cansas_reader.py @ 17e257b5

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 17e257b5 was 17e257b5, checked in by krzywon, 7 years ago
Fix the broken unit tests associated with the readers.
Property mode set to `100644`
File size: 63.4 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	msg = "CanSAS Reader could not load the file {}".format(xml_file)
160	if fc_exc.message is not None: # Propagate error messages from earlier
161	msg = fc_exc.message
162	if not self.extension in self.ext: # If the file has no associated loader
163	raise DefaultReaderException(msg)
164	raise FileContentsException(msg)
165	pass
166	else:
167	raise fc_exc
168	except Exception as e: # Convert all other exceptions to FileContentsExceptions
169	raise FileContentsException(e.message)
170
171
172	def load_file_and_schema(self, xml_file, schema_path=""):
173	base_name = xml_reader.__file__
174	base_name = base_name.replace("\\", "/")
175	base = base_name.split("/sas/")[0]
176
177	# Try and parse the XML file
178	try:
179	self.set_xml_file(xml_file)
180	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
181	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
182	raise FileContentsException(msg)
183
184	self.cansas_version = self.xmlroot.get("version", "1.0")
185	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
186
187	if schema_path == "":
188	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
189	base, self.cansas_defaults.get("schema").replace("\\", "/")
190	)
191	self.set_schema(schema_path)
192
193	def is_cansas(self, ext="xml"):
194	"""
195	Checks to see if the XML file is a CanSAS file
196
197	:param ext: The file extension of the data file
198	:raises FileContentsException: Raised if XML file isn't valid CanSAS
199	"""
200	if self.validate_xml(): # Check file is valid XML
201	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
202	value = self.xmlroot.get(name)
203	# Check schema CanSAS version matches file CanSAS version
204	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
205	return True
206	if ext == "svs":
207	return True # Why is this required?
208	# If we get to this point then file isn't valid CanSAS
209	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
210	raise FileContentsException("The file is not valid CanSAS")
211
212	def _parse_entry(self, dom, recurse=False):
213	if not self._is_call_local() and not recurse:
214	self.reset_state()
215	self.data = []
216	self.current_datainfo = DataInfo()
217	self.names.append("SASentry")
218	self.parent_class = "SASentry"
219	# Create an empty dataset if no data has been passed to the reader
220	if self.current_dataset is None:
221	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
222	np.empty(0), np.empty(0))
223	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
224
225	# Loop through each child in the parent element
226	for node in dom:
227	attr = node.attrib
228	name = attr.get("name", "")
229	type = attr.get("type", "")
230	# Get the element name and set the current names level
231	tagname = node.tag.replace(self.base_ns, "")
232	tagname_original = tagname
233	# Skip this iteration when loading in save state information
234	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
235	continue
236	# Get where to store content
237	self.names.append(tagname_original)
238	self.ns_list = CONSTANTS.iterate_namespace(self.names)
239	# If the element is a child element, recurse
240	if len(node.getchildren()) > 0:
241	self.parent_class = tagname_original
242	if tagname == 'SASdata':
243	self._initialize_new_data_set(node)
244	if isinstance(self.current_dataset, plottable_2D):
245	x_bins = attr.get("x_bins", "")
246	y_bins = attr.get("y_bins", "")
247	if x_bins is not "" and y_bins is not "":
248	self.current_dataset.shape = (x_bins, y_bins)
249	else:
250	self.current_dataset.shape = ()
251	# Recurse to access data within the group
252	self._parse_entry(node, recurse=True)
253	if tagname == "SASsample":
254	self.current_datainfo.sample.name = name
255	elif tagname == "beam_size":
256	self.current_datainfo.source.beam_size_name = name
257	elif tagname == "SAScollimation":
258	self.collimation.name = name
259	elif tagname == "aperture":
260	self.aperture.name = name
261	self.aperture.type = type
262	self._add_intermediate()
263	else:
264	if isinstance(self.current_dataset, plottable_2D):
265	data_point = node.text
266	unit = attr.get('unit', '')
267	else:
268	data_point, unit = self._get_node_value(node, tagname)
269
270	# If this is a dataset, store the data appropriately
271	if tagname == 'Run':
272	self.current_datainfo.run_name[data_point] = name
273	self.current_datainfo.run.append(data_point)
274	elif tagname == 'Title':
275	self.current_datainfo.title = data_point
276	elif tagname == 'SASnote':
277	self.current_datainfo.notes.append(data_point)
278
279	# I and Q points
280	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
281	unit_list = unit.split("\|")
282	if len(unit_list) > 1:
283	self.current_dataset.yaxis(unit_list[0].strip(),
284	unit_list[1].strip())
285	else:
286	self.current_dataset.yaxis("Intensity", unit)
287	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
288	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
289	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
290	elif tagname == 'Q':
291	unit_list = unit.split("\|")
292	if len(unit_list) > 1:
293	self.current_dataset.xaxis(unit_list[0].strip(),
294	unit_list[1].strip())
295	else:
296	self.current_dataset.xaxis("Q", unit)
297	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
298	elif tagname == 'Qdev':
299	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
300	elif tagname == 'dQw':
301	if self.current_dataset.dxw is None: self.current_dataset.dxw = np.empty(0)
302	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
303	elif tagname == 'dQl':
304	if self.current_dataset.dxl is None: self.current_dataset.dxl = np.empty(0)
305	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
306	elif tagname == 'Qmean':
307	pass
308	elif tagname == 'Shadowfactor':
309	pass
310	elif tagname == 'Sesans':
311	self.current_datainfo.isSesans = bool(data_point)
312	elif tagname == 'yacceptance':
313	self.current_datainfo.sample.yacceptance = (data_point, unit)
314	elif tagname == 'zacceptance':
315	self.current_datainfo.sample.zacceptance = (data_point, unit)
316
317	# I and Qx, Qy - 2D data
318	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
319	self.current_dataset.yaxis("Intensity", unit)
320	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
321	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
322	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
323	elif tagname == 'Qx':
324	self.current_dataset.xaxis("Qx", unit)
325	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
326	elif tagname == 'Qy':
327	self.current_dataset.yaxis("Qy", unit)
328	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
329	elif tagname == 'Qxdev':
330	self.current_dataset.xaxis("Qxdev", unit)
331	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
332	elif tagname == 'Qydev':
333	self.current_dataset.yaxis("Qydev", unit)
334	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
335	elif tagname == 'Mask':
336	inter = [item == "1" for item in data_point.split(",")]
337	self.current_dataset.mask = np.asarray(inter, dtype=bool)
338
339	# Sample Information
340	elif tagname == 'ID' and self.parent_class == 'SASsample':
341	self.current_datainfo.sample.ID = data_point
342	elif tagname == 'Title' and self.parent_class == 'SASsample':
343	self.current_datainfo.sample.name = data_point
344	elif tagname == 'thickness' and self.parent_class == 'SASsample':
345	self.current_datainfo.sample.thickness = data_point
346	self.current_datainfo.sample.thickness_unit = unit
347	elif tagname == 'transmission' and self.parent_class == 'SASsample':
348	self.current_datainfo.sample.transmission = data_point
349	elif tagname == 'temperature' and self.parent_class == 'SASsample':
350	self.current_datainfo.sample.temperature = data_point
351	self.current_datainfo.sample.temperature_unit = unit
352	elif tagname == 'details' and self.parent_class == 'SASsample':
353	self.current_datainfo.sample.details.append(data_point)
354	elif tagname == 'x' and self.parent_class == 'position':
355	self.current_datainfo.sample.position.x = data_point
356	self.current_datainfo.sample.position_unit = unit
357	elif tagname == 'y' and self.parent_class == 'position':
358	self.current_datainfo.sample.position.y = data_point
359	self.current_datainfo.sample.position_unit = unit
360	elif tagname == 'z' and self.parent_class == 'position':
361	self.current_datainfo.sample.position.z = data_point
362	self.current_datainfo.sample.position_unit = unit
363	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
364	self.current_datainfo.sample.orientation.x = data_point
365	self.current_datainfo.sample.orientation_unit = unit
366	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
367	self.current_datainfo.sample.orientation.y = data_point
368	self.current_datainfo.sample.orientation_unit = unit
369	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
370	self.current_datainfo.sample.orientation.z = data_point
371	self.current_datainfo.sample.orientation_unit = unit
372
373	# Instrumental Information
374	elif tagname == 'name' and self.parent_class == 'SASinstrument':
375	self.current_datainfo.instrument = data_point
376
377	# Detector Information
378	elif tagname == 'name' and self.parent_class == 'SASdetector':
379	self.detector.name = data_point
380	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
381	self.detector.distance = data_point
382	self.detector.distance_unit = unit
383	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
384	self.detector.slit_length = data_point
385	self.detector.slit_length_unit = unit
386	elif tagname == 'x' and self.parent_class == 'offset':
387	self.detector.offset.x = data_point
388	self.detector.offset_unit = unit
389	elif tagname == 'y' and self.parent_class == 'offset':
390	self.detector.offset.y = data_point
391	self.detector.offset_unit = unit
392	elif tagname == 'z' and self.parent_class == 'offset':
393	self.detector.offset.z = data_point
394	self.detector.offset_unit = unit
395	elif tagname == 'x' and self.parent_class == 'beam_center':
396	self.detector.beam_center.x = data_point
397	self.detector.beam_center_unit = unit
398	elif tagname == 'y' and self.parent_class == 'beam_center':
399	self.detector.beam_center.y = data_point
400	self.detector.beam_center_unit = unit
401	elif tagname == 'z' and self.parent_class == 'beam_center':
402	self.detector.beam_center.z = data_point
403	self.detector.beam_center_unit = unit
404	elif tagname == 'x' and self.parent_class == 'pixel_size':
405	self.detector.pixel_size.x = data_point
406	self.detector.pixel_size_unit = unit
407	elif tagname == 'y' and self.parent_class == 'pixel_size':
408	self.detector.pixel_size.y = data_point
409	self.detector.pixel_size_unit = unit
410	elif tagname == 'z' and self.parent_class == 'pixel_size':
411	self.detector.pixel_size.z = data_point
412	self.detector.pixel_size_unit = unit
413	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
414	self.detector.orientation.x = data_point
415	self.detector.orientation_unit = unit
416	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
417	self.detector.orientation.y = data_point
418	self.detector.orientation_unit = unit
419	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
420	self.detector.orientation.z = data_point
421	self.detector.orientation_unit = unit
422
423	# Collimation and Aperture
424	elif tagname == 'length' and self.parent_class == 'SAScollimation':
425	self.collimation.length = data_point
426	self.collimation.length_unit = unit
427	elif tagname == 'name' and self.parent_class == 'SAScollimation':
428	self.collimation.name = data_point
429	elif tagname == 'distance' and self.parent_class == 'aperture':
430	self.aperture.distance = data_point
431	self.aperture.distance_unit = unit
432	elif tagname == 'x' and self.parent_class == 'size':
433	self.aperture.size.x = data_point
434	self.collimation.size_unit = unit
435	elif tagname == 'y' and self.parent_class == 'size':
436	self.aperture.size.y = data_point
437	self.collimation.size_unit = unit
438	elif tagname == 'z' and self.parent_class == 'size':
439	self.aperture.size.z = data_point
440	self.collimation.size_unit = unit
441
442	# Process Information
443	elif tagname == 'name' and self.parent_class == 'SASprocess':
444	self.process.name = data_point
445	elif tagname == 'description' and self.parent_class == 'SASprocess':
446	self.process.description = data_point
447	elif tagname == 'date' and self.parent_class == 'SASprocess':
448	try:
449	self.process.date = datetime.datetime.fromtimestamp(data_point)
450	except:
451	self.process.date = data_point
452	elif tagname == 'SASprocessnote':
453	self.process.notes.append(data_point)
454	elif tagname == 'term' and self.parent_class == 'SASprocess':
455	unit = attr.get("unit", "")
456	dic = { "name": name, "value": data_point, "unit": unit }
457	self.process.term.append(dic)
458
459	# Transmission Spectrum
460	elif tagname == 'T' and self.parent_class == 'Tdata':
461	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
462	self.transspectrum.transmission_unit = unit
463	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
464	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
465	self.transspectrum.transmission_deviation_unit = unit
466	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
467	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
468	self.transspectrum.wavelength_unit = unit
469
470	# Source Information
471	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
472	self.current_datainfo.source.wavelength = data_point
473	self.current_datainfo.source.wavelength_unit = unit
474	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
475	self.current_datainfo.source.wavelength_min = data_point
476	self.current_datainfo.source.wavelength_min_unit = unit
477	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.wavelength_max = data_point
479	self.current_datainfo.source.wavelength_max_unit = unit
480	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
481	self.current_datainfo.source.wavelength_spread = data_point
482	self.current_datainfo.source.wavelength_spread_unit = unit
483	elif tagname == 'x' and self.parent_class == 'beam_size':
484	self.current_datainfo.source.beam_size.x = data_point
485	self.current_datainfo.source.beam_size_unit = unit
486	elif tagname == 'y' and self.parent_class == 'beam_size':
487	self.current_datainfo.source.beam_size.y = data_point
488	self.current_datainfo.source.beam_size_unit = unit
489	elif tagname == 'z' and self.parent_class == 'pixel_size':
490	self.current_datainfo.source.data_point.z = data_point
491	self.current_datainfo.source.beam_size_unit = unit
492	elif tagname == 'radiation' and self.parent_class == 'SASsource':
493	self.current_datainfo.source.radiation = data_point
494	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
495	self.current_datainfo.source.beam_shape = data_point
496
497	# Everything else goes in meta_data
498	else:
499	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
500	self.current_datainfo.meta_data[new_key] = data_point
501
502	self.names.remove(tagname_original)
503	length = 0
504	if len(self.names) > 1:
505	length = len(self.names) - 1
506	self.parent_class = self.names[length]
507	if not self._is_call_local() and not recurse:
508	self.frm = ""
509	self.current_datainfo.errors = set()
510	for error in self.errors:
511	self.current_datainfo.errors.add(error)
512	self.errors.clear()
513	self.send_to_output()
514	empty = None
515	return self.output[0], empty
516
517	def _is_call_local(self):
518	if self.frm == "":
519	inter = inspect.stack()
520	self.frm = inter[2]
521	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
522	mod_name = mod_name.replace(".py", "")
523	mod = mod_name.split("sas/")
524	mod_name = mod[1]
525	if mod_name != "sascalc/dataloader/readers/cansas_reader":
526	return False
527	return True
528
529	def _add_intermediate(self):
530	"""
531	This method stores any intermediate objects within the final data set after fully reading the set.
532	"""
533	if self.parent_class == 'SASprocess':
534	self.current_datainfo.process.append(self.process)
535	self.process = Process()
536	elif self.parent_class == 'SASdetector':
537	self.current_datainfo.detector.append(self.detector)
538	self.detector = Detector()
539	elif self.parent_class == 'SAStransmission_spectrum':
540	self.current_datainfo.trans_spectrum.append(self.transspectrum)
541	self.transspectrum = TransmissionSpectrum()
542	elif self.parent_class == 'SAScollimation':
543	self.current_datainfo.collimation.append(self.collimation)
544	self.collimation = Collimation()
545	elif self.parent_class == 'aperture':
546	self.collimation.aperture.append(self.aperture)
547	self.aperture = Aperture()
548	elif self.parent_class == 'SASdata':
549	self._check_for_empty_resolution()
550	self.data.append(self.current_dataset)
551
552	def _get_node_value(self, node, tagname):
553	"""
554	Get the value of a node and any applicable units
555
556	:param node: The XML node to get the value of
557	:param tagname: The tagname of the node
558	"""
559	#Get the text from the node and convert all whitespace to spaces
560	units = ''
561	node_value = node.text
562	if node_value is not None:
563	node_value = ' '.join(node_value.split())
564	else:
565	node_value = ""
566
567	# If the value is a float, compile with units.
568	if self.ns_list.ns_datatype == "float":
569	# If an empty value is given, set as zero.
570	if node_value is None or node_value.isspace() \
571	or node_value.lower() == "nan":
572	node_value = "0.0"
573	#Convert the value to the base units
574	node_value, units = self._unit_conversion(node, tagname, node_value)
575
576	# If the value is a timestamp, convert to a datetime object
577	elif self.ns_list.ns_datatype == "timestamp":
578	if node_value is None or node_value.isspace():
579	pass
580	else:
581	try:
582	node_value = \
583	datetime.datetime.fromtimestamp(node_value)
584	except ValueError:
585	node_value = None
586	return node_value, units
587
588	def _unit_conversion(self, node, tagname, node_value):
589	"""
590	A unit converter method used to convert the data included in the file
591	to the default units listed in data_info
592
593	:param node: XML node
594	:param tagname: name of the node
595	:param node_value: The value of the current dom node
596	"""
597	attr = node.attrib
598	value_unit = ''
599	err_msg = None
600	default_unit = None
601	if not isinstance(node_value, float):
602	node_value = float(node_value)
603	if 'unit' in attr and attr.get('unit') is not None:
604	try:
605	local_unit = attr['unit']
606	unitname = self.ns_list.current_level.get("unit", "")
607	if "SASdetector" in self.names:
608	save_in = "detector"
609	elif "aperture" in self.names:
610	save_in = "aperture"
611	elif "SAScollimation" in self.names:
612	save_in = "collimation"
613	elif "SAStransmission_spectrum" in self.names:
614	save_in = "transspectrum"
615	elif "SASdata" in self.names:
616	x = np.zeros(1)
617	y = np.zeros(1)
618	self.current_data1d = Data1D(x, y)
619	save_in = "current_data1d"
620	elif "SASsource" in self.names:
621	save_in = "current_datainfo.source"
622	elif "SASsample" in self.names:
623	save_in = "current_datainfo.sample"
624	elif "SASprocess" in self.names:
625	save_in = "process"
626	else:
627	save_in = "current_datainfo"
628	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
629	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
630	and local_unit.lower() != "none":
631	if HAS_CONVERTER == True:
632	# Check local units - bad units raise KeyError
633	data_conv_q = Converter(local_unit)
634	value_unit = default_unit
635	node_value = data_conv_q(node_value, units=default_unit)
636	else:
637	value_unit = local_unit
638	err_msg = "Unit converter is not available.\n"
639	else:
640	value_unit = local_unit
641	except KeyError:
642	err_msg = "CanSAS reader: unexpected "
643	err_msg += "\"{0}\" unit [{1}]; "
644	err_msg = err_msg.format(tagname, local_unit)
645	err_msg += "expecting [{0}]".format(default_unit)
646	value_unit = local_unit
647	except:
648	err_msg = "CanSAS reader: unknown error converting "
649	err_msg += "\"{0}\" unit [{1}]"
650	err_msg = err_msg.format(tagname, local_unit)
651	value_unit = local_unit
652	elif 'unit' in attr:
653	value_unit = attr['unit']
654	if err_msg:
655	self.errors.add(err_msg)
656	return node_value, value_unit
657
658	def _check_for_empty_resolution(self):
659	"""
660	a method to check all resolution data sets are the same size as I and q
661	"""
662	dql_exists = False
663	dqw_exists = False
664	dq_exists = False
665	di_exists = False
666	if self.current_dataset.dxl is not None:
667	dql_exists = True
668	if self.current_dataset.dxw is not None:
669	dqw_exists = True
670	if self.current_dataset.dx is not None:
671	dq_exists = True
672	if self.current_dataset.dy is not None:
673	di_exists = True
674	if dqw_exists and not dql_exists:
675	array_size = self.current_dataset.dxw.size - 1
676	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
677	np.zeros([array_size]))
678	elif dql_exists and not dqw_exists:
679	array_size = self.current_dataset.dxl.size - 1
680	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
681	np.zeros([array_size]))
682	elif not dql_exists and not dqw_exists and not dq_exists:
683	array_size = self.current_dataset.x.size - 1
684	self.current_dataset.dx = np.append(self.current_dataset.dx,
685	np.zeros([array_size]))
686	if not di_exists:
687	array_size = self.current_dataset.y.size - 1
688	self.current_dataset.dy = np.append(self.current_dataset.dy,
689	np.zeros([array_size]))
690
691	def _initialize_new_data_set(self, node=None):
692	if node is not None:
693	for child in node:
694	if child.tag.replace(self.base_ns, "") == "Idata":
695	for i_child in child:
696	if i_child.tag.replace(self.base_ns, "") == "Qx":
697	self.current_dataset = plottable_2D()
698	return
699	self.current_dataset = plottable_1D(np.array(0), np.array(0))
700
701	## Writing Methods
702	def write(self, filename, datainfo):
703	"""
704	Write the content of a Data1D as a CanSAS XML file
705
706	:param filename: name of the file to write
707	:param datainfo: Data1D object
708	"""
709	# Create XML document
710	doc, _ = self._to_xml_doc(datainfo)
711	# Write the file
712	file_ref = open(filename, 'w')
713	if self.encoding is None:
714	self.encoding = "UTF-8"
715	doc.write(file_ref, encoding=self.encoding,
716	pretty_print=True, xml_declaration=True)
717	file_ref.close()
718
719	def _to_xml_doc(self, datainfo):
720	"""
721	Create an XML document to contain the content of a Data1D
722
723	:param datainfo: Data1D object
724	"""
725	is_2d = False
726	if issubclass(datainfo.__class__, Data2D):
727	is_2d = True
728
729	# Get PIs and create root element
730	pi_string = self._get_pi_string()
731	# Define namespaces and create SASroot object
732	main_node = self._create_main_node()
733	# Create ElementTree, append SASroot and apply processing instructions
734	base_string = pi_string + self.to_string(main_node)
735	base_element = self.create_element_from_string(base_string)
736	doc = self.create_tree(base_element)
737	# Create SASentry Element
738	entry_node = self.create_element("SASentry")
739	root = doc.getroot()
740	root.append(entry_node)
741
742	# Add Title to SASentry
743	self.write_node(entry_node, "Title", datainfo.title)
744	# Add Run to SASentry
745	self._write_run_names(datainfo, entry_node)
746	# Add Data info to SASEntry
747	if is_2d:
748	self._write_data_2d(datainfo, entry_node)
749	else:
750	self._write_data(datainfo, entry_node)
751	# Transmission Spectrum Info
752	# TODO: fix the writer to linearize all data, including T_spectrum
753	# self._write_trans_spectrum(datainfo, entry_node)
754	# Sample info
755	self._write_sample_info(datainfo, entry_node)
756	# Instrument info
757	instr = self._write_instrument(datainfo, entry_node)
758	# Source
759	self._write_source(datainfo, instr)
760	# Collimation
761	self._write_collimation(datainfo, instr)
762	# Detectors
763	self._write_detectors(datainfo, instr)
764	# Processes info
765	self._write_process_notes(datainfo, entry_node)
766	# Note info
767	self._write_notes(datainfo, entry_node)
768	# Return the document, and the SASentry node associated with
769	# the data we just wrote
770	# If the calling function was not the cansas reader, return a minidom
771	# object rather than an lxml object.
772	self.frm = inspect.stack()[1]
773	doc, entry_node = self._check_origin(entry_node, doc)
774	return doc, entry_node
775
776	def write_node(self, parent, name, value, attr=None):
777	"""
778	:param doc: document DOM
779	:param parent: parent node
780	:param name: tag of the element
781	:param value: value of the child text node
782	:param attr: attribute dictionary
783
784	:return: True if something was appended, otherwise False
785	"""
786	if value is not None:
787	parent = self.ebuilder(parent, name, value, attr)
788	return True
789	return False
790
791	def _get_pi_string(self):
792	"""
793	Creates the processing instructions header for writing to file
794	"""
795	pis = self.return_processing_instructions()
796	if len(pis) > 0:
797	pi_tree = self.create_tree(pis[0])
798	i = 1
799	for i in range(1, len(pis) - 1):
800	pi_tree = self.append(pis[i], pi_tree)
801	pi_string = self.to_string(pi_tree)
802	else:
803	pi_string = ""
804	return pi_string
805
806	def _create_main_node(self):
807	"""
808	Creates the primary xml header used when writing to file
809	"""
810	xsi = "http://www.w3.org/2001/XMLSchema-instance"
811	version = self.cansas_version
812	n_s = CANSAS_NS.get(version).get("ns")
813	if version == "1.1":
814	url = "http://www.cansas.org/formats/1.1/"
815	else:
816	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
817	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
818	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
819	"version" : version}
820	nsmap = {'xsi' : xsi, None: n_s}
821
822	main_node = self.create_element("{" + n_s + "}SASroot",
823	attrib=attrib, nsmap=nsmap)
824	return main_node
825
826	def _write_run_names(self, datainfo, entry_node):
827	"""
828	Writes the run names to the XML file
829
830	:param datainfo: The Data1D object the information is coming from
831	:param entry_node: lxml node ElementTree object to be appended to
832	"""
833	if datainfo.run is None or datainfo.run == []:
834	datainfo.run.append(RUN_NAME_DEFAULT)
835	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
836	for item in datainfo.run:
837	runname = {}
838	if item in datainfo.run_name and \
839	len(str(datainfo.run_name[item])) > 1:
840	runname = {'name': datainfo.run_name[item]}
841	self.write_node(entry_node, "Run", item, runname)
842
843	def _write_data(self, datainfo, entry_node):
844	"""
845	Writes 1D I and Q data to the XML file
846
847	:param datainfo: The Data1D object the information is coming from
848	:param entry_node: lxml node ElementTree object to be appended to
849	"""
850	node = self.create_element("SASdata")
851	self.append(node, entry_node)
852
853	for i in range(len(datainfo.x)):
854	point = self.create_element("Idata")
855	node.append(point)
856	self.write_node(point, "Q", datainfo.x[i],
857	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
858	if len(datainfo.y) >= i:
859	self.write_node(point, "I", datainfo.y[i],
860	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
861	if datainfo.dy is not None and len(datainfo.dy) > i:
862	self.write_node(point, "Idev", datainfo.dy[i],
863	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
864	if datainfo.dx is not None and len(datainfo.dx) > i:
865	self.write_node(point, "Qdev", datainfo.dx[i],
866	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
867	if datainfo.dxw is not None and len(datainfo.dxw) > i:
868	self.write_node(point, "dQw", datainfo.dxw[i],
869	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
870	if datainfo.dxl is not None and len(datainfo.dxl) > i:
871	self.write_node(point, "dQl", datainfo.dxl[i],
872	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
873	if datainfo.isSesans:
874	sesans = self.create_element("Sesans")
875	sesans.text = str(datainfo.isSesans)
876	node.append(sesans)
877	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
878	{'unit': datainfo.sample.yacceptance[1]})
879	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
880	{'unit': datainfo.sample.zacceptance[1]})
881
882
883	def _write_data_2d(self, datainfo, entry_node):
884	"""
885	Writes 2D data to the XML file
886
887	:param datainfo: The Data2D object the information is coming from
888	:param entry_node: lxml node ElementTree object to be appended to
889	"""
890	attr = {}
891	if datainfo.data.shape:
892	attr["x_bins"] = str(len(datainfo.x_bins))
893	attr["y_bins"] = str(len(datainfo.y_bins))
894	node = self.create_element("SASdata", attr)
895	self.append(node, entry_node)
896
897	point = self.create_element("Idata")
898	node.append(point)
899	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
900	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
901	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
902
903	self.write_node(point, "Qx", qx,
904	{'unit': datainfo._xunit})
905	self.write_node(point, "Qy", qy,
906	{'unit': datainfo._yunit})
907	self.write_node(point, "I", intensity,
908	{'unit': datainfo._zunit})
909	if datainfo.err_data is not None:
910	err = ','.join([str(datainfo.err_data[i]) for i in
911	xrange(len(datainfo.err_data))])
912	self.write_node(point, "Idev", err,
913	{'unit': datainfo._zunit})
914	if datainfo.dqy_data is not None:
915	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
916	xrange(len(datainfo.dqy_data))])
917	self.write_node(point, "Qydev", dqy,
918	{'unit': datainfo._yunit})
919	if datainfo.dqx_data is not None:
920	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
921	xrange(len(datainfo.dqx_data))])
922	self.write_node(point, "Qxdev", dqx,
923	{'unit': datainfo._xunit})
924	if datainfo.mask is not None:
925	mask = ','.join(
926	["1" if datainfo.mask[i] else "0"
927	for i in xrange(len(datainfo.mask))])
928	self.write_node(point, "Mask", mask)
929
930	def _write_trans_spectrum(self, datainfo, entry_node):
931	"""
932	Writes the transmission spectrum data to the XML file
933
934	:param datainfo: The Data1D object the information is coming from
935	:param entry_node: lxml node ElementTree object to be appended to
936	"""
937	for i in range(len(datainfo.trans_spectrum)):
938	spectrum = datainfo.trans_spectrum[i]
939	node = self.create_element("SAStransmission_spectrum",
940	{"name" : spectrum.name})
941	self.append(node, entry_node)
942	if isinstance(spectrum.timestamp, datetime.datetime):
943	node.setAttribute("timestamp", spectrum.timestamp)
944	for i in range(len(spectrum.wavelength)):
945	point = self.create_element("Tdata")
946	node.append(point)
947	self.write_node(point, "Lambda", spectrum.wavelength[i],
948	{'unit': spectrum.wavelength_unit})
949	self.write_node(point, "T", spectrum.transmission[i],
950	{'unit': spectrum.transmission_unit})
951	if spectrum.transmission_deviation is not None \
952	and len(spectrum.transmission_deviation) >= i:
953	self.write_node(point, "Tdev",
954	spectrum.transmission_deviation[i],
955	{'unit':
956	spectrum.transmission_deviation_unit})
957
958	def _write_sample_info(self, datainfo, entry_node):
959	"""
960	Writes the sample information to the XML file
961
962	:param datainfo: The Data1D object the information is coming from
963	:param entry_node: lxml node ElementTree object to be appended to
964	"""
965	sample = self.create_element("SASsample")
966	if datainfo.sample.name is not None:
967	self.write_attribute(sample, "name",
968	str(datainfo.sample.name))
969	self.append(sample, entry_node)
970	self.write_node(sample, "ID", str(datainfo.sample.ID))
971	self.write_node(sample, "thickness", datainfo.sample.thickness,
972	{"unit": datainfo.sample.thickness_unit})
973	self.write_node(sample, "transmission", datainfo.sample.transmission)
974	self.write_node(sample, "temperature", datainfo.sample.temperature,
975	{"unit": datainfo.sample.temperature_unit})
976
977	pos = self.create_element("position")
978	written = self.write_node(pos,
979	"x",
980	datainfo.sample.position.x,
981	{"unit": datainfo.sample.position_unit})
982	written = written \| self.write_node( \
983	pos, "y", datainfo.sample.position.y,
984	{"unit": datainfo.sample.position_unit})
985	written = written \| self.write_node( \
986	pos, "z", datainfo.sample.position.z,
987	{"unit": datainfo.sample.position_unit})
988	if written == True:
989	self.append(pos, sample)
990
991	ori = self.create_element("orientation")
992	written = self.write_node(ori, "roll",
993	datainfo.sample.orientation.x,
994	{"unit": datainfo.sample.orientation_unit})
995	written = written \| self.write_node( \
996	ori, "pitch", datainfo.sample.orientation.y,
997	{"unit": datainfo.sample.orientation_unit})
998	written = written \| self.write_node( \
999	ori, "yaw", datainfo.sample.orientation.z,
1000	{"unit": datainfo.sample.orientation_unit})
1001	if written == True:
1002	self.append(ori, sample)
1003
1004	for item in datainfo.sample.details:
1005	self.write_node(sample, "details", item)
1006
1007	def _write_instrument(self, datainfo, entry_node):
1008	"""
1009	Writes the instrumental information to the XML file
1010
1011	:param datainfo: The Data1D object the information is coming from
1012	:param entry_node: lxml node ElementTree object to be appended to
1013	"""
1014	instr = self.create_element("SASinstrument")
1015	self.append(instr, entry_node)
1016	self.write_node(instr, "name", datainfo.instrument)
1017	return instr
1018
1019	def _write_source(self, datainfo, instr):
1020	"""
1021	Writes the source information to the XML file
1022
1023	:param datainfo: The Data1D object the information is coming from
1024	:param instr: instrument node to be appended to
1025	"""
1026	source = self.create_element("SASsource")
1027	if datainfo.source.name is not None:
1028	self.write_attribute(source, "name",
1029	str(datainfo.source.name))
1030	self.append(source, instr)
1031	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1032	datainfo.source.radiation = "neutron"
1033	self.write_node(source, "radiation", datainfo.source.radiation)
1034
1035	size = self.create_element("beam_size")
1036	if datainfo.source.beam_size_name is not None:
1037	self.write_attribute(size, "name",
1038	str(datainfo.source.beam_size_name))
1039	written = self.write_node( \
1040	size, "x", datainfo.source.beam_size.x,
1041	{"unit": datainfo.source.beam_size_unit})
1042	written = written \| self.write_node( \
1043	size, "y", datainfo.source.beam_size.y,
1044	{"unit": datainfo.source.beam_size_unit})
1045	written = written \| self.write_node( \
1046	size, "z", datainfo.source.beam_size.z,
1047	{"unit": datainfo.source.beam_size_unit})
1048	if written == True:
1049	self.append(size, source)
1050
1051	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1052	self.write_node(source, "wavelength",
1053	datainfo.source.wavelength,
1054	{"unit": datainfo.source.wavelength_unit})
1055	self.write_node(source, "wavelength_min",
1056	datainfo.source.wavelength_min,
1057	{"unit": datainfo.source.wavelength_min_unit})
1058	self.write_node(source, "wavelength_max",
1059	datainfo.source.wavelength_max,
1060	{"unit": datainfo.source.wavelength_max_unit})
1061	self.write_node(source, "wavelength_spread",
1062	datainfo.source.wavelength_spread,
1063	{"unit": datainfo.source.wavelength_spread_unit})
1064
1065	def _write_collimation(self, datainfo, instr):
1066	"""
1067	Writes the collimation information to the XML file
1068
1069	:param datainfo: The Data1D object the information is coming from
1070	:param instr: lxml node ElementTree object to be appended to
1071	"""
1072	if datainfo.collimation == [] or datainfo.collimation is None:
1073	coll = Collimation()
1074	datainfo.collimation.append(coll)
1075	for item in datainfo.collimation:
1076	coll = self.create_element("SAScollimation")
1077	if item.name is not None:
1078	self.write_attribute(coll, "name", str(item.name))
1079	self.append(coll, instr)
1080
1081	self.write_node(coll, "length", item.length,
1082	{"unit": item.length_unit})
1083
1084	for aperture in item.aperture:
1085	apert = self.create_element("aperture")
1086	if aperture.name is not None:
1087	self.write_attribute(apert, "name", str(aperture.name))
1088	if aperture.type is not None:
1089	self.write_attribute(apert, "type", str(aperture.type))
1090	self.append(apert, coll)
1091
1092	size = self.create_element("size")
1093	if aperture.size_name is not None:
1094	self.write_attribute(size, "name",
1095	str(aperture.size_name))
1096	written = self.write_node(size, "x", aperture.size.x,
1097	{"unit": aperture.size_unit})
1098	written = written \| self.write_node( \
1099	size, "y", aperture.size.y,
1100	{"unit": aperture.size_unit})
1101	written = written \| self.write_node( \
1102	size, "z", aperture.size.z,
1103	{"unit": aperture.size_unit})
1104	if written == True:
1105	self.append(size, apert)
1106
1107	self.write_node(apert, "distance", aperture.distance,
1108	{"unit": aperture.distance_unit})
1109
1110	def _write_detectors(self, datainfo, instr):
1111	"""
1112	Writes the detector information to the XML file
1113
1114	:param datainfo: The Data1D object the information is coming from
1115	:param inst: lxml instrument node to be appended to
1116	"""
1117	if datainfo.detector is None or datainfo.detector == []:
1118	det = Detector()
1119	det.name = ""
1120	datainfo.detector.append(det)
1121
1122	for item in datainfo.detector:
1123	det = self.create_element("SASdetector")
1124	written = self.write_node(det, "name", item.name)
1125	written = written \| self.write_node(det, "SDD", item.distance,
1126	{"unit": item.distance_unit})
1127	if written == True:
1128	self.append(det, instr)
1129
1130	off = self.create_element("offset")
1131	written = self.write_node(off, "x", item.offset.x,
1132	{"unit": item.offset_unit})
1133	written = written \| self.write_node(off, "y", item.offset.y,
1134	{"unit": item.offset_unit})
1135	written = written \| self.write_node(off, "z", item.offset.z,
1136	{"unit": item.offset_unit})
1137	if written == True:
1138	self.append(off, det)
1139
1140	ori = self.create_element("orientation")
1141	written = self.write_node(ori, "roll", item.orientation.x,
1142	{"unit": item.orientation_unit})
1143	written = written \| self.write_node(ori, "pitch",
1144	item.orientation.y,
1145	{"unit": item.orientation_unit})
1146	written = written \| self.write_node(ori, "yaw",
1147	item.orientation.z,
1148	{"unit": item.orientation_unit})
1149	if written == True:
1150	self.append(ori, det)
1151
1152	center = self.create_element("beam_center")
1153	written = self.write_node(center, "x", item.beam_center.x,
1154	{"unit": item.beam_center_unit})
1155	written = written \| self.write_node(center, "y",
1156	item.beam_center.y,
1157	{"unit": item.beam_center_unit})
1158	written = written \| self.write_node(center, "z",
1159	item.beam_center.z,
1160	{"unit": item.beam_center_unit})
1161	if written == True:
1162	self.append(center, det)
1163
1164	pix = self.create_element("pixel_size")
1165	written = self.write_node(pix, "x", item.pixel_size.x,
1166	{"unit": item.pixel_size_unit})
1167	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1168	{"unit": item.pixel_size_unit})
1169	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1170	{"unit": item.pixel_size_unit})
1171	if written == True:
1172	self.append(pix, det)
1173	self.write_node(det, "slit_length", item.slit_length,
1174	{"unit": item.slit_length_unit})
1175
1176
1177	def _write_process_notes(self, datainfo, entry_node):
1178	"""
1179	Writes the process notes to the XML file
1180
1181	:param datainfo: The Data1D object the information is coming from
1182	:param entry_node: lxml node ElementTree object to be appended to
1183
1184	"""
1185	for item in datainfo.process:
1186	node = self.create_element("SASprocess")
1187	self.append(node, entry_node)
1188	self.write_node(node, "name", item.name)
1189	self.write_node(node, "date", item.date)
1190	self.write_node(node, "description", item.description)
1191	for term in item.term:
1192	if isinstance(term, list):
1193	value = term['value']
1194	del term['value']
1195	elif isinstance(term, dict):
1196	value = term.get("value")
1197	del term['value']
1198	else:
1199	value = term
1200	self.write_node(node, "term", value, term)
1201	for note in item.notes:
1202	self.write_node(node, "SASprocessnote", note)
1203	if len(item.notes) == 0:
1204	self.write_node(node, "SASprocessnote", "")
1205
1206	def _write_notes(self, datainfo, entry_node):
1207	"""
1208	Writes the notes to the XML file and creates an empty note if none
1209	exist
1210
1211	:param datainfo: The Data1D object the information is coming from
1212	:param entry_node: lxml node ElementTree object to be appended to
1213
1214	"""
1215	if len(datainfo.notes) == 0:
1216	node = self.create_element("SASnote")
1217	self.append(node, entry_node)
1218	else:
1219	for item in datainfo.notes:
1220	node = self.create_element("SASnote")
1221	self.write_text(node, item)
1222	self.append(node, entry_node)
1223
1224	def _check_origin(self, entry_node, doc):
1225	"""
1226	Return the document, and the SASentry node associated with
1227	the data we just wrote.
1228	If the calling function was not the cansas reader, return a minidom
1229	object rather than an lxml object.
1230
1231	:param entry_node: lxml node ElementTree object to be appended to
1232	:param doc: entire xml tree
1233	"""
1234	if not self.frm:
1235	self.frm = inspect.stack()[1]
1236	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1237	mod_name = mod_name.replace(".py", "")
1238	mod = mod_name.split("sas/")
1239	mod_name = mod[1]
1240	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1241	string = self.to_string(doc, pretty_print=False)
1242	doc = parseString(string)
1243	node_name = entry_node.tag
1244	node_list = doc.getElementsByTagName(node_name)
1245	entry_node = node_list.item(0)
1246	return doc, entry_node
1247
1248	# DO NOT REMOVE - used in saving and loading panel states.
1249	def _store_float(self, location, node, variable, storage, optional=True):
1250	"""
1251	Get the content of a xpath location and store
1252	the result. Check that the units are compatible
1253	with the destination. The value is expected to
1254	be a float.
1255
1256	The xpath location might or might not exist.
1257	If it does not exist, nothing is done
1258
1259	:param location: xpath location to fetch
1260	:param node: node to read the data from
1261	:param variable: name of the data member to store it in [string]
1262	:param storage: data object that has the 'variable' data member
1263	:param optional: if True, no exception will be raised
1264	if unit conversion can't be done
1265
1266	:raise ValueError: raised when the units are not recognized
1267	"""
1268	entry = get_content(location, node)
1269	try:
1270	value = float(entry.text)
1271	except:
1272	value = None
1273
1274	if value is not None:
1275	# If the entry has units, check to see that they are
1276	# compatible with what we currently have in the data object
1277	units = entry.get('unit')
1278	if units is not None:
1279	toks = variable.split('.')
1280	local_unit = None
1281	exec "local_unit = storage.%s_unit" % toks[0]
1282	if local_unit is not None and units.lower() != local_unit.lower():
1283	if HAS_CONVERTER == True:
1284	try:
1285	conv = Converter(units)
1286	exec "storage.%s = %g" % \
1287	(variable, conv(value, units=local_unit))
1288	except:
1289	_, exc_value, _ = sys.exc_info()
1290	err_mess = "CanSAS reader: could not convert"
1291	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1292	% (variable, units, local_unit, exc_value)
1293	self.errors.add(err_mess)
1294	if optional:
1295	logger.info(err_mess)
1296	else:
1297	raise ValueError, err_mess
1298	else:
1299	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1300	% (variable, units)
1301	err_mess += " expecting [%s]" % local_unit
1302	self.errors.add(err_mess)
1303	if optional:
1304	logger.info(err_mess)
1305	else:
1306	raise ValueError, err_mess
1307	else:
1308	exec "storage.%s = value" % variable
1309	else:
1310	exec "storage.%s = value" % variable
1311
1312	# DO NOT REMOVE - used in saving and loading panel states.
1313	def _store_content(self, location, node, variable, storage):
1314	"""
1315	Get the content of a xpath location and store
1316	the result. The value is treated as a string.
1317
1318	The xpath location might or might not exist.
1319	If it does not exist, nothing is done
1320
1321	:param location: xpath location to fetch
1322	:param node: node to read the data from
1323	:param variable: name of the data member to store it in [string]
1324	:param storage: data object that has the 'variable' data member
1325
1326	:return: return a list of errors
1327	"""
1328	entry = get_content(location, node)
1329	if entry is not None and entry.text is not None:
1330	exec "storage.%s = entry.text.strip()" % variable
1331
1332	# DO NOT REMOVE Called by outside packages:
1333	# sas.sasgui.perspectives.invariant.invariant_state
1334	# sas.sasgui.perspectives.fitting.pagestate
1335	def get_content(location, node):
1336	"""
1337	Get the first instance of the content of a xpath location.
1338
1339	:param location: xpath location
1340	:param node: node to start at
1341
1342	:return: Element, or None
1343	"""
1344	nodes = node.xpath(location,
1345	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1346	if len(nodes) > 0:
1347	return nodes[0]
1348	else:
1349	return None
1350
1351	# DO NOT REMOVE Called by outside packages:
1352	# sas.sasgui.perspectives.fitting.pagestate
1353	def write_node(doc, parent, name, value, attr=None):
1354	"""
1355	:param doc: document DOM
1356	:param parent: parent node
1357	:param name: tag of the element
1358	:param value: value of the child text node
1359	:param attr: attribute dictionary
1360
1361	:return: True if something was appended, otherwise False
1362	"""
1363	if attr is None:
1364	attr = {}
1365	if value is not None:
1366	node = doc.createElement(name)
1367	node.appendChild(doc.createTextNode(str(value)))
1368	for item in attr:
1369	node.setAttribute(item, attr[item])
1370	parent.appendChild(node)
1371	return True
1372	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 17e257b5

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