cansas_reader_HDF5.py @ 7b50f14

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 7b50f14 was 7b50f14, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
restore python 2 functionality
Property mode set to `100644`
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Line
1	"""
2	CanSAS 2D data reader for reading HDF5 formatted CanSAS files.
3	"""
4
5	import h5py
6	import numpy as np
7	import re
8	import os
9	import sys
10
11	from ..data_info import plottable_1D, plottable_2D,\
12	Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \
13	TransmissionSpectrum, Detector
14	from ..data_info import combine_data_info_with_plottable
15	from ..loader_exceptions import FileContentsException, DefaultReaderException
16	from ..file_reader_base_class import FileReader, decode
17
18	def h5attr(node, key, default=None):
19	return decode(node.attrs.get(key, default))
20
21	class Reader(FileReader):
22	"""
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
33
34	:Dependencies:
35	The CanSAS HDF5 reader requires h5py => v2.5.0 or later.
36	"""
37
38	# CanSAS version
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
50	# Data type name
51	type_name = "CanSAS 2.0"
52	# Wildcards
53	type = ["CanSAS 2.0 HDF5 Files (.h5)\|.h5"]
54	# List of allowed extensions
55	ext = ['.h5', '.H5']
56	# Flag to bypass extension check
57	allow_all = True
58
59	def get_file_contents(self):
60	"""
61	This is the general read method that all SasView data_loaders must have.
62
63	:param filename: A path for an HDF5 formatted CanSAS 2D data file.
64	:return: List of Data1D/2D objects and/or a list of errors.
65	"""
66	# Reinitialize when loading a new data file to reset all class variables
67	self.reset_class_variables()
68
69	filename = self.f_open.name
70	self.f_open.close() # IO handled by h5py
71
72	# Check that the file exists
73	if os.path.isfile(filename):
74	basename = os.path.basename(filename)
75	_, extension = os.path.splitext(basename)
76	# If the file type is not allowed, return empty list
77	if extension in self.ext or self.allow_all:
78	# Load the data file
79	try:
80	self.raw_data = h5py.File(filename, 'r')
81	except Exception as e:
82	if extension not in self.ext:
83	msg = "CanSAS2.0 HDF5 Reader could not load file {}".format(basename + extension)
84	raise DefaultReaderException(msg)
85	raise FileContentsException(e.message)
86	try:
87	# Read in all child elements of top level SASroot
88	self.read_children(self.raw_data, [])
89	# Add the last data set to the list of outputs
90	self.add_data_set()
91	except Exception as exc:
92	raise FileContentsException(exc.message)
93	finally:
94	# Close the data file
95	self.raw_data.close()
96
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.")
102
103	def reset_class_variables(self):
104	"""
105	Create the reader object and define initial states for class variables
106	"""
107	self.current_datainfo = None
108	self.current_dataset = None
109	self.data1d = []
110	self.data2d = []
111	self.raw_data = None
112	self.errors = set()
113	self.logging = []
114	self.output = []
115	self.parent_class = u''
116	self.detector = Detector()
117	self.collimation = Collimation()
118	self.aperture = Aperture()
119	self.process = Process()
120	self.trans_spectrum = TransmissionSpectrum()
121
122	def read_children(self, data, parent_list):
123	"""
124	A recursive method for stepping through the hierarchical data file.
125
126	:param data: h5py Group object of any kind
127	:param parent: h5py Group parent name
128	"""
129
130	# Loop through each element of the parent and process accordingly
131	for key in data.keys():
132	# Get all information for the current key
133	value = data.get(key)
134	class_name = h5attr(value, u'canSAS_class')
135	if class_name is None:
136	class_name = h5attr(value, u'NX_class')
137	if class_name is not None:
138	class_prog = re.compile(class_name)
139	else:
140	class_prog = re.compile(value.name)
141
142	if isinstance(value, h5py.Group):
143	# Set parent class before recursion
144	self.parent_class = class_name
145	parent_list.append(key)
146	# If a new sasentry, store the current data sets and create
147	# a fresh Data1D/2D object
148	if class_prog.match(u'SASentry'):
149	self.add_data_set(key)
150	elif class_prog.match(u'SASdata'):
151	self._initialize_new_data_set(parent_list)
152	# Recursion step to access data within the group
153	self.read_children(value, parent_list)
154	# Reset parent class when returning from recursive method
155	self.parent_class = class_name
156	self.add_intermediate()
157	parent_list.remove(key)
158
159	elif isinstance(value, h5py.Dataset):
160	# If this is a dataset, store the data appropriately
161	data_set = data[key][:]
162	unit = self._get_unit(value)
163
164	# I and Q Data
165	if key == u'I':
166	if isinstance(self.current_dataset, plottable_2D):
167	self.current_dataset.data = data_set
168	self.current_dataset.zaxis("Intensity", unit)
169	else:
170	self.current_dataset.y = data_set.flatten()
171	self.current_dataset.yaxis("Intensity", unit)
172	continue
173	elif key == u'Idev':
174	if isinstance(self.current_dataset, plottable_2D):
175	self.current_dataset.err_data = data_set.flatten()
176	else:
177	self.current_dataset.dy = data_set.flatten()
178	continue
179	elif key == u'Q':
180	self.current_dataset.xaxis("Q", unit)
181	if isinstance(self.current_dataset, plottable_2D):
182	self.current_dataset.q = data_set.flatten()
183	else:
184	self.current_dataset.x = data_set.flatten()
185	continue
186	elif key == u'Qdev':
187	self.current_dataset.dx = data_set.flatten()
188	continue
189	elif key == u'dQw':
190	self.current_dataset.dxw = data_set.flatten()
191	continue
192	elif key == u'dQl':
193	self.current_dataset.dxl = data_set.flatten()
194	continue
195	elif key == u'Qy':
196	self.current_dataset.yaxis("Q_y", unit)
197	self.current_dataset.qy_data = data_set.flatten()
198	continue
199	elif key == u'Qydev':
200	self.current_dataset.dqy_data = data_set.flatten()
201	continue
202	elif key == u'Qx':
203	self.current_dataset.xaxis("Q_x", unit)
204	self.current_dataset.qx_data = data_set.flatten()
205	continue
206	elif key == u'Qxdev':
207	self.current_dataset.dqx_data = data_set.flatten()
208	continue
209	elif key == u'Mask':
210	self.current_dataset.mask = data_set.flatten()
211	continue
212	# Transmission Spectrum
213	elif (key == u'T'
214	and self.parent_class == u'SAStransmission_spectrum'):
215	self.trans_spectrum.transmission = data_set.flatten()
216	continue
217	elif (key == u'Tdev'
218	and self.parent_class == u'SAStransmission_spectrum'):
219	self.trans_spectrum.transmission_deviation = \
220	data_set.flatten()
221	continue
222	elif (key == u'lambda'
223	and self.parent_class == u'SAStransmission_spectrum'):
224	self.trans_spectrum.wavelength = data_set.flatten()
225	continue
226
227	for data_point in data_set:
228	if data_point.dtype.char == 'S':
229	data_point = decode(bytes(data_point))
230	# Top Level Meta Data
231	if key == u'definition':
232	self.current_datainfo.meta_data['reader'] = data_point
233	elif key == u'run':
234	self.current_datainfo.run.append(data_point)
235	try:
236	run_name = h5attr(value, 'name')
237	run_dict = {data_point: run_name}
238	self.current_datainfo.run_name = run_dict
239	except Exception:
240	pass
241	elif key == u'title':
242	self.current_datainfo.title = data_point
243	elif key == u'SASnote':
244	self.current_datainfo.notes.append(data_point)
245
246	# Sample Information
247	# CanSAS 2.0 format
248	elif key == u'Title' and self.parent_class == u'SASsample':
249	self.current_datainfo.sample.name = data_point
250	# NXcanSAS format
251	elif key == u'name' and self.parent_class == u'SASsample':
252	self.current_datainfo.sample.name = data_point
253	# NXcanSAS format
254	elif key == u'ID' and self.parent_class == u'SASsample':
255	self.current_datainfo.sample.name = data_point
256	elif (key == u'thickness'
257	and self.parent_class == u'SASsample'):
258	self.current_datainfo.sample.thickness = data_point
259	elif (key == u'temperature'
260	and self.parent_class == u'SASsample'):
261	self.current_datainfo.sample.temperature = data_point
262	elif (key == u'transmission'
263	and self.parent_class == u'SASsample'):
264	self.current_datainfo.sample.transmission = data_point
265	elif (key == u'x_position'
266	and self.parent_class == u'SASsample'):
267	self.current_datainfo.sample.position.x = data_point
268	elif (key == u'y_position'
269	and self.parent_class == u'SASsample'):
270	self.current_datainfo.sample.position.y = data_point
271	elif key == u'pitch' and self.parent_class == u'SASsample':
272	self.current_datainfo.sample.orientation.x = data_point
273	elif key == u'yaw' and self.parent_class == u'SASsample':
274	self.current_datainfo.sample.orientation.y = data_point
275	elif key == u'roll' and self.parent_class == u'SASsample':
276	self.current_datainfo.sample.orientation.z = data_point
277	elif (key == u'details'
278	and self.parent_class == u'SASsample'):
279	self.current_datainfo.sample.details.append(data_point)
280
281	# Instrumental Information
282	elif (key == u'name'
283	and self.parent_class == u'SASinstrument'):
284	self.current_datainfo.instrument = data_point
285	elif key == u'name' and self.parent_class == u'SASdetector':
286	self.detector.name = data_point
287	elif key == u'SDD' and self.parent_class == u'SASdetector':
288	self.detector.distance = float(data_point)
289	self.detector.distance_unit = unit
290	elif (key == u'slit_length'
291	and self.parent_class == u'SASdetector'):
292	self.detector.slit_length = float(data_point)
293	self.detector.slit_length_unit = unit
294	elif (key == u'x_position'
295	and self.parent_class == u'SASdetector'):
296	self.detector.offset.x = float(data_point)
297	self.detector.offset_unit = unit
298	elif (key == u'y_position'
299	and self.parent_class == u'SASdetector'):
300	self.detector.offset.y = float(data_point)
301	self.detector.offset_unit = unit
302	elif (key == u'pitch'
303	and self.parent_class == u'SASdetector'):
304	self.detector.orientation.x = float(data_point)
305	self.detector.orientation_unit = unit
306	elif key == u'roll' and self.parent_class == u'SASdetector':
307	self.detector.orientation.z = float(data_point)
308	self.detector.orientation_unit = unit
309	elif key == u'yaw' and self.parent_class == u'SASdetector':
310	self.detector.orientation.y = float(data_point)
311	self.detector.orientation_unit = unit
312	elif (key == u'beam_center_x'
313	and self.parent_class == u'SASdetector'):
314	self.detector.beam_center.x = float(data_point)
315	self.detector.beam_center_unit = unit
316	elif (key == u'beam_center_y'
317	and self.parent_class == u'SASdetector'):
318	self.detector.beam_center.y = float(data_point)
319	self.detector.beam_center_unit = unit
320	elif (key == u'x_pixel_size'
321	and self.parent_class == u'SASdetector'):
322	self.detector.pixel_size.x = float(data_point)
323	self.detector.pixel_size_unit = unit
324	elif (key == u'y_pixel_size'
325	and self.parent_class == u'SASdetector'):
326	self.detector.pixel_size.y = float(data_point)
327	self.detector.pixel_size_unit = unit
328	elif (key == u'distance'
329	and self.parent_class == u'SAScollimation'):
330	self.collimation.length = data_point
331	self.collimation.length_unit = unit
332	elif (key == u'name'
333	and self.parent_class == u'SAScollimation'):
334	self.collimation.name = data_point
335	elif (key == u'shape'
336	and self.parent_class == u'SASaperture'):
337	self.aperture.shape = data_point
338	elif (key == u'x_gap'
339	and self.parent_class == u'SASaperture'):
340	self.aperture.size.x = data_point
341	elif (key == u'y_gap'
342	and self.parent_class == u'SASaperture'):
343	self.aperture.size.y = data_point
344
345	# Process Information
346	elif (key == u'Title'
347	and self.parent_class == u'SASprocess'): # CanSAS 2.0
348	self.process.name = data_point
349	elif (key == u'name'
350	and self.parent_class == u'SASprocess'): # NXcanSAS
351	self.process.name = data_point
352	elif (key == u'description'
353	and self.parent_class == u'SASprocess'):
354	self.process.description = data_point
355	elif key == u'date' and self.parent_class == u'SASprocess':
356	self.process.date = data_point
357	elif key == u'term' and self.parent_class == u'SASprocess':
358	self.process.term = data_point
359	elif self.parent_class == u'SASprocess':
360	self.process.notes.append(data_point)
361
362	# Source
363	elif (key == u'wavelength'
364	and self.parent_class == u'SASdata'):
365	self.current_datainfo.source.wavelength = data_point
366	self.current_datainfo.source.wavelength_unit = unit
367	elif (key == u'incident_wavelength'
368	and self.parent_class == 'SASsource'):
369	self.current_datainfo.source.wavelength = data_point
370	self.current_datainfo.source.wavelength_unit = unit
371	elif (key == u'wavelength_max'
372	and self.parent_class == u'SASsource'):
373	self.current_datainfo.source.wavelength_max = data_point
374	self.current_datainfo.source.wavelength_max_unit = unit
375	elif (key == u'wavelength_min'
376	and self.parent_class == u'SASsource'):
377	self.current_datainfo.source.wavelength_min = data_point
378	self.current_datainfo.source.wavelength_min_unit = unit
379	elif (key == u'incident_wavelength_spread'
380	and self.parent_class == u'SASsource'):
381	self.current_datainfo.source.wavelength_spread = \
382	data_point
383	self.current_datainfo.source.wavelength_spread_unit = \
384	unit
385	elif (key == u'beam_size_x'
386	and self.parent_class == u'SASsource'):
387	self.current_datainfo.source.beam_size.x = data_point
388	self.current_datainfo.source.beam_size_unit = unit
389	elif (key == u'beam_size_y'
390	and self.parent_class == u'SASsource'):
391	self.current_datainfo.source.beam_size.y = data_point
392	self.current_datainfo.source.beam_size_unit = unit
393	elif (key == u'beam_shape'
394	and self.parent_class == u'SASsource'):
395	self.current_datainfo.source.beam_shape = data_point
396	elif (key == u'radiation'
397	and self.parent_class == u'SASsource'):
398	self.current_datainfo.source.radiation = data_point
399	elif (key == u'transmission'
400	and self.parent_class == u'SASdata'):
401	self.current_datainfo.sample.transmission = data_point
402
403	# Everything else goes in meta_data
404	else:
405	new_key = self._create_unique_key(
406	self.current_datainfo.meta_data, key)
407	self.current_datainfo.meta_data[new_key] = data_point
408
409	else:
410	# I don't know if this reachable code
411	self.errors.add("ShouldNeverHappenException")
412
413	def add_intermediate(self):
414	"""
415	This method stores any intermediate objects within the final data set
416	after fully reading the set.
417
418	:param parent: The NXclass name for the h5py Group object that just
419	finished being processed
420	"""
421
422	if self.parent_class == u'SASprocess':
423	self.current_datainfo.process.append(self.process)
424	self.process = Process()
425	elif self.parent_class == u'SASdetector':
426	self.current_datainfo.detector.append(self.detector)
427	self.detector = Detector()
428	elif self.parent_class == u'SAStransmission_spectrum':
429	self.current_datainfo.trans_spectrum.append(self.trans_spectrum)
430	self.trans_spectrum = TransmissionSpectrum()
431	elif self.parent_class == u'SAScollimation':
432	self.current_datainfo.collimation.append(self.collimation)
433	self.collimation = Collimation()
434	elif self.parent_class == u'SASaperture':
435	self.collimation.aperture.append(self.aperture)
436	self.aperture = Aperture()
437	elif self.parent_class == u'SASdata':
438	if isinstance(self.current_dataset, plottable_2D):
439	self.data2d.append(self.current_dataset)
440	elif isinstance(self.current_dataset, plottable_1D):
441	self.data1d.append(self.current_dataset)
442
443	def final_data_cleanup(self):
444	"""
445	Does some final cleanup and formatting on self.current_datainfo and
446	all data1D and data2D objects and then combines the data and info into
447	Data1D and Data2D objects
448	"""
449	# Type cast data arrays to float64
450	if len(self.current_datainfo.trans_spectrum) > 0:
451	spectrum_list = []
452	for spectrum in self.current_datainfo.trans_spectrum:
453	spectrum.transmission = np.delete(spectrum.transmission, [0])
454	spectrum.transmission = spectrum.transmission.astype(np.float64)
455	spectrum.transmission_deviation = np.delete(
456	spectrum.transmission_deviation, [0])
457	spectrum.transmission_deviation = \
458	spectrum.transmission_deviation.astype(np.float64)
459	spectrum.wavelength = np.delete(spectrum.wavelength, [0])
460	spectrum.wavelength = spectrum.wavelength.astype(np.float64)
461	if len(spectrum.transmission) > 0:
462	spectrum_list.append(spectrum)
463	self.current_datainfo.trans_spectrum = spectrum_list
464
465	# Append errors to dataset and reset class errors
466	self.current_datainfo.errors = self.errors
467	self.errors.clear()
468
469	# Combine all plottables with datainfo and append each to output
470	# Type cast data arrays to float64 and find min/max as appropriate
471	for dataset in self.data2d:
472	zeros = np.ones(dataset.data.size, dtype=bool)
473	try:
474	for i in range(0, dataset.mask.size - 1):
475	zeros[i] = dataset.mask[i]
476	except:
477	self.errors.add(sys.exc_value)
478	dataset.mask = zeros
479	# Calculate the actual Q matrix
480	try:
481	if dataset.q_data.size <= 1:
482	dataset.q_data = np.sqrt(dataset.qx_data
483	* dataset.qx_data
484	+ dataset.qy_data
485	* dataset.qy_data)
486	except:
487	dataset.q_data = None
488
489	if dataset.data.ndim == 2:
490	(n_rows, n_cols) = dataset.data.shape
491	dataset.y_bins = dataset.qy_data[0::n_cols]
492	dataset.x_bins = dataset.qx_data[:n_cols]
493	dataset.data = dataset.data.flatten()
494	self.current_dataset = dataset
495	self.send_to_output()
496
497	for dataset in self.data1d:
498	self.current_dataset = dataset
499	self.send_to_output()
500
501	def add_data_set(self, key=""):
502	"""
503	Adds the current_dataset to the list of outputs after preforming final
504	processing on the data and then calls a private method to generate a
505	new data set.
506
507	:param key: NeXus group name for current tree level
508	"""
509
510	if self.current_datainfo and self.current_dataset:
511	self.final_data_cleanup()
512	self.data1d = []
513	self.data2d = []
514	self.current_datainfo = DataInfo()
515
516
517	def _initialize_new_data_set(self, parent_list=None):
518	"""
519	A private class method to generate a new 1D or 2D data object based on
520	the type of data within the set. Outside methods should call
521	add_data_set() to be sure any existing data is stored properly.
522
523	:param parent_list: List of names of parent elements
524	"""
525
526	if parent_list is None:
527	parent_list = []
528	if self._find_intermediate(parent_list, "Qx"):
529	self.current_dataset = plottable_2D()
530	else:
531	x = np.array(0)
532	y = np.array(0)
533	self.current_dataset = plottable_1D(x, y)
534	self.current_datainfo.filename = self.raw_data.filename
535
536	def _find_intermediate(self, parent_list, basename=""):
537	"""
538	A private class used to find an entry by either using a direct key or
539	knowing the approximate basename.
540
541	:param parent_list: List of parents nodes in the HDF5 file
542	:param basename: Approximate name of an entry to search for
543	:return:
544	"""
545
546	entry = False
547	key_prog = re.compile(basename)
548	top = self.raw_data
549	for parent in parent_list:
550	top = top.get(parent)
551	for key in top.keys():
552	if key_prog.match(key):
553	entry = True
554	break
555	return entry
556
557	def _create_unique_key(self, dictionary, name, numb=0):
558	"""
559	Create a unique key value for any dictionary to prevent overwriting
560	Recurses until a unique key value is found.
561
562	:param dictionary: A dictionary with any number of entries
563	:param name: The index of the item to be added to dictionary
564	:param numb: The number to be appended to the name, starts at 0
565	:return: The new name for the dictionary entry
566	"""
567	if dictionary.get(name) is not None:
568	numb += 1
569	name = name.split("_")[0]
570	name += "_{0}".format(numb)
571	name = self._create_unique_key(dictionary, name, numb)
572	return name
573
574	def _get_unit(self, value):
575	"""
576	Find the unit for a particular value within the h5py dictionary
577
578	:param value: attribute dictionary for a particular value set
579	:return: unit for the value passed to the method
580	"""
581	unit = h5attr(value, u'units')
582	if unit is None:
583	unit = h5attr(value, u'unit')
584	# Convert the unit formats
585	if unit == "1/A":
586	unit = "A^{-1}"
587	elif unit == "1/cm":
588	unit = "cm^{-1}"
589	return unit

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py @ 7b50f14

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