cansas_reader_HDF5.py @ 5ae083b

Last change on this file since 5ae083b was 61f329f0, checked in by krzywon, 7 years ago
Reset file reader class data state each time a new data file is loaded.
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
[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
[61f329f0]	67	self.reset_state()
[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
[61f329f0]	103	def reset_state(self):
[d72567e]	104	"""
	105	Create the reader object and define initial states for class variables
	106	"""
[61f329f0]	107	super(Reader, self).reset_state()
[d72567e]	108	self.data1d = []
	109	self.data2d = []
	110	self.raw_data = None
	111	self.errors = set()
	112	self.logging = []
	113	self.parent_class = u''
	114	self.detector = Detector()
	115	self.collimation = Collimation()
	116	self.aperture = Aperture()
	117	self.process = Process()
	118	self.trans_spectrum = TransmissionSpectrum()
	119
	120	def read_children(self, data, parent_list):
[68aa210]	121	"""
[ad52d31]	122	A recursive method for stepping through the hierarchical data file.
[68aa210]	123
	124	:param data: h5py Group object of any kind
	125	:param parent: h5py Group parent name
	126	"""
	127
[082239e]	128	# Loop through each element of the parent and process accordingly
[68aa210]	129	for key in data.keys():
[082239e]	130	# Get all information for the current key
[68aa210]	131	value = data.get(key)
[7b50f14]	132	class_name = h5attr(value, u'canSAS_class')
	133	if class_name is None:
[5c5e7fd]	134	class_name = h5attr(value, u'NX_class')
[68aa210]	135	if class_name is not None:
	136	class_prog = re.compile(class_name)
	137	else:
	138	class_prog = re.compile(value.name)
	139
	140	if isinstance(value, h5py.Group):
[c9ecd1b]	141	# Set parent class before recursion
[d72567e]	142	self.parent_class = class_name
	143	parent_list.append(key)
[082239e]	144	# If a new sasentry, store the current data sets and create
	145	# a fresh Data1D/2D object
[68aa210]	146	if class_prog.match(u'SASentry'):
	147	self.add_data_set(key)
[d72567e]	148	elif class_prog.match(u'SASdata'):
	149	self._initialize_new_data_set(parent_list)
[082239e]	150	# Recursion step to access data within the group
[d72567e]	151	self.read_children(value, parent_list)
[c9ecd1b]	152	# Reset parent class when returning from recursive method
	153	self.parent_class = class_name
[d72567e]	154	self.add_intermediate()
	155	parent_list.remove(key)
[68aa210]	156
	157	elif isinstance(value, h5py.Dataset):
[082239e]	158	# If this is a dataset, store the data appropriately
[68aa210]	159	data_set = data[key][:]
[7bd6860a]	160	unit = self._get_unit(value)
[ac370c5]	161
[082239e]	162	# I and Q Data
[7bd6860a]	163	if key == u'I':
[082239e]	164	if isinstance(self.current_dataset, plottable_2D):
[ac370c5]	165	self.current_dataset.data = data_set
[7bd6860a]	166	self.current_dataset.zaxis("Intensity", unit)
	167	else:
	168	self.current_dataset.y = data_set.flatten()
	169	self.current_dataset.yaxis("Intensity", unit)
	170	continue
	171	elif key == u'Idev':
[082239e]	172	if isinstance(self.current_dataset, plottable_2D):
[7bd6860a]	173	self.current_dataset.err_data = data_set.flatten()
	174	else:
	175	self.current_dataset.dy = data_set.flatten()
	176	continue
	177	elif key == u'Q':
	178	self.current_dataset.xaxis("Q", unit)
[082239e]	179	if isinstance(self.current_dataset, plottable_2D):
[7bd6860a]	180	self.current_dataset.q = data_set.flatten()
	181	else:
	182	self.current_dataset.x = data_set.flatten()
	183	continue
[bbd0f37]	184	elif key == u'Qdev':
	185	self.current_dataset.dx = data_set.flatten()
	186	continue
[082239e]	187	elif key == u'dQw':
	188	self.current_dataset.dxw = data_set.flatten()
	189	continue
	190	elif key == u'dQl':
	191	self.current_dataset.dxl = data_set.flatten()
	192	continue
[7bd6860a]	193	elif key == u'Qy':
	194	self.current_dataset.yaxis("Q_y", unit)
	195	self.current_dataset.qy_data = data_set.flatten()
	196	continue
	197	elif key == u'Qydev':
	198	self.current_dataset.dqy_data = data_set.flatten()
	199	continue
	200	elif key == u'Qx':
	201	self.current_dataset.xaxis("Q_x", unit)
	202	self.current_dataset.qx_data = data_set.flatten()
	203	continue
	204	elif key == u'Qxdev':
	205	self.current_dataset.dqx_data = data_set.flatten()
	206	continue
	207	elif key == u'Mask':
	208	self.current_dataset.mask = data_set.flatten()
	209	continue
[082239e]	210	# Transmission Spectrum
[c94280c]	211	elif (key == u'T'
	212	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	213	self.trans_spectrum.transmission = data_set.flatten()
	214	continue
[c94280c]	215	elif (key == u'Tdev'
	216	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	217	self.trans_spectrum.transmission_deviation = \
	218	data_set.flatten()
	219	continue
[c94280c]	220	elif (key == u'lambda'
	221	and self.parent_class == u'SAStransmission_spectrum'):
[082239e]	222	self.trans_spectrum.wavelength = data_set.flatten()
	223	continue
[68aa210]	224
	225	for data_point in data_set:
[2b538cd]	226	if isinstance(data_point, np.ndarray):
	227	if data_point.dtype.char == 'S':
	228	data_point = decode(bytes(data_point))
	229	else:
	230	data_point = decode(data_point)
[082239e]	231	# Top Level Meta Data
[68aa210]	232	if key == u'definition':
[d72567e]	233	self.current_datainfo.meta_data['reader'] = data_point
[68aa210]	234	elif key == u'run':
[d72567e]	235	self.current_datainfo.run.append(data_point)
[be88076]	236	try:
[5c5e7fd]	237	run_name = h5attr(value, 'name')
[be88076]	238	run_dict = {data_point: run_name}
	239	self.current_datainfo.run_name = run_dict
[7b50f14]	240	except Exception:
[be88076]	241	pass
[68aa210]	242	elif key == u'title':
[d72567e]	243	self.current_datainfo.title = data_point
[68aa210]	244	elif key == u'SASnote':
[d72567e]	245	self.current_datainfo.notes.append(data_point)
[68aa210]	246
[082239e]	247	# Sample Information
	248	# CanSAS 2.0 format
	249	elif key == u'Title' and self.parent_class == u'SASsample':
[d72567e]	250	self.current_datainfo.sample.name = data_point
[082239e]	251	# NXcanSAS format
	252	elif key == u'name' and self.parent_class == u'SASsample':
[88d85c6]	253	self.current_datainfo.sample.name = data_point
[082239e]	254	# NXcanSAS format
	255	elif key == u'ID' and self.parent_class == u'SASsample':
	256	self.current_datainfo.sample.name = data_point
[c94280c]	257	elif (key == u'thickness'
	258	and self.parent_class == u'SASsample'):
[d72567e]	259	self.current_datainfo.sample.thickness = data_point
[c94280c]	260	elif (key == u'temperature'
	261	and self.parent_class == u'SASsample'):
[d72567e]	262	self.current_datainfo.sample.temperature = data_point
[c94280c]	263	elif (key == u'transmission'
	264	and self.parent_class == u'SASsample'):
[5e906207]	265	self.current_datainfo.sample.transmission = data_point
[c94280c]	266	elif (key == u'x_position'
	267	and self.parent_class == u'SASsample'):
[5e906207]	268	self.current_datainfo.sample.position.x = data_point
[c94280c]	269	elif (key == u'y_position'
	270	and self.parent_class == u'SASsample'):
[5e906207]	271	self.current_datainfo.sample.position.y = data_point
[082239e]	272	elif key == u'pitch' and self.parent_class == u'SASsample':
[5e906207]	273	self.current_datainfo.sample.orientation.x = data_point
[082239e]	274	elif key == u'yaw' and self.parent_class == u'SASsample':
	275	self.current_datainfo.sample.orientation.y = data_point
	276	elif key == u'roll' and self.parent_class == u'SASsample':
[5e906207]	277	self.current_datainfo.sample.orientation.z = data_point
[c94280c]	278	elif (key == u'details'
	279	and self.parent_class == u'SASsample'):
[5e906207]	280	self.current_datainfo.sample.details.append(data_point)
[68aa210]	281
[082239e]	282	# Instrumental Information
[c94280c]	283	elif (key == u'name'
	284	and self.parent_class == u'SASinstrument'):
[d72567e]	285	self.current_datainfo.instrument = data_point
	286	elif key == u'name' and self.parent_class == u'SASdetector':
[ad52d31]	287	self.detector.name = data_point
[d72567e]	288	elif key == u'SDD' and self.parent_class == u'SASdetector':
	289	self.detector.distance = float(data_point)
[d398285]	290	self.detector.distance_unit = unit
[c94280c]	291	elif (key == u'slit_length'
	292	and self.parent_class == u'SASdetector'):
[5e906207]	293	self.detector.slit_length = float(data_point)
	294	self.detector.slit_length_unit = unit
[c94280c]	295	elif (key == u'x_position'
	296	and self.parent_class == u'SASdetector'):
[5e906207]	297	self.detector.offset.x = float(data_point)
	298	self.detector.offset_unit = unit
[c94280c]	299	elif (key == u'y_position'
	300	and self.parent_class == u'SASdetector'):
[5e906207]	301	self.detector.offset.y = float(data_point)
	302	self.detector.offset_unit = unit
[c94280c]	303	elif (key == u'pitch'
	304	and self.parent_class == u'SASdetector'):
[5e906207]	305	self.detector.orientation.x = float(data_point)
	306	self.detector.orientation_unit = unit
[082239e]	307	elif key == u'roll' and self.parent_class == u'SASdetector':
[5e906207]	308	self.detector.orientation.z = float(data_point)
	309	self.detector.orientation_unit = unit
[082239e]	310	elif key == u'yaw' and self.parent_class == u'SASdetector':
	311	self.detector.orientation.y = float(data_point)
	312	self.detector.orientation_unit = unit
[c94280c]	313	elif (key == u'beam_center_x'
	314	and self.parent_class == u'SASdetector'):
[5e906207]	315	self.detector.beam_center.x = float(data_point)
	316	self.detector.beam_center_unit = unit
[c94280c]	317	elif (key == u'beam_center_y'
	318	and self.parent_class == u'SASdetector'):
[5e906207]	319	self.detector.beam_center.y = float(data_point)
	320	self.detector.beam_center_unit = unit
[c94280c]	321	elif (key == u'x_pixel_size'
	322	and self.parent_class == u'SASdetector'):
[5e906207]	323	self.detector.pixel_size.x = float(data_point)
	324	self.detector.pixel_size_unit = unit
[c94280c]	325	elif (key == u'y_pixel_size'
	326	and self.parent_class == u'SASdetector'):
[5e906207]	327	self.detector.pixel_size.y = float(data_point)
	328	self.detector.pixel_size_unit = unit
[c94280c]	329	elif (key == u'distance'
	330	and self.parent_class == u'SAScollimation'):
[ad52d31]	331	self.collimation.length = data_point
[d398285]	332	self.collimation.length_unit = unit
[c94280c]	333	elif (key == u'name'
	334	and self.parent_class == u'SAScollimation'):
[ad52d31]	335	self.collimation.name = data_point
[c94280c]	336	elif (key == u'shape'
	337	and self.parent_class == u'SASaperture'):
[082239e]	338	self.aperture.shape = data_point
[c94280c]	339	elif (key == u'x_gap'
	340	and self.parent_class == u'SASaperture'):
[082239e]	341	self.aperture.size.x = data_point
[c94280c]	342	elif (key == u'y_gap'
	343	and self.parent_class == u'SASaperture'):
[082239e]	344	self.aperture.size.y = data_point
	345
	346	# Process Information
[c94280c]	347	elif (key == u'Title'
	348	and self.parent_class == u'SASprocess'): # CanSAS 2.0
[68aa210]	349	self.process.name = data_point
[c94280c]	350	elif (key == u'name'
	351	and self.parent_class == u'SASprocess'): # NXcanSAS
[68aa210]	352	self.process.name = data_point
[c94280c]	353	elif (key == u'description'
	354	and self.parent_class == u'SASprocess'):
[68aa210]	355	self.process.description = data_point
[d72567e]	356	elif key == u'date' and self.parent_class == u'SASprocess':
[68aa210]	357	self.process.date = data_point
[082239e]	358	elif key == u'term' and self.parent_class == u'SASprocess':
	359	self.process.term = data_point
[d72567e]	360	elif self.parent_class == u'SASprocess':
[ad52d31]	361	self.process.notes.append(data_point)
	362
[082239e]	363	# Source
[c94280c]	364	elif (key == u'wavelength'
	365	and self.parent_class == u'SASdata'):
[d72567e]	366	self.current_datainfo.source.wavelength = data_point
[5e906207]	367	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	368	elif (key == u'incident_wavelength'
	369	and self.parent_class == 'SASsource'):
[5e906207]	370	self.current_datainfo.source.wavelength = data_point
	371	self.current_datainfo.source.wavelength_unit = unit
[c94280c]	372	elif (key == u'wavelength_max'
	373	and self.parent_class == u'SASsource'):
[5e906207]	374	self.current_datainfo.source.wavelength_max = data_point
	375	self.current_datainfo.source.wavelength_max_unit = unit
[c94280c]	376	elif (key == u'wavelength_min'
	377	and self.parent_class == u'SASsource'):
[5e906207]	378	self.current_datainfo.source.wavelength_min = data_point
	379	self.current_datainfo.source.wavelength_min_unit = unit
[c94280c]	380	elif (key == u'incident_wavelength_spread'
	381	and self.parent_class == u'SASsource'):
[082239e]	382	self.current_datainfo.source.wavelength_spread = \
	383	data_point
	384	self.current_datainfo.source.wavelength_spread_unit = \
	385	unit
[c94280c]	386	elif (key == u'beam_size_x'
	387	and self.parent_class == u'SASsource'):
[5e906207]	388	self.current_datainfo.source.beam_size.x = data_point
	389	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	390	elif (key == u'beam_size_y'
	391	and self.parent_class == u'SASsource'):
[5e906207]	392	self.current_datainfo.source.beam_size.y = data_point
	393	self.current_datainfo.source.beam_size_unit = unit
[c94280c]	394	elif (key == u'beam_shape'
	395	and self.parent_class == u'SASsource'):
[5e906207]	396	self.current_datainfo.source.beam_shape = data_point
[c94280c]	397	elif (key == u'radiation'
	398	and self.parent_class == u'SASsource'):
[d72567e]	399	self.current_datainfo.source.radiation = data_point
[c94280c]	400	elif (key == u'transmission'
	401	and self.parent_class == u'SASdata'):
[d72567e]	402	self.current_datainfo.sample.transmission = data_point
[68aa210]	403
[082239e]	404	# Everything else goes in meta_data
[68aa210]	405	else:
[082239e]	406	new_key = self._create_unique_key(
	407	self.current_datainfo.meta_data, key)
[d72567e]	408	self.current_datainfo.meta_data[new_key] = data_point
[68aa210]	409
	410	else:
[082239e]	411	# I don't know if this reachable code
[68aa210]	412	self.errors.add("ShouldNeverHappenException")
	413
[d72567e]	414	def add_intermediate(self):
[ad52d31]	415	"""
[082239e]	416	This method stores any intermediate objects within the final data set
	417	after fully reading the set.
[ad52d31]	418
[082239e]	419	:param parent: The NXclass name for the h5py Group object that just
	420	finished being processed
[ad52d31]	421	"""
	422
[d72567e]	423	if self.parent_class == u'SASprocess':
	424	self.current_datainfo.process.append(self.process)
[ad52d31]	425	self.process = Process()
[d72567e]	426	elif self.parent_class == u'SASdetector':
	427	self.current_datainfo.detector.append(self.detector)
[ad52d31]	428	self.detector = Detector()
[d72567e]	429	elif self.parent_class == u'SAStransmission_spectrum':
	430	self.current_datainfo.trans_spectrum.append(self.trans_spectrum)
[ad52d31]	431	self.trans_spectrum = TransmissionSpectrum()
[d72567e]	432	elif self.parent_class == u'SAScollimation':
	433	self.current_datainfo.collimation.append(self.collimation)
[ad52d31]	434	self.collimation = Collimation()
[d72567e]	435	elif self.parent_class == u'SASaperture':
[ad52d31]	436	self.collimation.aperture.append(self.aperture)
	437	self.aperture = Aperture()
[d72567e]	438	elif self.parent_class == u'SASdata':
[082239e]	439	if isinstance(self.current_dataset, plottable_2D):
[d72567e]	440	self.data2d.append(self.current_dataset)
[082239e]	441	elif isinstance(self.current_dataset, plottable_1D):
[d72567e]	442	self.data1d.append(self.current_dataset)
[68aa210]	443
	444	def final_data_cleanup(self):
	445	"""
[082239e]	446	Does some final cleanup and formatting on self.current_datainfo and
	447	all data1D and data2D objects and then combines the data and info into
	448	Data1D and Data2D objects
[68aa210]	449	"""
[082239e]	450	# Type cast data arrays to float64
[d72567e]	451	if len(self.current_datainfo.trans_spectrum) > 0:
[ad52d31]	452	spectrum_list = []
[d72567e]	453	for spectrum in self.current_datainfo.trans_spectrum:
[ad52d31]	454	spectrum.transmission = np.delete(spectrum.transmission, [0])
	455	spectrum.transmission = spectrum.transmission.astype(np.float64)
[082239e]	456	spectrum.transmission_deviation = np.delete(
	457	spectrum.transmission_deviation, [0])
	458	spectrum.transmission_deviation = \
	459	spectrum.transmission_deviation.astype(np.float64)
[ad52d31]	460	spectrum.wavelength = np.delete(spectrum.wavelength, [0])
	461	spectrum.wavelength = spectrum.wavelength.astype(np.float64)
[d72567e]	462	if len(spectrum.transmission) > 0:
	463	spectrum_list.append(spectrum)
	464	self.current_datainfo.trans_spectrum = spectrum_list
[68aa210]	465
[082239e]	466	# Append errors to dataset and reset class errors
[d72567e]	467	self.current_datainfo.errors = self.errors
[68aa210]	468	self.errors.clear()
	469
[082239e]	470	# Combine all plottables with datainfo and append each to output
	471	# Type cast data arrays to float64 and find min/max as appropriate
[d72567e]	472	for dataset in self.data2d:
	473	zeros = np.ones(dataset.data.size, dtype=bool)
	474	try:
[082239e]	475	for i in range(0, dataset.mask.size - 1):
[d72567e]	476	zeros[i] = dataset.mask[i]
	477	except:
	478	self.errors.add(sys.exc_value)
	479	dataset.mask = zeros
[082239e]	480	# Calculate the actual Q matrix
[d72567e]	481	try:
	482	if dataset.q_data.size <= 1:
[54544637]	483	dataset.q_data = np.sqrt(dataset.qx_data
	484	* dataset.qx_data
	485	+ dataset.qy_data
	486	* dataset.qy_data)
[d72567e]	487	except:
	488	dataset.q_data = None
[ac370c5]	489
	490	if dataset.data.ndim == 2:
	491	(n_rows, n_cols) = dataset.data.shape
[479799c]	492	dataset.y_bins = dataset.qy_data[0::n_cols]
[ac370c5]	493	dataset.x_bins = dataset.qx_data[:n_cols]
	494	dataset.data = dataset.data.flatten()
[9d786e5]	495	self.current_dataset = dataset
	496	self.send_to_output()
[d72567e]	497
	498	for dataset in self.data1d:
[9d786e5]	499	self.current_dataset = dataset
	500	self.send_to_output()
[d72567e]	501
[68aa210]	502	def add_data_set(self, key=""):
	503	"""
[082239e]	504	Adds the current_dataset to the list of outputs after preforming final
	505	processing on the data and then calls a private method to generate a
	506	new data set.
[68aa210]	507
	508	:param key: NeXus group name for current tree level
	509	"""
[d72567e]	510
	511	if self.current_datainfo and self.current_dataset:
[68aa210]	512	self.final_data_cleanup()
[d72567e]	513	self.data1d = []
	514	self.data2d = []
	515	self.current_datainfo = DataInfo()
[68aa210]	516
[54ba66e]	517
[082239e]	518	def _initialize_new_data_set(self, parent_list=None):
[68aa210]	519	"""
[082239e]	520	A private class method to generate a new 1D or 2D data object based on
	521	the type of data within the set. Outside methods should call
	522	add_data_set() to be sure any existing data is stored properly.
[68aa210]	523
[d72567e]	524	:param parent_list: List of names of parent elements
[68aa210]	525	"""
[d72567e]	526
	527	if parent_list is None:
	528	parent_list = []
	529	if self._find_intermediate(parent_list, "Qx"):
	530	self.current_dataset = plottable_2D()
[68aa210]	531	else:
	532	x = np.array(0)
	533	y = np.array(0)
[d72567e]	534	self.current_dataset = plottable_1D(x, y)
	535	self.current_datainfo.filename = self.raw_data.filename
[68aa210]	536
[d72567e]	537	def _find_intermediate(self, parent_list, basename=""):
[ad52d31]	538	"""
[082239e]	539	A private class used to find an entry by either using a direct key or
	540	knowing the approximate basename.
[ad52d31]	541
[082239e]	542	:param parent_list: List of parents nodes in the HDF5 file
[d72567e]	543	:param basename: Approximate name of an entry to search for
[ad52d31]	544	:return:
	545	"""
[d72567e]	546
	547	entry = False
	548	key_prog = re.compile(basename)
	549	top = self.raw_data
	550	for parent in parent_list:
	551	top = top.get(parent)
	552	for key in top.keys():
[082239e]	553	if key_prog.match(key):
[d72567e]	554	entry = True
	555	break
[ad52d31]	556	return entry
	557
[68aa210]	558	def _create_unique_key(self, dictionary, name, numb=0):
	559	"""
	560	Create a unique key value for any dictionary to prevent overwriting
	561	Recurses until a unique key value is found.
	562
	563	:param dictionary: A dictionary with any number of entries
	564	:param name: The index of the item to be added to dictionary
	565	:param numb: The number to be appended to the name, starts at 0
[d72567e]	566	:return: The new name for the dictionary entry
[68aa210]	567	"""
	568	if dictionary.get(name) is not None:
	569	numb += 1
	570	name = name.split("_")[0]
	571	name += "_{0}".format(numb)
	572	name = self._create_unique_key(dictionary, name, numb)
[d398285]	573	return name
	574
	575	def _get_unit(self, value):
	576	"""
	577	Find the unit for a particular value within the h5py dictionary
	578
	579	:param value: attribute dictionary for a particular value set
[d72567e]	580	:return: unit for the value passed to the method
[d398285]	581	"""
[5c5e7fd]	582	unit = h5attr(value, u'units')
[54544637]	583	if unit is None:
[5c5e7fd]	584	unit = h5attr(value, u'unit')
[082239e]	585	# Convert the unit formats
[d398285]	586	if unit == "1/A":
	587	unit = "A^{-1}"
	588	elif unit == "1/cm":
	589	unit = "cm^{-1}"
[54ba66e]	590	return unit

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py @ 5ae083b

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