cansas_reader.py @ c221349

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since c221349 was c221349, checked in by krzywon, 7 years ago
Split unit axis and label on "\|" and then strip whitespace.
Property mode set to `100644`
File size: 70.4 KB

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1	"""
2	CanSAS data reader - new recursive cansas_version.
3	"""
4	############################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#If you use DANSE applications to do scientific research that leads to
9	#publication, we ask that you acknowledge the use of the software with the
10	#following sentence:
11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
12	#copyright 2008,2009 University of Tennessee
13	#############################################################################
14
15	import logging
16	import numpy as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
23	plottable_1D, plottable_2D
24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
25	Detector, Process, Aperture
26	from sas.sascalc.dataloader.data_info import \
27	combine_data_info_with_plottable as combine_data
28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
31
32	# The following 2 imports ARE used. Do not remove either.
33	import xml.dom.minidom
34	from xml.dom.minidom import parseString
35
36	PREPROCESS = "xmlpreprocess"
37	ENCODING = "encoding"
38	RUN_NAME_DEFAULT = "None"
39	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
40	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
41	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
42	"as much of the data as possible.\n\n"
43	HAS_CONVERTER = True
44	try:
45	from sas.sascalc.data_util.nxsunit import Converter
46	except ImportError:
47	HAS_CONVERTER = False
48
49	CONSTANTS = CansasConstants()
50	CANSAS_FORMAT = CONSTANTS.format
51	CANSAS_NS = CONSTANTS.names
52	ALLOW_ALL = True
53
54	class Reader(XMLreader):
55	"""
56	Class to load cansas 1D XML files
57
58	:Dependencies:
59	The CanSAS reader requires PyXML 0.8.4 or later.
60	"""
61	# CanSAS version - defaults to version 1.0
62	cansas_version = "1.0"
63	base_ns = "{cansas1d/1.0}"
64	cansas_defaults = None
65	type_name = "canSAS"
66	invalid = True
67	frm = ""
68	# Log messages and errors
69	logging = None
70	errors = set()
71	# Namespace hierarchy for current xml_file object
72	names = None
73	ns_list = None
74	# Temporary storage location for loading multiple data sets in a single file
75	current_datainfo = None
76	current_dataset = None
77	current_data1d = None
78	data = None
79	# List of data1D objects to be sent back to SasView
80	output = None
81	# Wildcards
82	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
83	# List of allowed extensions
84	ext = ['.xml', '.XML', '.svs', '.SVS']
85	# Flag to bypass extension check
86	allow_all = True
87
88	def reset_state(self):
89	"""
90	Resets the class state to a base case when loading a new data file so previous
91	data files do not appear a second time
92	"""
93	self.current_datainfo = None
94	self.current_dataset = None
95	self.current_data1d = None
96	self.data = []
97	self.process = Process()
98	self.transspectrum = TransmissionSpectrum()
99	self.aperture = Aperture()
100	self.collimation = Collimation()
101	self.detector = Detector()
102	self.names = []
103	self.cansas_defaults = {}
104	self.output = []
105	self.ns_list = None
106	self.logging = []
107	self.encoding = None
108
109	def read(self, xml_file, schema_path="", invalid=True):
110	"""
111	Validate and read in an xml_file file in the canSAS format.
112
113	:param xml_file: A canSAS file path in proper XML format
114	:param schema_path: A file path to an XML schema to validate the xml_file against
115	"""
116	# For every file loaded, reset everything to a base state
117	self.reset_state()
118	self.invalid = invalid
119	# Check that the file exists
120	if os.path.isfile(xml_file):
121	basename, extension = os.path.splitext(os.path.basename(xml_file))
122	# If the file type is not allowed, return nothing
123	if extension in self.ext or self.allow_all:
124	# Get the file location of
125	self.load_file_and_schema(xml_file, schema_path)
126	self.add_data_set()
127	# Try to load the file, but raise an error if unable to.
128	# Check the file matches the XML schema
129	try:
130	self.is_cansas(extension)
131	self.invalid = False
132	# Get each SASentry from XML file and add it to a list.
133	entry_list = self.xmlroot.xpath(
134	'/ns:SASroot/ns:SASentry',
135	namespaces={'ns': self.cansas_defaults.get("ns")})
136	self.names.append("SASentry")
137
138	# Get all preprocessing events and encoding
139	self.set_processing_instructions()
140
141	# Parse each <SASentry> item
142	for entry in entry_list:
143	# Create a new DataInfo object for every <SASentry>
144
145	# Set the file name and then parse the entry.
146	self.current_datainfo.filename = basename + extension
147	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
148	self.current_datainfo.meta_data[PREPROCESS] = \
149	self.processing_instructions
150
151	# Parse the XML SASentry
152	self._parse_entry(entry)
153	# Combine datasets with datainfo
154	self.add_data_set()
155	except RuntimeError:
156	# If the file does not match the schema, raise this error
157	invalid_xml = self.find_invalid_xml()
158	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
159	self.errors.add(invalid_xml)
160	# Try again with an invalid CanSAS schema, that requires only a data set in each
161	base_name = xml_reader.__file__
162	base_name = base_name.replace("\\", "/")
163	base = base_name.split("/sas/")[0]
164	if self.cansas_version == "1.1":
165	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
166	else:
167	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
168	self.set_schema(invalid_schema)
169	try:
170	if self.invalid:
171	if self.is_cansas():
172	self.output = self.read(xml_file, invalid_schema, False)
173	else:
174	raise RuntimeError
175	else:
176	raise RuntimeError
177	except RuntimeError:
178	x = np.zeros(1)
179	y = np.zeros(1)
180	self.current_data1d = Data1D(x,y)
181	self.current_data1d.errors = self.errors
182	return [self.current_data1d]
183	else:
184	self.output.append("Not a valid file path.")
185	# Return a list of parsed entries that dataloader can manage
186	return self.output
187
188	def _parse_entry(self, dom, recurse=False):
189	"""
190	Parse a SASEntry - new recursive method for parsing the dom of
191	the CanSAS data format. This will allow multiple data files
192	and extra nodes to be read in simultaneously.
193
194	:param dom: dom object with a namespace base of names
195	"""
196
197	if not self._is_call_local() and not recurse:
198	self.reset_state()
199	self.add_data_set()
200	self.names.append("SASentry")
201	self.parent_class = "SASentry"
202	self._check_for_empty_data()
203	self.base_ns = "{0}{1}{2}".format("{", \
204	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
205
206	# Go through each child in the parent element
207	for node in dom:
208	attr = node.attrib
209	name = attr.get("name", "")
210	type = attr.get("type", "")
211	# Get the element name and set the current names level
212	tagname = node.tag.replace(self.base_ns, "")
213	tagname_original = tagname
214	# Skip this iteration when loading in save state information
215	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
216	continue
217
218	# Get where to store content
219	self.names.append(tagname_original)
220	self.ns_list = CONSTANTS.iterate_namespace(self.names)
221	# If the element is a child element, recurse
222	if len(node.getchildren()) > 0:
223	self.parent_class = tagname_original
224	if tagname == 'SASdata':
225	self._initialize_new_data_set(node)
226	if isinstance(self.current_dataset, plottable_2D):
227	x_bins = attr.get("x_bins", "")
228	y_bins = attr.get("y_bins", "")
229	if x_bins is not "" and y_bins is not "":
230	self.current_dataset.shape = (x_bins, y_bins)
231	else:
232	self.current_dataset.shape = ()
233	# Recursion step to access data within the group
234	self._parse_entry(node, True)
235	if tagname == "SASsample":
236	self.current_datainfo.sample.name = name
237	elif tagname == "beam_size":
238	self.current_datainfo.source.beam_size_name = name
239	elif tagname == "SAScollimation":
240	self.collimation.name = name
241	elif tagname == "aperture":
242	self.aperture.name = name
243	self.aperture.type = type
244	self.add_intermediate()
245	else:
246	if isinstance(self.current_dataset, plottable_2D):
247	data_point = node.text
248	unit = attr.get('unit', '')
249	else:
250	data_point, unit = self._get_node_value(node, tagname)
251
252	# If this is a dataset, store the data appropriately
253	if tagname == 'Run':
254	self.current_datainfo.run_name[data_point] = name
255	self.current_datainfo.run.append(data_point)
256	elif tagname == 'Title':
257	self.current_datainfo.title = data_point
258	elif tagname == 'SASnote':
259	self.current_datainfo.notes.append(data_point)
260
261	# I and Q - 1D data
262	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
263	unit_list = unit.split("\|")
264	if len(unit_list) > 1:
265	self.current_dataset.yaxis(unit_list[0].strip(),
266	unit_list[1].strip())
267	else:
268	self.current_dataset.yaxis("Intensity", unit)
269	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
270	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
271	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
272	elif tagname == 'Q':
273	unit_list = unit.split("\|")
274	if len(unit_list) > 1:
275	self.current_dataset.xaxis(unit_list[0].strip(),
276	unit_list[1].strip())
277	else:
278	self.current_dataset.xaxis("Q", unit)
279	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
280	elif tagname == 'Qdev':
281	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
282	elif tagname == 'dQw':
283	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
284	elif tagname == 'dQl':
285	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
286	elif tagname == 'Qmean':
287	pass
288	elif tagname == 'Shadowfactor':
289	pass
290	elif tagname == 'Sesans':
291	self.current_datainfo.isSesans = bool(data_point)
292	elif tagname == 'zacceptance':
293	self.current_datainfo.sample.zacceptance = (data_point, unit)
294
295	# I and Qx, Qy - 2D data
296	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
297	self.current_dataset.yaxis("Intensity", unit)
298	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
299	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
300	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
301	elif tagname == 'Qx':
302	self.current_dataset.xaxis("Qx", unit)
303	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
304	elif tagname == 'Qy':
305	self.current_dataset.yaxis("Qy", unit)
306	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
307	elif tagname == 'Qxdev':
308	self.current_dataset.xaxis("Qxdev", unit)
309	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
310	elif tagname == 'Qydev':
311	self.current_dataset.yaxis("Qydev", unit)
312	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
313	elif tagname == 'Mask':
314	inter = [item == "1" for item in data_point.split(",")]
315	self.current_dataset.mask = np.asarray(inter, dtype=bool)
316
317	# Sample Information
318	elif tagname == 'ID' and self.parent_class == 'SASsample':
319	self.current_datainfo.sample.ID = data_point
320	elif tagname == 'Title' and self.parent_class == 'SASsample':
321	self.current_datainfo.sample.name = data_point
322	elif tagname == 'thickness' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.thickness = data_point
324	self.current_datainfo.sample.thickness_unit = unit
325	elif tagname == 'transmission' and self.parent_class == 'SASsample':
326	self.current_datainfo.sample.transmission = data_point
327	elif tagname == 'temperature' and self.parent_class == 'SASsample':
328	self.current_datainfo.sample.temperature = data_point
329	self.current_datainfo.sample.temperature_unit = unit
330	elif tagname == 'details' and self.parent_class == 'SASsample':
331	self.current_datainfo.sample.details.append(data_point)
332	elif tagname == 'x' and self.parent_class == 'position':
333	self.current_datainfo.sample.position.x = data_point
334	self.current_datainfo.sample.position_unit = unit
335	elif tagname == 'y' and self.parent_class == 'position':
336	self.current_datainfo.sample.position.y = data_point
337	self.current_datainfo.sample.position_unit = unit
338	elif tagname == 'z' and self.parent_class == 'position':
339	self.current_datainfo.sample.position.z = data_point
340	self.current_datainfo.sample.position_unit = unit
341	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
342	self.current_datainfo.sample.orientation.x = data_point
343	self.current_datainfo.sample.orientation_unit = unit
344	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
345	self.current_datainfo.sample.orientation.y = data_point
346	self.current_datainfo.sample.orientation_unit = unit
347	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
348	self.current_datainfo.sample.orientation.z = data_point
349	self.current_datainfo.sample.orientation_unit = unit
350
351	# Instrumental Information
352	elif tagname == 'name' and self.parent_class == 'SASinstrument':
353	self.current_datainfo.instrument = data_point
354	# Detector Information
355	elif tagname == 'name' and self.parent_class == 'SASdetector':
356	self.detector.name = data_point
357	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
358	self.detector.distance = data_point
359	self.detector.distance_unit = unit
360	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
361	self.detector.slit_length = data_point
362	self.detector.slit_length_unit = unit
363	elif tagname == 'x' and self.parent_class == 'offset':
364	self.detector.offset.x = data_point
365	self.detector.offset_unit = unit
366	elif tagname == 'y' and self.parent_class == 'offset':
367	self.detector.offset.y = data_point
368	self.detector.offset_unit = unit
369	elif tagname == 'z' and self.parent_class == 'offset':
370	self.detector.offset.z = data_point
371	self.detector.offset_unit = unit
372	elif tagname == 'x' and self.parent_class == 'beam_center':
373	self.detector.beam_center.x = data_point
374	self.detector.beam_center_unit = unit
375	elif tagname == 'y' and self.parent_class == 'beam_center':
376	self.detector.beam_center.y = data_point
377	self.detector.beam_center_unit = unit
378	elif tagname == 'z' and self.parent_class == 'beam_center':
379	self.detector.beam_center.z = data_point
380	self.detector.beam_center_unit = unit
381	elif tagname == 'x' and self.parent_class == 'pixel_size':
382	self.detector.pixel_size.x = data_point
383	self.detector.pixel_size_unit = unit
384	elif tagname == 'y' and self.parent_class == 'pixel_size':
385	self.detector.pixel_size.y = data_point
386	self.detector.pixel_size_unit = unit
387	elif tagname == 'z' and self.parent_class == 'pixel_size':
388	self.detector.pixel_size.z = data_point
389	self.detector.pixel_size_unit = unit
390	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
391	self.detector.orientation.x = data_point
392	self.detector.orientation_unit = unit
393	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
394	self.detector.orientation.y = data_point
395	self.detector.orientation_unit = unit
396	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
397	self.detector.orientation.z = data_point
398	self.detector.orientation_unit = unit
399	# Collimation and Aperture
400	elif tagname == 'length' and self.parent_class == 'SAScollimation':
401	self.collimation.length = data_point
402	self.collimation.length_unit = unit
403	elif tagname == 'name' and self.parent_class == 'SAScollimation':
404	self.collimation.name = data_point
405	elif tagname == 'distance' and self.parent_class == 'aperture':
406	self.aperture.distance = data_point
407	self.aperture.distance_unit = unit
408	elif tagname == 'x' and self.parent_class == 'size':
409	self.aperture.size.x = data_point
410	self.collimation.size_unit = unit
411	elif tagname == 'y' and self.parent_class == 'size':
412	self.aperture.size.y = data_point
413	self.collimation.size_unit = unit
414	elif tagname == 'z' and self.parent_class == 'size':
415	self.aperture.size.z = data_point
416	self.collimation.size_unit = unit
417
418	# Process Information
419	elif tagname == 'name' and self.parent_class == 'SASprocess':
420	self.process.name = data_point
421	elif tagname == 'description' and self.parent_class == 'SASprocess':
422	self.process.description = data_point
423	elif tagname == 'date' and self.parent_class == 'SASprocess':
424	try:
425	self.process.date = datetime.datetime.fromtimestamp(data_point)
426	except:
427	self.process.date = data_point
428	elif tagname == 'SASprocessnote':
429	self.process.notes.append(data_point)
430	elif tagname == 'term' and self.parent_class == 'SASprocess':
431	unit = attr.get("unit", "")
432	dic = {}
433	dic["name"] = name
434	dic["value"] = data_point
435	dic["unit"] = unit
436	self.process.term.append(dic)
437
438	# Transmission Spectrum
439	elif tagname == 'T' and self.parent_class == 'Tdata':
440	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
441	self.transspectrum.transmission_unit = unit
442	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
443	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
444	self.transspectrum.transmission_deviation_unit = unit
445	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
446	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
447	self.transspectrum.wavelength_unit = unit
448
449	# Source Information
450	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
451	self.current_datainfo.source.wavelength = data_point
452	self.current_datainfo.source.wavelength_unit = unit
453	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
454	self.current_datainfo.source.wavelength_min = data_point
455	self.current_datainfo.source.wavelength_min_unit = unit
456	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
457	self.current_datainfo.source.wavelength_max = data_point
458	self.current_datainfo.source.wavelength_max_unit = unit
459	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
460	self.current_datainfo.source.wavelength_spread = data_point
461	self.current_datainfo.source.wavelength_spread_unit = unit
462	elif tagname == 'x' and self.parent_class == 'beam_size':
463	self.current_datainfo.source.beam_size.x = data_point
464	self.current_datainfo.source.beam_size_unit = unit
465	elif tagname == 'y' and self.parent_class == 'beam_size':
466	self.current_datainfo.source.beam_size.y = data_point
467	self.current_datainfo.source.beam_size_unit = unit
468	elif tagname == 'z' and self.parent_class == 'pixel_size':
469	self.current_datainfo.source.data_point.z = data_point
470	self.current_datainfo.source.beam_size_unit = unit
471	elif tagname == 'radiation' and self.parent_class == 'SASsource':
472	self.current_datainfo.source.radiation = data_point
473	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
474	self.current_datainfo.source.beam_shape = data_point
475
476	# Everything else goes in meta_data
477	else:
478	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
479	self.current_datainfo.meta_data[new_key] = data_point
480
481	self.names.remove(tagname_original)
482	length = 0
483	if len(self.names) > 1:
484	length = len(self.names) - 1
485	self.parent_class = self.names[length]
486	if not self._is_call_local() and not recurse:
487	self.frm = ""
488	self.add_data_set()
489	empty = None
490	return self.output[0], empty
491
492
493	def _is_call_local(self):
494	"""
495
496	"""
497	if self.frm == "":
498	inter = inspect.stack()
499	self.frm = inter[2]
500	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
501	mod_name = mod_name.replace(".py", "")
502	mod = mod_name.split("sas/")
503	mod_name = mod[1]
504	if mod_name != "sascalc/dataloader/readers/cansas_reader":
505	return False
506	return True
507
508	def is_cansas(self, ext="xml"):
509	"""
510	Checks to see if the xml file is a CanSAS file
511
512	:param ext: The file extension of the data file
513	"""
514	if self.validate_xml():
515	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
516	value = self.xmlroot.get(name)
517	if CANSAS_NS.get(self.cansas_version).get("ns") == \
518	value.rsplit(" ")[0]:
519	return True
520	if ext == "svs":
521	return True
522	raise RuntimeError
523
524	def load_file_and_schema(self, xml_file, schema_path=""):
525	"""
526	Loads the file and associates a schema, if a schema is passed in or if one already exists
527
528	:param xml_file: The xml file path sent to Reader.read
529	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
530	"""
531	base_name = xml_reader.__file__
532	base_name = base_name.replace("\\", "/")
533	base = base_name.split("/sas/")[0]
534
535	# Load in xml file and get the cansas version from the header
536	self.set_xml_file(xml_file)
537	self.cansas_version = self.xmlroot.get("version", "1.0")
538
539	# Generic values for the cansas file based on the version
540	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
541	if schema_path == "":
542	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
543	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
544
545	# Link a schema to the XML file.
546	self.set_schema(schema_path)
547
548	def add_data_set(self):
549	"""
550	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
551	private method to generate a new data set.
552
553	:param key: NeXus group name for current tree level
554	"""
555
556	if self.current_datainfo and self.current_dataset:
557	self._final_cleanup()
558	self.data = []
559	self.current_datainfo = DataInfo()
560
561	def _initialize_new_data_set(self, node=None):
562	"""
563	A private class method to generate a new 1D data object.
564	Outside methods should call add_data_set() to be sure any existing data is stored properly.
565
566	:param node: XML node to determine if 1D or 2D data
567	"""
568	x = np.array(0)
569	y = np.array(0)
570	for child in node:
571	if child.tag.replace(self.base_ns, "") == "Idata":
572	for i_child in child:
573	if i_child.tag.replace(self.base_ns, "") == "Qx":
574	self.current_dataset = plottable_2D()
575	return
576	self.current_dataset = plottable_1D(x, y)
577
578	def add_intermediate(self):
579	"""
580	This method stores any intermediate objects within the final data set after fully reading the set.
581
582	:param parent: The NXclass name for the h5py Group object that just finished being processed
583	"""
584
585	if self.parent_class == 'SASprocess':
586	self.current_datainfo.process.append(self.process)
587	self.process = Process()
588	elif self.parent_class == 'SASdetector':
589	self.current_datainfo.detector.append(self.detector)
590	self.detector = Detector()
591	elif self.parent_class == 'SAStransmission_spectrum':
592	self.current_datainfo.trans_spectrum.append(self.transspectrum)
593	self.transspectrum = TransmissionSpectrum()
594	elif self.parent_class == 'SAScollimation':
595	self.current_datainfo.collimation.append(self.collimation)
596	self.collimation = Collimation()
597	elif self.parent_class == 'aperture':
598	self.collimation.aperture.append(self.aperture)
599	self.aperture = Aperture()
600	elif self.parent_class == 'SASdata':
601	self._check_for_empty_resolution()
602	self.data.append(self.current_dataset)
603
604	def _final_cleanup(self):
605	"""
606	Final cleanup of the Data1D object to be sure it has all the
607	appropriate information needed for perspectives
608	"""
609
610	# Append errors to dataset and reset class errors
611	self.current_datainfo.errors = set()
612	for error in self.errors:
613	self.current_datainfo.errors.add(error)
614	self.errors.clear()
615
616	# Combine all plottables with datainfo and append each to output
617	# Type cast data arrays to float64 and find min/max as appropriate
618	for dataset in self.data:
619	if isinstance(dataset, plottable_1D):
620	if dataset.x is not None:
621	dataset.x = np.delete(dataset.x, [0])
622	dataset.x = dataset.x.astype(np.float64)
623	dataset.xmin = np.min(dataset.x)
624	dataset.xmax = np.max(dataset.x)
625	if dataset.y is not None:
626	dataset.y = np.delete(dataset.y, [0])
627	dataset.y = dataset.y.astype(np.float64)
628	dataset.ymin = np.min(dataset.y)
629	dataset.ymax = np.max(dataset.y)
630	if dataset.dx is not None:
631	dataset.dx = np.delete(dataset.dx, [0])
632	dataset.dx = dataset.dx.astype(np.float64)
633	if dataset.dxl is not None:
634	dataset.dxl = np.delete(dataset.dxl, [0])
635	dataset.dxl = dataset.dxl.astype(np.float64)
636	if dataset.dxw is not None:
637	dataset.dxw = np.delete(dataset.dxw, [0])
638	dataset.dxw = dataset.dxw.astype(np.float64)
639	if dataset.dy is not None:
640	dataset.dy = np.delete(dataset.dy, [0])
641	dataset.dy = dataset.dy.astype(np.float64)
642	np.trim_zeros(dataset.x)
643	np.trim_zeros(dataset.y)
644	np.trim_zeros(dataset.dy)
645	elif isinstance(dataset, plottable_2D):
646	dataset.data = dataset.data.astype(np.float64)
647	dataset.qx_data = dataset.qx_data.astype(np.float64)
648	dataset.xmin = np.min(dataset.qx_data)
649	dataset.xmax = np.max(dataset.qx_data)
650	dataset.qy_data = dataset.qy_data.astype(np.float64)
651	dataset.ymin = np.min(dataset.qy_data)
652	dataset.ymax = np.max(dataset.qy_data)
653	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
654	+ dataset.qy_data * dataset.qy_data)
655	if dataset.err_data is not None:
656	dataset.err_data = dataset.err_data.astype(np.float64)
657	if dataset.dqx_data is not None:
658	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
659	if dataset.dqy_data is not None:
660	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
661	if dataset.mask is not None:
662	dataset.mask = dataset.mask.astype(dtype=bool)
663
664	if len(dataset.shape) == 2:
665	n_rows, n_cols = dataset.shape
666	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
667	dataset.x_bins = dataset.qx_data[:int(n_cols)]
668	dataset.data = dataset.data.flatten()
669	else:
670	dataset.y_bins = []
671	dataset.x_bins = []
672	dataset.data = dataset.data.flatten()
673
674	final_dataset = combine_data(dataset, self.current_datainfo)
675	self.output.append(final_dataset)
676
677	def _create_unique_key(self, dictionary, name, numb=0):
678	"""
679	Create a unique key value for any dictionary to prevent overwriting
680	Recurse until a unique key value is found.
681
682	:param dictionary: A dictionary with any number of entries
683	:param name: The index of the item to be added to dictionary
684	:param numb: The number to be appended to the name, starts at 0
685	"""
686	if dictionary.get(name) is not None:
687	numb += 1
688	name = name.split("_")[0]
689	name += "_{0}".format(numb)
690	name = self._create_unique_key(dictionary, name, numb)
691	return name
692
693	def _get_node_value(self, node, tagname):
694	"""
695	Get the value of a node and any applicable units
696
697	:param node: The XML node to get the value of
698	:param tagname: The tagname of the node
699	"""
700	#Get the text from the node and convert all whitespace to spaces
701	units = ''
702	node_value = node.text
703	if node_value is not None:
704	node_value = ' '.join(node_value.split())
705	else:
706	node_value = ""
707
708	# If the value is a float, compile with units.
709	if self.ns_list.ns_datatype == "float":
710	# If an empty value is given, set as zero.
711	if node_value is None or node_value.isspace() \
712	or node_value.lower() == "nan":
713	node_value = "0.0"
714	#Convert the value to the base units
715	node_value, units = self._unit_conversion(node, tagname, node_value)
716
717	# If the value is a timestamp, convert to a datetime object
718	elif self.ns_list.ns_datatype == "timestamp":
719	if node_value is None or node_value.isspace():
720	pass
721	else:
722	try:
723	node_value = \
724	datetime.datetime.fromtimestamp(node_value)
725	except ValueError:
726	node_value = None
727	return node_value, units
728
729	def _unit_conversion(self, node, tagname, node_value):
730	"""
731	A unit converter method used to convert the data included in the file
732	to the default units listed in data_info
733
734	:param node: XML node
735	:param tagname: name of the node
736	:param node_value: The value of the current dom node
737	"""
738	attr = node.attrib
739	value_unit = ''
740	err_msg = None
741	default_unit = None
742	if not isinstance(node_value, float):
743	node_value = float(node_value)
744	if 'unit' in attr and attr.get('unit') is not None:
745	try:
746	local_unit = attr['unit']
747	unitname = self.ns_list.current_level.get("unit", "")
748	if "SASdetector" in self.names:
749	save_in = "detector"
750	elif "aperture" in self.names:
751	save_in = "aperture"
752	elif "SAScollimation" in self.names:
753	save_in = "collimation"
754	elif "SAStransmission_spectrum" in self.names:
755	save_in = "transspectrum"
756	elif "SASdata" in self.names:
757	x = np.zeros(1)
758	y = np.zeros(1)
759	self.current_data1d = Data1D(x, y)
760	save_in = "current_data1d"
761	elif "SASsource" in self.names:
762	save_in = "current_datainfo.source"
763	elif "SASsample" in self.names:
764	save_in = "current_datainfo.sample"
765	elif "SASprocess" in self.names:
766	save_in = "process"
767	else:
768	save_in = "current_datainfo"
769	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
770	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
771	and local_unit.lower() != "none":
772	if HAS_CONVERTER == True:
773	# Check local units - bad units raise KeyError
774	data_conv_q = Converter(local_unit)
775	value_unit = default_unit
776	node_value = data_conv_q(node_value, units=default_unit)
777	else:
778	value_unit = local_unit
779	err_msg = "Unit converter is not available.\n"
780	else:
781	value_unit = local_unit
782	except KeyError:
783	err_msg = "CanSAS reader: unexpected "
784	err_msg += "\"{0}\" unit [{1}]; "
785	err_msg = err_msg.format(tagname, local_unit)
786	err_msg += "expecting [{0}]".format(default_unit)
787	value_unit = local_unit
788	except:
789	err_msg = "CanSAS reader: unknown error converting "
790	err_msg += "\"{0}\" unit [{1}]"
791	err_msg = err_msg.format(tagname, local_unit)
792	value_unit = local_unit
793	elif 'unit' in attr:
794	value_unit = attr['unit']
795	if err_msg:
796	self.errors.add(err_msg)
797	return node_value, value_unit
798
799	def _check_for_empty_data(self):
800	"""
801	Creates an empty data set if no data is passed to the reader
802
803	:param data1d: presumably a Data1D object
804	"""
805	if self.current_dataset == None:
806	x_vals = np.empty(0)
807	y_vals = np.empty(0)
808	dx_vals = np.empty(0)
809	dy_vals = np.empty(0)
810	dxl = np.empty(0)
811	dxw = np.empty(0)
812	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
813	self.current_dataset.dxl = dxl
814	self.current_dataset.dxw = dxw
815
816	def _check_for_empty_resolution(self):
817	"""
818	A method to check all resolution data sets are the same size as I and Q
819	"""
820	if isinstance(self.current_dataset, plottable_1D):
821	dql_exists = False
822	dqw_exists = False
823	dq_exists = False
824	di_exists = False
825	if self.current_dataset.dxl is not None:
826	dql_exists = True
827	if self.current_dataset.dxw is not None:
828	dqw_exists = True
829	if self.current_dataset.dx is not None:
830	dq_exists = True
831	if self.current_dataset.dy is not None:
832	di_exists = True
833	if dqw_exists and not dql_exists:
834	array_size = self.current_dataset.dxw.size - 1
835	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
836	np.zeros([array_size]))
837	elif dql_exists and not dqw_exists:
838	array_size = self.current_dataset.dxl.size - 1
839	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
840	np.zeros([array_size]))
841	elif not dql_exists and not dqw_exists and not dq_exists:
842	array_size = self.current_dataset.x.size - 1
843	self.current_dataset.dx = np.append(self.current_dataset.dx,
844	np.zeros([array_size]))
845	if not di_exists:
846	array_size = self.current_dataset.y.size - 1
847	self.current_dataset.dy = np.append(self.current_dataset.dy,
848	np.zeros([array_size]))
849	elif isinstance(self.current_dataset, plottable_2D):
850	dqx_exists = False
851	dqy_exists = False
852	di_exists = False
853	mask_exists = False
854	if self.current_dataset.dqx_data is not None:
855	dqx_exists = True
856	if self.current_dataset.dqy_data is not None:
857	dqy_exists = True
858	if self.current_dataset.err_data is not None:
859	di_exists = True
860	if self.current_dataset.mask is not None:
861	mask_exists = True
862	if not dqy_exists:
863	array_size = self.current_dataset.qy_data.size - 1
864	self.current_dataset.dqy_data = np.append(
865	self.current_dataset.dqy_data, np.zeros([array_size]))
866	if not dqx_exists:
867	array_size = self.current_dataset.qx_data.size - 1
868	self.current_dataset.dqx_data = np.append(
869	self.current_dataset.dqx_data, np.zeros([array_size]))
870	if not di_exists:
871	array_size = self.current_dataset.data.size - 1
872	self.current_dataset.err_data = np.append(
873	self.current_dataset.err_data, np.zeros([array_size]))
874	if not mask_exists:
875	array_size = self.current_dataset.data.size - 1
876	self.current_dataset.mask = np.append(
877	self.current_dataset.mask,
878	np.ones([array_size] ,dtype=bool))
879
880	####### All methods below are for writing CanSAS XML files #######
881
882	def write(self, filename, datainfo):
883	"""
884	Write the content of a Data1D as a CanSAS XML file
885
886	:param filename: name of the file to write
887	:param datainfo: Data1D object
888	"""
889	# Create XML document
890	doc, _ = self._to_xml_doc(datainfo)
891	# Write the file
892	file_ref = open(filename, 'w')
893	if self.encoding == None:
894	self.encoding = "UTF-8"
895	doc.write(file_ref, encoding=self.encoding,
896	pretty_print=True, xml_declaration=True)
897	file_ref.close()
898
899	def _to_xml_doc(self, datainfo):
900	"""
901	Create an XML document to contain the content of a Data1D
902
903	:param datainfo: Data1D object
904	"""
905	is_2d = False
906	if issubclass(datainfo.__class__, Data2D):
907	is_2d = True
908
909	# Get PIs and create root element
910	pi_string = self._get_pi_string()
911	# Define namespaces and create SASroot object
912	main_node = self._create_main_node()
913	# Create ElementTree, append SASroot and apply processing instructions
914	base_string = pi_string + self.to_string(main_node)
915	base_element = self.create_element_from_string(base_string)
916	doc = self.create_tree(base_element)
917	# Create SASentry Element
918	entry_node = self.create_element("SASentry")
919	root = doc.getroot()
920	root.append(entry_node)
921
922	# Add Title to SASentry
923	self.write_node(entry_node, "Title", datainfo.title)
924	# Add Run to SASentry
925	self._write_run_names(datainfo, entry_node)
926	# Add Data info to SASEntry
927	if is_2d:
928	self._write_data_2d(datainfo, entry_node)
929	else:
930	self._write_data(datainfo, entry_node)
931	# Transmission Spectrum Info
932	self._write_trans_spectrum(datainfo, entry_node)
933	# Sample info
934	self._write_sample_info(datainfo, entry_node)
935	# Instrument info
936	instr = self._write_instrument(datainfo, entry_node)
937	# Source
938	self._write_source(datainfo, instr)
939	# Collimation
940	self._write_collimation(datainfo, instr)
941	# Detectors
942	self._write_detectors(datainfo, instr)
943	# Processes info
944	self._write_process_notes(datainfo, entry_node)
945	# Note info
946	self._write_notes(datainfo, entry_node)
947	# Return the document, and the SASentry node associated with
948	# the data we just wrote
949	# If the calling function was not the cansas reader, return a minidom
950	# object rather than an lxml object.
951	self.frm = inspect.stack()[1]
952	doc, entry_node = self._check_origin(entry_node, doc)
953	return doc, entry_node
954
955	def write_node(self, parent, name, value, attr=None):
956	"""
957	:param doc: document DOM
958	:param parent: parent node
959	:param name: tag of the element
960	:param value: value of the child text node
961	:param attr: attribute dictionary
962
963	:return: True if something was appended, otherwise False
964	"""
965	if value is not None:
966	parent = self.ebuilder(parent, name, value, attr)
967	return True
968	return False
969
970	def _get_pi_string(self):
971	"""
972	Creates the processing instructions header for writing to file
973	"""
974	pis = self.return_processing_instructions()
975	if len(pis) > 0:
976	pi_tree = self.create_tree(pis[0])
977	i = 1
978	for i in range(1, len(pis) - 1):
979	pi_tree = self.append(pis[i], pi_tree)
980	pi_string = self.to_string(pi_tree)
981	else:
982	pi_string = ""
983	return pi_string
984
985	def _create_main_node(self):
986	"""
987	Creates the primary xml header used when writing to file
988	"""
989	xsi = "http://www.w3.org/2001/XMLSchema-instance"
990	version = self.cansas_version
991	n_s = CANSAS_NS.get(version).get("ns")
992	if version == "1.1":
993	url = "http://www.cansas.org/formats/1.1/"
994	else:
995	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
996	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
997	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
998	"version" : version}
999	nsmap = {'xsi' : xsi, None: n_s}
1000
1001	main_node = self.create_element("{" + n_s + "}SASroot",
1002	attrib=attrib, nsmap=nsmap)
1003	return main_node
1004
1005	def _write_run_names(self, datainfo, entry_node):
1006	"""
1007	Writes the run names to the XML file
1008
1009	:param datainfo: The Data1D object the information is coming from
1010	:param entry_node: lxml node ElementTree object to be appended to
1011	"""
1012	if datainfo.run == None or datainfo.run == []:
1013	datainfo.run.append(RUN_NAME_DEFAULT)
1014	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1015	for item in datainfo.run:
1016	runname = {}
1017	if item in datainfo.run_name and \
1018	len(str(datainfo.run_name[item])) > 1:
1019	runname = {'name': datainfo.run_name[item]}
1020	self.write_node(entry_node, "Run", item, runname)
1021
1022	def _write_data(self, datainfo, entry_node):
1023	"""
1024	Writes 1D I and Q data to the XML file
1025
1026	:param datainfo: The Data1D object the information is coming from
1027	:param entry_node: lxml node ElementTree object to be appended to
1028	"""
1029	node = self.create_element("SASdata")
1030	self.append(node, entry_node)
1031
1032	for i in range(len(datainfo.x)):
1033	point = self.create_element("Idata")
1034	node.append(point)
1035	self.write_node(point, "Q", datainfo.x[i],
1036	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1037	if len(datainfo.y) >= i:
1038	self.write_node(point, "I", datainfo.y[i],
1039	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1040	if datainfo.dy is not None and len(datainfo.dy) > i:
1041	self.write_node(point, "Idev", datainfo.dy[i],
1042	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1043	if datainfo.dx is not None and len(datainfo.dx) > i:
1044	self.write_node(point, "Qdev", datainfo.dx[i],
1045	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1046	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1047	self.write_node(point, "dQw", datainfo.dxw[i],
1048	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1049	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1050	self.write_node(point, "dQl", datainfo.dxl[i],
1051	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1052	if datainfo.isSesans:
1053	sesans = self.create_element("Sesans")
1054	sesans.text = str(datainfo.isSesans)
1055	node.append(sesans)
1056	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1057	{'unit': datainfo.sample.zacceptance[1]})
1058
1059
1060	def _write_data_2d(self, datainfo, entry_node):
1061	"""
1062	Writes 2D data to the XML file
1063
1064	:param datainfo: The Data2D object the information is coming from
1065	:param entry_node: lxml node ElementTree object to be appended to
1066	"""
1067	attr = {}
1068	if datainfo.data.shape:
1069	attr["x_bins"] = str(len(datainfo.x_bins))
1070	attr["y_bins"] = str(len(datainfo.y_bins))
1071	node = self.create_element("SASdata", attr)
1072	self.append(node, entry_node)
1073
1074	point = self.create_element("Idata")
1075	node.append(point)
1076	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1077	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1078	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1079
1080	self.write_node(point, "Qx", qx,
1081	{'unit': datainfo._xunit})
1082	self.write_node(point, "Qy", qy,
1083	{'unit': datainfo._yunit})
1084	self.write_node(point, "I", intensity,
1085	{'unit': datainfo._zunit})
1086	if datainfo.err_data is not None:
1087	err = ','.join([str(datainfo.err_data[i]) for i in
1088	xrange(len(datainfo.err_data))])
1089	self.write_node(point, "Idev", err,
1090	{'unit': datainfo._zunit})
1091	if datainfo.dqy_data is not None:
1092	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1093	xrange(len(datainfo.dqy_data))])
1094	self.write_node(point, "Qydev", dqy,
1095	{'unit': datainfo._yunit})
1096	if datainfo.dqx_data is not None:
1097	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1098	xrange(len(datainfo.dqx_data))])
1099	self.write_node(point, "Qxdev", dqx,
1100	{'unit': datainfo._xunit})
1101	if datainfo.mask is not None:
1102	mask = ','.join(
1103	["1" if datainfo.mask[i] else "0"
1104	for i in xrange(len(datainfo.mask))])
1105	self.write_node(point, "Mask", mask)
1106
1107	def _write_trans_spectrum(self, datainfo, entry_node):
1108	"""
1109	Writes the transmission spectrum data to the XML file
1110
1111	:param datainfo: The Data1D object the information is coming from
1112	:param entry_node: lxml node ElementTree object to be appended to
1113	"""
1114	for i in range(len(datainfo.trans_spectrum)):
1115	spectrum = datainfo.trans_spectrum[i]
1116	node = self.create_element("SAStransmission_spectrum",
1117	{"name" : spectrum.name})
1118	self.append(node, entry_node)
1119	if isinstance(spectrum.timestamp, datetime.datetime):
1120	node.setAttribute("timestamp", spectrum.timestamp)
1121	for i in range(len(spectrum.wavelength)):
1122	point = self.create_element("Tdata")
1123	node.append(point)
1124	self.write_node(point, "Lambda", spectrum.wavelength[i],
1125	{'unit': spectrum.wavelength_unit})
1126	self.write_node(point, "T", spectrum.transmission[i],
1127	{'unit': spectrum.transmission_unit})
1128	if spectrum.transmission_deviation != None \
1129	and len(spectrum.transmission_deviation) >= i:
1130	self.write_node(point, "Tdev",
1131	spectrum.transmission_deviation[i],
1132	{'unit':
1133	spectrum.transmission_deviation_unit})
1134
1135	def _write_sample_info(self, datainfo, entry_node):
1136	"""
1137	Writes the sample information to the XML file
1138
1139	:param datainfo: The Data1D object the information is coming from
1140	:param entry_node: lxml node ElementTree object to be appended to
1141	"""
1142	sample = self.create_element("SASsample")
1143	if datainfo.sample.name is not None:
1144	self.write_attribute(sample, "name",
1145	str(datainfo.sample.name))
1146	self.append(sample, entry_node)
1147	self.write_node(sample, "ID", str(datainfo.sample.ID))
1148	self.write_node(sample, "thickness", datainfo.sample.thickness,
1149	{"unit": datainfo.sample.thickness_unit})
1150	self.write_node(sample, "transmission", datainfo.sample.transmission)
1151	self.write_node(sample, "temperature", datainfo.sample.temperature,
1152	{"unit": datainfo.sample.temperature_unit})
1153
1154	pos = self.create_element("position")
1155	written = self.write_node(pos,
1156	"x",
1157	datainfo.sample.position.x,
1158	{"unit": datainfo.sample.position_unit})
1159	written = written \| self.write_node( \
1160	pos, "y", datainfo.sample.position.y,
1161	{"unit": datainfo.sample.position_unit})
1162	written = written \| self.write_node( \
1163	pos, "z", datainfo.sample.position.z,
1164	{"unit": datainfo.sample.position_unit})
1165	if written == True:
1166	self.append(pos, sample)
1167
1168	ori = self.create_element("orientation")
1169	written = self.write_node(ori, "roll",
1170	datainfo.sample.orientation.x,
1171	{"unit": datainfo.sample.orientation_unit})
1172	written = written \| self.write_node( \
1173	ori, "pitch", datainfo.sample.orientation.y,
1174	{"unit": datainfo.sample.orientation_unit})
1175	written = written \| self.write_node( \
1176	ori, "yaw", datainfo.sample.orientation.z,
1177	{"unit": datainfo.sample.orientation_unit})
1178	if written == True:
1179	self.append(ori, sample)
1180
1181	for item in datainfo.sample.details:
1182	self.write_node(sample, "details", item)
1183
1184	def _write_instrument(self, datainfo, entry_node):
1185	"""
1186	Writes the instrumental information to the XML file
1187
1188	:param datainfo: The Data1D object the information is coming from
1189	:param entry_node: lxml node ElementTree object to be appended to
1190	"""
1191	instr = self.create_element("SASinstrument")
1192	self.append(instr, entry_node)
1193	self.write_node(instr, "name", datainfo.instrument)
1194	return instr
1195
1196	def _write_source(self, datainfo, instr):
1197	"""
1198	Writes the source information to the XML file
1199
1200	:param datainfo: The Data1D object the information is coming from
1201	:param instr: instrument node to be appended to
1202	"""
1203	source = self.create_element("SASsource")
1204	if datainfo.source.name is not None:
1205	self.write_attribute(source, "name",
1206	str(datainfo.source.name))
1207	self.append(source, instr)
1208	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1209	datainfo.source.radiation = "neutron"
1210	self.write_node(source, "radiation", datainfo.source.radiation)
1211
1212	size = self.create_element("beam_size")
1213	if datainfo.source.beam_size_name is not None:
1214	self.write_attribute(size, "name",
1215	str(datainfo.source.beam_size_name))
1216	written = self.write_node( \
1217	size, "x", datainfo.source.beam_size.x,
1218	{"unit": datainfo.source.beam_size_unit})
1219	written = written \| self.write_node( \
1220	size, "y", datainfo.source.beam_size.y,
1221	{"unit": datainfo.source.beam_size_unit})
1222	written = written \| self.write_node( \
1223	size, "z", datainfo.source.beam_size.z,
1224	{"unit": datainfo.source.beam_size_unit})
1225	if written == True:
1226	self.append(size, source)
1227
1228	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1229	self.write_node(source, "wavelength",
1230	datainfo.source.wavelength,
1231	{"unit": datainfo.source.wavelength_unit})
1232	self.write_node(source, "wavelength_min",
1233	datainfo.source.wavelength_min,
1234	{"unit": datainfo.source.wavelength_min_unit})
1235	self.write_node(source, "wavelength_max",
1236	datainfo.source.wavelength_max,
1237	{"unit": datainfo.source.wavelength_max_unit})
1238	self.write_node(source, "wavelength_spread",
1239	datainfo.source.wavelength_spread,
1240	{"unit": datainfo.source.wavelength_spread_unit})
1241
1242	def _write_collimation(self, datainfo, instr):
1243	"""
1244	Writes the collimation information to the XML file
1245
1246	:param datainfo: The Data1D object the information is coming from
1247	:param instr: lxml node ElementTree object to be appended to
1248	"""
1249	if datainfo.collimation == [] or datainfo.collimation == None:
1250	coll = Collimation()
1251	datainfo.collimation.append(coll)
1252	for item in datainfo.collimation:
1253	coll = self.create_element("SAScollimation")
1254	if item.name is not None:
1255	self.write_attribute(coll, "name", str(item.name))
1256	self.append(coll, instr)
1257
1258	self.write_node(coll, "length", item.length,
1259	{"unit": item.length_unit})
1260
1261	for aperture in item.aperture:
1262	apert = self.create_element("aperture")
1263	if aperture.name is not None:
1264	self.write_attribute(apert, "name", str(aperture.name))
1265	if aperture.type is not None:
1266	self.write_attribute(apert, "type", str(aperture.type))
1267	self.append(apert, coll)
1268
1269	size = self.create_element("size")
1270	if aperture.size_name is not None:
1271	self.write_attribute(size, "name",
1272	str(aperture.size_name))
1273	written = self.write_node(size, "x", aperture.size.x,
1274	{"unit": aperture.size_unit})
1275	written = written \| self.write_node( \
1276	size, "y", aperture.size.y,
1277	{"unit": aperture.size_unit})
1278	written = written \| self.write_node( \
1279	size, "z", aperture.size.z,
1280	{"unit": aperture.size_unit})
1281	if written == True:
1282	self.append(size, apert)
1283
1284	self.write_node(apert, "distance", aperture.distance,
1285	{"unit": aperture.distance_unit})
1286
1287	def _write_detectors(self, datainfo, instr):
1288	"""
1289	Writes the detector information to the XML file
1290
1291	:param datainfo: The Data1D object the information is coming from
1292	:param inst: lxml instrument node to be appended to
1293	"""
1294	if datainfo.detector == None or datainfo.detector == []:
1295	det = Detector()
1296	det.name = ""
1297	datainfo.detector.append(det)
1298
1299	for item in datainfo.detector:
1300	det = self.create_element("SASdetector")
1301	written = self.write_node(det, "name", item.name)
1302	written = written \| self.write_node(det, "SDD", item.distance,
1303	{"unit": item.distance_unit})
1304	if written == True:
1305	self.append(det, instr)
1306
1307	off = self.create_element("offset")
1308	written = self.write_node(off, "x", item.offset.x,
1309	{"unit": item.offset_unit})
1310	written = written \| self.write_node(off, "y", item.offset.y,
1311	{"unit": item.offset_unit})
1312	written = written \| self.write_node(off, "z", item.offset.z,
1313	{"unit": item.offset_unit})
1314	if written == True:
1315	self.append(off, det)
1316
1317	ori = self.create_element("orientation")
1318	written = self.write_node(ori, "roll", item.orientation.x,
1319	{"unit": item.orientation_unit})
1320	written = written \| self.write_node(ori, "pitch",
1321	item.orientation.y,
1322	{"unit": item.orientation_unit})
1323	written = written \| self.write_node(ori, "yaw",
1324	item.orientation.z,
1325	{"unit": item.orientation_unit})
1326	if written == True:
1327	self.append(ori, det)
1328
1329	center = self.create_element("beam_center")
1330	written = self.write_node(center, "x", item.beam_center.x,
1331	{"unit": item.beam_center_unit})
1332	written = written \| self.write_node(center, "y",
1333	item.beam_center.y,
1334	{"unit": item.beam_center_unit})
1335	written = written \| self.write_node(center, "z",
1336	item.beam_center.z,
1337	{"unit": item.beam_center_unit})
1338	if written == True:
1339	self.append(center, det)
1340
1341	pix = self.create_element("pixel_size")
1342	written = self.write_node(pix, "x", item.pixel_size.x,
1343	{"unit": item.pixel_size_unit})
1344	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1345	{"unit": item.pixel_size_unit})
1346	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1347	{"unit": item.pixel_size_unit})
1348	if written == True:
1349	self.append(pix, det)
1350	self.write_node(det, "slit_length", item.slit_length,
1351	{"unit": item.slit_length_unit})
1352
1353
1354	def _write_process_notes(self, datainfo, entry_node):
1355	"""
1356	Writes the process notes to the XML file
1357
1358	:param datainfo: The Data1D object the information is coming from
1359	:param entry_node: lxml node ElementTree object to be appended to
1360
1361	"""
1362	for item in datainfo.process:
1363	node = self.create_element("SASprocess")
1364	self.append(node, entry_node)
1365	self.write_node(node, "name", item.name)
1366	self.write_node(node, "date", item.date)
1367	self.write_node(node, "description", item.description)
1368	for term in item.term:
1369	if isinstance(term, list):
1370	value = term['value']
1371	del term['value']
1372	elif isinstance(term, dict):
1373	value = term.get("value")
1374	del term['value']
1375	else:
1376	value = term
1377	self.write_node(node, "term", value, term)
1378	for note in item.notes:
1379	self.write_node(node, "SASprocessnote", note)
1380	if len(item.notes) == 0:
1381	self.write_node(node, "SASprocessnote", "")
1382
1383	def _write_notes(self, datainfo, entry_node):
1384	"""
1385	Writes the notes to the XML file and creates an empty note if none
1386	exist
1387
1388	:param datainfo: The Data1D object the information is coming from
1389	:param entry_node: lxml node ElementTree object to be appended to
1390
1391	"""
1392	if len(datainfo.notes) == 0:
1393	node = self.create_element("SASnote")
1394	self.append(node, entry_node)
1395	else:
1396	for item in datainfo.notes:
1397	node = self.create_element("SASnote")
1398	self.write_text(node, item)
1399	self.append(node, entry_node)
1400
1401	def _check_origin(self, entry_node, doc):
1402	"""
1403	Return the document, and the SASentry node associated with
1404	the data we just wrote.
1405	If the calling function was not the cansas reader, return a minidom
1406	object rather than an lxml object.
1407
1408	:param entry_node: lxml node ElementTree object to be appended to
1409	:param doc: entire xml tree
1410	"""
1411	if not self.frm:
1412	self.frm = inspect.stack()[1]
1413	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1414	mod_name = mod_name.replace(".py", "")
1415	mod = mod_name.split("sas/")
1416	mod_name = mod[1]
1417	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1418	string = self.to_string(doc, pretty_print=False)
1419	doc = parseString(string)
1420	node_name = entry_node.tag
1421	node_list = doc.getElementsByTagName(node_name)
1422	entry_node = node_list.item(0)
1423	return doc, entry_node
1424
1425	# DO NOT REMOVE - used in saving and loading panel states.
1426	def _store_float(self, location, node, variable, storage, optional=True):
1427	"""
1428	Get the content of a xpath location and store
1429	the result. Check that the units are compatible
1430	with the destination. The value is expected to
1431	be a float.
1432
1433	The xpath location might or might not exist.
1434	If it does not exist, nothing is done
1435
1436	:param location: xpath location to fetch
1437	:param node: node to read the data from
1438	:param variable: name of the data member to store it in [string]
1439	:param storage: data object that has the 'variable' data member
1440	:param optional: if True, no exception will be raised
1441	if unit conversion can't be done
1442
1443	:raise ValueError: raised when the units are not recognized
1444	"""
1445	entry = get_content(location, node)
1446	try:
1447	value = float(entry.text)
1448	except:
1449	value = None
1450
1451	if value is not None:
1452	# If the entry has units, check to see that they are
1453	# compatible with what we currently have in the data object
1454	units = entry.get('unit')
1455	if units is not None:
1456	toks = variable.split('.')
1457	local_unit = None
1458	exec "local_unit = storage.%s_unit" % toks[0]
1459	if local_unit != None and units.lower() != local_unit.lower():
1460	if HAS_CONVERTER == True:
1461	try:
1462	conv = Converter(units)
1463	exec "storage.%s = %g" % \
1464	(variable, conv(value, units=local_unit))
1465	except:
1466	_, exc_value, _ = sys.exc_info()
1467	err_mess = "CanSAS reader: could not convert"
1468	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1469	% (variable, units, local_unit, exc_value)
1470	self.errors.add(err_mess)
1471	if optional:
1472	logging.info(err_mess)
1473	else:
1474	raise ValueError, err_mess
1475	else:
1476	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1477	% (variable, units)
1478	err_mess += " expecting [%s]" % local_unit
1479	self.errors.add(err_mess)
1480	if optional:
1481	logging.info(err_mess)
1482	else:
1483	raise ValueError, err_mess
1484	else:
1485	exec "storage.%s = value" % variable
1486	else:
1487	exec "storage.%s = value" % variable
1488
1489	# DO NOT REMOVE - used in saving and loading panel states.
1490	def _store_content(self, location, node, variable, storage):
1491	"""
1492	Get the content of a xpath location and store
1493	the result. The value is treated as a string.
1494
1495	The xpath location might or might not exist.
1496	If it does not exist, nothing is done
1497
1498	:param location: xpath location to fetch
1499	:param node: node to read the data from
1500	:param variable: name of the data member to store it in [string]
1501	:param storage: data object that has the 'variable' data member
1502
1503	:return: return a list of errors
1504	"""
1505	entry = get_content(location, node)
1506	if entry is not None and entry.text is not None:
1507	exec "storage.%s = entry.text.strip()" % variable
1508
1509
1510	# DO NOT REMOVE Called by outside packages:
1511	# sas.sasgui.perspectives.invariant.invariant_state
1512	# sas.sasgui.perspectives.fitting.pagestate
1513	def get_content(location, node):
1514	"""
1515	Get the first instance of the content of a xpath location.
1516
1517	:param location: xpath location
1518	:param node: node to start at
1519
1520	:return: Element, or None
1521	"""
1522	nodes = node.xpath(location,
1523	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1524	if len(nodes) > 0:
1525	return nodes[0]
1526	else:
1527	return None
1528
1529	# DO NOT REMOVE Called by outside packages:
1530	# sas.sasgui.perspectives.fitting.pagestate
1531	def write_node(doc, parent, name, value, attr=None):
1532	"""
1533	:param doc: document DOM
1534	:param parent: parent node
1535	:param name: tag of the element
1536	:param value: value of the child text node
1537	:param attr: attribute dictionary
1538
1539	:return: True if something was appended, otherwise False
1540	"""
1541	if attr is None:
1542	attr = {}
1543	if value is not None:
1544	node = doc.createElement(name)
1545	node.appendChild(doc.createTextNode(str(value)))
1546	for item in attr:
1547	node.setAttribute(item, attr[item])
1548	parent.appendChild(node)
1549	return True
1550	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ c221349

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