cansas_reader_HDF5.py @ 18d5af02

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since 18d5af02 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

Rev	Line
[68aa210]	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
[082239e]	11	from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\
	12	Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \
	13	TransmissionSpectrum, Detector
[132db16]	14	from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable
	15
[68aa210]	16
	17	class Reader():
	18	"""
[082239e]	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.
[d72567e]	24
[082239e]	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).
[5e906207]	27	Also supports reading NXcanSAS formatted HDF5 files
[68aa210]	28
	29	:Dependencies:
[132db16]	30	The CanSAS HDF5 reader requires h5py => v2.5.0 or later.
[68aa210]	31	"""
	32
[082239e]	33	# CanSAS version
[68aa210]	34	cansas_version = 2.0
[082239e]	35	# Logged warnings or messages
[68aa210]	36	logging = None
[082239e]	37	# List of errors for the current data set
[68aa210]	38	errors = None
[082239e]	39	# Raw file contents to be processed
[68aa210]	40	raw_data = None
[082239e]	41	# Data info currently being read in
[132db16]	42	current_datainfo = None
[082239e]	43	# SASdata set currently being read in
[68aa210]	44	current_dataset = None
[082239e]	45	# List of plottable1D objects that should be linked to the current_datainfo
[132db16]	46	data1d = None
[082239e]	47	# List of plottable2D objects that should be linked to the current_datainfo
[132db16]	48	data2d = None
[082239e]	49	# Data type name
[ad52d31]	50	type_name = "CanSAS 2.0"
[082239e]	51	# Wildcards
[ad52d31]	52	type = ["CanSAS 2.0 HDF5 Files (.h5)\|.h5"]
[082239e]	53	# List of allowed extensions
[68aa210]	54	ext = ['.h5', '.H5']
[082239e]	55	# Flag to bypass extension check
[54544637]	56	allow_all = True
[082239e]	57	# List of files to return
[68aa210]	58	output = None
	59
	60	def read(self, filename):
	61	"""
[ad52d31]	62	This is the general read method that all SasView data_loaders must have.
[68aa210]	63
	64	:param filename: A path for an HDF5 formatted CanSAS 2D data file.
[132db16]	65	:return: List of Data1D/2D objects and/or a list of errors.
[68aa210]	66	"""
[082239e]	67	# Reinitialize when loading a new data file to reset all class variables
[132db16]	68	self.reset_class_variables()
[082239e]	69	# Check that the file exists
[68aa210]	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:
[082239e]	75	# Load the data file
[68aa210]	76	self.raw_data = h5py.File(filename, 'r')
[082239e]	77	# Read in all child elements of top level SASroot
[132db16]	78	self.read_children(self.raw_data, [])
[082239e]	79	# Add the last data set to the list of outputs
[68aa210]	80	self.add_data_set()
[082239e]	81	# Close the data file
[995f4eb]	82	self.raw_data.close()
[082239e]	83	# Return data set(s)
[68aa210]	84	return self.output
	85
[132db16]	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):
[68aa210]	106	"""
[ad52d31]	107	A recursive method for stepping through the hierarchical data file.
[68aa210]	108
	109	:param data: h5py Group object of any kind
	110	:param parent: h5py Group parent name
	111	"""
	112
[082239e]	113	# Loop through each element of the parent and process accordingly
[68aa210]	114	for key in data.keys():
[082239e]	115	# Get all information for the current key
[68aa210]	116	value = data.get(key)
[d398285]	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')
[68aa210]	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):
[132db16]	127	self.parent_class = class_name
	128	parent_list.append(key)
[082239e]	129	# If a new sasentry, store the current data sets and create
	130	# a fresh Data1D/2D object
[68aa210]	131	if class_prog.match(u'SASentry'):
	132	self.add_data_set(key)
[132db16]	133	elif class_prog.match(u'SASdata'):
	134	self._initialize_new_data_set(parent_list)
[082239e]	135	# Recursion step to access data within the group
[132db16]	136	self.read_children(value, parent_list)
	137	self.add_intermediate()
	138	parent_list.remove(key)
[68aa210]	139
	140	elif isinstance(value, h5py.Dataset):
[082239e]	141	# If this is a dataset, store the data appropriately
[68aa210]	142	data_set = data[key][:]
[b76cf0d]	143	unit = self._get_unit(value)
[a9d3abb]	144
[082239e]	145	# I and Q Data
[b76cf0d]	146	if key == u'I':
[082239e]	147	if isinstance(self.current_dataset, plottable_2D):
[a9d3abb]	148	self.current_dataset.data = data_set
[b76cf0d]	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':
[082239e]	155	if isinstance(self.current_dataset, plottable_2D):
[b76cf0d]	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)
[082239e]	162	if isinstance(self.current_dataset, plottable_2D):
[b76cf0d]	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
[082239e]	184	# Transmission Spectrum
[c94280c]	185	elif (key == u'T'
	186	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	187	self.trans_spectrum.transmission = data_set.flatten()
	188	continue
[c94280c]	189	elif (key == u'Tdev'
	190	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	191	self.trans_spectrum.transmission_deviation = \
	192	data_set.flatten()
	193	continue
[c94280c]	194	elif (key == u'lambda'
	195	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	196	self.trans_spectrum.wavelength = data_set.flatten()
	197	continue
[68aa210]	198
	199	for data_point in data_set:
[082239e]	200	# Top Level Meta Data
[68aa210]	201	if key == u'definition':
[132db16]	202	self.current_datainfo.meta_data['reader'] = data_point
[68aa210]	203	elif key == u'run':
[132db16]	204	self.current_datainfo.run.append(data_point)
[68aa210]	205	elif key == u'title':
[132db16]	206	self.current_datainfo.title = data_point
[68aa210]	207	elif key == u'SASnote':
[132db16]	208	self.current_datainfo.notes.append(data_point)
[68aa210]	209
[082239e]	210	# Sample Information
	211	# CanSAS 2.0 format
	212	elif key == u'Title' and self.parent_class == u'SASsample':
[d72567e]	213	self.current_datainfo.sample.name = data_point
[082239e]	214	# NXcanSAS format
	215	elif key == u'name' and self.parent_class == u'SASsample':
[d72567e]	216	self.current_datainfo.sample.name = data_point
[082239e]	217	# NXcanSAS format
	218	elif key == u'ID' and self.parent_class == u'SASsample':
[132db16]	219	self.current_datainfo.sample.name = data_point
[c94280c]	220	elif (key == u'thickness'
	221	and self.parent_class == u'SASsample'):
[132db16]	222	self.current_datainfo.sample.thickness = data_point
[c94280c]	223	elif (key == u'temperature'
	224	and self.parent_class == u'SASsample'):
[132db16]	225	self.current_datainfo.sample.temperature = data_point
[c94280c]	226	elif (key == u'transmission'
	227	and self.parent_class == u'SASsample'):
[5e906207]	228	self.current_datainfo.sample.transmission = data_point
[c94280c]	229	elif (key == u'x_position'
	230	and self.parent_class == u'SASsample'):
[5e906207]	231	self.current_datainfo.sample.position.x = data_point
[c94280c]	232	elif (key == u'y_position'
	233	and self.parent_class == u'SASsample'):
[5e906207]	234	self.current_datainfo.sample.position.y = data_point
[082239e]	235	elif key == u'pitch' and self.parent_class == u'SASsample':
[5e906207]	236	self.current_datainfo.sample.orientation.x = data_point
[082239e]	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':
[5e906207]	240	self.current_datainfo.sample.orientation.z = data_point
[c94280c]	241	elif (key == u'details'
	242	and self.parent_class == u'SASsample'):
[5e906207]	243	self.current_datainfo.sample.details.append(data_point)
[68aa210]	244
[082239e]	245	# Instrumental Information
[c94280c]	246	elif (key == u'name'
	247	and self.parent_class == u'SASinstrument'):
[132db16]	248	self.current_datainfo.instrument = data_point
	249	elif key == u'name' and self.parent_class == u'SASdetector':
[ad52d31]	250	self.detector.name = data_point
[132db16]	251	elif key == u'SDD' and self.parent_class == u'SASdetector':
	252	self.detector.distance = float(data_point)
[d398285]	253	self.detector.distance_unit = unit
[c94280c]	254	elif (key == u'slit_length'
	255	and self.parent_class == u'SASdetector'):
[5e906207]	256	self.detector.slit_length = float(data_point)
	257	self.detector.slit_length_unit = unit
[c94280c]	258	elif (key == u'x_position'
	259	and self.parent_class == u'SASdetector'):
[5e906207]	260	self.detector.offset.x = float(data_point)
	261	self.detector.offset_unit = unit
[c94280c]	262	elif (key == u'y_position'
	263	and self.parent_class == u'SASdetector'):
[5e906207]	264	self.detector.offset.y = float(data_point)
	265	self.detector.offset_unit = unit
[c94280c]	266	elif (key == u'pitch'
	267	and self.parent_class == u'SASdetector'):
[5e906207]	268	self.detector.orientation.x = float(data_point)
	269	self.detector.orientation_unit = unit
[082239e]	270	elif key == u'roll' and self.parent_class == u'SASdetector':
[5e906207]	271	self.detector.orientation.z = float(data_point)
	272	self.detector.orientation_unit = unit
[082239e]	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
[c94280c]	276	elif (key == u'beam_center_x'
	277	and self.parent_class == u'SASdetector'):
[5e906207]	278	self.detector.beam_center.x = float(data_point)
	279	self.detector.beam_center_unit = unit
[c94280c]	280	elif (key == u'beam_center_y'
	281	and self.parent_class == u'SASdetector'):
[5e906207]	282	self.detector.beam_center.y = float(data_point)
	283	self.detector.beam_center_unit = unit
[c94280c]	284	elif (key == u'x_pixel_size'
	285	and self.parent_class == u'SASdetector'):
[5e906207]	286	self.detector.pixel_size.x = float(data_point)
	287	self.detector.pixel_size_unit = unit
[c94280c]	288	elif (key == u'y_pixel_size'
	289	and self.parent_class == u'SASdetector'):
[5e906207]	290	self.detector.pixel_size.y = float(data_point)
	291	self.detector.pixel_size_unit = unit
[c94280c]	292	elif (key == u'distance'
	293	and self.parent_class == u'SAScollimation'):
[ad52d31]	294	self.collimation.length = data_point
[d398285]	295	self.collimation.length_unit = unit
[c94280c]	296	elif (key == u'name'
	297	and self.parent_class == u'SAScollimation'):
[ad52d31]	298	self.collimation.name = data_point
[c94280c]	299	elif (key == u'shape'
	300	and self.parent_class == u'SASaperture'):
[082239e]	301	self.aperture.shape = data_point
[c94280c]	302	elif (key == u'x_gap'
	303	and self.parent_class == u'SASaperture'):
[082239e]	304	self.aperture.size.x = data_point
[c94280c]	305	elif (key == u'y_gap'
	306	and self.parent_class == u'SASaperture'):
[082239e]	307	self.aperture.size.y = data_point
	308
	309	# Process Information
[c94280c]	310	elif (key == u'Title'
	311	and self.parent_class == u'SASprocess'): # CanSAS 2.0
[68aa210]	312	self.process.name = data_point
[c94280c]	313	elif (key == u'name'
	314	and self.parent_class == u'SASprocess'): # NXcanSAS
[68aa210]	315	self.process.name = data_point
[c94280c]	316	elif (key == u'description'
	317	and self.parent_class == u'SASprocess'):
[68aa210]	318	self.process.description = data_point
[132db16]	319	elif key == u'date' and self.parent_class == u'SASprocess':
[68aa210]	320	self.process.date = data_point
[082239e]	321	elif key == u'term' and self.parent_class == u'SASprocess':
	322	self.process.term = data_point
[132db16]	323	elif self.parent_class == u'SASprocess':
[ad52d31]	324	self.process.notes.append(data_point)
	325
[082239e]	326	# Source
[c94280c]	327	elif (key == u'wavelength'
	328	and self.parent_class == u'SASdata'):
[132db16]	329	self.current_datainfo.source.wavelength = data_point
[5e906207]	330	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	331	elif (key == u'incident_wavelength'
	332	and self.parent_class == 'SASsource'):
[5e906207]	333	self.current_datainfo.source.wavelength = data_point
	334	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	335	elif (key == u'wavelength_max'
	336	and self.parent_class == u'SASsource'):
[5e906207]	337	self.current_datainfo.source.wavelength_max = data_point
	338	self.current_datainfo.source.wavelength_max_unit = unit
[c94280c]	339	elif (key == u'wavelength_min'
	340	and self.parent_class == u'SASsource'):
[5e906207]	341	self.current_datainfo.source.wavelength_min = data_point
	342	self.current_datainfo.source.wavelength_min_unit = unit
[c94280c]	343	elif (key == u'incident_wavelength_spread'
	344	and self.parent_class == u'SASsource'):
[082239e]	345	self.current_datainfo.source.wavelength_spread = \
	346	data_point
	347	self.current_datainfo.source.wavelength_spread_unit = \
	348	unit
[c94280c]	349	elif (key == u'beam_size_x'
	350	and self.parent_class == u'SASsource'):
[5e906207]	351	self.current_datainfo.source.beam_size.x = data_point
	352	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	353	elif (key == u'beam_size_y'
	354	and self.parent_class == u'SASsource'):
[5e906207]	355	self.current_datainfo.source.beam_size.y = data_point
	356	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	357	elif (key == u'beam_shape'
	358	and self.parent_class == u'SASsource'):
[5e906207]	359	self.current_datainfo.source.beam_shape = data_point
[c94280c]	360	elif (key == u'radiation'
	361	and self.parent_class == u'SASsource'):
[132db16]	362	self.current_datainfo.source.radiation = data_point
[c94280c]	363	elif (key == u'transmission'
	364	and self.parent_class == u'SASdata'):
[132db16]	365	self.current_datainfo.sample.transmission = data_point
[68aa210]	366
[082239e]	367	# Everything else goes in meta_data
[68aa210]	368	else:
[082239e]	369	new_key = self._create_unique_key(
	370	self.current_datainfo.meta_data, key)
[132db16]	371	self.current_datainfo.meta_data[new_key] = data_point
[68aa210]	372
	373	else:
[082239e]	374	# I don't know if this reachable code
[68aa210]	375	self.errors.add("ShouldNeverHappenException")
	376
[132db16]	377	def add_intermediate(self):
[ad52d31]	378	"""
[082239e]	379	This method stores any intermediate objects within the final data set
	380	after fully reading the set.
[ad52d31]	381
[082239e]	382	:param parent: The NXclass name for the h5py Group object that just
	383	finished being processed
[ad52d31]	384	"""
	385
[132db16]	386	if self.parent_class == u'SASprocess':
	387	self.current_datainfo.process.append(self.process)
[ad52d31]	388	self.process = Process()
[132db16]	389	elif self.parent_class == u'SASdetector':
	390	self.current_datainfo.detector.append(self.detector)
[ad52d31]	391	self.detector = Detector()
[132db16]	392	elif self.parent_class == u'SAStransmission_spectrum':
	393	self.current_datainfo.trans_spectrum.append(self.trans_spectrum)
[ad52d31]	394	self.trans_spectrum = TransmissionSpectrum()
[132db16]	395	elif self.parent_class == u'SAScollimation':
	396	self.current_datainfo.collimation.append(self.collimation)
[ad52d31]	397	self.collimation = Collimation()
[132db16]	398	elif self.parent_class == u'SASaperture':
[ad52d31]	399	self.collimation.aperture.append(self.aperture)
	400	self.aperture = Aperture()
[132db16]	401	elif self.parent_class == u'SASdata':
[082239e]	402	if isinstance(self.current_dataset, plottable_2D):
[132db16]	403	self.data2d.append(self.current_dataset)
[082239e]	404	elif isinstance(self.current_dataset, plottable_1D):
[132db16]	405	self.data1d.append(self.current_dataset)
[68aa210]	406
	407	def final_data_cleanup(self):
	408	"""
[082239e]	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
[68aa210]	412	"""
	413
[082239e]	414	# Type cast data arrays to float64
[132db16]	415	if len(self.current_datainfo.trans_spectrum) > 0:
[ad52d31]	416	spectrum_list = []
[132db16]	417	for spectrum in self.current_datainfo.trans_spectrum:
[ad52d31]	418	spectrum.transmission = np.delete(spectrum.transmission, [0])
	419	spectrum.transmission = spectrum.transmission.astype(np.float64)
[082239e]	420	spectrum.transmission_deviation = np.delete(
	421	spectrum.transmission_deviation, [0])
	422	spectrum.transmission_deviation = \
	423	spectrum.transmission_deviation.astype(np.float64)
[ad52d31]	424	spectrum.wavelength = np.delete(spectrum.wavelength, [0])
	425	spectrum.wavelength = spectrum.wavelength.astype(np.float64)
[132db16]	426	if len(spectrum.transmission) > 0:
	427	spectrum_list.append(spectrum)
	428	self.current_datainfo.trans_spectrum = spectrum_list
[68aa210]	429
[082239e]	430	# Append errors to dataset and reset class errors
[132db16]	431	self.current_datainfo.errors = self.errors
[68aa210]	432	self.errors.clear()
	433
[082239e]	434	# Combine all plottables with datainfo and append each to output
	435	# Type cast data arrays to float64 and find min/max as appropriate
[132db16]	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:
[082239e]	455	for i in range(0, dataset.mask.size - 1):
[132db16]	456	zeros[i] = dataset.mask[i]
	457	except:
	458	self.errors.add(sys.exc_value)
	459	dataset.mask = zeros
[082239e]	460	# Calculate the actual Q matrix
[132db16]	461	try:
	462	if dataset.q_data.size <= 1:
[54544637]	463	dataset.q_data = np.sqrt(dataset.qx_data
	464	* dataset.qx_data
	465	+ dataset.qy_data
	466	* dataset.qy_data)
[132db16]	467	except:
	468	dataset.q_data = None
[a9d3abb]	469
	470	if dataset.data.ndim == 2:
	471	(n_rows, n_cols) = dataset.data.shape
[1b06e13a]	472	dataset.y_bins = dataset.qy_data[0::n_cols]
[a9d3abb]	473	dataset.x_bins = dataset.qx_data[:n_cols]
	474	dataset.data = dataset.data.flatten()
	475
[082239e]	476	final_dataset = combine_data_info_with_plottable(
	477	dataset, self.current_datainfo)
[132db16]	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)
[082239e]	497	final_dataset = combine_data_info_with_plottable(
	498	dataset, self.current_datainfo)
[132db16]	499	self.output.append(final_dataset)
	500
[68aa210]	501	def add_data_set(self, key=""):
	502	"""
[082239e]	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.
[68aa210]	506
	507	:param key: NeXus group name for current tree level
	508	"""
[132db16]	509
	510	if self.current_datainfo and self.current_dataset:
[68aa210]	511	self.final_data_cleanup()
[132db16]	512	self.data1d = []
	513	self.data2d = []
	514	self.current_datainfo = DataInfo()
[68aa210]	515
[54ba66e]	516
[082239e]	517	def _initialize_new_data_set(self, parent_list=None):
[68aa210]	518	"""
[082239e]	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.
[68aa210]	522
[132db16]	523	:param parent_list: List of names of parent elements
[68aa210]	524	"""
[132db16]	525
	526	if parent_list is None:
	527	parent_list = []
	528	if self._find_intermediate(parent_list, "Qx"):
	529	self.current_dataset = plottable_2D()
[68aa210]	530	else:
	531	x = np.array(0)
	532	y = np.array(0)
[132db16]	533	self.current_dataset = plottable_1D(x, y)
	534	self.current_datainfo.filename = self.raw_data.filename
[68aa210]	535
[132db16]	536	def _find_intermediate(self, parent_list, basename=""):
[ad52d31]	537	"""
[082239e]	538	A private class used to find an entry by either using a direct key or
	539	knowing the approximate basename.
[ad52d31]	540
[082239e]	541	:param parent_list: List of parents nodes in the HDF5 file
[132db16]	542	:param basename: Approximate name of an entry to search for
[ad52d31]	543	:return:
	544	"""
[132db16]	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():
[082239e]	552	if key_prog.match(key):
[132db16]	553	entry = True
	554	break
[ad52d31]	555	return entry
	556
[68aa210]	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
[132db16]	565	:return: The new name for the dictionary entry
[68aa210]	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)
[d398285]	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
[132db16]	579	:return: unit for the value passed to the method
[d398285]	580	"""
	581	unit = value.attrs.get(u'units')
[54544637]	582	if unit is None:
[d398285]	583	unit = value.attrs.get(u'unit')
[082239e]	584	# Convert the unit formats
[d398285]	585	if unit == "1/A":
	586	unit = "A^{-1}"
	587	elif unit == "1/cm":
	588	unit = "cm^{-1}"
[54ba66e]	589	return unit

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py @ 18d5af02

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