Changeset c7634fd in sasview for src/sas/sascalc/dataloader
- Timestamp:
- Jun 21, 2018 2:04:35 PM (6 years ago)
- Branches:
- master, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, unittest-saveload
- Children:
- 3bab401
- Parents:
- 316b9c1 (diff), 6bd4235 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent. - Location:
- src/sas/sascalc/dataloader
- Files:
-
- 3 edited
-
readers/cansas_reader_HDF5.py (modified) (9 diffs)
-
file_reader_base_class.py (modified) (4 diffs)
-
loader.py (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py
r61f329f0 r18af6d2 38 38 # CanSAS version 39 39 cansas_version = 2.0 40 # Logged warnings or messages41 logging = None42 # List of errors for the current data set43 errors = None44 # Raw file contents to be processed45 raw_data = None46 # List of plottable1D objects that should be linked to the current_datainfo47 data1d = None48 # List of plottable2D objects that should be linked to the current_datainfo49 data2d = None50 40 # Data type name 51 41 type_name = "CanSAS 2.0" … … 111 101 self.errors = set() 112 102 self.logging = [] 103 self.q_name = [] 104 self.mask_name = u'' 105 self.i_name = u'' 106 self.i_node = u'' 107 self.q_uncertainties = u'' 108 self.q_resolutions = u'' 109 self.i_uncertainties = u'' 113 110 self.parent_class = u'' 114 111 self.detector = Detector() … … 147 144 self.add_data_set(key) 148 145 elif class_prog.match(u'SASdata'): 146 self._find_data_attributes(value) 149 147 self._initialize_new_data_set(parent_list) 150 148 # Recursion step to access data within the group … … 159 157 data_set = data[key][:] 160 158 unit = self._get_unit(value) 161 162 # I and Q Data163 if key == u'I':164 if isinstance(self.current_dataset, plottable_2D):165 self.current_dataset.data = data_set166 self.current_dataset.zaxis("Intensity", unit)167 else:168 self.current_dataset.y = data_set.flatten()169 self.current_dataset.yaxis("Intensity", unit)170 continue171 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 continue177 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 continue184 elif key == u'Qdev':185 self.current_dataset.dx = data_set.flatten()186 continue187 elif key == u'dQw':188 self.current_dataset.dxw = data_set.flatten()189 continue190 elif key == u'dQl':191 self.current_dataset.dxl = data_set.flatten()192 continue193 elif key == u'Qy':194 self.current_dataset.yaxis("Q_y", unit)195 self.current_dataset.qy_data = data_set.flatten()196 continue197 elif key == u'Qydev':198 self.current_dataset.dqy_data = data_set.flatten()199 continue200 elif key == u'Qx':201 self.current_dataset.xaxis("Q_x", unit)202 self.current_dataset.qx_data = data_set.flatten()203 continue204 elif key == u'Qxdev':205 self.current_dataset.dqx_data = data_set.flatten()206 continue207 elif key == u'Mask':208 self.current_dataset.mask = data_set.flatten()209 continue210 # Transmission Spectrum211 elif (key == u'T'212 and self.parent_class == u'SAStransmission_spectrum'):213 self.trans_spectrum.transmission = data_set.flatten()214 continue215 elif (key == u'Tdev'216 and self.parent_class == u'SAStransmission_spectrum'):217 self.trans_spectrum.transmission_deviation = \218 data_set.flatten()219 continue220 elif (key == u'lambda'221 and self.parent_class == u'SAStransmission_spectrum'):222 self.trans_spectrum.wavelength = data_set.flatten()223 continue224 159 225 160 for data_point in data_set: … … 232 167 if key == u'definition': 233 168 self.current_datainfo.meta_data['reader'] = data_point 169 # Run 234 170 elif key == u'run': 235 171 self.current_datainfo.run.append(data_point) … … 240 176 except Exception: 241 177 pass 178 # Title 242 179 elif key == u'title': 243 180 self.current_datainfo.title = data_point 181 # Note 244 182 elif key == u'SASnote': 245 183 self.current_datainfo.notes.append(data_point) 246 247 184 # Sample Information 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) 281 185 elif self.parent_class == u'SASsample': 186 self.process_sample(data_point, key) 282 187 # Instrumental Information 283 188 elif (key == u'name' 284 189 and self.parent_class == u'SASinstrument'): 285 190 self.current_datainfo.instrument = data_point 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 345 191 # Detector 192 elif self.parent_class == u'SASdetector': 193 self.process_detector(data_point, key, unit) 194 # Collimation 195 elif self.parent_class == u'SAScollimation': 196 self.process_collimation(data_point, key, unit) 197 # Aperture 198 elif self.parent_class == u'SASaperture': 199 self.process_aperture(data_point, key) 346 200 # Process Information 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) 362 201 elif self.parent_class == u'SASprocess': # CanSAS 2.0 202 self.process_process(data_point, key) 363 203 # Source 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 403 204 elif self.parent_class == u'SASsource': 205 self.process_source(data_point, key, unit) 404 206 # Everything else goes in meta_data 207 elif self.parent_class == u'SASdata': 208 self.process_data_object(data_set, key, unit) 209 break 210 elif self.parent_class == u'SAStransmission_spectrum': 211 self.process_trans_spectrum(data_set, key) 212 break 405 213 else: 406 214 new_key = self._create_unique_key( … … 411 219 # I don't know if this reachable code 412 220 self.errors.add("ShouldNeverHappenException") 221 222 def process_data_object(self, data_set, key, unit): 223 """ 224 SASdata processor method 225 :param data_set: data from HDF5 file 226 :param key: canSAS_class attribute 227 :param unit: unit attribute 228 """ 229 if key == self.i_name: 230 if isinstance(self.current_dataset, plottable_2D): 231 self.current_dataset.data = data_set 232 self.current_dataset.zaxis("Intensity", unit) 233 else: 234 self.current_dataset.y = data_set.flatten() 235 self.current_dataset.yaxis("Intensity", unit) 236 elif key == self.i_uncertainties: 237 if isinstance(self.current_dataset, plottable_2D): 238 self.current_dataset.err_data = data_set.flatten() 239 else: 240 self.current_dataset.dy = data_set.flatten() 241 elif key in self.q_name: 242 self.current_dataset.xaxis("Q", unit) 243 if isinstance(self.current_dataset, plottable_2D): 244 self.current_dataset.q = data_set.flatten() 245 else: 246 self.current_dataset.x = data_set.flatten() 247 elif key in self.q_resolutions: 248 if key == u'dQw': 249 self.current_dataset.dxw = data_set.flatten() 250 elif key == u'dQl': 251 self.current_dataset.dxl = data_set.flatten() 252 else: 253 self.current_dataset.dx = data_set.flatten() 254 elif key == u'Qy': 255 self.current_dataset.yaxis("Q_y", unit) 256 self.current_dataset.qy_data = data_set.flatten() 257 elif key == u'Qydev': 258 self.current_dataset.dqy_data = data_set.flatten() 259 elif key == u'Qx': 260 self.current_dataset.xaxis("Q_x", unit) 261 self.current_dataset.qx_data = data_set.flatten() 262 elif key == u'Qxdev': 263 self.current_dataset.dqx_data = data_set.flatten() 264 elif key == self.mask_name: 265 self.current_dataset.mask = data_set.flatten() 266 elif key == u'wavelength': 267 self.current_datainfo.source.wavelength = data_set[0] 268 self.current_datainfo.source.wavelength_unit = unit 269 270 def process_trans_spectrum(self, data_set, key): 271 """ 272 SAStransmission_spectrum processor 273 :param data_set: data from HDF5 file 274 :param key: canSAS_class attribute 275 """ 276 if key == u'T': 277 self.trans_spectrum.transmission = data_set.flatten() 278 elif key == u'Tdev': 279 self.trans_spectrum.transmission_deviation = data_set.flatten() 280 elif key == u'lambda': 281 self.trans_spectrum.wavelength = data_set.flatten() 282 283 def process_sample(self, data_point, key): 284 """ 285 SASsample processor 286 :param data_point: Single point from an HDF5 data file 287 :param key: class name data_point was taken from 288 """ 289 if key == u'Title': 290 self.current_datainfo.sample.name = data_point 291 elif key == u'name': 292 self.current_datainfo.sample.name = data_point 293 elif key == u'ID': 294 self.current_datainfo.sample.name = data_point 295 elif key == u'thickness': 296 self.current_datainfo.sample.thickness = data_point 297 elif key == u'temperature': 298 self.current_datainfo.sample.temperature = data_point 299 elif key == u'transmission': 300 self.current_datainfo.sample.transmission = data_point 301 elif key == u'x_position': 302 self.current_datainfo.sample.position.x = data_point 303 elif key == u'y_position': 304 self.current_datainfo.sample.position.y = data_point 305 elif key == u'pitch': 306 self.current_datainfo.sample.orientation.x = data_point 307 elif key == u'yaw': 308 self.current_datainfo.sample.orientation.y = data_point 309 elif key == u'roll': 310 self.current_datainfo.sample.orientation.z = data_point 311 elif key == u'details': 312 self.current_datainfo.sample.details.append(data_point) 313 314 def process_detector(self, data_point, key, unit): 315 """ 316 SASdetector processor 317 :param data_point: Single point from an HDF5 data file 318 :param key: class name data_point was taken from 319 :param unit: unit attribute from data set 320 """ 321 if key == u'name': 322 self.detector.name = data_point 323 elif key == u'SDD': 324 self.detector.distance = float(data_point) 325 self.detector.distance_unit = unit 326 elif key == u'slit_length': 327 self.detector.slit_length = float(data_point) 328 self.detector.slit_length_unit = unit 329 elif key == u'x_position': 330 self.detector.offset.x = float(data_point) 331 self.detector.offset_unit = unit 332 elif key == u'y_position': 333 self.detector.offset.y = float(data_point) 334 self.detector.offset_unit = unit 335 elif key == u'pitch': 336 self.detector.orientation.x = float(data_point) 337 self.detector.orientation_unit = unit 338 elif key == u'roll': 339 self.detector.orientation.z = float(data_point) 340 self.detector.orientation_unit = unit 341 elif key == u'yaw': 342 self.detector.orientation.y = float(data_point) 343 self.detector.orientation_unit = unit 344 elif key == u'beam_center_x': 345 self.detector.beam_center.x = float(data_point) 346 self.detector.beam_center_unit = unit 347 elif key == u'beam_center_y': 348 self.detector.beam_center.y = float(data_point) 349 self.detector.beam_center_unit = unit 350 elif key == u'x_pixel_size': 351 self.detector.pixel_size.x = float(data_point) 352 self.detector.pixel_size_unit = unit 353 elif key == u'y_pixel_size': 354 self.detector.pixel_size.y = float(data_point) 355 self.detector.pixel_size_unit = unit 356 357 def process_collimation(self, data_point, key, unit): 358 """ 359 SAScollimation processor 360 :param data_point: Single point from an HDF5 data file 361 :param key: class name data_point was taken from 362 :param unit: unit attribute from data set 363 """ 364 if key == u'distance': 365 self.collimation.length = data_point 366 self.collimation.length_unit = unit 367 elif key == u'name': 368 self.collimation.name = data_point 369 370 def process_aperture(self, data_point, key): 371 """ 372 SASaperture processor 373 :param data_point: Single point from an HDF5 data file 374 :param key: class name data_point was taken from 375 """ 376 if key == u'shape': 377 self.aperture.shape = data_point 378 elif key == u'x_gap': 379 self.aperture.size.x = data_point 380 elif key == u'y_gap': 381 self.aperture.size.y = data_point 382 383 def process_source(self, data_point, key, unit): 384 """ 385 SASsource processor 386 :param data_point: Single point from an HDF5 data file 387 :param key: class name data_point was taken from 388 :param unit: unit attribute from data set 389 """ 390 if key == u'incident_wavelength': 391 self.current_datainfo.source.wavelength = data_point 392 self.current_datainfo.source.wavelength_unit = unit 393 elif key == u'wavelength_max': 394 self.current_datainfo.source.wavelength_max = data_point 395 self.current_datainfo.source.wavelength_max_unit = unit 396 elif key == u'wavelength_min': 397 self.current_datainfo.source.wavelength_min = data_point 398 self.current_datainfo.source.wavelength_min_unit = unit 399 elif key == u'incident_wavelength_spread': 400 self.current_datainfo.source.wavelength_spread = data_point 401 self.current_datainfo.source.wavelength_spread_unit = unit 402 elif key == u'beam_size_x': 403 self.current_datainfo.source.beam_size.x = data_point 404 self.current_datainfo.source.beam_size_unit = unit 405 elif key == u'beam_size_y': 406 self.current_datainfo.source.beam_size.y = data_point 407 self.current_datainfo.source.beam_size_unit = unit 408 elif key == u'beam_shape': 409 self.current_datainfo.source.beam_shape = data_point 410 elif key == u'radiation': 411 self.current_datainfo.source.radiation = data_point 412 413 def process_process(self, data_point, key): 414 """ 415 SASprocess processor 416 :param data_point: Single point from an HDF5 data file 417 :param key: class name data_point was taken from 418 """ 419 if key == u'Title': # CanSAS 2.0 420 self.process.name = data_point 421 elif key == u'name': # NXcanSAS 422 self.process.name = data_point 423 elif key == u'description': 424 self.process.description = data_point 425 elif key == u'date': 426 self.process.date = data_point 427 elif key == u'term': 428 self.process.term = data_point 429 else: 430 self.process.notes.append(data_point) 413 431 414 432 def add_intermediate(self): … … 515 533 self.current_datainfo = DataInfo() 516 534 517 518 535 def _initialize_new_data_set(self, parent_list=None): 519 536 """ … … 534 551 self.current_dataset = plottable_1D(x, y) 535 552 self.current_datainfo.filename = self.raw_data.filename 553 self.mask_name = "" 554 self.i_name = "" 555 self.i_node = "" 556 self.q_name = [] 557 self.q_uncertainties = "" 558 self.q_resolutions = "" 559 self.i_uncertainties = "" 560 561 def _find_data_attributes(self, value): 562 """ 563 A class to find the indices for Q, the name of the Qdev and Idev, and 564 the name of the mask. 565 :param value: SASdata/NXdata HDF5 Group 566 """ 567 attrs = value.attrs 568 signal = attrs.get("signal") 569 i_axes = np.array(str(attrs.get("I_axes")).split(",")) 570 q_indices = np.int_(attrs.get("Q_indices").split(",")) 571 keys = value.keys() 572 self.mask_name = attrs.get("mask") 573 for val in q_indices: 574 self.q_name.append(i_axes[val]) 575 self.i_name = signal 576 self.i_node = value.get(self.i_name) 577 for item in self.q_name: 578 if item in keys: 579 q_vals = value.get(item) 580 self.q_uncertainties = q_vals.attrs.get("uncertainty") 581 self.q_resolutions = q_vals.attrs.get("resolution") 582 if self.i_name in keys: 583 i_vals = value.get(self.i_name) 584 self.i_uncertainties = i_vals.attrs.get("uncertainty") 536 585 537 586 def _find_intermediate(self, parent_list, basename=""): -
src/sas/sascalc/dataloader/file_reader_base_class.py
ra58b5a0 r4a8d55c 31 31 FIELDS_2D = ('data', 'qx_data', 'qy_data', 'q_data', 'err_data', 32 32 'dqx_data', 'dqy_data', 'mask') 33 33 DEPRECATION_MESSAGE = ("\rThe extension of this file suggests the data set migh" 34 "t not be fully reduced. Support for the reader associat" 35 "ed with this file type has been removed. An attempt to " 36 "load the file was made, but, should it be successful, " 37 "SasView cannot guarantee the accuracy of the data.") 34 38 35 39 class FileReader(object): … … 40 44 # List of allowed extensions 41 45 ext = ['.txt'] 46 # Deprecated extensions 47 deprecated_extensions = ['.asc', '.nxs'] 42 48 # Bypass extension check and try to load anyway 43 49 allow_all = False … … 87 93 if not self.f_open.closed: 88 94 self.f_open.close() 95 if any(filepath.lower().endswith(ext) for ext in 96 self.deprecated_extensions): 97 self.handle_error_message(DEPRECATION_MESSAGE) 89 98 if len(self.output) > 0: 90 99 # Sort the data that's been loaded … … 146 155 else: 147 156 logger.warning(msg) 157 raise NoKnownLoaderException(msg) 148 158 149 159 def send_to_output(self): -
src/sas/sascalc/dataloader/loader.py
rdc8d1c2 r4a8d55c 90 90 ascii_loader = ascii_reader.Reader() 91 91 return ascii_loader.read(path) 92 except NoKnownLoaderException: 93 pass # Try the Cansas XML reader 92 94 except DefaultReaderException: 93 95 pass # Loader specific error to try the cansas XML reader … … 100 102 cansas_loader = cansas_reader.Reader() 101 103 return cansas_loader.read(path) 104 except NoKnownLoaderException: 105 pass # Try the NXcanSAS reader 102 106 except DefaultReaderException: 103 107 pass # Loader specific error to try the NXcanSAS reader
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