cansas_reader.py @ 83c09af

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 83c09af was 83c09af, checked in by krzywon, 7 years ago
Fit states and projects are now able to save 2D data. Loading is still not working. #827
Property mode set to `100644`
File size: 63.0 KB

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

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 83c09af

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