cansas_reader_HDF5.py @ 9e308a3

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 9e308a3 was 7b50f14, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
restore python 2 functionality
Property mode set to `100644`
File size: 26.8 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
[7b50f14]	11	from ..data_info import plottable_1D, plottable_2D,\
[082239e]	12	Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \
	13	TransmissionSpectrum, Detector
[7b50f14]	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
[5c5e7fd]	17
	18	def h5attr(node, key, default=None):
	19	return decode(node.attrs.get(key, default))
[68aa210]	20
[9d786e5]	21	class Reader(FileReader):
[68aa210]	22	"""
[082239e]	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.
[d72567e]	28
[082239e]	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).
[68aa210]	31
[5e906207]	32	Also supports reading NXcanSAS formatted HDF5 files
	33
[68aa210]	34	:Dependencies:
[d72567e]	35	The CanSAS HDF5 reader requires h5py => v2.5.0 or later.
[68aa210]	36	"""
	37
[082239e]	38	# CanSAS version
[68aa210]	39	cansas_version = 2.0
[082239e]	40	# Logged warnings or messages
[68aa210]	41	logging = None
[082239e]	42	# List of errors for the current data set
[68aa210]	43	errors = None
[082239e]	44	# Raw file contents to be processed
[68aa210]	45	raw_data = None
[082239e]	46	# List of plottable1D objects that should be linked to the current_datainfo
[d72567e]	47	data1d = None
[082239e]	48	# List of plottable2D objects that should be linked to the current_datainfo
[d72567e]	49	data2d = None
[082239e]	50	# Data type name
[ad52d31]	51	type_name = "CanSAS 2.0"
[082239e]	52	# Wildcards
[ad52d31]	53	type = ["CanSAS 2.0 HDF5 Files (.h5)\|.h5"]
[082239e]	54	# List of allowed extensions
[68aa210]	55	ext = ['.h5', '.H5']
[082239e]	56	# Flag to bypass extension check
[54544637]	57	allow_all = True
[68aa210]	58
[9d786e5]	59	def get_file_contents(self):
[68aa210]	60	"""
[ad52d31]	61	This is the general read method that all SasView data_loaders must have.
[68aa210]	62
	63	:param filename: A path for an HDF5 formatted CanSAS 2D data file.
[d72567e]	64	:return: List of Data1D/2D objects and/or a list of errors.
[68aa210]	65	"""
[082239e]	66	# Reinitialize when loading a new data file to reset all class variables
[d72567e]	67	self.reset_class_variables()
[9d786e5]	68
	69	filename = self.f_open.name
	70	self.f_open.close() # IO handled by h5py
	71
[082239e]	72	# Check that the file exists
[68aa210]	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:
[082239e]	78	# Load the data file
[7f75a3f]	79	try:
	80	self.raw_data = h5py.File(filename, 'r')
	81	except Exception as e:
[8dec7e7]	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)
[dcb91cf]	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.")
[68aa210]	102
[d72567e]	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):
[68aa210]	123	"""
[ad52d31]	124	A recursive method for stepping through the hierarchical data file.
[68aa210]	125
	126	:param data: h5py Group object of any kind
	127	:param parent: h5py Group parent name
	128	"""
	129
[082239e]	130	# Loop through each element of the parent and process accordingly
[68aa210]	131	for key in data.keys():
[082239e]	132	# Get all information for the current key
[68aa210]	133	value = data.get(key)
[7b50f14]	134	class_name = h5attr(value, u'canSAS_class')
	135	if class_name is None:
[5c5e7fd]	136	class_name = h5attr(value, u'NX_class')
[68aa210]	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):
[c9ecd1b]	143	# Set parent class before recursion
[d72567e]	144	self.parent_class = class_name
	145	parent_list.append(key)
[082239e]	146	# If a new sasentry, store the current data sets and create
	147	# a fresh Data1D/2D object
[68aa210]	148	if class_prog.match(u'SASentry'):
	149	self.add_data_set(key)
[d72567e]	150	elif class_prog.match(u'SASdata'):
	151	self._initialize_new_data_set(parent_list)
[082239e]	152	# Recursion step to access data within the group
[d72567e]	153	self.read_children(value, parent_list)
[c9ecd1b]	154	# Reset parent class when returning from recursive method
	155	self.parent_class = class_name
[d72567e]	156	self.add_intermediate()
	157	parent_list.remove(key)
[68aa210]	158
	159	elif isinstance(value, h5py.Dataset):
[082239e]	160	# If this is a dataset, store the data appropriately
[68aa210]	161	data_set = data[key][:]
[7bd6860a]	162	unit = self._get_unit(value)
[ac370c5]	163
[082239e]	164	# I and Q Data
[7bd6860a]	165	if key == u'I':
[082239e]	166	if isinstance(self.current_dataset, plottable_2D):
[ac370c5]	167	self.current_dataset.data = data_set
[7bd6860a]	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':
[082239e]	174	if isinstance(self.current_dataset, plottable_2D):
[7bd6860a]	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)
[082239e]	181	if isinstance(self.current_dataset, plottable_2D):
[7bd6860a]	182	self.current_dataset.q = data_set.flatten()
	183	else:
	184	self.current_dataset.x = data_set.flatten()
	185	continue
[bbd0f37]	186	elif key == u'Qdev':
	187	self.current_dataset.dx = data_set.flatten()
	188	continue
[082239e]	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
[7bd6860a]	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
[082239e]	212	# Transmission Spectrum
[c94280c]	213	elif (key == u'T'
	214	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	215	self.trans_spectrum.transmission = data_set.flatten()
	216	continue
[c94280c]	217	elif (key == u'Tdev'
	218	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	219	self.trans_spectrum.transmission_deviation = \
	220	data_set.flatten()
	221	continue
[c94280c]	222	elif (key == u'lambda'
	223	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	224	self.trans_spectrum.wavelength = data_set.flatten()
	225	continue
[68aa210]	226
	227	for data_point in data_set:
[5c5e7fd]	228	if data_point.dtype.char == 'S':
	229	data_point = decode(bytes(data_point))
[082239e]	230	# Top Level Meta Data
[68aa210]	231	if key == u'definition':
[d72567e]	232	self.current_datainfo.meta_data['reader'] = data_point
[68aa210]	233	elif key == u'run':
[d72567e]	234	self.current_datainfo.run.append(data_point)
[be88076]	235	try:
[5c5e7fd]	236	run_name = h5attr(value, 'name')
[be88076]	237	run_dict = {data_point: run_name}
	238	self.current_datainfo.run_name = run_dict
[7b50f14]	239	except Exception:
[be88076]	240	pass
[68aa210]	241	elif key == u'title':
[d72567e]	242	self.current_datainfo.title = data_point
[68aa210]	243	elif key == u'SASnote':
[d72567e]	244	self.current_datainfo.notes.append(data_point)
[68aa210]	245
[082239e]	246	# Sample Information
	247	# CanSAS 2.0 format
	248	elif key == u'Title' and self.parent_class == u'SASsample':
[d72567e]	249	self.current_datainfo.sample.name = data_point
[082239e]	250	# NXcanSAS format
	251	elif key == u'name' and self.parent_class == u'SASsample':
[88d85c6]	252	self.current_datainfo.sample.name = data_point
[082239e]	253	# NXcanSAS format
	254	elif key == u'ID' and self.parent_class == u'SASsample':
	255	self.current_datainfo.sample.name = data_point
[c94280c]	256	elif (key == u'thickness'
	257	and self.parent_class == u'SASsample'):
[d72567e]	258	self.current_datainfo.sample.thickness = data_point
[c94280c]	259	elif (key == u'temperature'
	260	and self.parent_class == u'SASsample'):
[d72567e]	261	self.current_datainfo.sample.temperature = data_point
[c94280c]	262	elif (key == u'transmission'
	263	and self.parent_class == u'SASsample'):
[5e906207]	264	self.current_datainfo.sample.transmission = data_point
[c94280c]	265	elif (key == u'x_position'
	266	and self.parent_class == u'SASsample'):
[5e906207]	267	self.current_datainfo.sample.position.x = data_point
[c94280c]	268	elif (key == u'y_position'
	269	and self.parent_class == u'SASsample'):
[5e906207]	270	self.current_datainfo.sample.position.y = data_point
[082239e]	271	elif key == u'pitch' and self.parent_class == u'SASsample':
[5e906207]	272	self.current_datainfo.sample.orientation.x = data_point
[082239e]	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':
[5e906207]	276	self.current_datainfo.sample.orientation.z = data_point
[c94280c]	277	elif (key == u'details'
	278	and self.parent_class == u'SASsample'):
[5e906207]	279	self.current_datainfo.sample.details.append(data_point)
[68aa210]	280
[082239e]	281	# Instrumental Information
[c94280c]	282	elif (key == u'name'
	283	and self.parent_class == u'SASinstrument'):
[d72567e]	284	self.current_datainfo.instrument = data_point
	285	elif key == u'name' and self.parent_class == u'SASdetector':
[ad52d31]	286	self.detector.name = data_point
[d72567e]	287	elif key == u'SDD' and self.parent_class == u'SASdetector':
	288	self.detector.distance = float(data_point)
[d398285]	289	self.detector.distance_unit = unit
[c94280c]	290	elif (key == u'slit_length'
	291	and self.parent_class == u'SASdetector'):
[5e906207]	292	self.detector.slit_length = float(data_point)
	293	self.detector.slit_length_unit = unit
[c94280c]	294	elif (key == u'x_position'
	295	and self.parent_class == u'SASdetector'):
[5e906207]	296	self.detector.offset.x = float(data_point)
	297	self.detector.offset_unit = unit
[c94280c]	298	elif (key == u'y_position'
	299	and self.parent_class == u'SASdetector'):
[5e906207]	300	self.detector.offset.y = float(data_point)
	301	self.detector.offset_unit = unit
[c94280c]	302	elif (key == u'pitch'
	303	and self.parent_class == u'SASdetector'):
[5e906207]	304	self.detector.orientation.x = float(data_point)
	305	self.detector.orientation_unit = unit
[082239e]	306	elif key == u'roll' and self.parent_class == u'SASdetector':
[5e906207]	307	self.detector.orientation.z = float(data_point)
	308	self.detector.orientation_unit = unit
[082239e]	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
[c94280c]	312	elif (key == u'beam_center_x'
	313	and self.parent_class == u'SASdetector'):
[5e906207]	314	self.detector.beam_center.x = float(data_point)
	315	self.detector.beam_center_unit = unit
[c94280c]	316	elif (key == u'beam_center_y'
	317	and self.parent_class == u'SASdetector'):
[5e906207]	318	self.detector.beam_center.y = float(data_point)
	319	self.detector.beam_center_unit = unit
[c94280c]	320	elif (key == u'x_pixel_size'
	321	and self.parent_class == u'SASdetector'):
[5e906207]	322	self.detector.pixel_size.x = float(data_point)
	323	self.detector.pixel_size_unit = unit
[c94280c]	324	elif (key == u'y_pixel_size'
	325	and self.parent_class == u'SASdetector'):
[5e906207]	326	self.detector.pixel_size.y = float(data_point)
	327	self.detector.pixel_size_unit = unit
[c94280c]	328	elif (key == u'distance'
	329	and self.parent_class == u'SAScollimation'):
[ad52d31]	330	self.collimation.length = data_point
[d398285]	331	self.collimation.length_unit = unit
[c94280c]	332	elif (key == u'name'
	333	and self.parent_class == u'SAScollimation'):
[ad52d31]	334	self.collimation.name = data_point
[c94280c]	335	elif (key == u'shape'
	336	and self.parent_class == u'SASaperture'):
[082239e]	337	self.aperture.shape = data_point
[c94280c]	338	elif (key == u'x_gap'
	339	and self.parent_class == u'SASaperture'):
[082239e]	340	self.aperture.size.x = data_point
[c94280c]	341	elif (key == u'y_gap'
	342	and self.parent_class == u'SASaperture'):
[082239e]	343	self.aperture.size.y = data_point
	344
	345	# Process Information
[c94280c]	346	elif (key == u'Title'
	347	and self.parent_class == u'SASprocess'): # CanSAS 2.0
[68aa210]	348	self.process.name = data_point
[c94280c]	349	elif (key == u'name'
	350	and self.parent_class == u'SASprocess'): # NXcanSAS
[68aa210]	351	self.process.name = data_point
[c94280c]	352	elif (key == u'description'
	353	and self.parent_class == u'SASprocess'):
[68aa210]	354	self.process.description = data_point
[d72567e]	355	elif key == u'date' and self.parent_class == u'SASprocess':
[68aa210]	356	self.process.date = data_point
[082239e]	357	elif key == u'term' and self.parent_class == u'SASprocess':
	358	self.process.term = data_point
[d72567e]	359	elif self.parent_class == u'SASprocess':
[ad52d31]	360	self.process.notes.append(data_point)
	361
[082239e]	362	# Source
[c94280c]	363	elif (key == u'wavelength'
	364	and self.parent_class == u'SASdata'):
[d72567e]	365	self.current_datainfo.source.wavelength = data_point
[5e906207]	366	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	367	elif (key == u'incident_wavelength'
	368	and self.parent_class == 'SASsource'):
[5e906207]	369	self.current_datainfo.source.wavelength = data_point
	370	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	371	elif (key == u'wavelength_max'
	372	and self.parent_class == u'SASsource'):
[5e906207]	373	self.current_datainfo.source.wavelength_max = data_point
	374	self.current_datainfo.source.wavelength_max_unit = unit
[c94280c]	375	elif (key == u'wavelength_min'
	376	and self.parent_class == u'SASsource'):
[5e906207]	377	self.current_datainfo.source.wavelength_min = data_point
	378	self.current_datainfo.source.wavelength_min_unit = unit
[c94280c]	379	elif (key == u'incident_wavelength_spread'
	380	and self.parent_class == u'SASsource'):
[082239e]	381	self.current_datainfo.source.wavelength_spread = \
	382	data_point
	383	self.current_datainfo.source.wavelength_spread_unit = \
	384	unit
[c94280c]	385	elif (key == u'beam_size_x'
	386	and self.parent_class == u'SASsource'):
[5e906207]	387	self.current_datainfo.source.beam_size.x = data_point
	388	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	389	elif (key == u'beam_size_y'
	390	and self.parent_class == u'SASsource'):
[5e906207]	391	self.current_datainfo.source.beam_size.y = data_point
	392	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	393	elif (key == u'beam_shape'
	394	and self.parent_class == u'SASsource'):
[5e906207]	395	self.current_datainfo.source.beam_shape = data_point
[c94280c]	396	elif (key == u'radiation'
	397	and self.parent_class == u'SASsource'):
[d72567e]	398	self.current_datainfo.source.radiation = data_point
[c94280c]	399	elif (key == u'transmission'
	400	and self.parent_class == u'SASdata'):
[d72567e]	401	self.current_datainfo.sample.transmission = data_point
[68aa210]	402
[082239e]	403	# Everything else goes in meta_data
[68aa210]	404	else:
[082239e]	405	new_key = self._create_unique_key(
	406	self.current_datainfo.meta_data, key)
[d72567e]	407	self.current_datainfo.meta_data[new_key] = data_point
[68aa210]	408
	409	else:
[082239e]	410	# I don't know if this reachable code
[68aa210]	411	self.errors.add("ShouldNeverHappenException")
	412
[d72567e]	413	def add_intermediate(self):
[ad52d31]	414	"""
[082239e]	415	This method stores any intermediate objects within the final data set
	416	after fully reading the set.
[ad52d31]	417
[082239e]	418	:param parent: The NXclass name for the h5py Group object that just
	419	finished being processed
[ad52d31]	420	"""
	421
[d72567e]	422	if self.parent_class == u'SASprocess':
	423	self.current_datainfo.process.append(self.process)
[ad52d31]	424	self.process = Process()
[d72567e]	425	elif self.parent_class == u'SASdetector':
	426	self.current_datainfo.detector.append(self.detector)
[ad52d31]	427	self.detector = Detector()
[d72567e]	428	elif self.parent_class == u'SAStransmission_spectrum':
	429	self.current_datainfo.trans_spectrum.append(self.trans_spectrum)
[ad52d31]	430	self.trans_spectrum = TransmissionSpectrum()
[d72567e]	431	elif self.parent_class == u'SAScollimation':
	432	self.current_datainfo.collimation.append(self.collimation)
[ad52d31]	433	self.collimation = Collimation()
[d72567e]	434	elif self.parent_class == u'SASaperture':
[ad52d31]	435	self.collimation.aperture.append(self.aperture)
	436	self.aperture = Aperture()
[d72567e]	437	elif self.parent_class == u'SASdata':
[082239e]	438	if isinstance(self.current_dataset, plottable_2D):
[d72567e]	439	self.data2d.append(self.current_dataset)
[082239e]	440	elif isinstance(self.current_dataset, plottable_1D):
[d72567e]	441	self.data1d.append(self.current_dataset)
[68aa210]	442
	443	def final_data_cleanup(self):
	444	"""
[082239e]	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
[68aa210]	448	"""
[082239e]	449	# Type cast data arrays to float64
[d72567e]	450	if len(self.current_datainfo.trans_spectrum) > 0:
[ad52d31]	451	spectrum_list = []
[d72567e]	452	for spectrum in self.current_datainfo.trans_spectrum:
[ad52d31]	453	spectrum.transmission = np.delete(spectrum.transmission, [0])
	454	spectrum.transmission = spectrum.transmission.astype(np.float64)
[082239e]	455	spectrum.transmission_deviation = np.delete(
	456	spectrum.transmission_deviation, [0])
	457	spectrum.transmission_deviation = \
	458	spectrum.transmission_deviation.astype(np.float64)
[ad52d31]	459	spectrum.wavelength = np.delete(spectrum.wavelength, [0])
	460	spectrum.wavelength = spectrum.wavelength.astype(np.float64)
[d72567e]	461	if len(spectrum.transmission) > 0:
	462	spectrum_list.append(spectrum)
	463	self.current_datainfo.trans_spectrum = spectrum_list
[68aa210]	464
[082239e]	465	# Append errors to dataset and reset class errors
[d72567e]	466	self.current_datainfo.errors = self.errors
[68aa210]	467	self.errors.clear()
	468
[082239e]	469	# Combine all plottables with datainfo and append each to output
	470	# Type cast data arrays to float64 and find min/max as appropriate
[d72567e]	471	for dataset in self.data2d:
	472	zeros = np.ones(dataset.data.size, dtype=bool)
	473	try:
[082239e]	474	for i in range(0, dataset.mask.size - 1):
[d72567e]	475	zeros[i] = dataset.mask[i]
	476	except:
	477	self.errors.add(sys.exc_value)
	478	dataset.mask = zeros
[082239e]	479	# Calculate the actual Q matrix
[d72567e]	480	try:
	481	if dataset.q_data.size <= 1:
[54544637]	482	dataset.q_data = np.sqrt(dataset.qx_data
	483	* dataset.qx_data
	484	+ dataset.qy_data
	485	* dataset.qy_data)
[d72567e]	486	except:
	487	dataset.q_data = None
[ac370c5]	488
	489	if dataset.data.ndim == 2:
	490	(n_rows, n_cols) = dataset.data.shape
[479799c]	491	dataset.y_bins = dataset.qy_data[0::n_cols]
[ac370c5]	492	dataset.x_bins = dataset.qx_data[:n_cols]
	493	dataset.data = dataset.data.flatten()
[9d786e5]	494	self.current_dataset = dataset
	495	self.send_to_output()
[d72567e]	496
	497	for dataset in self.data1d:
[9d786e5]	498	self.current_dataset = dataset
	499	self.send_to_output()
[d72567e]	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	"""
[d72567e]	509
	510	if self.current_datainfo and self.current_dataset:
[68aa210]	511	self.final_data_cleanup()
[d72567e]	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
[d72567e]	523	:param parent_list: List of names of parent elements
[68aa210]	524	"""
[d72567e]	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)
[d72567e]	533	self.current_dataset = plottable_1D(x, y)
	534	self.current_datainfo.filename = self.raw_data.filename
[68aa210]	535
[d72567e]	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
[d72567e]	542	:param basename: Approximate name of an entry to search for
[ad52d31]	543	:return:
	544	"""
[d72567e]	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):
[d72567e]	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
[d72567e]	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
[d72567e]	579	:return: unit for the value passed to the method
[d398285]	580	"""
[5c5e7fd]	581	unit = h5attr(value, u'units')
[54544637]	582	if unit is None:
[5c5e7fd]	583	unit = h5attr(value, 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 @ 9e308a3

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