cansas_reader.py @ ad4632c

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 ad4632c was ad4632c, checked in by krzywon, 7 years ago
Save and load SESANS flag and zacceptance to/from project and analysis files.
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1	"""
2	CanSAS data reader - new recursive cansas_version.
3	"""
4	############################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#If you use DANSE applications to do scientific research that leads to
9	#publication, we ask that you acknowledge the use of the software with the
10	#following sentence:
11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
12	#copyright 2008,2009 University of Tennessee
13	#############################################################################
14
15	import logging
16	import numpy as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, 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	unit_list = unit.split(" \| ")
250	if len(unit_list) > 1:
251	self.current_dataset.yaxis(unit_list[0], unit_list[1])
252	else:
253	self.current_dataset.yaxis("Intensity", unit)
254	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
255	elif tagname == 'Idev':
256	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
257	elif tagname == 'Q':
258	unit_list = unit.split(" \| ")
259	if len(unit_list) > 1:
260	self.current_dataset.xaxis(unit_list[0], unit_list[1])
261	else:
262	self.current_dataset.xaxis("Q", unit)
263	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
264	elif tagname == 'Qdev':
265	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
266	elif tagname == 'dQw':
267	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
268	elif tagname == 'dQl':
269	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
270	elif tagname == 'Qmean':
271	pass
272	elif tagname == 'Shadowfactor':
273	pass
274	elif tagname == 'Sesans':
275	self.current_datainfo.isSesans = bool(data_point)
276	elif tagname == 'zacceptance':
277	self.current_datainfo.sample.zacceptance = (data_point, unit)
278
279	## Sample Information
280	elif tagname == 'ID' and self.parent_class == 'SASsample':
281	self.current_datainfo.sample.ID = data_point
282	elif tagname == 'Title' and self.parent_class == 'SASsample':
283	self.current_datainfo.sample.name = data_point
284	elif tagname == 'thickness' and self.parent_class == 'SASsample':
285	self.current_datainfo.sample.thickness = data_point
286	self.current_datainfo.sample.thickness_unit = unit
287	elif tagname == 'transmission' and self.parent_class == 'SASsample':
288	self.current_datainfo.sample.transmission = data_point
289	elif tagname == 'temperature' and self.parent_class == 'SASsample':
290	self.current_datainfo.sample.temperature = data_point
291	self.current_datainfo.sample.temperature_unit = unit
292	elif tagname == 'details' and self.parent_class == 'SASsample':
293	self.current_datainfo.sample.details.append(data_point)
294	elif tagname == 'x' and self.parent_class == 'position':
295	self.current_datainfo.sample.position.x = data_point
296	self.current_datainfo.sample.position_unit = unit
297	elif tagname == 'y' and self.parent_class == 'position':
298	self.current_datainfo.sample.position.y = data_point
299	self.current_datainfo.sample.position_unit = unit
300	elif tagname == 'z' and self.parent_class == 'position':
301	self.current_datainfo.sample.position.z = data_point
302	self.current_datainfo.sample.position_unit = unit
303	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
304	self.current_datainfo.sample.orientation.x = data_point
305	self.current_datainfo.sample.orientation_unit = unit
306	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
307	self.current_datainfo.sample.orientation.y = data_point
308	self.current_datainfo.sample.orientation_unit = unit
309	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
310	self.current_datainfo.sample.orientation.z = data_point
311	self.current_datainfo.sample.orientation_unit = unit
312
313	## Instrumental Information
314	elif tagname == 'name' and self.parent_class == 'SASinstrument':
315	self.current_datainfo.instrument = data_point
316	## Detector Information
317	elif tagname == 'name' and self.parent_class == 'SASdetector':
318	self.detector.name = data_point
319	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
320	self.detector.distance = data_point
321	self.detector.distance_unit = unit
322	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
323	self.detector.slit_length = data_point
324	self.detector.slit_length_unit = unit
325	elif tagname == 'x' and self.parent_class == 'offset':
326	self.detector.offset.x = data_point
327	self.detector.offset_unit = unit
328	elif tagname == 'y' and self.parent_class == 'offset':
329	self.detector.offset.y = data_point
330	self.detector.offset_unit = unit
331	elif tagname == 'z' and self.parent_class == 'offset':
332	self.detector.offset.z = data_point
333	self.detector.offset_unit = unit
334	elif tagname == 'x' and self.parent_class == 'beam_center':
335	self.detector.beam_center.x = data_point
336	self.detector.beam_center_unit = unit
337	elif tagname == 'y' and self.parent_class == 'beam_center':
338	self.detector.beam_center.y = data_point
339	self.detector.beam_center_unit = unit
340	elif tagname == 'z' and self.parent_class == 'beam_center':
341	self.detector.beam_center.z = data_point
342	self.detector.beam_center_unit = unit
343	elif tagname == 'x' and self.parent_class == 'pixel_size':
344	self.detector.pixel_size.x = data_point
345	self.detector.pixel_size_unit = unit
346	elif tagname == 'y' and self.parent_class == 'pixel_size':
347	self.detector.pixel_size.y = data_point
348	self.detector.pixel_size_unit = unit
349	elif tagname == 'z' and self.parent_class == 'pixel_size':
350	self.detector.pixel_size.z = data_point
351	self.detector.pixel_size_unit = unit
352	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
353	self.detector.orientation.x = data_point
354	self.detector.orientation_unit = unit
355	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
356	self.detector.orientation.y = data_point
357	self.detector.orientation_unit = unit
358	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
359	self.detector.orientation.z = data_point
360	self.detector.orientation_unit = unit
361	## Collimation and Aperture
362	elif tagname == 'length' and self.parent_class == 'SAScollimation':
363	self.collimation.length = data_point
364	self.collimation.length_unit = unit
365	elif tagname == 'name' and self.parent_class == 'SAScollimation':
366	self.collimation.name = data_point
367	elif tagname == 'distance' and self.parent_class == 'aperture':
368	self.aperture.distance = data_point
369	self.aperture.distance_unit = unit
370	elif tagname == 'x' and self.parent_class == 'size':
371	self.aperture.size.x = data_point
372	self.collimation.size_unit = unit
373	elif tagname == 'y' and self.parent_class == 'size':
374	self.aperture.size.y = data_point
375	self.collimation.size_unit = unit
376	elif tagname == 'z' and self.parent_class == 'size':
377	self.aperture.size.z = data_point
378	self.collimation.size_unit = unit
379
380	## Process Information
381	elif tagname == 'name' and self.parent_class == 'SASprocess':
382	self.process.name = data_point
383	elif tagname == 'description' and self.parent_class == 'SASprocess':
384	self.process.description = data_point
385	elif tagname == 'date' and self.parent_class == 'SASprocess':
386	try:
387	self.process.date = datetime.datetime.fromtimestamp(data_point)
388	except:
389	self.process.date = data_point
390	elif tagname == 'SASprocessnote':
391	self.process.notes.append(data_point)
392	elif tagname == 'term' and self.parent_class == 'SASprocess':
393	unit = attr.get("unit", "")
394	dic = {}
395	dic["name"] = name
396	dic["value"] = data_point
397	dic["unit"] = unit
398	self.process.term.append(dic)
399
400	## Transmission Spectrum
401	elif tagname == 'T' and self.parent_class == 'Tdata':
402	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
403	self.transspectrum.transmission_unit = unit
404	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
405	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
406	self.transspectrum.transmission_deviation_unit = unit
407	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
408	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
409	self.transspectrum.wavelength_unit = unit
410
411	## Source Information
412	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
413	self.current_datainfo.source.wavelength = data_point
414	self.current_datainfo.source.wavelength_unit = unit
415	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
416	self.current_datainfo.source.wavelength_min = data_point
417	self.current_datainfo.source.wavelength_min_unit = unit
418	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
419	self.current_datainfo.source.wavelength_max = data_point
420	self.current_datainfo.source.wavelength_max_unit = unit
421	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
422	self.current_datainfo.source.wavelength_spread = data_point
423	self.current_datainfo.source.wavelength_spread_unit = unit
424	elif tagname == 'x' and self.parent_class == 'beam_size':
425	self.current_datainfo.source.beam_size.x = data_point
426	self.current_datainfo.source.beam_size_unit = unit
427	elif tagname == 'y' and self.parent_class == 'beam_size':
428	self.current_datainfo.source.beam_size.y = data_point
429	self.current_datainfo.source.beam_size_unit = unit
430	elif tagname == 'z' and self.parent_class == 'pixel_size':
431	self.current_datainfo.source.data_point.z = data_point
432	self.current_datainfo.source.beam_size_unit = unit
433	elif tagname == 'radiation' and self.parent_class == 'SASsource':
434	self.current_datainfo.source.radiation = data_point
435	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
436	self.current_datainfo.source.beam_shape = data_point
437
438	## Everything else goes in meta_data
439	else:
440	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
441	self.current_datainfo.meta_data[new_key] = data_point
442
443	self.names.remove(tagname_original)
444	length = 0
445	if len(self.names) > 1:
446	length = len(self.names) - 1
447	self.parent_class = self.names[length]
448	if not self._is_call_local() and not recurse:
449	self.frm = ""
450	self.add_data_set()
451	empty = None
452	if self.output[0].dx is not None:
453	self.output[0].dxl = np.empty(0)
454	self.output[0].dxw = np.empty(0)
455	else:
456	self.output[0].dx = np.empty(0)
457	return self.output[0], empty
458
459
460	def _is_call_local(self):
461	"""
462
463	"""
464	if self.frm == "":
465	inter = inspect.stack()
466	self.frm = inter[2]
467	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
468	mod_name = mod_name.replace(".py", "")
469	mod = mod_name.split("sas/")
470	mod_name = mod[1]
471	if mod_name != "sascalc/dataloader/readers/cansas_reader":
472	return False
473	return True
474
475	def is_cansas(self, ext="xml"):
476	"""
477	Checks to see if the xml file is a CanSAS file
478
479	:param ext: The file extension of the data file
480	"""
481	if self.validate_xml():
482	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
483	value = self.xmlroot.get(name)
484	if CANSAS_NS.get(self.cansas_version).get("ns") == \
485	value.rsplit(" ")[0]:
486	return True
487	if ext == "svs":
488	return True
489	raise RuntimeError
490
491	def load_file_and_schema(self, xml_file, schema_path=""):
492	"""
493	Loads the file and associates a schema, if a schema is passed in or if one already exists
494
495	:param xml_file: The xml file path sent to Reader.read
496	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
497	"""
498	base_name = xml_reader.__file__
499	base_name = base_name.replace("\\", "/")
500	base = base_name.split("/sas/")[0]
501
502	# Load in xml file and get the cansas version from the header
503	self.set_xml_file(xml_file)
504	self.cansas_version = self.xmlroot.get("version", "1.0")
505
506	# Generic values for the cansas file based on the version
507	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
508	if schema_path == "":
509	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
510	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
511
512	# Link a schema to the XML file.
513	self.set_schema(schema_path)
514
515	def add_data_set(self):
516	"""
517	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
518	private method to generate a new data set.
519
520	:param key: NeXus group name for current tree level
521	"""
522
523	if self.current_datainfo and self.current_dataset:
524	self._final_cleanup()
525	self.data = []
526	self.current_datainfo = DataInfo()
527
528	def _initialize_new_data_set(self, parent_list=None):
529	"""
530	A private class method to generate a new 1D data object.
531	Outside methods should call add_data_set() to be sure any existing data is stored properly.
532
533	:param parent_list: List of names of parent elements
534	"""
535
536	if parent_list is None:
537	parent_list = []
538	x = np.array(0)
539	y = np.array(0)
540	self.current_dataset = plottable_1D(x, y)
541
542	def add_intermediate(self):
543	"""
544	This method stores any intermediate objects within the final data set after fully reading the set.
545
546	:param parent: The NXclass name for the h5py Group object that just finished being processed
547	"""
548
549	if self.parent_class == 'SASprocess':
550	self.current_datainfo.process.append(self.process)
551	self.process = Process()
552	elif self.parent_class == 'SASdetector':
553	self.current_datainfo.detector.append(self.detector)
554	self.detector = Detector()
555	elif self.parent_class == 'SAStransmission_spectrum':
556	self.current_datainfo.trans_spectrum.append(self.transspectrum)
557	self.transspectrum = TransmissionSpectrum()
558	elif self.parent_class == 'SAScollimation':
559	self.current_datainfo.collimation.append(self.collimation)
560	self.collimation = Collimation()
561	elif self.parent_class == 'aperture':
562	self.collimation.aperture.append(self.aperture)
563	self.aperture = Aperture()
564	elif self.parent_class == 'SASdata':
565	self._check_for_empty_resolution()
566	self.data.append(self.current_dataset)
567
568	def _final_cleanup(self):
569	"""
570	Final cleanup of the Data1D object to be sure it has all the
571	appropriate information needed for perspectives
572	"""
573
574	## Append errors to dataset and reset class errors
575	self.current_datainfo.errors = set()
576	for error in self.errors:
577	self.current_datainfo.errors.add(error)
578	self.errors.clear()
579
580	## Combine all plottables with datainfo and append each to output
581	## Type cast data arrays to float64 and find min/max as appropriate
582	for dataset in self.data:
583	if dataset.x is not None:
584	dataset.x = np.delete(dataset.x, [0])
585	dataset.x = dataset.x.astype(np.float64)
586	dataset.xmin = np.min(dataset.x)
587	dataset.xmax = np.max(dataset.x)
588	if dataset.y is not None:
589	dataset.y = np.delete(dataset.y, [0])
590	dataset.y = dataset.y.astype(np.float64)
591	dataset.ymin = np.min(dataset.y)
592	dataset.ymax = np.max(dataset.y)
593	if dataset.dx is not None:
594	dataset.dx = np.delete(dataset.dx, [0])
595	dataset.dx = dataset.dx.astype(np.float64)
596	if dataset.dxl is not None:
597	dataset.dxl = np.delete(dataset.dxl, [0])
598	dataset.dxl = dataset.dxl.astype(np.float64)
599	if dataset.dxw is not None:
600	dataset.dxw = np.delete(dataset.dxw, [0])
601	dataset.dxw = dataset.dxw.astype(np.float64)
602	if dataset.dy is not None:
603	dataset.dy = np.delete(dataset.dy, [0])
604	dataset.dy = dataset.dy.astype(np.float64)
605	np.trim_zeros(dataset.x)
606	np.trim_zeros(dataset.y)
607	np.trim_zeros(dataset.dy)
608	final_dataset = combine_data(dataset, self.current_datainfo)
609	self.output.append(final_dataset)
610
611	def _create_unique_key(self, dictionary, name, numb=0):
612	"""
613	Create a unique key value for any dictionary to prevent overwriting
614	Recurse until a unique key value is found.
615
616	:param dictionary: A dictionary with any number of entries
617	:param name: The index of the item to be added to dictionary
618	:param numb: The number to be appended to the name, starts at 0
619	"""
620	if dictionary.get(name) is not None:
621	numb += 1
622	name = name.split("_")[0]
623	name += "_{0}".format(numb)
624	name = self._create_unique_key(dictionary, name, numb)
625	return name
626
627	def _get_node_value(self, node, tagname):
628	"""
629	Get the value of a node and any applicable units
630
631	:param node: The XML node to get the value of
632	:param tagname: The tagname of the node
633	"""
634	#Get the text from the node and convert all whitespace to spaces
635	units = ''
636	node_value = node.text
637	if node_value is not None:
638	node_value = ' '.join(node_value.split())
639	else:
640	node_value = ""
641
642	# If the value is a float, compile with units.
643	if self.ns_list.ns_datatype == "float":
644	# If an empty value is given, set as zero.
645	if node_value is None or node_value.isspace() \
646	or node_value.lower() == "nan":
647	node_value = "0.0"
648	#Convert the value to the base units
649	node_value, units = self._unit_conversion(node, tagname, node_value)
650
651	# If the value is a timestamp, convert to a datetime object
652	elif self.ns_list.ns_datatype == "timestamp":
653	if node_value is None or node_value.isspace():
654	pass
655	else:
656	try:
657	node_value = \
658	datetime.datetime.fromtimestamp(node_value)
659	except ValueError:
660	node_value = None
661	return node_value, units
662
663	def _unit_conversion(self, node, tagname, node_value):
664	"""
665	A unit converter method used to convert the data included in the file
666	to the default units listed in data_info
667
668	:param node: XML node
669	:param tagname: name of the node
670	:param node_value: The value of the current dom node
671	"""
672	attr = node.attrib
673	value_unit = ''
674	err_msg = None
675	default_unit = None
676	if not isinstance(node_value, float):
677	node_value = float(node_value)
678	if 'unit' in attr and attr.get('unit') is not None:
679	try:
680	local_unit = attr['unit']
681	unitname = self.ns_list.current_level.get("unit", "")
682	if "SASdetector" in self.names:
683	save_in = "detector"
684	elif "aperture" in self.names:
685	save_in = "aperture"
686	elif "SAScollimation" in self.names:
687	save_in = "collimation"
688	elif "SAStransmission_spectrum" in self.names:
689	save_in = "transspectrum"
690	elif "SASdata" in self.names:
691	x = np.zeros(1)
692	y = np.zeros(1)
693	self.current_data1d = Data1D(x, y)
694	save_in = "current_data1d"
695	elif "SASsource" in self.names:
696	save_in = "current_datainfo.source"
697	elif "SASsample" in self.names:
698	save_in = "current_datainfo.sample"
699	elif "SASprocess" in self.names:
700	save_in = "process"
701	else:
702	save_in = "current_datainfo"
703	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
704	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
705	and local_unit.lower() != "none":
706	if HAS_CONVERTER == True:
707	## Check local units - bad units raise KeyError
708	data_conv_q = Converter(local_unit)
709	value_unit = default_unit
710	node_value = data_conv_q(node_value, units=default_unit)
711	else:
712	value_unit = local_unit
713	err_msg = "Unit converter is not available.\n"
714	else:
715	value_unit = local_unit
716	except KeyError:
717	err_msg = "CanSAS reader: unexpected "
718	err_msg += "\"{0}\" unit [{1}]; "
719	err_msg = err_msg.format(tagname, local_unit)
720	err_msg += "expecting [{0}]".format(default_unit)
721	value_unit = local_unit
722	except:
723	err_msg = "CanSAS reader: unknown error converting "
724	err_msg += "\"{0}\" unit [{1}]"
725	err_msg = err_msg.format(tagname, local_unit)
726	value_unit = local_unit
727	elif 'unit' in attr:
728	value_unit = attr['unit']
729	if err_msg:
730	self.errors.add(err_msg)
731	return node_value, value_unit
732
733	def _check_for_empty_data(self):
734	"""
735	Creates an empty data set if no data is passed to the reader
736
737	:param data1d: presumably a Data1D object
738	"""
739	if self.current_dataset == None:
740	x_vals = np.empty(0)
741	y_vals = np.empty(0)
742	dx_vals = np.empty(0)
743	dy_vals = np.empty(0)
744	dxl = np.empty(0)
745	dxw = np.empty(0)
746	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
747	self.current_dataset.dxl = dxl
748	self.current_dataset.dxw = dxw
749
750	def _check_for_empty_resolution(self):
751	"""
752	A method to check all resolution data sets are the same size as I and Q
753	"""
754	dql_exists = False
755	dqw_exists = False
756	dq_exists = False
757	di_exists = False
758	if self.current_dataset.dxl is not None:
759	dql_exists = True
760	if self.current_dataset.dxw is not None:
761	dqw_exists = True
762	if self.current_dataset.dx is not None:
763	dq_exists = True
764	if self.current_dataset.dy is not None:
765	di_exists = True
766	if dqw_exists and not dql_exists:
767	array_size = self.current_dataset.dxw.size - 1
768	self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size]))
769	elif dql_exists and not dqw_exists:
770	array_size = self.current_dataset.dxl.size - 1
771	self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size]))
772	elif not dql_exists and not dqw_exists and not dq_exists:
773	array_size = self.current_dataset.x.size - 1
774	self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size]))
775	if not di_exists:
776	array_size = self.current_dataset.y.size - 1
777	self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size]))
778
779
780	####### All methods below are for writing CanSAS XML files #######
781
782
783	def write(self, filename, datainfo):
784	"""
785	Write the content of a Data1D as a CanSAS XML file
786
787	:param filename: name of the file to write
788	:param datainfo: Data1D object
789	"""
790	# Create XML document
791	doc, _ = self._to_xml_doc(datainfo)
792	# Write the file
793	file_ref = open(filename, 'w')
794	if self.encoding == None:
795	self.encoding = "UTF-8"
796	doc.write(file_ref, encoding=self.encoding,
797	pretty_print=True, xml_declaration=True)
798	file_ref.close()
799
800	def _to_xml_doc(self, datainfo):
801	"""
802	Create an XML document to contain the content of a Data1D
803
804	:param datainfo: Data1D object
805	"""
806	if not issubclass(datainfo.__class__, Data1D):
807	raise RuntimeError, "The cansas writer expects a Data1D instance"
808
809	# Get PIs and create root element
810	pi_string = self._get_pi_string()
811	# Define namespaces and create SASroot object
812	main_node = self._create_main_node()
813	# Create ElementTree, append SASroot and apply processing instructions
814	base_string = pi_string + self.to_string(main_node)
815	base_element = self.create_element_from_string(base_string)
816	doc = self.create_tree(base_element)
817	# Create SASentry Element
818	entry_node = self.create_element("SASentry")
819	root = doc.getroot()
820	root.append(entry_node)
821
822	# Add Title to SASentry
823	self.write_node(entry_node, "Title", datainfo.title)
824	# Add Run to SASentry
825	self._write_run_names(datainfo, entry_node)
826	# Add Data info to SASEntry
827	self._write_data(datainfo, entry_node)
828	# Transmission Spectrum Info
829	self._write_trans_spectrum(datainfo, entry_node)
830	# Sample info
831	self._write_sample_info(datainfo, entry_node)
832	# Instrument info
833	instr = self._write_instrument(datainfo, entry_node)
834	# Source
835	self._write_source(datainfo, instr)
836	# Collimation
837	self._write_collimation(datainfo, instr)
838	# Detectors
839	self._write_detectors(datainfo, instr)
840	# Processes info
841	self._write_process_notes(datainfo, entry_node)
842	# Note info
843	self._write_notes(datainfo, entry_node)
844	# Return the document, and the SASentry node associated with
845	# the data we just wrote
846	# If the calling function was not the cansas reader, return a minidom
847	# object rather than an lxml object.
848	self.frm = inspect.stack()[1]
849	doc, entry_node = self._check_origin(entry_node, doc)
850	return doc, entry_node
851
852	def write_node(self, parent, name, value, attr=None):
853	"""
854	:param doc: document DOM
855	:param parent: parent node
856	:param name: tag of the element
857	:param value: value of the child text node
858	:param attr: attribute dictionary
859
860	:return: True if something was appended, otherwise False
861	"""
862	if value is not None:
863	parent = self.ebuilder(parent, name, value, attr)
864	return True
865	return False
866
867	def _get_pi_string(self):
868	"""
869	Creates the processing instructions header for writing to file
870	"""
871	pis = self.return_processing_instructions()
872	if len(pis) > 0:
873	pi_tree = self.create_tree(pis[0])
874	i = 1
875	for i in range(1, len(pis) - 1):
876	pi_tree = self.append(pis[i], pi_tree)
877	pi_string = self.to_string(pi_tree)
878	else:
879	pi_string = ""
880	return pi_string
881
882	def _create_main_node(self):
883	"""
884	Creates the primary xml header used when writing to file
885	"""
886	xsi = "http://www.w3.org/2001/XMLSchema-instance"
887	version = self.cansas_version
888	n_s = CANSAS_NS.get(version).get("ns")
889	if version == "1.1":
890	url = "http://www.cansas.org/formats/1.1/"
891	else:
892	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
893	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
894	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
895	"version" : version}
896	nsmap = {'xsi' : xsi, None: n_s}
897
898	main_node = self.create_element("{" + n_s + "}SASroot",
899	attrib=attrib, nsmap=nsmap)
900	return main_node
901
902	def _write_run_names(self, datainfo, entry_node):
903	"""
904	Writes the run names to the XML file
905
906	:param datainfo: The Data1D object the information is coming from
907	:param entry_node: lxml node ElementTree object to be appended to
908	"""
909	if datainfo.run == None or datainfo.run == []:
910	datainfo.run.append(RUN_NAME_DEFAULT)
911	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
912	for item in datainfo.run:
913	runname = {}
914	if item in datainfo.run_name and \
915	len(str(datainfo.run_name[item])) > 1:
916	runname = {'name': datainfo.run_name[item]}
917	self.write_node(entry_node, "Run", item, runname)
918
919	def _write_data(self, datainfo, entry_node):
920	"""
921	Writes the I and Q data to the XML file
922
923	:param datainfo: The Data1D object the information is coming from
924	:param entry_node: lxml node ElementTree object to be appended to
925	"""
926	node = self.create_element("SASdata")
927	self.append(node, entry_node)
928
929	for i in range(len(datainfo.x)):
930	point = self.create_element("Idata")
931	node.append(point)
932	self.write_node(point, "Q", datainfo.x[i],
933	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
934	if len(datainfo.y) >= i:
935	self.write_node(point, "I", datainfo.y[i],
936	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
937	if datainfo.dy is not None and len(datainfo.dy) > i:
938	self.write_node(point, "Idev", datainfo.dy[i],
939	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
940	if datainfo.dx is not None and len(datainfo.dx) > i:
941	self.write_node(point, "Qdev", datainfo.dx[i],
942	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
943	if datainfo.dxw is not None and len(datainfo.dxw) > i:
944	self.write_node(point, "dQw", datainfo.dxw[i],
945	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
946	if datainfo.dxl is not None and len(datainfo.dxl) > i:
947	self.write_node(point, "dQl", datainfo.dxl[i],
948	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
949	if datainfo.isSesans:
950	sesans = self.create_element("Sesans")
951	sesans.text = str(datainfo.isSesans)
952	node.append(sesans)
953	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
954	{'unit': datainfo.sample.zacceptance[1]})
955
956
957	def _write_trans_spectrum(self, datainfo, entry_node):
958	"""
959	Writes the transmission spectrum data to the XML file
960
961	:param datainfo: The Data1D object the information is coming from
962	:param entry_node: lxml node ElementTree object to be appended to
963	"""
964	for i in range(len(datainfo.trans_spectrum)):
965	spectrum = datainfo.trans_spectrum[i]
966	node = self.create_element("SAStransmission_spectrum",
967	{"name" : spectrum.name})
968	self.append(node, entry_node)
969	if isinstance(spectrum.timestamp, datetime.datetime):
970	node.setAttribute("timestamp", spectrum.timestamp)
971	for i in range(len(spectrum.wavelength)):
972	point = self.create_element("Tdata")
973	node.append(point)
974	self.write_node(point, "Lambda", spectrum.wavelength[i],
975	{'unit': spectrum.wavelength_unit})
976	self.write_node(point, "T", spectrum.transmission[i],
977	{'unit': spectrum.transmission_unit})
978	if spectrum.transmission_deviation != None \
979	and len(spectrum.transmission_deviation) >= i:
980	self.write_node(point, "Tdev",
981	spectrum.transmission_deviation[i],
982	{'unit':
983	spectrum.transmission_deviation_unit})
984
985	def _write_sample_info(self, datainfo, entry_node):
986	"""
987	Writes the sample information to the XML file
988
989	:param datainfo: The Data1D object the information is coming from
990	:param entry_node: lxml node ElementTree object to be appended to
991	"""
992	sample = self.create_element("SASsample")
993	if datainfo.sample.name is not None:
994	self.write_attribute(sample, "name",
995	str(datainfo.sample.name))
996	self.append(sample, entry_node)
997	self.write_node(sample, "ID", str(datainfo.sample.ID))
998	self.write_node(sample, "thickness", datainfo.sample.thickness,
999	{"unit": datainfo.sample.thickness_unit})
1000	self.write_node(sample, "transmission", datainfo.sample.transmission)
1001	self.write_node(sample, "temperature", datainfo.sample.temperature,
1002	{"unit": datainfo.sample.temperature_unit})
1003
1004	pos = self.create_element("position")
1005	written = self.write_node(pos,
1006	"x",
1007	datainfo.sample.position.x,
1008	{"unit": datainfo.sample.position_unit})
1009	written = written \| self.write_node( \
1010	pos, "y", datainfo.sample.position.y,
1011	{"unit": datainfo.sample.position_unit})
1012	written = written \| self.write_node( \
1013	pos, "z", datainfo.sample.position.z,
1014	{"unit": datainfo.sample.position_unit})
1015	if written == True:
1016	self.append(pos, sample)
1017
1018	ori = self.create_element("orientation")
1019	written = self.write_node(ori, "roll",
1020	datainfo.sample.orientation.x,
1021	{"unit": datainfo.sample.orientation_unit})
1022	written = written \| self.write_node( \
1023	ori, "pitch", datainfo.sample.orientation.y,
1024	{"unit": datainfo.sample.orientation_unit})
1025	written = written \| self.write_node( \
1026	ori, "yaw", datainfo.sample.orientation.z,
1027	{"unit": datainfo.sample.orientation_unit})
1028	if written == True:
1029	self.append(ori, sample)
1030
1031	for item in datainfo.sample.details:
1032	self.write_node(sample, "details", item)
1033
1034	def _write_instrument(self, datainfo, entry_node):
1035	"""
1036	Writes the instrumental information to the XML file
1037
1038	:param datainfo: The Data1D object the information is coming from
1039	:param entry_node: lxml node ElementTree object to be appended to
1040	"""
1041	instr = self.create_element("SASinstrument")
1042	self.append(instr, entry_node)
1043	self.write_node(instr, "name", datainfo.instrument)
1044	return instr
1045
1046	def _write_source(self, datainfo, instr):
1047	"""
1048	Writes the source information to the XML file
1049
1050	:param datainfo: The Data1D object the information is coming from
1051	:param instr: instrument node to be appended to
1052	"""
1053	source = self.create_element("SASsource")
1054	if datainfo.source.name is not None:
1055	self.write_attribute(source, "name",
1056	str(datainfo.source.name))
1057	self.append(source, instr)
1058	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1059	datainfo.source.radiation = "neutron"
1060	self.write_node(source, "radiation", datainfo.source.radiation)
1061
1062	size = self.create_element("beam_size")
1063	if datainfo.source.beam_size_name is not None:
1064	self.write_attribute(size, "name",
1065	str(datainfo.source.beam_size_name))
1066	written = self.write_node( \
1067	size, "x", datainfo.source.beam_size.x,
1068	{"unit": datainfo.source.beam_size_unit})
1069	written = written \| self.write_node( \
1070	size, "y", datainfo.source.beam_size.y,
1071	{"unit": datainfo.source.beam_size_unit})
1072	written = written \| self.write_node( \
1073	size, "z", datainfo.source.beam_size.z,
1074	{"unit": datainfo.source.beam_size_unit})
1075	if written == True:
1076	self.append(size, source)
1077
1078	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1079	self.write_node(source, "wavelength",
1080	datainfo.source.wavelength,
1081	{"unit": datainfo.source.wavelength_unit})
1082	self.write_node(source, "wavelength_min",
1083	datainfo.source.wavelength_min,
1084	{"unit": datainfo.source.wavelength_min_unit})
1085	self.write_node(source, "wavelength_max",
1086	datainfo.source.wavelength_max,
1087	{"unit": datainfo.source.wavelength_max_unit})
1088	self.write_node(source, "wavelength_spread",
1089	datainfo.source.wavelength_spread,
1090	{"unit": datainfo.source.wavelength_spread_unit})
1091
1092	def _write_collimation(self, datainfo, instr):
1093	"""
1094	Writes the collimation information to the XML file
1095
1096	:param datainfo: The Data1D object the information is coming from
1097	:param instr: lxml node ElementTree object to be appended to
1098	"""
1099	if datainfo.collimation == [] or datainfo.collimation == None:
1100	coll = Collimation()
1101	datainfo.collimation.append(coll)
1102	for item in datainfo.collimation:
1103	coll = self.create_element("SAScollimation")
1104	if item.name is not None:
1105	self.write_attribute(coll, "name", str(item.name))
1106	self.append(coll, instr)
1107
1108	self.write_node(coll, "length", item.length,
1109	{"unit": item.length_unit})
1110
1111	for aperture in item.aperture:
1112	apert = self.create_element("aperture")
1113	if aperture.name is not None:
1114	self.write_attribute(apert, "name", str(aperture.name))
1115	if aperture.type is not None:
1116	self.write_attribute(apert, "type", str(aperture.type))
1117	self.append(apert, coll)
1118
1119	size = self.create_element("size")
1120	if aperture.size_name is not None:
1121	self.write_attribute(size, "name",
1122	str(aperture.size_name))
1123	written = self.write_node(size, "x", aperture.size.x,
1124	{"unit": aperture.size_unit})
1125	written = written \| self.write_node( \
1126	size, "y", aperture.size.y,
1127	{"unit": aperture.size_unit})
1128	written = written \| self.write_node( \
1129	size, "z", aperture.size.z,
1130	{"unit": aperture.size_unit})
1131	if written == True:
1132	self.append(size, apert)
1133
1134	self.write_node(apert, "distance", aperture.distance,
1135	{"unit": aperture.distance_unit})
1136
1137	def _write_detectors(self, datainfo, instr):
1138	"""
1139	Writes the detector information to the XML file
1140
1141	:param datainfo: The Data1D object the information is coming from
1142	:param inst: lxml instrument node to be appended to
1143	"""
1144	if datainfo.detector == None or datainfo.detector == []:
1145	det = Detector()
1146	det.name = ""
1147	datainfo.detector.append(det)
1148
1149	for item in datainfo.detector:
1150	det = self.create_element("SASdetector")
1151	written = self.write_node(det, "name", item.name)
1152	written = written \| self.write_node(det, "SDD", item.distance,
1153	{"unit": item.distance_unit})
1154	if written == True:
1155	self.append(det, instr)
1156
1157	off = self.create_element("offset")
1158	written = self.write_node(off, "x", item.offset.x,
1159	{"unit": item.offset_unit})
1160	written = written \| self.write_node(off, "y", item.offset.y,
1161	{"unit": item.offset_unit})
1162	written = written \| self.write_node(off, "z", item.offset.z,
1163	{"unit": item.offset_unit})
1164	if written == True:
1165	self.append(off, det)
1166
1167	ori = self.create_element("orientation")
1168	written = self.write_node(ori, "roll", item.orientation.x,
1169	{"unit": item.orientation_unit})
1170	written = written \| self.write_node(ori, "pitch",
1171	item.orientation.y,
1172	{"unit": item.orientation_unit})
1173	written = written \| self.write_node(ori, "yaw",
1174	item.orientation.z,
1175	{"unit": item.orientation_unit})
1176	if written == True:
1177	self.append(ori, det)
1178
1179	center = self.create_element("beam_center")
1180	written = self.write_node(center, "x", item.beam_center.x,
1181	{"unit": item.beam_center_unit})
1182	written = written \| self.write_node(center, "y",
1183	item.beam_center.y,
1184	{"unit": item.beam_center_unit})
1185	written = written \| self.write_node(center, "z",
1186	item.beam_center.z,
1187	{"unit": item.beam_center_unit})
1188	if written == True:
1189	self.append(center, det)
1190
1191	pix = self.create_element("pixel_size")
1192	written = self.write_node(pix, "x", item.pixel_size.x,
1193	{"unit": item.pixel_size_unit})
1194	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1195	{"unit": item.pixel_size_unit})
1196	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1197	{"unit": item.pixel_size_unit})
1198	if written == True:
1199	self.append(pix, det)
1200	self.write_node(det, "slit_length", item.slit_length,
1201	{"unit": item.slit_length_unit})
1202
1203
1204	def _write_process_notes(self, datainfo, entry_node):
1205	"""
1206	Writes the process notes to the XML file
1207
1208	:param datainfo: The Data1D object the information is coming from
1209	:param entry_node: lxml node ElementTree object to be appended to
1210
1211	"""
1212	for item in datainfo.process:
1213	node = self.create_element("SASprocess")
1214	self.append(node, entry_node)
1215	self.write_node(node, "name", item.name)
1216	self.write_node(node, "date", item.date)
1217	self.write_node(node, "description", item.description)
1218	for term in item.term:
1219	if isinstance(term, list):
1220	value = term['value']
1221	del term['value']
1222	elif isinstance(term, dict):
1223	value = term.get("value")
1224	del term['value']
1225	else:
1226	value = term
1227	self.write_node(node, "term", value, term)
1228	for note in item.notes:
1229	self.write_node(node, "SASprocessnote", note)
1230	if len(item.notes) == 0:
1231	self.write_node(node, "SASprocessnote", "")
1232
1233	def _write_notes(self, datainfo, entry_node):
1234	"""
1235	Writes the notes to the XML file and creates an empty note if none
1236	exist
1237
1238	:param datainfo: The Data1D object the information is coming from
1239	:param entry_node: lxml node ElementTree object to be appended to
1240
1241	"""
1242	if len(datainfo.notes) == 0:
1243	node = self.create_element("SASnote")
1244	self.append(node, entry_node)
1245	else:
1246	for item in datainfo.notes:
1247	node = self.create_element("SASnote")
1248	self.write_text(node, item)
1249	self.append(node, entry_node)
1250
1251	def _check_origin(self, entry_node, doc):
1252	"""
1253	Return the document, and the SASentry node associated with
1254	the data we just wrote.
1255	If the calling function was not the cansas reader, return a minidom
1256	object rather than an lxml object.
1257
1258	:param entry_node: lxml node ElementTree object to be appended to
1259	:param doc: entire xml tree
1260	"""
1261	if not self.frm:
1262	self.frm = inspect.stack()[1]
1263	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1264	mod_name = mod_name.replace(".py", "")
1265	mod = mod_name.split("sas/")
1266	mod_name = mod[1]
1267	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1268	string = self.to_string(doc, pretty_print=False)
1269	doc = parseString(string)
1270	node_name = entry_node.tag
1271	node_list = doc.getElementsByTagName(node_name)
1272	entry_node = node_list.item(0)
1273	return doc, entry_node
1274
1275	# DO NOT REMOVE - used in saving and loading panel states.
1276	def _store_float(self, location, node, variable, storage, optional=True):
1277	"""
1278	Get the content of a xpath location and store
1279	the result. Check that the units are compatible
1280	with the destination. The value is expected to
1281	be a float.
1282
1283	The xpath location might or might not exist.
1284	If it does not exist, nothing is done
1285
1286	:param location: xpath location to fetch
1287	:param node: node to read the data from
1288	:param variable: name of the data member to store it in [string]
1289	:param storage: data object that has the 'variable' data member
1290	:param optional: if True, no exception will be raised
1291	if unit conversion can't be done
1292
1293	:raise ValueError: raised when the units are not recognized
1294	"""
1295	entry = get_content(location, node)
1296	try:
1297	value = float(entry.text)
1298	except:
1299	value = None
1300
1301	if value is not None:
1302	# If the entry has units, check to see that they are
1303	# compatible with what we currently have in the data object
1304	units = entry.get('unit')
1305	if units is not None:
1306	toks = variable.split('.')
1307	local_unit = None
1308	exec "local_unit = storage.%s_unit" % toks[0]
1309	if local_unit != None and units.lower() != local_unit.lower():
1310	if HAS_CONVERTER == True:
1311	try:
1312	conv = Converter(units)
1313	exec "storage.%s = %g" % \
1314	(variable, conv(value, units=local_unit))
1315	except:
1316	_, exc_value, _ = sys.exc_info()
1317	err_mess = "CanSAS reader: could not convert"
1318	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1319	% (variable, units, local_unit, exc_value)
1320	self.errors.add(err_mess)
1321	if optional:
1322	logging.info(err_mess)
1323	else:
1324	raise ValueError, err_mess
1325	else:
1326	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1327	% (variable, units)
1328	err_mess += " expecting [%s]" % local_unit
1329	self.errors.add(err_mess)
1330	if optional:
1331	logging.info(err_mess)
1332	else:
1333	raise ValueError, err_mess
1334	else:
1335	exec "storage.%s = value" % variable
1336	else:
1337	exec "storage.%s = value" % variable
1338
1339	# DO NOT REMOVE - used in saving and loading panel states.
1340	def _store_content(self, location, node, variable, storage):
1341	"""
1342	Get the content of a xpath location and store
1343	the result. The value is treated as a string.
1344
1345	The xpath location might or might not exist.
1346	If it does not exist, nothing is done
1347
1348	:param location: xpath location to fetch
1349	:param node: node to read the data from
1350	:param variable: name of the data member to store it in [string]
1351	:param storage: data object that has the 'variable' data member
1352
1353	:return: return a list of errors
1354	"""
1355	entry = get_content(location, node)
1356	if entry is not None and entry.text is not None:
1357	exec "storage.%s = entry.text.strip()" % variable
1358
1359
1360	# DO NOT REMOVE Called by outside packages:
1361	# sas.sasgui.perspectives.invariant.invariant_state
1362	# sas.sasgui.perspectives.fitting.pagestate
1363	def get_content(location, node):
1364	"""
1365	Get the first instance of the content of a xpath location.
1366
1367	:param location: xpath location
1368	:param node: node to start at
1369
1370	:return: Element, or None
1371	"""
1372	nodes = node.xpath(location,
1373	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1374	if len(nodes) > 0:
1375	return nodes[0]
1376	else:
1377	return None
1378
1379	# DO NOT REMOVE Called by outside packages:
1380	# sas.sasgui.perspectives.fitting.pagestate
1381	def write_node(doc, parent, name, value, attr=None):
1382	"""
1383	:param doc: document DOM
1384	:param parent: parent node
1385	:param name: tag of the element
1386	:param value: value of the child text node
1387	:param attr: attribute dictionary
1388
1389	:return: True if something was appended, otherwise False
1390	"""
1391	if attr is None:
1392	attr = {}
1393	if value is not None:
1394	node = doc.createElement(name)
1395	node.appendChild(doc.createTextNode(str(value)))
1396	for item in attr:
1397	node.setAttribute(item, attr[item])
1398	parent.appendChild(node)
1399	return True
1400	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ ad4632c

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