cansas_reader.py @ 7ad12e9f

ticket-1094-headless

Last change on this file since 7ad12e9f was f0b9bce, checked in by Paul Kienzle <pkienzle@…>, 6 years ago
Merge branch 'ticket-1243' into ticket-1094-headless
Property mode set to `100644`
File size: 61.0 KB

Line
1	import logging
2	import os
3	import sys
4	import datetime
5	import inspect
6
7	import numpy as np
8
9	# The following 2 imports ARE used. Do not remove either.
10	import xml.dom.minidom
11	from xml.dom.minidom import parseString
12
13	from lxml import etree
14
15	from sas.sascalc.data_util.nxsunit import Converter
16
17	# For saving individual sections of data
18	from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \
19	Collimation, TransmissionSpectrum, Detector, Process, Aperture, \
20	combine_data_info_with_plottable as combine_data
21	from ..loader_exceptions import FileContentsException, DefaultReaderException, \
22	DataReaderException
23	from . import xml_reader
24	from .xml_reader import XMLreader
25	from .cansas_constants import CansasConstants, CurrentLevel
26
27	logger = logging.getLogger(__name__)
28
29	PREPROCESS = "xmlpreprocess"
30	ENCODING = "encoding"
31	RUN_NAME_DEFAULT = "None"
32	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
33	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
34	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
35	"as much of the data as possible.\n\n"
36
37	CONSTANTS = CansasConstants()
38	CANSAS_FORMAT = CONSTANTS.format
39	CANSAS_NS = CONSTANTS.names
40	ALLOW_ALL = True
41
42	class Reader(XMLreader):
43	cansas_version = "1.0"
44	base_ns = "{cansas1d/1.0}"
45	cansas_defaults = None
46	type_name = "canSAS"
47	invalid = True
48	frm = ""
49	# Log messages and errors
50	logging = None
51	errors = set()
52	# Namespace hierarchy for current xml_file object
53	names = None
54	ns_list = None
55	# Temporary storage location for loading multiple data sets in a single file
56	current_data1d = None
57	data = None
58	# Wildcards
59	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
60	# List of allowed extensions
61	ext = ['.xml', '.XML', '.svs', '.SVS']
62	# Flag to bypass extension check
63	allow_all = True
64
65	def reset_state(self):
66	"""
67	Resets the class state to a base case when loading a new data file so previous
68	data files do not appear a second time
69	"""
70	super(Reader, self).reset_state()
71	self.data = []
72	self.process = Process()
73	self.transspectrum = TransmissionSpectrum()
74	self.aperture = Aperture()
75	self.collimation = Collimation()
76	self.detector = Detector()
77	self.names = []
78	self.cansas_defaults = {}
79	self.ns_list = None
80	self.logging = []
81	self.encoding = None
82
83	def read(self, xml_file, schema_path="", invalid=True):
84	if schema_path != "" or not invalid:
85	# read has been called from self.get_file_contents because xml file doens't conform to schema
86	_, self.extension = os.path.splitext(os.path.basename(xml_file))
87	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
88
89	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
90	return super(XMLreader, self).read(xml_file)
91
92	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
93	# Reset everything since we're loading a new file
94	self.reset_state()
95	self.invalid = invalid
96	if xml_file is None:
97	xml_file = self.f_open.name
98	# We don't sure f_open since lxml handles opnening/closing files
99	try:
100	# Raises FileContentsException
101	self.load_file_and_schema(xml_file, schema_path)
102	# Parse each SASentry
103	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
104	namespaces={
105	'ns': self.cansas_defaults.get(
106	"ns")
107	})
108	self.is_cansas(self.extension)
109	self.set_processing_instructions()
110	for entry in entry_list:
111	self._parse_entry(entry)
112	self.data_cleanup()
113	except FileContentsException as fc_exc:
114	# File doesn't meet schema - try loading with a less strict schema
115	base_name = xml_reader.__file__
116	base_name = base_name.replace("\\", "/")
117	base = base_name.split("/sas/")[0]
118	if self.cansas_version == "1.1":
119	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
120	else:
121	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
122	self.set_schema(invalid_schema)
123	if self.invalid:
124	try:
125	# Load data with less strict schema
126	self.read(xml_file, invalid_schema, False)
127
128	# File can still be read but doesn't match schema, so raise exception
129	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
130	invalid_xml = self.find_invalid_xml()
131	if invalid_xml != "":
132	basename, _ = os.path.splitext(
133	os.path.basename(self.f_open.name))
134	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
135	raise DataReaderException(invalid_xml) # Handled by base class
136	except FileContentsException as fc_exc:
137	msg = "CanSAS Reader could not load the file {}".format(xml_file)
138	if fc_exc.message is not None: # Propagate error messages from earlier
139	msg = fc_exc.message
140	if not self.extension in self.ext: # If the file has no associated loader
141	raise DefaultReaderException(msg)
142	raise FileContentsException(msg)
143	pass
144	else:
145	raise fc_exc
146	except Exception as e: # Convert all other exceptions to FileContentsExceptions
147	raise FileContentsException(str(e))
148	finally:
149	if not self.f_open.closed:
150	self.f_open.close()
151
152	def load_file_and_schema(self, xml_file, schema_path=""):
153	base_name = xml_reader.__file__
154	base_name = base_name.replace("\\", "/")
155	base = base_name.split("/sas/")[0]
156
157	# Try and parse the XML file
158	try:
159	self.set_xml_file(xml_file)
160	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
161	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
162	raise FileContentsException(msg)
163
164	self.cansas_version = self.xmlroot.get("version", "1.0")
165	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
166
167	if schema_path == "":
168	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
169	base, self.cansas_defaults.get("schema").replace("\\", "/")
170	)
171	self.set_schema(schema_path)
172
173	def is_cansas(self, ext="xml"):
174	"""
175	Checks to see if the XML file is a CanSAS file
176
177	:param ext: The file extension of the data file
178	:raises FileContentsException: Raised if XML file isn't valid CanSAS
179	"""
180	if self.validate_xml(): # Check file is valid XML
181	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
182	value = self.xmlroot.get(name)
183	# Check schema CanSAS version matches file CanSAS version
184	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
185	return True
186	if ext == "svs":
187	return True # Why is this required?
188	# If we get to this point then file isn't valid CanSAS
189	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
190	raise FileContentsException("The file is not valid CanSAS")
191
192	def _parse_entry(self, dom, recurse=False):
193	if not self._is_call_local() and not recurse:
194	self.reset_state()
195	if not recurse:
196	self.current_datainfo = DataInfo()
197	# Raises FileContentsException if file doesn't meet CanSAS schema
198	self.invalid = False
199	# Look for a SASentry
200	self.data = []
201	self.parent_class = "SASentry"
202	self.names.append("SASentry")
203	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
204	self.current_datainfo.meta_data[
205	PREPROCESS] = self.processing_instructions
206	if self._is_call_local() and not recurse:
207	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
208	self.current_datainfo.filename = basename + self.extension
209	# Create an empty dataset if no data has been passed to the reader
210	if self.current_dataset is None:
211	self._initialize_new_data_set(dom)
212	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
213
214	# Loop through each child in the parent element
215	for node in dom:
216	attr = node.attrib
217	name = attr.get("name", "")
218	type = attr.get("type", "")
219	# Get the element name and set the current names level
220	tagname = node.tag.replace(self.base_ns, "")
221	tagname_original = tagname
222	# Skip this iteration when loading in save state information
223	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
224	continue
225	# Get where to store content
226	self.names.append(tagname_original)
227	self.ns_list = CONSTANTS.iterate_namespace(self.names)
228	# If the element is a child element, recurse
229	if len(node.getchildren()) > 0:
230	self.parent_class = tagname_original
231	if tagname == 'SASdata':
232	self._initialize_new_data_set(node)
233	if isinstance(self.current_dataset, plottable_2D):
234	x_bins = attr.get("x_bins", "")
235	y_bins = attr.get("y_bins", "")
236	if x_bins is not "" and y_bins is not "":
237	self.current_dataset.shape = (x_bins, y_bins)
238	else:
239	self.current_dataset.shape = ()
240	# Recurse to access data within the group
241	self._parse_entry(node, recurse=True)
242	if tagname == "SASsample":
243	self.current_datainfo.sample.name = name
244	elif tagname == "beam_size":
245	self.current_datainfo.source.beam_size_name = name
246	elif tagname == "SAScollimation":
247	self.collimation.name = name
248	elif tagname == "aperture":
249	self.aperture.name = name
250	self.aperture.type = type
251	self._add_intermediate()
252	else:
253	# TODO: Clean this up to make it faster (fewer if/elifs)
254	if isinstance(self.current_dataset, plottable_2D):
255	data_point = node.text
256	unit = attr.get('unit', '')
257	else:
258	data_point, unit = self._get_node_value(node, tagname)
259
260	# If this is a dataset, store the data appropriately
261	if tagname == 'Run':
262	self.current_datainfo.run_name[data_point] = name
263	self.current_datainfo.run.append(data_point)
264	elif tagname == 'Title':
265	self.current_datainfo.title = data_point
266	elif tagname == 'SASnote':
267	self.current_datainfo.notes.append(data_point)
268
269	# I and Q points
270	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
271	self.current_dataset.yaxis("Intensity", unit)
272	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
273	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
274	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
275	elif tagname == 'Q':
276	self.current_dataset.xaxis("Q", unit)
277	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
278	elif tagname == 'Qdev':
279	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
280	elif tagname == 'dQw':
281	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
282	elif tagname == 'dQl':
283	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
284	elif tagname == 'Qmean':
285	pass
286	elif tagname == 'Shadowfactor':
287	pass
288	elif tagname == 'Sesans':
289	self.current_datainfo.isSesans = bool(data_point)
290	self.current_dataset.xaxis(attr.get('x_axis'),
291	attr.get('x_unit'))
292	self.current_dataset.yaxis(attr.get('y_axis'),
293	attr.get('y_unit'))
294	elif tagname == 'yacceptance':
295	self.current_datainfo.sample.yacceptance = (data_point, unit)
296	elif tagname == 'zacceptance':
297	self.current_datainfo.sample.zacceptance = (data_point, unit)
298
299	# I and Qx, Qy - 2D data
300	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
301	self.current_dataset.yaxis("Intensity", unit)
302	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
303	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
304	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qx':
306	self.current_dataset.xaxis("Qx", unit)
307	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qy':
309	self.current_dataset.yaxis("Qy", unit)
310	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qxdev':
312	self.current_dataset.xaxis("Qxdev", unit)
313	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qydev':
315	self.current_dataset.yaxis("Qydev", unit)
316	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Mask':
318	inter = [item == "1" for item in data_point.split(",")]
319	self.current_dataset.mask = np.asarray(inter, dtype=bool)
320
321	# Sample Information
322	elif tagname == 'ID' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.ID = data_point
324	elif tagname == 'Title' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.name = data_point
326	elif tagname == 'thickness' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.thickness = data_point
328	self.current_datainfo.sample.thickness_unit = unit
329	elif tagname == 'transmission' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.transmission = data_point
331	elif tagname == 'temperature' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.temperature = data_point
333	self.current_datainfo.sample.temperature_unit = unit
334	elif tagname == 'details' and self.parent_class == 'SASsample':
335	self.current_datainfo.sample.details.append(data_point)
336	elif tagname == 'x' and self.parent_class == 'position':
337	self.current_datainfo.sample.position.x = data_point
338	self.current_datainfo.sample.position_unit = unit
339	elif tagname == 'y' and self.parent_class == 'position':
340	self.current_datainfo.sample.position.y = data_point
341	self.current_datainfo.sample.position_unit = unit
342	elif tagname == 'z' and self.parent_class == 'position':
343	self.current_datainfo.sample.position.z = data_point
344	self.current_datainfo.sample.position_unit = unit
345	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
346	self.current_datainfo.sample.orientation.x = data_point
347	self.current_datainfo.sample.orientation_unit = unit
348	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
349	self.current_datainfo.sample.orientation.y = data_point
350	self.current_datainfo.sample.orientation_unit = unit
351	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
352	self.current_datainfo.sample.orientation.z = data_point
353	self.current_datainfo.sample.orientation_unit = unit
354
355	# Instrumental Information
356	elif tagname == 'name' and self.parent_class == 'SASinstrument':
357	self.current_datainfo.instrument = data_point
358
359	# Detector Information
360	elif tagname == 'name' and self.parent_class == 'SASdetector':
361	self.detector.name = data_point
362	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
363	self.detector.distance = data_point
364	self.detector.distance_unit = unit
365	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
366	self.detector.slit_length = data_point
367	self.detector.slit_length_unit = unit
368	elif tagname == 'x' and self.parent_class == 'offset':
369	self.detector.offset.x = data_point
370	self.detector.offset_unit = unit
371	elif tagname == 'y' and self.parent_class == 'offset':
372	self.detector.offset.y = data_point
373	self.detector.offset_unit = unit
374	elif tagname == 'z' and self.parent_class == 'offset':
375	self.detector.offset.z = data_point
376	self.detector.offset_unit = unit
377	elif tagname == 'x' and self.parent_class == 'beam_center':
378	self.detector.beam_center.x = data_point
379	self.detector.beam_center_unit = unit
380	elif tagname == 'y' and self.parent_class == 'beam_center':
381	self.detector.beam_center.y = data_point
382	self.detector.beam_center_unit = unit
383	elif tagname == 'z' and self.parent_class == 'beam_center':
384	self.detector.beam_center.z = data_point
385	self.detector.beam_center_unit = unit
386	elif tagname == 'x' and self.parent_class == 'pixel_size':
387	self.detector.pixel_size.x = data_point
388	self.detector.pixel_size_unit = unit
389	elif tagname == 'y' and self.parent_class == 'pixel_size':
390	self.detector.pixel_size.y = data_point
391	self.detector.pixel_size_unit = unit
392	elif tagname == 'z' and self.parent_class == 'pixel_size':
393	self.detector.pixel_size.z = data_point
394	self.detector.pixel_size_unit = unit
395	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
396	self.detector.orientation.x = data_point
397	self.detector.orientation_unit = unit
398	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
399	self.detector.orientation.y = data_point
400	self.detector.orientation_unit = unit
401	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
402	self.detector.orientation.z = data_point
403	self.detector.orientation_unit = unit
404
405	# Collimation and Aperture
406	elif tagname == 'length' and self.parent_class == 'SAScollimation':
407	self.collimation.length = data_point
408	self.collimation.length_unit = unit
409	elif tagname == 'name' and self.parent_class == 'SAScollimation':
410	self.collimation.name = data_point
411	elif tagname == 'distance' and self.parent_class == 'aperture':
412	self.aperture.distance = data_point
413	self.aperture.distance_unit = unit
414	elif tagname == 'x' and self.parent_class == 'size':
415	self.aperture.size.x = data_point
416	self.collimation.size_unit = unit
417	elif tagname == 'y' and self.parent_class == 'size':
418	self.aperture.size.y = data_point
419	self.collimation.size_unit = unit
420	elif tagname == 'z' and self.parent_class == 'size':
421	self.aperture.size.z = data_point
422	self.collimation.size_unit = unit
423
424	# Process Information
425	elif tagname == 'name' and self.parent_class == 'SASprocess':
426	self.process.name = data_point
427	elif tagname == 'description' and self.parent_class == 'SASprocess':
428	self.process.description = data_point
429	elif tagname == 'date' and self.parent_class == 'SASprocess':
430	try:
431	self.process.date = datetime.datetime.fromtimestamp(data_point)
432	except:
433	self.process.date = data_point
434	elif tagname == 'SASprocessnote':
435	self.process.notes.append(data_point)
436	elif tagname == 'term' and self.parent_class == 'SASprocess':
437	unit = attr.get("unit", "")
438	dic = { "name": name, "value": data_point, "unit": unit }
439	self.process.term.append(dic)
440
441	# Transmission Spectrum
442	elif tagname == 'T' and self.parent_class == 'Tdata':
443	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
444	self.transspectrum.transmission_unit = unit
445	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
446	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
447	self.transspectrum.transmission_deviation_unit = unit
448	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
449	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
450	self.transspectrum.wavelength_unit = unit
451
452	# Source Information
453	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
454	self.current_datainfo.source.wavelength = data_point
455	self.current_datainfo.source.wavelength_unit = unit
456	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
457	self.current_datainfo.source.wavelength_min = data_point
458	self.current_datainfo.source.wavelength_min_unit = unit
459	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
460	self.current_datainfo.source.wavelength_max = data_point
461	self.current_datainfo.source.wavelength_max_unit = unit
462	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
463	self.current_datainfo.source.wavelength_spread = data_point
464	self.current_datainfo.source.wavelength_spread_unit = unit
465	elif tagname == 'x' and self.parent_class == 'beam_size':
466	self.current_datainfo.source.beam_size.x = data_point
467	self.current_datainfo.source.beam_size_unit = unit
468	elif tagname == 'y' and self.parent_class == 'beam_size':
469	self.current_datainfo.source.beam_size.y = data_point
470	self.current_datainfo.source.beam_size_unit = unit
471	elif tagname == 'z' and self.parent_class == 'pixel_size':
472	self.current_datainfo.source.data_point.z = data_point
473	self.current_datainfo.source.beam_size_unit = unit
474	elif tagname == 'radiation' and self.parent_class == 'SASsource':
475	self.current_datainfo.source.radiation = data_point
476	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.beam_shape = data_point
478
479	# Everything else goes in meta_data
480	else:
481	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
482	self.current_datainfo.meta_data[new_key] = data_point
483
484	self.names.remove(tagname_original)
485	length = 0
486	if len(self.names) > 1:
487	length = len(self.names) - 1
488	self.parent_class = self.names[length]
489	if not self._is_call_local() and not recurse:
490	self.frm = ""
491	self.current_datainfo.errors = set()
492	for error in self.errors:
493	self.current_datainfo.errors.add(error)
494	self.data_cleanup()
495	self.sort_data()
496	self.reset_data_list()
497	return self.output[0], None
498
499	def _is_call_local(self):
500	if self.frm == "":
501	inter = inspect.stack()
502	self.frm = inter[2]
503	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
504	mod_name = mod_name.replace(".py", "")
505	mod = mod_name.split("sas/")
506	mod_name = mod[1]
507	if mod_name != "sascalc/dataloader/readers/cansas_reader":
508	return False
509	return True
510
511	def _add_intermediate(self):
512	"""
513	This method stores any intermediate objects within the final data set after fully reading the set.
514	"""
515	if self.parent_class == 'SASprocess':
516	self.current_datainfo.process.append(self.process)
517	self.process = Process()
518	elif self.parent_class == 'SASdetector':
519	self.current_datainfo.detector.append(self.detector)
520	self.detector = Detector()
521	elif self.parent_class == 'SAStransmission_spectrum':
522	self.current_datainfo.trans_spectrum.append(self.transspectrum)
523	self.transspectrum = TransmissionSpectrum()
524	elif self.parent_class == 'SAScollimation':
525	self.current_datainfo.collimation.append(self.collimation)
526	self.collimation = Collimation()
527	elif self.parent_class == 'aperture':
528	self.collimation.aperture.append(self.aperture)
529	self.aperture = Aperture()
530	elif self.parent_class == 'SASdata':
531	self.data.append(self.current_dataset)
532
533	def _get_node_value(self, node, tagname):
534	"""
535	Get the value of a node and any applicable units
536
537	:param node: The XML node to get the value of
538	:param tagname: The tagname of the node
539	"""
540	#Get the text from the node and convert all whitespace to spaces
541	units = ''
542	node_value = node.text
543	if node_value is not None:
544	node_value = ' '.join(node_value.split())
545	else:
546	node_value = ""
547
548	# If the value is a float, compile with units.
549	if self.ns_list.ns_datatype == "float":
550	# If an empty value is given, set as zero.
551	if node_value is None or node_value.isspace() \
552	or node_value.lower() == "nan":
553	node_value = "0.0"
554	#Convert the value to the base units
555	node_value, units = self._unit_conversion(node, tagname, node_value)
556
557	# If the value is a timestamp, convert to a datetime object
558	elif self.ns_list.ns_datatype == "timestamp":
559	if node_value is None or node_value.isspace():
560	pass
561	else:
562	try:
563	node_value = \
564	datetime.datetime.fromtimestamp(node_value)
565	except ValueError:
566	node_value = None
567	return node_value, units
568
569	def _unit_conversion(self, node, tagname, node_value):
570	"""
571	A unit converter method used to convert the data included in the file
572	to the default units listed in data_info
573
574	:param node: XML node
575	:param tagname: name of the node
576	:param node_value: The value of the current dom node
577	"""
578	attr = node.attrib
579	value_unit = ''
580	err_msg = None
581	default_unit = None
582	if not isinstance(node_value, float):
583	node_value = float(node_value)
584	if 'unit' in attr and attr.get('unit') is not None:
585	try:
586	unit = attr['unit']
587	# Split the units to retain backwards compatibility with
588	# projects, analyses, and saved data from v4.1.0
589	unit_list = unit.split("\|")
590	if len(unit_list) > 1:
591	local_unit = unit_list[1]
592	else:
593	local_unit = unit
594	unitname = self.ns_list.current_level.get("unit", "")
595	if "SASdetector" in self.names:
596	save_in = "detector"
597	elif "aperture" in self.names:
598	save_in = "aperture"
599	elif "SAScollimation" in self.names:
600	save_in = "collimation"
601	elif "SAStransmission_spectrum" in self.names:
602	save_in = "transspectrum"
603	elif "SASdata" in self.names:
604	x = np.zeros(1)
605	y = np.zeros(1)
606	self.current_data1d = Data1D(x, y)
607	save_in = "current_data1d"
608	elif "SASsource" in self.names:
609	save_in = "current_datainfo.source"
610	elif "SASsample" in self.names:
611	save_in = "current_datainfo.sample"
612	elif "SASprocess" in self.names:
613	save_in = "process"
614	else:
615	save_in = "current_datainfo"
616	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
617	if (local_unit and default_unit
618	and local_unit.lower() != default_unit.lower()
619	and local_unit.lower() != "none"):
620	# Check local units - bad units raise KeyError
621	#print("loading", tagname, node_value, local_unit, default_unit)
622	data_conv_q = Converter(local_unit)
623	value_unit = default_unit
624	node_value = data_conv_q(node_value, units=default_unit)
625	else:
626	value_unit = local_unit
627	except KeyError:
628	# Do not throw an error for loading Sesans data in cansas xml
629	# This is a temporary fix.
630	if local_unit != "A" and local_unit != 'pol':
631	err_msg = "CanSAS reader: unexpected "
632	err_msg += "\"{0}\" unit [{1}]; "
633	err_msg = err_msg.format(tagname, local_unit)
634	err_msg += "expecting [{0}]".format(default_unit)
635	value_unit = local_unit
636	except Exception:
637	err_msg = "CanSAS reader: unknown error converting "
638	err_msg += "\"{0}\" unit [{1}]"
639	err_msg = err_msg.format(tagname, local_unit)
640	value_unit = local_unit
641	elif 'unit' in attr:
642	value_unit = attr['unit']
643	if err_msg:
644	self.errors.add(err_msg)
645	return node_value, value_unit
646
647	def _initialize_new_data_set(self, node=None):
648	if node is not None:
649	for child in node:
650	if child.tag.replace(self.base_ns, "") == "Idata":
651	for i_child in child:
652	if i_child.tag.replace(self.base_ns, "") == "Qx":
653	self.current_dataset = plottable_2D()
654	return
655	self.current_dataset = plottable_1D(np.array(0), np.array(0))
656
657	## Writing Methods
658	def write(self, filename, datainfo):
659	"""
660	Write the content of a Data1D as a CanSAS XML file
661
662	:param filename: name of the file to write
663	:param datainfo: Data1D object
664	"""
665	# Create XML document
666	doc, _ = self._to_xml_doc(datainfo)
667	# Write the file
668	file_ref = open(filename, 'wb')
669	if self.encoding is None:
670	self.encoding = "UTF-8"
671	doc.write(file_ref, encoding=self.encoding,
672	pretty_print=True, xml_declaration=True)
673	file_ref.close()
674
675	def _to_xml_doc(self, datainfo):
676	"""
677	Create an XML document to contain the content of a Data1D
678
679	:param datainfo: Data1D object
680	"""
681	is_2d = False
682	if issubclass(datainfo.__class__, Data2D):
683	is_2d = True
684
685	# Get PIs and create root element
686	pi_string = self._get_pi_string()
687	# Define namespaces and create SASroot object
688	main_node = self._create_main_node()
689	# Create ElementTree, append SASroot and apply processing instructions
690	base_string = pi_string + self.to_string(main_node)
691	base_element = self.create_element_from_string(base_string)
692	doc = self.create_tree(base_element)
693	# Create SASentry Element
694	entry_node = self.create_element("SASentry")
695	root = doc.getroot()
696	root.append(entry_node)
697
698	# Add Title to SASentry
699	self.write_node(entry_node, "Title", datainfo.title)
700	# Add Run to SASentry
701	self._write_run_names(datainfo, entry_node)
702	# Add Data info to SASEntry
703	if is_2d:
704	self._write_data_2d(datainfo, entry_node)
705	else:
706	self._write_data(datainfo, entry_node)
707	# Transmission Spectrum Info
708	# TODO: fix the writer to linearize all data, including T_spectrum
709	# self._write_trans_spectrum(datainfo, entry_node)
710	# Sample info
711	self._write_sample_info(datainfo, entry_node)
712	# Instrument info
713	instr = self._write_instrument(datainfo, entry_node)
714	# Source
715	self._write_source(datainfo, instr)
716	# Collimation
717	self._write_collimation(datainfo, instr)
718	# Detectors
719	self._write_detectors(datainfo, instr)
720	# Processes info
721	self._write_process_notes(datainfo, entry_node)
722	# Note info
723	self._write_notes(datainfo, entry_node)
724	# Return the document, and the SASentry node associated with
725	# the data we just wrote
726	# If the calling function was not the cansas reader, return a minidom
727	# object rather than an lxml object.
728	self.frm = inspect.stack()[1]
729	doc, entry_node = self._check_origin(entry_node, doc)
730	return doc, entry_node
731
732	def write_node(self, parent, name, value, attr=None):
733	"""
734	:param doc: document DOM
735	:param parent: parent node
736	:param name: tag of the element
737	:param value: value of the child text node
738	:param attr: attribute dictionary
739
740	:return: True if something was appended, otherwise False
741	"""
742	if value is not None:
743	parent = self.ebuilder(parent, name, value, attr)
744	return True
745	return False
746
747	def _get_pi_string(self):
748	"""
749	Creates the processing instructions header for writing to file
750	"""
751	pis = self.return_processing_instructions()
752	if len(pis) > 0:
753	pi_tree = self.create_tree(pis[0])
754	i = 1
755	for i in range(1, len(pis) - 1):
756	pi_tree = self.append(pis[i], pi_tree)
757	pi_string = self.to_string(pi_tree)
758	else:
759	pi_string = ""
760	return pi_string
761
762	def _create_main_node(self):
763	"""
764	Creates the primary xml header used when writing to file
765	"""
766	xsi = "http://www.w3.org/2001/XMLSchema-instance"
767	version = self.cansas_version
768	n_s = CANSAS_NS.get(version).get("ns")
769	if version == "1.1":
770	url = "http://www.cansas.org/formats/1.1/"
771	else:
772	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
773	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
774	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
775	"version" : version}
776	nsmap = {'xsi' : xsi, None: n_s}
777
778	main_node = self.create_element("{" + n_s + "}SASroot",
779	attrib=attrib, nsmap=nsmap)
780	return main_node
781
782	def _write_run_names(self, datainfo, entry_node):
783	"""
784	Writes the run names to the XML file
785
786	:param datainfo: The Data1D object the information is coming from
787	:param entry_node: lxml node ElementTree object to be appended to
788	"""
789	if datainfo.run is None or datainfo.run == []:
790	datainfo.run.append(RUN_NAME_DEFAULT)
791	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
792	for item in datainfo.run:
793	runname = {}
794	if item in datainfo.run_name and \
795	len(str(datainfo.run_name[item])) > 1:
796	runname = {'name': datainfo.run_name[item]}
797	self.write_node(entry_node, "Run", item, runname)
798
799	def _write_data(self, datainfo, entry_node):
800	"""
801	Writes 1D I and Q data to the XML file
802
803	:param datainfo: The Data1D object the information is coming from
804	:param entry_node: lxml node ElementTree object to be appended to
805	"""
806	node = self.create_element("SASdata")
807	self.append(node, entry_node)
808
809	for i in range(len(datainfo.x)):
810	point = self.create_element("Idata")
811	node.append(point)
812	self.write_node(point, "Q", datainfo.x[i],
813	{'unit': datainfo._xunit})
814	if len(datainfo.y) >= i:
815	self.write_node(point, "I", datainfo.y[i],
816	{'unit': datainfo._yunit})
817	if datainfo.dy is not None and len(datainfo.dy) > i:
818	self.write_node(point, "Idev", datainfo.dy[i],
819	{'unit': datainfo._yunit})
820	if datainfo.dx is not None and len(datainfo.dx) > i:
821	self.write_node(point, "Qdev", datainfo.dx[i],
822	{'unit': datainfo._xunit})
823	if datainfo.dxw is not None and len(datainfo.dxw) > i:
824	self.write_node(point, "dQw", datainfo.dxw[i],
825	{'unit': datainfo._xunit})
826	if datainfo.dxl is not None and len(datainfo.dxl) > i:
827	self.write_node(point, "dQl", datainfo.dxl[i],
828	{'unit': datainfo._xunit})
829	if datainfo.isSesans:
830	sesans_attrib = {'x_axis': datainfo._xaxis,
831	'y_axis': datainfo._yaxis,
832	'x_unit': datainfo.x_unit,
833	'y_unit': datainfo.y_unit}
834	sesans = self.create_element("Sesans", attrib=sesans_attrib)
835	sesans.text = str(datainfo.isSesans)
836	entry_node.append(sesans)
837	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
838	{'unit': datainfo.sample.yacceptance[1]})
839	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
840	{'unit': datainfo.sample.zacceptance[1]})
841
842
843	def _write_data_2d(self, datainfo, entry_node):
844	"""
845	Writes 2D data to the XML file
846
847	:param datainfo: The Data2D object the information is coming from
848	:param entry_node: lxml node ElementTree object to be appended to
849	"""
850	attr = {}
851	if datainfo.data.shape:
852	attr["x_bins"] = str(len(datainfo.x_bins))
853	attr["y_bins"] = str(len(datainfo.y_bins))
854	node = self.create_element("SASdata", attr)
855	self.append(node, entry_node)
856
857	point = self.create_element("Idata")
858	node.append(point)
859	qx = ','.join(str(v) for v in datainfo.qx_data)
860	qy = ','.join(str(v) for v in datainfo.qy_data)
861	intensity = ','.join(str(v) for v in datainfo.data)
862
863	self.write_node(point, "Qx", qx,
864	{'unit': datainfo._xunit})
865	self.write_node(point, "Qy", qy,
866	{'unit': datainfo._yunit})
867	self.write_node(point, "I", intensity,
868	{'unit': datainfo._zunit})
869	if datainfo.err_data is not None:
870	err = ','.join(str(v) for v in datainfo.err_data)
871	self.write_node(point, "Idev", err,
872	{'unit': datainfo._zunit})
873	if datainfo.dqy_data is not None:
874	dqy = ','.join(str(v) for v in datainfo.dqy_data)
875	self.write_node(point, "Qydev", dqy,
876	{'unit': datainfo._yunit})
877	if datainfo.dqx_data is not None:
878	dqx = ','.join(str(v) for v in datainfo.dqx_data)
879	self.write_node(point, "Qxdev", dqx,
880	{'unit': datainfo._xunit})
881	if datainfo.mask is not None:
882	mask = ','.join("1" if v else "0" for v in datainfo.mask)
883	self.write_node(point, "Mask", mask)
884
885	def _write_trans_spectrum(self, datainfo, entry_node):
886	"""
887	Writes the transmission spectrum data to the XML file
888
889	:param datainfo: The Data1D object the information is coming from
890	:param entry_node: lxml node ElementTree object to be appended to
891	"""
892	for i in range(len(datainfo.trans_spectrum)):
893	spectrum = datainfo.trans_spectrum[i]
894	node = self.create_element("SAStransmission_spectrum",
895	{"name" : spectrum.name})
896	self.append(node, entry_node)
897	if isinstance(spectrum.timestamp, datetime.datetime):
898	node.setAttribute("timestamp", spectrum.timestamp)
899	for i in range(len(spectrum.wavelength)):
900	point = self.create_element("Tdata")
901	node.append(point)
902	self.write_node(point, "Lambda", spectrum.wavelength[i],
903	{'unit': spectrum.wavelength_unit})
904	self.write_node(point, "T", spectrum.transmission[i],
905	{'unit': spectrum.transmission_unit})
906	if spectrum.transmission_deviation is not None \
907	and len(spectrum.transmission_deviation) >= i:
908	self.write_node(point, "Tdev",
909	spectrum.transmission_deviation[i],
910	{'unit':
911	spectrum.transmission_deviation_unit})
912
913	def _write_sample_info(self, datainfo, entry_node):
914	"""
915	Writes the sample information 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	sample = self.create_element("SASsample")
921	if datainfo.sample.name is not None:
922	self.write_attribute(sample, "name",
923	str(datainfo.sample.name))
924	self.append(sample, entry_node)
925	self.write_node(sample, "ID", str(datainfo.sample.ID))
926	self.write_node(sample, "thickness", datainfo.sample.thickness,
927	{"unit": datainfo.sample.thickness_unit})
928	self.write_node(sample, "transmission", datainfo.sample.transmission)
929	self.write_node(sample, "temperature", datainfo.sample.temperature,
930	{"unit": datainfo.sample.temperature_unit})
931
932	pos = self.create_element("position")
933	written = self.write_node(pos,
934	"x",
935	datainfo.sample.position.x,
936	{"unit": datainfo.sample.position_unit})
937	written = written \| self.write_node( \
938	pos, "y", datainfo.sample.position.y,
939	{"unit": datainfo.sample.position_unit})
940	written = written \| self.write_node( \
941	pos, "z", datainfo.sample.position.z,
942	{"unit": datainfo.sample.position_unit})
943	if written:
944	self.append(pos, sample)
945
946	ori = self.create_element("orientation")
947	written = self.write_node(ori, "roll",
948	datainfo.sample.orientation.x,
949	{"unit": datainfo.sample.orientation_unit})
950	written = written \| self.write_node( \
951	ori, "pitch", datainfo.sample.orientation.y,
952	{"unit": datainfo.sample.orientation_unit})
953	written = written \| self.write_node( \
954	ori, "yaw", datainfo.sample.orientation.z,
955	{"unit": datainfo.sample.orientation_unit})
956	if written:
957	self.append(ori, sample)
958
959	for item in datainfo.sample.details:
960	self.write_node(sample, "details", item)
961
962	def _write_instrument(self, datainfo, entry_node):
963	"""
964	Writes the instrumental information to the XML file
965
966	:param datainfo: The Data1D object the information is coming from
967	:param entry_node: lxml node ElementTree object to be appended to
968	"""
969	instr = self.create_element("SASinstrument")
970	self.append(instr, entry_node)
971	self.write_node(instr, "name", datainfo.instrument)
972	return instr
973
974	def _write_source(self, datainfo, instr):
975	"""
976	Writes the source information to the XML file
977
978	:param datainfo: The Data1D object the information is coming from
979	:param instr: instrument node to be appended to
980	"""
981	source = self.create_element("SASsource")
982	if datainfo.source.name is not None:
983	self.write_attribute(source, "name",
984	str(datainfo.source.name))
985	self.append(source, instr)
986	if datainfo.source.radiation is None or datainfo.source.radiation == '':
987	datainfo.source.radiation = "neutron"
988	self.write_node(source, "radiation", datainfo.source.radiation)
989
990	size = self.create_element("beam_size")
991	if datainfo.source.beam_size_name is not None:
992	self.write_attribute(size, "name",
993	str(datainfo.source.beam_size_name))
994	written = self.write_node( \
995	size, "x", datainfo.source.beam_size.x,
996	{"unit": datainfo.source.beam_size_unit})
997	written = written \| self.write_node( \
998	size, "y", datainfo.source.beam_size.y,
999	{"unit": datainfo.source.beam_size_unit})
1000	written = written \| self.write_node( \
1001	size, "z", datainfo.source.beam_size.z,
1002	{"unit": datainfo.source.beam_size_unit})
1003	if written:
1004	self.append(size, source)
1005
1006	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1007	self.write_node(source, "wavelength",
1008	datainfo.source.wavelength,
1009	{"unit": datainfo.source.wavelength_unit})
1010	self.write_node(source, "wavelength_min",
1011	datainfo.source.wavelength_min,
1012	{"unit": datainfo.source.wavelength_min_unit})
1013	self.write_node(source, "wavelength_max",
1014	datainfo.source.wavelength_max,
1015	{"unit": datainfo.source.wavelength_max_unit})
1016	self.write_node(source, "wavelength_spread",
1017	datainfo.source.wavelength_spread,
1018	{"unit": datainfo.source.wavelength_spread_unit})
1019
1020	def _write_collimation(self, datainfo, instr):
1021	"""
1022	Writes the collimation information to the XML file
1023
1024	:param datainfo: The Data1D object the information is coming from
1025	:param instr: lxml node ElementTree object to be appended to
1026	"""
1027	if datainfo.collimation == [] or datainfo.collimation is None:
1028	coll = Collimation()
1029	datainfo.collimation.append(coll)
1030	for item in datainfo.collimation:
1031	coll = self.create_element("SAScollimation")
1032	if item.name is not None:
1033	self.write_attribute(coll, "name", str(item.name))
1034	self.append(coll, instr)
1035
1036	self.write_node(coll, "length", item.length,
1037	{"unit": item.length_unit})
1038
1039	for aperture in item.aperture:
1040	apert = self.create_element("aperture")
1041	if aperture.name is not None:
1042	self.write_attribute(apert, "name", str(aperture.name))
1043	if aperture.type is not None:
1044	self.write_attribute(apert, "type", str(aperture.type))
1045	self.append(apert, coll)
1046
1047	size = self.create_element("size")
1048	if aperture.size_name is not None:
1049	self.write_attribute(size, "name",
1050	str(aperture.size_name))
1051	written = self.write_node(size, "x", aperture.size.x,
1052	{"unit": aperture.size_unit})
1053	written = written \| self.write_node( \
1054	size, "y", aperture.size.y,
1055	{"unit": aperture.size_unit})
1056	written = written \| self.write_node( \
1057	size, "z", aperture.size.z,
1058	{"unit": aperture.size_unit})
1059	if written:
1060	self.append(size, apert)
1061
1062	self.write_node(apert, "distance", aperture.distance,
1063	{"unit": aperture.distance_unit})
1064
1065	def _write_detectors(self, datainfo, instr):
1066	"""
1067	Writes the detector information to the XML file
1068
1069	:param datainfo: The Data1D object the information is coming from
1070	:param inst: lxml instrument node to be appended to
1071	"""
1072	if datainfo.detector is None or datainfo.detector == []:
1073	det = Detector()
1074	det.name = ""
1075	datainfo.detector.append(det)
1076
1077	for item in datainfo.detector:
1078	det = self.create_element("SASdetector")
1079	written = self.write_node(det, "name", item.name)
1080	written = written \| self.write_node(det, "SDD", item.distance,
1081	{"unit": item.distance_unit})
1082	if written:
1083	self.append(det, instr)
1084
1085	off = self.create_element("offset")
1086	written = self.write_node(off, "x", item.offset.x,
1087	{"unit": item.offset_unit})
1088	written = written \| self.write_node(off, "y", item.offset.y,
1089	{"unit": item.offset_unit})
1090	written = written \| self.write_node(off, "z", item.offset.z,
1091	{"unit": item.offset_unit})
1092	if written:
1093	self.append(off, det)
1094
1095	ori = self.create_element("orientation")
1096	written = self.write_node(ori, "roll", item.orientation.x,
1097	{"unit": item.orientation_unit})
1098	written = written \| self.write_node(ori, "pitch",
1099	item.orientation.y,
1100	{"unit": item.orientation_unit})
1101	written = written \| self.write_node(ori, "yaw",
1102	item.orientation.z,
1103	{"unit": item.orientation_unit})
1104	if written:
1105	self.append(ori, det)
1106
1107	center = self.create_element("beam_center")
1108	written = self.write_node(center, "x", item.beam_center.x,
1109	{"unit": item.beam_center_unit})
1110	written = written \| self.write_node(center, "y",
1111	item.beam_center.y,
1112	{"unit": item.beam_center_unit})
1113	written = written \| self.write_node(center, "z",
1114	item.beam_center.z,
1115	{"unit": item.beam_center_unit})
1116	if written:
1117	self.append(center, det)
1118
1119	pix = self.create_element("pixel_size")
1120	written = self.write_node(pix, "x", item.pixel_size.x,
1121	{"unit": item.pixel_size_unit})
1122	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1123	{"unit": item.pixel_size_unit})
1124	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1125	{"unit": item.pixel_size_unit})
1126	if written:
1127	self.append(pix, det)
1128	self.write_node(det, "slit_length", item.slit_length,
1129	{"unit": item.slit_length_unit})
1130
1131
1132	def _write_process_notes(self, datainfo, entry_node):
1133	"""
1134	Writes the process notes to the XML file
1135
1136	:param datainfo: The Data1D object the information is coming from
1137	:param entry_node: lxml node ElementTree object to be appended to
1138
1139	"""
1140	for item in datainfo.process:
1141	node = self.create_element("SASprocess")
1142	self.append(node, entry_node)
1143	self.write_node(node, "name", item.name)
1144	self.write_node(node, "date", item.date)
1145	self.write_node(node, "description", item.description)
1146	for term in item.term:
1147	if isinstance(term, list):
1148	value = term['value']
1149	del term['value']
1150	elif isinstance(term, dict):
1151	value = term.get("value")
1152	del term['value']
1153	else:
1154	value = term
1155	self.write_node(node, "term", value, term)
1156	for note in item.notes:
1157	self.write_node(node, "SASprocessnote", note)
1158	if len(item.notes) == 0:
1159	self.write_node(node, "SASprocessnote", "")
1160
1161	def _write_notes(self, datainfo, entry_node):
1162	"""
1163	Writes the notes to the XML file and creates an empty note if none
1164	exist
1165
1166	:param datainfo: The Data1D object the information is coming from
1167	:param entry_node: lxml node ElementTree object to be appended to
1168
1169	"""
1170	if len(datainfo.notes) == 0:
1171	node = self.create_element("SASnote")
1172	self.append(node, entry_node)
1173	else:
1174	for item in datainfo.notes:
1175	node = self.create_element("SASnote")
1176	self.write_text(node, item)
1177	self.append(node, entry_node)
1178
1179	def _check_origin(self, entry_node, doc):
1180	"""
1181	Return the document, and the SASentry node associated with
1182	the data we just wrote.
1183	If the calling function was not the cansas reader, return a minidom
1184	object rather than an lxml object.
1185
1186	:param entry_node: lxml node ElementTree object to be appended to
1187	:param doc: entire xml tree
1188	"""
1189	if not self.frm:
1190	self.frm = inspect.stack()[1]
1191	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1192	mod_name = mod_name.replace(".py", "")
1193	mod = mod_name.split("sas/")
1194	mod_name = mod[1]
1195	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1196	string = self.to_string(doc, pretty_print=False)
1197	doc = parseString(string)
1198	node_name = entry_node.tag
1199	node_list = doc.getElementsByTagName(node_name)
1200	entry_node = node_list.item(0)
1201	return doc, entry_node
1202
1203	# DO NOT REMOVE - used in saving and loading panel states.
1204	def _store_float(self, location, node, variable, storage, optional=True):
1205	"""
1206	Get the content of a xpath location and store
1207	the result. Check that the units are compatible
1208	with the destination. The value is expected to
1209	be a float.
1210
1211	The xpath location might or might not exist.
1212	If it does not exist, nothing is done
1213
1214	:param location: xpath location to fetch
1215	:param node: node to read the data from
1216	:param variable: name of the data member to store it in [string]
1217	:param storage: data object that has the 'variable' data member
1218	:param optional: if True, no exception will be raised
1219	if unit conversion can't be done
1220
1221	:raise ValueError: raised when the units are not recognized
1222	"""
1223	entry = get_content(location, node)
1224	try:
1225	value = float(entry.text)
1226	except ValueError:
1227	value = None
1228
1229	if value is not None:
1230	# If the entry has units, check to see that they are
1231	# compatible with what we currently have in the data object
1232	units = entry.get('unit')
1233	if units is not None:
1234	toks = variable.split('.')
1235	local_unit = getattr(storage, toks[0]+"_unit")
1236	if local_unit is not None and units.lower() != local_unit.lower():
1237	try:
1238	conv = Converter(units)
1239	setattrchain(storage, variable, conv(value, units=local_unit))
1240	except Exception as exc:
1241	err_mess = "CanSAS reader: could not convert"
1242	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1243	% (variable, units, local_unit, exc)
1244	self.errors.add(err_mess)
1245	if optional:
1246	logger.info(err_mess)
1247	else:
1248	raise ValueError(err_mess)
1249	else:
1250	setattrchain(storage, variable, value)
1251	else:
1252	setattrchain(storage, variable, value)
1253
1254	# DO NOT REMOVE - used in saving and loading panel states.
1255	def _store_content(self, location, node, variable, storage):
1256	"""
1257	Get the content of a xpath location and store
1258	the result. The value is treated as a string.
1259
1260	The xpath location might or might not exist.
1261	If it does not exist, nothing is done
1262
1263	:param location: xpath location to fetch
1264	:param node: node to read the data from
1265	:param variable: name of the data member to store it in [string]
1266	:param storage: data object that has the 'variable' data member
1267
1268	:return: return a list of errors
1269	"""
1270	entry = get_content(location, node)
1271	if entry is not None and entry.text is not None:
1272	setattrchain(storage, variable, entry.text.strip())
1273
1274	# DO NOT REMOVE Called by outside packages:
1275	# sas.sasgui.perspectives.invariant.invariant_state
1276	# sas.sasgui.perspectives.fitting.pagestate
1277	def get_content(location, node):
1278	"""
1279	Get the first instance of the content of a xpath location.
1280
1281	:param location: xpath location
1282	:param node: node to start at
1283
1284	:return: Element, or None
1285	"""
1286	nodes = node.xpath(location,
1287	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1288	if len(nodes) > 0:
1289	return nodes[0]
1290	else:
1291	return None
1292
1293	# DO NOT REMOVE Called by outside packages:
1294	# sas.sasgui.perspectives.fitting.pagestate
1295	def write_node(doc, parent, name, value, attr=None):
1296	"""
1297	:param doc: document DOM
1298	:param parent: parent node
1299	:param name: tag of the element
1300	:param value: value of the child text node
1301	:param attr: attribute dictionary
1302
1303	:return: True if something was appended, otherwise False
1304	"""
1305	if attr is None:
1306	attr = {}
1307	if value is not None:
1308	node = doc.createElement(name)
1309	node.appendChild(doc.createTextNode(str(value)))
1310	for item in attr:
1311	node.setAttribute(item, attr[item])
1312	parent.appendChild(node)
1313	return True
1314	return False
1315
1316	def getattrchain(obj, chain, default=None):
1317	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
1318	for part in chain.split('.'):
1319	if hasattr(obj, part):
1320	obj = getattr(obj, part, None)
1321	else:
1322	return default
1323	return obj
1324
1325	def setattrchain(obj, chain, value):
1326	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
1327	parts = list(chain.split('.'))
1328	for part in parts[-1]:
1329	obj = getattr(obj, part, None)
1330	if obj is None:
1331	raise ValueError("missing parent object "+part)
1332	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 7ad12e9f

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