cansas_reader.py @ 24d9e84

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 24d9e84 was 62160509, checked in by krzywon, 7 years ago
Check for units saved in v4.1.0 and convert to current.
Property mode set to `100644`
File size: 62.0 KB

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1	import logging
2	import numpy as np
3	import os
4	import sys
5	import datetime
6	import inspect
7	# For saving individual sections of data
8	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
9	plottable_1D, plottable_2D
10	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
11	Detector, Process, Aperture
12	from sas.sascalc.dataloader.data_info import \
13	combine_data_info_with_plottable as combine_data
14	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
15	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
16	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
17	from sas.sascalc.dataloader.loader_exceptions import FileContentsException, \
18	DefaultReaderException, DataReaderException
19
20	# The following 2 imports ARE used. Do not remove either.
21	import xml.dom.minidom
22	from xml.dom.minidom import parseString
23
24	from lxml import etree
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	HAS_CONVERTER = True
36	try:
37	from sas.sascalc.data_util.nxsunit import Converter
38	except ImportError:
39	HAS_CONVERTER = False
40
41	CONSTANTS = CansasConstants()
42	CANSAS_FORMAT = CONSTANTS.format
43	CANSAS_NS = CONSTANTS.names
44	ALLOW_ALL = True
45
46	class Reader(XMLreader):
47	cansas_version = "1.0"
48	base_ns = "{cansas1d/1.0}"
49	cansas_defaults = None
50	type_name = "canSAS"
51	invalid = True
52	frm = ""
53	# Log messages and errors
54	logging = None
55	errors = set()
56	# Namespace hierarchy for current xml_file object
57	names = None
58	ns_list = None
59	# Temporary storage location for loading multiple data sets in a single file
60	current_data1d = None
61	data = None
62	# Wildcards
63	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
64	# List of allowed extensions
65	ext = ['.xml', '.XML', '.svs', '.SVS']
66	# Flag to bypass extension check
67	allow_all = True
68
69	def reset_state(self):
70	"""
71	Resets the class state to a base case when loading a new data file so previous
72	data files do not appear a second time
73	"""
74	self.current_datainfo = None
75	self.current_dataset = None
76	self.current_data1d = None
77	self.data = []
78	self.process = Process()
79	self.transspectrum = TransmissionSpectrum()
80	self.aperture = Aperture()
81	self.collimation = Collimation()
82	self.detector = Detector()
83	self.names = []
84	self.cansas_defaults = {}
85	self.output = []
86	self.ns_list = None
87	self.logging = []
88	self.encoding = None
89
90	def read(self, xml_file, schema_path="", invalid=True):
91	if schema_path != "" or invalid != True:
92	# read has been called from self.get_file_contents because xml file doens't conform to schema
93	_, self.extension = os.path.splitext(os.path.basename(xml_file))
94	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
95
96	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
97	return super(XMLreader, self).read(xml_file)
98
99	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
100	# Reset everything since we're loading a new file
101	self.reset_state()
102	self.invalid = invalid
103	if xml_file is None:
104	xml_file = self.f_open.name
105	# We don't sure f_open since lxml handles opnening/closing files
106	try:
107	# Raises FileContentsException
108	self.load_file_and_schema(xml_file, schema_path)
109	# Parse each SASentry
110	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
111	namespaces={
112	'ns': self.cansas_defaults.get(
113	"ns")
114	})
115	self.is_cansas(self.extension)
116	self.set_processing_instructions()
117	for entry in entry_list:
118	self._parse_entry(entry)
119	self.data_cleanup()
120	except FileContentsException as fc_exc:
121	# File doesn't meet schema - try loading with a less strict schema
122	base_name = xml_reader.__file__
123	base_name = base_name.replace("\\", "/")
124	base = base_name.split("/sas/")[0]
125	if self.cansas_version == "1.1":
126	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
127	else:
128	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
129	self.set_schema(invalid_schema)
130	if self.invalid:
131	try:
132	# Load data with less strict schema
133	self.read(xml_file, invalid_schema, False)
134
135	# File can still be read but doesn't match schema, so raise exception
136	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
137	invalid_xml = self.find_invalid_xml()
138	if invalid_xml != "":
139	basename, _ = os.path.splitext(
140	os.path.basename(self.f_open.name))
141	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
142	raise DataReaderException(invalid_xml) # Handled by base class
143	except FileContentsException as fc_exc:
144	msg = "CanSAS Reader could not load the file {}".format(xml_file)
145	if fc_exc.message is not None: # Propagate error messages from earlier
146	msg = fc_exc.message
147	if not self.extension in self.ext: # If the file has no associated loader
148	raise DefaultReaderException(msg)
149	raise FileContentsException(msg)
150	pass
151	else:
152	raise fc_exc
153	except Exception as e: # Convert all other exceptions to FileContentsExceptions
154	raise FileContentsException(e.message)
155	finally:
156	if not self.f_open.closed:
157	self.f_open.close()
158
159	def load_file_and_schema(self, xml_file, schema_path=""):
160	base_name = xml_reader.__file__
161	base_name = base_name.replace("\\", "/")
162	base = base_name.split("/sas/")[0]
163
164	# Try and parse the XML file
165	try:
166	self.set_xml_file(xml_file)
167	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
168	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
169	raise FileContentsException(msg)
170
171	self.cansas_version = self.xmlroot.get("version", "1.0")
172	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
173
174	if schema_path == "":
175	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
176	base, self.cansas_defaults.get("schema").replace("\\", "/")
177	)
178	self.set_schema(schema_path)
179
180	def is_cansas(self, ext="xml"):
181	"""
182	Checks to see if the XML file is a CanSAS file
183
184	:param ext: The file extension of the data file
185	:raises FileContentsException: Raised if XML file isn't valid CanSAS
186	"""
187	if self.validate_xml(): # Check file is valid XML
188	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
189	value = self.xmlroot.get(name)
190	# Check schema CanSAS version matches file CanSAS version
191	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
192	return True
193	if ext == "svs":
194	return True # Why is this required?
195	# If we get to this point then file isn't valid CanSAS
196	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
197	raise FileContentsException("The file is not valid CanSAS")
198
199	def _parse_entry(self, dom, recurse=False):
200	if not self._is_call_local() and not recurse:
201	self.reset_state()
202	if not recurse:
203	self.current_datainfo = DataInfo()
204	# Raises FileContentsException if file doesn't meet CanSAS schema
205	self.invalid = False
206	# Look for a SASentry
207	self.data = []
208	self.parent_class = "SASentry"
209	self.names.append("SASentry")
210	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
211	self.current_datainfo.meta_data[
212	PREPROCESS] = self.processing_instructions
213	if self._is_call_local() and not recurse:
214	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
215	self.current_datainfo.filename = basename + self.extension
216	# Create an empty dataset if no data has been passed to the reader
217	if self.current_dataset is None:
218	self._initialize_new_data_set(dom)
219	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
220
221	# Loop through each child in the parent element
222	for node in dom:
223	attr = node.attrib
224	name = attr.get("name", "")
225	type = attr.get("type", "")
226	# Get the element name and set the current names level
227	tagname = node.tag.replace(self.base_ns, "")
228	tagname_original = tagname
229	# Skip this iteration when loading in save state information
230	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
231	continue
232	# Get where to store content
233	self.names.append(tagname_original)
234	self.ns_list = CONSTANTS.iterate_namespace(self.names)
235	# If the element is a child element, recurse
236	if len(node.getchildren()) > 0:
237	self.parent_class = tagname_original
238	if tagname == 'SASdata':
239	self._initialize_new_data_set(node)
240	if isinstance(self.current_dataset, plottable_2D):
241	x_bins = attr.get("x_bins", "")
242	y_bins = attr.get("y_bins", "")
243	if x_bins is not "" and y_bins is not "":
244	self.current_dataset.shape = (x_bins, y_bins)
245	else:
246	self.current_dataset.shape = ()
247	# Recurse to access data within the group
248	self._parse_entry(node, recurse=True)
249	if tagname == "SASsample":
250	self.current_datainfo.sample.name = name
251	elif tagname == "beam_size":
252	self.current_datainfo.source.beam_size_name = name
253	elif tagname == "SAScollimation":
254	self.collimation.name = name
255	elif tagname == "aperture":
256	self.aperture.name = name
257	self.aperture.type = type
258	self._add_intermediate()
259	else:
260	# TODO: Clean this up to make it faster (fewer if/elifs)
261	if isinstance(self.current_dataset, plottable_2D):
262	data_point = node.text
263	unit = attr.get('unit', '')
264	else:
265	data_point, unit = self._get_node_value(node, tagname)
266
267	# If this is a dataset, store the data appropriately
268	if tagname == 'Run':
269	self.current_datainfo.run_name[data_point] = name
270	self.current_datainfo.run.append(data_point)
271	elif tagname == 'Title':
272	self.current_datainfo.title = data_point
273	elif tagname == 'SASnote':
274	self.current_datainfo.notes.append(data_point)
275
276	# I and Q points
277	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
278	self.current_dataset.yaxis("Intensity", unit)
279	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
280	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
281	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
282	elif tagname == 'Q':
283	self.current_dataset.xaxis("Q", unit)
284	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
285	elif tagname == 'Qdev':
286	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
287	elif tagname == 'dQw':
288	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
289	elif tagname == 'dQl':
290	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
291	elif tagname == 'Qmean':
292	pass
293	elif tagname == 'Shadowfactor':
294	pass
295	elif tagname == 'Sesans':
296	self.current_datainfo.isSesans = bool(data_point)
297	self.current_dataset.xaxis(attr.get('x_axis'),
298	attr.get('x_unit'))
299	self.current_dataset.yaxis(attr.get('y_axis'),
300	attr.get('y_unit'))
301	elif tagname == 'yacceptance':
302	self.current_datainfo.sample.yacceptance = (data_point, unit)
303	elif tagname == 'zacceptance':
304	self.current_datainfo.sample.zacceptance = (data_point, unit)
305
306	# I and Qx, Qy - 2D data
307	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
308	self.current_dataset.yaxis("Intensity", unit)
309	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
310	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
311	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
312	elif tagname == 'Qx':
313	self.current_dataset.xaxis("Qx", unit)
314	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
315	elif tagname == 'Qy':
316	self.current_dataset.yaxis("Qy", unit)
317	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
318	elif tagname == 'Qxdev':
319	self.current_dataset.xaxis("Qxdev", unit)
320	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
321	elif tagname == 'Qydev':
322	self.current_dataset.yaxis("Qydev", unit)
323	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
324	elif tagname == 'Mask':
325	inter = [item == "1" for item in data_point.split(",")]
326	self.current_dataset.mask = np.asarray(inter, dtype=bool)
327
328	# Sample Information
329	elif tagname == 'ID' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.ID = data_point
331	elif tagname == 'Title' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.name = data_point
333	elif tagname == 'thickness' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.thickness = data_point
335	self.current_datainfo.sample.thickness_unit = unit
336	elif tagname == 'transmission' and self.parent_class == 'SASsample':
337	self.current_datainfo.sample.transmission = data_point
338	elif tagname == 'temperature' and self.parent_class == 'SASsample':
339	self.current_datainfo.sample.temperature = data_point
340	self.current_datainfo.sample.temperature_unit = unit
341	elif tagname == 'details' and self.parent_class == 'SASsample':
342	self.current_datainfo.sample.details.append(data_point)
343	elif tagname == 'x' and self.parent_class == 'position':
344	self.current_datainfo.sample.position.x = data_point
345	self.current_datainfo.sample.position_unit = unit
346	elif tagname == 'y' and self.parent_class == 'position':
347	self.current_datainfo.sample.position.y = data_point
348	self.current_datainfo.sample.position_unit = unit
349	elif tagname == 'z' and self.parent_class == 'position':
350	self.current_datainfo.sample.position.z = data_point
351	self.current_datainfo.sample.position_unit = unit
352	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
353	self.current_datainfo.sample.orientation.x = data_point
354	self.current_datainfo.sample.orientation_unit = unit
355	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
356	self.current_datainfo.sample.orientation.y = data_point
357	self.current_datainfo.sample.orientation_unit = unit
358	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
359	self.current_datainfo.sample.orientation.z = data_point
360	self.current_datainfo.sample.orientation_unit = unit
361
362	# Instrumental Information
363	elif tagname == 'name' and self.parent_class == 'SASinstrument':
364	self.current_datainfo.instrument = data_point
365
366	# Detector Information
367	elif tagname == 'name' and self.parent_class == 'SASdetector':
368	self.detector.name = data_point
369	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
370	self.detector.distance = data_point
371	self.detector.distance_unit = unit
372	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
373	self.detector.slit_length = data_point
374	self.detector.slit_length_unit = unit
375	elif tagname == 'x' and self.parent_class == 'offset':
376	self.detector.offset.x = data_point
377	self.detector.offset_unit = unit
378	elif tagname == 'y' and self.parent_class == 'offset':
379	self.detector.offset.y = data_point
380	self.detector.offset_unit = unit
381	elif tagname == 'z' and self.parent_class == 'offset':
382	self.detector.offset.z = data_point
383	self.detector.offset_unit = unit
384	elif tagname == 'x' and self.parent_class == 'beam_center':
385	self.detector.beam_center.x = data_point
386	self.detector.beam_center_unit = unit
387	elif tagname == 'y' and self.parent_class == 'beam_center':
388	self.detector.beam_center.y = data_point
389	self.detector.beam_center_unit = unit
390	elif tagname == 'z' and self.parent_class == 'beam_center':
391	self.detector.beam_center.z = data_point
392	self.detector.beam_center_unit = unit
393	elif tagname == 'x' and self.parent_class == 'pixel_size':
394	self.detector.pixel_size.x = data_point
395	self.detector.pixel_size_unit = unit
396	elif tagname == 'y' and self.parent_class == 'pixel_size':
397	self.detector.pixel_size.y = data_point
398	self.detector.pixel_size_unit = unit
399	elif tagname == 'z' and self.parent_class == 'pixel_size':
400	self.detector.pixel_size.z = data_point
401	self.detector.pixel_size_unit = unit
402	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
403	self.detector.orientation.x = data_point
404	self.detector.orientation_unit = unit
405	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
406	self.detector.orientation.y = data_point
407	self.detector.orientation_unit = unit
408	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
409	self.detector.orientation.z = data_point
410	self.detector.orientation_unit = unit
411
412	# Collimation and Aperture
413	elif tagname == 'length' and self.parent_class == 'SAScollimation':
414	self.collimation.length = data_point
415	self.collimation.length_unit = unit
416	elif tagname == 'name' and self.parent_class == 'SAScollimation':
417	self.collimation.name = data_point
418	elif tagname == 'distance' and self.parent_class == 'aperture':
419	self.aperture.distance = data_point
420	self.aperture.distance_unit = unit
421	elif tagname == 'x' and self.parent_class == 'size':
422	self.aperture.size.x = data_point
423	self.collimation.size_unit = unit
424	elif tagname == 'y' and self.parent_class == 'size':
425	self.aperture.size.y = data_point
426	self.collimation.size_unit = unit
427	elif tagname == 'z' and self.parent_class == 'size':
428	self.aperture.size.z = data_point
429	self.collimation.size_unit = unit
430
431	# Process Information
432	elif tagname == 'name' and self.parent_class == 'SASprocess':
433	self.process.name = data_point
434	elif tagname == 'description' and self.parent_class == 'SASprocess':
435	self.process.description = data_point
436	elif tagname == 'date' and self.parent_class == 'SASprocess':
437	try:
438	self.process.date = datetime.datetime.fromtimestamp(data_point)
439	except:
440	self.process.date = data_point
441	elif tagname == 'SASprocessnote':
442	self.process.notes.append(data_point)
443	elif tagname == 'term' and self.parent_class == 'SASprocess':
444	unit = attr.get("unit", "")
445	dic = { "name": name, "value": data_point, "unit": unit }
446	self.process.term.append(dic)
447
448	# Transmission Spectrum
449	elif tagname == 'T' and self.parent_class == 'Tdata':
450	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
451	self.transspectrum.transmission_unit = unit
452	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
453	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
454	self.transspectrum.transmission_deviation_unit = unit
455	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
456	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
457	self.transspectrum.wavelength_unit = unit
458
459	# Source Information
460	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
461	self.current_datainfo.source.wavelength = data_point
462	self.current_datainfo.source.wavelength_unit = unit
463	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
464	self.current_datainfo.source.wavelength_min = data_point
465	self.current_datainfo.source.wavelength_min_unit = unit
466	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
467	self.current_datainfo.source.wavelength_max = data_point
468	self.current_datainfo.source.wavelength_max_unit = unit
469	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
470	self.current_datainfo.source.wavelength_spread = data_point
471	self.current_datainfo.source.wavelength_spread_unit = unit
472	elif tagname == 'x' and self.parent_class == 'beam_size':
473	self.current_datainfo.source.beam_size.x = data_point
474	self.current_datainfo.source.beam_size_unit = unit
475	elif tagname == 'y' and self.parent_class == 'beam_size':
476	self.current_datainfo.source.beam_size.y = data_point
477	self.current_datainfo.source.beam_size_unit = unit
478	elif tagname == 'z' and self.parent_class == 'pixel_size':
479	self.current_datainfo.source.data_point.z = data_point
480	self.current_datainfo.source.beam_size_unit = unit
481	elif tagname == 'radiation' and self.parent_class == 'SASsource':
482	self.current_datainfo.source.radiation = data_point
483	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
484	self.current_datainfo.source.beam_shape = data_point
485
486	# Everything else goes in meta_data
487	else:
488	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
489	self.current_datainfo.meta_data[new_key] = data_point
490
491	self.names.remove(tagname_original)
492	length = 0
493	if len(self.names) > 1:
494	length = len(self.names) - 1
495	self.parent_class = self.names[length]
496	if not self._is_call_local() and not recurse:
497	self.frm = ""
498	self.current_datainfo.errors = set()
499	for error in self.errors:
500	self.current_datainfo.errors.add(error)
501	self.data_cleanup()
502	self.sort_one_d_data()
503	self.sort_two_d_data()
504	self.reset_data_list()
505	return self.output[0], None
506
507	def _is_call_local(self):
508	if self.frm == "":
509	inter = inspect.stack()
510	self.frm = inter[2]
511	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
512	mod_name = mod_name.replace(".py", "")
513	mod = mod_name.split("sas/")
514	mod_name = mod[1]
515	if mod_name != "sascalc/dataloader/readers/cansas_reader":
516	return False
517	return True
518
519	def _add_intermediate(self):
520	"""
521	This method stores any intermediate objects within the final data set after fully reading the set.
522	"""
523	if self.parent_class == 'SASprocess':
524	self.current_datainfo.process.append(self.process)
525	self.process = Process()
526	elif self.parent_class == 'SASdetector':
527	self.current_datainfo.detector.append(self.detector)
528	self.detector = Detector()
529	elif self.parent_class == 'SAStransmission_spectrum':
530	self.current_datainfo.trans_spectrum.append(self.transspectrum)
531	self.transspectrum = TransmissionSpectrum()
532	elif self.parent_class == 'SAScollimation':
533	self.current_datainfo.collimation.append(self.collimation)
534	self.collimation = Collimation()
535	elif self.parent_class == 'aperture':
536	self.collimation.aperture.append(self.aperture)
537	self.aperture = Aperture()
538	elif self.parent_class == 'SASdata':
539	self.data.append(self.current_dataset)
540
541	def _get_node_value(self, node, tagname):
542	"""
543	Get the value of a node and any applicable units
544
545	:param node: The XML node to get the value of
546	:param tagname: The tagname of the node
547	"""
548	#Get the text from the node and convert all whitespace to spaces
549	units = ''
550	node_value = node.text
551	if node_value is not None:
552	node_value = ' '.join(node_value.split())
553	else:
554	node_value = ""
555
556	# If the value is a float, compile with units.
557	if self.ns_list.ns_datatype == "float":
558	# If an empty value is given, set as zero.
559	if node_value is None or node_value.isspace() \
560	or node_value.lower() == "nan":
561	node_value = "0.0"
562	#Convert the value to the base units
563	node_value, units = self._unit_conversion(node, tagname, node_value)
564
565	# If the value is a timestamp, convert to a datetime object
566	elif self.ns_list.ns_datatype == "timestamp":
567	if node_value is None or node_value.isspace():
568	pass
569	else:
570	try:
571	node_value = \
572	datetime.datetime.fromtimestamp(node_value)
573	except ValueError:
574	node_value = None
575	return node_value, units
576
577	def _unit_conversion(self, node, tagname, node_value):
578	"""
579	A unit converter method used to convert the data included in the file
580	to the default units listed in data_info
581
582	:param node: XML node
583	:param tagname: name of the node
584	:param node_value: The value of the current dom node
585	"""
586	attr = node.attrib
587	value_unit = ''
588	err_msg = None
589	default_unit = None
590	if not isinstance(node_value, float):
591	node_value = float(node_value)
592	if 'unit' in attr and attr.get('unit') is not None:
593	try:
594	unit = attr['unit']
595	unit_list = unit.split("\|")
596	if len(unit_list) > 1:
597	self.current_dataset.xaxis(unit_list[0].strip(),
598	unit_list[1].strip())
599	local_unit = unit_list[1]
600	else:
601	local_unit = unit
602	unitname = self.ns_list.current_level.get("unit", "")
603	if "SASdetector" in self.names:
604	save_in = "detector"
605	elif "aperture" in self.names:
606	save_in = "aperture"
607	elif "SAScollimation" in self.names:
608	save_in = "collimation"
609	elif "SAStransmission_spectrum" in self.names:
610	save_in = "transspectrum"
611	elif "SASdata" in self.names:
612	x = np.zeros(1)
613	y = np.zeros(1)
614	self.current_data1d = Data1D(x, y)
615	save_in = "current_data1d"
616	elif "SASsource" in self.names:
617	save_in = "current_datainfo.source"
618	elif "SASsample" in self.names:
619	save_in = "current_datainfo.sample"
620	elif "SASprocess" in self.names:
621	save_in = "process"
622	else:
623	save_in = "current_datainfo"
624	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
625	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
626	and local_unit.lower() != "none":
627	if HAS_CONVERTER == True:
628	# Check local units - bad units raise KeyError
629	data_conv_q = Converter(local_unit)
630	value_unit = default_unit
631	node_value = data_conv_q(node_value, units=default_unit)
632	else:
633	value_unit = local_unit
634	err_msg = "Unit converter is not available.\n"
635	else:
636	value_unit = local_unit
637	except KeyError:
638	# Do not throw an error for loading Sesans data in cansas xml
639	# This is a temporary fix.
640	if local_unit != "A" and local_unit != 'pol':
641	err_msg = "CanSAS reader: unexpected "
642	err_msg += "\"{0}\" unit [{1}]; "
643	err_msg = err_msg.format(tagname, local_unit)
644	err_msg += "expecting [{0}]".format(default_unit)
645	value_unit = local_unit
646	except:
647	err_msg = "CanSAS reader: unknown error converting "
648	err_msg += "\"{0}\" unit [{1}]"
649	err_msg = err_msg.format(tagname, local_unit)
650	value_unit = local_unit
651	elif 'unit' in attr:
652	value_unit = attr['unit']
653	if err_msg:
654	self.errors.add(err_msg)
655	return node_value, value_unit
656
657	def _initialize_new_data_set(self, node=None):
658	if node is not None:
659	for child in node:
660	if child.tag.replace(self.base_ns, "") == "Idata":
661	for i_child in child:
662	if i_child.tag.replace(self.base_ns, "") == "Qx":
663	self.current_dataset = plottable_2D()
664	return
665	self.current_dataset = plottable_1D(np.array(0), np.array(0))
666
667	## Writing Methods
668	def write(self, filename, datainfo):
669	"""
670	Write the content of a Data1D as a CanSAS XML file
671
672	:param filename: name of the file to write
673	:param datainfo: Data1D object
674	"""
675	# Create XML document
676	doc, _ = self._to_xml_doc(datainfo)
677	# Write the file
678	file_ref = open(filename, 'w')
679	if self.encoding is None:
680	self.encoding = "UTF-8"
681	doc.write(file_ref, encoding=self.encoding,
682	pretty_print=True, xml_declaration=True)
683	file_ref.close()
684
685	def _to_xml_doc(self, datainfo):
686	"""
687	Create an XML document to contain the content of a Data1D
688
689	:param datainfo: Data1D object
690	"""
691	is_2d = False
692	if issubclass(datainfo.__class__, Data2D):
693	is_2d = True
694
695	# Get PIs and create root element
696	pi_string = self._get_pi_string()
697	# Define namespaces and create SASroot object
698	main_node = self._create_main_node()
699	# Create ElementTree, append SASroot and apply processing instructions
700	base_string = pi_string + self.to_string(main_node)
701	base_element = self.create_element_from_string(base_string)
702	doc = self.create_tree(base_element)
703	# Create SASentry Element
704	entry_node = self.create_element("SASentry")
705	root = doc.getroot()
706	root.append(entry_node)
707
708	# Add Title to SASentry
709	self.write_node(entry_node, "Title", datainfo.title)
710	# Add Run to SASentry
711	self._write_run_names(datainfo, entry_node)
712	# Add Data info to SASEntry
713	if is_2d:
714	self._write_data_2d(datainfo, entry_node)
715	else:
716	self._write_data(datainfo, entry_node)
717	# Transmission Spectrum Info
718	# TODO: fix the writer to linearize all data, including T_spectrum
719	# self._write_trans_spectrum(datainfo, entry_node)
720	# Sample info
721	self._write_sample_info(datainfo, entry_node)
722	# Instrument info
723	instr = self._write_instrument(datainfo, entry_node)
724	# Source
725	self._write_source(datainfo, instr)
726	# Collimation
727	self._write_collimation(datainfo, instr)
728	# Detectors
729	self._write_detectors(datainfo, instr)
730	# Processes info
731	self._write_process_notes(datainfo, entry_node)
732	# Note info
733	self._write_notes(datainfo, entry_node)
734	# Return the document, and the SASentry node associated with
735	# the data we just wrote
736	# If the calling function was not the cansas reader, return a minidom
737	# object rather than an lxml object.
738	self.frm = inspect.stack()[1]
739	doc, entry_node = self._check_origin(entry_node, doc)
740	return doc, entry_node
741
742	def write_node(self, parent, name, value, attr=None):
743	"""
744	:param doc: document DOM
745	:param parent: parent node
746	:param name: tag of the element
747	:param value: value of the child text node
748	:param attr: attribute dictionary
749
750	:return: True if something was appended, otherwise False
751	"""
752	if value is not None:
753	parent = self.ebuilder(parent, name, value, attr)
754	return True
755	return False
756
757	def _get_pi_string(self):
758	"""
759	Creates the processing instructions header for writing to file
760	"""
761	pis = self.return_processing_instructions()
762	if len(pis) > 0:
763	pi_tree = self.create_tree(pis[0])
764	i = 1
765	for i in range(1, len(pis) - 1):
766	pi_tree = self.append(pis[i], pi_tree)
767	pi_string = self.to_string(pi_tree)
768	else:
769	pi_string = ""
770	return pi_string
771
772	def _create_main_node(self):
773	"""
774	Creates the primary xml header used when writing to file
775	"""
776	xsi = "http://www.w3.org/2001/XMLSchema-instance"
777	version = self.cansas_version
778	n_s = CANSAS_NS.get(version).get("ns")
779	if version == "1.1":
780	url = "http://www.cansas.org/formats/1.1/"
781	else:
782	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
783	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
784	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
785	"version" : version}
786	nsmap = {'xsi' : xsi, None: n_s}
787
788	main_node = self.create_element("{" + n_s + "}SASroot",
789	attrib=attrib, nsmap=nsmap)
790	return main_node
791
792	def _write_run_names(self, datainfo, entry_node):
793	"""
794	Writes the run names to the XML file
795
796	:param datainfo: The Data1D object the information is coming from
797	:param entry_node: lxml node ElementTree object to be appended to
798	"""
799	if datainfo.run is None or datainfo.run == []:
800	datainfo.run.append(RUN_NAME_DEFAULT)
801	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
802	for item in datainfo.run:
803	runname = {}
804	if item in datainfo.run_name and \
805	len(str(datainfo.run_name[item])) > 1:
806	runname = {'name': datainfo.run_name[item]}
807	self.write_node(entry_node, "Run", item, runname)
808
809	def _write_data(self, datainfo, entry_node):
810	"""
811	Writes 1D I and Q data to the XML file
812
813	:param datainfo: The Data1D object the information is coming from
814	:param entry_node: lxml node ElementTree object to be appended to
815	"""
816	node = self.create_element("SASdata")
817	self.append(node, entry_node)
818
819	for i in range(len(datainfo.x)):
820	point = self.create_element("Idata")
821	node.append(point)
822	self.write_node(point, "Q", datainfo.x[i],
823	{'unit': datainfo.x_unit})
824	if len(datainfo.y) >= i:
825	self.write_node(point, "I", datainfo.y[i],
826	{'unit': datainfo.y_unit})
827	if datainfo.dy is not None and len(datainfo.dy) > i:
828	self.write_node(point, "Idev", datainfo.dy[i],
829	{'unit': datainfo.y_unit})
830	if datainfo.dx is not None and len(datainfo.dx) > i:
831	self.write_node(point, "Qdev", datainfo.dx[i],
832	{'unit': datainfo.x_unit})
833	if datainfo.dxw is not None and len(datainfo.dxw) > i:
834	self.write_node(point, "dQw", datainfo.dxw[i],
835	{'unit': datainfo.x_unit})
836	if datainfo.dxl is not None and len(datainfo.dxl) > i:
837	self.write_node(point, "dQl", datainfo.dxl[i],
838	{'unit': datainfo.x_unit})
839	if datainfo.isSesans:
840	sesans_attrib = {'x_axis': datainfo._xaxis,
841	'y_axis': datainfo._yaxis,
842	'x_unit': datainfo.x_unit,
843	'y_unit': datainfo.y_unit}
844	sesans = self.create_element("Sesans", attrib=sesans_attrib)
845	sesans.text = str(datainfo.isSesans)
846	entry_node.append(sesans)
847	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
848	{'unit': datainfo.sample.yacceptance[1]})
849	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
850	{'unit': datainfo.sample.zacceptance[1]})
851
852
853	def _write_data_2d(self, datainfo, entry_node):
854	"""
855	Writes 2D data to the XML file
856
857	:param datainfo: The Data2D object the information is coming from
858	:param entry_node: lxml node ElementTree object to be appended to
859	"""
860	attr = {}
861	if datainfo.data.shape:
862	attr["x_bins"] = str(len(datainfo.x_bins))
863	attr["y_bins"] = str(len(datainfo.y_bins))
864	node = self.create_element("SASdata", attr)
865	self.append(node, entry_node)
866
867	point = self.create_element("Idata")
868	node.append(point)
869	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
870	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
871	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
872
873	self.write_node(point, "Qx", qx,
874	{'unit': datainfo._xunit})
875	self.write_node(point, "Qy", qy,
876	{'unit': datainfo._yunit})
877	self.write_node(point, "I", intensity,
878	{'unit': datainfo._zunit})
879	if datainfo.err_data is not None:
880	err = ','.join([str(datainfo.err_data[i]) for i in
881	xrange(len(datainfo.err_data))])
882	self.write_node(point, "Idev", err,
883	{'unit': datainfo._zunit})
884	if datainfo.dqy_data is not None:
885	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
886	xrange(len(datainfo.dqy_data))])
887	self.write_node(point, "Qydev", dqy,
888	{'unit': datainfo._yunit})
889	if datainfo.dqx_data is not None:
890	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
891	xrange(len(datainfo.dqx_data))])
892	self.write_node(point, "Qxdev", dqx,
893	{'unit': datainfo._xunit})
894	if datainfo.mask is not None:
895	mask = ','.join(
896	["1" if datainfo.mask[i] else "0"
897	for i in xrange(len(datainfo.mask))])
898	self.write_node(point, "Mask", mask)
899
900	def _write_trans_spectrum(self, datainfo, entry_node):
901	"""
902	Writes the transmission spectrum data to the XML file
903
904	:param datainfo: The Data1D object the information is coming from
905	:param entry_node: lxml node ElementTree object to be appended to
906	"""
907	for i in range(len(datainfo.trans_spectrum)):
908	spectrum = datainfo.trans_spectrum[i]
909	node = self.create_element("SAStransmission_spectrum",
910	{"name" : spectrum.name})
911	self.append(node, entry_node)
912	if isinstance(spectrum.timestamp, datetime.datetime):
913	node.setAttribute("timestamp", spectrum.timestamp)
914	for i in range(len(spectrum.wavelength)):
915	point = self.create_element("Tdata")
916	node.append(point)
917	self.write_node(point, "Lambda", spectrum.wavelength[i],
918	{'unit': spectrum.wavelength_unit})
919	self.write_node(point, "T", spectrum.transmission[i],
920	{'unit': spectrum.transmission_unit})
921	if spectrum.transmission_deviation is not None \
922	and len(spectrum.transmission_deviation) >= i:
923	self.write_node(point, "Tdev",
924	spectrum.transmission_deviation[i],
925	{'unit':
926	spectrum.transmission_deviation_unit})
927
928	def _write_sample_info(self, datainfo, entry_node):
929	"""
930	Writes the sample information to the XML file
931
932	:param datainfo: The Data1D object the information is coming from
933	:param entry_node: lxml node ElementTree object to be appended to
934	"""
935	sample = self.create_element("SASsample")
936	if datainfo.sample.name is not None:
937	self.write_attribute(sample, "name",
938	str(datainfo.sample.name))
939	self.append(sample, entry_node)
940	self.write_node(sample, "ID", str(datainfo.sample.ID))
941	self.write_node(sample, "thickness", datainfo.sample.thickness,
942	{"unit": datainfo.sample.thickness_unit})
943	self.write_node(sample, "transmission", datainfo.sample.transmission)
944	self.write_node(sample, "temperature", datainfo.sample.temperature,
945	{"unit": datainfo.sample.temperature_unit})
946
947	pos = self.create_element("position")
948	written = self.write_node(pos,
949	"x",
950	datainfo.sample.position.x,
951	{"unit": datainfo.sample.position_unit})
952	written = written \| self.write_node( \
953	pos, "y", datainfo.sample.position.y,
954	{"unit": datainfo.sample.position_unit})
955	written = written \| self.write_node( \
956	pos, "z", datainfo.sample.position.z,
957	{"unit": datainfo.sample.position_unit})
958	if written == True:
959	self.append(pos, sample)
960
961	ori = self.create_element("orientation")
962	written = self.write_node(ori, "roll",
963	datainfo.sample.orientation.x,
964	{"unit": datainfo.sample.orientation_unit})
965	written = written \| self.write_node( \
966	ori, "pitch", datainfo.sample.orientation.y,
967	{"unit": datainfo.sample.orientation_unit})
968	written = written \| self.write_node( \
969	ori, "yaw", datainfo.sample.orientation.z,
970	{"unit": datainfo.sample.orientation_unit})
971	if written == True:
972	self.append(ori, sample)
973
974	for item in datainfo.sample.details:
975	self.write_node(sample, "details", item)
976
977	def _write_instrument(self, datainfo, entry_node):
978	"""
979	Writes the instrumental information to the XML file
980
981	:param datainfo: The Data1D object the information is coming from
982	:param entry_node: lxml node ElementTree object to be appended to
983	"""
984	instr = self.create_element("SASinstrument")
985	self.append(instr, entry_node)
986	self.write_node(instr, "name", datainfo.instrument)
987	return instr
988
989	def _write_source(self, datainfo, instr):
990	"""
991	Writes the source information to the XML file
992
993	:param datainfo: The Data1D object the information is coming from
994	:param instr: instrument node to be appended to
995	"""
996	source = self.create_element("SASsource")
997	if datainfo.source.name is not None:
998	self.write_attribute(source, "name",
999	str(datainfo.source.name))
1000	self.append(source, instr)
1001	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1002	datainfo.source.radiation = "neutron"
1003	self.write_node(source, "radiation", datainfo.source.radiation)
1004
1005	size = self.create_element("beam_size")
1006	if datainfo.source.beam_size_name is not None:
1007	self.write_attribute(size, "name",
1008	str(datainfo.source.beam_size_name))
1009	written = self.write_node( \
1010	size, "x", datainfo.source.beam_size.x,
1011	{"unit": datainfo.source.beam_size_unit})
1012	written = written \| self.write_node( \
1013	size, "y", datainfo.source.beam_size.y,
1014	{"unit": datainfo.source.beam_size_unit})
1015	written = written \| self.write_node( \
1016	size, "z", datainfo.source.beam_size.z,
1017	{"unit": datainfo.source.beam_size_unit})
1018	if written == True:
1019	self.append(size, source)
1020
1021	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1022	self.write_node(source, "wavelength",
1023	datainfo.source.wavelength,
1024	{"unit": datainfo.source.wavelength_unit})
1025	self.write_node(source, "wavelength_min",
1026	datainfo.source.wavelength_min,
1027	{"unit": datainfo.source.wavelength_min_unit})
1028	self.write_node(source, "wavelength_max",
1029	datainfo.source.wavelength_max,
1030	{"unit": datainfo.source.wavelength_max_unit})
1031	self.write_node(source, "wavelength_spread",
1032	datainfo.source.wavelength_spread,
1033	{"unit": datainfo.source.wavelength_spread_unit})
1034
1035	def _write_collimation(self, datainfo, instr):
1036	"""
1037	Writes the collimation information to the XML file
1038
1039	:param datainfo: The Data1D object the information is coming from
1040	:param instr: lxml node ElementTree object to be appended to
1041	"""
1042	if datainfo.collimation == [] or datainfo.collimation is None:
1043	coll = Collimation()
1044	datainfo.collimation.append(coll)
1045	for item in datainfo.collimation:
1046	coll = self.create_element("SAScollimation")
1047	if item.name is not None:
1048	self.write_attribute(coll, "name", str(item.name))
1049	self.append(coll, instr)
1050
1051	self.write_node(coll, "length", item.length,
1052	{"unit": item.length_unit})
1053
1054	for aperture in item.aperture:
1055	apert = self.create_element("aperture")
1056	if aperture.name is not None:
1057	self.write_attribute(apert, "name", str(aperture.name))
1058	if aperture.type is not None:
1059	self.write_attribute(apert, "type", str(aperture.type))
1060	self.append(apert, coll)
1061
1062	size = self.create_element("size")
1063	if aperture.size_name is not None:
1064	self.write_attribute(size, "name",
1065	str(aperture.size_name))
1066	written = self.write_node(size, "x", aperture.size.x,
1067	{"unit": aperture.size_unit})
1068	written = written \| self.write_node( \
1069	size, "y", aperture.size.y,
1070	{"unit": aperture.size_unit})
1071	written = written \| self.write_node( \
1072	size, "z", aperture.size.z,
1073	{"unit": aperture.size_unit})
1074	if written == True:
1075	self.append(size, apert)
1076
1077	self.write_node(apert, "distance", aperture.distance,
1078	{"unit": aperture.distance_unit})
1079
1080	def _write_detectors(self, datainfo, instr):
1081	"""
1082	Writes the detector information to the XML file
1083
1084	:param datainfo: The Data1D object the information is coming from
1085	:param inst: lxml instrument node to be appended to
1086	"""
1087	if datainfo.detector is None or datainfo.detector == []:
1088	det = Detector()
1089	det.name = ""
1090	datainfo.detector.append(det)
1091
1092	for item in datainfo.detector:
1093	det = self.create_element("SASdetector")
1094	written = self.write_node(det, "name", item.name)
1095	written = written \| self.write_node(det, "SDD", item.distance,
1096	{"unit": item.distance_unit})
1097	if written == True:
1098	self.append(det, instr)
1099
1100	off = self.create_element("offset")
1101	written = self.write_node(off, "x", item.offset.x,
1102	{"unit": item.offset_unit})
1103	written = written \| self.write_node(off, "y", item.offset.y,
1104	{"unit": item.offset_unit})
1105	written = written \| self.write_node(off, "z", item.offset.z,
1106	{"unit": item.offset_unit})
1107	if written == True:
1108	self.append(off, det)
1109
1110	ori = self.create_element("orientation")
1111	written = self.write_node(ori, "roll", item.orientation.x,
1112	{"unit": item.orientation_unit})
1113	written = written \| self.write_node(ori, "pitch",
1114	item.orientation.y,
1115	{"unit": item.orientation_unit})
1116	written = written \| self.write_node(ori, "yaw",
1117	item.orientation.z,
1118	{"unit": item.orientation_unit})
1119	if written == True:
1120	self.append(ori, det)
1121
1122	center = self.create_element("beam_center")
1123	written = self.write_node(center, "x", item.beam_center.x,
1124	{"unit": item.beam_center_unit})
1125	written = written \| self.write_node(center, "y",
1126	item.beam_center.y,
1127	{"unit": item.beam_center_unit})
1128	written = written \| self.write_node(center, "z",
1129	item.beam_center.z,
1130	{"unit": item.beam_center_unit})
1131	if written == True:
1132	self.append(center, det)
1133
1134	pix = self.create_element("pixel_size")
1135	written = self.write_node(pix, "x", item.pixel_size.x,
1136	{"unit": item.pixel_size_unit})
1137	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1138	{"unit": item.pixel_size_unit})
1139	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1140	{"unit": item.pixel_size_unit})
1141	if written == True:
1142	self.append(pix, det)
1143	self.write_node(det, "slit_length", item.slit_length,
1144	{"unit": item.slit_length_unit})
1145
1146
1147	def _write_process_notes(self, datainfo, entry_node):
1148	"""
1149	Writes the process notes to the XML file
1150
1151	:param datainfo: The Data1D object the information is coming from
1152	:param entry_node: lxml node ElementTree object to be appended to
1153
1154	"""
1155	for item in datainfo.process:
1156	node = self.create_element("SASprocess")
1157	self.append(node, entry_node)
1158	self.write_node(node, "name", item.name)
1159	self.write_node(node, "date", item.date)
1160	self.write_node(node, "description", item.description)
1161	for term in item.term:
1162	if isinstance(term, list):
1163	value = term['value']
1164	del term['value']
1165	elif isinstance(term, dict):
1166	value = term.get("value")
1167	del term['value']
1168	else:
1169	value = term
1170	self.write_node(node, "term", value, term)
1171	for note in item.notes:
1172	self.write_node(node, "SASprocessnote", note)
1173	if len(item.notes) == 0:
1174	self.write_node(node, "SASprocessnote", "")
1175
1176	def _write_notes(self, datainfo, entry_node):
1177	"""
1178	Writes the notes to the XML file and creates an empty note if none
1179	exist
1180
1181	:param datainfo: The Data1D object the information is coming from
1182	:param entry_node: lxml node ElementTree object to be appended to
1183
1184	"""
1185	if len(datainfo.notes) == 0:
1186	node = self.create_element("SASnote")
1187	self.append(node, entry_node)
1188	else:
1189	for item in datainfo.notes:
1190	node = self.create_element("SASnote")
1191	self.write_text(node, item)
1192	self.append(node, entry_node)
1193
1194	def _check_origin(self, entry_node, doc):
1195	"""
1196	Return the document, and the SASentry node associated with
1197	the data we just wrote.
1198	If the calling function was not the cansas reader, return a minidom
1199	object rather than an lxml object.
1200
1201	:param entry_node: lxml node ElementTree object to be appended to
1202	:param doc: entire xml tree
1203	"""
1204	if not self.frm:
1205	self.frm = inspect.stack()[1]
1206	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1207	mod_name = mod_name.replace(".py", "")
1208	mod = mod_name.split("sas/")
1209	mod_name = mod[1]
1210	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1211	string = self.to_string(doc, pretty_print=False)
1212	doc = parseString(string)
1213	node_name = entry_node.tag
1214	node_list = doc.getElementsByTagName(node_name)
1215	entry_node = node_list.item(0)
1216	return doc, entry_node
1217
1218	# DO NOT REMOVE - used in saving and loading panel states.
1219	def _store_float(self, location, node, variable, storage, optional=True):
1220	"""
1221	Get the content of a xpath location and store
1222	the result. Check that the units are compatible
1223	with the destination. The value is expected to
1224	be a float.
1225
1226	The xpath location might or might not exist.
1227	If it does not exist, nothing is done
1228
1229	:param location: xpath location to fetch
1230	:param node: node to read the data from
1231	:param variable: name of the data member to store it in [string]
1232	:param storage: data object that has the 'variable' data member
1233	:param optional: if True, no exception will be raised
1234	if unit conversion can't be done
1235
1236	:raise ValueError: raised when the units are not recognized
1237	"""
1238	entry = get_content(location, node)
1239	try:
1240	value = float(entry.text)
1241	except:
1242	value = None
1243
1244	if value is not None:
1245	# If the entry has units, check to see that they are
1246	# compatible with what we currently have in the data object
1247	units = entry.get('unit')
1248	if units is not None:
1249	toks = variable.split('.')
1250	local_unit = None
1251	exec "local_unit = storage.%s_unit" % toks[0]
1252	if local_unit is not None and units.lower() != local_unit.lower():
1253	if HAS_CONVERTER == True:
1254	try:
1255	conv = Converter(units)
1256	exec "storage.%s = %g" % \
1257	(variable, conv(value, units=local_unit))
1258	except:
1259	_, exc_value, _ = sys.exc_info()
1260	err_mess = "CanSAS reader: could not convert"
1261	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1262	% (variable, units, local_unit, exc_value)
1263	self.errors.add(err_mess)
1264	if optional:
1265	logger.info(err_mess)
1266	else:
1267	raise ValueError, err_mess
1268	else:
1269	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1270	% (variable, units)
1271	err_mess += " expecting [%s]" % local_unit
1272	self.errors.add(err_mess)
1273	if optional:
1274	logger.info(err_mess)
1275	else:
1276	raise ValueError, err_mess
1277	else:
1278	exec "storage.%s = value" % variable
1279	else:
1280	exec "storage.%s = value" % variable
1281
1282	# DO NOT REMOVE - used in saving and loading panel states.
1283	def _store_content(self, location, node, variable, storage):
1284	"""
1285	Get the content of a xpath location and store
1286	the result. The value is treated as a string.
1287
1288	The xpath location might or might not exist.
1289	If it does not exist, nothing is done
1290
1291	:param location: xpath location to fetch
1292	:param node: node to read the data from
1293	:param variable: name of the data member to store it in [string]
1294	:param storage: data object that has the 'variable' data member
1295
1296	:return: return a list of errors
1297	"""
1298	entry = get_content(location, node)
1299	if entry is not None and entry.text is not None:
1300	exec "storage.%s = entry.text.strip()" % variable
1301
1302	# DO NOT REMOVE Called by outside packages:
1303	# sas.sasgui.perspectives.invariant.invariant_state
1304	# sas.sasgui.perspectives.fitting.pagestate
1305	def get_content(location, node):
1306	"""
1307	Get the first instance of the content of a xpath location.
1308
1309	:param location: xpath location
1310	:param node: node to start at
1311
1312	:return: Element, or None
1313	"""
1314	nodes = node.xpath(location,
1315	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1316	if len(nodes) > 0:
1317	return nodes[0]
1318	else:
1319	return None
1320
1321	# DO NOT REMOVE Called by outside packages:
1322	# sas.sasgui.perspectives.fitting.pagestate
1323	def write_node(doc, parent, name, value, attr=None):
1324	"""
1325	:param doc: document DOM
1326	:param parent: parent node
1327	:param name: tag of the element
1328	:param value: value of the child text node
1329	:param attr: attribute dictionary
1330
1331	:return: True if something was appended, otherwise False
1332	"""
1333	if attr is None:
1334	attr = {}
1335	if value is not None:
1336	node = doc.createElement(name)
1337	node.appendChild(doc.createTextNode(str(value)))
1338	for item in attr:
1339	node.setAttribute(item, attr[item])
1340	parent.appendChild(node)
1341	return True
1342	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 24d9e84

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