cansas_reader.py @ 67d8b1b

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 67d8b1b was ae69c690, checked in by krzywon, 7 years ago
Ensure dxl and dxw and the same length as each other and as x.
Property mode set to `100644`
File size: 63.5 KB

Line
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	self.data_cleanup()
133	except FileContentsException as fc_exc:
134	# File doesn't meet schema - try loading with a less strict schema
135	base_name = xml_reader.__file__
136	base_name = base_name.replace("\\", "/")
137	base = base_name.split("/sas/")[0]
138	if self.cansas_version == "1.1":
139	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
140	else:
141	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
142	self.set_schema(invalid_schema)
143	if self.invalid:
144	try:
145	# Load data with less strict schema
146	self.read(xml_file, invalid_schema, False)
147
148	# File can still be read but doesn't match schema, so raise exception
149	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
150	invalid_xml = self.find_invalid_xml()
151	if invalid_xml != "":
152	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
153	raise DataReaderException(invalid_xml) # Handled by base class
154	except FileContentsException as fc_exc:
155	msg = "CanSAS Reader could not load the file {}".format(xml_file)
156	if fc_exc.message is not None: # Propagate error messages from earlier
157	msg = fc_exc.message
158	if not self.extension in self.ext: # If the file has no associated loader
159	raise DefaultReaderException(msg)
160	raise FileContentsException(msg)
161	pass
162	else:
163	raise fc_exc
164	except Exception as e: # Convert all other exceptions to FileContentsExceptions
165	raise FileContentsException(e.message)
166
167
168	def load_file_and_schema(self, xml_file, schema_path=""):
169	base_name = xml_reader.__file__
170	base_name = base_name.replace("\\", "/")
171	base = base_name.split("/sas/")[0]
172
173	# Try and parse the XML file
174	try:
175	self.set_xml_file(xml_file)
176	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
177	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
178	raise FileContentsException(msg)
179
180	self.cansas_version = self.xmlroot.get("version", "1.0")
181	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
182
183	if schema_path == "":
184	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
185	base, self.cansas_defaults.get("schema").replace("\\", "/")
186	)
187	self.set_schema(schema_path)
188
189	def is_cansas(self, ext="xml"):
190	"""
191	Checks to see if the XML file is a CanSAS file
192
193	:param ext: The file extension of the data file
194	:raises FileContentsException: Raised if XML file isn't valid CanSAS
195	"""
196	if self.validate_xml(): # Check file is valid XML
197	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
198	value = self.xmlroot.get(name)
199	# Check schema CanSAS version matches file CanSAS version
200	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
201	return True
202	if ext == "svs":
203	return True # Why is this required?
204	# If we get to this point then file isn't valid CanSAS
205	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
206	raise FileContentsException("The file is not valid CanSAS")
207
208	def _parse_entry(self, dom, recurse=False):
209	if not self._is_call_local() and not recurse:
210	self.reset_state()
211	self.data = []
212	self.current_datainfo = DataInfo()
213	self.names.append("SASentry")
214	self.parent_class = "SASentry"
215	# Create an empty dataset if no data has been passed to the reader
216	if self.current_dataset is None:
217	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
218	np.empty(0), np.empty(0))
219	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
220
221	# Loop through each child in the parent element
222	for node in dom:
223	attr = node.attrib
224	name = attr.get("name", "")
225	type = attr.get("type", "")
226	# Get the element name and set the current names level
227	tagname = node.tag.replace(self.base_ns, "")
228	tagname_original = tagname
229	# Skip this iteration when loading in save state information
230	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
231	continue
232	# Get where to store content
233	self.names.append(tagname_original)
234	self.ns_list = CONSTANTS.iterate_namespace(self.names)
235	# If the element is a child element, recurse
236	if len(node.getchildren()) > 0:
237	self.parent_class = tagname_original
238	if tagname == 'SASdata':
239	self._initialize_new_data_set(node)
240	if isinstance(self.current_dataset, plottable_2D):
241	x_bins = attr.get("x_bins", "")
242	y_bins = attr.get("y_bins", "")
243	if x_bins is not "" and y_bins is not "":
244	self.current_dataset.shape = (x_bins, y_bins)
245	else:
246	self.current_dataset.shape = ()
247	# Recurse to access data within the group
248	self._parse_entry(node, recurse=True)
249	if tagname == "SASsample":
250	self.current_datainfo.sample.name = name
251	elif tagname == "beam_size":
252	self.current_datainfo.source.beam_size_name = name
253	elif tagname == "SAScollimation":
254	self.collimation.name = name
255	elif tagname == "aperture":
256	self.aperture.name = name
257	self.aperture.type = type
258	self._add_intermediate()
259	else:
260	if isinstance(self.current_dataset, plottable_2D):
261	data_point = node.text
262	unit = attr.get('unit', '')
263	else:
264	data_point, unit = self._get_node_value(node, tagname)
265
266	# If this is a dataset, store the data appropriately
267	if tagname == 'Run':
268	self.current_datainfo.run_name[data_point] = name
269	self.current_datainfo.run.append(data_point)
270	elif tagname == 'Title':
271	self.current_datainfo.title = data_point
272	elif tagname == 'SASnote':
273	self.current_datainfo.notes.append(data_point)
274
275	# I and Q points
276	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
277	self.current_dataset.yaxis("Intensity", unit)
278	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
279	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
280	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
281	elif tagname == 'Q':
282	self.current_dataset.xaxis("Q", unit)
283	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
284	elif tagname == 'Qdev':
285	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
286	elif tagname == 'dQw':
287	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
288	elif tagname == 'dQl':
289	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
290	elif tagname == 'Qmean':
291	pass
292	elif tagname == 'Shadowfactor':
293	pass
294	elif tagname == 'Sesans':
295	self.current_datainfo.isSesans = bool(data_point)
296	self.current_dataset.xaxis(attr.get('x_axis'),
297	attr.get('x_unit'))
298	self.current_dataset.yaxis(attr.get('y_axis'),
299	attr.get('y_unit'))
300	elif tagname == 'yacceptance':
301	self.current_datainfo.sample.yacceptance = (data_point, unit)
302	elif tagname == 'zacceptance':
303	self.current_datainfo.sample.zacceptance = (data_point, unit)
304
305	# I and Qx, Qy - 2D data
306	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
307	self.current_dataset.yaxis("Intensity", unit)
308	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
309	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
310	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qx':
312	self.current_dataset.xaxis("Qx", unit)
313	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qy':
315	self.current_dataset.yaxis("Qy", unit)
316	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Qxdev':
318	self.current_dataset.xaxis("Qxdev", unit)
319	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
320	elif tagname == 'Qydev':
321	self.current_dataset.yaxis("Qydev", unit)
322	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
323	elif tagname == 'Mask':
324	inter = [item == "1" for item in data_point.split(",")]
325	self.current_dataset.mask = np.asarray(inter, dtype=bool)
326
327	# Sample Information
328	elif tagname == 'ID' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.ID = data_point
330	elif tagname == 'Title' and self.parent_class == 'SASsample':
331	self.current_datainfo.sample.name = data_point
332	elif tagname == 'thickness' and self.parent_class == 'SASsample':
333	self.current_datainfo.sample.thickness = data_point
334	self.current_datainfo.sample.thickness_unit = unit
335	elif tagname == 'transmission' and self.parent_class == 'SASsample':
336	self.current_datainfo.sample.transmission = data_point
337	elif tagname == 'temperature' and self.parent_class == 'SASsample':
338	self.current_datainfo.sample.temperature = data_point
339	self.current_datainfo.sample.temperature_unit = unit
340	elif tagname == 'details' and self.parent_class == 'SASsample':
341	self.current_datainfo.sample.details.append(data_point)
342	elif tagname == 'x' and self.parent_class == 'position':
343	self.current_datainfo.sample.position.x = data_point
344	self.current_datainfo.sample.position_unit = unit
345	elif tagname == 'y' and self.parent_class == 'position':
346	self.current_datainfo.sample.position.y = data_point
347	self.current_datainfo.sample.position_unit = unit
348	elif tagname == 'z' and self.parent_class == 'position':
349	self.current_datainfo.sample.position.z = data_point
350	self.current_datainfo.sample.position_unit = unit
351	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
352	self.current_datainfo.sample.orientation.x = data_point
353	self.current_datainfo.sample.orientation_unit = unit
354	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
355	self.current_datainfo.sample.orientation.y = data_point
356	self.current_datainfo.sample.orientation_unit = unit
357	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
358	self.current_datainfo.sample.orientation.z = data_point
359	self.current_datainfo.sample.orientation_unit = unit
360
361	# Instrumental Information
362	elif tagname == 'name' and self.parent_class == 'SASinstrument':
363	self.current_datainfo.instrument = data_point
364
365	# Detector Information
366	elif tagname == 'name' and self.parent_class == 'SASdetector':
367	self.detector.name = data_point
368	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
369	self.detector.distance = data_point
370	self.detector.distance_unit = unit
371	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
372	self.detector.slit_length = data_point
373	self.detector.slit_length_unit = unit
374	elif tagname == 'x' and self.parent_class == 'offset':
375	self.detector.offset.x = data_point
376	self.detector.offset_unit = unit
377	elif tagname == 'y' and self.parent_class == 'offset':
378	self.detector.offset.y = data_point
379	self.detector.offset_unit = unit
380	elif tagname == 'z' and self.parent_class == 'offset':
381	self.detector.offset.z = data_point
382	self.detector.offset_unit = unit
383	elif tagname == 'x' and self.parent_class == 'beam_center':
384	self.detector.beam_center.x = data_point
385	self.detector.beam_center_unit = unit
386	elif tagname == 'y' and self.parent_class == 'beam_center':
387	self.detector.beam_center.y = data_point
388	self.detector.beam_center_unit = unit
389	elif tagname == 'z' and self.parent_class == 'beam_center':
390	self.detector.beam_center.z = data_point
391	self.detector.beam_center_unit = unit
392	elif tagname == 'x' and self.parent_class == 'pixel_size':
393	self.detector.pixel_size.x = data_point
394	self.detector.pixel_size_unit = unit
395	elif tagname == 'y' and self.parent_class == 'pixel_size':
396	self.detector.pixel_size.y = data_point
397	self.detector.pixel_size_unit = unit
398	elif tagname == 'z' and self.parent_class == 'pixel_size':
399	self.detector.pixel_size.z = data_point
400	self.detector.pixel_size_unit = unit
401	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
402	self.detector.orientation.x = data_point
403	self.detector.orientation_unit = unit
404	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
405	self.detector.orientation.y = data_point
406	self.detector.orientation_unit = unit
407	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
408	self.detector.orientation.z = data_point
409	self.detector.orientation_unit = unit
410
411	# Collimation and Aperture
412	elif tagname == 'length' and self.parent_class == 'SAScollimation':
413	self.collimation.length = data_point
414	self.collimation.length_unit = unit
415	elif tagname == 'name' and self.parent_class == 'SAScollimation':
416	self.collimation.name = data_point
417	elif tagname == 'distance' and self.parent_class == 'aperture':
418	self.aperture.distance = data_point
419	self.aperture.distance_unit = unit
420	elif tagname == 'x' and self.parent_class == 'size':
421	self.aperture.size.x = data_point
422	self.collimation.size_unit = unit
423	elif tagname == 'y' and self.parent_class == 'size':
424	self.aperture.size.y = data_point
425	self.collimation.size_unit = unit
426	elif tagname == 'z' and self.parent_class == 'size':
427	self.aperture.size.z = data_point
428	self.collimation.size_unit = unit
429
430	# Process Information
431	elif tagname == 'name' and self.parent_class == 'SASprocess':
432	self.process.name = data_point
433	elif tagname == 'description' and self.parent_class == 'SASprocess':
434	self.process.description = data_point
435	elif tagname == 'date' and self.parent_class == 'SASprocess':
436	try:
437	self.process.date = datetime.datetime.fromtimestamp(data_point)
438	except:
439	self.process.date = data_point
440	elif tagname == 'SASprocessnote':
441	self.process.notes.append(data_point)
442	elif tagname == 'term' and self.parent_class == 'SASprocess':
443	unit = attr.get("unit", "")
444	dic = { "name": name, "value": data_point, "unit": unit }
445	self.process.term.append(dic)
446
447	# Transmission Spectrum
448	elif tagname == 'T' and self.parent_class == 'Tdata':
449	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
450	self.transspectrum.transmission_unit = unit
451	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
452	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
453	self.transspectrum.transmission_deviation_unit = unit
454	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
455	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
456	self.transspectrum.wavelength_unit = unit
457
458	# Source Information
459	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
460	self.current_datainfo.source.wavelength = data_point
461	self.current_datainfo.source.wavelength_unit = unit
462	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
463	self.current_datainfo.source.wavelength_min = data_point
464	self.current_datainfo.source.wavelength_min_unit = unit
465	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
466	self.current_datainfo.source.wavelength_max = data_point
467	self.current_datainfo.source.wavelength_max_unit = unit
468	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
469	self.current_datainfo.source.wavelength_spread = data_point
470	self.current_datainfo.source.wavelength_spread_unit = unit
471	elif tagname == 'x' and self.parent_class == 'beam_size':
472	self.current_datainfo.source.beam_size.x = data_point
473	self.current_datainfo.source.beam_size_unit = unit
474	elif tagname == 'y' and self.parent_class == 'beam_size':
475	self.current_datainfo.source.beam_size.y = data_point
476	self.current_datainfo.source.beam_size_unit = unit
477	elif tagname == 'z' and self.parent_class == 'pixel_size':
478	self.current_datainfo.source.data_point.z = data_point
479	self.current_datainfo.source.beam_size_unit = unit
480	elif tagname == 'radiation' and self.parent_class == 'SASsource':
481	self.current_datainfo.source.radiation = data_point
482	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
483	self.current_datainfo.source.beam_shape = data_point
484
485	# Everything else goes in meta_data
486	else:
487	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
488	self.current_datainfo.meta_data[new_key] = data_point
489
490	self.names.remove(tagname_original)
491	length = 0
492	if len(self.names) > 1:
493	length = len(self.names) - 1
494	self.parent_class = self.names[length]
495	if not self._is_call_local() and not recurse:
496	self.frm = ""
497	self.current_datainfo.errors = set()
498	for error in self.errors:
499	self.current_datainfo.errors.add(error)
500	self.data_cleanup()
501	self.sort_one_d_data()
502	self.sort_two_d_data()
503	self.reset_data_list()
504	empty = None
505	return self.output[0], empty
506
507	def data_cleanup(self):
508	"""
509	Clean up the data sets and refresh everything
510	:return: None
511	"""
512	has_error_dx = self.current_dataset.dx is not None
513	has_error_dxl = self.current_dataset.dxl is not None
514	has_error_dxw = self.current_dataset.dxw is not None
515	has_error_dy = self.current_dataset.dy is not None
516	self.remove_empty_q_values(has_error_dx=has_error_dx,
517	has_error_dxl=has_error_dxl,
518	has_error_dxw=has_error_dxw,
519	has_error_dy=has_error_dy)
520	self.send_to_output() # Combine datasets with DataInfo
521	self.current_datainfo = DataInfo() # Reset DataInfo
522
523	def _is_call_local(self):
524	if self.frm == "":
525	inter = inspect.stack()
526	self.frm = inter[2]
527	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
528	mod_name = mod_name.replace(".py", "")
529	mod = mod_name.split("sas/")
530	mod_name = mod[1]
531	if mod_name != "sascalc/dataloader/readers/cansas_reader":
532	return False
533	return True
534
535	def _add_intermediate(self):
536	"""
537	This method stores any intermediate objects within the final data set after fully reading the set.
538	"""
539	if self.parent_class == 'SASprocess':
540	self.current_datainfo.process.append(self.process)
541	self.process = Process()
542	elif self.parent_class == 'SASdetector':
543	self.current_datainfo.detector.append(self.detector)
544	self.detector = Detector()
545	elif self.parent_class == 'SAStransmission_spectrum':
546	self.current_datainfo.trans_spectrum.append(self.transspectrum)
547	self.transspectrum = TransmissionSpectrum()
548	elif self.parent_class == 'SAScollimation':
549	self.current_datainfo.collimation.append(self.collimation)
550	self.collimation = Collimation()
551	elif self.parent_class == 'aperture':
552	self.collimation.aperture.append(self.aperture)
553	self.aperture = Aperture()
554	elif self.parent_class == 'SASdata':
555	self._check_for_empty_resolution()
556	self.data.append(self.current_dataset)
557
558	def _get_node_value(self, node, tagname):
559	"""
560	Get the value of a node and any applicable units
561
562	:param node: The XML node to get the value of
563	:param tagname: The tagname of the node
564	"""
565	#Get the text from the node and convert all whitespace to spaces
566	units = ''
567	node_value = node.text
568	if node_value is not None:
569	node_value = ' '.join(node_value.split())
570	else:
571	node_value = ""
572
573	# If the value is a float, compile with units.
574	if self.ns_list.ns_datatype == "float":
575	# If an empty value is given, set as zero.
576	if node_value is None or node_value.isspace() \
577	or node_value.lower() == "nan":
578	node_value = "0.0"
579	#Convert the value to the base units
580	node_value, units = self._unit_conversion(node, tagname, node_value)
581
582	# If the value is a timestamp, convert to a datetime object
583	elif self.ns_list.ns_datatype == "timestamp":
584	if node_value is None or node_value.isspace():
585	pass
586	else:
587	try:
588	node_value = \
589	datetime.datetime.fromtimestamp(node_value)
590	except ValueError:
591	node_value = None
592	return node_value, units
593
594	def _unit_conversion(self, node, tagname, node_value):
595	"""
596	A unit converter method used to convert the data included in the file
597	to the default units listed in data_info
598
599	:param node: XML node
600	:param tagname: name of the node
601	:param node_value: The value of the current dom node
602	"""
603	attr = node.attrib
604	value_unit = ''
605	err_msg = None
606	default_unit = None
607	if not isinstance(node_value, float):
608	node_value = float(node_value)
609	if 'unit' in attr and attr.get('unit') is not None:
610	try:
611	local_unit = attr['unit']
612	unitname = self.ns_list.current_level.get("unit", "")
613	if "SASdetector" in self.names:
614	save_in = "detector"
615	elif "aperture" in self.names:
616	save_in = "aperture"
617	elif "SAScollimation" in self.names:
618	save_in = "collimation"
619	elif "SAStransmission_spectrum" in self.names:
620	save_in = "transspectrum"
621	elif "SASdata" in self.names:
622	x = np.zeros(1)
623	y = np.zeros(1)
624	self.current_data1d = Data1D(x, y)
625	save_in = "current_data1d"
626	elif "SASsource" in self.names:
627	save_in = "current_datainfo.source"
628	elif "SASsample" in self.names:
629	save_in = "current_datainfo.sample"
630	elif "SASprocess" in self.names:
631	save_in = "process"
632	else:
633	save_in = "current_datainfo"
634	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
635	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
636	and local_unit.lower() != "none":
637	if HAS_CONVERTER == True:
638	# Check local units - bad units raise KeyError
639	data_conv_q = Converter(local_unit)
640	value_unit = default_unit
641	node_value = data_conv_q(node_value, units=default_unit)
642	else:
643	value_unit = local_unit
644	err_msg = "Unit converter is not available.\n"
645	else:
646	value_unit = local_unit
647	except KeyError:
648	# Do not throw an error for loading Sesans data in cansas xml
649	# This is a temporary fix.
650	if local_unit != "A" and local_unit != 'pol':
651	err_msg = "CanSAS reader: unexpected "
652	err_msg += "\"{0}\" unit [{1}]; "
653	err_msg = err_msg.format(tagname, local_unit)
654	err_msg += "expecting [{0}]".format(default_unit)
655	value_unit = local_unit
656	except:
657	err_msg = "CanSAS reader: unknown error converting "
658	err_msg += "\"{0}\" unit [{1}]"
659	err_msg = err_msg.format(tagname, local_unit)
660	value_unit = local_unit
661	elif 'unit' in attr:
662	value_unit = attr['unit']
663	if err_msg:
664	self.errors.add(err_msg)
665	return node_value, value_unit
666
667	def _check_for_empty_resolution(self):
668	"""
669	a method to check all resolution data sets are the same size as I and q
670	"""
671	dql_exists = False
672	dqw_exists = False
673	dq_exists = False
674	di_exists = False
675	if self.current_dataset.dxl is not None:
676	dql_exists = True
677	if self.current_dataset.dxw is not None:
678	dqw_exists = True
679	if self.current_dataset.dx is not None:
680	dq_exists = True
681	if self.current_dataset.dy is not None:
682	di_exists = True
683	if dqw_exists and not dql_exists:
684	array_size = self.current_dataset.dxw.size
685	self.current_dataset.dxl = np.zeros(array_size)
686	elif dql_exists and not dqw_exists:
687	array_size = self.current_dataset.dxl.size
688	self.current_dataset.dxw = np.zeros(array_size)
689	elif not dql_exists and not dqw_exists and not dq_exists:
690	array_size = self.current_dataset.x.size
691	self.current_dataset.dx = np.append(self.current_dataset.dx,
692	np.zeros([array_size]))
693	if not di_exists:
694	array_size = self.current_dataset.y.size
695	self.current_dataset.dy = np.append(self.current_dataset.dy,
696	np.zeros([array_size]))
697
698	def _initialize_new_data_set(self, node=None):
699	if node is not None:
700	for child in node:
701	if child.tag.replace(self.base_ns, "") == "Idata":
702	for i_child in child:
703	if i_child.tag.replace(self.base_ns, "") == "Qx":
704	self.current_dataset = plottable_2D()
705	return
706	self.current_dataset = plottable_1D(np.array(0), np.array(0))
707
708	## Writing Methods
709	def write(self, filename, datainfo):
710	"""
711	Write the content of a Data1D as a CanSAS XML file
712
713	:param filename: name of the file to write
714	:param datainfo: Data1D object
715	"""
716	# Create XML document
717	doc, _ = self._to_xml_doc(datainfo)
718	# Write the file
719	file_ref = open(filename, 'w')
720	if self.encoding is None:
721	self.encoding = "UTF-8"
722	doc.write(file_ref, encoding=self.encoding,
723	pretty_print=True, xml_declaration=True)
724	file_ref.close()
725
726	def _to_xml_doc(self, datainfo):
727	"""
728	Create an XML document to contain the content of a Data1D
729
730	:param datainfo: Data1D object
731	"""
732	is_2d = False
733	if issubclass(datainfo.__class__, Data2D):
734	is_2d = True
735
736	# Get PIs and create root element
737	pi_string = self._get_pi_string()
738	# Define namespaces and create SASroot object
739	main_node = self._create_main_node()
740	# Create ElementTree, append SASroot and apply processing instructions
741	base_string = pi_string + self.to_string(main_node)
742	base_element = self.create_element_from_string(base_string)
743	doc = self.create_tree(base_element)
744	# Create SASentry Element
745	entry_node = self.create_element("SASentry")
746	root = doc.getroot()
747	root.append(entry_node)
748
749	# Add Title to SASentry
750	self.write_node(entry_node, "Title", datainfo.title)
751	# Add Run to SASentry
752	self._write_run_names(datainfo, entry_node)
753	# Add Data info to SASEntry
754	if is_2d:
755	self._write_data_2d(datainfo, entry_node)
756	else:
757	self._write_data(datainfo, entry_node)
758	# Transmission Spectrum Info
759	# TODO: fix the writer to linearize all data, including T_spectrum
760	# self._write_trans_spectrum(datainfo, entry_node)
761	# Sample info
762	self._write_sample_info(datainfo, entry_node)
763	# Instrument info
764	instr = self._write_instrument(datainfo, entry_node)
765	# Source
766	self._write_source(datainfo, instr)
767	# Collimation
768	self._write_collimation(datainfo, instr)
769	# Detectors
770	self._write_detectors(datainfo, instr)
771	# Processes info
772	self._write_process_notes(datainfo, entry_node)
773	# Note info
774	self._write_notes(datainfo, entry_node)
775	# Return the document, and the SASentry node associated with
776	# the data we just wrote
777	# If the calling function was not the cansas reader, return a minidom
778	# object rather than an lxml object.
779	self.frm = inspect.stack()[1]
780	doc, entry_node = self._check_origin(entry_node, doc)
781	return doc, entry_node
782
783	def write_node(self, parent, name, value, attr=None):
784	"""
785	:param doc: document DOM
786	:param parent: parent node
787	:param name: tag of the element
788	:param value: value of the child text node
789	:param attr: attribute dictionary
790
791	:return: True if something was appended, otherwise False
792	"""
793	if value is not None:
794	parent = self.ebuilder(parent, name, value, attr)
795	return True
796	return False
797
798	def _get_pi_string(self):
799	"""
800	Creates the processing instructions header for writing to file
801	"""
802	pis = self.return_processing_instructions()
803	if len(pis) > 0:
804	pi_tree = self.create_tree(pis[0])
805	i = 1
806	for i in range(1, len(pis) - 1):
807	pi_tree = self.append(pis[i], pi_tree)
808	pi_string = self.to_string(pi_tree)
809	else:
810	pi_string = ""
811	return pi_string
812
813	def _create_main_node(self):
814	"""
815	Creates the primary xml header used when writing to file
816	"""
817	xsi = "http://www.w3.org/2001/XMLSchema-instance"
818	version = self.cansas_version
819	n_s = CANSAS_NS.get(version).get("ns")
820	if version == "1.1":
821	url = "http://www.cansas.org/formats/1.1/"
822	else:
823	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
824	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
825	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
826	"version" : version}
827	nsmap = {'xsi' : xsi, None: n_s}
828
829	main_node = self.create_element("{" + n_s + "}SASroot",
830	attrib=attrib, nsmap=nsmap)
831	return main_node
832
833	def _write_run_names(self, datainfo, entry_node):
834	"""
835	Writes the run names to the XML file
836
837	:param datainfo: The Data1D object the information is coming from
838	:param entry_node: lxml node ElementTree object to be appended to
839	"""
840	if datainfo.run is None or datainfo.run == []:
841	datainfo.run.append(RUN_NAME_DEFAULT)
842	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
843	for item in datainfo.run:
844	runname = {}
845	if item in datainfo.run_name and \
846	len(str(datainfo.run_name[item])) > 1:
847	runname = {'name': datainfo.run_name[item]}
848	self.write_node(entry_node, "Run", item, runname)
849
850	def _write_data(self, datainfo, entry_node):
851	"""
852	Writes 1D I and Q data to the XML file
853
854	:param datainfo: The Data1D object the information is coming from
855	:param entry_node: lxml node ElementTree object to be appended to
856	"""
857	node = self.create_element("SASdata")
858	self.append(node, entry_node)
859
860	for i in range(len(datainfo.x)):
861	point = self.create_element("Idata")
862	node.append(point)
863	self.write_node(point, "Q", datainfo.x[i],
864	{'unit': datainfo.x_unit})
865	if len(datainfo.y) >= i:
866	self.write_node(point, "I", datainfo.y[i],
867	{'unit': datainfo.y_unit})
868	if datainfo.dy is not None and len(datainfo.dy) > i:
869	self.write_node(point, "Idev", datainfo.dy[i],
870	{'unit': datainfo.y_unit})
871	if datainfo.dx is not None and len(datainfo.dx) > i:
872	self.write_node(point, "Qdev", datainfo.dx[i],
873	{'unit': datainfo.x_unit})
874	if datainfo.dxw is not None and len(datainfo.dxw) > i:
875	self.write_node(point, "dQw", datainfo.dxw[i],
876	{'unit': datainfo.x_unit})
877	if datainfo.dxl is not None and len(datainfo.dxl) > i:
878	self.write_node(point, "dQl", datainfo.dxl[i],
879	{'unit': datainfo.x_unit})
880	if datainfo.isSesans:
881	sesans_attrib = {'x_axis': datainfo._xaxis,
882	'y_axis': datainfo._yaxis,
883	'x_unit': datainfo.x_unit,
884	'y_unit': datainfo.y_unit}
885	sesans = self.create_element("Sesans", attrib=sesans_attrib)
886	sesans.text = str(datainfo.isSesans)
887	entry_node.append(sesans)
888	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
889	{'unit': datainfo.sample.yacceptance[1]})
890	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
891	{'unit': datainfo.sample.zacceptance[1]})
892
893
894	def _write_data_2d(self, datainfo, entry_node):
895	"""
896	Writes 2D data to the XML file
897
898	:param datainfo: The Data2D object the information is coming from
899	:param entry_node: lxml node ElementTree object to be appended to
900	"""
901	attr = {}
902	if datainfo.data.shape:
903	attr["x_bins"] = str(len(datainfo.x_bins))
904	attr["y_bins"] = str(len(datainfo.y_bins))
905	node = self.create_element("SASdata", attr)
906	self.append(node, entry_node)
907
908	point = self.create_element("Idata")
909	node.append(point)
910	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
911	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
912	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
913
914	self.write_node(point, "Qx", qx,
915	{'unit': datainfo._xunit})
916	self.write_node(point, "Qy", qy,
917	{'unit': datainfo._yunit})
918	self.write_node(point, "I", intensity,
919	{'unit': datainfo._zunit})
920	if datainfo.err_data is not None:
921	err = ','.join([str(datainfo.err_data[i]) for i in
922	xrange(len(datainfo.err_data))])
923	self.write_node(point, "Idev", err,
924	{'unit': datainfo._zunit})
925	if datainfo.dqy_data is not None:
926	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
927	xrange(len(datainfo.dqy_data))])
928	self.write_node(point, "Qydev", dqy,
929	{'unit': datainfo._yunit})
930	if datainfo.dqx_data is not None:
931	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
932	xrange(len(datainfo.dqx_data))])
933	self.write_node(point, "Qxdev", dqx,
934	{'unit': datainfo._xunit})
935	if datainfo.mask is not None:
936	mask = ','.join(
937	["1" if datainfo.mask[i] else "0"
938	for i in xrange(len(datainfo.mask))])
939	self.write_node(point, "Mask", mask)
940
941	def _write_trans_spectrum(self, datainfo, entry_node):
942	"""
943	Writes the transmission spectrum data to the XML file
944
945	:param datainfo: The Data1D object the information is coming from
946	:param entry_node: lxml node ElementTree object to be appended to
947	"""
948	for i in range(len(datainfo.trans_spectrum)):
949	spectrum = datainfo.trans_spectrum[i]
950	node = self.create_element("SAStransmission_spectrum",
951	{"name" : spectrum.name})
952	self.append(node, entry_node)
953	if isinstance(spectrum.timestamp, datetime.datetime):
954	node.setAttribute("timestamp", spectrum.timestamp)
955	for i in range(len(spectrum.wavelength)):
956	point = self.create_element("Tdata")
957	node.append(point)
958	self.write_node(point, "Lambda", spectrum.wavelength[i],
959	{'unit': spectrum.wavelength_unit})
960	self.write_node(point, "T", spectrum.transmission[i],
961	{'unit': spectrum.transmission_unit})
962	if spectrum.transmission_deviation is not None \
963	and len(spectrum.transmission_deviation) >= i:
964	self.write_node(point, "Tdev",
965	spectrum.transmission_deviation[i],
966	{'unit':
967	spectrum.transmission_deviation_unit})
968
969	def _write_sample_info(self, datainfo, entry_node):
970	"""
971	Writes the sample information to the XML file
972
973	:param datainfo: The Data1D object the information is coming from
974	:param entry_node: lxml node ElementTree object to be appended to
975	"""
976	sample = self.create_element("SASsample")
977	if datainfo.sample.name is not None:
978	self.write_attribute(sample, "name",
979	str(datainfo.sample.name))
980	self.append(sample, entry_node)
981	self.write_node(sample, "ID", str(datainfo.sample.ID))
982	self.write_node(sample, "thickness", datainfo.sample.thickness,
983	{"unit": datainfo.sample.thickness_unit})
984	self.write_node(sample, "transmission", datainfo.sample.transmission)
985	self.write_node(sample, "temperature", datainfo.sample.temperature,
986	{"unit": datainfo.sample.temperature_unit})
987
988	pos = self.create_element("position")
989	written = self.write_node(pos,
990	"x",
991	datainfo.sample.position.x,
992	{"unit": datainfo.sample.position_unit})
993	written = written \| self.write_node( \
994	pos, "y", datainfo.sample.position.y,
995	{"unit": datainfo.sample.position_unit})
996	written = written \| self.write_node( \
997	pos, "z", datainfo.sample.position.z,
998	{"unit": datainfo.sample.position_unit})
999	if written == True:
1000	self.append(pos, sample)
1001
1002	ori = self.create_element("orientation")
1003	written = self.write_node(ori, "roll",
1004	datainfo.sample.orientation.x,
1005	{"unit": datainfo.sample.orientation_unit})
1006	written = written \| self.write_node( \
1007	ori, "pitch", datainfo.sample.orientation.y,
1008	{"unit": datainfo.sample.orientation_unit})
1009	written = written \| self.write_node( \
1010	ori, "yaw", datainfo.sample.orientation.z,
1011	{"unit": datainfo.sample.orientation_unit})
1012	if written == True:
1013	self.append(ori, sample)
1014
1015	for item in datainfo.sample.details:
1016	self.write_node(sample, "details", item)
1017
1018	def _write_instrument(self, datainfo, entry_node):
1019	"""
1020	Writes the instrumental information to the XML file
1021
1022	:param datainfo: The Data1D object the information is coming from
1023	:param entry_node: lxml node ElementTree object to be appended to
1024	"""
1025	instr = self.create_element("SASinstrument")
1026	self.append(instr, entry_node)
1027	self.write_node(instr, "name", datainfo.instrument)
1028	return instr
1029
1030	def _write_source(self, datainfo, instr):
1031	"""
1032	Writes the source information to the XML file
1033
1034	:param datainfo: The Data1D object the information is coming from
1035	:param instr: instrument node to be appended to
1036	"""
1037	source = self.create_element("SASsource")
1038	if datainfo.source.name is not None:
1039	self.write_attribute(source, "name",
1040	str(datainfo.source.name))
1041	self.append(source, instr)
1042	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1043	datainfo.source.radiation = "neutron"
1044	self.write_node(source, "radiation", datainfo.source.radiation)
1045
1046	size = self.create_element("beam_size")
1047	if datainfo.source.beam_size_name is not None:
1048	self.write_attribute(size, "name",
1049	str(datainfo.source.beam_size_name))
1050	written = self.write_node( \
1051	size, "x", datainfo.source.beam_size.x,
1052	{"unit": datainfo.source.beam_size_unit})
1053	written = written \| self.write_node( \
1054	size, "y", datainfo.source.beam_size.y,
1055	{"unit": datainfo.source.beam_size_unit})
1056	written = written \| self.write_node( \
1057	size, "z", datainfo.source.beam_size.z,
1058	{"unit": datainfo.source.beam_size_unit})
1059	if written == True:
1060	self.append(size, source)
1061
1062	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1063	self.write_node(source, "wavelength",
1064	datainfo.source.wavelength,
1065	{"unit": datainfo.source.wavelength_unit})
1066	self.write_node(source, "wavelength_min",
1067	datainfo.source.wavelength_min,
1068	{"unit": datainfo.source.wavelength_min_unit})
1069	self.write_node(source, "wavelength_max",
1070	datainfo.source.wavelength_max,
1071	{"unit": datainfo.source.wavelength_max_unit})
1072	self.write_node(source, "wavelength_spread",
1073	datainfo.source.wavelength_spread,
1074	{"unit": datainfo.source.wavelength_spread_unit})
1075
1076	def _write_collimation(self, datainfo, instr):
1077	"""
1078	Writes the collimation information to the XML file
1079
1080	:param datainfo: The Data1D object the information is coming from
1081	:param instr: lxml node ElementTree object to be appended to
1082	"""
1083	if datainfo.collimation == [] or datainfo.collimation is None:
1084	coll = Collimation()
1085	datainfo.collimation.append(coll)
1086	for item in datainfo.collimation:
1087	coll = self.create_element("SAScollimation")
1088	if item.name is not None:
1089	self.write_attribute(coll, "name", str(item.name))
1090	self.append(coll, instr)
1091
1092	self.write_node(coll, "length", item.length,
1093	{"unit": item.length_unit})
1094
1095	for aperture in item.aperture:
1096	apert = self.create_element("aperture")
1097	if aperture.name is not None:
1098	self.write_attribute(apert, "name", str(aperture.name))
1099	if aperture.type is not None:
1100	self.write_attribute(apert, "type", str(aperture.type))
1101	self.append(apert, coll)
1102
1103	size = self.create_element("size")
1104	if aperture.size_name is not None:
1105	self.write_attribute(size, "name",
1106	str(aperture.size_name))
1107	written = self.write_node(size, "x", aperture.size.x,
1108	{"unit": aperture.size_unit})
1109	written = written \| self.write_node( \
1110	size, "y", aperture.size.y,
1111	{"unit": aperture.size_unit})
1112	written = written \| self.write_node( \
1113	size, "z", aperture.size.z,
1114	{"unit": aperture.size_unit})
1115	if written == True:
1116	self.append(size, apert)
1117
1118	self.write_node(apert, "distance", aperture.distance,
1119	{"unit": aperture.distance_unit})
1120
1121	def _write_detectors(self, datainfo, instr):
1122	"""
1123	Writes the detector information to the XML file
1124
1125	:param datainfo: The Data1D object the information is coming from
1126	:param inst: lxml instrument node to be appended to
1127	"""
1128	if datainfo.detector is None or datainfo.detector == []:
1129	det = Detector()
1130	det.name = ""
1131	datainfo.detector.append(det)
1132
1133	for item in datainfo.detector:
1134	det = self.create_element("SASdetector")
1135	written = self.write_node(det, "name", item.name)
1136	written = written \| self.write_node(det, "SDD", item.distance,
1137	{"unit": item.distance_unit})
1138	if written == True:
1139	self.append(det, instr)
1140
1141	off = self.create_element("offset")
1142	written = self.write_node(off, "x", item.offset.x,
1143	{"unit": item.offset_unit})
1144	written = written \| self.write_node(off, "y", item.offset.y,
1145	{"unit": item.offset_unit})
1146	written = written \| self.write_node(off, "z", item.offset.z,
1147	{"unit": item.offset_unit})
1148	if written == True:
1149	self.append(off, det)
1150
1151	ori = self.create_element("orientation")
1152	written = self.write_node(ori, "roll", item.orientation.x,
1153	{"unit": item.orientation_unit})
1154	written = written \| self.write_node(ori, "pitch",
1155	item.orientation.y,
1156	{"unit": item.orientation_unit})
1157	written = written \| self.write_node(ori, "yaw",
1158	item.orientation.z,
1159	{"unit": item.orientation_unit})
1160	if written == True:
1161	self.append(ori, det)
1162
1163	center = self.create_element("beam_center")
1164	written = self.write_node(center, "x", item.beam_center.x,
1165	{"unit": item.beam_center_unit})
1166	written = written \| self.write_node(center, "y",
1167	item.beam_center.y,
1168	{"unit": item.beam_center_unit})
1169	written = written \| self.write_node(center, "z",
1170	item.beam_center.z,
1171	{"unit": item.beam_center_unit})
1172	if written == True:
1173	self.append(center, det)
1174
1175	pix = self.create_element("pixel_size")
1176	written = self.write_node(pix, "x", item.pixel_size.x,
1177	{"unit": item.pixel_size_unit})
1178	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1179	{"unit": item.pixel_size_unit})
1180	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1181	{"unit": item.pixel_size_unit})
1182	if written == True:
1183	self.append(pix, det)
1184	self.write_node(det, "slit_length", item.slit_length,
1185	{"unit": item.slit_length_unit})
1186
1187
1188	def _write_process_notes(self, datainfo, entry_node):
1189	"""
1190	Writes the process notes to the XML file
1191
1192	:param datainfo: The Data1D object the information is coming from
1193	:param entry_node: lxml node ElementTree object to be appended to
1194
1195	"""
1196	for item in datainfo.process:
1197	node = self.create_element("SASprocess")
1198	self.append(node, entry_node)
1199	self.write_node(node, "name", item.name)
1200	self.write_node(node, "date", item.date)
1201	self.write_node(node, "description", item.description)
1202	for term in item.term:
1203	if isinstance(term, list):
1204	value = term['value']
1205	del term['value']
1206	elif isinstance(term, dict):
1207	value = term.get("value")
1208	del term['value']
1209	else:
1210	value = term
1211	self.write_node(node, "term", value, term)
1212	for note in item.notes:
1213	self.write_node(node, "SASprocessnote", note)
1214	if len(item.notes) == 0:
1215	self.write_node(node, "SASprocessnote", "")
1216
1217	def _write_notes(self, datainfo, entry_node):
1218	"""
1219	Writes the notes to the XML file and creates an empty note if none
1220	exist
1221
1222	:param datainfo: The Data1D object the information is coming from
1223	:param entry_node: lxml node ElementTree object to be appended to
1224
1225	"""
1226	if len(datainfo.notes) == 0:
1227	node = self.create_element("SASnote")
1228	self.append(node, entry_node)
1229	else:
1230	for item in datainfo.notes:
1231	node = self.create_element("SASnote")
1232	self.write_text(node, item)
1233	self.append(node, entry_node)
1234
1235	def _check_origin(self, entry_node, doc):
1236	"""
1237	Return the document, and the SASentry node associated with
1238	the data we just wrote.
1239	If the calling function was not the cansas reader, return a minidom
1240	object rather than an lxml object.
1241
1242	:param entry_node: lxml node ElementTree object to be appended to
1243	:param doc: entire xml tree
1244	"""
1245	if not self.frm:
1246	self.frm = inspect.stack()[1]
1247	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1248	mod_name = mod_name.replace(".py", "")
1249	mod = mod_name.split("sas/")
1250	mod_name = mod[1]
1251	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1252	string = self.to_string(doc, pretty_print=False)
1253	doc = parseString(string)
1254	node_name = entry_node.tag
1255	node_list = doc.getElementsByTagName(node_name)
1256	entry_node = node_list.item(0)
1257	return doc, entry_node
1258
1259	# DO NOT REMOVE - used in saving and loading panel states.
1260	def _store_float(self, location, node, variable, storage, optional=True):
1261	"""
1262	Get the content of a xpath location and store
1263	the result. Check that the units are compatible
1264	with the destination. The value is expected to
1265	be a float.
1266
1267	The xpath location might or might not exist.
1268	If it does not exist, nothing is done
1269
1270	:param location: xpath location to fetch
1271	:param node: node to read the data from
1272	:param variable: name of the data member to store it in [string]
1273	:param storage: data object that has the 'variable' data member
1274	:param optional: if True, no exception will be raised
1275	if unit conversion can't be done
1276
1277	:raise ValueError: raised when the units are not recognized
1278	"""
1279	entry = get_content(location, node)
1280	try:
1281	value = float(entry.text)
1282	except:
1283	value = None
1284
1285	if value is not None:
1286	# If the entry has units, check to see that they are
1287	# compatible with what we currently have in the data object
1288	units = entry.get('unit')
1289	if units is not None:
1290	toks = variable.split('.')
1291	local_unit = None
1292	exec "local_unit = storage.%s_unit" % toks[0]
1293	if local_unit is not None and units.lower() != local_unit.lower():
1294	if HAS_CONVERTER == True:
1295	try:
1296	conv = Converter(units)
1297	exec "storage.%s = %g" % \
1298	(variable, conv(value, units=local_unit))
1299	except:
1300	_, exc_value, _ = sys.exc_info()
1301	err_mess = "CanSAS reader: could not convert"
1302	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1303	% (variable, units, local_unit, exc_value)
1304	self.errors.add(err_mess)
1305	if optional:
1306	logger.info(err_mess)
1307	else:
1308	raise ValueError, err_mess
1309	else:
1310	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1311	% (variable, units)
1312	err_mess += " expecting [%s]" % local_unit
1313	self.errors.add(err_mess)
1314	if optional:
1315	logger.info(err_mess)
1316	else:
1317	raise ValueError, err_mess
1318	else:
1319	exec "storage.%s = value" % variable
1320	else:
1321	exec "storage.%s = value" % variable
1322
1323	# DO NOT REMOVE - used in saving and loading panel states.
1324	def _store_content(self, location, node, variable, storage):
1325	"""
1326	Get the content of a xpath location and store
1327	the result. The value is treated as a string.
1328
1329	The xpath location might or might not exist.
1330	If it does not exist, nothing is done
1331
1332	:param location: xpath location to fetch
1333	:param node: node to read the data from
1334	:param variable: name of the data member to store it in [string]
1335	:param storage: data object that has the 'variable' data member
1336
1337	:return: return a list of errors
1338	"""
1339	entry = get_content(location, node)
1340	if entry is not None and entry.text is not None:
1341	exec "storage.%s = entry.text.strip()" % variable
1342
1343	# DO NOT REMOVE Called by outside packages:
1344	# sas.sasgui.perspectives.invariant.invariant_state
1345	# sas.sasgui.perspectives.fitting.pagestate
1346	def get_content(location, node):
1347	"""
1348	Get the first instance of the content of a xpath location.
1349
1350	:param location: xpath location
1351	:param node: node to start at
1352
1353	:return: Element, or None
1354	"""
1355	nodes = node.xpath(location,
1356	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1357	if len(nodes) > 0:
1358	return nodes[0]
1359	else:
1360	return None
1361
1362	# DO NOT REMOVE Called by outside packages:
1363	# sas.sasgui.perspectives.fitting.pagestate
1364	def write_node(doc, parent, name, value, attr=None):
1365	"""
1366	:param doc: document DOM
1367	:param parent: parent node
1368	:param name: tag of the element
1369	:param value: value of the child text node
1370	:param attr: attribute dictionary
1371
1372	:return: True if something was appended, otherwise False
1373	"""
1374	if attr is None:
1375	attr = {}
1376	if value is not None:
1377	node = doc.createElement(name)
1378	node.appendChild(doc.createTextNode(str(value)))
1379	for item in attr:
1380	node.setAttribute(item, attr[item])
1381	parent.appendChild(node)
1382	return True
1383	return False

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 67d8b1b

Download in other formats: