cansas_reader.py @ cd57c7d4

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 cd57c7d4 was cd57c7d4, checked in by krzywon, 7 years ago

Merge branch 'master' into 4_1_issues

# Conflicts:
# src/sas/sascalc/dataloader/readers/cansas_reader.py

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File size: 63.5 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	if not self.f_open.closed:
107	self.f_open.close()
108
109	basename, _ = os.path.splitext(os.path.basename(xml_file))
110
111	try:
112	# Raises FileContentsException
113	self.load_file_and_schema(xml_file, schema_path)
114	self.current_datainfo = DataInfo()
115	# Raises FileContentsException if file doesn't meet CanSAS schema
116	self.is_cansas(self.extension)
117	self.invalid = False # If we reach this point then file must be valid CanSAS
118
119	# Parse each SASentry
120	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
121	'ns': self.cansas_defaults.get("ns")
122	})
123	# Look for a SASentry
124	self.names.append("SASentry")
125	self.set_processing_instructions()
126
127	for entry in entry_list:
128	self.current_datainfo.filename = basename + self.extension
129	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
130	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
131	self._parse_entry(entry)
132	has_error_dx = self.current_dataset.dx is not None
133	has_error_dy = self.current_dataset.dy is not None
134	self.remove_empty_q_values(has_error_dx=has_error_dx,
135	has_error_dy=has_error_dy)
136	self.send_to_output() # Combine datasets with DataInfo
137	self.current_datainfo = DataInfo() # Reset DataInfo
138	except FileContentsException as fc_exc:
139	# File doesn't meet schema - try loading with a less strict schema
140	base_name = xml_reader.__file__
141	base_name = base_name.replace("\\", "/")
142	base = base_name.split("/sas/")[0]
143	if self.cansas_version == "1.1":
144	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
145	else:
146	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
147	self.set_schema(invalid_schema)
148	if self.invalid:
149	try:
150	# Load data with less strict schema
151	self.read(xml_file, invalid_schema, False)
152
153	# File can still be read but doesn't match schema, so raise exception
154	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
155	invalid_xml = self.find_invalid_xml()
156	if invalid_xml != "":
157	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
158	raise DataReaderException(invalid_xml) # Handled by base class
159	except FileContentsException as fc_exc:
160	msg = "CanSAS Reader could not load the file {}".format(xml_file)
161	if fc_exc.message is not None: # Propagate error messages from earlier
162	msg = fc_exc.message
163	if not self.extension in self.ext: # If the file has no associated loader
164	raise DefaultReaderException(msg)
165	raise FileContentsException(msg)
166	pass
167	else:
168	raise fc_exc
169	except Exception as e: # Convert all other exceptions to FileContentsExceptions
170	raise FileContentsException(e.message)
171
172
173	def load_file_and_schema(self, xml_file, schema_path=""):
174	base_name = xml_reader.__file__
175	base_name = base_name.replace("\\", "/")
176	base = base_name.split("/sas/")[0]
177
178	# Try and parse the XML file
179	try:
180	self.set_xml_file(xml_file)
181	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
182	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
183	raise FileContentsException(msg)
184
185	self.cansas_version = self.xmlroot.get("version", "1.0")
186	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
187
188	if schema_path == "":
189	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
190	base, self.cansas_defaults.get("schema").replace("\\", "/")
191	)
192	self.set_schema(schema_path)
193
194	def is_cansas(self, ext="xml"):
195	"""
196	Checks to see if the XML file is a CanSAS file
197
198	:param ext: The file extension of the data file
199	:raises FileContentsException: Raised if XML file isn't valid CanSAS
200	"""
201	if self.validate_xml(): # Check file is valid XML
202	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
203	value = self.xmlroot.get(name)
204	# Check schema CanSAS version matches file CanSAS version
205	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
206	return True
207	if ext == "svs":
208	return True # Why is this required?
209	# If we get to this point then file isn't valid CanSAS
210	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
211	raise FileContentsException("The file is not valid CanSAS")
212
213	def _parse_entry(self, dom, recurse=False):
214	if not self._is_call_local() and not recurse:
215	self.reset_state()
216	self.data = []
217	self.current_datainfo = DataInfo()
218	self.names.append("SASentry")
219	self.parent_class = "SASentry"
220	# Create an empty dataset if no data has been passed to the reader
221	if self.current_dataset is None:
222	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
223	np.empty(0), np.empty(0))
224	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
225
226	# Loop through each child in the parent element
227	for node in dom:
228	attr = node.attrib
229	name = attr.get("name", "")
230	type = attr.get("type", "")
231	# Get the element name and set the current names level
232	tagname = node.tag.replace(self.base_ns, "")
233	tagname_original = tagname
234	# Skip this iteration when loading in save state information
235	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
236	continue
237	# Get where to store content
238	self.names.append(tagname_original)
239	self.ns_list = CONSTANTS.iterate_namespace(self.names)
240	# If the element is a child element, recurse
241	if len(node.getchildren()) > 0:
242	self.parent_class = tagname_original
243	if tagname == 'SASdata':
244	self._initialize_new_data_set(node)
245	if isinstance(self.current_dataset, plottable_2D):
246	x_bins = attr.get("x_bins", "")
247	y_bins = attr.get("y_bins", "")
248	if x_bins is not "" and y_bins is not "":
249	self.current_dataset.shape = (x_bins, y_bins)
250	else:
251	self.current_dataset.shape = ()
252	# Recurse to access data within the group
253	self._parse_entry(node, recurse=True)
254	if tagname == "SASsample":
255	self.current_datainfo.sample.name = name
256	elif tagname == "beam_size":
257	self.current_datainfo.source.beam_size_name = name
258	elif tagname == "SAScollimation":
259	self.collimation.name = name
260	elif tagname == "aperture":
261	self.aperture.name = name
262	self.aperture.type = type
263	self._add_intermediate()
264	else:
265	if isinstance(self.current_dataset, plottable_2D):
266	data_point = node.text
267	unit = attr.get('unit', '')
268	else:
269	data_point, unit = self._get_node_value(node, tagname)
270
271	# If this is a dataset, store the data appropriately
272	if tagname == 'Run':
273	self.current_datainfo.run_name[data_point] = name
274	self.current_datainfo.run.append(data_point)
275	elif tagname == 'Title':
276	self.current_datainfo.title = data_point
277	elif tagname == 'SASnote':
278	self.current_datainfo.notes.append(data_point)
279
280	# I and Q points
281	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
282	self.current_dataset.yaxis("Intensity", unit)
283	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
284	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
285	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
286	elif tagname == 'Q':
287	self.current_dataset.xaxis("Q", unit)
288	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
289	elif tagname == 'Qdev':
290	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
291	elif tagname == 'dQw':
292	if self.current_dataset.dxw is None:
293	self.current_dataset.dxw = np.empty(0)
294	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
295	elif tagname == 'dQl':
296	if self.current_dataset.dxl is None:
297	self.current_dataset.dxl = np.empty(0)
298	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
299	elif tagname == 'Qmean':
300	pass
301	elif tagname == 'Shadowfactor':
302	pass
303	elif tagname == 'Sesans':
304	self.current_datainfo.isSesans = bool(data_point)
305	self.current_dataset.xaxis(attr.get('x_axis'),
306	attr.get('x_unit'))
307	self.current_dataset.yaxis(attr.get('y_axis'),
308	attr.get('y_unit'))
309	elif tagname == 'yacceptance':
310	self.current_datainfo.sample.yacceptance = (data_point, unit)
311	elif tagname == 'zacceptance':
312	self.current_datainfo.sample.zacceptance = (data_point, unit)
313
314	# I and Qx, Qy - 2D data
315	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
316	self.current_dataset.yaxis("Intensity", unit)
317	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
318	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
319	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
320	elif tagname == 'Qx':
321	self.current_dataset.xaxis("Qx", unit)
322	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
323	elif tagname == 'Qy':
324	self.current_dataset.yaxis("Qy", unit)
325	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
326	elif tagname == 'Qxdev':
327	self.current_dataset.xaxis("Qxdev", unit)
328	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
329	elif tagname == 'Qydev':
330	self.current_dataset.yaxis("Qydev", unit)
331	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
332	elif tagname == 'Mask':
333	inter = [item == "1" for item in data_point.split(",")]
334	self.current_dataset.mask = np.asarray(inter, dtype=bool)
335
336	# Sample Information
337	elif tagname == 'ID' and self.parent_class == 'SASsample':
338	self.current_datainfo.sample.ID = data_point
339	elif tagname == 'Title' and self.parent_class == 'SASsample':
340	self.current_datainfo.sample.name = data_point
341	elif tagname == 'thickness' and self.parent_class == 'SASsample':
342	self.current_datainfo.sample.thickness = data_point
343	self.current_datainfo.sample.thickness_unit = unit
344	elif tagname == 'transmission' and self.parent_class == 'SASsample':
345	self.current_datainfo.sample.transmission = data_point
346	elif tagname == 'temperature' and self.parent_class == 'SASsample':
347	self.current_datainfo.sample.temperature = data_point
348	self.current_datainfo.sample.temperature_unit = unit
349	elif tagname == 'details' and self.parent_class == 'SASsample':
350	self.current_datainfo.sample.details.append(data_point)
351	elif tagname == 'x' and self.parent_class == 'position':
352	self.current_datainfo.sample.position.x = data_point
353	self.current_datainfo.sample.position_unit = unit
354	elif tagname == 'y' and self.parent_class == 'position':
355	self.current_datainfo.sample.position.y = data_point
356	self.current_datainfo.sample.position_unit = unit
357	elif tagname == 'z' and self.parent_class == 'position':
358	self.current_datainfo.sample.position.z = data_point
359	self.current_datainfo.sample.position_unit = unit
360	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
361	self.current_datainfo.sample.orientation.x = data_point
362	self.current_datainfo.sample.orientation_unit = unit
363	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
364	self.current_datainfo.sample.orientation.y = data_point
365	self.current_datainfo.sample.orientation_unit = unit
366	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
367	self.current_datainfo.sample.orientation.z = data_point
368	self.current_datainfo.sample.orientation_unit = unit
369
370	# Instrumental Information
371	elif tagname == 'name' and self.parent_class == 'SASinstrument':
372	self.current_datainfo.instrument = data_point
373
374	# Detector Information
375	elif tagname == 'name' and self.parent_class == 'SASdetector':
376	self.detector.name = data_point
377	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
378	self.detector.distance = data_point
379	self.detector.distance_unit = unit
380	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
381	self.detector.slit_length = data_point
382	self.detector.slit_length_unit = unit
383	elif tagname == 'x' and self.parent_class == 'offset':
384	self.detector.offset.x = data_point
385	self.detector.offset_unit = unit
386	elif tagname == 'y' and self.parent_class == 'offset':
387	self.detector.offset.y = data_point
388	self.detector.offset_unit = unit
389	elif tagname == 'z' and self.parent_class == 'offset':
390	self.detector.offset.z = data_point
391	self.detector.offset_unit = unit
392	elif tagname == 'x' and self.parent_class == 'beam_center':
393	self.detector.beam_center.x = data_point
394	self.detector.beam_center_unit = unit
395	elif tagname == 'y' and self.parent_class == 'beam_center':
396	self.detector.beam_center.y = data_point
397	self.detector.beam_center_unit = unit
398	elif tagname == 'z' and self.parent_class == 'beam_center':
399	self.detector.beam_center.z = data_point
400	self.detector.beam_center_unit = unit
401	elif tagname == 'x' and self.parent_class == 'pixel_size':
402	self.detector.pixel_size.x = data_point
403	self.detector.pixel_size_unit = unit
404	elif tagname == 'y' and self.parent_class == 'pixel_size':
405	self.detector.pixel_size.y = data_point
406	self.detector.pixel_size_unit = unit
407	elif tagname == 'z' and self.parent_class == 'pixel_size':
408	self.detector.pixel_size.z = data_point
409	self.detector.pixel_size_unit = unit
410	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
411	self.detector.orientation.x = data_point
412	self.detector.orientation_unit = unit
413	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
414	self.detector.orientation.y = data_point
415	self.detector.orientation_unit = unit
416	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
417	self.detector.orientation.z = data_point
418	self.detector.orientation_unit = unit
419
420	# Collimation and Aperture
421	elif tagname == 'length' and self.parent_class == 'SAScollimation':
422	self.collimation.length = data_point
423	self.collimation.length_unit = unit
424	elif tagname == 'name' and self.parent_class == 'SAScollimation':
425	self.collimation.name = data_point
426	elif tagname == 'distance' and self.parent_class == 'aperture':
427	self.aperture.distance = data_point
428	self.aperture.distance_unit = unit
429	elif tagname == 'x' and self.parent_class == 'size':
430	self.aperture.size.x = data_point
431	self.collimation.size_unit = unit
432	elif tagname == 'y' and self.parent_class == 'size':
433	self.aperture.size.y = data_point
434	self.collimation.size_unit = unit
435	elif tagname == 'z' and self.parent_class == 'size':
436	self.aperture.size.z = data_point
437	self.collimation.size_unit = unit
438
439	# Process Information
440	elif tagname == 'name' and self.parent_class == 'SASprocess':
441	self.process.name = data_point
442	elif tagname == 'description' and self.parent_class == 'SASprocess':
443	self.process.description = data_point
444	elif tagname == 'date' and self.parent_class == 'SASprocess':
445	try:
446	self.process.date = datetime.datetime.fromtimestamp(data_point)
447	except:
448	self.process.date = data_point
449	elif tagname == 'SASprocessnote':
450	self.process.notes.append(data_point)
451	elif tagname == 'term' and self.parent_class == 'SASprocess':
452	unit = attr.get("unit", "")
453	dic = { "name": name, "value": data_point, "unit": unit }
454	self.process.term.append(dic)
455
456	# Transmission Spectrum
457	elif tagname == 'T' and self.parent_class == 'Tdata':
458	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
459	self.transspectrum.transmission_unit = unit
460	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
461	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
462	self.transspectrum.transmission_deviation_unit = unit
463	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
464	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
465	self.transspectrum.wavelength_unit = unit
466
467	# Source Information
468	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
469	self.current_datainfo.source.wavelength = data_point
470	self.current_datainfo.source.wavelength_unit = unit
471	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
472	self.current_datainfo.source.wavelength_min = data_point
473	self.current_datainfo.source.wavelength_min_unit = unit
474	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
475	self.current_datainfo.source.wavelength_max = data_point
476	self.current_datainfo.source.wavelength_max_unit = unit
477	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.wavelength_spread = data_point
479	self.current_datainfo.source.wavelength_spread_unit = unit
480	elif tagname == 'x' and self.parent_class == 'beam_size':
481	self.current_datainfo.source.beam_size.x = data_point
482	self.current_datainfo.source.beam_size_unit = unit
483	elif tagname == 'y' and self.parent_class == 'beam_size':
484	self.current_datainfo.source.beam_size.y = data_point
485	self.current_datainfo.source.beam_size_unit = unit
486	elif tagname == 'z' and self.parent_class == 'pixel_size':
487	self.current_datainfo.source.data_point.z = data_point
488	self.current_datainfo.source.beam_size_unit = unit
489	elif tagname == 'radiation' and self.parent_class == 'SASsource':
490	self.current_datainfo.source.radiation = data_point
491	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
492	self.current_datainfo.source.beam_shape = data_point
493
494	# Everything else goes in meta_data
495	else:
496	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
497	self.current_datainfo.meta_data[new_key] = data_point
498
499	self.names.remove(tagname_original)
500	length = 0
501	if len(self.names) > 1:
502	length = len(self.names) - 1
503	self.parent_class = self.names[length]
504	if not self._is_call_local() and not recurse:
505	self.frm = ""
506	self.current_datainfo.errors = set()
507	for error in self.errors:
508	self.current_datainfo.errors.add(error)
509	self.errors.clear()
510	self.send_to_output()
511	empty = None
512	return self.output[0], empty
513
514	def _is_call_local(self):
515	if self.frm == "":
516	inter = inspect.stack()
517	self.frm = inter[2]
518	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
519	mod_name = mod_name.replace(".py", "")
520	mod = mod_name.split("sas/")
521	mod_name = mod[1]
522	if mod_name != "sascalc/dataloader/readers/cansas_reader":
523	return False
524	return True
525
526	def _add_intermediate(self):
527	"""
528	This method stores any intermediate objects within the final data set after fully reading the set.
529	"""
530	if self.parent_class == 'SASprocess':
531	self.current_datainfo.process.append(self.process)
532	self.process = Process()
533	elif self.parent_class == 'SASdetector':
534	self.current_datainfo.detector.append(self.detector)
535	self.detector = Detector()
536	elif self.parent_class == 'SAStransmission_spectrum':
537	self.current_datainfo.trans_spectrum.append(self.transspectrum)
538	self.transspectrum = TransmissionSpectrum()
539	elif self.parent_class == 'SAScollimation':
540	self.current_datainfo.collimation.append(self.collimation)
541	self.collimation = Collimation()
542	elif self.parent_class == 'aperture':
543	self.collimation.aperture.append(self.aperture)
544	self.aperture = Aperture()
545	elif self.parent_class == 'SASdata':
546	self._check_for_empty_resolution()
547	self.data.append(self.current_dataset)
548
549	def _get_node_value(self, node, tagname):
550	"""
551	Get the value of a node and any applicable units
552
553	:param node: The XML node to get the value of
554	:param tagname: The tagname of the node
555	"""
556	#Get the text from the node and convert all whitespace to spaces
557	units = ''
558	node_value = node.text
559	if node_value is not None:
560	node_value = ' '.join(node_value.split())
561	else:
562	node_value = ""
563
564	# If the value is a float, compile with units.
565	if self.ns_list.ns_datatype == "float":
566	# If an empty value is given, set as zero.
567	if node_value is None or node_value.isspace() \
568	or node_value.lower() == "nan":
569	node_value = "0.0"
570	#Convert the value to the base units
571	node_value, units = self._unit_conversion(node, tagname, node_value)
572
573	# If the value is a timestamp, convert to a datetime object
574	elif self.ns_list.ns_datatype == "timestamp":
575	if node_value is None or node_value.isspace():
576	pass
577	else:
578	try:
579	node_value = \
580	datetime.datetime.fromtimestamp(node_value)
581	except ValueError:
582	node_value = None
583	return node_value, units
584
585	def _unit_conversion(self, node, tagname, node_value):
586	"""
587	A unit converter method used to convert the data included in the file
588	to the default units listed in data_info
589
590	:param node: XML node
591	:param tagname: name of the node
592	:param node_value: The value of the current dom node
593	"""
594	attr = node.attrib
595	value_unit = ''
596	err_msg = None
597	default_unit = None
598	if not isinstance(node_value, float):
599	node_value = float(node_value)
600	if 'unit' in attr and attr.get('unit') is not None:
601	try:
602	local_unit = attr['unit']
603	unitname = self.ns_list.current_level.get("unit", "")
604	if "SASdetector" in self.names:
605	save_in = "detector"
606	elif "aperture" in self.names:
607	save_in = "aperture"
608	elif "SAScollimation" in self.names:
609	save_in = "collimation"
610	elif "SAStransmission_spectrum" in self.names:
611	save_in = "transspectrum"
612	elif "SASdata" in self.names:
613	x = np.zeros(1)
614	y = np.zeros(1)
615	self.current_data1d = Data1D(x, y)
616	save_in = "current_data1d"
617	elif "SASsource" in self.names:
618	save_in = "current_datainfo.source"
619	elif "SASsample" in self.names:
620	save_in = "current_datainfo.sample"
621	elif "SASprocess" in self.names:
622	save_in = "process"
623	else:
624	save_in = "current_datainfo"
625	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
626	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
627	and local_unit.lower() != "none":
628	if HAS_CONVERTER == True:
629	# Check local units - bad units raise KeyError
630	data_conv_q = Converter(local_unit)
631	value_unit = default_unit
632	node_value = data_conv_q(node_value, units=default_unit)
633	else:
634	value_unit = local_unit
635	err_msg = "Unit converter is not available.\n"
636	else:
637	value_unit = local_unit
638	except KeyError:
639	# Do not throw an error for loading Sesans data in cansas xml
640	# This is a temporary fix.
641	if local_unit != "A" and local_unit != 'pol':
642	err_msg = "CanSAS reader: unexpected "
643	err_msg += "\"{0}\" unit [{1}]; "
644	err_msg = err_msg.format(tagname, local_unit)
645	err_msg += "expecting [{0}]".format(default_unit)
646	value_unit = local_unit
647	except:
648	err_msg = "CanSAS reader: unknown error converting "
649	err_msg += "\"{0}\" unit [{1}]"
650	err_msg = err_msg.format(tagname, local_unit)
651	value_unit = local_unit
652	elif 'unit' in attr:
653	value_unit = attr['unit']
654	if err_msg:
655	self.errors.add(err_msg)
656	return node_value, value_unit
657
658	def _check_for_empty_resolution(self):
659	"""
660	a method to check all resolution data sets are the same size as I and q
661	"""
662	dql_exists = False
663	dqw_exists = False
664	dq_exists = False
665	di_exists = False
666	if self.current_dataset.dxl is not None:
667	dql_exists = True
668	if self.current_dataset.dxw is not None:
669	dqw_exists = True
670	if self.current_dataset.dx is not None:
671	dq_exists = True
672	if self.current_dataset.dy is not None:
673	di_exists = True
674	if dqw_exists and not dql_exists:
675	array_size = self.current_dataset.dxw.size - 1
676	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
677	np.zeros([array_size]))
678	elif dql_exists and not dqw_exists:
679	array_size = self.current_dataset.dxl.size - 1
680	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
681	np.zeros([array_size]))
682	elif not dql_exists and not dqw_exists and not dq_exists:
683	array_size = self.current_dataset.x.size - 1
684	self.current_dataset.dx = np.append(self.current_dataset.dx,
685	np.zeros([array_size]))
686	if not di_exists:
687	array_size = self.current_dataset.y.size - 1
688	self.current_dataset.dy = np.append(self.current_dataset.dy,
689	np.zeros([array_size]))
690
691	def _initialize_new_data_set(self, node=None):
692	if node is not None:
693	for child in node:
694	if child.tag.replace(self.base_ns, "") == "Idata":
695	for i_child in child:
696	if i_child.tag.replace(self.base_ns, "") == "Qx":
697	self.current_dataset = plottable_2D()
698	return
699	self.current_dataset = plottable_1D(np.array(0), np.array(0))
700
701	## Writing Methods
702	def write(self, filename, datainfo):
703	"""
704	Write the content of a Data1D as a CanSAS XML file
705
706	:param filename: name of the file to write
707	:param datainfo: Data1D object
708	"""
709	# Create XML document
710	doc, _ = self._to_xml_doc(datainfo)
711	# Write the file
712	file_ref = open(filename, 'w')
713	if self.encoding is None:
714	self.encoding = "UTF-8"
715	doc.write(file_ref, encoding=self.encoding,
716	pretty_print=True, xml_declaration=True)
717	file_ref.close()
718
719	def _to_xml_doc(self, datainfo):
720	"""
721	Create an XML document to contain the content of a Data1D
722
723	:param datainfo: Data1D object
724	"""
725	is_2d = False
726	if issubclass(datainfo.__class__, Data2D):
727	is_2d = True
728
729	# Get PIs and create root element
730	pi_string = self._get_pi_string()
731	# Define namespaces and create SASroot object
732	main_node = self._create_main_node()
733	# Create ElementTree, append SASroot and apply processing instructions
734	base_string = pi_string + self.to_string(main_node)
735	base_element = self.create_element_from_string(base_string)
736	doc = self.create_tree(base_element)
737	# Create SASentry Element
738	entry_node = self.create_element("SASentry")
739	root = doc.getroot()
740	root.append(entry_node)
741
742	# Add Title to SASentry
743	self.write_node(entry_node, "Title", datainfo.title)
744	# Add Run to SASentry
745	self._write_run_names(datainfo, entry_node)
746	# Add Data info to SASEntry
747	if is_2d:
748	self._write_data_2d(datainfo, entry_node)
749	else:
750	self._write_data(datainfo, entry_node)
751	# Transmission Spectrum Info
752	# TODO: fix the writer to linearize all data, including T_spectrum
753	# self._write_trans_spectrum(datainfo, entry_node)
754	# Sample info
755	self._write_sample_info(datainfo, entry_node)
756	# Instrument info
757	instr = self._write_instrument(datainfo, entry_node)
758	# Source
759	self._write_source(datainfo, instr)
760	# Collimation
761	self._write_collimation(datainfo, instr)
762	# Detectors
763	self._write_detectors(datainfo, instr)
764	# Processes info
765	self._write_process_notes(datainfo, entry_node)
766	# Note info
767	self._write_notes(datainfo, entry_node)
768	# Return the document, and the SASentry node associated with
769	# the data we just wrote
770	# If the calling function was not the cansas reader, return a minidom
771	# object rather than an lxml object.
772	self.frm = inspect.stack()[1]
773	doc, entry_node = self._check_origin(entry_node, doc)
774	return doc, entry_node
775
776	def write_node(self, parent, name, value, attr=None):
777	"""
778	:param doc: document DOM
779	:param parent: parent node
780	:param name: tag of the element
781	:param value: value of the child text node
782	:param attr: attribute dictionary
783
784	:return: True if something was appended, otherwise False
785	"""
786	if value is not None:
787	parent = self.ebuilder(parent, name, value, attr)
788	return True
789	return False
790
791	def _get_pi_string(self):
792	"""
793	Creates the processing instructions header for writing to file
794	"""
795	pis = self.return_processing_instructions()
796	if len(pis) > 0:
797	pi_tree = self.create_tree(pis[0])
798	i = 1
799	for i in range(1, len(pis) - 1):
800	pi_tree = self.append(pis[i], pi_tree)
801	pi_string = self.to_string(pi_tree)
802	else:
803	pi_string = ""
804	return pi_string
805
806	def _create_main_node(self):
807	"""
808	Creates the primary xml header used when writing to file
809	"""
810	xsi = "http://www.w3.org/2001/XMLSchema-instance"
811	version = self.cansas_version
812	n_s = CANSAS_NS.get(version).get("ns")
813	if version == "1.1":
814	url = "http://www.cansas.org/formats/1.1/"
815	else:
816	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
817	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
818	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
819	"version" : version}
820	nsmap = {'xsi' : xsi, None: n_s}
821
822	main_node = self.create_element("{" + n_s + "}SASroot",
823	attrib=attrib, nsmap=nsmap)
824	return main_node
825
826	def _write_run_names(self, datainfo, entry_node):
827	"""
828	Writes the run names to the XML file
829
830	:param datainfo: The Data1D object the information is coming from
831	:param entry_node: lxml node ElementTree object to be appended to
832	"""
833	if datainfo.run is None or datainfo.run == []:
834	datainfo.run.append(RUN_NAME_DEFAULT)
835	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
836	for item in datainfo.run:
837	runname = {}
838	if item in datainfo.run_name and \
839	len(str(datainfo.run_name[item])) > 1:
840	runname = {'name': datainfo.run_name[item]}
841	self.write_node(entry_node, "Run", item, runname)
842
843	def _write_data(self, datainfo, entry_node):
844	"""
845	Writes 1D I and Q data to the XML file
846
847	:param datainfo: The Data1D object the information is coming from
848	:param entry_node: lxml node ElementTree object to be appended to
849	"""
850	node = self.create_element("SASdata")
851	self.append(node, entry_node)
852
853	for i in range(len(datainfo.x)):
854	point = self.create_element("Idata")
855	node.append(point)
856	self.write_node(point, "Q", datainfo.x[i],
857	{'unit': datainfo.x_unit})
858	if len(datainfo.y) >= i:
859	self.write_node(point, "I", datainfo.y[i],
860	{'unit': datainfo.y_unit})
861	if datainfo.dy is not None and len(datainfo.dy) > i:
862	self.write_node(point, "Idev", datainfo.dy[i],
863	{'unit': datainfo.y_unit})
864	if datainfo.dx is not None and len(datainfo.dx) > i:
865	self.write_node(point, "Qdev", datainfo.dx[i],
866	{'unit': datainfo.x_unit})
867	if datainfo.dxw is not None and len(datainfo.dxw) > i:
868	self.write_node(point, "dQw", datainfo.dxw[i],
869	{'unit': datainfo.x_unit})
870	if datainfo.dxl is not None and len(datainfo.dxl) > i:
871	self.write_node(point, "dQl", datainfo.dxl[i],
872	{'unit': datainfo.x_unit})
873	if datainfo.isSesans:
874	sesans_attrib = {'x_axis': datainfo._xaxis,
875	'y_axis': datainfo._yaxis,
876	'x_unit': datainfo.x_unit,
877	'y_unit': datainfo.y_unit}
878	sesans = self.create_element("Sesans", attrib=sesans_attrib)
879	sesans.text = str(datainfo.isSesans)
880	entry_node.append(sesans)
881	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
882	{'unit': datainfo.sample.yacceptance[1]})
883	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
884	{'unit': datainfo.sample.zacceptance[1]})
885
886
887	def _write_data_2d(self, datainfo, entry_node):
888	"""
889	Writes 2D data to the XML file
890
891	:param datainfo: The Data2D object the information is coming from
892	:param entry_node: lxml node ElementTree object to be appended to
893	"""
894	attr = {}
895	if datainfo.data.shape:
896	attr["x_bins"] = str(len(datainfo.x_bins))
897	attr["y_bins"] = str(len(datainfo.y_bins))
898	node = self.create_element("SASdata", attr)
899	self.append(node, entry_node)
900
901	point = self.create_element("Idata")
902	node.append(point)
903	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
904	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
905	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
906
907	self.write_node(point, "Qx", qx,
908	{'unit': datainfo._xunit})
909	self.write_node(point, "Qy", qy,
910	{'unit': datainfo._yunit})
911	self.write_node(point, "I", intensity,
912	{'unit': datainfo._zunit})
913	if datainfo.err_data is not None:
914	err = ','.join([str(datainfo.err_data[i]) for i in
915	xrange(len(datainfo.err_data))])
916	self.write_node(point, "Idev", err,
917	{'unit': datainfo._zunit})
918	if datainfo.dqy_data is not None:
919	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
920	xrange(len(datainfo.dqy_data))])
921	self.write_node(point, "Qydev", dqy,
922	{'unit': datainfo._yunit})
923	if datainfo.dqx_data is not None:
924	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
925	xrange(len(datainfo.dqx_data))])
926	self.write_node(point, "Qxdev", dqx,
927	{'unit': datainfo._xunit})
928	if datainfo.mask is not None:
929	mask = ','.join(
930	["1" if datainfo.mask[i] else "0"
931	for i in xrange(len(datainfo.mask))])
932	self.write_node(point, "Mask", mask)
933
934	def _write_trans_spectrum(self, datainfo, entry_node):
935	"""
936	Writes the transmission spectrum data to the XML file
937
938	:param datainfo: The Data1D object the information is coming from
939	:param entry_node: lxml node ElementTree object to be appended to
940	"""
941	for i in range(len(datainfo.trans_spectrum)):
942	spectrum = datainfo.trans_spectrum[i]
943	node = self.create_element("SAStransmission_spectrum",
944	{"name" : spectrum.name})
945	self.append(node, entry_node)
946	if isinstance(spectrum.timestamp, datetime.datetime):
947	node.setAttribute("timestamp", spectrum.timestamp)
948	for i in range(len(spectrum.wavelength)):
949	point = self.create_element("Tdata")
950	node.append(point)
951	self.write_node(point, "Lambda", spectrum.wavelength[i],
952	{'unit': spectrum.wavelength_unit})
953	self.write_node(point, "T", spectrum.transmission[i],
954	{'unit': spectrum.transmission_unit})
955	if spectrum.transmission_deviation is not None \
956	and len(spectrum.transmission_deviation) >= i:
957	self.write_node(point, "Tdev",
958	spectrum.transmission_deviation[i],
959	{'unit':
960	spectrum.transmission_deviation_unit})
961
962	def _write_sample_info(self, datainfo, entry_node):
963	"""
964	Writes the sample information to the XML file
965
966	:param datainfo: The Data1D object the information is coming from
967	:param entry_node: lxml node ElementTree object to be appended to
968	"""
969	sample = self.create_element("SASsample")
970	if datainfo.sample.name is not None:
971	self.write_attribute(sample, "name",
972	str(datainfo.sample.name))
973	self.append(sample, entry_node)
974	self.write_node(sample, "ID", str(datainfo.sample.ID))
975	self.write_node(sample, "thickness", datainfo.sample.thickness,
976	{"unit": datainfo.sample.thickness_unit})
977	self.write_node(sample, "transmission", datainfo.sample.transmission)
978	self.write_node(sample, "temperature", datainfo.sample.temperature,
979	{"unit": datainfo.sample.temperature_unit})
980
981	pos = self.create_element("position")
982	written = self.write_node(pos,
983	"x",
984	datainfo.sample.position.x,
985	{"unit": datainfo.sample.position_unit})
986	written = written \| self.write_node( \
987	pos, "y", datainfo.sample.position.y,
988	{"unit": datainfo.sample.position_unit})
989	written = written \| self.write_node( \
990	pos, "z", datainfo.sample.position.z,
991	{"unit": datainfo.sample.position_unit})
992	if written == True:
993	self.append(pos, sample)
994
995	ori = self.create_element("orientation")
996	written = self.write_node(ori, "roll",
997	datainfo.sample.orientation.x,
998	{"unit": datainfo.sample.orientation_unit})
999	written = written \| self.write_node( \
1000	ori, "pitch", datainfo.sample.orientation.y,
1001	{"unit": datainfo.sample.orientation_unit})
1002	written = written \| self.write_node( \
1003	ori, "yaw", datainfo.sample.orientation.z,
1004	{"unit": datainfo.sample.orientation_unit})
1005	if written == True:
1006	self.append(ori, sample)
1007
1008	for item in datainfo.sample.details:
1009	self.write_node(sample, "details", item)
1010
1011	def _write_instrument(self, datainfo, entry_node):
1012	"""
1013	Writes the instrumental information to the XML file
1014
1015	:param datainfo: The Data1D object the information is coming from
1016	:param entry_node: lxml node ElementTree object to be appended to
1017	"""
1018	instr = self.create_element("SASinstrument")
1019	self.append(instr, entry_node)
1020	self.write_node(instr, "name", datainfo.instrument)
1021	return instr
1022
1023	def _write_source(self, datainfo, instr):
1024	"""
1025	Writes the source information to the XML file
1026
1027	:param datainfo: The Data1D object the information is coming from
1028	:param instr: instrument node to be appended to
1029	"""
1030	source = self.create_element("SASsource")
1031	if datainfo.source.name is not None:
1032	self.write_attribute(source, "name",
1033	str(datainfo.source.name))
1034	self.append(source, instr)
1035	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1036	datainfo.source.radiation = "neutron"
1037	self.write_node(source, "radiation", datainfo.source.radiation)
1038
1039	size = self.create_element("beam_size")
1040	if datainfo.source.beam_size_name is not None:
1041	self.write_attribute(size, "name",
1042	str(datainfo.source.beam_size_name))
1043	written = self.write_node( \
1044	size, "x", datainfo.source.beam_size.x,
1045	{"unit": datainfo.source.beam_size_unit})
1046	written = written \| self.write_node( \
1047	size, "y", datainfo.source.beam_size.y,
1048	{"unit": datainfo.source.beam_size_unit})
1049	written = written \| self.write_node( \
1050	size, "z", datainfo.source.beam_size.z,
1051	{"unit": datainfo.source.beam_size_unit})
1052	if written == True:
1053	self.append(size, source)
1054
1055	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1056	self.write_node(source, "wavelength",
1057	datainfo.source.wavelength,
1058	{"unit": datainfo.source.wavelength_unit})
1059	self.write_node(source, "wavelength_min",
1060	datainfo.source.wavelength_min,
1061	{"unit": datainfo.source.wavelength_min_unit})
1062	self.write_node(source, "wavelength_max",
1063	datainfo.source.wavelength_max,
1064	{"unit": datainfo.source.wavelength_max_unit})
1065	self.write_node(source, "wavelength_spread",
1066	datainfo.source.wavelength_spread,
1067	{"unit": datainfo.source.wavelength_spread_unit})
1068
1069	def _write_collimation(self, datainfo, instr):
1070	"""
1071	Writes the collimation information to the XML file
1072
1073	:param datainfo: The Data1D object the information is coming from
1074	:param instr: lxml node ElementTree object to be appended to
1075	"""
1076	if datainfo.collimation == [] or datainfo.collimation is None:
1077	coll = Collimation()
1078	datainfo.collimation.append(coll)
1079	for item in datainfo.collimation:
1080	coll = self.create_element("SAScollimation")
1081	if item.name is not None:
1082	self.write_attribute(coll, "name", str(item.name))
1083	self.append(coll, instr)
1084
1085	self.write_node(coll, "length", item.length,
1086	{"unit": item.length_unit})
1087
1088	for aperture in item.aperture:
1089	apert = self.create_element("aperture")
1090	if aperture.name is not None:
1091	self.write_attribute(apert, "name", str(aperture.name))
1092	if aperture.type is not None:
1093	self.write_attribute(apert, "type", str(aperture.type))
1094	self.append(apert, coll)
1095
1096	size = self.create_element("size")
1097	if aperture.size_name is not None:
1098	self.write_attribute(size, "name",
1099	str(aperture.size_name))
1100	written = self.write_node(size, "x", aperture.size.x,
1101	{"unit": aperture.size_unit})
1102	written = written \| self.write_node( \
1103	size, "y", aperture.size.y,
1104	{"unit": aperture.size_unit})
1105	written = written \| self.write_node( \
1106	size, "z", aperture.size.z,
1107	{"unit": aperture.size_unit})
1108	if written == True:
1109	self.append(size, apert)
1110
1111	self.write_node(apert, "distance", aperture.distance,
1112	{"unit": aperture.distance_unit})
1113
1114	def _write_detectors(self, datainfo, instr):
1115	"""
1116	Writes the detector information to the XML file
1117
1118	:param datainfo: The Data1D object the information is coming from
1119	:param inst: lxml instrument node to be appended to
1120	"""
1121	if datainfo.detector is None or datainfo.detector == []:
1122	det = Detector()
1123	det.name = ""
1124	datainfo.detector.append(det)
1125
1126	for item in datainfo.detector:
1127	det = self.create_element("SASdetector")
1128	written = self.write_node(det, "name", item.name)
1129	written = written \| self.write_node(det, "SDD", item.distance,
1130	{"unit": item.distance_unit})
1131	if written == True:
1132	self.append(det, instr)
1133
1134	off = self.create_element("offset")
1135	written = self.write_node(off, "x", item.offset.x,
1136	{"unit": item.offset_unit})
1137	written = written \| self.write_node(off, "y", item.offset.y,
1138	{"unit": item.offset_unit})
1139	written = written \| self.write_node(off, "z", item.offset.z,
1140	{"unit": item.offset_unit})
1141	if written == True:
1142	self.append(off, det)
1143
1144	ori = self.create_element("orientation")
1145	written = self.write_node(ori, "roll", item.orientation.x,
1146	{"unit": item.orientation_unit})
1147	written = written \| self.write_node(ori, "pitch",
1148	item.orientation.y,
1149	{"unit": item.orientation_unit})
1150	written = written \| self.write_node(ori, "yaw",
1151	item.orientation.z,
1152	{"unit": item.orientation_unit})
1153	if written == True:
1154	self.append(ori, det)
1155
1156	center = self.create_element("beam_center")
1157	written = self.write_node(center, "x", item.beam_center.x,
1158	{"unit": item.beam_center_unit})
1159	written = written \| self.write_node(center, "y",
1160	item.beam_center.y,
1161	{"unit": item.beam_center_unit})
1162	written = written \| self.write_node(center, "z",
1163	item.beam_center.z,
1164	{"unit": item.beam_center_unit})
1165	if written == True:
1166	self.append(center, det)
1167
1168	pix = self.create_element("pixel_size")
1169	written = self.write_node(pix, "x", item.pixel_size.x,
1170	{"unit": item.pixel_size_unit})
1171	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1172	{"unit": item.pixel_size_unit})
1173	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1174	{"unit": item.pixel_size_unit})
1175	if written == True:
1176	self.append(pix, det)
1177	self.write_node(det, "slit_length", item.slit_length,
1178	{"unit": item.slit_length_unit})
1179
1180
1181	def _write_process_notes(self, datainfo, entry_node):
1182	"""
1183	Writes the process notes to the XML file
1184
1185	:param datainfo: The Data1D object the information is coming from
1186	:param entry_node: lxml node ElementTree object to be appended to
1187
1188	"""
1189	for item in datainfo.process:
1190	node = self.create_element("SASprocess")
1191	self.append(node, entry_node)
1192	self.write_node(node, "name", item.name)
1193	self.write_node(node, "date", item.date)
1194	self.write_node(node, "description", item.description)
1195	for term in item.term:
1196	if isinstance(term, list):
1197	value = term['value']
1198	del term['value']
1199	elif isinstance(term, dict):
1200	value = term.get("value")
1201	del term['value']
1202	else:
1203	value = term
1204	self.write_node(node, "term", value, term)
1205	for note in item.notes:
1206	self.write_node(node, "SASprocessnote", note)
1207	if len(item.notes) == 0:
1208	self.write_node(node, "SASprocessnote", "")
1209
1210	def _write_notes(self, datainfo, entry_node):
1211	"""
1212	Writes the notes to the XML file and creates an empty note if none
1213	exist
1214
1215	:param datainfo: The Data1D object the information is coming from
1216	:param entry_node: lxml node ElementTree object to be appended to
1217
1218	"""
1219	if len(datainfo.notes) == 0:
1220	node = self.create_element("SASnote")
1221	self.append(node, entry_node)
1222	else:
1223	for item in datainfo.notes:
1224	node = self.create_element("SASnote")
1225	self.write_text(node, item)
1226	self.append(node, entry_node)
1227
1228	def _check_origin(self, entry_node, doc):
1229	"""
1230	Return the document, and the SASentry node associated with
1231	the data we just wrote.
1232	If the calling function was not the cansas reader, return a minidom
1233	object rather than an lxml object.
1234
1235	:param entry_node: lxml node ElementTree object to be appended to
1236	:param doc: entire xml tree
1237	"""
1238	if not self.frm:
1239	self.frm = inspect.stack()[1]
1240	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1241	mod_name = mod_name.replace(".py", "")
1242	mod = mod_name.split("sas/")
1243	mod_name = mod[1]
1244	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1245	string = self.to_string(doc, pretty_print=False)
1246	doc = parseString(string)
1247	node_name = entry_node.tag
1248	node_list = doc.getElementsByTagName(node_name)
1249	entry_node = node_list.item(0)
1250	return doc, entry_node
1251
1252	# DO NOT REMOVE - used in saving and loading panel states.
1253	def _store_float(self, location, node, variable, storage, optional=True):
1254	"""
1255	Get the content of a xpath location and store
1256	the result. Check that the units are compatible
1257	with the destination. The value is expected to
1258	be a float.
1259
1260	The xpath location might or might not exist.
1261	If it does not exist, nothing is done
1262
1263	:param location: xpath location to fetch
1264	:param node: node to read the data from
1265	:param variable: name of the data member to store it in [string]
1266	:param storage: data object that has the 'variable' data member
1267	:param optional: if True, no exception will be raised
1268	if unit conversion can't be done
1269
1270	:raise ValueError: raised when the units are not recognized
1271	"""
1272	entry = get_content(location, node)
1273	try:
1274	value = float(entry.text)
1275	except:
1276	value = None
1277
1278	if value is not None:
1279	# If the entry has units, check to see that they are
1280	# compatible with what we currently have in the data object
1281	units = entry.get('unit')
1282	if units is not None:
1283	toks = variable.split('.')
1284	local_unit = None
1285	exec "local_unit = storage.%s_unit" % toks[0]
1286	if local_unit is not None and units.lower() != local_unit.lower():
1287	if HAS_CONVERTER == True:
1288	try:
1289	conv = Converter(units)
1290	exec "storage.%s = %g" % \
1291	(variable, conv(value, units=local_unit))
1292	except:
1293	_, exc_value, _ = sys.exc_info()
1294	err_mess = "CanSAS reader: could not convert"
1295	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1296	% (variable, units, local_unit, exc_value)
1297	self.errors.add(err_mess)
1298	if optional:
1299	logger.info(err_mess)
1300	else:
1301	raise ValueError, err_mess
1302	else:
1303	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1304	% (variable, units)
1305	err_mess += " expecting [%s]" % local_unit
1306	self.errors.add(err_mess)
1307	if optional:
1308	logger.info(err_mess)
1309	else:
1310	raise ValueError, err_mess
1311	else:
1312	exec "storage.%s = value" % variable
1313	else:
1314	exec "storage.%s = value" % variable
1315
1316	# DO NOT REMOVE - used in saving and loading panel states.
1317	def _store_content(self, location, node, variable, storage):
1318	"""
1319	Get the content of a xpath location and store
1320	the result. The value is treated as a string.
1321
1322	The xpath location might or might not exist.
1323	If it does not exist, nothing is done
1324
1325	:param location: xpath location to fetch
1326	:param node: node to read the data from
1327	:param variable: name of the data member to store it in [string]
1328	:param storage: data object that has the 'variable' data member
1329
1330	:return: return a list of errors
1331	"""
1332	entry = get_content(location, node)
1333	if entry is not None and entry.text is not None:
1334	exec "storage.%s = entry.text.strip()" % variable
1335
1336	# DO NOT REMOVE Called by outside packages:
1337	# sas.sasgui.perspectives.invariant.invariant_state
1338	# sas.sasgui.perspectives.fitting.pagestate
1339	def get_content(location, node):
1340	"""
1341	Get the first instance of the content of a xpath location.
1342
1343	:param location: xpath location
1344	:param node: node to start at
1345
1346	:return: Element, or None
1347	"""
1348	nodes = node.xpath(location,
1349	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1350	if len(nodes) > 0:
1351	return nodes[0]
1352	else:
1353	return None
1354
1355	# DO NOT REMOVE Called by outside packages:
1356	# sas.sasgui.perspectives.fitting.pagestate
1357	def write_node(doc, parent, name, value, attr=None):
1358	"""
1359	:param doc: document DOM
1360	:param parent: parent node
1361	:param name: tag of the element
1362	:param value: value of the child text node
1363	:param attr: attribute dictionary
1364
1365	:return: True if something was appended, otherwise False
1366	"""
1367	if attr is None:
1368	attr = {}
1369	if value is not None:
1370	node = doc.createElement(name)
1371	node.appendChild(doc.createTextNode(str(value)))
1372	for item in attr:
1373	node.setAttribute(item, attr[item])
1374	parent.appendChild(node)
1375	return True
1376	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ cd57c7d4

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