cansas_reader.py @ 2a52b0e

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 2a52b0e was 248ff73, checked in by lewis, 7 years ago

Ensure unit tests pass

utest_averaging still fails as it relies on loading in an Igor 2D file,
which is no longer possible

Property mode set to 100644

File size: 63.3 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	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	if not self.extension in self.ext: # If the file has no associated loader
160	raise DefaultReaderException(msg)
161	msg = "CanSAS Reader could not load the file {}".format(xml_file)
162	if fc_exc.message is not None: # Propagate error messages from earlier
163	msg = fc_exc.message
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 = "Cansas cannot load {}.\n Invalid 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	raise FileContentsException("The file is not valid CanSAS")
210
211	def _parse_entry(self, dom, recurse=False):
212	if not self._is_call_local() and not recurse:
213	self.reset_state()
214	self.data = []
215	self.current_datainfo = DataInfo()
216	self.names.append("SASentry")
217	self.parent_class = "SASentry"
218	# Create an empty dataset if no data has been passed to the reader
219	if self.current_dataset is None:
220	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
221	np.empty(0), np.empty(0))
222	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
223
224	# Loop through each child in the parent element
225	for node in dom:
226	attr = node.attrib
227	name = attr.get("name", "")
228	type = attr.get("type", "")
229	# Get the element name and set the current names level
230	tagname = node.tag.replace(self.base_ns, "")
231	tagname_original = tagname
232	# Skip this iteration when loading in save state information
233	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
234	continue
235	# Get where to store content
236	self.names.append(tagname_original)
237	self.ns_list = CONSTANTS.iterate_namespace(self.names)
238	# If the element is a child element, recurse
239	if len(node.getchildren()) > 0:
240	self.parent_class = tagname_original
241	if tagname == 'SASdata':
242	self._initialize_new_data_set(node)
243	if isinstance(self.current_dataset, plottable_2D):
244	x_bins = attr.get("x_bins", "")
245	y_bins = attr.get("y_bins", "")
246	if x_bins is not "" and y_bins is not "":
247	self.current_dataset.shape = (x_bins, y_bins)
248	else:
249	self.current_dataset.shape = ()
250	# Recurse to access data within the group
251	self._parse_entry(node, recurse=True)
252	if tagname == "SASsample":
253	self.current_datainfo.sample.name = name
254	elif tagname == "beam_size":
255	self.current_datainfo.source.beam_size_name = name
256	elif tagname == "SAScollimation":
257	self.collimation.name = name
258	elif tagname == "aperture":
259	self.aperture.name = name
260	self.aperture.type = type
261	self._add_intermediate()
262	else:
263	if isinstance(self.current_dataset, plottable_2D):
264	data_point = node.text
265	unit = attr.get('unit', '')
266	else:
267	data_point, unit = self._get_node_value(node, tagname)
268
269	# If this is a dataset, store the data appropriately
270	if tagname == 'Run':
271	self.current_datainfo.run_name[data_point] = name
272	self.current_datainfo.run.append(data_point)
273	elif tagname == 'Title':
274	self.current_datainfo.title = data_point
275	elif tagname == 'SASnote':
276	self.current_datainfo.notes.append(data_point)
277
278	# I and Q points
279	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
280	unit_list = unit.split("\|")
281	if len(unit_list) > 1:
282	self.current_dataset.yaxis(unit_list[0].strip(),
283	unit_list[1].strip())
284	else:
285	self.current_dataset.yaxis("Intensity", unit)
286	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
287	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
288	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
289	elif tagname == 'Q':
290	unit_list = unit.split("\|")
291	if len(unit_list) > 1:
292	self.current_dataset.xaxis(unit_list[0].strip(),
293	unit_list[1].strip())
294	else:
295	self.current_dataset.xaxis("Q", unit)
296	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
297	elif tagname == 'Qdev':
298	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
299	elif tagname == 'dQw':
300	if self.current_dataset.dqw is None: self.current_dataset.dqw = np.empty(0)
301	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
302	elif tagname == 'dQl':
303	if self.current_dataset.dxl is None: self.current_dataset.dxl = np.empty(0)
304	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
305	elif tagname == 'Qmean':
306	pass
307	elif tagname == 'Shadowfactor':
308	pass
309	elif tagname == 'Sesans':
310	self.current_datainfo.isSesans = bool(data_point)
311	elif tagname == 'yacceptance':
312	self.current_datainfo.sample.yacceptance = (data_point, unit)
313	elif tagname == 'zacceptance':
314	self.current_datainfo.sample.zacceptance = (data_point, unit)
315
316	# I and Qx, Qy - 2D data
317	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
318	self.current_dataset.yaxis("Intensity", unit)
319	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
320	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
321	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
322	elif tagname == 'Qx':
323	self.current_dataset.xaxis("Qx", unit)
324	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
325	elif tagname == 'Qy':
326	self.current_dataset.yaxis("Qy", unit)
327	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
328	elif tagname == 'Qxdev':
329	self.current_dataset.xaxis("Qxdev", unit)
330	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
331	elif tagname == 'Qydev':
332	self.current_dataset.yaxis("Qydev", unit)
333	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
334	elif tagname == 'Mask':
335	inter = [item == "1" for item in data_point.split(",")]
336	self.current_dataset.mask = np.asarray(inter, dtype=bool)
337
338	# Sample Information
339	elif tagname == 'ID' and self.parent_class == 'SASsample':
340	self.current_datainfo.sample.ID = data_point
341	elif tagname == 'Title' and self.parent_class == 'SASsample':
342	self.current_datainfo.sample.name = data_point
343	elif tagname == 'thickness' and self.parent_class == 'SASsample':
344	self.current_datainfo.sample.thickness = data_point
345	self.current_datainfo.sample.thickness_unit = unit
346	elif tagname == 'transmission' and self.parent_class == 'SASsample':
347	self.current_datainfo.sample.transmission = data_point
348	elif tagname == 'temperature' and self.parent_class == 'SASsample':
349	self.current_datainfo.sample.temperature = data_point
350	self.current_datainfo.sample.temperature_unit = unit
351	elif tagname == 'details' and self.parent_class == 'SASsample':
352	self.current_datainfo.sample.details.append(data_point)
353	elif tagname == 'x' and self.parent_class == 'position':
354	self.current_datainfo.sample.position.x = data_point
355	self.current_datainfo.sample.position_unit = unit
356	elif tagname == 'y' and self.parent_class == 'position':
357	self.current_datainfo.sample.position.y = data_point
358	self.current_datainfo.sample.position_unit = unit
359	elif tagname == 'z' and self.parent_class == 'position':
360	self.current_datainfo.sample.position.z = data_point
361	self.current_datainfo.sample.position_unit = unit
362	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
363	self.current_datainfo.sample.orientation.x = data_point
364	self.current_datainfo.sample.orientation_unit = unit
365	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
366	self.current_datainfo.sample.orientation.y = data_point
367	self.current_datainfo.sample.orientation_unit = unit
368	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
369	self.current_datainfo.sample.orientation.z = data_point
370	self.current_datainfo.sample.orientation_unit = unit
371
372	# Instrumental Information
373	elif tagname == 'name' and self.parent_class == 'SASinstrument':
374	self.current_datainfo.instrument = data_point
375
376	# Detector Information
377	elif tagname == 'name' and self.parent_class == 'SASdetector':
378	self.detector.name = data_point
379	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
380	self.detector.distance = data_point
381	self.detector.distance_unit = unit
382	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
383	self.detector.slit_length = data_point
384	self.detector.slit_length_unit = unit
385	elif tagname == 'x' and self.parent_class == 'offset':
386	self.detector.offset.x = data_point
387	self.detector.offset_unit = unit
388	elif tagname == 'y' and self.parent_class == 'offset':
389	self.detector.offset.y = data_point
390	self.detector.offset_unit = unit
391	elif tagname == 'z' and self.parent_class == 'offset':
392	self.detector.offset.z = data_point
393	self.detector.offset_unit = unit
394	elif tagname == 'x' and self.parent_class == 'beam_center':
395	self.detector.beam_center.x = data_point
396	self.detector.beam_center_unit = unit
397	elif tagname == 'y' and self.parent_class == 'beam_center':
398	self.detector.beam_center.y = data_point
399	self.detector.beam_center_unit = unit
400	elif tagname == 'z' and self.parent_class == 'beam_center':
401	self.detector.beam_center.z = data_point
402	self.detector.beam_center_unit = unit
403	elif tagname == 'x' and self.parent_class == 'pixel_size':
404	self.detector.pixel_size.x = data_point
405	self.detector.pixel_size_unit = unit
406	elif tagname == 'y' and self.parent_class == 'pixel_size':
407	self.detector.pixel_size.y = data_point
408	self.detector.pixel_size_unit = unit
409	elif tagname == 'z' and self.parent_class == 'pixel_size':
410	self.detector.pixel_size.z = data_point
411	self.detector.pixel_size_unit = unit
412	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
413	self.detector.orientation.x = data_point
414	self.detector.orientation_unit = unit
415	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
416	self.detector.orientation.y = data_point
417	self.detector.orientation_unit = unit
418	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
419	self.detector.orientation.z = data_point
420	self.detector.orientation_unit = unit
421
422	# Collimation and Aperture
423	elif tagname == 'length' and self.parent_class == 'SAScollimation':
424	self.collimation.length = data_point
425	self.collimation.length_unit = unit
426	elif tagname == 'name' and self.parent_class == 'SAScollimation':
427	self.collimation.name = data_point
428	elif tagname == 'distance' and self.parent_class == 'aperture':
429	self.aperture.distance = data_point
430	self.aperture.distance_unit = unit
431	elif tagname == 'x' and self.parent_class == 'size':
432	self.aperture.size.x = data_point
433	self.collimation.size_unit = unit
434	elif tagname == 'y' and self.parent_class == 'size':
435	self.aperture.size.y = data_point
436	self.collimation.size_unit = unit
437	elif tagname == 'z' and self.parent_class == 'size':
438	self.aperture.size.z = data_point
439	self.collimation.size_unit = unit
440
441	# Process Information
442	elif tagname == 'name' and self.parent_class == 'SASprocess':
443	self.process.name = data_point
444	elif tagname == 'description' and self.parent_class == 'SASprocess':
445	self.process.description = data_point
446	elif tagname == 'date' and self.parent_class == 'SASprocess':
447	try:
448	self.process.date = datetime.datetime.fromtimestamp(data_point)
449	except:
450	self.process.date = data_point
451	elif tagname == 'SASprocessnote':
452	self.process.notes.append(data_point)
453	elif tagname == 'term' and self.parent_class == 'SASprocess':
454	unit = attr.get("unit", "")
455	dic = { "name": name, "value": data_point, "unit": unit }
456	self.process.term.append(dic)
457
458	# Transmission Spectrum
459	elif tagname == 'T' and self.parent_class == 'Tdata':
460	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
461	self.transspectrum.transmission_unit = unit
462	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
463	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
464	self.transspectrum.transmission_deviation_unit = unit
465	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
466	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
467	self.transspectrum.wavelength_unit = unit
468
469	# Source Information
470	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
471	self.current_datainfo.source.wavelength = data_point
472	self.current_datainfo.source.wavelength_unit = unit
473	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
474	self.current_datainfo.source.wavelength_min = data_point
475	self.current_datainfo.source.wavelength_min_unit = unit
476	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.wavelength_max = data_point
478	self.current_datainfo.source.wavelength_max_unit = unit
479	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
480	self.current_datainfo.source.wavelength_spread = data_point
481	self.current_datainfo.source.wavelength_spread_unit = unit
482	elif tagname == 'x' and self.parent_class == 'beam_size':
483	self.current_datainfo.source.beam_size.x = data_point
484	self.current_datainfo.source.beam_size_unit = unit
485	elif tagname == 'y' and self.parent_class == 'beam_size':
486	self.current_datainfo.source.beam_size.y = data_point
487	self.current_datainfo.source.beam_size_unit = unit
488	elif tagname == 'z' and self.parent_class == 'pixel_size':
489	self.current_datainfo.source.data_point.z = data_point
490	self.current_datainfo.source.beam_size_unit = unit
491	elif tagname == 'radiation' and self.parent_class == 'SASsource':
492	self.current_datainfo.source.radiation = data_point
493	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
494	self.current_datainfo.source.beam_shape = data_point
495
496	# Everything else goes in meta_data
497	else:
498	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
499	self.current_datainfo.meta_data[new_key] = data_point
500
501	self.names.remove(tagname_original)
502	length = 0
503	if len(self.names) > 1:
504	length = len(self.names) - 1
505	self.parent_class = self.names[length]
506	if not self._is_call_local() and not recurse:
507	self.frm = ""
508	self.current_datainfo.errors = set()
509	for error in self.errors:
510	self.current_datainfo.errors.add(error)
511	self.errors.clear()
512	self.send_to_output()
513	empty = None
514	return self.output[0], empty
515
516	def _is_call_local(self):
517	if self.frm == "":
518	inter = inspect.stack()
519	self.frm = inter[2]
520	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
521	mod_name = mod_name.replace(".py", "")
522	mod = mod_name.split("sas/")
523	mod_name = mod[1]
524	if mod_name != "sascalc/dataloader/readers/cansas_reader":
525	return False
526	return True
527
528	def _add_intermediate(self):
529	"""
530	This method stores any intermediate objects within the final data set after fully reading the set.
531	"""
532	if self.parent_class == 'SASprocess':
533	self.current_datainfo.process.append(self.process)
534	self.process = Process()
535	elif self.parent_class == 'SASdetector':
536	self.current_datainfo.detector.append(self.detector)
537	self.detector = Detector()
538	elif self.parent_class == 'SAStransmission_spectrum':
539	self.current_datainfo.trans_spectrum.append(self.transspectrum)
540	self.transspectrum = TransmissionSpectrum()
541	elif self.parent_class == 'SAScollimation':
542	self.current_datainfo.collimation.append(self.collimation)
543	self.collimation = Collimation()
544	elif self.parent_class == 'aperture':
545	self.collimation.aperture.append(self.aperture)
546	self.aperture = Aperture()
547	elif self.parent_class == 'SASdata':
548	self._check_for_empty_resolution()
549	self.data.append(self.current_dataset)
550
551	def _get_node_value(self, node, tagname):
552	"""
553	Get the value of a node and any applicable units
554
555	:param node: The XML node to get the value of
556	:param tagname: The tagname of the node
557	"""
558	#Get the text from the node and convert all whitespace to spaces
559	units = ''
560	node_value = node.text
561	if node_value is not None:
562	node_value = ' '.join(node_value.split())
563	else:
564	node_value = ""
565
566	# If the value is a float, compile with units.
567	if self.ns_list.ns_datatype == "float":
568	# If an empty value is given, set as zero.
569	if node_value is None or node_value.isspace() \
570	or node_value.lower() == "nan":
571	node_value = "0.0"
572	#Convert the value to the base units
573	node_value, units = self._unit_conversion(node, tagname, node_value)
574
575	# If the value is a timestamp, convert to a datetime object
576	elif self.ns_list.ns_datatype == "timestamp":
577	if node_value is None or node_value.isspace():
578	pass
579	else:
580	try:
581	node_value = \
582	datetime.datetime.fromtimestamp(node_value)
583	except ValueError:
584	node_value = None
585	return node_value, units
586
587	def _unit_conversion(self, node, tagname, node_value):
588	"""
589	A unit converter method used to convert the data included in the file
590	to the default units listed in data_info
591
592	:param node: XML node
593	:param tagname: name of the node
594	:param node_value: The value of the current dom node
595	"""
596	attr = node.attrib
597	value_unit = ''
598	err_msg = None
599	default_unit = None
600	if not isinstance(node_value, float):
601	node_value = float(node_value)
602	if 'unit' in attr and attr.get('unit') is not None:
603	try:
604	local_unit = attr['unit']
605	unitname = self.ns_list.current_level.get("unit", "")
606	if "SASdetector" in self.names:
607	save_in = "detector"
608	elif "aperture" in self.names:
609	save_in = "aperture"
610	elif "SAScollimation" in self.names:
611	save_in = "collimation"
612	elif "SAStransmission_spectrum" in self.names:
613	save_in = "transspectrum"
614	elif "SASdata" in self.names:
615	x = np.zeros(1)
616	y = np.zeros(1)
617	self.current_data1d = Data1D(x, y)
618	save_in = "current_data1d"
619	elif "SASsource" in self.names:
620	save_in = "current_datainfo.source"
621	elif "SASsample" in self.names:
622	save_in = "current_datainfo.sample"
623	elif "SASprocess" in self.names:
624	save_in = "process"
625	else:
626	save_in = "current_datainfo"
627	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
628	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
629	and local_unit.lower() != "none":
630	if HAS_CONVERTER == True:
631	# Check local units - bad units raise KeyError
632	data_conv_q = Converter(local_unit)
633	value_unit = default_unit
634	node_value = data_conv_q(node_value, units=default_unit)
635	else:
636	value_unit = local_unit
637	err_msg = "Unit converter is not available.\n"
638	else:
639	value_unit = local_unit
640	except KeyError:
641	err_msg = "CanSAS reader: unexpected "
642	err_msg += "\"{0}\" unit [{1}]; "
643	err_msg = err_msg.format(tagname, local_unit)
644	err_msg += "expecting [{0}]".format(default_unit)
645	value_unit = local_unit
646	except:
647	err_msg = "CanSAS reader: unknown error converting "
648	err_msg += "\"{0}\" unit [{1}]"
649	err_msg = err_msg.format(tagname, local_unit)
650	value_unit = local_unit
651	elif 'unit' in attr:
652	value_unit = attr['unit']
653	if err_msg:
654	self.errors.add(err_msg)
655	return node_value, value_unit
656
657	def _check_for_empty_resolution(self):
658	"""
659	a method to check all resolution data sets are the same size as I and q
660	"""
661	dql_exists = False
662	dqw_exists = False
663	dq_exists = False
664	di_exists = False
665	if self.current_dataset.dxl is not None:
666	dql_exists = True
667	if self.current_dataset.dxw is not None:
668	dqw_exists = True
669	if self.current_dataset.dx is not None:
670	dq_exists = True
671	if self.current_dataset.dy is not None:
672	di_exists = True
673	if dqw_exists and not dql_exists:
674	array_size = self.current_dataset.dxw.size - 1
675	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
676	np.zeros([array_size]))
677	elif dql_exists and not dqw_exists:
678	array_size = self.current_dataset.dxl.size - 1
679	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
680	np.zeros([array_size]))
681	elif not dql_exists and not dqw_exists and not dq_exists:
682	array_size = self.current_dataset.x.size - 1
683	self.current_dataset.dx = np.append(self.current_dataset.dx,
684	np.zeros([array_size]))
685	if not di_exists:
686	array_size = self.current_dataset.y.size - 1
687	self.current_dataset.dy = np.append(self.current_dataset.dy,
688	np.zeros([array_size]))
689
690	def _initialize_new_data_set(self, node=None):
691	if node is not None:
692	for child in node:
693	if child.tag.replace(self.base_ns, "") == "Idata":
694	for i_child in child:
695	if i_child.tag.replace(self.base_ns, "") == "Qx":
696	self.current_dataset = plottable_2D()
697	return
698	self.current_dataset = plottable_1D(np.array(0), np.array(0))
699
700	## Writing Methods
701	def write(self, filename, datainfo):
702	"""
703	Write the content of a Data1D as a CanSAS XML file
704
705	:param filename: name of the file to write
706	:param datainfo: Data1D object
707	"""
708	# Create XML document
709	doc, _ = self._to_xml_doc(datainfo)
710	# Write the file
711	file_ref = open(filename, 'w')
712	if self.encoding is None:
713	self.encoding = "UTF-8"
714	doc.write(file_ref, encoding=self.encoding,
715	pretty_print=True, xml_declaration=True)
716	file_ref.close()
717
718	def _to_xml_doc(self, datainfo):
719	"""
720	Create an XML document to contain the content of a Data1D
721
722	:param datainfo: Data1D object
723	"""
724	is_2d = False
725	if issubclass(datainfo.__class__, Data2D):
726	is_2d = True
727
728	# Get PIs and create root element
729	pi_string = self._get_pi_string()
730	# Define namespaces and create SASroot object
731	main_node = self._create_main_node()
732	# Create ElementTree, append SASroot and apply processing instructions
733	base_string = pi_string + self.to_string(main_node)
734	base_element = self.create_element_from_string(base_string)
735	doc = self.create_tree(base_element)
736	# Create SASentry Element
737	entry_node = self.create_element("SASentry")
738	root = doc.getroot()
739	root.append(entry_node)
740
741	# Add Title to SASentry
742	self.write_node(entry_node, "Title", datainfo.title)
743	# Add Run to SASentry
744	self._write_run_names(datainfo, entry_node)
745	# Add Data info to SASEntry
746	if is_2d:
747	self._write_data_2d(datainfo, entry_node)
748	else:
749	self._write_data(datainfo, entry_node)
750	# Transmission Spectrum Info
751	# TODO: fix the writer to linearize all data, including T_spectrum
752	# self._write_trans_spectrum(datainfo, entry_node)
753	# Sample info
754	self._write_sample_info(datainfo, entry_node)
755	# Instrument info
756	instr = self._write_instrument(datainfo, entry_node)
757	# Source
758	self._write_source(datainfo, instr)
759	# Collimation
760	self._write_collimation(datainfo, instr)
761	# Detectors
762	self._write_detectors(datainfo, instr)
763	# Processes info
764	self._write_process_notes(datainfo, entry_node)
765	# Note info
766	self._write_notes(datainfo, entry_node)
767	# Return the document, and the SASentry node associated with
768	# the data we just wrote
769	# If the calling function was not the cansas reader, return a minidom
770	# object rather than an lxml object.
771	self.frm = inspect.stack()[1]
772	doc, entry_node = self._check_origin(entry_node, doc)
773	return doc, entry_node
774
775	def write_node(self, parent, name, value, attr=None):
776	"""
777	:param doc: document DOM
778	:param parent: parent node
779	:param name: tag of the element
780	:param value: value of the child text node
781	:param attr: attribute dictionary
782
783	:return: True if something was appended, otherwise False
784	"""
785	if value is not None:
786	parent = self.ebuilder(parent, name, value, attr)
787	return True
788	return False
789
790	def _get_pi_string(self):
791	"""
792	Creates the processing instructions header for writing to file
793	"""
794	pis = self.return_processing_instructions()
795	if len(pis) > 0:
796	pi_tree = self.create_tree(pis[0])
797	i = 1
798	for i in range(1, len(pis) - 1):
799	pi_tree = self.append(pis[i], pi_tree)
800	pi_string = self.to_string(pi_tree)
801	else:
802	pi_string = ""
803	return pi_string
804
805	def _create_main_node(self):
806	"""
807	Creates the primary xml header used when writing to file
808	"""
809	xsi = "http://www.w3.org/2001/XMLSchema-instance"
810	version = self.cansas_version
811	n_s = CANSAS_NS.get(version).get("ns")
812	if version == "1.1":
813	url = "http://www.cansas.org/formats/1.1/"
814	else:
815	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
816	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
817	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
818	"version" : version}
819	nsmap = {'xsi' : xsi, None: n_s}
820
821	main_node = self.create_element("{" + n_s + "}SASroot",
822	attrib=attrib, nsmap=nsmap)
823	return main_node
824
825	def _write_run_names(self, datainfo, entry_node):
826	"""
827	Writes the run names to the XML file
828
829	:param datainfo: The Data1D object the information is coming from
830	:param entry_node: lxml node ElementTree object to be appended to
831	"""
832	if datainfo.run is None or datainfo.run == []:
833	datainfo.run.append(RUN_NAME_DEFAULT)
834	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
835	for item in datainfo.run:
836	runname = {}
837	if item in datainfo.run_name and \
838	len(str(datainfo.run_name[item])) > 1:
839	runname = {'name': datainfo.run_name[item]}
840	self.write_node(entry_node, "Run", item, runname)
841
842	def _write_data(self, datainfo, entry_node):
843	"""
844	Writes 1D I and Q data to the XML file
845
846	:param datainfo: The Data1D object the information is coming from
847	:param entry_node: lxml node ElementTree object to be appended to
848	"""
849	node = self.create_element("SASdata")
850	self.append(node, entry_node)
851
852	for i in range(len(datainfo.x)):
853	point = self.create_element("Idata")
854	node.append(point)
855	self.write_node(point, "Q", datainfo.x[i],
856	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
857	if len(datainfo.y) >= i:
858	self.write_node(point, "I", datainfo.y[i],
859	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
860	if datainfo.dy is not None and len(datainfo.dy) > i:
861	self.write_node(point, "Idev", datainfo.dy[i],
862	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
863	if datainfo.dx is not None and len(datainfo.dx) > i:
864	self.write_node(point, "Qdev", datainfo.dx[i],
865	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
866	if datainfo.dxw is not None and len(datainfo.dxw) > i:
867	self.write_node(point, "dQw", datainfo.dxw[i],
868	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
869	if datainfo.dxl is not None and len(datainfo.dxl) > i:
870	self.write_node(point, "dQl", datainfo.dxl[i],
871	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
872	if datainfo.isSesans:
873	sesans = self.create_element("Sesans")
874	sesans.text = str(datainfo.isSesans)
875	node.append(sesans)
876	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
877	{'unit': datainfo.sample.yacceptance[1]})
878	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
879	{'unit': datainfo.sample.zacceptance[1]})
880
881
882	def _write_data_2d(self, datainfo, entry_node):
883	"""
884	Writes 2D data to the XML file
885
886	:param datainfo: The Data2D object the information is coming from
887	:param entry_node: lxml node ElementTree object to be appended to
888	"""
889	attr = {}
890	if datainfo.data.shape:
891	attr["x_bins"] = str(len(datainfo.x_bins))
892	attr["y_bins"] = str(len(datainfo.y_bins))
893	node = self.create_element("SASdata", attr)
894	self.append(node, entry_node)
895
896	point = self.create_element("Idata")
897	node.append(point)
898	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
899	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
900	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
901
902	self.write_node(point, "Qx", qx,
903	{'unit': datainfo._xunit})
904	self.write_node(point, "Qy", qy,
905	{'unit': datainfo._yunit})
906	self.write_node(point, "I", intensity,
907	{'unit': datainfo._zunit})
908	if datainfo.err_data is not None:
909	err = ','.join([str(datainfo.err_data[i]) for i in
910	xrange(len(datainfo.err_data))])
911	self.write_node(point, "Idev", err,
912	{'unit': datainfo._zunit})
913	if datainfo.dqy_data is not None:
914	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
915	xrange(len(datainfo.dqy_data))])
916	self.write_node(point, "Qydev", dqy,
917	{'unit': datainfo._yunit})
918	if datainfo.dqx_data is not None:
919	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
920	xrange(len(datainfo.dqx_data))])
921	self.write_node(point, "Qxdev", dqx,
922	{'unit': datainfo._xunit})
923	if datainfo.mask is not None:
924	mask = ','.join(
925	["1" if datainfo.mask[i] else "0"
926	for i in xrange(len(datainfo.mask))])
927	self.write_node(point, "Mask", mask)
928
929	def _write_trans_spectrum(self, datainfo, entry_node):
930	"""
931	Writes the transmission spectrum data to the XML file
932
933	:param datainfo: The Data1D object the information is coming from
934	:param entry_node: lxml node ElementTree object to be appended to
935	"""
936	for i in range(len(datainfo.trans_spectrum)):
937	spectrum = datainfo.trans_spectrum[i]
938	node = self.create_element("SAStransmission_spectrum",
939	{"name" : spectrum.name})
940	self.append(node, entry_node)
941	if isinstance(spectrum.timestamp, datetime.datetime):
942	node.setAttribute("timestamp", spectrum.timestamp)
943	for i in range(len(spectrum.wavelength)):
944	point = self.create_element("Tdata")
945	node.append(point)
946	self.write_node(point, "Lambda", spectrum.wavelength[i],
947	{'unit': spectrum.wavelength_unit})
948	self.write_node(point, "T", spectrum.transmission[i],
949	{'unit': spectrum.transmission_unit})
950	if spectrum.transmission_deviation is not None \
951	and len(spectrum.transmission_deviation) >= i:
952	self.write_node(point, "Tdev",
953	spectrum.transmission_deviation[i],
954	{'unit':
955	spectrum.transmission_deviation_unit})
956
957	def _write_sample_info(self, datainfo, entry_node):
958	"""
959	Writes the sample information to the XML file
960
961	:param datainfo: The Data1D object the information is coming from
962	:param entry_node: lxml node ElementTree object to be appended to
963	"""
964	sample = self.create_element("SASsample")
965	if datainfo.sample.name is not None:
966	self.write_attribute(sample, "name",
967	str(datainfo.sample.name))
968	self.append(sample, entry_node)
969	self.write_node(sample, "ID", str(datainfo.sample.ID))
970	self.write_node(sample, "thickness", datainfo.sample.thickness,
971	{"unit": datainfo.sample.thickness_unit})
972	self.write_node(sample, "transmission", datainfo.sample.transmission)
973	self.write_node(sample, "temperature", datainfo.sample.temperature,
974	{"unit": datainfo.sample.temperature_unit})
975
976	pos = self.create_element("position")
977	written = self.write_node(pos,
978	"x",
979	datainfo.sample.position.x,
980	{"unit": datainfo.sample.position_unit})
981	written = written \| self.write_node( \
982	pos, "y", datainfo.sample.position.y,
983	{"unit": datainfo.sample.position_unit})
984	written = written \| self.write_node( \
985	pos, "z", datainfo.sample.position.z,
986	{"unit": datainfo.sample.position_unit})
987	if written == True:
988	self.append(pos, sample)
989
990	ori = self.create_element("orientation")
991	written = self.write_node(ori, "roll",
992	datainfo.sample.orientation.x,
993	{"unit": datainfo.sample.orientation_unit})
994	written = written \| self.write_node( \
995	ori, "pitch", datainfo.sample.orientation.y,
996	{"unit": datainfo.sample.orientation_unit})
997	written = written \| self.write_node( \
998	ori, "yaw", datainfo.sample.orientation.z,
999	{"unit": datainfo.sample.orientation_unit})
1000	if written == True:
1001	self.append(ori, sample)
1002
1003	for item in datainfo.sample.details:
1004	self.write_node(sample, "details", item)
1005
1006	def _write_instrument(self, datainfo, entry_node):
1007	"""
1008	Writes the instrumental information to the XML file
1009
1010	:param datainfo: The Data1D object the information is coming from
1011	:param entry_node: lxml node ElementTree object to be appended to
1012	"""
1013	instr = self.create_element("SASinstrument")
1014	self.append(instr, entry_node)
1015	self.write_node(instr, "name", datainfo.instrument)
1016	return instr
1017
1018	def _write_source(self, datainfo, instr):
1019	"""
1020	Writes the source information to the XML file
1021
1022	:param datainfo: The Data1D object the information is coming from
1023	:param instr: instrument node to be appended to
1024	"""
1025	source = self.create_element("SASsource")
1026	if datainfo.source.name is not None:
1027	self.write_attribute(source, "name",
1028	str(datainfo.source.name))
1029	self.append(source, instr)
1030	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1031	datainfo.source.radiation = "neutron"
1032	self.write_node(source, "radiation", datainfo.source.radiation)
1033
1034	size = self.create_element("beam_size")
1035	if datainfo.source.beam_size_name is not None:
1036	self.write_attribute(size, "name",
1037	str(datainfo.source.beam_size_name))
1038	written = self.write_node( \
1039	size, "x", datainfo.source.beam_size.x,
1040	{"unit": datainfo.source.beam_size_unit})
1041	written = written \| self.write_node( \
1042	size, "y", datainfo.source.beam_size.y,
1043	{"unit": datainfo.source.beam_size_unit})
1044	written = written \| self.write_node( \
1045	size, "z", datainfo.source.beam_size.z,
1046	{"unit": datainfo.source.beam_size_unit})
1047	if written == True:
1048	self.append(size, source)
1049
1050	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1051	self.write_node(source, "wavelength",
1052	datainfo.source.wavelength,
1053	{"unit": datainfo.source.wavelength_unit})
1054	self.write_node(source, "wavelength_min",
1055	datainfo.source.wavelength_min,
1056	{"unit": datainfo.source.wavelength_min_unit})
1057	self.write_node(source, "wavelength_max",
1058	datainfo.source.wavelength_max,
1059	{"unit": datainfo.source.wavelength_max_unit})
1060	self.write_node(source, "wavelength_spread",
1061	datainfo.source.wavelength_spread,
1062	{"unit": datainfo.source.wavelength_spread_unit})
1063
1064	def _write_collimation(self, datainfo, instr):
1065	"""
1066	Writes the collimation information to the XML file
1067
1068	:param datainfo: The Data1D object the information is coming from
1069	:param instr: lxml node ElementTree object to be appended to
1070	"""
1071	if datainfo.collimation == [] or datainfo.collimation is None:
1072	coll = Collimation()
1073	datainfo.collimation.append(coll)
1074	for item in datainfo.collimation:
1075	coll = self.create_element("SAScollimation")
1076	if item.name is not None:
1077	self.write_attribute(coll, "name", str(item.name))
1078	self.append(coll, instr)
1079
1080	self.write_node(coll, "length", item.length,
1081	{"unit": item.length_unit})
1082
1083	for aperture in item.aperture:
1084	apert = self.create_element("aperture")
1085	if aperture.name is not None:
1086	self.write_attribute(apert, "name", str(aperture.name))
1087	if aperture.type is not None:
1088	self.write_attribute(apert, "type", str(aperture.type))
1089	self.append(apert, coll)
1090
1091	size = self.create_element("size")
1092	if aperture.size_name is not None:
1093	self.write_attribute(size, "name",
1094	str(aperture.size_name))
1095	written = self.write_node(size, "x", aperture.size.x,
1096	{"unit": aperture.size_unit})
1097	written = written \| self.write_node( \
1098	size, "y", aperture.size.y,
1099	{"unit": aperture.size_unit})
1100	written = written \| self.write_node( \
1101	size, "z", aperture.size.z,
1102	{"unit": aperture.size_unit})
1103	if written == True:
1104	self.append(size, apert)
1105
1106	self.write_node(apert, "distance", aperture.distance,
1107	{"unit": aperture.distance_unit})
1108
1109	def _write_detectors(self, datainfo, instr):
1110	"""
1111	Writes the detector information to the XML file
1112
1113	:param datainfo: The Data1D object the information is coming from
1114	:param inst: lxml instrument node to be appended to
1115	"""
1116	if datainfo.detector is None or datainfo.detector == []:
1117	det = Detector()
1118	det.name = ""
1119	datainfo.detector.append(det)
1120
1121	for item in datainfo.detector:
1122	det = self.create_element("SASdetector")
1123	written = self.write_node(det, "name", item.name)
1124	written = written \| self.write_node(det, "SDD", item.distance,
1125	{"unit": item.distance_unit})
1126	if written == True:
1127	self.append(det, instr)
1128
1129	off = self.create_element("offset")
1130	written = self.write_node(off, "x", item.offset.x,
1131	{"unit": item.offset_unit})
1132	written = written \| self.write_node(off, "y", item.offset.y,
1133	{"unit": item.offset_unit})
1134	written = written \| self.write_node(off, "z", item.offset.z,
1135	{"unit": item.offset_unit})
1136	if written == True:
1137	self.append(off, det)
1138
1139	ori = self.create_element("orientation")
1140	written = self.write_node(ori, "roll", item.orientation.x,
1141	{"unit": item.orientation_unit})
1142	written = written \| self.write_node(ori, "pitch",
1143	item.orientation.y,
1144	{"unit": item.orientation_unit})
1145	written = written \| self.write_node(ori, "yaw",
1146	item.orientation.z,
1147	{"unit": item.orientation_unit})
1148	if written == True:
1149	self.append(ori, det)
1150
1151	center = self.create_element("beam_center")
1152	written = self.write_node(center, "x", item.beam_center.x,
1153	{"unit": item.beam_center_unit})
1154	written = written \| self.write_node(center, "y",
1155	item.beam_center.y,
1156	{"unit": item.beam_center_unit})
1157	written = written \| self.write_node(center, "z",
1158	item.beam_center.z,
1159	{"unit": item.beam_center_unit})
1160	if written == True:
1161	self.append(center, det)
1162
1163	pix = self.create_element("pixel_size")
1164	written = self.write_node(pix, "x", item.pixel_size.x,
1165	{"unit": item.pixel_size_unit})
1166	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1167	{"unit": item.pixel_size_unit})
1168	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1169	{"unit": item.pixel_size_unit})
1170	if written == True:
1171	self.append(pix, det)
1172	self.write_node(det, "slit_length", item.slit_length,
1173	{"unit": item.slit_length_unit})
1174
1175
1176	def _write_process_notes(self, datainfo, entry_node):
1177	"""
1178	Writes the process notes to the XML file
1179
1180	:param datainfo: The Data1D object the information is coming from
1181	:param entry_node: lxml node ElementTree object to be appended to
1182
1183	"""
1184	for item in datainfo.process:
1185	node = self.create_element("SASprocess")
1186	self.append(node, entry_node)
1187	self.write_node(node, "name", item.name)
1188	self.write_node(node, "date", item.date)
1189	self.write_node(node, "description", item.description)
1190	for term in item.term:
1191	if isinstance(term, list):
1192	value = term['value']
1193	del term['value']
1194	elif isinstance(term, dict):
1195	value = term.get("value")
1196	del term['value']
1197	else:
1198	value = term
1199	self.write_node(node, "term", value, term)
1200	for note in item.notes:
1201	self.write_node(node, "SASprocessnote", note)
1202	if len(item.notes) == 0:
1203	self.write_node(node, "SASprocessnote", "")
1204
1205	def _write_notes(self, datainfo, entry_node):
1206	"""
1207	Writes the notes to the XML file and creates an empty note if none
1208	exist
1209
1210	:param datainfo: The Data1D object the information is coming from
1211	:param entry_node: lxml node ElementTree object to be appended to
1212
1213	"""
1214	if len(datainfo.notes) == 0:
1215	node = self.create_element("SASnote")
1216	self.append(node, entry_node)
1217	else:
1218	for item in datainfo.notes:
1219	node = self.create_element("SASnote")
1220	self.write_text(node, item)
1221	self.append(node, entry_node)
1222
1223	def _check_origin(self, entry_node, doc):
1224	"""
1225	Return the document, and the SASentry node associated with
1226	the data we just wrote.
1227	If the calling function was not the cansas reader, return a minidom
1228	object rather than an lxml object.
1229
1230	:param entry_node: lxml node ElementTree object to be appended to
1231	:param doc: entire xml tree
1232	"""
1233	if not self.frm:
1234	self.frm = inspect.stack()[1]
1235	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1236	mod_name = mod_name.replace(".py", "")
1237	mod = mod_name.split("sas/")
1238	mod_name = mod[1]
1239	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1240	string = self.to_string(doc, pretty_print=False)
1241	doc = parseString(string)
1242	node_name = entry_node.tag
1243	node_list = doc.getElementsByTagName(node_name)
1244	entry_node = node_list.item(0)
1245	return doc, entry_node
1246
1247	# DO NOT REMOVE - used in saving and loading panel states.
1248	def _store_float(self, location, node, variable, storage, optional=True):
1249	"""
1250	Get the content of a xpath location and store
1251	the result. Check that the units are compatible
1252	with the destination. The value is expected to
1253	be a float.
1254
1255	The xpath location might or might not exist.
1256	If it does not exist, nothing is done
1257
1258	:param location: xpath location to fetch
1259	:param node: node to read the data from
1260	:param variable: name of the data member to store it in [string]
1261	:param storage: data object that has the 'variable' data member
1262	:param optional: if True, no exception will be raised
1263	if unit conversion can't be done
1264
1265	:raise ValueError: raised when the units are not recognized
1266	"""
1267	entry = get_content(location, node)
1268	try:
1269	value = float(entry.text)
1270	except:
1271	value = None
1272
1273	if value is not None:
1274	# If the entry has units, check to see that they are
1275	# compatible with what we currently have in the data object
1276	units = entry.get('unit')
1277	if units is not None:
1278	toks = variable.split('.')
1279	local_unit = None
1280	exec "local_unit = storage.%s_unit" % toks[0]
1281	if local_unit is not None and units.lower() != local_unit.lower():
1282	if HAS_CONVERTER == True:
1283	try:
1284	conv = Converter(units)
1285	exec "storage.%s = %g" % \
1286	(variable, conv(value, units=local_unit))
1287	except:
1288	_, exc_value, _ = sys.exc_info()
1289	err_mess = "CanSAS reader: could not convert"
1290	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1291	% (variable, units, local_unit, exc_value)
1292	self.errors.add(err_mess)
1293	if optional:
1294	logger.info(err_mess)
1295	else:
1296	raise ValueError, err_mess
1297	else:
1298	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1299	% (variable, units)
1300	err_mess += " expecting [%s]" % local_unit
1301	self.errors.add(err_mess)
1302	if optional:
1303	logger.info(err_mess)
1304	else:
1305	raise ValueError, err_mess
1306	else:
1307	exec "storage.%s = value" % variable
1308	else:
1309	exec "storage.%s = value" % variable
1310
1311	# DO NOT REMOVE - used in saving and loading panel states.
1312	def _store_content(self, location, node, variable, storage):
1313	"""
1314	Get the content of a xpath location and store
1315	the result. The value is treated as a string.
1316
1317	The xpath location might or might not exist.
1318	If it does not exist, nothing is done
1319
1320	:param location: xpath location to fetch
1321	:param node: node to read the data from
1322	:param variable: name of the data member to store it in [string]
1323	:param storage: data object that has the 'variable' data member
1324
1325	:return: return a list of errors
1326	"""
1327	entry = get_content(location, node)
1328	if entry is not None and entry.text is not None:
1329	exec "storage.%s = entry.text.strip()" % variable
1330
1331	# DO NOT REMOVE Called by outside packages:
1332	# sas.sasgui.perspectives.invariant.invariant_state
1333	# sas.sasgui.perspectives.fitting.pagestate
1334	def get_content(location, node):
1335	"""
1336	Get the first instance of the content of a xpath location.
1337
1338	:param location: xpath location
1339	:param node: node to start at
1340
1341	:return: Element, or None
1342	"""
1343	nodes = node.xpath(location,
1344	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1345	if len(nodes) > 0:
1346	return nodes[0]
1347	else:
1348	return None
1349
1350	# DO NOT REMOVE Called by outside packages:
1351	# sas.sasgui.perspectives.fitting.pagestate
1352	def write_node(doc, parent, name, value, attr=None):
1353	"""
1354	:param doc: document DOM
1355	:param parent: parent node
1356	:param name: tag of the element
1357	:param value: value of the child text node
1358	:param attr: attribute dictionary
1359
1360	:return: True if something was appended, otherwise False
1361	"""
1362	if attr is None:
1363	attr = {}
1364	if value is not None:
1365	node = doc.createElement(name)
1366	node.appendChild(doc.createTextNode(str(value)))
1367	for item in attr:
1368	node.setAttribute(item, attr[item])
1369	parent.appendChild(node)
1370	return True
1371	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 2a52b0e

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