cansas_reader.py @ a78a02f

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since a78a02f was a78a02f, checked in by krzywon, 7 years ago
Make suggested changes for unit test fixes.
Property mode set to `100644`
File size: 63.4 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	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
157	raise DataReaderException(invalid_xml) # Handled by base class
158	except FileContentsException as fc_exc:
159	msg = "CanSAS Reader could not load the file {}".format(xml_file)
160	if fc_exc.message is not None: # Propagate error messages from earlier
161	msg = fc_exc.message
162	if not self.extension in self.ext: # If the file has no associated loader
163	raise DefaultReaderException(msg)
164	raise FileContentsException(msg)
165	pass
166	else:
167	raise fc_exc
168	except Exception as e: # Convert all other exceptions to FileContentsExceptions
169	raise FileContentsException(e.message)
170
171
172	def load_file_and_schema(self, xml_file, schema_path=""):
173	base_name = xml_reader.__file__
174	base_name = base_name.replace("\\", "/")
175	base = base_name.split("/sas/")[0]
176
177	# Try and parse the XML file
178	try:
179	self.set_xml_file(xml_file)
180	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
181	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
182	raise FileContentsException(msg)
183
184	self.cansas_version = self.xmlroot.get("version", "1.0")
185	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
186
187	if schema_path == "":
188	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
189	base, self.cansas_defaults.get("schema").replace("\\", "/")
190	)
191	self.set_schema(schema_path)
192
193	def is_cansas(self, ext="xml"):
194	"""
195	Checks to see if the XML file is a CanSAS file
196
197	:param ext: The file extension of the data file
198	:raises FileContentsException: Raised if XML file isn't valid CanSAS
199	"""
200	if self.validate_xml(): # Check file is valid XML
201	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
202	value = self.xmlroot.get(name)
203	# Check schema CanSAS version matches file CanSAS version
204	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
205	return True
206	if ext == "svs":
207	return True # Why is this required?
208	# If we get to this point then file isn't valid CanSAS
209	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
210	raise FileContentsException("The file is not valid CanSAS")
211
212	def _parse_entry(self, dom, recurse=False):
213	if not self._is_call_local() and not recurse:
214	self.reset_state()
215	self.data = []
216	self.current_datainfo = DataInfo()
217	self.names.append("SASentry")
218	self.parent_class = "SASentry"
219	# Create an empty dataset if no data has been passed to the reader
220	if self.current_dataset is None:
221	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
222	np.empty(0), np.empty(0))
223	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
224
225	# Loop through each child in the parent element
226	for node in dom:
227	attr = node.attrib
228	name = attr.get("name", "")
229	type = attr.get("type", "")
230	# Get the element name and set the current names level
231	tagname = node.tag.replace(self.base_ns, "")
232	tagname_original = tagname
233	# Skip this iteration when loading in save state information
234	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
235	continue
236	# Get where to store content
237	self.names.append(tagname_original)
238	self.ns_list = CONSTANTS.iterate_namespace(self.names)
239	# If the element is a child element, recurse
240	if len(node.getchildren()) > 0:
241	self.parent_class = tagname_original
242	if tagname == 'SASdata':
243	self._initialize_new_data_set(node)
244	if isinstance(self.current_dataset, plottable_2D):
245	x_bins = attr.get("x_bins", "")
246	y_bins = attr.get("y_bins", "")
247	if x_bins is not "" and y_bins is not "":
248	self.current_dataset.shape = (x_bins, y_bins)
249	else:
250	self.current_dataset.shape = ()
251	# Recurse to access data within the group
252	self._parse_entry(node, recurse=True)
253	if tagname == "SASsample":
254	self.current_datainfo.sample.name = name
255	elif tagname == "beam_size":
256	self.current_datainfo.source.beam_size_name = name
257	elif tagname == "SAScollimation":
258	self.collimation.name = name
259	elif tagname == "aperture":
260	self.aperture.name = name
261	self.aperture.type = type
262	self._add_intermediate()
263	else:
264	if isinstance(self.current_dataset, plottable_2D):
265	data_point = node.text
266	unit = attr.get('unit', '')
267	else:
268	data_point, unit = self._get_node_value(node, tagname)
269
270	# If this is a dataset, store the data appropriately
271	if tagname == 'Run':
272	self.current_datainfo.run_name[data_point] = name
273	self.current_datainfo.run.append(data_point)
274	elif tagname == 'Title':
275	self.current_datainfo.title = data_point
276	elif tagname == 'SASnote':
277	self.current_datainfo.notes.append(data_point)
278
279	# I and Q points
280	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
281	unit_list = unit.split("\|")
282	if len(unit_list) > 1:
283	self.current_dataset.yaxis(unit_list[0].strip(),
284	unit_list[1].strip())
285	else:
286	self.current_dataset.yaxis("Intensity", unit)
287	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
288	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
289	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
290	elif tagname == 'Q':
291	unit_list = unit.split("\|")
292	if len(unit_list) > 1:
293	self.current_dataset.xaxis(unit_list[0].strip(),
294	unit_list[1].strip())
295	else:
296	self.current_dataset.xaxis("Q", unit)
297	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
298	elif tagname == 'Qdev':
299	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
300	elif tagname == 'dQw':
301	if self.current_dataset.dxw is None:
302	self.current_dataset.dxw = np.empty(0)
303	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
304	elif tagname == 'dQl':
305	if self.current_dataset.dxl is None:
306	self.current_dataset.dxl = np.empty(0)
307	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
308	elif tagname == 'Qmean':
309	pass
310	elif tagname == 'Shadowfactor':
311	pass
312	elif tagname == 'Sesans':
313	self.current_datainfo.isSesans = bool(data_point)
314	elif tagname == 'yacceptance':
315	self.current_datainfo.sample.yacceptance = (data_point, unit)
316	elif tagname == 'zacceptance':
317	self.current_datainfo.sample.zacceptance = (data_point, unit)
318
319	# I and Qx, Qy - 2D data
320	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
321	self.current_dataset.yaxis("Intensity", unit)
322	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
323	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
324	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
325	elif tagname == 'Qx':
326	self.current_dataset.xaxis("Qx", unit)
327	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
328	elif tagname == 'Qy':
329	self.current_dataset.yaxis("Qy", unit)
330	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
331	elif tagname == 'Qxdev':
332	self.current_dataset.xaxis("Qxdev", unit)
333	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
334	elif tagname == 'Qydev':
335	self.current_dataset.yaxis("Qydev", unit)
336	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
337	elif tagname == 'Mask':
338	inter = [item == "1" for item in data_point.split(",")]
339	self.current_dataset.mask = np.asarray(inter, dtype=bool)
340
341	# Sample Information
342	elif tagname == 'ID' and self.parent_class == 'SASsample':
343	self.current_datainfo.sample.ID = data_point
344	elif tagname == 'Title' and self.parent_class == 'SASsample':
345	self.current_datainfo.sample.name = data_point
346	elif tagname == 'thickness' and self.parent_class == 'SASsample':
347	self.current_datainfo.sample.thickness = data_point
348	self.current_datainfo.sample.thickness_unit = unit
349	elif tagname == 'transmission' and self.parent_class == 'SASsample':
350	self.current_datainfo.sample.transmission = data_point
351	elif tagname == 'temperature' and self.parent_class == 'SASsample':
352	self.current_datainfo.sample.temperature = data_point
353	self.current_datainfo.sample.temperature_unit = unit
354	elif tagname == 'details' and self.parent_class == 'SASsample':
355	self.current_datainfo.sample.details.append(data_point)
356	elif tagname == 'x' and self.parent_class == 'position':
357	self.current_datainfo.sample.position.x = data_point
358	self.current_datainfo.sample.position_unit = unit
359	elif tagname == 'y' and self.parent_class == 'position':
360	self.current_datainfo.sample.position.y = data_point
361	self.current_datainfo.sample.position_unit = unit
362	elif tagname == 'z' and self.parent_class == 'position':
363	self.current_datainfo.sample.position.z = data_point
364	self.current_datainfo.sample.position_unit = unit
365	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
366	self.current_datainfo.sample.orientation.x = data_point
367	self.current_datainfo.sample.orientation_unit = unit
368	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
369	self.current_datainfo.sample.orientation.y = data_point
370	self.current_datainfo.sample.orientation_unit = unit
371	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
372	self.current_datainfo.sample.orientation.z = data_point
373	self.current_datainfo.sample.orientation_unit = unit
374
375	# Instrumental Information
376	elif tagname == 'name' and self.parent_class == 'SASinstrument':
377	self.current_datainfo.instrument = data_point
378
379	# Detector Information
380	elif tagname == 'name' and self.parent_class == 'SASdetector':
381	self.detector.name = data_point
382	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
383	self.detector.distance = data_point
384	self.detector.distance_unit = unit
385	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
386	self.detector.slit_length = data_point
387	self.detector.slit_length_unit = unit
388	elif tagname == 'x' and self.parent_class == 'offset':
389	self.detector.offset.x = data_point
390	self.detector.offset_unit = unit
391	elif tagname == 'y' and self.parent_class == 'offset':
392	self.detector.offset.y = data_point
393	self.detector.offset_unit = unit
394	elif tagname == 'z' and self.parent_class == 'offset':
395	self.detector.offset.z = data_point
396	self.detector.offset_unit = unit
397	elif tagname == 'x' and self.parent_class == 'beam_center':
398	self.detector.beam_center.x = data_point
399	self.detector.beam_center_unit = unit
400	elif tagname == 'y' and self.parent_class == 'beam_center':
401	self.detector.beam_center.y = data_point
402	self.detector.beam_center_unit = unit
403	elif tagname == 'z' and self.parent_class == 'beam_center':
404	self.detector.beam_center.z = data_point
405	self.detector.beam_center_unit = unit
406	elif tagname == 'x' and self.parent_class == 'pixel_size':
407	self.detector.pixel_size.x = data_point
408	self.detector.pixel_size_unit = unit
409	elif tagname == 'y' and self.parent_class == 'pixel_size':
410	self.detector.pixel_size.y = data_point
411	self.detector.pixel_size_unit = unit
412	elif tagname == 'z' and self.parent_class == 'pixel_size':
413	self.detector.pixel_size.z = data_point
414	self.detector.pixel_size_unit = unit
415	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
416	self.detector.orientation.x = data_point
417	self.detector.orientation_unit = unit
418	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
419	self.detector.orientation.y = data_point
420	self.detector.orientation_unit = unit
421	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
422	self.detector.orientation.z = data_point
423	self.detector.orientation_unit = unit
424
425	# Collimation and Aperture
426	elif tagname == 'length' and self.parent_class == 'SAScollimation':
427	self.collimation.length = data_point
428	self.collimation.length_unit = unit
429	elif tagname == 'name' and self.parent_class == 'SAScollimation':
430	self.collimation.name = data_point
431	elif tagname == 'distance' and self.parent_class == 'aperture':
432	self.aperture.distance = data_point
433	self.aperture.distance_unit = unit
434	elif tagname == 'x' and self.parent_class == 'size':
435	self.aperture.size.x = data_point
436	self.collimation.size_unit = unit
437	elif tagname == 'y' and self.parent_class == 'size':
438	self.aperture.size.y = data_point
439	self.collimation.size_unit = unit
440	elif tagname == 'z' and self.parent_class == 'size':
441	self.aperture.size.z = data_point
442	self.collimation.size_unit = unit
443
444	# Process Information
445	elif tagname == 'name' and self.parent_class == 'SASprocess':
446	self.process.name = data_point
447	elif tagname == 'description' and self.parent_class == 'SASprocess':
448	self.process.description = data_point
449	elif tagname == 'date' and self.parent_class == 'SASprocess':
450	try:
451	self.process.date = datetime.datetime.fromtimestamp(data_point)
452	except:
453	self.process.date = data_point
454	elif tagname == 'SASprocessnote':
455	self.process.notes.append(data_point)
456	elif tagname == 'term' and self.parent_class == 'SASprocess':
457	unit = attr.get("unit", "")
458	dic = { "name": name, "value": data_point, "unit": unit }
459	self.process.term.append(dic)
460
461	# Transmission Spectrum
462	elif tagname == 'T' and self.parent_class == 'Tdata':
463	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
464	self.transspectrum.transmission_unit = unit
465	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
466	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
467	self.transspectrum.transmission_deviation_unit = unit
468	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
469	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
470	self.transspectrum.wavelength_unit = unit
471
472	# Source Information
473	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
474	self.current_datainfo.source.wavelength = data_point
475	self.current_datainfo.source.wavelength_unit = unit
476	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.wavelength_min = data_point
478	self.current_datainfo.source.wavelength_min_unit = unit
479	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
480	self.current_datainfo.source.wavelength_max = data_point
481	self.current_datainfo.source.wavelength_max_unit = unit
482	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
483	self.current_datainfo.source.wavelength_spread = data_point
484	self.current_datainfo.source.wavelength_spread_unit = unit
485	elif tagname == 'x' and self.parent_class == 'beam_size':
486	self.current_datainfo.source.beam_size.x = data_point
487	self.current_datainfo.source.beam_size_unit = unit
488	elif tagname == 'y' and self.parent_class == 'beam_size':
489	self.current_datainfo.source.beam_size.y = data_point
490	self.current_datainfo.source.beam_size_unit = unit
491	elif tagname == 'z' and self.parent_class == 'pixel_size':
492	self.current_datainfo.source.data_point.z = data_point
493	self.current_datainfo.source.beam_size_unit = unit
494	elif tagname == 'radiation' and self.parent_class == 'SASsource':
495	self.current_datainfo.source.radiation = data_point
496	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
497	self.current_datainfo.source.beam_shape = data_point
498
499	# Everything else goes in meta_data
500	else:
501	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
502	self.current_datainfo.meta_data[new_key] = data_point
503
504	self.names.remove(tagname_original)
505	length = 0
506	if len(self.names) > 1:
507	length = len(self.names) - 1
508	self.parent_class = self.names[length]
509	if not self._is_call_local() and not recurse:
510	self.frm = ""
511	self.current_datainfo.errors = set()
512	for error in self.errors:
513	self.current_datainfo.errors.add(error)
514	self.errors.clear()
515	self.send_to_output()
516	empty = None
517	return self.output[0], empty
518
519	def _is_call_local(self):
520	if self.frm == "":
521	inter = inspect.stack()
522	self.frm = inter[2]
523	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
524	mod_name = mod_name.replace(".py", "")
525	mod = mod_name.split("sas/")
526	mod_name = mod[1]
527	if mod_name != "sascalc/dataloader/readers/cansas_reader":
528	return False
529	return True
530
531	def _add_intermediate(self):
532	"""
533	This method stores any intermediate objects within the final data set after fully reading the set.
534	"""
535	if self.parent_class == 'SASprocess':
536	self.current_datainfo.process.append(self.process)
537	self.process = Process()
538	elif self.parent_class == 'SASdetector':
539	self.current_datainfo.detector.append(self.detector)
540	self.detector = Detector()
541	elif self.parent_class == 'SAStransmission_spectrum':
542	self.current_datainfo.trans_spectrum.append(self.transspectrum)
543	self.transspectrum = TransmissionSpectrum()
544	elif self.parent_class == 'SAScollimation':
545	self.current_datainfo.collimation.append(self.collimation)
546	self.collimation = Collimation()
547	elif self.parent_class == 'aperture':
548	self.collimation.aperture.append(self.aperture)
549	self.aperture = Aperture()
550	elif self.parent_class == 'SASdata':
551	self._check_for_empty_resolution()
552	self.data.append(self.current_dataset)
553
554	def _get_node_value(self, node, tagname):
555	"""
556	Get the value of a node and any applicable units
557
558	:param node: The XML node to get the value of
559	:param tagname: The tagname of the node
560	"""
561	#Get the text from the node and convert all whitespace to spaces
562	units = ''
563	node_value = node.text
564	if node_value is not None:
565	node_value = ' '.join(node_value.split())
566	else:
567	node_value = ""
568
569	# If the value is a float, compile with units.
570	if self.ns_list.ns_datatype == "float":
571	# If an empty value is given, set as zero.
572	if node_value is None or node_value.isspace() \
573	or node_value.lower() == "nan":
574	node_value = "0.0"
575	#Convert the value to the base units
576	node_value, units = self._unit_conversion(node, tagname, node_value)
577
578	# If the value is a timestamp, convert to a datetime object
579	elif self.ns_list.ns_datatype == "timestamp":
580	if node_value is None or node_value.isspace():
581	pass
582	else:
583	try:
584	node_value = \
585	datetime.datetime.fromtimestamp(node_value)
586	except ValueError:
587	node_value = None
588	return node_value, units
589
590	def _unit_conversion(self, node, tagname, node_value):
591	"""
592	A unit converter method used to convert the data included in the file
593	to the default units listed in data_info
594
595	:param node: XML node
596	:param tagname: name of the node
597	:param node_value: The value of the current dom node
598	"""
599	attr = node.attrib
600	value_unit = ''
601	err_msg = None
602	default_unit = None
603	if not isinstance(node_value, float):
604	node_value = float(node_value)
605	if 'unit' in attr and attr.get('unit') is not None:
606	try:
607	local_unit = attr['unit']
608	unitname = self.ns_list.current_level.get("unit", "")
609	if "SASdetector" in self.names:
610	save_in = "detector"
611	elif "aperture" in self.names:
612	save_in = "aperture"
613	elif "SAScollimation" in self.names:
614	save_in = "collimation"
615	elif "SAStransmission_spectrum" in self.names:
616	save_in = "transspectrum"
617	elif "SASdata" in self.names:
618	x = np.zeros(1)
619	y = np.zeros(1)
620	self.current_data1d = Data1D(x, y)
621	save_in = "current_data1d"
622	elif "SASsource" in self.names:
623	save_in = "current_datainfo.source"
624	elif "SASsample" in self.names:
625	save_in = "current_datainfo.sample"
626	elif "SASprocess" in self.names:
627	save_in = "process"
628	else:
629	save_in = "current_datainfo"
630	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
631	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
632	and local_unit.lower() != "none":
633	if HAS_CONVERTER == True:
634	# Check local units - bad units raise KeyError
635	data_conv_q = Converter(local_unit)
636	value_unit = default_unit
637	node_value = data_conv_q(node_value, units=default_unit)
638	else:
639	value_unit = local_unit
640	err_msg = "Unit converter is not available.\n"
641	else:
642	value_unit = local_unit
643	except KeyError:
644	err_msg = "CanSAS reader: unexpected "
645	err_msg += "\"{0}\" unit [{1}]; "
646	err_msg = err_msg.format(tagname, local_unit)
647	err_msg += "expecting [{0}]".format(default_unit)
648	value_unit = local_unit
649	except:
650	err_msg = "CanSAS reader: unknown error converting "
651	err_msg += "\"{0}\" unit [{1}]"
652	err_msg = err_msg.format(tagname, local_unit)
653	value_unit = local_unit
654	elif 'unit' in attr:
655	value_unit = attr['unit']
656	if err_msg:
657	self.errors.add(err_msg)
658	return node_value, value_unit
659
660	def _check_for_empty_resolution(self):
661	"""
662	a method to check all resolution data sets are the same size as I and q
663	"""
664	dql_exists = False
665	dqw_exists = False
666	dq_exists = False
667	di_exists = False
668	if self.current_dataset.dxl is not None:
669	dql_exists = True
670	if self.current_dataset.dxw is not None:
671	dqw_exists = True
672	if self.current_dataset.dx is not None:
673	dq_exists = True
674	if self.current_dataset.dy is not None:
675	di_exists = True
676	if dqw_exists and not dql_exists:
677	array_size = self.current_dataset.dxw.size - 1
678	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
679	np.zeros([array_size]))
680	elif dql_exists and not dqw_exists:
681	array_size = self.current_dataset.dxl.size - 1
682	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
683	np.zeros([array_size]))
684	elif not dql_exists and not dqw_exists and not dq_exists:
685	array_size = self.current_dataset.x.size - 1
686	self.current_dataset.dx = np.append(self.current_dataset.dx,
687	np.zeros([array_size]))
688	if not di_exists:
689	array_size = self.current_dataset.y.size - 1
690	self.current_dataset.dy = np.append(self.current_dataset.dy,
691	np.zeros([array_size]))
692
693	def _initialize_new_data_set(self, node=None):
694	if node is not None:
695	for child in node:
696	if child.tag.replace(self.base_ns, "") == "Idata":
697	for i_child in child:
698	if i_child.tag.replace(self.base_ns, "") == "Qx":
699	self.current_dataset = plottable_2D()
700	return
701	self.current_dataset = plottable_1D(np.array(0), np.array(0))
702
703	## Writing Methods
704	def write(self, filename, datainfo):
705	"""
706	Write the content of a Data1D as a CanSAS XML file
707
708	:param filename: name of the file to write
709	:param datainfo: Data1D object
710	"""
711	# Create XML document
712	doc, _ = self._to_xml_doc(datainfo)
713	# Write the file
714	file_ref = open(filename, 'w')
715	if self.encoding is None:
716	self.encoding = "UTF-8"
717	doc.write(file_ref, encoding=self.encoding,
718	pretty_print=True, xml_declaration=True)
719	file_ref.close()
720
721	def _to_xml_doc(self, datainfo):
722	"""
723	Create an XML document to contain the content of a Data1D
724
725	:param datainfo: Data1D object
726	"""
727	is_2d = False
728	if issubclass(datainfo.__class__, Data2D):
729	is_2d = True
730
731	# Get PIs and create root element
732	pi_string = self._get_pi_string()
733	# Define namespaces and create SASroot object
734	main_node = self._create_main_node()
735	# Create ElementTree, append SASroot and apply processing instructions
736	base_string = pi_string + self.to_string(main_node)
737	base_element = self.create_element_from_string(base_string)
738	doc = self.create_tree(base_element)
739	# Create SASentry Element
740	entry_node = self.create_element("SASentry")
741	root = doc.getroot()
742	root.append(entry_node)
743
744	# Add Title to SASentry
745	self.write_node(entry_node, "Title", datainfo.title)
746	# Add Run to SASentry
747	self._write_run_names(datainfo, entry_node)
748	# Add Data info to SASEntry
749	if is_2d:
750	self._write_data_2d(datainfo, entry_node)
751	else:
752	self._write_data(datainfo, entry_node)
753	# Transmission Spectrum Info
754	# TODO: fix the writer to linearize all data, including T_spectrum
755	# self._write_trans_spectrum(datainfo, entry_node)
756	# Sample info
757	self._write_sample_info(datainfo, entry_node)
758	# Instrument info
759	instr = self._write_instrument(datainfo, entry_node)
760	# Source
761	self._write_source(datainfo, instr)
762	# Collimation
763	self._write_collimation(datainfo, instr)
764	# Detectors
765	self._write_detectors(datainfo, instr)
766	# Processes info
767	self._write_process_notes(datainfo, entry_node)
768	# Note info
769	self._write_notes(datainfo, entry_node)
770	# Return the document, and the SASentry node associated with
771	# the data we just wrote
772	# If the calling function was not the cansas reader, return a minidom
773	# object rather than an lxml object.
774	self.frm = inspect.stack()[1]
775	doc, entry_node = self._check_origin(entry_node, doc)
776	return doc, entry_node
777
778	def write_node(self, parent, name, value, attr=None):
779	"""
780	:param doc: document DOM
781	:param parent: parent node
782	:param name: tag of the element
783	:param value: value of the child text node
784	:param attr: attribute dictionary
785
786	:return: True if something was appended, otherwise False
787	"""
788	if value is not None:
789	parent = self.ebuilder(parent, name, value, attr)
790	return True
791	return False
792
793	def _get_pi_string(self):
794	"""
795	Creates the processing instructions header for writing to file
796	"""
797	pis = self.return_processing_instructions()
798	if len(pis) > 0:
799	pi_tree = self.create_tree(pis[0])
800	i = 1
801	for i in range(1, len(pis) - 1):
802	pi_tree = self.append(pis[i], pi_tree)
803	pi_string = self.to_string(pi_tree)
804	else:
805	pi_string = ""
806	return pi_string
807
808	def _create_main_node(self):
809	"""
810	Creates the primary xml header used when writing to file
811	"""
812	xsi = "http://www.w3.org/2001/XMLSchema-instance"
813	version = self.cansas_version
814	n_s = CANSAS_NS.get(version).get("ns")
815	if version == "1.1":
816	url = "http://www.cansas.org/formats/1.1/"
817	else:
818	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
819	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
820	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
821	"version" : version}
822	nsmap = {'xsi' : xsi, None: n_s}
823
824	main_node = self.create_element("{" + n_s + "}SASroot",
825	attrib=attrib, nsmap=nsmap)
826	return main_node
827
828	def _write_run_names(self, datainfo, entry_node):
829	"""
830	Writes the run names to the XML file
831
832	:param datainfo: The Data1D object the information is coming from
833	:param entry_node: lxml node ElementTree object to be appended to
834	"""
835	if datainfo.run is None or datainfo.run == []:
836	datainfo.run.append(RUN_NAME_DEFAULT)
837	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
838	for item in datainfo.run:
839	runname = {}
840	if item in datainfo.run_name and \
841	len(str(datainfo.run_name[item])) > 1:
842	runname = {'name': datainfo.run_name[item]}
843	self.write_node(entry_node, "Run", item, runname)
844
845	def _write_data(self, datainfo, entry_node):
846	"""
847	Writes 1D I and Q data to the XML file
848
849	:param datainfo: The Data1D object the information is coming from
850	:param entry_node: lxml node ElementTree object to be appended to
851	"""
852	node = self.create_element("SASdata")
853	self.append(node, entry_node)
854
855	for i in range(len(datainfo.x)):
856	point = self.create_element("Idata")
857	node.append(point)
858	self.write_node(point, "Q", datainfo.x[i],
859	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
860	if len(datainfo.y) >= i:
861	self.write_node(point, "I", datainfo.y[i],
862	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
863	if datainfo.dy is not None and len(datainfo.dy) > i:
864	self.write_node(point, "Idev", datainfo.dy[i],
865	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
866	if datainfo.dx is not None and len(datainfo.dx) > i:
867	self.write_node(point, "Qdev", datainfo.dx[i],
868	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
869	if datainfo.dxw is not None and len(datainfo.dxw) > i:
870	self.write_node(point, "dQw", datainfo.dxw[i],
871	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
872	if datainfo.dxl is not None and len(datainfo.dxl) > i:
873	self.write_node(point, "dQl", datainfo.dxl[i],
874	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
875	if datainfo.isSesans:
876	sesans = self.create_element("Sesans")
877	sesans.text = str(datainfo.isSesans)
878	node.append(sesans)
879	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
880	{'unit': datainfo.sample.yacceptance[1]})
881	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
882	{'unit': datainfo.sample.zacceptance[1]})
883
884
885	def _write_data_2d(self, datainfo, entry_node):
886	"""
887	Writes 2D data to the XML file
888
889	:param datainfo: The Data2D object the information is coming from
890	:param entry_node: lxml node ElementTree object to be appended to
891	"""
892	attr = {}
893	if datainfo.data.shape:
894	attr["x_bins"] = str(len(datainfo.x_bins))
895	attr["y_bins"] = str(len(datainfo.y_bins))
896	node = self.create_element("SASdata", attr)
897	self.append(node, entry_node)
898
899	point = self.create_element("Idata")
900	node.append(point)
901	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
902	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
903	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
904
905	self.write_node(point, "Qx", qx,
906	{'unit': datainfo._xunit})
907	self.write_node(point, "Qy", qy,
908	{'unit': datainfo._yunit})
909	self.write_node(point, "I", intensity,
910	{'unit': datainfo._zunit})
911	if datainfo.err_data is not None:
912	err = ','.join([str(datainfo.err_data[i]) for i in
913	xrange(len(datainfo.err_data))])
914	self.write_node(point, "Idev", err,
915	{'unit': datainfo._zunit})
916	if datainfo.dqy_data is not None:
917	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
918	xrange(len(datainfo.dqy_data))])
919	self.write_node(point, "Qydev", dqy,
920	{'unit': datainfo._yunit})
921	if datainfo.dqx_data is not None:
922	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
923	xrange(len(datainfo.dqx_data))])
924	self.write_node(point, "Qxdev", dqx,
925	{'unit': datainfo._xunit})
926	if datainfo.mask is not None:
927	mask = ','.join(
928	["1" if datainfo.mask[i] else "0"
929	for i in xrange(len(datainfo.mask))])
930	self.write_node(point, "Mask", mask)
931
932	def _write_trans_spectrum(self, datainfo, entry_node):
933	"""
934	Writes the transmission spectrum data to the XML file
935
936	:param datainfo: The Data1D object the information is coming from
937	:param entry_node: lxml node ElementTree object to be appended to
938	"""
939	for i in range(len(datainfo.trans_spectrum)):
940	spectrum = datainfo.trans_spectrum[i]
941	node = self.create_element("SAStransmission_spectrum",
942	{"name" : spectrum.name})
943	self.append(node, entry_node)
944	if isinstance(spectrum.timestamp, datetime.datetime):
945	node.setAttribute("timestamp", spectrum.timestamp)
946	for i in range(len(spectrum.wavelength)):
947	point = self.create_element("Tdata")
948	node.append(point)
949	self.write_node(point, "Lambda", spectrum.wavelength[i],
950	{'unit': spectrum.wavelength_unit})
951	self.write_node(point, "T", spectrum.transmission[i],
952	{'unit': spectrum.transmission_unit})
953	if spectrum.transmission_deviation is not None \
954	and len(spectrum.transmission_deviation) >= i:
955	self.write_node(point, "Tdev",
956	spectrum.transmission_deviation[i],
957	{'unit':
958	spectrum.transmission_deviation_unit})
959
960	def _write_sample_info(self, datainfo, entry_node):
961	"""
962	Writes the sample information to the XML file
963
964	:param datainfo: The Data1D object the information is coming from
965	:param entry_node: lxml node ElementTree object to be appended to
966	"""
967	sample = self.create_element("SASsample")
968	if datainfo.sample.name is not None:
969	self.write_attribute(sample, "name",
970	str(datainfo.sample.name))
971	self.append(sample, entry_node)
972	self.write_node(sample, "ID", str(datainfo.sample.ID))
973	self.write_node(sample, "thickness", datainfo.sample.thickness,
974	{"unit": datainfo.sample.thickness_unit})
975	self.write_node(sample, "transmission", datainfo.sample.transmission)
976	self.write_node(sample, "temperature", datainfo.sample.temperature,
977	{"unit": datainfo.sample.temperature_unit})
978
979	pos = self.create_element("position")
980	written = self.write_node(pos,
981	"x",
982	datainfo.sample.position.x,
983	{"unit": datainfo.sample.position_unit})
984	written = written \| self.write_node( \
985	pos, "y", datainfo.sample.position.y,
986	{"unit": datainfo.sample.position_unit})
987	written = written \| self.write_node( \
988	pos, "z", datainfo.sample.position.z,
989	{"unit": datainfo.sample.position_unit})
990	if written == True:
991	self.append(pos, sample)
992
993	ori = self.create_element("orientation")
994	written = self.write_node(ori, "roll",
995	datainfo.sample.orientation.x,
996	{"unit": datainfo.sample.orientation_unit})
997	written = written \| self.write_node( \
998	ori, "pitch", datainfo.sample.orientation.y,
999	{"unit": datainfo.sample.orientation_unit})
1000	written = written \| self.write_node( \
1001	ori, "yaw", datainfo.sample.orientation.z,
1002	{"unit": datainfo.sample.orientation_unit})
1003	if written == True:
1004	self.append(ori, sample)
1005
1006	for item in datainfo.sample.details:
1007	self.write_node(sample, "details", item)
1008
1009	def _write_instrument(self, datainfo, entry_node):
1010	"""
1011	Writes the instrumental information to the XML file
1012
1013	:param datainfo: The Data1D object the information is coming from
1014	:param entry_node: lxml node ElementTree object to be appended to
1015	"""
1016	instr = self.create_element("SASinstrument")
1017	self.append(instr, entry_node)
1018	self.write_node(instr, "name", datainfo.instrument)
1019	return instr
1020
1021	def _write_source(self, datainfo, instr):
1022	"""
1023	Writes the source information to the XML file
1024
1025	:param datainfo: The Data1D object the information is coming from
1026	:param instr: instrument node to be appended to
1027	"""
1028	source = self.create_element("SASsource")
1029	if datainfo.source.name is not None:
1030	self.write_attribute(source, "name",
1031	str(datainfo.source.name))
1032	self.append(source, instr)
1033	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1034	datainfo.source.radiation = "neutron"
1035	self.write_node(source, "radiation", datainfo.source.radiation)
1036
1037	size = self.create_element("beam_size")
1038	if datainfo.source.beam_size_name is not None:
1039	self.write_attribute(size, "name",
1040	str(datainfo.source.beam_size_name))
1041	written = self.write_node( \
1042	size, "x", datainfo.source.beam_size.x,
1043	{"unit": datainfo.source.beam_size_unit})
1044	written = written \| self.write_node( \
1045	size, "y", datainfo.source.beam_size.y,
1046	{"unit": datainfo.source.beam_size_unit})
1047	written = written \| self.write_node( \
1048	size, "z", datainfo.source.beam_size.z,
1049	{"unit": datainfo.source.beam_size_unit})
1050	if written == True:
1051	self.append(size, source)
1052
1053	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1054	self.write_node(source, "wavelength",
1055	datainfo.source.wavelength,
1056	{"unit": datainfo.source.wavelength_unit})
1057	self.write_node(source, "wavelength_min",
1058	datainfo.source.wavelength_min,
1059	{"unit": datainfo.source.wavelength_min_unit})
1060	self.write_node(source, "wavelength_max",
1061	datainfo.source.wavelength_max,
1062	{"unit": datainfo.source.wavelength_max_unit})
1063	self.write_node(source, "wavelength_spread",
1064	datainfo.source.wavelength_spread,
1065	{"unit": datainfo.source.wavelength_spread_unit})
1066
1067	def _write_collimation(self, datainfo, instr):
1068	"""
1069	Writes the collimation information to the XML file
1070
1071	:param datainfo: The Data1D object the information is coming from
1072	:param instr: lxml node ElementTree object to be appended to
1073	"""
1074	if datainfo.collimation == [] or datainfo.collimation is None:
1075	coll = Collimation()
1076	datainfo.collimation.append(coll)
1077	for item in datainfo.collimation:
1078	coll = self.create_element("SAScollimation")
1079	if item.name is not None:
1080	self.write_attribute(coll, "name", str(item.name))
1081	self.append(coll, instr)
1082
1083	self.write_node(coll, "length", item.length,
1084	{"unit": item.length_unit})
1085
1086	for aperture in item.aperture:
1087	apert = self.create_element("aperture")
1088	if aperture.name is not None:
1089	self.write_attribute(apert, "name", str(aperture.name))
1090	if aperture.type is not None:
1091	self.write_attribute(apert, "type", str(aperture.type))
1092	self.append(apert, coll)
1093
1094	size = self.create_element("size")
1095	if aperture.size_name is not None:
1096	self.write_attribute(size, "name",
1097	str(aperture.size_name))
1098	written = self.write_node(size, "x", aperture.size.x,
1099	{"unit": aperture.size_unit})
1100	written = written \| self.write_node( \
1101	size, "y", aperture.size.y,
1102	{"unit": aperture.size_unit})
1103	written = written \| self.write_node( \
1104	size, "z", aperture.size.z,
1105	{"unit": aperture.size_unit})
1106	if written == True:
1107	self.append(size, apert)
1108
1109	self.write_node(apert, "distance", aperture.distance,
1110	{"unit": aperture.distance_unit})
1111
1112	def _write_detectors(self, datainfo, instr):
1113	"""
1114	Writes the detector information to the XML file
1115
1116	:param datainfo: The Data1D object the information is coming from
1117	:param inst: lxml instrument node to be appended to
1118	"""
1119	if datainfo.detector is None or datainfo.detector == []:
1120	det = Detector()
1121	det.name = ""
1122	datainfo.detector.append(det)
1123
1124	for item in datainfo.detector:
1125	det = self.create_element("SASdetector")
1126	written = self.write_node(det, "name", item.name)
1127	written = written \| self.write_node(det, "SDD", item.distance,
1128	{"unit": item.distance_unit})
1129	if written == True:
1130	self.append(det, instr)
1131
1132	off = self.create_element("offset")
1133	written = self.write_node(off, "x", item.offset.x,
1134	{"unit": item.offset_unit})
1135	written = written \| self.write_node(off, "y", item.offset.y,
1136	{"unit": item.offset_unit})
1137	written = written \| self.write_node(off, "z", item.offset.z,
1138	{"unit": item.offset_unit})
1139	if written == True:
1140	self.append(off, det)
1141
1142	ori = self.create_element("orientation")
1143	written = self.write_node(ori, "roll", item.orientation.x,
1144	{"unit": item.orientation_unit})
1145	written = written \| self.write_node(ori, "pitch",
1146	item.orientation.y,
1147	{"unit": item.orientation_unit})
1148	written = written \| self.write_node(ori, "yaw",
1149	item.orientation.z,
1150	{"unit": item.orientation_unit})
1151	if written == True:
1152	self.append(ori, det)
1153
1154	center = self.create_element("beam_center")
1155	written = self.write_node(center, "x", item.beam_center.x,
1156	{"unit": item.beam_center_unit})
1157	written = written \| self.write_node(center, "y",
1158	item.beam_center.y,
1159	{"unit": item.beam_center_unit})
1160	written = written \| self.write_node(center, "z",
1161	item.beam_center.z,
1162	{"unit": item.beam_center_unit})
1163	if written == True:
1164	self.append(center, det)
1165
1166	pix = self.create_element("pixel_size")
1167	written = self.write_node(pix, "x", item.pixel_size.x,
1168	{"unit": item.pixel_size_unit})
1169	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1170	{"unit": item.pixel_size_unit})
1171	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1172	{"unit": item.pixel_size_unit})
1173	if written == True:
1174	self.append(pix, det)
1175	self.write_node(det, "slit_length", item.slit_length,
1176	{"unit": item.slit_length_unit})
1177
1178
1179	def _write_process_notes(self, datainfo, entry_node):
1180	"""
1181	Writes the process notes to the XML file
1182
1183	:param datainfo: The Data1D object the information is coming from
1184	:param entry_node: lxml node ElementTree object to be appended to
1185
1186	"""
1187	for item in datainfo.process:
1188	node = self.create_element("SASprocess")
1189	self.append(node, entry_node)
1190	self.write_node(node, "name", item.name)
1191	self.write_node(node, "date", item.date)
1192	self.write_node(node, "description", item.description)
1193	for term in item.term:
1194	if isinstance(term, list):
1195	value = term['value']
1196	del term['value']
1197	elif isinstance(term, dict):
1198	value = term.get("value")
1199	del term['value']
1200	else:
1201	value = term
1202	self.write_node(node, "term", value, term)
1203	for note in item.notes:
1204	self.write_node(node, "SASprocessnote", note)
1205	if len(item.notes) == 0:
1206	self.write_node(node, "SASprocessnote", "")
1207
1208	def _write_notes(self, datainfo, entry_node):
1209	"""
1210	Writes the notes to the XML file and creates an empty note if none
1211	exist
1212
1213	:param datainfo: The Data1D object the information is coming from
1214	:param entry_node: lxml node ElementTree object to be appended to
1215
1216	"""
1217	if len(datainfo.notes) == 0:
1218	node = self.create_element("SASnote")
1219	self.append(node, entry_node)
1220	else:
1221	for item in datainfo.notes:
1222	node = self.create_element("SASnote")
1223	self.write_text(node, item)
1224	self.append(node, entry_node)
1225
1226	def _check_origin(self, entry_node, doc):
1227	"""
1228	Return the document, and the SASentry node associated with
1229	the data we just wrote.
1230	If the calling function was not the cansas reader, return a minidom
1231	object rather than an lxml object.
1232
1233	:param entry_node: lxml node ElementTree object to be appended to
1234	:param doc: entire xml tree
1235	"""
1236	if not self.frm:
1237	self.frm = inspect.stack()[1]
1238	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1239	mod_name = mod_name.replace(".py", "")
1240	mod = mod_name.split("sas/")
1241	mod_name = mod[1]
1242	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1243	string = self.to_string(doc, pretty_print=False)
1244	doc = parseString(string)
1245	node_name = entry_node.tag
1246	node_list = doc.getElementsByTagName(node_name)
1247	entry_node = node_list.item(0)
1248	return doc, entry_node
1249
1250	# DO NOT REMOVE - used in saving and loading panel states.
1251	def _store_float(self, location, node, variable, storage, optional=True):
1252	"""
1253	Get the content of a xpath location and store
1254	the result. Check that the units are compatible
1255	with the destination. The value is expected to
1256	be a float.
1257
1258	The xpath location might or might not exist.
1259	If it does not exist, nothing is done
1260
1261	:param location: xpath location to fetch
1262	:param node: node to read the data from
1263	:param variable: name of the data member to store it in [string]
1264	:param storage: data object that has the 'variable' data member
1265	:param optional: if True, no exception will be raised
1266	if unit conversion can't be done
1267
1268	:raise ValueError: raised when the units are not recognized
1269	"""
1270	entry = get_content(location, node)
1271	try:
1272	value = float(entry.text)
1273	except:
1274	value = None
1275
1276	if value is not None:
1277	# If the entry has units, check to see that they are
1278	# compatible with what we currently have in the data object
1279	units = entry.get('unit')
1280	if units is not None:
1281	toks = variable.split('.')
1282	local_unit = None
1283	exec "local_unit = storage.%s_unit" % toks[0]
1284	if local_unit is not None and units.lower() != local_unit.lower():
1285	if HAS_CONVERTER == True:
1286	try:
1287	conv = Converter(units)
1288	exec "storage.%s = %g" % \
1289	(variable, conv(value, units=local_unit))
1290	except:
1291	_, exc_value, _ = sys.exc_info()
1292	err_mess = "CanSAS reader: could not convert"
1293	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1294	% (variable, units, local_unit, exc_value)
1295	self.errors.add(err_mess)
1296	if optional:
1297	logger.info(err_mess)
1298	else:
1299	raise ValueError, err_mess
1300	else:
1301	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1302	% (variable, units)
1303	err_mess += " expecting [%s]" % local_unit
1304	self.errors.add(err_mess)
1305	if optional:
1306	logger.info(err_mess)
1307	else:
1308	raise ValueError, err_mess
1309	else:
1310	exec "storage.%s = value" % variable
1311	else:
1312	exec "storage.%s = value" % variable
1313
1314	# DO NOT REMOVE - used in saving and loading panel states.
1315	def _store_content(self, location, node, variable, storage):
1316	"""
1317	Get the content of a xpath location and store
1318	the result. The value is treated as a string.
1319
1320	The xpath location might or might not exist.
1321	If it does not exist, nothing is done
1322
1323	:param location: xpath location to fetch
1324	:param node: node to read the data from
1325	:param variable: name of the data member to store it in [string]
1326	:param storage: data object that has the 'variable' data member
1327
1328	:return: return a list of errors
1329	"""
1330	entry = get_content(location, node)
1331	if entry is not None and entry.text is not None:
1332	exec "storage.%s = entry.text.strip()" % variable
1333
1334	# DO NOT REMOVE Called by outside packages:
1335	# sas.sasgui.perspectives.invariant.invariant_state
1336	# sas.sasgui.perspectives.fitting.pagestate
1337	def get_content(location, node):
1338	"""
1339	Get the first instance of the content of a xpath location.
1340
1341	:param location: xpath location
1342	:param node: node to start at
1343
1344	:return: Element, or None
1345	"""
1346	nodes = node.xpath(location,
1347	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1348	if len(nodes) > 0:
1349	return nodes[0]
1350	else:
1351	return None
1352
1353	# DO NOT REMOVE Called by outside packages:
1354	# sas.sasgui.perspectives.fitting.pagestate
1355	def write_node(doc, parent, name, value, attr=None):
1356	"""
1357	:param doc: document DOM
1358	:param parent: parent node
1359	:param name: tag of the element
1360	:param value: value of the child text node
1361	:param attr: attribute dictionary
1362
1363	:return: True if something was appended, otherwise False
1364	"""
1365	if attr is None:
1366	attr = {}
1367	if value is not None:
1368	node = doc.createElement(name)
1369	node.appendChild(doc.createTextNode(str(value)))
1370	for item in attr:
1371	node.setAttribute(item, attr[item])
1372	parent.appendChild(node)
1373	return True
1374	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ a78a02f

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