '_str_tree', None)):
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147 # If data is likely an NXobject, print its tree representation
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148 # (since NXobjects' str representations are just their nxname -- not
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149 # very helpful).
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150 print(data._str_tree(attrs=True, recursive=True))
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151 else:
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152 print(str(data))
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153
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154 return(data)
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155
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156 class NexusToNumpyProcessor(Processor):
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157 '''A class to convert the default plottable data in an `NXobject` into an
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158 `numpy.ndarray`.
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159 '''
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160
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161 def _process(self, data):
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162 '''Return the default plottable data signal in `data` as an
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163 `numpy.ndarray`.
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164
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165 :param data: input NeXus structure
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166 :type data: nexusformat.nexus.tree.NXobject
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167 :raises ValueError: if `data` has no default plottable data signal
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168 :return: default plottable data signal in `data`
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169 :rtype: numpy.ndarray
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170 '''
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171
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172 default_data = data.plottable_data
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173
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174 if default_data is None:
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175 default_data_path = data.attrs['default']
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176 default_data = data.get(default_data_path)
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177 if default_data is None:
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178 raise(ValueError(f'The structure of {data} contains no default data'))
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179
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180 default_signal = default_data.attrs.get('signal')
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181 if default_signal is None:
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182 raise(ValueError(f'The signal of {default_data} is unknown'))
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183 default_signal = default_signal.nxdata
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184
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185 np_data = default_data[default_signal].nxdata
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186
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187 return(np_data)
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188
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189 class NexusToXarrayProcessor(Processor):
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190 '''A class to convert the default plottable data in an `NXobject` into an
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191 `xarray.DataArray`.'''
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192
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193 def _process(self, data):
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194 '''Return the default plottable data signal in `data` as an
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195 `xarray.DataArray`.
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196
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197 :param data: input NeXus structure
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198 :type data: nexusformat.nexus.tree.NXobject
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199 :raises ValueError: if metadata for `xarray` is absen from `data`
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200 :return: default plottable data signal in `data`
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201 :rtype: xarray.DataArray
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202 '''
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203
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204 from xarray import DataArray
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205
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206 default_data = data.plottable_data
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207
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208 if default_data is None:
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209 default_data_path = data.attrs['default']
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210 default_data = data.get(default_data_path)
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211 if default_data is None:
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212 raise(ValueError(f'The structure of {data} contains no default data'))
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213
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214 default_signal = default_data.attrs.get('signal')
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215 if default_signal is None:
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216 raise(ValueError(f'The signal of {default_data} is unknown'))
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217 default_signal = default_signal.nxdata
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218
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219 signal_data = default_data[default_signal].nxdata
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220
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221 axes = default_data.attrs['axes']
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222 coords = {}
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223 for axis_name in axes:
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224 axis = default_data[axis_name]
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225 coords[axis_name] = (axis_name,
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226 axis.nxdata,
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227 axis.attrs)
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228
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229 dims = tuple(axes)
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230
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231 name = default_signal
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232
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233 attrs = default_data[default_signal].attrs
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234
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235 return(DataArray(data=signal_data,
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236 coords=coords,
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237 dims=dims,
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238 name=name,
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239 attrs=attrs))
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240
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241 class XarrayToNexusProcessor(Processor):
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242 '''A class to convert the data in an `xarray` structure to an
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243 `nexusformat.nexus.NXdata`.
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244 '''
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245
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246 def _process(self, data):
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247 '''Return `data` represented as an `nexusformat.nexus.NXdata`.
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248
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249 :param data: The input `xarray` structure
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250 :type data: typing.Union[xarray.DataArray, xarray.Dataset]
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251 :return: The data and metadata in `data`
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252 :rtype: nexusformat.nexus.NXdata
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253 '''
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254
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255 from nexusformat.nexus import NXdata, NXfield
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256
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257 signal = NXfield(value=data.data, name=data.name, attrs=data.attrs)
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258
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259 axes = []
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260 for name, coord in data.coords.items():
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261 axes.append(NXfield(value=coord.data, name=name, attrs=coord.attrs))
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262 axes = tuple(axes)
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263
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264 return(NXdata(signal=signal, axes=axes))
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265
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266 class XarrayToNumpyProcessor(Processor):
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267 '''A class to convert the data in an `xarray.DataArray` structure to an
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268 `numpy.ndarray`.
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269 '''
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270
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271 def _process(self, data):
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272 '''Return just the signal values contained in `data`.
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273
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274 :param data: The input `xarray.DataArray`
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275 :type data: xarray.DataArray
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276 :return: The data in `data`
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277 :rtype: numpy.ndarray
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278 '''
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279
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280 return(data.data)
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281
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282 class MapProcessor(Processor):
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283 '''Class representing a process that takes a map configuration and returns a
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284 `nexusformat.nexus.NXentry` representing that map's metadata and any
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285 scalar-valued raw data requseted by the supplied map configuration.
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286 '''
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287
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288 def _process(self, data):
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289 '''Process the output of a `Reader` that contains a map configuration and
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290 return a `nexusformat.nexus.NXentry` representing the map.
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291
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292 :param data: Result of `Reader.read` where at least one item has the
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293 value `'MapConfig'` for the `'schema'` key.
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294 :type data: list[dict[str,object]]
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295 :return: Map data & metadata (SPEC only, no detector)
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296 :rtype: nexusformat.nexus.NXentry
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297 '''
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298
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299 map_config = self.get_map_config(data)
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300 nxentry = self.__class__.get_nxentry(map_config)
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301
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302 return(nxentry)
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303
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304 def get_map_config(self, data):
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305 '''Get an instance of `MapConfig` from a returned value of `Reader.read`
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306
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307 :param data: Result of `Reader.read` where at least one item has the
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308 value `'MapConfig'` for the `'schema'` key.
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309 :type data: list[dict[str,object]]
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310 :raises Exception: If a valid `MapConfig` cannot be constructed from `data`.
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311 :return: a valid instance of `MapConfig` with field values taken from `data`.
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312 :rtype: MapConfig
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313 '''
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314
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315 from CHAP.models.map import MapConfig
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316
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317 map_config = False
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318 if isinstance(data, list):
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319 for item in data:
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320 if isinstance(item, dict):
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321 if item.get('schema') == 'MapConfig':
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322 map_config = item.get('data')
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323 break
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324
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325 if not map_config:
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326 raise(ValueError('No map configuration found'))
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327
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328 return(MapConfig(**map_config))
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329
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330 @staticmethod
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331 def get_nxentry(map_config):
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332 '''Use a `MapConfig` to construct a `nexusformat.nexus.NXentry`
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333
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334 :param map_config: a valid map configuration
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335 :type map_config: MapConfig
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336 :return: the map's data and metadata contained in a NeXus structure
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337 :rtype: nexusformat.nexus.NXentry
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338 '''
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339
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340 from nexusformat.nexus import (NXcollection,
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341 NXdata,
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342 NXentry,
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343 NXfield,
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344 NXsample)
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345 import numpy as np
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346
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347 nxentry = NXentry(name=map_config.title)
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348
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349 nxentry.map_config = json.dumps(map_config.dict())
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350
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351 nxentry[map_config.sample.name] = NXsample(**map_config.sample.dict())
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352
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353 nxentry.attrs['station'] = map_config.station
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354
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355 nxentry.spec_scans = NXcollection()
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356 for scans in map_config.spec_scans:
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357 nxentry.spec_scans[scans.scanparsers[0].scan_name] = \
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358 NXfield(value=scans.scan_numbers,
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359 dtype='int8',
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360 attrs={'spec_file':str(scans.spec_file)})
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361
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362 nxentry.data = NXdata()
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363 nxentry.data.attrs['axes'] = map_config.dims
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364 for i,dim in enumerate(map_config.independent_dimensions[::-1]):
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365 nxentry.data[dim.label] = NXfield(value=map_config.coords[dim.label],
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366 units=dim.units,
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367 attrs={'long_name': f'{dim.label} ({dim.units})',
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368 'data_type': dim.data_type,
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369 'local_name': dim.name})
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370 nxentry.data.attrs[f'{dim.label}_indices'] = i
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371
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372 signal = False
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373 auxilliary_signals = []
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374 for data in map_config.all_scalar_data:
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375 nxentry.data[data.label] = NXfield(value=np.empty(map_config.shape),
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376 units=data.units,
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377 attrs={'long_name': f'{data.label} ({data.units})',
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378 'data_type': data.data_type,
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379 'local_name': data.name})
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380 if not signal:
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381 signal = data.label
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382 else:
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383 auxilliary_signals.append(data.label)
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384
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385 if signal:
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386 nxentry.data.attrs['signal'] = signal
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387 nxentry.data.attrs['auxilliary_signals'] = auxilliary_signals
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388
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389 for scans in map_config.spec_scans:
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390 for scan_number in scans.scan_numbers:
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391 scanparser = scans.get_scanparser(scan_number)
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392 for scan_step_index in range(scanparser.spec_scan_npts):
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393 map_index = scans.get_index(scan_number, scan_step_index, map_config)
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394 for data in map_config.all_scalar_data:
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395 nxentry.data[data.label][map_index] = data.get_value(scans, scan_number, scan_step_index)
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396
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397 return(nxentry)
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398
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399 class IntegrationProcessor(Processor):
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400 '''Class for integrating 2D detector data
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401 '''
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402
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403 def _process(self, data):
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404 '''Integrate the input data with the integration method and keyword
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405 arguments supplied and return the results.
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406
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407 :param data: input data, including raw data, integration method, and
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408 keyword args for the integration method.
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409 :type data: tuple[typing.Union[numpy.ndarray, list[numpy.ndarray]],
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410 callable,
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411 dict]
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412 :param integration_method: the method of a
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413 `pyFAI.azimuthalIntegrator.AzimuthalIntegrator` or
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414 `pyFAI.multi_geometry.MultiGeometry` that returns the desired
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415 integration results.
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416 :return: integrated raw data
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417 :rtype: pyFAI.containers.IntegrateResult
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418 '''
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419
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420 detector_data, integration_method, integration_kwargs = data
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421
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422 return(integration_method(detector_data, **integration_kwargs))
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423
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424 class IntegrateMapProcessor(Processor):
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425 '''Class representing a process that takes a map and integration
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426 configuration and returns a `nexusformat.nexus.NXprocess` containing a map of
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427 the integrated detector data requested.
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428 '''
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429
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430 def _process(self, data):
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431 '''Process the output of a `Reader` that contains a map and integration
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432 configuration and return a `nexusformat.nexus.NXprocess` containing a map
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433 of the integrated detector data requested
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434
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435 :param data: Result of `Reader.read` where at least one item has the
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436 value `'MapConfig'` for the `'schema'` key, and at least one item has
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437 the value `'IntegrationConfig'` for the `'schema'` key.
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438 :type data: list[dict[str,object]]
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439 :return: integrated data and process metadata
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440 :rtype: nexusformat.nexus.NXprocess
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441 '''
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442
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443 map_config, integration_config = self.get_configs(data)
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444 nxprocess = self.get_nxprocess(map_config, integration_config)
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445
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446 return(nxprocess)
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447
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448 def get_configs(self, data):
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449 '''Return valid instances of `MapConfig` and `IntegrationConfig` from the
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450 input supplied by `MultipleReader`.
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451
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452 :param data: Result of `Reader.read` where at least one item has the
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453 value `'MapConfig'` for the `'schema'` key, and at least one item has
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454 the value `'IntegrationConfig'` for the `'schema'` key.
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455 :type data: list[dict[str,object]]
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456 :raises ValueError: if `data` cannot be parsed into map and integration configurations.
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457 :return: valid map and integration configuration objects.
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458 :rtype: tuple[MapConfig, IntegrationConfig]
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459 '''
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460
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461 self.logger.debug('Getting configuration objects')
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462 t0 = time()
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463
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464 from CHAP.models.map import MapConfig
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465 from CHAP.models.integration import IntegrationConfig
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466
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diff changeset
467 map_config = False
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diff changeset
468 integration_config = False
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
469 if isinstance(data, list):
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diff changeset
470 for item in data:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
471 if isinstance(item, dict):
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diff changeset
472 schema = item.get('schema')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
473 if schema == 'MapConfig':
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diff changeset
474 map_config = item.get('data')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
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diff changeset
475 elif schema == 'IntegrationConfig':
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diff changeset
476 integration_config = item.get('data')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
477
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
478 if not map_config:
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diff changeset
479 raise(ValueError('No map configuration found'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
480 if not integration_config:
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diff changeset
481 raise(ValueError('No integration configuration found'))
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diff changeset
482
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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483 map_config = MapConfig(**map_config)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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484 integration_config = IntegrationConfig(**integration_config)
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485
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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486 self.logger.debug(f'Got configuration objects in {time()-t0:.3f} seconds')
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487
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488 return(map_config, integration_config)
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489
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490 def get_nxprocess(self, map_config, integration_config):
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491 '''Use a `MapConfig` and `IntegrationConfig` to construct a
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492 `nexusformat.nexus.NXprocess`
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493
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diff changeset
494 :param map_config: a valid map configuration
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495 :type map_config: MapConfig
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496 :param integration_config: a valid integration configuration
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497 :type integration_config" IntegrationConfig
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498 :return: the integrated detector data and metadata contained in a NeXus
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499 structure
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500 :rtype: nexusformat.nexus.NXprocess
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501 '''
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502
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diff changeset
503 self.logger.debug('Constructing NXprocess')
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504 t0 = time()
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diff changeset
505
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diff changeset
506 from nexusformat.nexus import (NXdata,
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diff changeset
507 NXdetector,
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diff changeset
508 NXfield,
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diff changeset
509 NXprocess)
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diff changeset
510 import numpy as np
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511 import pyFAI
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diff changeset
512
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513 nxprocess = NXprocess(name=integration_config.title)
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diff changeset
514
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diff changeset
515 nxprocess.map_config = json.dumps(map_config.dict())
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diff changeset
516 nxprocess.integration_config = json.dumps(integration_config.dict())
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diff changeset
517
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diff changeset
518 nxprocess.program = 'pyFAI'
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diff changeset
519 nxprocess.version = pyFAI.version
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diff changeset
520
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521 for k,v in integration_config.dict().items():
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diff changeset
522 if k == 'detectors':
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diff changeset
523 continue
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diff changeset
524 nxprocess.attrs[k] = v
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diff changeset
525
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diff changeset
526 for detector in integration_config.detectors:
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diff changeset
527 nxprocess[detector.prefix] = NXdetector()
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528 nxprocess[detector.prefix].local_name = detector.prefix
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529 nxprocess[detector.prefix].distance = detector.azimuthal_integrator.dist
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530 nxprocess[detector.prefix].distance.attrs['units'] = 'm'
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531 nxprocess[detector.prefix].calibration_wavelength = detector.azimuthal_integrator.wavelength
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532 nxprocess[detector.prefix].calibration_wavelength.attrs['units'] = 'm'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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533 nxprocess[detector.prefix].attrs['poni_file'] = str(detector.poni_file)
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534 nxprocess[detector.prefix].attrs['mask_file'] = str(detector.mask_file)
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535 nxprocess[detector.prefix].raw_data_files = np.full(map_config.shape, '', dtype='|S256')
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diff changeset
536
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537 nxprocess.data = NXdata()
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538
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539 nxprocess.data.attrs['axes'] = (*map_config.dims, *integration_config.integrated_data_dims)
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540 for i,dim in enumerate(map_config.independent_dimensions[::-1]):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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541 nxprocess.data[dim.label] = NXfield(value=map_config.coords[dim.label],
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542 units=dim.units,
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543 attrs={'long_name': f'{dim.label} ({dim.units})',
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544 'data_type': dim.data_type,
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diff changeset
545 'local_name': dim.name})
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546 nxprocess.data.attrs[f'{dim.label}_indices'] = i
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diff changeset
547
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548 for i,(coord_name,coord_values) in enumerate(integration_config.integrated_data_coordinates.items()):
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549 if coord_name == 'radial':
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550 type_ = pyFAI.units.RADIAL_UNITS
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551 elif coord_name == 'azimuthal':
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552 type_ = pyFAI.units.AZIMUTHAL_UNITS
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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553 coord_units = pyFAI.units.to_unit(getattr(integration_config, f'{coord_name}_units'), type_=type_)
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diff changeset
554 nxprocess.data[coord_units.name] = coord_values
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555 nxprocess.data.attrs[f'{coord_units.name}_indices'] = i+len(map_config.coords)
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556 nxprocess.data[coord_units.name].units = coord_units.unit_symbol
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557 nxprocess.data[coord_units.name].attrs['long_name'] = coord_units.label
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558
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559 nxprocess.data.attrs['signal'] = 'I'
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560 nxprocess.data.I = NXfield(value=np.empty((*tuple([len(coord_values) for coord_name,coord_values in map_config.coords.items()][::-1]), *integration_config.integrated_data_shape)),
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561 units='a.u',
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562 attrs={'long_name':'Intensity (a.u)'})
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563
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564 integrator = integration_config.get_multi_geometry_integrator()
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565 if integration_config.integration_type == 'azimuthal':
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566 integration_method = integrator.integrate1d
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567 integration_kwargs = {
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568 'lst_mask': [detector.mask_array for detector in integration_config.detectors],
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569 'npt': integration_config.radial_npt
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570 }
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571 elif integration_config.integration_type == 'cake':
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572 integration_method = integrator.integrate2d
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573 integration_kwargs = {
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574 'lst_mask': [detector.mask_array for detector in integration_config.detectors],
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575 'npt_rad': integration_config.radial_npt,
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576 'npt_azim': integration_config.azimuthal_npt,
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577 'method': 'bbox'
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578 }
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579
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580 integration_processor = IntegrationProcessor()
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581 integration_processor.logger.setLevel(self.logger.getEffectiveLevel())
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582 integration_processor.logger.addHandler(self.logger.handlers[0])
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583 lst_args = []
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584 for scans in map_config.spec_scans:
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585 for scan_number in scans.scan_numbers:
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586 scanparser = scans.get_scanparser(scan_number)
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587 for scan_step_index in range(scanparser.spec_scan_npts):
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588 map_index = scans.get_index(scan_number, scan_step_index, map_config)
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589 detector_data = scans.get_detector_data(integration_config.detectors, scan_number, scan_step_index)
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590 result = integration_processor.process((detector_data, integration_method, integration_kwargs))
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591 nxprocess.data.I[map_index] = result.intensity
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592 for detector in integration_config.detectors:
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593 nxprocess[detector.prefix].raw_data_files[map_index] = scanparser.get_detector_data_file(detector.prefix, scan_step_index)
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594
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diff changeset
595 self.logger.debug(f'Constructed NXprocess in {time()-t0:.3f} seconds')
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diff changeset
596
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diff changeset
597 return(nxprocess)
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598
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599 class MCACeriaCalibrationProcessor(Processor):
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600 '''Class representing the procedure to use a CeO2 scan to obtain tuned values
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diff changeset
601 for the bragg diffraction angle and linear correction parameters for MCA
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602 channel energies for an EDD experimental setup.
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603 '''
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604
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605 def _process(self, data):
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606 '''Return tuned values for 2&theta and linear correction parameters for
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diff changeset
607 the MCA channel energies.
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608
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609 :param data: input configuration for the raw data & tuning procedure
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610 :type data: list[dict[str,object]]
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611 :return: original configuration dictionary with tuned values added
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612 :rtype: dict[str,float]
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613 '''
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614
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615 calibration_config = self.get_config(data)
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616
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617 tth, slope, intercept = self.calibrate(calibration_config)
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618
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diff changeset
619 calibration_config.tth_calibrated = tth
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620 calibration_config.slope_calibrated = slope
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621 calibration_config.intercept_calibrated = intercept
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622
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623 return(calibration_config.dict())
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624
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625 def get_config(self, data):
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626 '''Get an instance of the configuration object needed by this
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627 `Processor` from a returned value of `Reader.read`
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628
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629 :param data: Result of `Reader.read` where at least one item has the
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630 value `'MCACeriaCalibrationConfig'` for the `'schema'` key.
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631 :type data: list[dict[str,object]]
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632 :raises Exception: If a valid config object cannot be constructed from `data`.
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633 :return: a valid instance of a configuration object with field values
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634 taken from `data`.
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635 :rtype: MCACeriaCalibrationConfig
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636 '''
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637
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638 from CHAP.models.edd import MCACeriaCalibrationConfig
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639
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640 calibration_config = False
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641 if isinstance(data, list):
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642 for item in data:
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643 if isinstance(item, dict):
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644 if item.get('schema') == 'MCACeriaCalibrationConfig':
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645 calibration_config = item.get('data')
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646 break
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647
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648 if not calibration_config:
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649 raise(ValueError('No MCA ceria calibration configuration found in input data'))
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650
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651 return(MCACeriaCalibrationConfig(**calibration_config))
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652
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653 def calibrate(self, calibration_config):
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654 '''Iteratively calibrate 2&theta by fitting selected peaks of an MCA
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655 spectrum until the computed strain is sufficiently small. Use the fitted
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656 peak locations to determine linear correction parameters for the MCA's
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657 channel energies.
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658
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659 :param calibration_config: object configuring the CeO2 calibration procedure
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660 :type calibration_config: MCACeriaCalibrationConfig
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661 :return: calibrated values of 2&theta and linear correction parameters
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662 for MCA channel energies : tth, slope, intercept
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663 :rtype: float, float, float
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664 '''
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665
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666 from msnctools.fit import Fit, FitMultipeak
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667 import numpy as np
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668 from scipy.constants import physical_constants
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669
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670 hc = physical_constants['Planck constant in eV/Hz'][0] * \
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671 physical_constants['speed of light in vacuum'][0] * \
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672 1e7 # We'll work in keV and A, not eV and m.
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673
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674 # Collect raw MCA data of interest
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675 mca_data = calibration_config.mca_data()
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676 mca_bin_energies = np.arange(0, calibration_config.num_bins) * \
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677 (calibration_config.max_energy_kev / calibration_config.num_bins)
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678
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679 # Mask out the corrected MCA data for fitting
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680 mca_mask = calibration_config.mca_mask()
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681 fit_mca_energies = mca_bin_energies[mca_mask]
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682 fit_mca_intensities = mca_data[mca_mask]
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683
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684 # Correct raw MCA data for variable flux at different energies
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685 flux_correct = calibration_config.flux_correction_interpolation_function()
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686 mca_intensity_weights = flux_correct(fit_mca_energies)
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687 fit_mca_intensities = fit_mca_intensities / mca_intensity_weights
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688
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689 # Get the HKLs and lattice spacings that will be used for fitting
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690 tth = calibration_config.tth_initial_guess
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691 fit_hkls, fit_ds = calibration_config.fit_ds()
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692 c_1 = fit_hkls[:,0]**2 + fit_hkls[:,1]**2 + fit_hkls[:,2]**2
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693
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694 for iter_i in range(calibration_config.max_iter):
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695
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696 ### Perform the uniform fit first ###
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697
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698 # Get expected peak energy locations for this iteration's starting
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699 # value of tth
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700 fit_lambda = 2.0 * fit_ds * np.sin(0.5*np.radians(tth))
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701 fit_E0 = hc / fit_lambda
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702
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703 # Run the uniform fit
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704 best_fit, residual, best_values, best_errors, redchi, success = \
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705 FitMultipeak.fit_multipeak(fit_mca_intensities,
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706 fit_E0,
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707 x=fit_mca_energies,
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708 fit_type='uniform')
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709
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710 # Extract values of interest from the best values for the uniform fit
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711 # parameters
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712 uniform_fit_centers = [best_values[f'peak{i+1}_center'] for i in range(len(calibration_config.fit_hkls))]
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713 # uniform_a = best_values['scale_factor']
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714 # uniform_strain = np.log(uniform_a / calibration_config.lattice_parameter_angstrom)
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715 # uniform_tth = tth * (1.0 + uniform_strain)
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716 # uniform_rel_rms_error = np.linalg.norm(residual) / np.linalg.norm(fit_mca_intensities)
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717
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718 ### Next, perform the unconstrained fit ###
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719
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720 # Use the peak locations found in the uniform fit as the initial
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721 # guesses for peak locations in the unconstrained fit
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722 best_fit, residual, best_values, best_errors, redchi, success = \
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723 FitMultipeak.fit_multipeak(fit_mca_intensities,
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724 uniform_fit_centers,
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725 x=fit_mca_energies,
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726 fit_type='unconstrained')
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727
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728 # Extract values of interest from the best values for the
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729 # unconstrained fit parameters
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730 unconstrained_fit_centers = np.array([best_values[f'peak{i+1}_center'] for i in range(len(calibration_config.fit_hkls))])
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731 unconstrained_a = 0.5 * hc * np.sqrt(c_1) / (unconstrained_fit_centers * abs(np.sin(0.5*np.radians(tth))))
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732 unconstrained_strains = np.log(unconstrained_a / calibration_config.lattice_parameter_angstrom)
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733 unconstrained_strain = np.mean(unconstrained_strains)
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734 unconstrained_tth = tth * (1.0 + unconstrained_strain)
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735 # unconstrained_rel_rms_error = np.linalg.norm(residual) / np.linalg.norm(fit_mca_intensities)
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736
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diff changeset
737
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
738 # Update tth for the next iteration of tuning
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
739 prev_tth = tth
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
740 tth = unconstrained_tth
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
741
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
742 # Stop tuning tth at this iteration if differences are small enough
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
743 if abs(tth - prev_tth) < calibration_config.tune_tth_tol:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
744 break
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
745
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
746 # Fit line to expected / computed peak locations from the last
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
747 # unconstrained fit.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
748 fit = Fit.fit_data(fit_E0,'linear', x=unconstrained_fit_centers, nan_policy='omit')
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parents:
diff changeset
749 slope = fit.best_values['slope']
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parents:
diff changeset
750 intercept = fit.best_values['intercept']
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parents:
diff changeset
751
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
752 return(float(tth), float(slope), float(intercept))
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parents:
diff changeset
753
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
754 class MCADataProcessor(Processor):
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parents:
diff changeset
755 '''Class representing a process to return data from a MCA, restuctured to
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
756 incorporate the shape & metadata associated with a map configuration to
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
757 which the MCA data belongs, and linearly transformed according to the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
758 results of a ceria calibration.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
759 '''
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parents:
diff changeset
760
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
761 def _process(self, data):
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parents:
diff changeset
762 '''Process configurations for a map and MCA detector(s), and return the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
763 raw MCA data collected over the map.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
764
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kls286
parents:
diff changeset
765 :param data: input map configuration and results of ceria calibration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
766 :type data: list[dict[str,object]]
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parents:
diff changeset
767 :return: calibrated and flux-corrected MCA data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
768 :rtype: nexusformat.nexus.NXentry
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
769 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
770
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
771 map_config, calibration_config = self.get_configs(data)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
772 nxroot = self.get_nxroot(map_config, calibration_config)
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parents:
diff changeset
773
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
774 return(nxroot)
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parents:
diff changeset
775
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parents:
diff changeset
776 def get_configs(self, data):
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diff changeset
777 '''Get instances of the configuration objects needed by this
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
778 `Processor` from a returned value of `Reader.read`
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parents:
diff changeset
779
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kls286
parents:
diff changeset
780 :param data: Result of `Reader.read` where at least one item has the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
781 value `'MapConfig'` for the `'schema'` key, and at least one item has
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
782 the value `'MCACeriaCalibrationConfig'` for the `'schema'` key.
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diff changeset
783 :type data: list[dict[str,object]]
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diff changeset
784 :raises Exception: If valid config objects cannot be constructed from `data`.
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diff changeset
785 :return: valid instances of the configuration objects with field values
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
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diff changeset
786 taken from `data`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
787 :rtype: tuple[MapConfig, MCACeriaCalibrationConfig]
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parents:
diff changeset
788 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
789
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
790 from CHAP.models.map import MapConfig
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diff changeset
791 from CHAP.models.edd import MCACeriaCalibrationConfig
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parents:
diff changeset
792
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parents:
diff changeset
793 map_config = False
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diff changeset
794 calibration_config = False
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diff changeset
795 if isinstance(data, list):
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diff changeset
796 for item in data:
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diff changeset
797 if isinstance(item, dict):
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diff changeset
798 schema = item.get('schema')
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parents:
diff changeset
799 if schema == 'MapConfig':
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diff changeset
800 map_config = item.get('data')
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parents:
diff changeset
801 elif schema == 'MCACeriaCalibrationConfig':
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diff changeset
802 calibration_config = item.get('data')
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parents:
diff changeset
803
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
804 if not map_config:
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diff changeset
805 raise(ValueError('No map configuration found in input data'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
806 if not calibration_config:
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parents:
diff changeset
807 raise(ValueError('No MCA ceria calibration configuration found in input data'))
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parents:
diff changeset
808
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
809 return(MapConfig(**map_config), MCACeriaCalibrationConfig(**calibration_config))
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parents:
diff changeset
810
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parents:
diff changeset
811 def get_nxroot(self, map_config, calibration_config):
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diff changeset
812 '''Get a map of the MCA data collected by the scans in `map_config`. The
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
813 MCA data will be calibrated and flux-corrected according to the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
814 parameters included in `calibration_config`. The data will be returned
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
815 along with relevant metadata in the form of a NeXus structure.
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diff changeset
816
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diff changeset
817 :param map_config: the map configuration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
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diff changeset
818 :type map_config: MapConfig
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diff changeset
819 :param calibration_config: the calibration configuration
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diff changeset
820 :type calibration_config: MCACeriaCalibrationConfig
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diff changeset
821 :return: a map of the calibrated and flux-corrected MCA data
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diff changeset
822 :rtype: nexusformat.nexus.NXroot
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diff changeset
823 '''
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parents:
diff changeset
824
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kls286
parents:
diff changeset
825 from nexusformat.nexus import (NXdata,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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diff changeset
826 NXdetector,
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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parents:
diff changeset
827 NXentry,
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parents:
diff changeset
828 NXinstrument,
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diff changeset
829 NXroot)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
830 import numpy as np
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
831
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
832 nxroot = NXroot()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
833
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
834 nxroot[map_config.title] = MapProcessor.get_nxentry(map_config)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
835 nxentry = nxroot[map_config.title]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
836
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
837 nxentry.instrument = NXinstrument()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
838 nxentry.instrument.detector = NXdetector()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
839 nxentry.instrument.detector.calibration_configuration = json.dumps(calibration_config.dict())
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
840
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
841 nxentry.instrument.detector.data = NXdata()
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
842 nxdata = nxentry.instrument.detector.data
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
843 nxdata.raw = np.empty((*map_config.shape, calibration_config.num_bins))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
844 nxdata.raw.attrs['units'] = 'counts'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
845 nxdata.channel_energy = calibration_config.slope_calibrated * \
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
846 np.arange(0, calibration_config.num_bins) * \
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
847 (calibration_config.max_energy_kev / calibration_config.num_bins) + \
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
848 calibration_config.intercept_calibrated
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
849 nxdata.channel_energy.attrs['units'] = 'keV'
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
850
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
851 for scans in map_config.spec_scans:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
852 for scan_number in scans.scan_numbers:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
853 scanparser = scans.get_scanparser(scan_number)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
854 for scan_step_index in range(scanparser.spec_scan_npts):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
855 map_index = scans.get_index(scan_number, scan_step_index, map_config)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
856 nxdata.raw[map_index] = scanparser.get_detector_data(calibration_config.detector_name, scan_step_index)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
857
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
858 nxentry.data.makelink(nxdata.raw, name=calibration_config.detector_name)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
859 nxentry.data.makelink(nxdata.channel_energy, name=f'{calibration_config.detector_name}_channel_energy')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
860 if isinstance(nxentry.data.attrs['axes'], str):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
861 nxentry.data.attrs['axes'] = [nxentry.data.attrs['axes'], f'{calibration_config.detector_name}_channel_energy']
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
862 else:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
863 nxentry.data.attrs['axes'] += [f'{calibration_config.detector_name}_channel_energy']
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
864 nxentry.data.attrs['signal'] = calibration_config.detector_name
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
865
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
866 return(nxroot)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
867
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
868 class StrainAnalysisProcessor(Processor):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
869 '''Class representing a process to compute a map of sample strains by fitting
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
870 bragg peaks in 1D detector data and analyzing the difference between measured
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
871 peak locations and expected peak locations for the sample measured.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
872 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
873
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
874 def _process(self, data):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
875 '''Process the input map detector data & configuration for the strain
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
876 analysis procedure, and return a map of sample strains.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
877
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
878 :param data: results of `MutlipleReader.read` containing input map
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
879 detector data and strain analysis configuration
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
880 :type data: dict[list[str,object]]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
881 :return: map of sample strains
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
882 :rtype: xarray.Dataset
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
883 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
884
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
885 strain_analysis_config = self.get_config(data)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
886
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
887 return(data)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
888
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
889 def get_config(self, data):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
890 '''Get instances of the configuration objects needed by this
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
891 `Processor` from a returned value of `Reader.read`
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
892
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
893 :param data: Result of `Reader.read` where at least one item has the
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
894 value `'StrainAnalysisConfig'` for the `'schema'` key.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
895 :type data: list[dict[str,object]]
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
896 :raises Exception: If valid config objects cannot be constructed from `data`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
897 :return: valid instances of the configuration objects with field values
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
898 taken from `data`.
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
899 :rtype: StrainAnalysisConfig
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
900 '''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
901
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
902 strain_analysis_config = False
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
903 if isinstance(data, list):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
904 for item in data:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
905 if isinstance(item, dict):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
906 schema = item.get('schema')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
907 if item.get('schema') == 'StrainAnalysisConfig':
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
908 strain_analysis_config = item.get('data')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
909
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
910 if not strain_analysis_config:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
911 raise(ValueError('No strain analysis configuration found in input data'))
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
912
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
913 return(strain_analysis_config)
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
914
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
915
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
916 class OptionParser():
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
917 '''User based option parser'''
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
918 def __init__(self):
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
919 self.parser = argparse.ArgumentParser(prog='PROG')
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
kls286
parents:
diff changeset
920 self.parser.add_argument("--data", action="store",
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921 dest="data", default="", help="Input data")
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922 self.parser.add_argument("--processor", action="store",
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923 dest="processor", default="Processor", help="Processor class name")
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924 self.parser.add_argument('--log-level', choices=logging._nameToLevel.keys(),
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925 dest='log_level', default='INFO', help='logging level')
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926
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927 def main():
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928 '''Main function'''
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929 optmgr = OptionParser()
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930 opts = optmgr.parser.parse_args()
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931 clsName = opts.processor
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kls286
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diff changeset
932 try:
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kls286
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933 processorCls = getattr(sys.modules[__name__],clsName)
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kls286
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934 except:
cbbe42422d56 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline/tree/galaxy commit 1401a7e1ae007a6bda260d147f9b879e789b73e0-dirty
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935 print(f'Unsupported processor {clsName}')
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936 sys.exit(1)
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937
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kls286
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938 processor = processorCls()
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939 processor.logger.setLevel(getattr(logging, opts.log_level))
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940 log_handler = logging.StreamHandler()
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941 log_handler.setFormatter(logging.Formatter('{name:20}: {message}', style='{'))
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kls286
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942 processor.logger.addHandler(log_handler)
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943 data = processor.process(opts.data)
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944
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945 print(f"Processor {processor} operates on data {data}")
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946
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947 if __name__ == '__main__':
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948 main()