Changes in src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py [109afbd:61f329f0] in sasview
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src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py
r109afbd r61f329f0 1 1 """ 2 NXcanSASdata reader for reading HDF5 formatted CanSAS files.2 CanSAS 2D data reader for reading HDF5 formatted CanSAS files. 3 3 """ 4 4 … … 12 12 Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ 13 13 TransmissionSpectrum, Detector 14 from ..data_info import combine_data_info_with_plottable 14 15 from ..loader_exceptions import FileContentsException, DefaultReaderException 15 16 from ..file_reader_base_class import FileReader, decode 16 17 17 try:18 basestring19 except NameError: # CRUFT: python 2 support20 basestring = str21 22 23 18 def h5attr(node, key, default=None): 24 19 return decode(node.attrs.get(key, default)) 25 20 26 27 21 class Reader(FileReader): 28 22 """ 29 A class for reading in NXcanSAS data files. The current implementation has30 been tested to load data generated by multiple facilities, all of which are31 known to produce NXcanSAS standards compliant data. Any number of data sets32 may be present within the file and any dimensionality of data may be used.33 Currently 1D and 2D SAS data sets are supported, but should be immediately34 extensible to SESANS data. 35 36 Any number of SASdata groups may be present in a SASentry and the data37 within each SASdata group can be a single 1D I(Q), multi-framed 1D I(Q), 38 2D I(Qx, Qy) or multi-framed 2D I(Qx, Qy).23 A class for reading in CanSAS v2.0 data files. The existing iteration opens 24 Mantid generated HDF5 formatted files with file extension .h5/.H5. Any 25 number of data sets may be present within the file and any dimensionality 26 of data may be used. Currently 1D and 2D SAS data sets are supported, but 27 future implementations will include 1D and 2D SESANS data. 28 29 Any number of SASdata sets may be present in a SASentry and the data within 30 can be either 1D I(Q) or 2D I(Qx, Qy). 31 32 Also supports reading NXcanSAS formatted HDF5 files 39 33 40 34 :Dependencies: 41 The NXcanSAS HDF5 reader requires h5py => v2.5.0 or later.35 The CanSAS HDF5 reader requires h5py => v2.5.0 or later. 42 36 """ 43 37 44 38 # CanSAS version 45 39 cansas_version = 2.0 40 # Logged warnings or messages 41 logging = None 42 # List of errors for the current data set 43 errors = None 44 # Raw file contents to be processed 45 raw_data = None 46 # List of plottable1D objects that should be linked to the current_datainfo 47 data1d = None 48 # List of plottable2D objects that should be linked to the current_datainfo 49 data2d = None 46 50 # Data type name 47 type_name = " NXcanSAS"51 type_name = "CanSAS 2.0" 48 52 # Wildcards 49 type = [" NXcanSAS HDF5 Files (*.h5)|*.h5|"]53 type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] 50 54 # List of allowed extensions 51 55 ext = ['.h5', '.H5'] … … 77 81 except Exception as e: 78 82 if extension not in self.ext: 79 msg = "NXcanSAS Reader could not load file {}".format( 80 basename + extension) 83 msg = "CanSAS2.0 HDF5 Reader could not load file {}".format(basename + extension) 81 84 raise DefaultReaderException(msg) 82 85 raise FileContentsException(e.message) … … 92 95 self.raw_data.close() 93 96 94 for data_set in self.output: 95 if isinstance(data_set, Data1D): 96 if data_set.x.size < 5: 97 exception = FileContentsException( 98 "Fewer than 5 data points found.") 99 data_set.errors.append(exception) 97 for dataset in self.output: 98 if isinstance(dataset, Data1D): 99 if dataset.x.size < 5: 100 self.output = [] 101 raise FileContentsException("Fewer than 5 data points found.") 100 102 101 103 def reset_state(self): … … 107 109 self.data2d = [] 108 110 self.raw_data = None 109 self.multi_frame = False 110 self.data_frames = [] 111 self.data_uncertainty_frames = [] 112 self.errors = [] 111 self.errors = set() 113 112 self.logging = [] 114 self.q_names = []115 self.mask_name = u''116 self.i_name = u''117 self.i_node = u''118 self.i_uncertainties_name = u''119 self.q_uncertainty_names = []120 self.q_resolution_names = []121 113 self.parent_class = u'' 122 114 self.detector = Detector() … … 139 131 value = data.get(key) 140 132 class_name = h5attr(value, u'canSAS_class') 141 if isinstance(class_name, (list, tuple, np.ndarray)):142 class_name = class_name[0]143 133 if class_name is None: 144 134 class_name = h5attr(value, u'NX_class') … … 150 140 if isinstance(value, h5py.Group): 151 141 # Set parent class before recursion 152 last_parent_class = self.parent_class153 142 self.parent_class = class_name 154 143 parent_list.append(key) … … 158 147 self.add_data_set(key) 159 148 elif class_prog.match(u'SASdata'): 160 self._find_data_attributes(value) 161 self._initialize_new_data_set(value) 149 self._initialize_new_data_set(parent_list) 162 150 # Recursion step to access data within the group 163 151 self.read_children(value, parent_list) 152 # Reset parent class when returning from recursive method 153 self.parent_class = class_name 164 154 self.add_intermediate() 165 # Reset parent class when returning from recursive method166 self.parent_class = last_parent_class167 155 parent_list.remove(key) 168 156 169 157 elif isinstance(value, h5py.Dataset): 170 158 # If this is a dataset, store the data appropriately 171 data_set = value.value159 data_set = data[key][:] 172 160 unit = self._get_unit(value) 161 162 # I and Q Data 163 if key == u'I': 164 if isinstance(self.current_dataset, plottable_2D): 165 self.current_dataset.data = data_set 166 self.current_dataset.zaxis("Intensity", unit) 167 else: 168 self.current_dataset.y = data_set.flatten() 169 self.current_dataset.yaxis("Intensity", unit) 170 continue 171 elif key == u'Idev': 172 if isinstance(self.current_dataset, plottable_2D): 173 self.current_dataset.err_data = data_set.flatten() 174 else: 175 self.current_dataset.dy = data_set.flatten() 176 continue 177 elif key == u'Q': 178 self.current_dataset.xaxis("Q", unit) 179 if isinstance(self.current_dataset, plottable_2D): 180 self.current_dataset.q = data_set.flatten() 181 else: 182 self.current_dataset.x = data_set.flatten() 183 continue 184 elif key == u'Qdev': 185 self.current_dataset.dx = data_set.flatten() 186 continue 187 elif key == u'dQw': 188 self.current_dataset.dxw = data_set.flatten() 189 continue 190 elif key == u'dQl': 191 self.current_dataset.dxl = data_set.flatten() 192 continue 193 elif key == u'Qy': 194 self.current_dataset.yaxis("Q_y", unit) 195 self.current_dataset.qy_data = data_set.flatten() 196 continue 197 elif key == u'Qydev': 198 self.current_dataset.dqy_data = data_set.flatten() 199 continue 200 elif key == u'Qx': 201 self.current_dataset.xaxis("Q_x", unit) 202 self.current_dataset.qx_data = data_set.flatten() 203 continue 204 elif key == u'Qxdev': 205 self.current_dataset.dqx_data = data_set.flatten() 206 continue 207 elif key == u'Mask': 208 self.current_dataset.mask = data_set.flatten() 209 continue 210 # Transmission Spectrum 211 elif (key == u'T' 212 and self.parent_class == u'SAStransmission_spectrum'): 213 self.trans_spectrum.transmission = data_set.flatten() 214 continue 215 elif (key == u'Tdev' 216 and self.parent_class == u'SAStransmission_spectrum'): 217 self.trans_spectrum.transmission_deviation = \ 218 data_set.flatten() 219 continue 220 elif (key == u'lambda' 221 and self.parent_class == u'SAStransmission_spectrum'): 222 self.trans_spectrum.wavelength = data_set.flatten() 223 continue 173 224 174 225 for data_point in data_set: … … 180 231 # Top Level Meta Data 181 232 if key == u'definition': 182 if isinstance(data_set, basestring): 183 self.current_datainfo.meta_data['reader'] = data_set 184 break 185 else: 186 self.current_datainfo.meta_data[ 187 'reader'] = data_point 188 # Run 233 self.current_datainfo.meta_data['reader'] = data_point 189 234 elif key == u'run': 235 self.current_datainfo.run.append(data_point) 190 236 try: 191 237 run_name = h5attr(value, 'name') 192 run_dict = {data_ set: run_name}238 run_dict = {data_point: run_name} 193 239 self.current_datainfo.run_name = run_dict 194 240 except Exception: 195 241 pass 196 if isinstance(data_set, basestring):197 self.current_datainfo.run.append(data_set)198 break199 else:200 self.current_datainfo.run.append(data_point)201 # Title202 242 elif key == u'title': 203 if isinstance(data_set, basestring): 204 self.current_datainfo.title = data_set 205 break 206 else: 207 self.current_datainfo.title = data_point 208 # Note 243 self.current_datainfo.title = data_point 209 244 elif key == u'SASnote': 210 self.current_datainfo.notes.append(data_ set)211 break 245 self.current_datainfo.notes.append(data_point) 246 212 247 # Sample Information 213 elif self.parent_class == u'SASsample': 214 self.process_sample(data_point, key) 248 # CanSAS 2.0 format 249 elif key == u'Title' and self.parent_class == u'SASsample': 250 self.current_datainfo.sample.name = data_point 251 # NXcanSAS format 252 elif key == u'name' and self.parent_class == u'SASsample': 253 self.current_datainfo.sample.name = data_point 254 # NXcanSAS format 255 elif key == u'ID' and self.parent_class == u'SASsample': 256 self.current_datainfo.sample.name = data_point 257 elif (key == u'thickness' 258 and self.parent_class == u'SASsample'): 259 self.current_datainfo.sample.thickness = data_point 260 elif (key == u'temperature' 261 and self.parent_class == u'SASsample'): 262 self.current_datainfo.sample.temperature = data_point 263 elif (key == u'transmission' 264 and self.parent_class == u'SASsample'): 265 self.current_datainfo.sample.transmission = data_point 266 elif (key == u'x_position' 267 and self.parent_class == u'SASsample'): 268 self.current_datainfo.sample.position.x = data_point 269 elif (key == u'y_position' 270 and self.parent_class == u'SASsample'): 271 self.current_datainfo.sample.position.y = data_point 272 elif key == u'pitch' and self.parent_class == u'SASsample': 273 self.current_datainfo.sample.orientation.x = data_point 274 elif key == u'yaw' and self.parent_class == u'SASsample': 275 self.current_datainfo.sample.orientation.y = data_point 276 elif key == u'roll' and self.parent_class == u'SASsample': 277 self.current_datainfo.sample.orientation.z = data_point 278 elif (key == u'details' 279 and self.parent_class == u'SASsample'): 280 self.current_datainfo.sample.details.append(data_point) 281 215 282 # Instrumental Information 216 283 elif (key == u'name' 217 284 and self.parent_class == u'SASinstrument'): 218 285 self.current_datainfo.instrument = data_point 219 # Detector 220 elif self.parent_class == u'SASdetector': 221 self.process_detector(data_point, key, unit) 222 # Collimation 223 elif self.parent_class == u'SAScollimation': 224 self.process_collimation(data_point, key, unit) 225 # Aperture 226 elif self.parent_class == u'SASaperture': 227 self.process_aperture(data_point, key) 286 elif key == u'name' and self.parent_class == u'SASdetector': 287 self.detector.name = data_point 288 elif key == u'SDD' and self.parent_class == u'SASdetector': 289 self.detector.distance = float(data_point) 290 self.detector.distance_unit = unit 291 elif (key == u'slit_length' 292 and self.parent_class == u'SASdetector'): 293 self.detector.slit_length = float(data_point) 294 self.detector.slit_length_unit = unit 295 elif (key == u'x_position' 296 and self.parent_class == u'SASdetector'): 297 self.detector.offset.x = float(data_point) 298 self.detector.offset_unit = unit 299 elif (key == u'y_position' 300 and self.parent_class == u'SASdetector'): 301 self.detector.offset.y = float(data_point) 302 self.detector.offset_unit = unit 303 elif (key == u'pitch' 304 and self.parent_class == u'SASdetector'): 305 self.detector.orientation.x = float(data_point) 306 self.detector.orientation_unit = unit 307 elif key == u'roll' and self.parent_class == u'SASdetector': 308 self.detector.orientation.z = float(data_point) 309 self.detector.orientation_unit = unit 310 elif key == u'yaw' and self.parent_class == u'SASdetector': 311 self.detector.orientation.y = float(data_point) 312 self.detector.orientation_unit = unit 313 elif (key == u'beam_center_x' 314 and self.parent_class == u'SASdetector'): 315 self.detector.beam_center.x = float(data_point) 316 self.detector.beam_center_unit = unit 317 elif (key == u'beam_center_y' 318 and self.parent_class == u'SASdetector'): 319 self.detector.beam_center.y = float(data_point) 320 self.detector.beam_center_unit = unit 321 elif (key == u'x_pixel_size' 322 and self.parent_class == u'SASdetector'): 323 self.detector.pixel_size.x = float(data_point) 324 self.detector.pixel_size_unit = unit 325 elif (key == u'y_pixel_size' 326 and self.parent_class == u'SASdetector'): 327 self.detector.pixel_size.y = float(data_point) 328 self.detector.pixel_size_unit = unit 329 elif (key == u'distance' 330 and self.parent_class == u'SAScollimation'): 331 self.collimation.length = data_point 332 self.collimation.length_unit = unit 333 elif (key == u'name' 334 and self.parent_class == u'SAScollimation'): 335 self.collimation.name = data_point 336 elif (key == u'shape' 337 and self.parent_class == u'SASaperture'): 338 self.aperture.shape = data_point 339 elif (key == u'x_gap' 340 and self.parent_class == u'SASaperture'): 341 self.aperture.size.x = data_point 342 elif (key == u'y_gap' 343 and self.parent_class == u'SASaperture'): 344 self.aperture.size.y = data_point 345 228 346 # Process Information 229 elif self.parent_class == u'SASprocess': # CanSAS 2.0 230 self.process_process(data_point, key) 347 elif (key == u'Title' 348 and self.parent_class == u'SASprocess'): # CanSAS 2.0 349 self.process.name = data_point 350 elif (key == u'name' 351 and self.parent_class == u'SASprocess'): # NXcanSAS 352 self.process.name = data_point 353 elif (key == u'description' 354 and self.parent_class == u'SASprocess'): 355 self.process.description = data_point 356 elif key == u'date' and self.parent_class == u'SASprocess': 357 self.process.date = data_point 358 elif key == u'term' and self.parent_class == u'SASprocess': 359 self.process.term = data_point 360 elif self.parent_class == u'SASprocess': 361 self.process.notes.append(data_point) 362 231 363 # Source 232 elif self.parent_class == u'SASsource': 233 self.process_source(data_point, key, unit) 364 elif (key == u'wavelength' 365 and self.parent_class == u'SASdata'): 366 self.current_datainfo.source.wavelength = data_point 367 self.current_datainfo.source.wavelength_unit = unit 368 elif (key == u'incident_wavelength' 369 and self.parent_class == 'SASsource'): 370 self.current_datainfo.source.wavelength = data_point 371 self.current_datainfo.source.wavelength_unit = unit 372 elif (key == u'wavelength_max' 373 and self.parent_class == u'SASsource'): 374 self.current_datainfo.source.wavelength_max = data_point 375 self.current_datainfo.source.wavelength_max_unit = unit 376 elif (key == u'wavelength_min' 377 and self.parent_class == u'SASsource'): 378 self.current_datainfo.source.wavelength_min = data_point 379 self.current_datainfo.source.wavelength_min_unit = unit 380 elif (key == u'incident_wavelength_spread' 381 and self.parent_class == u'SASsource'): 382 self.current_datainfo.source.wavelength_spread = \ 383 data_point 384 self.current_datainfo.source.wavelength_spread_unit = \ 385 unit 386 elif (key == u'beam_size_x' 387 and self.parent_class == u'SASsource'): 388 self.current_datainfo.source.beam_size.x = data_point 389 self.current_datainfo.source.beam_size_unit = unit 390 elif (key == u'beam_size_y' 391 and self.parent_class == u'SASsource'): 392 self.current_datainfo.source.beam_size.y = data_point 393 self.current_datainfo.source.beam_size_unit = unit 394 elif (key == u'beam_shape' 395 and self.parent_class == u'SASsource'): 396 self.current_datainfo.source.beam_shape = data_point 397 elif (key == u'radiation' 398 and self.parent_class == u'SASsource'): 399 self.current_datainfo.source.radiation = data_point 400 elif (key == u'transmission' 401 and self.parent_class == u'SASdata'): 402 self.current_datainfo.sample.transmission = data_point 403 234 404 # Everything else goes in meta_data 235 elif self.parent_class == u'SASdata':236 if isinstance(self.current_dataset, plottable_2D):237 self.process_2d_data_object(data_set, key, unit)238 else:239 self.process_1d_data_object(data_set, key, unit)240 241 break242 elif self.parent_class == u'SAStransmission_spectrum':243 self.process_trans_spectrum(data_set, key)244 break245 405 else: 246 406 new_key = self._create_unique_key( … … 250 410 else: 251 411 # I don't know if this reachable code 252 self.errors.append("ShouldNeverHappenException") 253 254 def process_1d_data_object(self, data_set, key, unit): 255 """ 256 SASdata processor method for 1d data items 257 :param data_set: data from HDF5 file 258 :param key: canSAS_class attribute 259 :param unit: unit attribute 260 """ 261 if key == self.i_name: 262 if self.multi_frame: 263 for x in range(0, data_set.shape[0]): 264 self.data_frames.append(data_set[x].flatten()) 265 else: 266 self.current_dataset.y = data_set.flatten() 267 self.current_dataset.yaxis("Intensity", unit) 268 elif key == self.i_uncertainties_name: 269 if self.multi_frame: 270 for x in range(0, data_set.shape[0]): 271 self.data_uncertainty_frames.append(data_set[x].flatten()) 272 self.current_dataset.dy = data_set.flatten() 273 elif key in self.q_names: 274 self.current_dataset.xaxis("Q", unit) 275 self.current_dataset.x = data_set.flatten() 276 elif key in self.q_resolution_names: 277 if (len(self.q_resolution_names) > 1 278 and np.where(self.q_resolution_names == key)[0] == 0): 279 self.current_dataset.dxw = data_set.flatten() 280 elif (len(self.q_resolution_names) > 1 281 and np.where(self.q_resolution_names == key)[0] == 1): 282 self.current_dataset.dxl = data_set.flatten() 283 else: 284 self.current_dataset.dx = data_set.flatten() 285 elif key in self.q_uncertainty_names: 286 if (len(self.q_uncertainty_names) > 1 287 and np.where(self.q_uncertainty_names == key)[0] == 0): 288 self.current_dataset.dxw = data_set.flatten() 289 elif (len(self.q_uncertainty_names) > 1 290 and np.where(self.q_uncertainty_names == key)[0] == 1): 291 self.current_dataset.dxl = data_set.flatten() 292 else: 293 self.current_dataset.dx = data_set.flatten() 294 elif key == self.mask_name: 295 self.current_dataset.mask = data_set.flatten() 296 elif key == u'wavelength': 297 self.current_datainfo.source.wavelength = data_set[0] 298 self.current_datainfo.source.wavelength_unit = unit 299 300 def process_2d_data_object(self, data_set, key, unit): 301 if key == self.i_name: 302 self.current_dataset.data = data_set 303 self.current_dataset.zaxis("Intensity", unit) 304 elif key == self.i_uncertainties_name: 305 self.current_dataset.err_data = data_set.flatten() 306 elif key in self.q_names: 307 self.current_dataset.xaxis("Q_x", unit) 308 self.current_dataset.yaxis("Q_y", unit) 309 if self.q_names[0] == self.q_names[1]: 310 # All q data in a single array 311 self.current_dataset.qx_data = data_set[0] 312 self.current_dataset.qy_data = data_set[1] 313 elif self.q_names.index(key) == 0: 314 self.current_dataset.qx_data = data_set 315 elif self.q_names.index(key) == 1: 316 self.current_dataset.qy_data = data_set 317 elif key in self.q_uncertainty_names or key in self.q_resolution_names: 318 if ((self.q_uncertainty_names[0] == self.q_uncertainty_names[1]) or 319 (self.q_resolution_names[0] == self.q_resolution_names[1])): 320 # All q data in a single array 321 self.current_dataset.dqx_data = data_set[0].flatten() 322 self.current_dataset.dqy_data = data_set[1].flatten() 323 elif (self.q_uncertainty_names.index(key) == 0 or 324 self.q_resolution_names.index(key) == 0): 325 self.current_dataset.dqx_data = data_set.flatten() 326 elif (self.q_uncertainty_names.index(key) == 1 or 327 self.q_resolution_names.index(key) == 1): 328 self.current_dataset.dqy_data = data_set.flatten() 329 self.current_dataset.yaxis("Q_y", unit) 330 elif key == self.mask_name: 331 self.current_dataset.mask = data_set.flatten() 332 elif key == u'Qy': 333 self.current_dataset.yaxis("Q_y", unit) 334 self.current_dataset.qy_data = data_set.flatten() 335 elif key == u'Qydev': 336 self.current_dataset.dqy_data = data_set.flatten() 337 elif key == u'Qx': 338 self.current_dataset.xaxis("Q_x", unit) 339 self.current_dataset.qx_data = data_set.flatten() 340 elif key == u'Qxdev': 341 self.current_dataset.dqx_data = data_set.flatten() 342 343 def process_trans_spectrum(self, data_set, key): 344 """ 345 SAStransmission_spectrum processor 346 :param data_set: data from HDF5 file 347 :param key: canSAS_class attribute 348 """ 349 if key == u'T': 350 self.trans_spectrum.transmission = data_set.flatten() 351 elif key == u'Tdev': 352 self.trans_spectrum.transmission_deviation = data_set.flatten() 353 elif key == u'lambda': 354 self.trans_spectrum.wavelength = data_set.flatten() 355 356 def process_sample(self, data_point, key): 357 """ 358 SASsample processor 359 :param data_point: Single point from an HDF5 data file 360 :param key: class name data_point was taken from 361 """ 362 if key == u'Title': 363 self.current_datainfo.sample.name = data_point 364 elif key == u'name': 365 self.current_datainfo.sample.name = data_point 366 elif key == u'ID': 367 self.current_datainfo.sample.name = data_point 368 elif key == u'thickness': 369 self.current_datainfo.sample.thickness = data_point 370 elif key == u'temperature': 371 self.current_datainfo.sample.temperature = data_point 372 elif key == u'transmission': 373 self.current_datainfo.sample.transmission = data_point 374 elif key == u'x_position': 375 self.current_datainfo.sample.position.x = data_point 376 elif key == u'y_position': 377 self.current_datainfo.sample.position.y = data_point 378 elif key == u'pitch': 379 self.current_datainfo.sample.orientation.x = data_point 380 elif key == u'yaw': 381 self.current_datainfo.sample.orientation.y = data_point 382 elif key == u'roll': 383 self.current_datainfo.sample.orientation.z = data_point 384 elif key == u'details': 385 self.current_datainfo.sample.details.append(data_point) 386 387 def process_detector(self, data_point, key, unit): 388 """ 389 SASdetector processor 390 :param data_point: Single point from an HDF5 data file 391 :param key: class name data_point was taken from 392 :param unit: unit attribute from data set 393 """ 394 if key == u'name': 395 self.detector.name = data_point 396 elif key == u'SDD': 397 self.detector.distance = float(data_point) 398 self.detector.distance_unit = unit 399 elif key == u'slit_length': 400 self.detector.slit_length = float(data_point) 401 self.detector.slit_length_unit = unit 402 elif key == u'x_position': 403 self.detector.offset.x = float(data_point) 404 self.detector.offset_unit = unit 405 elif key == u'y_position': 406 self.detector.offset.y = float(data_point) 407 self.detector.offset_unit = unit 408 elif key == u'pitch': 409 self.detector.orientation.x = float(data_point) 410 self.detector.orientation_unit = unit 411 elif key == u'roll': 412 self.detector.orientation.z = float(data_point) 413 self.detector.orientation_unit = unit 414 elif key == u'yaw': 415 self.detector.orientation.y = float(data_point) 416 self.detector.orientation_unit = unit 417 elif key == u'beam_center_x': 418 self.detector.beam_center.x = float(data_point) 419 self.detector.beam_center_unit = unit 420 elif key == u'beam_center_y': 421 self.detector.beam_center.y = float(data_point) 422 self.detector.beam_center_unit = unit 423 elif key == u'x_pixel_size': 424 self.detector.pixel_size.x = float(data_point) 425 self.detector.pixel_size_unit = unit 426 elif key == u'y_pixel_size': 427 self.detector.pixel_size.y = float(data_point) 428 self.detector.pixel_size_unit = unit 429 430 def process_collimation(self, data_point, key, unit): 431 """ 432 SAScollimation processor 433 :param data_point: Single point from an HDF5 data file 434 :param key: class name data_point was taken from 435 :param unit: unit attribute from data set 436 """ 437 if key == u'distance': 438 self.collimation.length = data_point 439 self.collimation.length_unit = unit 440 elif key == u'name': 441 self.collimation.name = data_point 442 443 def process_aperture(self, data_point, key): 444 """ 445 SASaperture processor 446 :param data_point: Single point from an HDF5 data file 447 :param key: class name data_point was taken from 448 """ 449 if key == u'shape': 450 self.aperture.shape = data_point 451 elif key == u'x_gap': 452 self.aperture.size.x = data_point 453 elif key == u'y_gap': 454 self.aperture.size.y = data_point 455 456 def process_source(self, data_point, key, unit): 457 """ 458 SASsource processor 459 :param data_point: Single point from an HDF5 data file 460 :param key: class name data_point was taken from 461 :param unit: unit attribute from data set 462 """ 463 if key == u'incident_wavelength': 464 self.current_datainfo.source.wavelength = data_point 465 self.current_datainfo.source.wavelength_unit = unit 466 elif key == u'wavelength_max': 467 self.current_datainfo.source.wavelength_max = data_point 468 self.current_datainfo.source.wavelength_max_unit = unit 469 elif key == u'wavelength_min': 470 self.current_datainfo.source.wavelength_min = data_point 471 self.current_datainfo.source.wavelength_min_unit = unit 472 elif key == u'incident_wavelength_spread': 473 self.current_datainfo.source.wavelength_spread = data_point 474 self.current_datainfo.source.wavelength_spread_unit = unit 475 elif key == u'beam_size_x': 476 self.current_datainfo.source.beam_size.x = data_point 477 self.current_datainfo.source.beam_size_unit = unit 478 elif key == u'beam_size_y': 479 self.current_datainfo.source.beam_size.y = data_point 480 self.current_datainfo.source.beam_size_unit = unit 481 elif key == u'beam_shape': 482 self.current_datainfo.source.beam_shape = data_point 483 elif key == u'radiation': 484 self.current_datainfo.source.radiation = data_point 485 486 def process_process(self, data_point, key): 487 """ 488 SASprocess processor 489 :param data_point: Single point from an HDF5 data file 490 :param key: class name data_point was taken from 491 """ 492 term_match = re.compile(u'^term[0-9]+$') 493 if key == u'Title': # CanSAS 2.0 494 self.process.name = data_point 495 elif key == u'name': # NXcanSAS 496 self.process.name = data_point 497 elif key == u'description': 498 self.process.description = data_point 499 elif key == u'date': 500 self.process.date = data_point 501 elif term_match.match(key): 502 self.process.term.append(data_point) 503 else: 504 self.process.notes.append(data_point) 412 self.errors.add("ShouldNeverHappenException") 505 413 506 414 def add_intermediate(self): … … 532 440 self.data2d.append(self.current_dataset) 533 441 elif isinstance(self.current_dataset, plottable_1D): 534 if self.multi_frame: 535 for x in range(0, len(self.data_frames)): 536 self.current_dataset.y = self.data_frames[x] 537 if len(self.data_uncertainty_frames) > x: 538 self.current_dataset.dy = \ 539 self.data_uncertainty_frames[x] 540 self.data1d.append(self.current_dataset) 541 else: 542 self.data1d.append(self.current_dataset) 442 self.data1d.append(self.current_dataset) 543 443 544 444 def final_data_cleanup(self): … … 552 452 spectrum_list = [] 553 453 for spectrum in self.current_datainfo.trans_spectrum: 454 spectrum.transmission = np.delete(spectrum.transmission, [0]) 554 455 spectrum.transmission = spectrum.transmission.astype(np.float64) 456 spectrum.transmission_deviation = np.delete( 457 spectrum.transmission_deviation, [0]) 555 458 spectrum.transmission_deviation = \ 556 459 spectrum.transmission_deviation.astype(np.float64) 460 spectrum.wavelength = np.delete(spectrum.wavelength, [0]) 557 461 spectrum.wavelength = spectrum.wavelength.astype(np.float64) 558 462 if len(spectrum.transmission) > 0: … … 562 466 # Append errors to dataset and reset class errors 563 467 self.current_datainfo.errors = self.errors 564 self.errors = []468 self.errors.clear() 565 469 566 470 # Combine all plottables with datainfo and append each to output 567 471 # Type cast data arrays to float64 and find min/max as appropriate 568 472 for dataset in self.data2d: 473 zeros = np.ones(dataset.data.size, dtype=bool) 474 try: 475 for i in range(0, dataset.mask.size - 1): 476 zeros[i] = dataset.mask[i] 477 except: 478 self.errors.add(sys.exc_value) 479 dataset.mask = zeros 569 480 # Calculate the actual Q matrix 570 481 try: … … 573 484 * dataset.qx_data 574 485 + dataset.qy_data 575 * dataset.qy_data) .flatten()486 * dataset.qy_data) 576 487 except: 577 488 dataset.q_data = None 578 489 579 490 if dataset.data.ndim == 2: 580 dataset.y_bins = np.unique(dataset.qy_data.flatten()) 581 dataset.x_bins = np.unique(dataset.qx_data.flatten()) 491 (n_rows, n_cols) = dataset.data.shape 492 dataset.y_bins = dataset.qy_data[0::n_cols] 493 dataset.x_bins = dataset.qx_data[:n_cols] 582 494 dataset.data = dataset.data.flatten() 583 dataset.qx_data = dataset.qx_data.flatten()584 dataset.qy_data = dataset.qy_data.flatten()585 586 try:587 iter(dataset.mask)588 dataset.mask = np.invert(np.asarray(dataset.mask, dtype=bool))589 except TypeError:590 dataset.mask = np.ones(dataset.data.shape, dtype=bool)591 495 self.current_dataset = dataset 592 496 self.send_to_output() … … 607 511 if self.current_datainfo and self.current_dataset: 608 512 self.final_data_cleanup() 609 self.data_frames = []610 self.data_uncertainty_frames = []611 513 self.data1d = [] 612 514 self.data2d = [] 613 515 self.current_datainfo = DataInfo() 614 516 615 def _initialize_new_data_set(self, value=None): 517 518 def _initialize_new_data_set(self, parent_list=None): 616 519 """ 617 520 A private class method to generate a new 1D or 2D data object based on … … 621 524 :param parent_list: List of names of parent elements 622 525 """ 623 if self._is_2d_not_multi_frame(value): 526 527 if parent_list is None: 528 parent_list = [] 529 if self._find_intermediate(parent_list, "Qx"): 624 530 self.current_dataset = plottable_2D() 625 531 else: … … 629 535 self.current_datainfo.filename = self.raw_data.filename 630 536 631 @staticmethod 632 def as_list_or_array(iterable): 633 """ 634 Return value as a list if not already a list or array. 635 :param iterable: 537 def _find_intermediate(self, parent_list, basename=""): 538 """ 539 A private class used to find an entry by either using a direct key or 540 knowing the approximate basename. 541 542 :param parent_list: List of parents nodes in the HDF5 file 543 :param basename: Approximate name of an entry to search for 636 544 :return: 637 545 """ 638 if not (isinstance(iterable, np.ndarray) or isinstance(iterable, list)): 639 iterable = iterable.split(",") if isinstance(iterable, basestring)\ 640 else [iterable] 641 return iterable 642 643 def _find_data_attributes(self, value): 644 """ 645 A class to find the indices for Q, the name of the Qdev and Idev, and 646 the name of the mask. 647 :param value: SASdata/NXdata HDF5 Group 648 """ 649 # Initialize values to base types 650 self.mask_name = u'' 651 self.i_name = u'' 652 self.i_node = u'' 653 self.i_uncertainties_name = u'' 654 self.q_names = [] 655 self.q_uncertainty_names = [] 656 self.q_resolution_names = [] 657 # Get attributes 658 attrs = value.attrs 659 signal = attrs.get("signal", "I") 660 i_axes = attrs.get("I_axes", ["Q"]) 661 q_indices = attrs.get("Q_indices", [0]) 662 i_axes = self.as_list_or_array(i_axes) 663 keys = value.keys() 664 # Assign attributes to appropriate class variables 665 self.q_names = [i_axes[int(v)] for v in self.as_list_or_array(q_indices)] 666 self.mask_name = attrs.get("mask") 667 self.i_name = signal 668 self.i_node = value.get(self.i_name) 669 for item in self.q_names: 670 if item in keys: 671 q_vals = value.get(item) 672 if q_vals.attrs.get("uncertainties") is not None: 673 self.q_uncertainty_names = q_vals.attrs.get("uncertainties") 674 elif q_vals.attrs.get("uncertainty") is not None: 675 self.q_uncertainty_names = q_vals.attrs.get("uncertainty") 676 if isinstance(self.q_uncertainty_names, basestring): 677 self.q_uncertainty_names = self.q_uncertainty_names.split(",") 678 if q_vals.attrs.get("resolutions") is not None: 679 self.q_resolution_names = q_vals.attrs.get("resolutions") 680 if isinstance(self.q_resolution_names, basestring): 681 self.q_resolution_names = self.q_resolution_names.split(",") 682 if self.i_name in keys: 683 i_vals = value.get(self.i_name) 684 self.i_uncertainties_name = i_vals.attrs.get("uncertainties") 685 if self.i_uncertainties_name is None: 686 self.i_uncertainties_name = i_vals.attrs.get("uncertainty") 687 688 def _is_2d_not_multi_frame(self, value, i_base="", q_base=""): 689 """ 690 A private class to determine if the data set is 1d or 2d. 691 692 :param value: Nexus/NXcanSAS data group 693 :param basename: Approximate name of an entry to search for 694 :return: True if 2D, otherwise false 695 """ 696 i_basename = i_base if i_base != "" else self.i_name 697 i_vals = value.get(i_basename) 698 q_basename = q_base if q_base != "" else self.q_names 699 q_vals = value.get(q_basename[0]) 700 self.multi_frame = (i_vals is not None and q_vals is not None 701 and len(i_vals.shape) != 1 702 and len(q_vals.shape) == 1) 703 return (i_vals is not None and len(i_vals.shape) != 1 704 and not self.multi_frame) 546 547 entry = False 548 key_prog = re.compile(basename) 549 top = self.raw_data 550 for parent in parent_list: 551 top = top.get(parent) 552 for key in top.keys(): 553 if key_prog.match(key): 554 entry = True 555 break 556 return entry 705 557 706 558 def _create_unique_key(self, dictionary, name, numb=0): … … 731 583 if unit is None: 732 584 unit = h5attr(value, u'unit') 585 # Convert the unit formats 586 if unit == "1/A": 587 unit = "A^{-1}" 588 elif unit == "1/cm": 589 unit = "cm^{-1}" 733 590 return unit
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