cansas_reader.py @ 67b0a99

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 67b0a99 was 0639476, checked in by GitHub <noreply@…>, 8 years ago

Merge pull request #12 from lewisodriscoll/file-converter

Implement File Converter Tool

Property mode set to 100644

File size: 61.4 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	frm = ""
65	## Log messages and errors
66	logging = None
67	errors = set()
68	## Namespace hierarchy for current xml_file object
69	names = None
70	ns_list = None
71	## Temporary storage location for loading multiple data sets in a single file
72	current_datainfo = None
73	current_dataset = None
74	current_data1d = None
75	data = None
76	## List of data1D objects to be sent back to SasView
77	output = None
78	## Wildcards
79	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
80	## List of allowed extensions
81	ext = ['.xml', '.XML', '.svs', '.SVS']
82	## Flag to bypass extension check
83	allow_all = True
84
85	def reset_state(self):
86	"""
87	Resets the class state to a base case when loading a new data file so previous
88	data files do not appear a second time
89	"""
90	self.current_datainfo = None
91	self.current_dataset = None
92	self.current_data1d = None
93	self.data = []
94	self.process = Process()
95	self.transspectrum = TransmissionSpectrum()
96	self.aperture = Aperture()
97	self.collimation = Collimation()
98	self.detector = Detector()
99	self.names = []
100	self.cansas_defaults = {}
101	self.output = []
102	self.ns_list = None
103	self.logging = []
104	self.encoding = None
105
106	def read(self, xml_file, schema_path="", invalid=True):
107	"""
108	Validate and read in an xml_file file in the canSAS format.
109
110	:param xml_file: A canSAS file path in proper XML format
111	:param schema_path: A file path to an XML schema to validate the xml_file against
112	"""
113	# For every file loaded, reset everything to a base state
114	self.reset_state()
115	self.invalid = invalid
116	# Check that the file exists
117	if os.path.isfile(xml_file):
118	basename, extension = os.path.splitext(os.path.basename(xml_file))
119	# If the file type is not allowed, return nothing
120	if extension in self.ext or self.allow_all:
121	# Get the file location of
122	self.load_file_and_schema(xml_file, schema_path)
123	self.add_data_set()
124	# Try to load the file, but raise an error if unable to.
125	# Check the file matches the XML schema
126	try:
127	self.is_cansas(extension)
128	self.invalid = False
129	# Get each SASentry from XML file and add it to a list.
130	entry_list = self.xmlroot.xpath(
131	'/ns:SASroot/ns:SASentry',
132	namespaces={'ns': self.cansas_defaults.get("ns")})
133	self.names.append("SASentry")
134
135	# Get all preprocessing events and encoding
136	self.set_processing_instructions()
137
138	# Parse each <SASentry> item
139	for entry in entry_list:
140	# Create a new DataInfo object for every <SASentry>
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, recurse=False):
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	if not self._is_call_local() and not recurse:
195	self.reset_state()
196	self.add_data_set()
197	self.names.append("SASentry")
198	self.parent_class = "SASentry"
199	self._check_for_empty_data()
200	self.base_ns = "{0}{1}{2}".format("{", \
201	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
202
203	# Go through each child in the parent element
204	for node in dom:
205	attr = node.attrib
206	name = attr.get("name", "")
207	type = attr.get("type", "")
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, True)
225	if tagname == "SASsample":
226	self.current_datainfo.sample.name = name
227	elif tagname == "beam_size":
228	self.current_datainfo.source.beam_size_name = name
229	elif tagname == "SAScollimation":
230	self.collimation.name = name
231	elif tagname == "aperture":
232	self.aperture.name = name
233	self.aperture.type = type
234	self.add_intermediate()
235	else:
236	data_point, unit = self._get_node_value(node, tagname)
237
238	## If this is a dataset, store the data appropriately
239	if tagname == 'Run':
240	self.current_datainfo.run_name[data_point] = name
241	self.current_datainfo.run.append(data_point)
242	elif tagname == 'Title':
243	self.current_datainfo.title = data_point
244	elif tagname == 'SASnote':
245	self.current_datainfo.notes.append(data_point)
246
247	## I and Q Data
248	elif tagname == 'I':
249	self.current_dataset.yaxis("Intensity", unit)
250	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
251	elif tagname == 'Idev':
252	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
253	elif tagname == 'Q':
254	self.current_dataset.xaxis("Q", unit)
255	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
256	elif tagname == 'Qdev':
257	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
258	elif tagname == 'dQw':
259	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
260	elif tagname == 'dQl':
261	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
262	elif tagname == 'Qmean':
263	pass
264	elif tagname == 'Shadowfactor':
265	pass
266
267	## Sample Information
268	elif tagname == 'ID' and self.parent_class == 'SASsample':
269	self.current_datainfo.sample.ID = data_point
270	elif tagname == 'Title' and self.parent_class == 'SASsample':
271	self.current_datainfo.sample.name = data_point
272	elif tagname == 'thickness' and self.parent_class == 'SASsample':
273	self.current_datainfo.sample.thickness = data_point
274	self.current_datainfo.sample.thickness_unit = unit
275	elif tagname == 'transmission' and self.parent_class == 'SASsample':
276	self.current_datainfo.sample.transmission = data_point
277	elif tagname == 'temperature' and self.parent_class == 'SASsample':
278	self.current_datainfo.sample.temperature = data_point
279	self.current_datainfo.sample.temperature_unit = unit
280	elif tagname == 'details' and self.parent_class == 'SASsample':
281	self.current_datainfo.sample.details.append(data_point)
282	elif tagname == 'x' and self.parent_class == 'position':
283	self.current_datainfo.sample.position.x = data_point
284	self.current_datainfo.sample.position_unit = unit
285	elif tagname == 'y' and self.parent_class == 'position':
286	self.current_datainfo.sample.position.y = data_point
287	self.current_datainfo.sample.position_unit = unit
288	elif tagname == 'z' and self.parent_class == 'position':
289	self.current_datainfo.sample.position.z = data_point
290	self.current_datainfo.sample.position_unit = unit
291	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
292	self.current_datainfo.sample.orientation.x = data_point
293	self.current_datainfo.sample.orientation_unit = unit
294	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
295	self.current_datainfo.sample.orientation.y = data_point
296	self.current_datainfo.sample.orientation_unit = unit
297	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
298	self.current_datainfo.sample.orientation.z = data_point
299	self.current_datainfo.sample.orientation_unit = unit
300
301	## Instrumental Information
302	elif tagname == 'name' and self.parent_class == 'SASinstrument':
303	self.current_datainfo.instrument = data_point
304	## Detector Information
305	elif tagname == 'name' and self.parent_class == 'SASdetector':
306	self.detector.name = data_point
307	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
308	self.detector.distance = data_point
309	self.detector.distance_unit = unit
310	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
311	self.detector.slit_length = data_point
312	self.detector.slit_length_unit = unit
313	elif tagname == 'x' and self.parent_class == 'offset':
314	self.detector.offset.x = data_point
315	self.detector.offset_unit = unit
316	elif tagname == 'y' and self.parent_class == 'offset':
317	self.detector.offset.y = data_point
318	self.detector.offset_unit = unit
319	elif tagname == 'z' and self.parent_class == 'offset':
320	self.detector.offset.z = data_point
321	self.detector.offset_unit = unit
322	elif tagname == 'x' and self.parent_class == 'beam_center':
323	self.detector.beam_center.x = data_point
324	self.detector.beam_center_unit = unit
325	elif tagname == 'y' and self.parent_class == 'beam_center':
326	self.detector.beam_center.y = data_point
327	self.detector.beam_center_unit = unit
328	elif tagname == 'z' and self.parent_class == 'beam_center':
329	self.detector.beam_center.z = data_point
330	self.detector.beam_center_unit = unit
331	elif tagname == 'x' and self.parent_class == 'pixel_size':
332	self.detector.pixel_size.x = data_point
333	self.detector.pixel_size_unit = unit
334	elif tagname == 'y' and self.parent_class == 'pixel_size':
335	self.detector.pixel_size.y = data_point
336	self.detector.pixel_size_unit = unit
337	elif tagname == 'z' and self.parent_class == 'pixel_size':
338	self.detector.pixel_size.z = data_point
339	self.detector.pixel_size_unit = unit
340	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
341	self.detector.orientation.x = data_point
342	self.detector.orientation_unit = unit
343	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
344	self.detector.orientation.y = data_point
345	self.detector.orientation_unit = unit
346	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
347	self.detector.orientation.z = data_point
348	self.detector.orientation_unit = unit
349	## Collimation and Aperture
350	elif tagname == 'length' and self.parent_class == 'SAScollimation':
351	self.collimation.length = data_point
352	self.collimation.length_unit = unit
353	elif tagname == 'name' and self.parent_class == 'SAScollimation':
354	self.collimation.name = data_point
355	elif tagname == 'distance' and self.parent_class == 'aperture':
356	self.aperture.distance = data_point
357	self.aperture.distance_unit = unit
358	elif tagname == 'x' and self.parent_class == 'size':
359	self.aperture.size.x = data_point
360	self.collimation.size_unit = unit
361	elif tagname == 'y' and self.parent_class == 'size':
362	self.aperture.size.y = data_point
363	self.collimation.size_unit = unit
364	elif tagname == 'z' and self.parent_class == 'size':
365	self.aperture.size.z = data_point
366	self.collimation.size_unit = unit
367
368	## Process Information
369	elif tagname == 'name' and self.parent_class == 'SASprocess':
370	self.process.name = data_point
371	elif tagname == 'description' and self.parent_class == 'SASprocess':
372	self.process.description = data_point
373	elif tagname == 'date' and self.parent_class == 'SASprocess':
374	try:
375	self.process.date = datetime.datetime.fromtimestamp(data_point)
376	except:
377	self.process.date = data_point
378	elif tagname == 'SASprocessnote':
379	self.process.notes.append(data_point)
380	elif tagname == 'term' and self.parent_class == 'SASprocess':
381	unit = attr.get("unit", "")
382	dic = {}
383	dic["name"] = name
384	dic["value"] = data_point
385	dic["unit"] = unit
386	self.process.term.append(dic)
387
388	## Transmission Spectrum
389	elif tagname == 'T' and self.parent_class == 'Tdata':
390	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
391	self.transspectrum.transmission_unit = unit
392	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
393	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
394	self.transspectrum.transmission_deviation_unit = unit
395	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
396	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
397	self.transspectrum.wavelength_unit = unit
398
399	## Source Information
400	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
401	self.current_datainfo.source.wavelength = data_point
402	self.current_datainfo.source.wavelength_unit = unit
403	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
404	self.current_datainfo.source.wavelength_min = data_point
405	self.current_datainfo.source.wavelength_min_unit = unit
406	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
407	self.current_datainfo.source.wavelength_max = data_point
408	self.current_datainfo.source.wavelength_max_unit = unit
409	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
410	self.current_datainfo.source.wavelength_spread = data_point
411	self.current_datainfo.source.wavelength_spread_unit = unit
412	elif tagname == 'x' and self.parent_class == 'beam_size':
413	self.current_datainfo.source.beam_size.x = data_point
414	self.current_datainfo.source.beam_size_unit = unit
415	elif tagname == 'y' and self.parent_class == 'beam_size':
416	self.current_datainfo.source.beam_size.y = data_point
417	self.current_datainfo.source.beam_size_unit = unit
418	elif tagname == 'z' and self.parent_class == 'pixel_size':
419	self.current_datainfo.source.data_point.z = data_point
420	self.current_datainfo.source.beam_size_unit = unit
421	elif tagname == 'radiation' and self.parent_class == 'SASsource':
422	self.current_datainfo.source.radiation = data_point
423	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
424	self.current_datainfo.source.beam_shape = data_point
425
426	## Everything else goes in meta_data
427	else:
428	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
429	self.current_datainfo.meta_data[new_key] = data_point
430
431	self.names.remove(tagname_original)
432	length = 0
433	if len(self.names) > 1:
434	length = len(self.names) - 1
435	self.parent_class = self.names[length]
436	if not self._is_call_local() and not recurse:
437	self.frm = ""
438	self.add_data_set()
439	empty = None
440	if self.output[0].dx is not None:
441	self.output[0].dxl = np.empty(0)
442	self.output[0].dxw = np.empty(0)
443	else:
444	self.output[0].dx = np.empty(0)
445	return self.output[0], empty
446
447
448	def _is_call_local(self):
449	"""
450
451	"""
452	if self.frm == "":
453	inter = inspect.stack()
454	self.frm = inter[2]
455	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
456	mod_name = mod_name.replace(".py", "")
457	mod = mod_name.split("sas/")
458	mod_name = mod[1]
459	if mod_name != "sascalc/dataloader/readers/cansas_reader":
460	return False
461	return True
462
463	def is_cansas(self, ext="xml"):
464	"""
465	Checks to see if the xml file is a CanSAS file
466
467	:param ext: The file extension of the data file
468	"""
469	if self.validate_xml():
470	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
471	value = self.xmlroot.get(name)
472	if CANSAS_NS.get(self.cansas_version).get("ns") == \
473	value.rsplit(" ")[0]:
474	return True
475	if ext == "svs":
476	return True
477	raise RuntimeError
478
479	def load_file_and_schema(self, xml_file, schema_path=""):
480	"""
481	Loads the file and associates a schema, if a schema is passed in or if one already exists
482
483	:param xml_file: The xml file path sent to Reader.read
484	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
485	"""
486	base_name = xml_reader.__file__
487	base_name = base_name.replace("\\", "/")
488	base = base_name.split("/sas/")[0]
489
490	# Load in xml file and get the cansas version from the header
491	self.set_xml_file(xml_file)
492	self.cansas_version = self.xmlroot.get("version", "1.0")
493
494	# Generic values for the cansas file based on the version
495	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
496	if schema_path == "":
497	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
498	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
499
500	# Link a schema to the XML file.
501	self.set_schema(schema_path)
502
503	def add_data_set(self):
504	"""
505	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
506	private method to generate a new data set.
507
508	:param key: NeXus group name for current tree level
509	"""
510
511	if self.current_datainfo and self.current_dataset:
512	self._final_cleanup()
513	self.data = []
514	self.current_datainfo = DataInfo()
515
516	def _initialize_new_data_set(self, parent_list=None):
517	"""
518	A private class method to generate a new 1D data object.
519	Outside methods should call add_data_set() to be sure any existing data is stored properly.
520
521	:param parent_list: List of names of parent elements
522	"""
523
524	if parent_list is None:
525	parent_list = []
526	x = np.array(0)
527	y = np.array(0)
528	self.current_dataset = plottable_1D(x, y)
529
530	def add_intermediate(self):
531	"""
532	This method stores any intermediate objects within the final data set after fully reading the set.
533
534	:param parent: The NXclass name for the h5py Group object that just finished being processed
535	"""
536
537	if self.parent_class == 'SASprocess':
538	self.current_datainfo.process.append(self.process)
539	self.process = Process()
540	elif self.parent_class == 'SASdetector':
541	self.current_datainfo.detector.append(self.detector)
542	self.detector = Detector()
543	elif self.parent_class == 'SAStransmission_spectrum':
544	self.current_datainfo.trans_spectrum.append(self.transspectrum)
545	self.transspectrum = TransmissionSpectrum()
546	elif self.parent_class == 'SAScollimation':
547	self.current_datainfo.collimation.append(self.collimation)
548	self.collimation = Collimation()
549	elif self.parent_class == 'aperture':
550	self.collimation.aperture.append(self.aperture)
551	self.aperture = Aperture()
552	elif self.parent_class == 'SASdata':
553	self._check_for_empty_resolution()
554	self.data.append(self.current_dataset)
555
556	def _final_cleanup(self):
557	"""
558	Final cleanup of the Data1D object to be sure it has all the
559	appropriate information needed for perspectives
560	"""
561
562	## Append errors to dataset and reset class errors
563	self.current_datainfo.errors = set()
564	for error in self.errors:
565	self.current_datainfo.errors.add(error)
566	self.errors.clear()
567
568	## Combine all plottables with datainfo and append each to output
569	## Type cast data arrays to float64 and find min/max as appropriate
570	for dataset in self.data:
571	if dataset.x is not None:
572	dataset.x = np.delete(dataset.x, [0])
573	dataset.x = dataset.x.astype(np.float64)
574	dataset.xmin = np.min(dataset.x)
575	dataset.xmax = np.max(dataset.x)
576	if dataset.y is not None:
577	dataset.y = np.delete(dataset.y, [0])
578	dataset.y = dataset.y.astype(np.float64)
579	dataset.ymin = np.min(dataset.y)
580	dataset.ymax = np.max(dataset.y)
581	if dataset.dx is not None:
582	dataset.dx = np.delete(dataset.dx, [0])
583	dataset.dx = dataset.dx.astype(np.float64)
584	if dataset.dxl is not None:
585	dataset.dxl = np.delete(dataset.dxl, [0])
586	dataset.dxl = dataset.dxl.astype(np.float64)
587	if dataset.dxw is not None:
588	dataset.dxw = np.delete(dataset.dxw, [0])
589	dataset.dxw = dataset.dxw.astype(np.float64)
590	if dataset.dy is not None:
591	dataset.dy = np.delete(dataset.dy, [0])
592	dataset.dy = dataset.dy.astype(np.float64)
593	np.trim_zeros(dataset.x)
594	np.trim_zeros(dataset.y)
595	np.trim_zeros(dataset.dy)
596	final_dataset = combine_data(dataset, self.current_datainfo)
597	self.output.append(final_dataset)
598
599	def _create_unique_key(self, dictionary, name, numb=0):
600	"""
601	Create a unique key value for any dictionary to prevent overwriting
602	Recurse until a unique key value is found.
603
604	:param dictionary: A dictionary with any number of entries
605	:param name: The index of the item to be added to dictionary
606	:param numb: The number to be appended to the name, starts at 0
607	"""
608	if dictionary.get(name) is not None:
609	numb += 1
610	name = name.split("_")[0]
611	name += "_{0}".format(numb)
612	name = self._create_unique_key(dictionary, name, numb)
613	return name
614
615	def _get_node_value(self, node, tagname):
616	"""
617	Get the value of a node and any applicable units
618
619	:param node: The XML node to get the value of
620	:param tagname: The tagname of the node
621	"""
622	#Get the text from the node and convert all whitespace to spaces
623	units = ''
624	node_value = node.text
625	if node_value is not None:
626	node_value = ' '.join(node_value.split())
627	else:
628	node_value = ""
629
630	# If the value is a float, compile with units.
631	if self.ns_list.ns_datatype == "float":
632	# If an empty value is given, set as zero.
633	if node_value is None or node_value.isspace() \
634	or node_value.lower() == "nan":
635	node_value = "0.0"
636	#Convert the value to the base units
637	node_value, units = self._unit_conversion(node, tagname, node_value)
638
639	# If the value is a timestamp, convert to a datetime object
640	elif self.ns_list.ns_datatype == "timestamp":
641	if node_value is None or node_value.isspace():
642	pass
643	else:
644	try:
645	node_value = \
646	datetime.datetime.fromtimestamp(node_value)
647	except ValueError:
648	node_value = None
649	return node_value, units
650
651	def _unit_conversion(self, node, tagname, node_value):
652	"""
653	A unit converter method used to convert the data included in the file
654	to the default units listed in data_info
655
656	:param node: XML node
657	:param tagname: name of the node
658	:param node_value: The value of the current dom node
659	"""
660	attr = node.attrib
661	value_unit = ''
662	err_msg = None
663	default_unit = None
664	if not isinstance(node_value, float):
665	node_value = float(node_value)
666	if 'unit' in attr and attr.get('unit') is not None:
667	try:
668	local_unit = attr['unit']
669	unitname = self.ns_list.current_level.get("unit", "")
670	if "SASdetector" in self.names:
671	save_in = "detector"
672	elif "aperture" in self.names:
673	save_in = "aperture"
674	elif "SAScollimation" in self.names:
675	save_in = "collimation"
676	elif "SAStransmission_spectrum" in self.names:
677	save_in = "transspectrum"
678	elif "SASdata" in self.names:
679	x = np.zeros(1)
680	y = np.zeros(1)
681	self.current_data1d = Data1D(x, y)
682	save_in = "current_data1d"
683	elif "SASsource" in self.names:
684	save_in = "current_datainfo.source"
685	elif "SASsample" in self.names:
686	save_in = "current_datainfo.sample"
687	elif "SASprocess" in self.names:
688	save_in = "process"
689	else:
690	save_in = "current_datainfo"
691	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
692	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
693	and local_unit.lower() != "none":
694	if HAS_CONVERTER == True:
695	## Check local units - bad units raise KeyError
696	data_conv_q = Converter(local_unit)
697	value_unit = default_unit
698	node_value = data_conv_q(node_value, units=default_unit)
699	else:
700	value_unit = local_unit
701	err_msg = "Unit converter is not available.\n"
702	else:
703	value_unit = local_unit
704	except KeyError:
705	err_msg = "CanSAS reader: unexpected "
706	err_msg += "\"{0}\" unit [{1}]; "
707	err_msg = err_msg.format(tagname, local_unit)
708	err_msg += "expecting [{0}]".format(default_unit)
709	value_unit = local_unit
710	except:
711	err_msg = "CanSAS reader: unknown error converting "
712	err_msg += "\"{0}\" unit [{1}]"
713	err_msg = err_msg.format(tagname, local_unit)
714	value_unit = local_unit
715	elif 'unit' in attr:
716	value_unit = attr['unit']
717	if err_msg:
718	self.errors.add(err_msg)
719	return node_value, value_unit
720
721	def _check_for_empty_data(self):
722	"""
723	Creates an empty data set if no data is passed to the reader
724
725	:param data1d: presumably a Data1D object
726	"""
727	if self.current_dataset == None:
728	x_vals = np.empty(0)
729	y_vals = np.empty(0)
730	dx_vals = np.empty(0)
731	dy_vals = np.empty(0)
732	dxl = np.empty(0)
733	dxw = np.empty(0)
734	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
735	self.current_dataset.dxl = dxl
736	self.current_dataset.dxw = dxw
737
738	def _check_for_empty_resolution(self):
739	"""
740	A method to check all resolution data sets are the same size as I and Q
741	"""
742	dql_exists = False
743	dqw_exists = False
744	dq_exists = False
745	di_exists = False
746	if self.current_dataset.dxl is not None:
747	dql_exists = True
748	if self.current_dataset.dxw is not None:
749	dqw_exists = True
750	if self.current_dataset.dx is not None:
751	dq_exists = True
752	if self.current_dataset.dy is not None:
753	di_exists = True
754	if dqw_exists and not dql_exists:
755	array_size = self.current_dataset.dxw.size - 1
756	self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size]))
757	elif dql_exists and not dqw_exists:
758	array_size = self.current_dataset.dxl.size - 1
759	self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size]))
760	elif not dql_exists and not dqw_exists and not dq_exists:
761	array_size = self.current_dataset.x.size - 1
762	self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size]))
763	if not di_exists:
764	array_size = self.current_dataset.y.size - 1
765	self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size]))
766
767
768	####### All methods below are for writing CanSAS XML files #######
769
770
771	def write(self, filename, datainfo):
772	"""
773	Write the content of a Data1D as a CanSAS XML file
774
775	:param filename: name of the file to write
776	:param datainfo: Data1D object
777	"""
778	# Create XML document
779	doc, _ = self._to_xml_doc(datainfo)
780	# Write the file
781	file_ref = open(filename, 'w')
782	if self.encoding == None:
783	self.encoding = "UTF-8"
784	doc.write(file_ref, encoding=self.encoding,
785	pretty_print=True, xml_declaration=True)
786	file_ref.close()
787
788	def _to_xml_doc(self, datainfo):
789	"""
790	Create an XML document to contain the content of a Data1D
791
792	:param datainfo: Data1D object
793	"""
794	if not issubclass(datainfo.__class__, Data1D):
795	raise RuntimeError, "The cansas writer expects a Data1D instance"
796
797	# Get PIs and create root element
798	pi_string = self._get_pi_string()
799	# Define namespaces and create SASroot object
800	main_node = self._create_main_node()
801	# Create ElementTree, append SASroot and apply processing instructions
802	base_string = pi_string + self.to_string(main_node)
803	base_element = self.create_element_from_string(base_string)
804	doc = self.create_tree(base_element)
805	# Create SASentry Element
806	entry_node = self.create_element("SASentry")
807	root = doc.getroot()
808	root.append(entry_node)
809
810	# Add Title to SASentry
811	self.write_node(entry_node, "Title", datainfo.title)
812	# Add Run to SASentry
813	self._write_run_names(datainfo, entry_node)
814	# Add Data info to SASEntry
815	self._write_data(datainfo, entry_node)
816	# Transmission Spectrum Info
817	self._write_trans_spectrum(datainfo, entry_node)
818	# Sample info
819	self._write_sample_info(datainfo, entry_node)
820	# Instrument info
821	instr = self._write_instrument(datainfo, entry_node)
822	# Source
823	self._write_source(datainfo, instr)
824	# Collimation
825	self._write_collimation(datainfo, instr)
826	# Detectors
827	self._write_detectors(datainfo, instr)
828	# Processes info
829	self._write_process_notes(datainfo, entry_node)
830	# Note info
831	self._write_notes(datainfo, entry_node)
832	# Return the document, and the SASentry node associated with
833	# the data we just wrote
834	# If the calling function was not the cansas reader, return a minidom
835	# object rather than an lxml object.
836	self.frm = inspect.stack()[1]
837	doc, entry_node = self._check_origin(entry_node, doc)
838	return doc, entry_node
839
840	def write_node(self, parent, name, value, attr=None):
841	"""
842	:param doc: document DOM
843	:param parent: parent node
844	:param name: tag of the element
845	:param value: value of the child text node
846	:param attr: attribute dictionary
847
848	:return: True if something was appended, otherwise False
849	"""
850	if value is not None:
851	parent = self.ebuilder(parent, name, value, attr)
852	return True
853	return False
854
855	def _get_pi_string(self):
856	"""
857	Creates the processing instructions header for writing to file
858	"""
859	pis = self.return_processing_instructions()
860	if len(pis) > 0:
861	pi_tree = self.create_tree(pis[0])
862	i = 1
863	for i in range(1, len(pis) - 1):
864	pi_tree = self.append(pis[i], pi_tree)
865	pi_string = self.to_string(pi_tree)
866	else:
867	pi_string = ""
868	return pi_string
869
870	def _create_main_node(self):
871	"""
872	Creates the primary xml header used when writing to file
873	"""
874	xsi = "http://www.w3.org/2001/XMLSchema-instance"
875	version = self.cansas_version
876	n_s = CANSAS_NS.get(version).get("ns")
877	if version == "1.1":
878	url = "http://www.cansas.org/formats/1.1/"
879	else:
880	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
881	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
882	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
883	"version" : version}
884	nsmap = {'xsi' : xsi, None: n_s}
885
886	main_node = self.create_element("{" + n_s + "}SASroot",
887	attrib=attrib, nsmap=nsmap)
888	return main_node
889
890	def _write_run_names(self, datainfo, entry_node):
891	"""
892	Writes the run names to the XML file
893
894	:param datainfo: The Data1D object the information is coming from
895	:param entry_node: lxml node ElementTree object to be appended to
896	"""
897	if datainfo.run == None or datainfo.run == []:
898	datainfo.run.append(RUN_NAME_DEFAULT)
899	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
900	for item in datainfo.run:
901	runname = {}
902	if item in datainfo.run_name and \
903	len(str(datainfo.run_name[item])) > 1:
904	runname = {'name': datainfo.run_name[item]}
905	self.write_node(entry_node, "Run", item, runname)
906
907	def _write_data(self, datainfo, entry_node):
908	"""
909	Writes the I and Q data to the XML file
910
911	:param datainfo: The Data1D object the information is coming from
912	:param entry_node: lxml node ElementTree object to be appended to
913	"""
914	node = self.create_element("SASdata")
915	self.append(node, entry_node)
916
917	for i in range(len(datainfo.x)):
918	point = self.create_element("Idata")
919	node.append(point)
920	self.write_node(point, "Q", datainfo.x[i],
921	{'unit': datainfo.x_unit})
922	if len(datainfo.y) >= i:
923	self.write_node(point, "I", datainfo.y[i],
924	{'unit': datainfo.y_unit})
925	if datainfo.dy is not None and len(datainfo.dy) > i:
926	self.write_node(point, "Idev", datainfo.dy[i],
927	{'unit': datainfo.y_unit})
928	if datainfo.dx is not None and len(datainfo.dx) > i:
929	self.write_node(point, "Qdev", datainfo.dx[i],
930	{'unit': datainfo.x_unit})
931	if datainfo.dxw is not None and len(datainfo.dxw) > i:
932	self.write_node(point, "dQw", datainfo.dxw[i],
933	{'unit': datainfo.x_unit})
934	if datainfo.dxl is not None and len(datainfo.dxl) > i:
935	self.write_node(point, "dQl", datainfo.dxl[i],
936	{'unit': datainfo.x_unit})
937
938	def _write_trans_spectrum(self, datainfo, entry_node):
939	"""
940	Writes the transmission spectrum data to the XML file
941
942	:param datainfo: The Data1D object the information is coming from
943	:param entry_node: lxml node ElementTree object to be appended to
944	"""
945	for i in range(len(datainfo.trans_spectrum)):
946	spectrum = datainfo.trans_spectrum[i]
947	node = self.create_element("SAStransmission_spectrum",
948	{"name" : spectrum.name})
949	self.append(node, entry_node)
950	if isinstance(spectrum.timestamp, datetime.datetime):
951	node.setAttribute("timestamp", spectrum.timestamp)
952	for i in range(len(spectrum.wavelength)):
953	point = self.create_element("Tdata")
954	node.append(point)
955	self.write_node(point, "Lambda", spectrum.wavelength[i],
956	{'unit': spectrum.wavelength_unit})
957	self.write_node(point, "T", spectrum.transmission[i],
958	{'unit': spectrum.transmission_unit})
959	if spectrum.transmission_deviation != None \
960	and len(spectrum.transmission_deviation) >= i:
961	self.write_node(point, "Tdev",
962	spectrum.transmission_deviation[i],
963	{'unit':
964	spectrum.transmission_deviation_unit})
965
966	def _write_sample_info(self, datainfo, entry_node):
967	"""
968	Writes the sample information to the XML file
969
970	:param datainfo: The Data1D object the information is coming from
971	:param entry_node: lxml node ElementTree object to be appended to
972	"""
973	sample = self.create_element("SASsample")
974	if datainfo.sample.name is not None:
975	self.write_attribute(sample, "name",
976	str(datainfo.sample.name))
977	self.append(sample, entry_node)
978	self.write_node(sample, "ID", str(datainfo.sample.ID))
979	self.write_node(sample, "thickness", datainfo.sample.thickness,
980	{"unit": datainfo.sample.thickness_unit})
981	self.write_node(sample, "transmission", datainfo.sample.transmission)
982	self.write_node(sample, "temperature", datainfo.sample.temperature,
983	{"unit": datainfo.sample.temperature_unit})
984
985	pos = self.create_element("position")
986	written = self.write_node(pos,
987	"x",
988	datainfo.sample.position.x,
989	{"unit": datainfo.sample.position_unit})
990	written = written \| self.write_node( \
991	pos, "y", datainfo.sample.position.y,
992	{"unit": datainfo.sample.position_unit})
993	written = written \| self.write_node( \
994	pos, "z", datainfo.sample.position.z,
995	{"unit": datainfo.sample.position_unit})
996	if written == True:
997	self.append(pos, sample)
998
999	ori = self.create_element("orientation")
1000	written = self.write_node(ori, "roll",
1001	datainfo.sample.orientation.x,
1002	{"unit": datainfo.sample.orientation_unit})
1003	written = written \| self.write_node( \
1004	ori, "pitch", datainfo.sample.orientation.y,
1005	{"unit": datainfo.sample.orientation_unit})
1006	written = written \| self.write_node( \
1007	ori, "yaw", datainfo.sample.orientation.z,
1008	{"unit": datainfo.sample.orientation_unit})
1009	if written == True:
1010	self.append(ori, sample)
1011
1012	for item in datainfo.sample.details:
1013	self.write_node(sample, "details", item)
1014
1015	def _write_instrument(self, datainfo, entry_node):
1016	"""
1017	Writes the instrumental information to the XML file
1018
1019	:param datainfo: The Data1D object the information is coming from
1020	:param entry_node: lxml node ElementTree object to be appended to
1021	"""
1022	instr = self.create_element("SASinstrument")
1023	self.append(instr, entry_node)
1024	self.write_node(instr, "name", datainfo.instrument)
1025	return instr
1026
1027	def _write_source(self, datainfo, instr):
1028	"""
1029	Writes the source information to the XML file
1030
1031	:param datainfo: The Data1D object the information is coming from
1032	:param instr: instrument node to be appended to
1033	"""
1034	source = self.create_element("SASsource")
1035	if datainfo.source.name is not None:
1036	self.write_attribute(source, "name",
1037	str(datainfo.source.name))
1038	self.append(source, instr)
1039	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1040	datainfo.source.radiation = "neutron"
1041	self.write_node(source, "radiation", datainfo.source.radiation)
1042
1043	size = self.create_element("beam_size")
1044	if datainfo.source.beam_size_name is not None:
1045	self.write_attribute(size, "name",
1046	str(datainfo.source.beam_size_name))
1047	written = self.write_node( \
1048	size, "x", datainfo.source.beam_size.x,
1049	{"unit": datainfo.source.beam_size_unit})
1050	written = written \| self.write_node( \
1051	size, "y", datainfo.source.beam_size.y,
1052	{"unit": datainfo.source.beam_size_unit})
1053	written = written \| self.write_node( \
1054	size, "z", datainfo.source.beam_size.z,
1055	{"unit": datainfo.source.beam_size_unit})
1056	if written == True:
1057	self.append(size, source)
1058
1059	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1060	self.write_node(source, "wavelength",
1061	datainfo.source.wavelength,
1062	{"unit": datainfo.source.wavelength_unit})
1063	self.write_node(source, "wavelength_min",
1064	datainfo.source.wavelength_min,
1065	{"unit": datainfo.source.wavelength_min_unit})
1066	self.write_node(source, "wavelength_max",
1067	datainfo.source.wavelength_max,
1068	{"unit": datainfo.source.wavelength_max_unit})
1069	self.write_node(source, "wavelength_spread",
1070	datainfo.source.wavelength_spread,
1071	{"unit": datainfo.source.wavelength_spread_unit})
1072
1073	def _write_collimation(self, datainfo, instr):
1074	"""
1075	Writes the collimation information to the XML file
1076
1077	:param datainfo: The Data1D object the information is coming from
1078	:param instr: lxml node ElementTree object to be appended to
1079	"""
1080	if datainfo.collimation == [] or datainfo.collimation == None:
1081	coll = Collimation()
1082	datainfo.collimation.append(coll)
1083	for item in datainfo.collimation:
1084	coll = self.create_element("SAScollimation")
1085	if item.name is not None:
1086	self.write_attribute(coll, "name", str(item.name))
1087	self.append(coll, instr)
1088
1089	self.write_node(coll, "length", item.length,
1090	{"unit": item.length_unit})
1091
1092	for aperture in item.aperture:
1093	apert = self.create_element("aperture")
1094	if aperture.name is not None:
1095	self.write_attribute(apert, "name", str(aperture.name))
1096	if aperture.type is not None:
1097	self.write_attribute(apert, "type", str(aperture.type))
1098	self.append(apert, coll)
1099
1100	size = self.create_element("size")
1101	if aperture.size_name is not None:
1102	self.write_attribute(size, "name",
1103	str(aperture.size_name))
1104	written = self.write_node(size, "x", aperture.size.x,
1105	{"unit": aperture.size_unit})
1106	written = written \| self.write_node( \
1107	size, "y", aperture.size.y,
1108	{"unit": aperture.size_unit})
1109	written = written \| self.write_node( \
1110	size, "z", aperture.size.z,
1111	{"unit": aperture.size_unit})
1112	if written == True:
1113	self.append(size, apert)
1114
1115	self.write_node(apert, "distance", aperture.distance,
1116	{"unit": aperture.distance_unit})
1117
1118	def _write_detectors(self, datainfo, instr):
1119	"""
1120	Writes the detector information to the XML file
1121
1122	:param datainfo: The Data1D object the information is coming from
1123	:param inst: lxml instrument node to be appended to
1124	"""
1125	if datainfo.detector == None or datainfo.detector == []:
1126	det = Detector()
1127	det.name = ""
1128	datainfo.detector.append(det)
1129
1130	for item in datainfo.detector:
1131	det = self.create_element("SASdetector")
1132	written = self.write_node(det, "name", item.name)
1133	written = written \| self.write_node(det, "SDD", item.distance,
1134	{"unit": item.distance_unit})
1135	if written == True:
1136	self.append(det, instr)
1137
1138	off = self.create_element("offset")
1139	written = self.write_node(off, "x", item.offset.x,
1140	{"unit": item.offset_unit})
1141	written = written \| self.write_node(off, "y", item.offset.y,
1142	{"unit": item.offset_unit})
1143	written = written \| self.write_node(off, "z", item.offset.z,
1144	{"unit": item.offset_unit})
1145	if written == True:
1146	self.append(off, det)
1147
1148	ori = self.create_element("orientation")
1149	written = self.write_node(ori, "roll", item.orientation.x,
1150	{"unit": item.orientation_unit})
1151	written = written \| self.write_node(ori, "pitch",
1152	item.orientation.y,
1153	{"unit": item.orientation_unit})
1154	written = written \| self.write_node(ori, "yaw",
1155	item.orientation.z,
1156	{"unit": item.orientation_unit})
1157	if written == True:
1158	self.append(ori, det)
1159
1160	center = self.create_element("beam_center")
1161	written = self.write_node(center, "x", item.beam_center.x,
1162	{"unit": item.beam_center_unit})
1163	written = written \| self.write_node(center, "y",
1164	item.beam_center.y,
1165	{"unit": item.beam_center_unit})
1166	written = written \| self.write_node(center, "z",
1167	item.beam_center.z,
1168	{"unit": item.beam_center_unit})
1169	if written == True:
1170	self.append(center, det)
1171
1172	pix = self.create_element("pixel_size")
1173	written = self.write_node(pix, "x", item.pixel_size.x,
1174	{"unit": item.pixel_size_unit})
1175	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1176	{"unit": item.pixel_size_unit})
1177	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1178	{"unit": item.pixel_size_unit})
1179	if written == True:
1180	self.append(pix, det)
1181	self.write_node(det, "slit_length", item.slit_length,
1182	{"unit": item.slit_length_unit})
1183
1184
1185	def _write_process_notes(self, datainfo, entry_node):
1186	"""
1187	Writes the process notes to the XML file
1188
1189	:param datainfo: The Data1D object the information is coming from
1190	:param entry_node: lxml node ElementTree object to be appended to
1191
1192	"""
1193	for item in datainfo.process:
1194	node = self.create_element("SASprocess")
1195	self.append(node, entry_node)
1196	self.write_node(node, "name", item.name)
1197	self.write_node(node, "date", item.date)
1198	self.write_node(node, "description", item.description)
1199	for term in item.term:
1200	if isinstance(term, list):
1201	value = term['value']
1202	del term['value']
1203	elif isinstance(term, dict):
1204	value = term.get("value")
1205	del term['value']
1206	else:
1207	value = term
1208	self.write_node(node, "term", value, term)
1209	for note in item.notes:
1210	self.write_node(node, "SASprocessnote", note)
1211	if len(item.notes) == 0:
1212	self.write_node(node, "SASprocessnote", "")
1213
1214	def _write_notes(self, datainfo, entry_node):
1215	"""
1216	Writes the notes to the XML file and creates an empty note if none
1217	exist
1218
1219	:param datainfo: The Data1D object the information is coming from
1220	:param entry_node: lxml node ElementTree object to be appended to
1221
1222	"""
1223	if len(datainfo.notes) == 0:
1224	node = self.create_element("SASnote")
1225	self.append(node, entry_node)
1226	else:
1227	for item in datainfo.notes:
1228	node = self.create_element("SASnote")
1229	self.write_text(node, item)
1230	self.append(node, entry_node)
1231
1232	def _check_origin(self, entry_node, doc):
1233	"""
1234	Return the document, and the SASentry node associated with
1235	the data we just wrote.
1236	If the calling function was not the cansas reader, return a minidom
1237	object rather than an lxml object.
1238
1239	:param entry_node: lxml node ElementTree object to be appended to
1240	:param doc: entire xml tree
1241	"""
1242	if not self.frm:
1243	self.frm = inspect.stack()[1]
1244	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1245	mod_name = mod_name.replace(".py", "")
1246	mod = mod_name.split("sas/")
1247	mod_name = mod[1]
1248	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1249	string = self.to_string(doc, pretty_print=False)
1250	doc = parseString(string)
1251	node_name = entry_node.tag
1252	node_list = doc.getElementsByTagName(node_name)
1253	entry_node = node_list.item(0)
1254	return doc, entry_node
1255
1256	# DO NOT REMOVE - used in saving and loading panel states.
1257	def _store_float(self, location, node, variable, storage, optional=True):
1258	"""
1259	Get the content of a xpath location and store
1260	the result. Check that the units are compatible
1261	with the destination. The value is expected to
1262	be a float.
1263
1264	The xpath location might or might not exist.
1265	If it does not exist, nothing is done
1266
1267	:param location: xpath location to fetch
1268	:param node: node to read the data from
1269	:param variable: name of the data member to store it in [string]
1270	:param storage: data object that has the 'variable' data member
1271	:param optional: if True, no exception will be raised
1272	if unit conversion can't be done
1273
1274	:raise ValueError: raised when the units are not recognized
1275	"""
1276	entry = get_content(location, node)
1277	try:
1278	value = float(entry.text)
1279	except:
1280	value = None
1281
1282	if value is not None:
1283	# If the entry has units, check to see that they are
1284	# compatible with what we currently have in the data object
1285	units = entry.get('unit')
1286	if units is not None:
1287	toks = variable.split('.')
1288	local_unit = None
1289	exec "local_unit = storage.%s_unit" % toks[0]
1290	if local_unit != None and units.lower() != local_unit.lower():
1291	if HAS_CONVERTER == True:
1292	try:
1293	conv = Converter(units)
1294	exec "storage.%s = %g" % \
1295	(variable, conv(value, units=local_unit))
1296	except:
1297	_, exc_value, _ = sys.exc_info()
1298	err_mess = "CanSAS reader: could not convert"
1299	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1300	% (variable, units, local_unit, exc_value)
1301	self.errors.add(err_mess)
1302	if optional:
1303	logging.info(err_mess)
1304	else:
1305	raise ValueError, err_mess
1306	else:
1307	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1308	% (variable, units)
1309	err_mess += " expecting [%s]" % local_unit
1310	self.errors.add(err_mess)
1311	if optional:
1312	logging.info(err_mess)
1313	else:
1314	raise ValueError, err_mess
1315	else:
1316	exec "storage.%s = value" % variable
1317	else:
1318	exec "storage.%s = value" % variable
1319
1320	# DO NOT REMOVE - used in saving and loading panel states.
1321	def _store_content(self, location, node, variable, storage):
1322	"""
1323	Get the content of a xpath location and store
1324	the result. The value is treated as a string.
1325
1326	The xpath location might or might not exist.
1327	If it does not exist, nothing is done
1328
1329	:param location: xpath location to fetch
1330	:param node: node to read the data from
1331	:param variable: name of the data member to store it in [string]
1332	:param storage: data object that has the 'variable' data member
1333
1334	:return: return a list of errors
1335	"""
1336	entry = get_content(location, node)
1337	if entry is not None and entry.text is not None:
1338	exec "storage.%s = entry.text.strip()" % variable
1339
1340
1341	# DO NOT REMOVE Called by outside packages:
1342	# sas.sasgui.perspectives.invariant.invariant_state
1343	# sas.sasgui.perspectives.fitting.pagestate
1344	def get_content(location, node):
1345	"""
1346	Get the first instance of the content of a xpath location.
1347
1348	:param location: xpath location
1349	:param node: node to start at
1350
1351	:return: Element, or None
1352	"""
1353	nodes = node.xpath(location,
1354	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1355	if len(nodes) > 0:
1356	return nodes[0]
1357	else:
1358	return None
1359
1360	# DO NOT REMOVE Called by outside packages:
1361	# sas.sasgui.perspectives.fitting.pagestate
1362	def write_node(doc, parent, name, value, attr=None):
1363	"""
1364	:param doc: document DOM
1365	:param parent: parent node
1366	:param name: tag of the element
1367	:param value: value of the child text node
1368	:param attr: attribute dictionary
1369
1370	:return: True if something was appended, otherwise False
1371	"""
1372	if attr is None:
1373	attr = {}
1374	if value is not None:
1375	node = doc.createElement(name)
1376	node.appendChild(doc.createTextNode(str(value)))
1377	for item in attr:
1378	node.setAttribute(item, attr[item])
1379	parent.appendChild(node)
1380	return True
1381	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 67b0a99

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