cansas_reader.py @ 15fd91b

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since 15fd91b was 158cb9e, checked in by Piotr Rozyczko <rozyczko@…>, 8 years ago
Added compatibility with save/load projects and analysis.
Property mode set to `100644`
File size: 60.6 KB

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

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 15fd91b

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