cansas_reader_HDF5.py @ a7067ef2

Last change on this file since a7067ef2 was c416a17, checked in by Piotr Rozyczko <rozyczko@…>, 8 years ago
Merge branch 'master' into ESS_GUI
Property mode set to `100644`
File size: 26.9 KB

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 sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\
12	Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \
13	TransmissionSpectrum, Detector
14	from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable
15
16
17	class Reader():
18	"""
19	A class for reading in CanSAS v2.0 data files. The existing iteration opens
20	Mantid generated HDF5 formatted files with file extension .h5/.H5. Any
21	number of data sets may be present within the file and any dimensionality
22	of data may be used. Currently 1D and 2D SAS data sets are supported, but
23	future implementations will include 1D and 2D SESANS data.
24
25	Any number of SASdata sets may be present in a SASentry and the data within
26	can be either 1D I(Q) or 2D I(Qx, Qy).
27	Also supports reading NXcanSAS formatted HDF5 files
28
29	:Dependencies:
30	The CanSAS HDF5 reader requires h5py => v2.5.0 or later.
31	"""
32
33	# CanSAS version
34	cansas_version = 2.0
35	# Logged warnings or messages
36	logging = None
37	# List of errors for the current data set
38	errors = None
39	# Raw file contents to be processed
40	raw_data = None
41	# Data info currently being read in
42	current_datainfo = None
43	# SASdata set currently being read in
44	current_dataset = None
45	# List of plottable1D objects that should be linked to the current_datainfo
46	data1d = None
47	# List of plottable2D objects that should be linked to the current_datainfo
48	data2d = None
49	# Data type name
50	type_name = "CanSAS 2.0"
51	# Wildcards
52	type = ["CanSAS 2.0 HDF5 Files (.h5)\|.h5"]
53	# List of allowed extensions
54	ext = ['.h5', '.H5']
55	# Flag to bypass extension check
56	allow_all = True
57	# List of files to return
58	output = None
59
60	def read(self, filename):
61	"""
62	This is the general read method that all SasView data_loaders must have.
63
64	:param filename: A path for an HDF5 formatted CanSAS 2D data file.
65	:return: List of Data1D/2D objects and/or a list of errors.
66	"""
67	# Reinitialize when loading a new data file to reset all class variables
68	self.reset_class_variables()
69	# Check that the file exists
70	if os.path.isfile(filename):
71	basename = os.path.basename(filename)
72	_, extension = os.path.splitext(basename)
73	# If the file type is not allowed, return empty list
74	if extension in self.ext or self.allow_all:
75	# Load the data file
76	self.raw_data = h5py.File(filename, 'r')
77	# Read in all child elements of top level SASroot
78	self.read_children(self.raw_data, [])
79	# Add the last data set to the list of outputs
80	self.add_data_set()
81	# Close the data file
82	self.raw_data.close()
83	# Return data set(s)
84	return self.output
85
86	def reset_class_variables(self):
87	"""
88	Create the reader object and define initial states for class variables
89	"""
90	self.current_datainfo = None
91	self.current_dataset = None
92	self.data1d = []
93	self.data2d = []
94	self.raw_data = None
95	self.errors = set()
96	self.logging = []
97	self.output = []
98	self.parent_class = u''
99	self.detector = Detector()
100	self.collimation = Collimation()
101	self.aperture = Aperture()
102	self.process = Process()
103	self.trans_spectrum = TransmissionSpectrum()
104
105	def read_children(self, data, parent_list):
106	"""
107	A recursive method for stepping through the hierarchical data file.
108
109	:param data: h5py Group object of any kind
110	:param parent: h5py Group parent name
111	"""
112
113	# Loop through each element of the parent and process accordingly
114	for key in data.keys():
115	# Get all information for the current key
116	value = data.get(key)
117	if value.attrs.get(u'canSAS_class') is not None:
118	class_name = value.attrs.get(u'canSAS_class')
119	else:
120	class_name = value.attrs.get(u'NX_class')
121	if class_name is not None:
122	class_prog = re.compile(class_name)
123	else:
124	class_prog = re.compile(value.name)
125
126	if isinstance(value, h5py.Group):
127	self.parent_class = class_name
128	parent_list.append(key)
129	# If a new sasentry, store the current data sets and create
130	# a fresh Data1D/2D object
131	if class_prog.match(u'SASentry'):
132	self.add_data_set(key)
133	elif class_prog.match(u'SASdata'):
134	self._initialize_new_data_set(parent_list)
135	# Recursion step to access data within the group
136	self.read_children(value, parent_list)
137	self.add_intermediate()
138	parent_list.remove(key)
139
140	elif isinstance(value, h5py.Dataset):
141	# If this is a dataset, store the data appropriately
142	data_set = data[key][:]
143	unit = self._get_unit(value)
144
145	# I and Q Data
146	if key == u'I':
147	if isinstance(self.current_dataset, plottable_2D):
148	self.current_dataset.data = data_set
149	self.current_dataset.zaxis("Intensity", unit)
150	else:
151	self.current_dataset.y = data_set.flatten()
152	self.current_dataset.yaxis("Intensity", unit)
153	continue
154	elif key == u'Idev':
155	if isinstance(self.current_dataset, plottable_2D):
156	self.current_dataset.err_data = data_set.flatten()
157	else:
158	self.current_dataset.dy = data_set.flatten()
159	continue
160	elif key == u'Q':
161	self.current_dataset.xaxis("Q", unit)
162	if isinstance(self.current_dataset, plottable_2D):
163	self.current_dataset.q = data_set.flatten()
164	else:
165	self.current_dataset.x = data_set.flatten()
166	continue
167	elif key == u'Qy':
168	self.current_dataset.yaxis("Q_y", unit)
169	self.current_dataset.qy_data = data_set.flatten()
170	continue
171	elif key == u'Qydev':
172	self.current_dataset.dqy_data = data_set.flatten()
173	continue
174	elif key == u'Qx':
175	self.current_dataset.xaxis("Q_x", unit)
176	self.current_dataset.qx_data = data_set.flatten()
177	continue
178	elif key == u'Qxdev':
179	self.current_dataset.dqx_data = data_set.flatten()
180	continue
181	elif key == u'Mask':
182	self.current_dataset.mask = data_set.flatten()
183	continue
184	# Transmission Spectrum
185	elif (key == u'T'
186	and self.parent_class == u'SAStransmission_spectrum'):
187	self.trans_spectrum.transmission = data_set.flatten()
188	continue
189	elif (key == u'Tdev'
190	and self.parent_class == u'SAStransmission_spectrum'):
191	self.trans_spectrum.transmission_deviation = \
192	data_set.flatten()
193	continue
194	elif (key == u'lambda'
195	and self.parent_class == u'SAStransmission_spectrum'):
196	self.trans_spectrum.wavelength = data_set.flatten()
197	continue
198
199	for data_point in data_set:
200	# Top Level Meta Data
201	if key == u'definition':
202	self.current_datainfo.meta_data['reader'] = data_point
203	elif key == u'run':
204	self.current_datainfo.run.append(data_point)
205	elif key == u'title':
206	self.current_datainfo.title = data_point
207	elif key == u'SASnote':
208	self.current_datainfo.notes.append(data_point)
209
210	# Sample Information
211	# CanSAS 2.0 format
212	elif key == u'Title' and self.parent_class == u'SASsample':
213	self.current_datainfo.sample.name = data_point
214	# NXcanSAS format
215	elif key == u'name' and self.parent_class == u'SASsample':
216	self.current_datainfo.sample.name = data_point
217	# NXcanSAS format
218	elif key == u'ID' and self.parent_class == u'SASsample':
219	self.current_datainfo.sample.name = data_point
220	elif (key == u'thickness'
221	and self.parent_class == u'SASsample'):
222	self.current_datainfo.sample.thickness = data_point
223	elif (key == u'temperature'
224	and self.parent_class == u'SASsample'):
225	self.current_datainfo.sample.temperature = data_point
226	elif (key == u'transmission'
227	and self.parent_class == u'SASsample'):
228	self.current_datainfo.sample.transmission = data_point
229	elif (key == u'x_position'
230	and self.parent_class == u'SASsample'):
231	self.current_datainfo.sample.position.x = data_point
232	elif (key == u'y_position'
233	and self.parent_class == u'SASsample'):
234	self.current_datainfo.sample.position.y = data_point
235	elif key == u'pitch' and self.parent_class == u'SASsample':
236	self.current_datainfo.sample.orientation.x = data_point
237	elif key == u'yaw' and self.parent_class == u'SASsample':
238	self.current_datainfo.sample.orientation.y = data_point
239	elif key == u'roll' and self.parent_class == u'SASsample':
240	self.current_datainfo.sample.orientation.z = data_point
241	elif (key == u'details'
242	and self.parent_class == u'SASsample'):
243	self.current_datainfo.sample.details.append(data_point)
244
245	# Instrumental Information
246	elif (key == u'name'
247	and self.parent_class == u'SASinstrument'):
248	self.current_datainfo.instrument = data_point
249	elif key == u'name' and self.parent_class == u'SASdetector':
250	self.detector.name = data_point
251	elif key == u'SDD' and self.parent_class == u'SASdetector':
252	self.detector.distance = float(data_point)
253	self.detector.distance_unit = unit
254	elif (key == u'slit_length'
255	and self.parent_class == u'SASdetector'):
256	self.detector.slit_length = float(data_point)
257	self.detector.slit_length_unit = unit
258	elif (key == u'x_position'
259	and self.parent_class == u'SASdetector'):
260	self.detector.offset.x = float(data_point)
261	self.detector.offset_unit = unit
262	elif (key == u'y_position'
263	and self.parent_class == u'SASdetector'):
264	self.detector.offset.y = float(data_point)
265	self.detector.offset_unit = unit
266	elif (key == u'pitch'
267	and self.parent_class == u'SASdetector'):
268	self.detector.orientation.x = float(data_point)
269	self.detector.orientation_unit = unit
270	elif key == u'roll' and self.parent_class == u'SASdetector':
271	self.detector.orientation.z = float(data_point)
272	self.detector.orientation_unit = unit
273	elif key == u'yaw' and self.parent_class == u'SASdetector':
274	self.detector.orientation.y = float(data_point)
275	self.detector.orientation_unit = unit
276	elif (key == u'beam_center_x'
277	and self.parent_class == u'SASdetector'):
278	self.detector.beam_center.x = float(data_point)
279	self.detector.beam_center_unit = unit
280	elif (key == u'beam_center_y'
281	and self.parent_class == u'SASdetector'):
282	self.detector.beam_center.y = float(data_point)
283	self.detector.beam_center_unit = unit
284	elif (key == u'x_pixel_size'
285	and self.parent_class == u'SASdetector'):
286	self.detector.pixel_size.x = float(data_point)
287	self.detector.pixel_size_unit = unit
288	elif (key == u'y_pixel_size'
289	and self.parent_class == u'SASdetector'):
290	self.detector.pixel_size.y = float(data_point)
291	self.detector.pixel_size_unit = unit
292	elif (key == u'distance'
293	and self.parent_class == u'SAScollimation'):
294	self.collimation.length = data_point
295	self.collimation.length_unit = unit
296	elif (key == u'name'
297	and self.parent_class == u'SAScollimation'):
298	self.collimation.name = data_point
299	elif (key == u'shape'
300	and self.parent_class == u'SASaperture'):
301	self.aperture.shape = data_point
302	elif (key == u'x_gap'
303	and self.parent_class == u'SASaperture'):
304	self.aperture.size.x = data_point
305	elif (key == u'y_gap'
306	and self.parent_class == u'SASaperture'):
307	self.aperture.size.y = data_point
308
309	# Process Information
310	elif (key == u'Title'
311	and self.parent_class == u'SASprocess'): # CanSAS 2.0
312	self.process.name = data_point
313	elif (key == u'name'
314	and self.parent_class == u'SASprocess'): # NXcanSAS
315	self.process.name = data_point
316	elif (key == u'description'
317	and self.parent_class == u'SASprocess'):
318	self.process.description = data_point
319	elif key == u'date' and self.parent_class == u'SASprocess':
320	self.process.date = data_point
321	elif key == u'term' and self.parent_class == u'SASprocess':
322	self.process.term = data_point
323	elif self.parent_class == u'SASprocess':
324	self.process.notes.append(data_point)
325
326	# Source
327	elif (key == u'wavelength'
328	and self.parent_class == u'SASdata'):
329	self.current_datainfo.source.wavelength = data_point
330	self.current_datainfo.source.wavelength_unit = unit
331	elif (key == u'incident_wavelength'
332	and self.parent_class == 'SASsource'):
333	self.current_datainfo.source.wavelength = data_point
334	self.current_datainfo.source.wavelength_unit = unit
335	elif (key == u'wavelength_max'
336	and self.parent_class == u'SASsource'):
337	self.current_datainfo.source.wavelength_max = data_point
338	self.current_datainfo.source.wavelength_max_unit = unit
339	elif (key == u'wavelength_min'
340	and self.parent_class == u'SASsource'):
341	self.current_datainfo.source.wavelength_min = data_point
342	self.current_datainfo.source.wavelength_min_unit = unit
343	elif (key == u'incident_wavelength_spread'
344	and self.parent_class == u'SASsource'):
345	self.current_datainfo.source.wavelength_spread = \
346	data_point
347	self.current_datainfo.source.wavelength_spread_unit = \
348	unit
349	elif (key == u'beam_size_x'
350	and self.parent_class == u'SASsource'):
351	self.current_datainfo.source.beam_size.x = data_point
352	self.current_datainfo.source.beam_size_unit = unit
353	elif (key == u'beam_size_y'
354	and self.parent_class == u'SASsource'):
355	self.current_datainfo.source.beam_size.y = data_point
356	self.current_datainfo.source.beam_size_unit = unit
357	elif (key == u'beam_shape'
358	and self.parent_class == u'SASsource'):
359	self.current_datainfo.source.beam_shape = data_point
360	elif (key == u'radiation'
361	and self.parent_class == u'SASsource'):
362	self.current_datainfo.source.radiation = data_point
363	elif (key == u'transmission'
364	and self.parent_class == u'SASdata'):
365	self.current_datainfo.sample.transmission = data_point
366
367	# Everything else goes in meta_data
368	else:
369	new_key = self._create_unique_key(
370	self.current_datainfo.meta_data, key)
371	self.current_datainfo.meta_data[new_key] = data_point
372
373	else:
374	# I don't know if this reachable code
375	self.errors.add("ShouldNeverHappenException")
376
377	def add_intermediate(self):
378	"""
379	This method stores any intermediate objects within the final data set
380	after fully reading the set.
381
382	:param parent: The NXclass name for the h5py Group object that just
383	finished being processed
384	"""
385
386	if self.parent_class == u'SASprocess':
387	self.current_datainfo.process.append(self.process)
388	self.process = Process()
389	elif self.parent_class == u'SASdetector':
390	self.current_datainfo.detector.append(self.detector)
391	self.detector = Detector()
392	elif self.parent_class == u'SAStransmission_spectrum':
393	self.current_datainfo.trans_spectrum.append(self.trans_spectrum)
394	self.trans_spectrum = TransmissionSpectrum()
395	elif self.parent_class == u'SAScollimation':
396	self.current_datainfo.collimation.append(self.collimation)
397	self.collimation = Collimation()
398	elif self.parent_class == u'SASaperture':
399	self.collimation.aperture.append(self.aperture)
400	self.aperture = Aperture()
401	elif self.parent_class == u'SASdata':
402	if isinstance(self.current_dataset, plottable_2D):
403	self.data2d.append(self.current_dataset)
404	elif isinstance(self.current_dataset, plottable_1D):
405	self.data1d.append(self.current_dataset)
406
407	def final_data_cleanup(self):
408	"""
409	Does some final cleanup and formatting on self.current_datainfo and
410	all data1D and data2D objects and then combines the data and info into
411	Data1D and Data2D objects
412	"""
413
414	# Type cast data arrays to float64
415	if len(self.current_datainfo.trans_spectrum) > 0:
416	spectrum_list = []
417	for spectrum in self.current_datainfo.trans_spectrum:
418	spectrum.transmission = np.delete(spectrum.transmission, [0])
419	spectrum.transmission = spectrum.transmission.astype(np.float64)
420	spectrum.transmission_deviation = np.delete(
421	spectrum.transmission_deviation, [0])
422	spectrum.transmission_deviation = \
423	spectrum.transmission_deviation.astype(np.float64)
424	spectrum.wavelength = np.delete(spectrum.wavelength, [0])
425	spectrum.wavelength = spectrum.wavelength.astype(np.float64)
426	if len(spectrum.transmission) > 0:
427	spectrum_list.append(spectrum)
428	self.current_datainfo.trans_spectrum = spectrum_list
429
430	# Append errors to dataset and reset class errors
431	self.current_datainfo.errors = self.errors
432	self.errors.clear()
433
434	# Combine all plottables with datainfo and append each to output
435	# Type cast data arrays to float64 and find min/max as appropriate
436	for dataset in self.data2d:
437	dataset.data = dataset.data.astype(np.float64)
438	dataset.err_data = dataset.err_data.astype(np.float64)
439	if dataset.qx_data is not None:
440	dataset.xmin = np.min(dataset.qx_data)
441	dataset.xmax = np.max(dataset.qx_data)
442	dataset.qx_data = dataset.qx_data.astype(np.float64)
443	if dataset.dqx_data is not None:
444	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
445	if dataset.qy_data is not None:
446	dataset.ymin = np.min(dataset.qy_data)
447	dataset.ymax = np.max(dataset.qy_data)
448	dataset.qy_data = dataset.qy_data.astype(np.float64)
449	if dataset.dqy_data is not None:
450	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
451	if dataset.q_data is not None:
452	dataset.q_data = dataset.q_data.astype(np.float64)
453	zeros = np.ones(dataset.data.size, dtype=bool)
454	try:
455	for i in range(0, dataset.mask.size - 1):
456	zeros[i] = dataset.mask[i]
457	except:
458	self.errors.add(sys.exc_value)
459	dataset.mask = zeros
460	# Calculate the actual Q matrix
461	try:
462	if dataset.q_data.size <= 1:
463	dataset.q_data = np.sqrt(dataset.qx_data
464	* dataset.qx_data
465	+ dataset.qy_data
466	* dataset.qy_data)
467	except:
468	dataset.q_data = None
469
470	if dataset.data.ndim == 2:
471	(n_rows, n_cols) = dataset.data.shape
472	dataset.y_bins = dataset.qy_data[0::n_cols]
473	dataset.x_bins = dataset.qx_data[:n_cols]
474	dataset.data = dataset.data.flatten()
475
476	final_dataset = combine_data_info_with_plottable(
477	dataset, self.current_datainfo)
478	self.output.append(final_dataset)
479
480	for dataset in self.data1d:
481	if dataset.x is not None:
482	dataset.x = dataset.x.astype(np.float64)
483	dataset.xmin = np.min(dataset.x)
484	dataset.xmax = np.max(dataset.x)
485	if dataset.y is not None:
486	dataset.y = dataset.y.astype(np.float64)
487	dataset.ymin = np.min(dataset.y)
488	dataset.ymax = np.max(dataset.y)
489	if dataset.dx is not None:
490	dataset.dx = dataset.dx.astype(np.float64)
491	if dataset.dxl is not None:
492	dataset.dxl = dataset.dxl.astype(np.float64)
493	if dataset.dxw is not None:
494	dataset.dxw = dataset.dxw.astype(np.float64)
495	if dataset.dy is not None:
496	dataset.dy = dataset.dy.astype(np.float64)
497	final_dataset = combine_data_info_with_plottable(
498	dataset, self.current_datainfo)
499	self.output.append(final_dataset)
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 = value.attrs.get(u'units')
582	if unit is None:
583	unit = value.attrs.get(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 @ a7067ef2

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