cansas_reader.py @ 0e0c645

ticket-1243

Last change on this file since 0e0c645 was 0e0c645, checked in by Jeff Krzywon <jkrzywon@…>, 5 years ago
Fix for loading 2D saved projects and small clean up of cansas XML reader.
Property mode set to `100644`
File size: 61.1 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	from ..loader_exceptions import FileContentsException, DefaultReaderException, \
21	DataReaderException
22	from . import xml_reader
23	from .xml_reader import XMLreader
24	from .cansas_constants import CansasConstants
25
26	logger = logging.getLogger(__name__)
27
28	PREPROCESS = "xmlpreprocess"
29	ENCODING = "encoding"
30	RUN_NAME_DEFAULT = "None"
31	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
32	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
33	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
34	"as much of the data as possible.\n\n"
35
36	CONSTANTS = CansasConstants()
37	CANSAS_FORMAT = CONSTANTS.format
38	CANSAS_NS = CONSTANTS.names
39	ALLOW_ALL = True
40
41	class Reader(XMLreader):
42	cansas_version = "1.0"
43	base_ns = "{cansas1d/1.0}"
44	cansas_defaults = None
45	type_name = "canSAS"
46	invalid = True
47	frm = ""
48	# Log messages and errors
49	logging = None
50	errors = set()
51	# Namespace hierarchy for current xml_file object
52	names = None
53	ns_list = None
54	# Temporary storage location for loading multiple data sets in a single file
55	current_data1d = None
56	data = None
57	# Wildcards
58	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
59	# List of allowed extensions
60	ext = ['.xml', '.svs']
61	# Flag to bypass extension check
62	allow_all = True
63
64	def reset_state(self):
65	"""
66	Resets the class state to a base case when loading a new data file so previous
67	data files do not appear a second time
68	"""
69	super(Reader, self).reset_state()
70	self.data = []
71	self.process = Process()
72	self.transspectrum = TransmissionSpectrum()
73	self.aperture = Aperture()
74	self.collimation = Collimation()
75	self.detector = Detector()
76	self.names = []
77	self.cansas_defaults = {}
78	self.ns_list = None
79	self.logging = []
80	self.encoding = None
81
82	def _read(self, xml_file, schema_path="", invalid=True):
83	if schema_path != "" or not invalid:
84	# read has been called from self.get_file_contents because xml file doens't conform to schema
85	_, self.extension = os.path.splitext(os.path.basename(xml_file))
86	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
87
88	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
89	return super(XMLreader, self).read(xml_file)
90
91	def get_file_contents(self):
92	return self._get_file_contents(xml_file=None, schema_path="", invalid=True)
93
94	def _get_file_contents(self, xml_file=None, schema_path="", invalid=True):
95	# Reset everything since we're loading a new file
96	self.reset_state()
97	self.invalid = invalid
98	if xml_file is None:
99	xml_file = self.f_open.name
100	# We don't sure f_open since lxml handles opnening/closing files
101	try:
102	# Raises FileContentsException
103	self.load_file_and_schema(xml_file, schema_path)
104	# Parse each SASentry
105	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
106	namespaces={
107	'ns': self.cansas_defaults.get(
108	"ns")
109	})
110	self.is_cansas(self.extension)
111	self.set_processing_instructions()
112	for entry in entry_list:
113	self._parse_entry(entry)
114	self.data_cleanup()
115	except FileContentsException as fc_exc:
116	# File doesn't meet schema - try loading with a less strict schema
117	base_name = xml_reader.__file__
118	base_name = base_name.replace("\\", "/")
119	base = base_name.split("/sas/")[0]
120	if self.cansas_version == "1.1":
121	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
122	else:
123	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
124	self.set_schema(invalid_schema)
125	if self.invalid:
126	try:
127	# Load data with less strict schema
128	self._get_file_contents(xml_file, invalid_schema, False)
129
130	# File can still be read but doesn't match schema, so raise exception
131	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
132	invalid_xml = self.find_invalid_xml()
133	if invalid_xml != "":
134	basename, _ = os.path.splitext(
135	os.path.basename(self.f_open.name))
136	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
137	raise DataReaderException(invalid_xml) # Handled by base class
138	except FileContentsException as fc_exc:
139	msg = "CanSAS Reader could not load the file {}".format(xml_file)
140	if fc_exc.message is not None: # Propagate error messages from earlier
141	msg = fc_exc.message
142	if not self.extension in self.ext: # If the file has no associated loader
143	raise DefaultReaderException(msg)
144	raise FileContentsException(msg)
145	pass
146	else:
147	raise fc_exc
148	except Exception as e: # Convert all other exceptions to FileContentsExceptions
149	raise FileContentsException(str(e))
150	finally:
151	if not self.f_open.closed:
152	self.f_open.close()
153
154	def load_file_and_schema(self, xml_file, schema_path=""):
155	base_name = xml_reader.__file__
156	base_name = base_name.replace("\\", "/")
157	base = base_name.split("/sas/")[0]
158
159	# Try and parse the XML file
160	try:
161	self.set_xml_file(xml_file)
162	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
163	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
164	raise FileContentsException(msg)
165
166	self.cansas_version = self.xmlroot.get("version", "1.0")
167	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
168
169	if schema_path == "":
170	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
171	base, self.cansas_defaults.get("schema").replace("\\", "/")
172	)
173	self.set_schema(schema_path)
174
175	def is_cansas(self, ext="xml"):
176	"""
177	Checks to see if the XML file is a CanSAS file
178
179	:param ext: The file extension of the data file
180	:raises FileContentsException: Raised if XML file isn't valid CanSAS
181	"""
182	if self.validate_xml(): # Check file is valid XML
183	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
184	value = self.xmlroot.get(name)
185	# Check schema CanSAS version matches file CanSAS version
186	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
187	return True
188	if ext == "svs":
189	return True # Why is this required?
190	# If we get to this point then file isn't valid CanSAS
191	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
192	raise FileContentsException("The file is not valid CanSAS")
193
194	def _parse_entry(self, dom, recurse=False):
195	if not self._is_call_local() and not recurse:
196	self.reset_state()
197	if not recurse:
198	self.current_datainfo = DataInfo()
199	# Raises FileContentsException if file doesn't meet CanSAS schema
200	self.invalid = False
201	# Look for a SASentry
202	self.data = []
203	self.parent_class = "SASentry"
204	self.names.append("SASentry")
205	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
206	self.current_datainfo.meta_data[
207	PREPROCESS] = self.processing_instructions
208	if self._is_call_local() and not recurse:
209	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
210	self.current_datainfo.filename = basename + self.extension
211	# Create an empty dataset if no data has been passed to the reader
212	if self.current_dataset is None:
213	self._initialize_new_data_set(dom)
214	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
215
216	# Loop through each child in the parent element
217	for node in dom:
218	attr = node.attrib
219	name = attr.get("name", "")
220	type = attr.get("type", "")
221	# Get the element name and set the current names level
222	tagname = node.tag.replace(self.base_ns, "")
223	tagname_original = tagname
224	# Skip this iteration when loading in save state information
225	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
226	continue
227	# Get where to store content
228	self.names.append(tagname_original)
229	self.ns_list = CONSTANTS.iterate_namespace(self.names)
230	# If the element is a child element, recurse
231	if len(node.getchildren()) > 0:
232	self.parent_class = tagname_original
233	if tagname == 'SASdata':
234	self._initialize_new_data_set(node)
235	if isinstance(self.current_dataset, plottable_2D):
236	x_bins = attr.get("x_bins", "")
237	y_bins = attr.get("y_bins", "")
238	if x_bins is not "" and y_bins is not "":
239	self.current_dataset.shape = (x_bins, y_bins)
240	else:
241	self.current_dataset.shape = ()
242	# Recurse to access data within the group
243	self._parse_entry(node, recurse=True)
244	if tagname == "SASsample":
245	self.current_datainfo.sample.name = name
246	elif tagname == "beam_size":
247	self.current_datainfo.source.beam_size_name = name
248	elif tagname == "SAScollimation":
249	self.collimation.name = name
250	elif tagname == "aperture":
251	self.aperture.name = name
252	self.aperture.type = type
253	self._add_intermediate()
254	else:
255	# TODO: Clean this up to make it faster (fewer if/elifs)
256	if isinstance(self.current_dataset, plottable_2D):
257	data_point = node.text
258	unit = attr.get('unit', '')
259	else:
260	data_point, unit = self._get_node_value(node, tagname)
261
262	# If this is a dataset, store the data appropriately
263	if tagname == 'Run':
264	self.current_datainfo.run_name[data_point] = name
265	self.current_datainfo.run.append(data_point)
266	elif tagname == 'Title':
267	self.current_datainfo.title = data_point
268	elif tagname == 'SASnote':
269	self.current_datainfo.notes.append(data_point)
270
271	# I and Q points
272	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
273	self.current_dataset.yaxis("Intensity", unit)
274	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
275	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
276	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
277	elif tagname == 'Q':
278	self.current_dataset.xaxis("Q", unit)
279	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
280	elif tagname == 'Qdev':
281	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
282	elif tagname == 'dQw':
283	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
284	elif tagname == 'dQl':
285	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
286	elif tagname == 'Qmean':
287	pass
288	elif tagname == 'Shadowfactor':
289	pass
290	elif tagname == 'Sesans':
291	self.current_datainfo.isSesans = bool(data_point)
292	self.current_dataset.xaxis(attr.get('x_axis'),
293	attr.get('x_unit'))
294	self.current_dataset.yaxis(attr.get('y_axis'),
295	attr.get('y_unit'))
296	elif tagname == 'yacceptance':
297	self.current_datainfo.sample.yacceptance = (data_point, unit)
298	elif tagname == 'zacceptance':
299	self.current_datainfo.sample.zacceptance = (data_point, unit)
300
301	# I and Qx, Qy - 2D data
302	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
303	self.current_dataset.yaxis("Intensity", unit)
304	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
306	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
307	elif tagname == 'Qx':
308	self.current_dataset.xaxis("Qx", unit)
309	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
310	elif tagname == 'Qy':
311	self.current_dataset.yaxis("Qy", unit)
312	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
313	elif tagname == 'Qxdev':
314	self.current_dataset.xaxis("Qxdev", unit)
315	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
316	elif tagname == 'Qydev':
317	self.current_dataset.yaxis("Qydev", unit)
318	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
319	elif tagname == 'Mask':
320	inter = [item == "1" for item in data_point.split(",")]
321	self.current_dataset.mask = np.asarray(inter, dtype=bool)
322
323	# Sample Information
324	elif tagname == 'ID' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.ID = data_point
326	elif tagname == 'Title' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.name = data_point
328	elif tagname == 'thickness' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.thickness = data_point
330	self.current_datainfo.sample.thickness_unit = unit
331	elif tagname == 'transmission' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.transmission = data_point
333	elif tagname == 'temperature' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.temperature = data_point
335	self.current_datainfo.sample.temperature_unit = unit
336	elif tagname == 'details' and self.parent_class == 'SASsample':
337	self.current_datainfo.sample.details.append(data_point)
338	elif tagname == 'x' and self.parent_class == 'position':
339	self.current_datainfo.sample.position.x = data_point
340	self.current_datainfo.sample.position_unit = unit
341	elif tagname == 'y' and self.parent_class == 'position':
342	self.current_datainfo.sample.position.y = data_point
343	self.current_datainfo.sample.position_unit = unit
344	elif tagname == 'z' and self.parent_class == 'position':
345	self.current_datainfo.sample.position.z = data_point
346	self.current_datainfo.sample.position_unit = unit
347	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
348	self.current_datainfo.sample.orientation.x = data_point
349	self.current_datainfo.sample.orientation_unit = unit
350	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
351	self.current_datainfo.sample.orientation.y = data_point
352	self.current_datainfo.sample.orientation_unit = unit
353	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
354	self.current_datainfo.sample.orientation.z = data_point
355	self.current_datainfo.sample.orientation_unit = unit
356
357	# Instrumental Information
358	elif tagname == 'name' and self.parent_class == 'SASinstrument':
359	self.current_datainfo.instrument = data_point
360
361	# Detector Information
362	elif tagname == 'name' and self.parent_class == 'SASdetector':
363	self.detector.name = data_point
364	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
365	self.detector.distance = data_point
366	self.detector.distance_unit = unit
367	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
368	self.detector.slit_length = data_point
369	self.detector.slit_length_unit = unit
370	elif tagname == 'x' and self.parent_class == 'offset':
371	self.detector.offset.x = data_point
372	self.detector.offset_unit = unit
373	elif tagname == 'y' and self.parent_class == 'offset':
374	self.detector.offset.y = data_point
375	self.detector.offset_unit = unit
376	elif tagname == 'z' and self.parent_class == 'offset':
377	self.detector.offset.z = data_point
378	self.detector.offset_unit = unit
379	elif tagname == 'x' and self.parent_class == 'beam_center':
380	self.detector.beam_center.x = data_point
381	self.detector.beam_center_unit = unit
382	elif tagname == 'y' and self.parent_class == 'beam_center':
383	self.detector.beam_center.y = data_point
384	self.detector.beam_center_unit = unit
385	elif tagname == 'z' and self.parent_class == 'beam_center':
386	self.detector.beam_center.z = data_point
387	self.detector.beam_center_unit = unit
388	elif tagname == 'x' and self.parent_class == 'pixel_size':
389	self.detector.pixel_size.x = data_point
390	self.detector.pixel_size_unit = unit
391	elif tagname == 'y' and self.parent_class == 'pixel_size':
392	self.detector.pixel_size.y = data_point
393	self.detector.pixel_size_unit = unit
394	elif tagname == 'z' and self.parent_class == 'pixel_size':
395	self.detector.pixel_size.z = data_point
396	self.detector.pixel_size_unit = unit
397	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
398	self.detector.orientation.x = data_point
399	self.detector.orientation_unit = unit
400	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
401	self.detector.orientation.y = data_point
402	self.detector.orientation_unit = unit
403	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
404	self.detector.orientation.z = data_point
405	self.detector.orientation_unit = unit
406
407	# Collimation and Aperture
408	elif tagname == 'length' and self.parent_class == 'SAScollimation':
409	self.collimation.length = data_point
410	self.collimation.length_unit = unit
411	elif tagname == 'name' and self.parent_class == 'SAScollimation':
412	self.collimation.name = data_point
413	elif tagname == 'distance' and self.parent_class == 'aperture':
414	self.aperture.distance = data_point
415	self.aperture.distance_unit = unit
416	elif tagname == 'x' and self.parent_class == 'size':
417	self.aperture.size.x = data_point
418	self.collimation.size_unit = unit
419	elif tagname == 'y' and self.parent_class == 'size':
420	self.aperture.size.y = data_point
421	self.collimation.size_unit = unit
422	elif tagname == 'z' and self.parent_class == 'size':
423	self.aperture.size.z = data_point
424	self.collimation.size_unit = unit
425
426	# Process Information
427	elif tagname == 'name' and self.parent_class == 'SASprocess':
428	self.process.name = data_point
429	elif tagname == 'description' and self.parent_class == 'SASprocess':
430	self.process.description = data_point
431	elif tagname == 'date' and self.parent_class == 'SASprocess':
432	try:
433	self.process.date = datetime.datetime.fromtimestamp(data_point)
434	except:
435	self.process.date = data_point
436	elif tagname == 'SASprocessnote':
437	self.process.notes.append(data_point)
438	elif tagname == 'term' and self.parent_class == 'SASprocess':
439	unit = attr.get("unit", "")
440	dic = { "name": name, "value": data_point, "unit": unit }
441	self.process.term.append(dic)
442
443	# Transmission Spectrum
444	elif tagname == 'T' and self.parent_class == 'Tdata':
445	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
446	self.transspectrum.transmission_unit = unit
447	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
448	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
449	self.transspectrum.transmission_deviation_unit = unit
450	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
451	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
452	self.transspectrum.wavelength_unit = unit
453
454	# Source Information
455	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
456	self.current_datainfo.source.wavelength = data_point
457	self.current_datainfo.source.wavelength_unit = unit
458	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
459	self.current_datainfo.source.wavelength_min = data_point
460	self.current_datainfo.source.wavelength_min_unit = unit
461	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
462	self.current_datainfo.source.wavelength_max = data_point
463	self.current_datainfo.source.wavelength_max_unit = unit
464	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
465	self.current_datainfo.source.wavelength_spread = data_point
466	self.current_datainfo.source.wavelength_spread_unit = unit
467	elif tagname == 'x' and self.parent_class == 'beam_size':
468	self.current_datainfo.source.beam_size.x = data_point
469	self.current_datainfo.source.beam_size_unit = unit
470	elif tagname == 'y' and self.parent_class == 'beam_size':
471	self.current_datainfo.source.beam_size.y = data_point
472	self.current_datainfo.source.beam_size_unit = unit
473	elif tagname == 'z' and self.parent_class == 'pixel_size':
474	self.current_datainfo.source.data_point.z = data_point
475	self.current_datainfo.source.beam_size_unit = unit
476	elif tagname == 'radiation' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.radiation = data_point
478	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
479	self.current_datainfo.source.beam_shape = data_point
480
481	# Everything else goes in meta_data
482	else:
483	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
484	self.current_datainfo.meta_data[new_key] = data_point
485
486	self.names.remove(tagname_original)
487	length = 0
488	if len(self.names) > 1:
489	length = len(self.names) - 1
490	self.parent_class = self.names[length]
491	if not self._is_call_local() and not recurse:
492	self.frm = ""
493	self.current_datainfo.errors = set()
494	for error in self.errors:
495	self.current_datainfo.errors.add(error)
496	self.data_cleanup()
497	self.sort_data()
498	self.reset_data_list()
499	return self.output[0], None
500
501	def _is_call_local(self):
502	if self.frm == "":
503	inter = inspect.stack()
504	self.frm = inter[2]
505	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
506	mod_name = mod_name.replace(".py", "")
507	mod = mod_name.split("sas/")
508	mod_name = mod[1]
509	if mod_name != "sascalc/dataloader/readers/cansas_reader":
510	return False
511	return True
512
513	def _add_intermediate(self):
514	"""
515	This method stores any intermediate objects within the final data set after fully reading the set.
516	"""
517	if self.parent_class == 'SASprocess':
518	self.current_datainfo.process.append(self.process)
519	self.process = Process()
520	elif self.parent_class == 'SASdetector':
521	self.current_datainfo.detector.append(self.detector)
522	self.detector = Detector()
523	elif self.parent_class == 'SAStransmission_spectrum':
524	self.current_datainfo.trans_spectrum.append(self.transspectrum)
525	self.transspectrum = TransmissionSpectrum()
526	elif self.parent_class == 'SAScollimation':
527	self.current_datainfo.collimation.append(self.collimation)
528	self.collimation = Collimation()
529	elif self.parent_class == 'aperture':
530	self.collimation.aperture.append(self.aperture)
531	self.aperture = Aperture()
532	elif self.parent_class == 'SASdata':
533	self.data.append(self.current_dataset)
534
535	def _get_node_value(self, node, tagname):
536	"""
537	Get the value of a node and any applicable units
538
539	:param node: The XML node to get the value of
540	:param tagname: The tagname of the node
541	"""
542	#Get the text from the node and convert all whitespace to spaces
543	units = ''
544	node_value = node.text
545	if node_value is not None:
546	node_value = ' '.join(node_value.split())
547	else:
548	node_value = ""
549
550	# If the value is a float, compile with units.
551	if self.ns_list.ns_datatype == "float":
552	# If an empty value is given, set as zero.
553	if node_value is None or node_value.isspace() \
554	or node_value.lower() == "nan":
555	node_value = "0.0"
556	#Convert the value to the base units
557	node_value, units = self._unit_conversion(node, tagname, node_value)
558
559	# If the value is a timestamp, convert to a datetime object
560	elif self.ns_list.ns_datatype == "timestamp":
561	if node_value is None or node_value.isspace():
562	pass
563	else:
564	try:
565	node_value = \
566	datetime.datetime.fromtimestamp(node_value)
567	except ValueError:
568	node_value = None
569	return node_value, units
570
571	def _unit_conversion(self, node, tagname, node_value):
572	"""
573	A unit converter method used to convert the data included in the file
574	to the default units listed in data_info
575
576	:param node: XML node
577	:param tagname: name of the node
578	:param node_value: The value of the current dom node
579	"""
580	attr = node.attrib
581	value_unit = ''
582	err_msg = None
583	default_unit = None
584	if not isinstance(node_value, float):
585	node_value = float(node_value)
586	if 'unit' in attr and attr.get('unit') is not None:
587	try:
588	unit = attr['unit']
589	# Split the units to retain backwards compatibility with
590	# projects, analyses, and saved data from v4.1.0
591	unit_list = unit.split("\|")
592	if len(unit_list) > 1:
593	local_unit = unit_list[1]
594	else:
595	local_unit = unit
596	unitname = self.ns_list.current_level.get("unit", "")
597	if "SASdetector" in self.names:
598	save_in = "detector"
599	elif "aperture" in self.names:
600	save_in = "aperture"
601	elif "SAScollimation" in self.names:
602	save_in = "collimation"
603	elif "SAStransmission_spectrum" in self.names:
604	save_in = "transspectrum"
605	elif "SASdata" in self.names:
606	x = np.zeros(1)
607	y = np.zeros(1)
608	self.current_data1d = Data1D(x, y)
609	save_in = "current_data1d"
610	elif "SASsource" in self.names:
611	save_in = "current_datainfo.source"
612	elif "SASsample" in self.names:
613	save_in = "current_datainfo.sample"
614	elif "SASprocess" in self.names:
615	save_in = "process"
616	else:
617	save_in = "current_datainfo"
618	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
619	if (local_unit and default_unit
620	and local_unit.lower() != default_unit.lower()
621	and local_unit.lower() != "none"):
622	# Check local units - bad units raise KeyError
623	#print("loading", tagname, node_value, local_unit, default_unit)
624	data_conv_q = Converter(local_unit)
625	value_unit = default_unit
626	node_value = data_conv_q(node_value, units=default_unit)
627	else:
628	value_unit = local_unit
629	except KeyError:
630	# Do not throw an error for loading Sesans data in cansas xml
631	# This is a temporary fix.
632	if local_unit != "A" and local_unit != 'pol':
633	err_msg = "CanSAS reader: unexpected "
634	err_msg += "\"{0}\" unit [{1}]; "
635	err_msg = err_msg.format(tagname, local_unit)
636	err_msg += "expecting [{0}]".format(default_unit)
637	value_unit = local_unit
638	except Exception:
639	err_msg = "CanSAS reader: unknown error converting "
640	err_msg += "\"{0}\" unit [{1}]"
641	err_msg = err_msg.format(tagname, local_unit)
642	value_unit = local_unit
643	elif 'unit' in attr:
644	value_unit = attr['unit']
645	if err_msg:
646	self.errors.add(err_msg)
647	return node_value, value_unit
648
649	def _initialize_new_data_set(self, node=None):
650	if node is not None:
651	for child in node:
652	if child.tag.replace(self.base_ns, "") == "Idata":
653	for i_child in child:
654	if i_child.tag.replace(self.base_ns, "") == "Qx":
655	self.current_dataset = plottable_2D()
656	return
657	self.current_dataset = plottable_1D(np.array(0), np.array(0))
658
659	## Writing Methods
660	def write(self, filename, datainfo):
661	"""
662	Write the content of a Data1D as a CanSAS XML file
663
664	:param filename: name of the file to write
665	:param datainfo: Data1D object
666	"""
667	# Create XML document
668	doc, _ = self._to_xml_doc(datainfo)
669	# Write the file
670	file_ref = open(filename, 'wb')
671	if self.encoding is None:
672	self.encoding = "UTF-8"
673	doc.write(file_ref, encoding=self.encoding,
674	pretty_print=True, xml_declaration=True)
675	file_ref.close()
676
677	def _to_xml_doc(self, datainfo):
678	"""
679	Create an XML document to contain the content of a Data1D
680
681	:param datainfo: Data1D object
682	"""
683	is_2d = False
684	if issubclass(datainfo.__class__, Data2D):
685	is_2d = True
686
687	# Get PIs and create root element
688	pi_string = self._get_pi_string()
689	# Define namespaces and create SASroot object
690	main_node = self._create_main_node()
691	# Create ElementTree, append SASroot and apply processing instructions
692	base_string = pi_string + self.to_string(main_node)
693	base_element = self.create_element_from_string(base_string)
694	doc = self.create_tree(base_element)
695	# Create SASentry Element
696	entry_node = self.create_element("SASentry")
697	root = doc.getroot()
698	root.append(entry_node)
699
700	# Add Title to SASentry
701	self.write_node(entry_node, "Title", datainfo.title)
702	# Add Run to SASentry
703	self._write_run_names(datainfo, entry_node)
704	# Add Data info to SASEntry
705	if is_2d:
706	self._write_data_2d(datainfo, entry_node)
707	else:
708	self._write_data(datainfo, entry_node)
709	# Transmission Spectrum Info
710	# TODO: fix the writer to linearize all data, including T_spectrum
711	# self._write_trans_spectrum(datainfo, entry_node)
712	# Sample info
713	self._write_sample_info(datainfo, entry_node)
714	# Instrument info
715	instr = self._write_instrument(datainfo, entry_node)
716	# Source
717	self._write_source(datainfo, instr)
718	# Collimation
719	self._write_collimation(datainfo, instr)
720	# Detectors
721	self._write_detectors(datainfo, instr)
722	# Processes info
723	self._write_process_notes(datainfo, entry_node)
724	# Note info
725	self._write_notes(datainfo, entry_node)
726	# Return the document, and the SASentry node associated with
727	# the data we just wrote
728	# If the calling function was not the cansas reader, return a minidom
729	# object rather than an lxml object.
730	self.frm = inspect.stack()[1]
731	doc, entry_node = self._check_origin(entry_node, doc)
732	return doc, entry_node
733
734	def write_node(self, parent, name, value, attr=None):
735	"""
736	:param doc: document DOM
737	:param parent: parent node
738	:param name: tag of the element
739	:param value: value of the child text node
740	:param attr: attribute dictionary
741
742	:return: True if something was appended, otherwise False
743	"""
744	if value is not None:
745	parent = self.ebuilder(parent, name, value, attr)
746	return True
747	return False
748
749	def _get_pi_string(self):
750	"""
751	Creates the processing instructions header for writing to file
752	"""
753	pis = self.return_processing_instructions()
754	if len(pis) > 0:
755	pi_tree = self.create_tree(pis[0])
756	i = 1
757	for i in range(1, len(pis) - 1):
758	pi_tree = self.append(pis[i], pi_tree)
759	pi_string = self.to_string(pi_tree)
760	else:
761	pi_string = ""
762	return pi_string
763
764	def _create_main_node(self):
765	"""
766	Creates the primary xml header used when writing to file
767	"""
768	xsi = "http://www.w3.org/2001/XMLSchema-instance"
769	version = self.cansas_version
770	n_s = CANSAS_NS.get(version).get("ns")
771	if version == "1.1":
772	url = "http://www.cansas.org/formats/1.1/"
773	else:
774	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
775	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
776	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
777	"version" : version}
778	nsmap = {'xsi' : xsi, None: n_s}
779
780	main_node = self.create_element("{" + n_s + "}SASroot",
781	attrib=attrib, nsmap=nsmap)
782	return main_node
783
784	def _write_run_names(self, datainfo, entry_node):
785	"""
786	Writes the run names to the XML file
787
788	:param datainfo: The Data1D object the information is coming from
789	:param entry_node: lxml node ElementTree object to be appended to
790	"""
791	if datainfo.run is None or datainfo.run == []:
792	datainfo.run.append(RUN_NAME_DEFAULT)
793	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
794	for item in datainfo.run:
795	runname = {}
796	if item in datainfo.run_name and \
797	len(str(datainfo.run_name[item])) > 1:
798	runname = {'name': datainfo.run_name[item]}
799	self.write_node(entry_node, "Run", item, runname)
800
801	def _write_data(self, datainfo, entry_node):
802	"""
803	Writes 1D I and Q data to the XML file
804
805	:param datainfo: The Data1D object the information is coming from
806	:param entry_node: lxml node ElementTree object to be appended to
807	"""
808	node = self.create_element("SASdata")
809	self.append(node, entry_node)
810
811	for i in range(len(datainfo.x)):
812	point = self.create_element("Idata")
813	node.append(point)
814	self.write_node(point, "Q", datainfo.x[i],
815	{'unit': datainfo._xunit})
816	if len(datainfo.y) >= i:
817	self.write_node(point, "I", datainfo.y[i],
818	{'unit': datainfo._yunit})
819	if datainfo.dy is not None and len(datainfo.dy) > i:
820	self.write_node(point, "Idev", datainfo.dy[i],
821	{'unit': datainfo._yunit})
822	if datainfo.dx is not None and len(datainfo.dx) > i:
823	self.write_node(point, "Qdev", datainfo.dx[i],
824	{'unit': datainfo._xunit})
825	if datainfo.dxw is not None and len(datainfo.dxw) > i:
826	self.write_node(point, "dQw", datainfo.dxw[i],
827	{'unit': datainfo._xunit})
828	if datainfo.dxl is not None and len(datainfo.dxl) > i:
829	self.write_node(point, "dQl", datainfo.dxl[i],
830	{'unit': datainfo._xunit})
831	if datainfo.isSesans:
832	sesans_attrib = {'x_axis': datainfo._xaxis,
833	'y_axis': datainfo._yaxis,
834	'x_unit': datainfo.x_unit,
835	'y_unit': datainfo.y_unit}
836	sesans = self.create_element("Sesans", attrib=sesans_attrib)
837	sesans.text = str(datainfo.isSesans)
838	entry_node.append(sesans)
839	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
840	{'unit': datainfo.sample.yacceptance[1]})
841	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
842	{'unit': datainfo.sample.zacceptance[1]})
843
844
845	def _write_data_2d(self, datainfo, entry_node):
846	"""
847	Writes 2D data to the XML file
848
849	:param datainfo: The Data2D object the information is coming from
850	:param entry_node: lxml node ElementTree object to be appended to
851	"""
852	attr = {}
853	if datainfo.data.shape:
854	attr["x_bins"] = str(len(datainfo.x_bins))
855	attr["y_bins"] = str(len(datainfo.y_bins))
856	node = self.create_element("SASdata", attr)
857	self.append(node, entry_node)
858
859	point = self.create_element("Idata")
860	node.append(point)
861	qx = ','.join(str(v) for v in datainfo.qx_data)
862	qy = ','.join(str(v) for v in datainfo.qy_data)
863	intensity = ','.join(str(v) for v in datainfo.data)
864
865	self.write_node(point, "Qx", qx,
866	{'unit': datainfo._xunit})
867	self.write_node(point, "Qy", qy,
868	{'unit': datainfo._yunit})
869	self.write_node(point, "I", intensity,
870	{'unit': datainfo._zunit})
871	if datainfo.err_data is not None:
872	err = ','.join(str(v) for v in datainfo.err_data)
873	self.write_node(point, "Idev", err,
874	{'unit': datainfo._zunit})
875	if datainfo.dqy_data is not None:
876	dqy = ','.join(str(v) for v in datainfo.dqy_data)
877	self.write_node(point, "Qydev", dqy,
878	{'unit': datainfo._yunit})
879	if datainfo.dqx_data is not None:
880	dqx = ','.join(str(v) for v in datainfo.dqx_data)
881	self.write_node(point, "Qxdev", dqx,
882	{'unit': datainfo._xunit})
883	if datainfo.mask is not None:
884	mask = ','.join("1" if v else "0" for v in datainfo.mask)
885	self.write_node(point, "Mask", mask)
886
887	def _write_trans_spectrum(self, datainfo, entry_node):
888	"""
889	Writes the transmission spectrum data to the XML file
890
891	:param datainfo: The Data1D object the information is coming from
892	:param entry_node: lxml node ElementTree object to be appended to
893	"""
894	for i in range(len(datainfo.trans_spectrum)):
895	spectrum = datainfo.trans_spectrum[i]
896	node = self.create_element("SAStransmission_spectrum",
897	{"name" : spectrum.name})
898	self.append(node, entry_node)
899	if isinstance(spectrum.timestamp, datetime.datetime):
900	node.setAttribute("timestamp", spectrum.timestamp)
901	for i in range(len(spectrum.wavelength)):
902	point = self.create_element("Tdata")
903	node.append(point)
904	self.write_node(point, "Lambda", spectrum.wavelength[i],
905	{'unit': spectrum.wavelength_unit})
906	self.write_node(point, "T", spectrum.transmission[i],
907	{'unit': spectrum.transmission_unit})
908	if spectrum.transmission_deviation is not None \
909	and len(spectrum.transmission_deviation) >= i:
910	self.write_node(point, "Tdev",
911	spectrum.transmission_deviation[i],
912	{'unit':
913	spectrum.transmission_deviation_unit})
914
915	def _write_sample_info(self, datainfo, entry_node):
916	"""
917	Writes the sample information to the XML file
918
919	:param datainfo: The Data1D object the information is coming from
920	:param entry_node: lxml node ElementTree object to be appended to
921	"""
922	sample = self.create_element("SASsample")
923	if datainfo.sample.name is not None:
924	self.write_attribute(sample, "name",
925	str(datainfo.sample.name))
926	self.append(sample, entry_node)
927	self.write_node(sample, "ID", str(datainfo.sample.ID))
928	self.write_node(sample, "thickness", datainfo.sample.thickness,
929	{"unit": datainfo.sample.thickness_unit})
930	self.write_node(sample, "transmission", datainfo.sample.transmission)
931	self.write_node(sample, "temperature", datainfo.sample.temperature,
932	{"unit": datainfo.sample.temperature_unit})
933
934	pos = self.create_element("position")
935	written = self.write_node(pos,
936	"x",
937	datainfo.sample.position.x,
938	{"unit": datainfo.sample.position_unit})
939	written = written \| self.write_node( \
940	pos, "y", datainfo.sample.position.y,
941	{"unit": datainfo.sample.position_unit})
942	written = written \| self.write_node( \
943	pos, "z", datainfo.sample.position.z,
944	{"unit": datainfo.sample.position_unit})
945	if written:
946	self.append(pos, sample)
947
948	ori = self.create_element("orientation")
949	written = self.write_node(ori, "roll",
950	datainfo.sample.orientation.x,
951	{"unit": datainfo.sample.orientation_unit})
952	written = written \| self.write_node( \
953	ori, "pitch", datainfo.sample.orientation.y,
954	{"unit": datainfo.sample.orientation_unit})
955	written = written \| self.write_node( \
956	ori, "yaw", datainfo.sample.orientation.z,
957	{"unit": datainfo.sample.orientation_unit})
958	if written:
959	self.append(ori, sample)
960
961	for item in datainfo.sample.details:
962	self.write_node(sample, "details", item)
963
964	def _write_instrument(self, datainfo, entry_node):
965	"""
966	Writes the instrumental information to the XML file
967
968	:param datainfo: The Data1D object the information is coming from
969	:param entry_node: lxml node ElementTree object to be appended to
970	"""
971	instr = self.create_element("SASinstrument")
972	self.append(instr, entry_node)
973	self.write_node(instr, "name", datainfo.instrument)
974	return instr
975
976	def _write_source(self, datainfo, instr):
977	"""
978	Writes the source information to the XML file
979
980	:param datainfo: The Data1D object the information is coming from
981	:param instr: instrument node to be appended to
982	"""
983	source = self.create_element("SASsource")
984	if datainfo.source.name is not None:
985	self.write_attribute(source, "name",
986	str(datainfo.source.name))
987	self.append(source, instr)
988	if datainfo.source.radiation is None or datainfo.source.radiation == '':
989	datainfo.source.radiation = "neutron"
990	self.write_node(source, "radiation", datainfo.source.radiation)
991
992	size = self.create_element("beam_size")
993	if datainfo.source.beam_size_name is not None:
994	self.write_attribute(size, "name",
995	str(datainfo.source.beam_size_name))
996	written = self.write_node( \
997	size, "x", datainfo.source.beam_size.x,
998	{"unit": datainfo.source.beam_size_unit})
999	written = written \| self.write_node( \
1000	size, "y", datainfo.source.beam_size.y,
1001	{"unit": datainfo.source.beam_size_unit})
1002	written = written \| self.write_node( \
1003	size, "z", datainfo.source.beam_size.z,
1004	{"unit": datainfo.source.beam_size_unit})
1005	if written:
1006	self.append(size, source)
1007
1008	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1009	self.write_node(source, "wavelength",
1010	datainfo.source.wavelength,
1011	{"unit": datainfo.source.wavelength_unit})
1012	self.write_node(source, "wavelength_min",
1013	datainfo.source.wavelength_min,
1014	{"unit": datainfo.source.wavelength_min_unit})
1015	self.write_node(source, "wavelength_max",
1016	datainfo.source.wavelength_max,
1017	{"unit": datainfo.source.wavelength_max_unit})
1018	self.write_node(source, "wavelength_spread",
1019	datainfo.source.wavelength_spread,
1020	{"unit": datainfo.source.wavelength_spread_unit})
1021
1022	def _write_collimation(self, datainfo, instr):
1023	"""
1024	Writes the collimation information to the XML file
1025
1026	:param datainfo: The Data1D object the information is coming from
1027	:param instr: lxml node ElementTree object to be appended to
1028	"""
1029	if datainfo.collimation == [] or datainfo.collimation is None:
1030	coll = Collimation()
1031	datainfo.collimation.append(coll)
1032	for item in datainfo.collimation:
1033	coll = self.create_element("SAScollimation")
1034	if item.name is not None:
1035	self.write_attribute(coll, "name", str(item.name))
1036	self.append(coll, instr)
1037
1038	self.write_node(coll, "length", item.length,
1039	{"unit": item.length_unit})
1040
1041	for aperture in item.aperture:
1042	apert = self.create_element("aperture")
1043	if aperture.name is not None:
1044	self.write_attribute(apert, "name", str(aperture.name))
1045	if aperture.type is not None:
1046	self.write_attribute(apert, "type", str(aperture.type))
1047	self.append(apert, coll)
1048
1049	size = self.create_element("size")
1050	if aperture.size_name is not None:
1051	self.write_attribute(size, "name",
1052	str(aperture.size_name))
1053	written = self.write_node(size, "x", aperture.size.x,
1054	{"unit": aperture.size_unit})
1055	written = written \| self.write_node( \
1056	size, "y", aperture.size.y,
1057	{"unit": aperture.size_unit})
1058	written = written \| self.write_node( \
1059	size, "z", aperture.size.z,
1060	{"unit": aperture.size_unit})
1061	if written:
1062	self.append(size, apert)
1063
1064	self.write_node(apert, "distance", aperture.distance,
1065	{"unit": aperture.distance_unit})
1066
1067	def _write_detectors(self, datainfo, instr):
1068	"""
1069	Writes the detector information to the XML file
1070
1071	:param datainfo: The Data1D object the information is coming from
1072	:param inst: lxml instrument node to be appended to
1073	"""
1074	if datainfo.detector is None or datainfo.detector == []:
1075	det = Detector()
1076	det.name = ""
1077	datainfo.detector.append(det)
1078
1079	for item in datainfo.detector:
1080	det = self.create_element("SASdetector")
1081	written = self.write_node(det, "name", item.name)
1082	written = written \| self.write_node(det, "SDD", item.distance,
1083	{"unit": item.distance_unit})
1084	if written:
1085	self.append(det, instr)
1086
1087	off = self.create_element("offset")
1088	written = self.write_node(off, "x", item.offset.x,
1089	{"unit": item.offset_unit})
1090	written = written \| self.write_node(off, "y", item.offset.y,
1091	{"unit": item.offset_unit})
1092	written = written \| self.write_node(off, "z", item.offset.z,
1093	{"unit": item.offset_unit})
1094	if written:
1095	self.append(off, det)
1096
1097	ori = self.create_element("orientation")
1098	written = self.write_node(ori, "roll", item.orientation.x,
1099	{"unit": item.orientation_unit})
1100	written = written \| self.write_node(ori, "pitch",
1101	item.orientation.y,
1102	{"unit": item.orientation_unit})
1103	written = written \| self.write_node(ori, "yaw",
1104	item.orientation.z,
1105	{"unit": item.orientation_unit})
1106	if written:
1107	self.append(ori, det)
1108
1109	center = self.create_element("beam_center")
1110	written = self.write_node(center, "x", item.beam_center.x,
1111	{"unit": item.beam_center_unit})
1112	written = written \| self.write_node(center, "y",
1113	item.beam_center.y,
1114	{"unit": item.beam_center_unit})
1115	written = written \| self.write_node(center, "z",
1116	item.beam_center.z,
1117	{"unit": item.beam_center_unit})
1118	if written:
1119	self.append(center, det)
1120
1121	pix = self.create_element("pixel_size")
1122	written = self.write_node(pix, "x", item.pixel_size.x,
1123	{"unit": item.pixel_size_unit})
1124	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1125	{"unit": item.pixel_size_unit})
1126	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1127	{"unit": item.pixel_size_unit})
1128	if written:
1129	self.append(pix, det)
1130	self.write_node(det, "slit_length", item.slit_length,
1131	{"unit": item.slit_length_unit})
1132
1133
1134	def _write_process_notes(self, datainfo, entry_node):
1135	"""
1136	Writes the process notes to the XML file
1137
1138	:param datainfo: The Data1D object the information is coming from
1139	:param entry_node: lxml node ElementTree object to be appended to
1140
1141	"""
1142	for item in datainfo.process:
1143	node = self.create_element("SASprocess")
1144	self.append(node, entry_node)
1145	self.write_node(node, "name", item.name)
1146	self.write_node(node, "date", item.date)
1147	self.write_node(node, "description", item.description)
1148	for term in item.term:
1149	if isinstance(term, list):
1150	value = term['value']
1151	del term['value']
1152	elif isinstance(term, dict):
1153	value = term.get("value")
1154	del term['value']
1155	else:
1156	value = term
1157	self.write_node(node, "term", value, term)
1158	for note in item.notes:
1159	self.write_node(node, "SASprocessnote", note)
1160	if len(item.notes) == 0:
1161	self.write_node(node, "SASprocessnote", "")
1162
1163	def _write_notes(self, datainfo, entry_node):
1164	"""
1165	Writes the notes to the XML file and creates an empty note if none
1166	exist
1167
1168	:param datainfo: The Data1D object the information is coming from
1169	:param entry_node: lxml node ElementTree object to be appended to
1170
1171	"""
1172	if len(datainfo.notes) == 0:
1173	node = self.create_element("SASnote")
1174	self.append(node, entry_node)
1175	else:
1176	for item in datainfo.notes:
1177	node = self.create_element("SASnote")
1178	self.write_text(node, item)
1179	self.append(node, entry_node)
1180
1181	def _check_origin(self, entry_node, doc):
1182	"""
1183	Return the document, and the SASentry node associated with
1184	the data we just wrote.
1185	If the calling function was not the cansas reader, return a minidom
1186	object rather than an lxml object.
1187
1188	:param entry_node: lxml node ElementTree object to be appended to
1189	:param doc: entire xml tree
1190	"""
1191	if not self.frm:
1192	self.frm = inspect.stack()[1]
1193	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1194	mod_name = mod_name.replace(".py", "")
1195	mod = mod_name.split("sas/")
1196	mod_name = mod[1]
1197	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1198	string = self.to_string(doc, pretty_print=False)
1199	doc = parseString(string)
1200	node_name = entry_node.tag
1201	node_list = doc.getElementsByTagName(node_name)
1202	entry_node = node_list.item(0)
1203	return doc, entry_node
1204
1205	# DO NOT REMOVE - used in saving and loading panel states.
1206	def _store_float(self, location, node, variable, storage, optional=True):
1207	"""
1208	Get the content of a xpath location and store
1209	the result. Check that the units are compatible
1210	with the destination. The value is expected to
1211	be a float.
1212
1213	The xpath location might or might not exist.
1214	If it does not exist, nothing is done
1215
1216	:param location: xpath location to fetch
1217	:param node: node to read the data from
1218	:param variable: name of the data member to store it in [string]
1219	:param storage: data object that has the 'variable' data member
1220	:param optional: if True, no exception will be raised
1221	if unit conversion can't be done
1222
1223	:raise ValueError: raised when the units are not recognized
1224	"""
1225	entry = get_content(location, node)
1226	try:
1227	value = float(entry.text)
1228	except ValueError:
1229	value = None
1230
1231	if value is not None:
1232	# If the entry has units, check to see that they are
1233	# compatible with what we currently have in the data object
1234	units = entry.get('unit')
1235	if units is not None:
1236	toks = variable.split('.')
1237	local_unit = getattr(storage, toks[0]+"_unit")
1238	if local_unit is not None and units.lower() != local_unit.lower():
1239	try:
1240	conv = Converter(units)
1241	setattrchain(storage, variable, conv(value, units=local_unit))
1242	except Exception:
1243	_, exc_value, _ = sys.exc_info()
1244	err_mess = "CanSAS reader: could not convert"
1245	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1246	% (variable, units, local_unit, exc_value)
1247	self.errors.add(err_mess)
1248	if optional:
1249	logger.info(err_mess)
1250	else:
1251	raise ValueError(err_mess)
1252	else:
1253	setattrchain(storage, variable, value)
1254	else:
1255	setattrchain(storage, variable, value)
1256
1257	# DO NOT REMOVE - used in saving and loading panel states.
1258	def _store_content(self, location, node, variable, storage):
1259	"""
1260	Get the content of a xpath location and store
1261	the result. The value is treated as a string.
1262
1263	The xpath location might or might not exist.
1264	If it does not exist, nothing is done
1265
1266	:param location: xpath location to fetch
1267	:param node: node to read the data from
1268	:param variable: name of the data member to store it in [string]
1269	:param storage: data object that has the 'variable' data member
1270
1271	:return: return a list of errors
1272	"""
1273	entry = get_content(location, node)
1274	if entry is not None and entry.text is not None:
1275	setattrchain(storage, variable, entry.text.strip())
1276
1277	# DO NOT REMOVE Called by outside packages:
1278	# sas.sasgui.perspectives.invariant.invariant_state
1279	# sas.sasgui.perspectives.fitting.pagestate
1280	def get_content(location, node):
1281	"""
1282	Get the first instance of the content of a xpath location.
1283
1284	:param location: xpath location
1285	:param node: node to start at
1286
1287	:return: Element, or None
1288	"""
1289	nodes = node.xpath(location,
1290	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1291	if len(nodes) > 0:
1292	return nodes[0]
1293	else:
1294	return None
1295
1296	# DO NOT REMOVE Called by outside packages:
1297	# sas.sasgui.perspectives.fitting.pagestate
1298	def write_node(doc, parent, name, value, attr=None):
1299	"""
1300	:param doc: document DOM
1301	:param parent: parent node
1302	:param name: tag of the element
1303	:param value: value of the child text node
1304	:param attr: attribute dictionary
1305
1306	:return: True if something was appended, otherwise False
1307	"""
1308	if attr is None:
1309	attr = {}
1310	if value is not None:
1311	node = doc.createElement(name)
1312	node.appendChild(doc.createTextNode(str(value)))
1313	for item in attr:
1314	node.setAttribute(item, attr[item])
1315	parent.appendChild(node)
1316	return True
1317	return False
1318
1319	def getattrchain(obj, chain, default=None):
1320	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
1321	for part in chain.split('.'):
1322	if hasattr(obj, part):
1323	obj = getattr(obj, part, None)
1324	else:
1325	return default
1326	return obj
1327
1328	def setattrchain(obj, chain, value):
1329	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
1330	parts = list(chain.split('.'))
1331	for part in parts[-1]:
1332	obj = getattr(obj, part, None)
1333	if obj is None:
1334	raise ValueError("missing parent object "+part)
1335	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 0e0c645

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