Changeset 8cb1a07 in sasview
- Timestamp:
- Aug 18, 2016 7:03:43 AM (8 years ago)
- Branches:
- master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- eb98f24
- Parents:
- 1f6d293
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py
r1f6d293 r8cb1a07 390 390 :param filename: Where to write the CanSAS 2.0 file 391 391 """ 392 is_1d = all([isinstance(d, Data1D) for d in dataset])393 is_2d = all([isinstance(d, Data2D) for d in dataset])394 395 if not (is_1d or is_2d):396 msg = ("All elements of dataset must be of the same class "397 "(Data1D or Data2D)")398 raise ValueError(msg)399 392 400 393 def _h5_string(string): … … 414 407 return np.array(x, dtype=np.float32) 415 408 409 valid_data = all([issubclass(d.__class__, (Data1D, Data2D)) for d in dataset]) 410 if not valid_data: 411 raise ValueError("All entries of dataset must be Data1D or Data2D objects") 412 416 413 # Get run name and number from first Data object 417 414 data_info = dataset[0] … … 434 431 i = 1 435 432 436 if is_1d: 437 for data_obj in dataset: 438 data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i)) 439 data_entry.attrs['canSAS_class'] = 'SASdata' 440 data_entry.attrs['signal'] = 'I' 441 data_entry.attrs['I_axes'] = 'Q' 442 data_entry.attrs['I_uncertainties'] = 'Idev' 443 data_entry.attrs['Q_indicies'] = 0 444 Q_data = data_entry.create_dataset('Q', data=data_obj.x) 445 I_data = data_entry.create_dataset('I', data=data_obj.y) 446 dI_data = data_entry.create_dataset('Idev', data=data_obj.dy) 433 for data_obj in dataset: 434 data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i)) 435 data_entry.attrs['canSAS_class'] = 'SASdata' 436 if isinstance(data_obj, Data1D): 437 self._write_1d_data(data_obj, data_entry) 438 elif isinstance(data_obj, Data2D): 439 self._write_2d_data(data_obj, data_entry) 440 i += 1 441 442 data_info = dataset[0] 443 sample_entry = sasentry.create_group('sassample') 444 sample_entry.attrs['canSAS_class'] = 'SASsample' 445 sample_entry['name'] = _h5_string(data_info.sample.name) 446 sample_attrs = ['thickness', 'temperature'] 447 for key in sample_attrs: 448 if getattr(data_info.sample, key) is not None: 449 sample_entry.create_dataset(key, data=np.array([getattr(data_info.sample, key)])) 450 451 instrument_entry = sasentry.create_group('sasinstrument') 452 instrument_entry.attrs['canSAS_class'] = 'SASinstrument' 453 instrument_entry['name'] = _h5_string(data_info.instrument) 454 455 source_entry = instrument_entry.create_group('sassource') 456 source_entry.attrs['canSAS_class'] = 'SASsource' 457 if data_info.source.radiation is None: 458 source_entry['radiation'] = _h5_string('neutron') 459 else: 460 source_entry['radiation'] = _h5_string(data_info.source.radiation) 461 462 if len(data_info.collimation) > 0: 463 i = 1 464 for coll_info in data_info.collimation: 465 collimation_entry = instrument_entry.create_group( 466 'sascollimation{0:0=2d}'.format(i)) 467 collimation_entry.attrs['canSAS_class'] = 'SAScollimation' 468 if coll_info.length is not None: 469 collimation_entry['SDD'] = _h5_float(coll_info.length) 470 collimation_entry['SDD'].attrs['units'] = coll_info.length_unit 471 if coll_info.name is not None: 472 collimation_entry['name'] = _h5_string(coll_info.name) 473 else: 474 collimation_entry = instrument_entry.create_group('sascollimation01') 475 476 if len(data_info.detector) > 0: 477 i = 1 478 for det_info in data_info.detector: 479 detector_entry = instrument_entry.create_group( 480 'sasdetector{0:0=2d}'.format(i)) 481 detector_entry.attrs['canSAS_class'] = 'SASdetector' 482 if det_info.distance is not None: 483 detector_entry['SDD'] = _h5_float(det_info.distance) 484 detector_entry['SDD'].attrs['units'] = det_info.distance_unit 485 if det_info.name is not None: 486 detector_entry['name'] = _h5_string(det_info.name) 487 else: 488 detector_entry['name'] = _h5_string('') 447 489 i += 1 448 449 data_info = dataset[0] 450 sample_entry = sasentry.create_group('sassample') 451 sample_entry.attrs['canSAS_class'] = 'SASsample' 452 sample_entry['name'] = _h5_string(data_info.sample.name) 453 sample_attrs = ['thickness', 'temperature'] 454 for key in sample_attrs: 455 if getattr(data_info.sample, key) is not None: 456 sample_entry.create_dataset(key, data=np.array([getattr(data_info.sample, key)])) 457 458 instrument_entry = sasentry.create_group('sasinstrument') 459 instrument_entry.attrs['canSAS_class'] = 'SASinstrument' 460 instrument_entry['name'] = _h5_string(data_info.instrument) 461 462 source_entry = instrument_entry.create_group('sassource') 463 source_entry.attrs['canSAS_class'] = 'SASsource' 464 if data_info.source.radiation is None: 465 source_entry['radiation'] = _h5_string('neutron') 466 else: 467 source_entry['radiation'] = _h5_string(data_info.source.radiation) 468 469 if len(data_info.collimation) > 0: 470 i = 1 471 for coll_info in data_info.collimation: 472 collimation_entry = instrument_entry.create_group( 473 'sascollimation{0:0=2d}'.format(i)) 474 collimation_entry.attrs['canSAS_class'] = 'SAScollimation' 475 if coll_info.length is not None: 476 collimation_entry['SDD'] = _h5_float(coll_info.length) 477 collimation_entry['SDD'].attrs['units'] = coll_info.length_unit 478 if coll_info.name is not None: 479 collimation_entry['name'] = _h5_string(coll_info.name) 480 else: 481 collimation_entry = instrument_entry.create_group('sascollimation01') 482 483 if len(data_info.detector) > 0: 484 i = 1 485 for det_info in data_info.detector: 486 detector_entry = instrument_entry.create_group( 487 'sasdetector{0:0=2d}'.format(i)) 488 detector_entry.attrs['canSAS_class'] = 'SASdetector' 489 if det_info.distance is not None: 490 detector_entry['SDD'] = _h5_float(det_info.distance) 491 detector_entry['SDD'].attrs['units'] = det_info.distance_unit 492 if det_info.name is not None: 493 detector_entry['name'] = _h5_string(det_info.name) 494 else: 495 detector_entry['name'] = _h5_string('') 496 i += 1 497 else: 498 detector_entry = instrument_entry.create_group('sasdetector01') 499 detector_entry.attrs['canSAS_class'] = 'SASdetector' 500 detector_entry.attrs['name'] = '' 501 502 # TODO: implement writing SASnote 503 note_entry = sasentry.create_group('sasnote{0:0=2d}'.format(i)) 504 note_entry.attrs['canSAS_class'] = 'SASnote' 505 506 elif is_2d: 507 f.close() 508 raise NotImplementedError("Saving 2D data as CanSAS 2.0 is not yet implemented") 490 else: 491 detector_entry = instrument_entry.create_group('sasdetector01') 492 detector_entry.attrs['canSAS_class'] = 'SASdetector' 493 detector_entry.attrs['name'] = '' 494 495 # TODO: implement writing SASnote 496 note_entry = sasentry.create_group('sasnote{0:0=2d}'.format(i)) 497 note_entry.attrs['canSAS_class'] = 'SASnote' 509 498 510 499 f.close() 500 501 def _write_1d_data(self, data_obj, data_entry): 502 """ 503 Writes the contents of a Data1D object to a SASdata h5py Group 504 505 :param data_obj: A Data1D object to write to the file 506 :param data_entry: A h5py Group object representing the SASdata 507 """ 508 data_entry.attrs['signal'] = 'I' 509 data_entry.attrs['I_axes'] = 'Q' 510 data_entry.attrs['I_uncertainties'] = 'Idev' 511 data_entry.attrs['Q_indicies'] = 0 512 data_entry.create_dataset('Q', data=data_obj.x) 513 data_entry.create_dataset('I', data=data_obj.y) 514 data_entry.create_dataset('Idev', data=data_obj.dy) 515 516 def _write_2d_data(self, data, data_entry): 517 """ 518 Writes the contents of a Data2D object to a SASdata h5py Group 519 520 :param data: A Data2D object to write to the file 521 :param data_entry: A h5py Group object representing the SASdata 522 """ 523 data_entry.attrs['signal'] = 'I' 524 data_entry.attrs['I_axes'] = 'Q,Q' 525 data_entry.attrs['I_uncertainties'] = 'Idev' 526 data_entry.attrs['Q_indicies'] = [0,1] 527 528 # Calculate rows and columns, assuming detector is square 529 # Same logic as used in PlotPanel.py _get_bins 530 n_cols = int(np.floor(np.sqrt(len(data.qy_data)))) 531 n_rows = int(np.floor(len(data.qy_data) / n_cols)) 532 533 if n_rows * n_cols != len(data.qy_data): 534 raise ValueError("Unable to calculate dimensions of data") 535 536 I = np.reshape(data.data, (n_rows, n_cols)) 537 dI = np.reshape(data.err_data, (n_rows, n_cols)) 538 qx = np.reshape(data.qx_data, (n_rows, n_cols)) 539 qy = np.reshape(data.qy_data, (n_rows, n_cols)) 540 I_entry = data_entry.create_dataset('I', data=I) 541 I_entry.attrs['units'] = data.I_unit 542 Qx_entry = data_entry.create_dataset('Qx', data=qx) 543 Qx_entry.attrs['units'] = data.Q_unit 544 Qy_entry = data_entry.create_dataset('Qy', data=qy) 545 Qy_entry.attrs['units'] = data.Q_unit 511 546 512 547
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