cansas_reader.py @ f00072f

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since f00072f was e6e89c4, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
exec magic for dereferencing default units didn't work in python 3
Property mode set to `100644`
File size: 63.7 KB

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1	import logging
2	import os
3	import sys
4	import datetime
5	import inspect
6
7	import numpy as np
8
9	# The following 2 imports ARE used. Do not remove either.
10	import xml.dom.minidom
11	from xml.dom.minidom import parseString
12
13	from lxml import etree
14
15	from sas.sascalc.data_util.nxsunit import Converter
16
17	# For saving individual sections of data
18	from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \
19	Collimation, TransmissionSpectrum, Detector, Process, Aperture, \
20	combine_data_info_with_plottable as combine_data
21	from ..loader_exceptions import FileContentsException, DefaultReaderException, \
22	DataReaderException
23	from . import xml_reader
24	from .xml_reader import XMLreader
25	from .cansas_constants import CansasConstants, CurrentLevel
26
27	logger = logging.getLogger(__name__)
28
29	PREPROCESS = "xmlpreprocess"
30	ENCODING = "encoding"
31	RUN_NAME_DEFAULT = "None"
32	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
33	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
34	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
35	"as much of the data as possible.\n\n"
36	HAS_CONVERTER = True
37
38	CONSTANTS = CansasConstants()
39	CANSAS_FORMAT = CONSTANTS.format
40	CANSAS_NS = CONSTANTS.names
41	ALLOW_ALL = True
42
43	class Reader(XMLreader):
44	cansas_version = "1.0"
45	base_ns = "{cansas1d/1.0}"
46	cansas_defaults = None
47	type_name = "canSAS"
48	invalid = True
49	frm = ""
50	# Log messages and errors
51	logging = None
52	errors = set()
53	# Namespace hierarchy for current xml_file object
54	names = None
55	ns_list = None
56	# Temporary storage location for loading multiple data sets in a single file
57	current_data1d = None
58	data = None
59	# Wildcards
60	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
61	# List of allowed extensions
62	ext = ['.xml', '.XML', '.svs', '.SVS']
63	# Flag to bypass extension check
64	allow_all = True
65
66	def reset_state(self):
67	"""
68	Resets the class state to a base case when loading a new data file so previous
69	data files do not appear a second time
70	"""
71	self.current_datainfo = None
72	self.current_dataset = None
73	self.current_data1d = None
74	self.data = []
75	self.process = Process()
76	self.transspectrum = TransmissionSpectrum()
77	self.aperture = Aperture()
78	self.collimation = Collimation()
79	self.detector = Detector()
80	self.names = []
81	self.cansas_defaults = {}
82	self.output = []
83	self.ns_list = None
84	self.logging = []
85	self.encoding = None
86
87	def read(self, xml_file, schema_path="", invalid=True):
88	if schema_path != "" or invalid != True:
89	# read has been called from self.get_file_contents because xml file doens't conform to schema
90	_, self.extension = os.path.splitext(os.path.basename(xml_file))
91	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
92
93	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
94	return super(XMLreader, self).read(xml_file)
95
96	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
97	# Reset everything since we're loading a new file
98	self.reset_state()
99	self.invalid = invalid
100	if xml_file is None:
101	xml_file = self.f_open.name
102	# We don't sure f_open since lxml handles opnening/closing files
103	if not self.f_open.closed:
104	self.f_open.close()
105
106	basename, _ = os.path.splitext(os.path.basename(xml_file))
107
108	try:
109	# Raises FileContentsException
110	self.load_file_and_schema(xml_file, schema_path)
111	self.current_datainfo = DataInfo()
112	# Raises FileContentsException if file doesn't meet CanSAS schema
113	self.is_cansas(self.extension)
114	self.invalid = False # If we reach this point then file must be valid CanSAS
115
116	# Parse each SASentry
117	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
118	'ns': self.cansas_defaults.get("ns")
119	})
120	# Look for a SASentry
121	self.names.append("SASentry")
122	self.set_processing_instructions()
123
124	for entry in entry_list:
125	self.current_datainfo.filename = basename + self.extension
126	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
127	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
128	self._parse_entry(entry)
129	self.data_cleanup()
130	except FileContentsException as fc_exc:
131	# File doesn't meet schema - try loading with a less strict schema
132	base_name = xml_reader.__file__
133	base_name = base_name.replace("\\", "/")
134	base = base_name.split("/sas/")[0]
135	if self.cansas_version == "1.1":
136	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
137	else:
138	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
139	self.set_schema(invalid_schema)
140	if self.invalid:
141	try:
142	# Load data with less strict schema
143	self.read(xml_file, invalid_schema, False)
144
145	# File can still be read but doesn't match schema, so raise exception
146	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
147	invalid_xml = self.find_invalid_xml()
148	if invalid_xml != "":
149	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
150	raise DataReaderException(invalid_xml) # Handled by base class
151	except FileContentsException as fc_exc:
152	msg = "CanSAS Reader could not load the file {}".format(xml_file)
153	if fc_exc.message is not None: # Propagate error messages from earlier
154	msg = fc_exc.message
155	if not self.extension in self.ext: # If the file has no associated loader
156	raise DefaultReaderException(msg)
157	raise FileContentsException(msg)
158	pass
159	else:
160	raise fc_exc
161	except Exception as e: # Convert all other exceptions to FileContentsExceptions
162	raise
163	raise FileContentsException(str(e))
164
165
166	def load_file_and_schema(self, xml_file, schema_path=""):
167	base_name = xml_reader.__file__
168	base_name = base_name.replace("\\", "/")
169	base = base_name.split("/sas/")[0]
170
171	# Try and parse the XML file
172	try:
173	self.set_xml_file(xml_file)
174	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
175	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
176	raise FileContentsException(msg)
177
178	self.cansas_version = self.xmlroot.get("version", "1.0")
179	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
180
181	if schema_path == "":
182	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
183	base, self.cansas_defaults.get("schema").replace("\\", "/")
184	)
185	self.set_schema(schema_path)
186
187	def is_cansas(self, ext="xml"):
188	"""
189	Checks to see if the XML file is a CanSAS file
190
191	:param ext: The file extension of the data file
192	:raises FileContentsException: Raised if XML file isn't valid CanSAS
193	"""
194	if self.validate_xml(): # Check file is valid XML
195	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
196	value = self.xmlroot.get(name)
197	# Check schema CanSAS version matches file CanSAS version
198	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
199	return True
200	if ext == "svs":
201	return True # Why is this required?
202	# If we get to this point then file isn't valid CanSAS
203	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
204	raise FileContentsException("The file is not valid CanSAS")
205
206	def _parse_entry(self, dom, recurse=False):
207	if not self._is_call_local() and not recurse:
208	self.reset_state()
209	self.data = []
210	self.current_datainfo = DataInfo()
211	self.names.append("SASentry")
212	self.parent_class = "SASentry"
213	# Create an empty dataset if no data has been passed to the reader
214	if self.current_dataset is None:
215	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
216	np.empty(0), np.empty(0))
217	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
218
219	# Loop through each child in the parent element
220	for node in dom:
221	attr = node.attrib
222	name = attr.get("name", "")
223	type = attr.get("type", "")
224	# Get the element name and set the current names level
225	tagname = node.tag.replace(self.base_ns, "")
226	tagname_original = tagname
227	# Skip this iteration when loading in save state information
228	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
229	continue
230	# Get where to store content
231	self.names.append(tagname_original)
232	self.ns_list = CONSTANTS.iterate_namespace(self.names)
233	# If the element is a child element, recurse
234	if len(node.getchildren()) > 0:
235	self.parent_class = tagname_original
236	if tagname == 'SASdata':
237	self._initialize_new_data_set(node)
238	if isinstance(self.current_dataset, plottable_2D):
239	x_bins = attr.get("x_bins", "")
240	y_bins = attr.get("y_bins", "")
241	if x_bins is not "" and y_bins is not "":
242	self.current_dataset.shape = (x_bins, y_bins)
243	else:
244	self.current_dataset.shape = ()
245	# Recurse to access data within the group
246	self._parse_entry(node, recurse=True)
247	if tagname == "SASsample":
248	self.current_datainfo.sample.name = name
249	elif tagname == "beam_size":
250	self.current_datainfo.source.beam_size_name = name
251	elif tagname == "SAScollimation":
252	self.collimation.name = name
253	elif tagname == "aperture":
254	self.aperture.name = name
255	self.aperture.type = type
256	self._add_intermediate()
257	else:
258	if isinstance(self.current_dataset, plottable_2D):
259	data_point = node.text
260	unit = attr.get('unit', '')
261	else:
262	data_point, unit = self._get_node_value(node, tagname)
263
264	# If this is a dataset, store the data appropriately
265	if tagname == 'Run':
266	self.current_datainfo.run_name[data_point] = name
267	self.current_datainfo.run.append(data_point)
268	elif tagname == 'Title':
269	self.current_datainfo.title = data_point
270	elif tagname == 'SASnote':
271	self.current_datainfo.notes.append(data_point)
272
273	# I and Q points
274	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
275	self.current_dataset.yaxis("Intensity", unit)
276	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
277	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
278	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
279	elif tagname == 'Q':
280	self.current_dataset.xaxis("Q", unit)
281	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
282	elif tagname == 'Qdev':
283	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
284	elif tagname == 'dQw':
285	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
286	elif tagname == 'dQl':
287	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
288	elif tagname == 'Qmean':
289	pass
290	elif tagname == 'Shadowfactor':
291	pass
292	elif tagname == 'Sesans':
293	self.current_datainfo.isSesans = bool(data_point)
294	self.current_dataset.xaxis(attr.get('x_axis'),
295	attr.get('x_unit'))
296	self.current_dataset.yaxis(attr.get('y_axis'),
297	attr.get('y_unit'))
298	elif tagname == 'yacceptance':
299	self.current_datainfo.sample.yacceptance = (data_point, unit)
300	elif tagname == 'zacceptance':
301	self.current_datainfo.sample.zacceptance = (data_point, unit)
302
303	# I and Qx, Qy - 2D data
304	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
305	self.current_dataset.yaxis("Intensity", unit)
306	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
307	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
308	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
309	elif tagname == 'Qx':
310	self.current_dataset.xaxis("Qx", unit)
311	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
312	elif tagname == 'Qy':
313	self.current_dataset.yaxis("Qy", unit)
314	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
315	elif tagname == 'Qxdev':
316	self.current_dataset.xaxis("Qxdev", unit)
317	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
318	elif tagname == 'Qydev':
319	self.current_dataset.yaxis("Qydev", unit)
320	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
321	elif tagname == 'Mask':
322	inter = [item == "1" for item in data_point.split(",")]
323	self.current_dataset.mask = np.asarray(inter, dtype=bool)
324
325	# Sample Information
326	elif tagname == 'ID' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.ID = data_point
328	elif tagname == 'Title' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.name = data_point
330	elif tagname == 'thickness' and self.parent_class == 'SASsample':
331	self.current_datainfo.sample.thickness = data_point
332	self.current_datainfo.sample.thickness_unit = unit
333	elif tagname == 'transmission' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.transmission = data_point
335	elif tagname == 'temperature' and self.parent_class == 'SASsample':
336	self.current_datainfo.sample.temperature = data_point
337	self.current_datainfo.sample.temperature_unit = unit
338	elif tagname == 'details' and self.parent_class == 'SASsample':
339	self.current_datainfo.sample.details.append(data_point)
340	elif tagname == 'x' and self.parent_class == 'position':
341	self.current_datainfo.sample.position.x = data_point
342	self.current_datainfo.sample.position_unit = unit
343	elif tagname == 'y' and self.parent_class == 'position':
344	self.current_datainfo.sample.position.y = data_point
345	self.current_datainfo.sample.position_unit = unit
346	elif tagname == 'z' and self.parent_class == 'position':
347	self.current_datainfo.sample.position.z = data_point
348	self.current_datainfo.sample.position_unit = unit
349	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
350	self.current_datainfo.sample.orientation.x = data_point
351	self.current_datainfo.sample.orientation_unit = unit
352	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
353	self.current_datainfo.sample.orientation.y = data_point
354	self.current_datainfo.sample.orientation_unit = unit
355	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
356	self.current_datainfo.sample.orientation.z = data_point
357	self.current_datainfo.sample.orientation_unit = unit
358
359	# Instrumental Information
360	elif tagname == 'name' and self.parent_class == 'SASinstrument':
361	self.current_datainfo.instrument = data_point
362
363	# Detector Information
364	elif tagname == 'name' and self.parent_class == 'SASdetector':
365	self.detector.name = data_point
366	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
367	self.detector.distance = data_point
368	self.detector.distance_unit = unit
369	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
370	self.detector.slit_length = data_point
371	self.detector.slit_length_unit = unit
372	elif tagname == 'x' and self.parent_class == 'offset':
373	self.detector.offset.x = data_point
374	self.detector.offset_unit = unit
375	elif tagname == 'y' and self.parent_class == 'offset':
376	self.detector.offset.y = data_point
377	self.detector.offset_unit = unit
378	elif tagname == 'z' and self.parent_class == 'offset':
379	self.detector.offset.z = data_point
380	self.detector.offset_unit = unit
381	elif tagname == 'x' and self.parent_class == 'beam_center':
382	self.detector.beam_center.x = data_point
383	self.detector.beam_center_unit = unit
384	elif tagname == 'y' and self.parent_class == 'beam_center':
385	self.detector.beam_center.y = data_point
386	self.detector.beam_center_unit = unit
387	elif tagname == 'z' and self.parent_class == 'beam_center':
388	self.detector.beam_center.z = data_point
389	self.detector.beam_center_unit = unit
390	elif tagname == 'x' and self.parent_class == 'pixel_size':
391	self.detector.pixel_size.x = data_point
392	self.detector.pixel_size_unit = unit
393	elif tagname == 'y' and self.parent_class == 'pixel_size':
394	self.detector.pixel_size.y = data_point
395	self.detector.pixel_size_unit = unit
396	elif tagname == 'z' and self.parent_class == 'pixel_size':
397	self.detector.pixel_size.z = data_point
398	self.detector.pixel_size_unit = unit
399	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
400	self.detector.orientation.x = data_point
401	self.detector.orientation_unit = unit
402	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
403	self.detector.orientation.y = data_point
404	self.detector.orientation_unit = unit
405	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
406	self.detector.orientation.z = data_point
407	self.detector.orientation_unit = unit
408
409	# Collimation and Aperture
410	elif tagname == 'length' and self.parent_class == 'SAScollimation':
411	self.collimation.length = data_point
412	self.collimation.length_unit = unit
413	elif tagname == 'name' and self.parent_class == 'SAScollimation':
414	self.collimation.name = data_point
415	elif tagname == 'distance' and self.parent_class == 'aperture':
416	self.aperture.distance = data_point
417	self.aperture.distance_unit = unit
418	elif tagname == 'x' and self.parent_class == 'size':
419	self.aperture.size.x = data_point
420	self.collimation.size_unit = unit
421	elif tagname == 'y' and self.parent_class == 'size':
422	self.aperture.size.y = data_point
423	self.collimation.size_unit = unit
424	elif tagname == 'z' and self.parent_class == 'size':
425	self.aperture.size.z = data_point
426	self.collimation.size_unit = unit
427
428	# Process Information
429	elif tagname == 'name' and self.parent_class == 'SASprocess':
430	self.process.name = data_point
431	elif tagname == 'description' and self.parent_class == 'SASprocess':
432	self.process.description = data_point
433	elif tagname == 'date' and self.parent_class == 'SASprocess':
434	try:
435	self.process.date = datetime.datetime.fromtimestamp(data_point)
436	except:
437	self.process.date = data_point
438	elif tagname == 'SASprocessnote':
439	self.process.notes.append(data_point)
440	elif tagname == 'term' and self.parent_class == 'SASprocess':
441	unit = attr.get("unit", "")
442	dic = { "name": name, "value": data_point, "unit": unit }
443	self.process.term.append(dic)
444
445	# Transmission Spectrum
446	elif tagname == 'T' and self.parent_class == 'Tdata':
447	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
448	self.transspectrum.transmission_unit = unit
449	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
450	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
451	self.transspectrum.transmission_deviation_unit = unit
452	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
453	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
454	self.transspectrum.wavelength_unit = unit
455
456	# Source Information
457	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
458	self.current_datainfo.source.wavelength = data_point
459	self.current_datainfo.source.wavelength_unit = unit
460	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
461	self.current_datainfo.source.wavelength_min = data_point
462	self.current_datainfo.source.wavelength_min_unit = unit
463	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
464	self.current_datainfo.source.wavelength_max = data_point
465	self.current_datainfo.source.wavelength_max_unit = unit
466	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
467	self.current_datainfo.source.wavelength_spread = data_point
468	self.current_datainfo.source.wavelength_spread_unit = unit
469	elif tagname == 'x' and self.parent_class == 'beam_size':
470	self.current_datainfo.source.beam_size.x = data_point
471	self.current_datainfo.source.beam_size_unit = unit
472	elif tagname == 'y' and self.parent_class == 'beam_size':
473	self.current_datainfo.source.beam_size.y = data_point
474	self.current_datainfo.source.beam_size_unit = unit
475	elif tagname == 'z' and self.parent_class == 'pixel_size':
476	self.current_datainfo.source.data_point.z = data_point
477	self.current_datainfo.source.beam_size_unit = unit
478	elif tagname == 'radiation' and self.parent_class == 'SASsource':
479	self.current_datainfo.source.radiation = data_point
480	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
481	self.current_datainfo.source.beam_shape = data_point
482
483	# Everything else goes in meta_data
484	else:
485	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
486	self.current_datainfo.meta_data[new_key] = data_point
487
488	self.names.remove(tagname_original)
489	length = 0
490	if len(self.names) > 1:
491	length = len(self.names) - 1
492	self.parent_class = self.names[length]
493	if not self._is_call_local() and not recurse:
494	self.frm = ""
495	self.current_datainfo.errors = set()
496	for error in self.errors:
497	self.current_datainfo.errors.add(error)
498	self.data_cleanup()
499	self.sort_one_d_data()
500	self.sort_two_d_data()
501	self.reset_data_list()
502	empty = None
503	return self.output[0], empty
504
505	def data_cleanup(self):
506	"""
507	Clean up the data sets and refresh everything
508	:return: None
509	"""
510	has_error_dx = self.current_dataset.dx is not None
511	has_error_dxl = self.current_dataset.dxl is not None
512	has_error_dxw = self.current_dataset.dxw is not None
513	has_error_dy = self.current_dataset.dy is not None
514	self.remove_empty_q_values(has_error_dx=has_error_dx,
515	has_error_dxl=has_error_dxl,
516	has_error_dxw=has_error_dxw,
517	has_error_dy=has_error_dy)
518	self.send_to_output() # Combine datasets with DataInfo
519	self.current_datainfo = DataInfo() # Reset DataInfo
520
521	def _is_call_local(self):
522	if self.frm == "":
523	inter = inspect.stack()
524	self.frm = inter[2]
525	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
526	mod_name = mod_name.replace(".py", "")
527	mod = mod_name.split("sas/")
528	mod_name = mod[1]
529	if mod_name != "sascalc/dataloader/readers/cansas_reader":
530	return False
531	return True
532
533	def _add_intermediate(self):
534	"""
535	This method stores any intermediate objects within the final data set after fully reading the set.
536	"""
537	if self.parent_class == 'SASprocess':
538	self.current_datainfo.process.append(self.process)
539	self.process = Process()
540	elif self.parent_class == 'SASdetector':
541	self.current_datainfo.detector.append(self.detector)
542	self.detector = Detector()
543	elif self.parent_class == 'SAStransmission_spectrum':
544	self.current_datainfo.trans_spectrum.append(self.transspectrum)
545	self.transspectrum = TransmissionSpectrum()
546	elif self.parent_class == 'SAScollimation':
547	self.current_datainfo.collimation.append(self.collimation)
548	self.collimation = Collimation()
549	elif self.parent_class == 'aperture':
550	self.collimation.aperture.append(self.aperture)
551	self.aperture = Aperture()
552	elif self.parent_class == 'SASdata':
553	self._check_for_empty_resolution()
554	self.data.append(self.current_dataset)
555
556	def _get_node_value(self, node, tagname):
557	"""
558	Get the value of a node and any applicable units
559
560	:param node: The XML node to get the value of
561	:param tagname: The tagname of the node
562	"""
563	#Get the text from the node and convert all whitespace to spaces
564	units = ''
565	node_value = node.text
566	if node_value is not None:
567	node_value = ' '.join(node_value.split())
568	else:
569	node_value = ""
570
571	# If the value is a float, compile with units.
572	if self.ns_list.ns_datatype == "float":
573	# If an empty value is given, set as zero.
574	if node_value is None or node_value.isspace() \
575	or node_value.lower() == "nan":
576	node_value = "0.0"
577	#Convert the value to the base units
578	node_value, units = self._unit_conversion(node, tagname, node_value)
579
580	# If the value is a timestamp, convert to a datetime object
581	elif self.ns_list.ns_datatype == "timestamp":
582	if node_value is None or node_value.isspace():
583	pass
584	else:
585	try:
586	node_value = \
587	datetime.datetime.fromtimestamp(node_value)
588	except ValueError:
589	node_value = None
590	return node_value, units
591
592	def _unit_conversion(self, node, tagname, node_value):
593	"""
594	A unit converter method used to convert the data included in the file
595	to the default units listed in data_info
596
597	:param node: XML node
598	:param tagname: name of the node
599	:param node_value: The value of the current dom node
600	"""
601	attr = node.attrib
602	value_unit = ''
603	err_msg = None
604	default_unit = None
605	if not isinstance(node_value, float):
606	node_value = float(node_value)
607	if 'unit' in attr and attr.get('unit') is not None:
608	try:
609	local_unit = attr['unit']
610	unitname = self.ns_list.current_level.get("unit", "")
611	if "SASdetector" in self.names:
612	save_in = "detector"
613	elif "aperture" in self.names:
614	save_in = "aperture"
615	elif "SAScollimation" in self.names:
616	save_in = "collimation"
617	elif "SAStransmission_spectrum" in self.names:
618	save_in = "transspectrum"
619	elif "SASdata" in self.names:
620	x = np.zeros(1)
621	y = np.zeros(1)
622	self.current_data1d = Data1D(x, y)
623	save_in = "current_data1d"
624	elif "SASsource" in self.names:
625	save_in = "current_datainfo.source"
626	elif "SASsample" in self.names:
627	save_in = "current_datainfo.sample"
628	elif "SASprocess" in self.names:
629	save_in = "process"
630	else:
631	save_in = "current_datainfo"
632	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
633	if (local_unit and default_unit
634	and local_unit.lower() != default_unit.lower()
635	and local_unit.lower() != "none"):
636	if HAS_CONVERTER:
637	# Check local units - bad units raise KeyError
638	#print("loading", tagname, node_value, local_unit, default_unit)
639	data_conv_q = Converter(local_unit)
640	value_unit = default_unit
641	node_value = data_conv_q(node_value, units=default_unit)
642	else:
643	value_unit = local_unit
644	err_msg = "Unit converter is not available.\n"
645	else:
646	value_unit = local_unit
647	except KeyError:
648	# Do not throw an error for loading Sesans data in cansas xml
649	# This is a temporary fix.
650	if local_unit != "A" and local_unit != 'pol':
651	err_msg = "CanSAS reader: unexpected "
652	err_msg += "\"{0}\" unit [{1}]; "
653	err_msg = err_msg.format(tagname, local_unit)
654	err_msg += "expecting [{0}]".format(default_unit)
655	value_unit = local_unit
656	except Exception:
657	err_msg = "CanSAS reader: unknown error converting "
658	err_msg += "\"{0}\" unit [{1}]"
659	err_msg = err_msg.format(tagname, local_unit)
660	value_unit = local_unit
661	elif 'unit' in attr:
662	value_unit = attr['unit']
663	if err_msg:
664	self.errors.add(err_msg)
665	return node_value, value_unit
666
667	def _check_for_empty_resolution(self):
668	"""
669	a method to check all resolution data sets are the same size as I and q
670	"""
671	dql_exists = False
672	dqw_exists = False
673	dq_exists = False
674	di_exists = False
675	if self.current_dataset.dxl is not None:
676	dql_exists = True
677	if self.current_dataset.dxw is not None:
678	dqw_exists = True
679	if self.current_dataset.dx is not None:
680	dq_exists = True
681	if self.current_dataset.dy is not None:
682	di_exists = True
683	if dqw_exists and not dql_exists:
684	array_size = self.current_dataset.dxw.size
685	self.current_dataset.dxl = np.zeros(array_size)
686	elif dql_exists and not dqw_exists:
687	array_size = self.current_dataset.dxl.size
688	self.current_dataset.dxw = np.zeros(array_size)
689	elif not dql_exists and not dqw_exists and not dq_exists:
690	array_size = self.current_dataset.x.size
691	self.current_dataset.dx = np.append(self.current_dataset.dx,
692	np.zeros([array_size]))
693	if not di_exists:
694	array_size = self.current_dataset.y.size
695	self.current_dataset.dy = np.append(self.current_dataset.dy,
696	np.zeros([array_size]))
697
698	def _initialize_new_data_set(self, node=None):
699	if node is not None:
700	for child in node:
701	if child.tag.replace(self.base_ns, "") == "Idata":
702	for i_child in child:
703	if i_child.tag.replace(self.base_ns, "") == "Qx":
704	self.current_dataset = plottable_2D()
705	return
706	self.current_dataset = plottable_1D(np.array(0), np.array(0))
707
708	## Writing Methods
709	def write(self, filename, datainfo):
710	"""
711	Write the content of a Data1D as a CanSAS XML file
712
713	:param filename: name of the file to write
714	:param datainfo: Data1D object
715	"""
716	# Create XML document
717	doc, _ = self._to_xml_doc(datainfo)
718	# Write the file
719	file_ref = open(filename, 'wb')
720	if self.encoding is None:
721	self.encoding = "UTF-8"
722	doc.write(file_ref, encoding=self.encoding,
723	pretty_print=True, xml_declaration=True)
724	file_ref.close()
725
726	def _to_xml_doc(self, datainfo):
727	"""
728	Create an XML document to contain the content of a Data1D
729
730	:param datainfo: Data1D object
731	"""
732	is_2d = False
733	if issubclass(datainfo.__class__, Data2D):
734	is_2d = True
735
736	# Get PIs and create root element
737	pi_string = self._get_pi_string()
738	# Define namespaces and create SASroot object
739	main_node = self._create_main_node()
740	# Create ElementTree, append SASroot and apply processing instructions
741	base_string = pi_string + self.to_string(main_node)
742	base_element = self.create_element_from_string(base_string)
743	doc = self.create_tree(base_element)
744	# Create SASentry Element
745	entry_node = self.create_element("SASentry")
746	root = doc.getroot()
747	root.append(entry_node)
748
749	# Add Title to SASentry
750	self.write_node(entry_node, "Title", datainfo.title)
751	# Add Run to SASentry
752	self._write_run_names(datainfo, entry_node)
753	# Add Data info to SASEntry
754	if is_2d:
755	self._write_data_2d(datainfo, entry_node)
756	else:
757	self._write_data(datainfo, entry_node)
758	# Transmission Spectrum Info
759	# TODO: fix the writer to linearize all data, including T_spectrum
760	# self._write_trans_spectrum(datainfo, entry_node)
761	# Sample info
762	self._write_sample_info(datainfo, entry_node)
763	# Instrument info
764	instr = self._write_instrument(datainfo, entry_node)
765	# Source
766	self._write_source(datainfo, instr)
767	# Collimation
768	self._write_collimation(datainfo, instr)
769	# Detectors
770	self._write_detectors(datainfo, instr)
771	# Processes info
772	self._write_process_notes(datainfo, entry_node)
773	# Note info
774	self._write_notes(datainfo, entry_node)
775	# Return the document, and the SASentry node associated with
776	# the data we just wrote
777	# If the calling function was not the cansas reader, return a minidom
778	# object rather than an lxml object.
779	self.frm = inspect.stack()[1]
780	doc, entry_node = self._check_origin(entry_node, doc)
781	return doc, entry_node
782
783	def write_node(self, parent, name, value, attr=None):
784	"""
785	:param doc: document DOM
786	:param parent: parent node
787	:param name: tag of the element
788	:param value: value of the child text node
789	:param attr: attribute dictionary
790
791	:return: True if something was appended, otherwise False
792	"""
793	if value is not None:
794	parent = self.ebuilder(parent, name, value, attr)
795	return True
796	return False
797
798	def _get_pi_string(self):
799	"""
800	Creates the processing instructions header for writing to file
801	"""
802	pis = self.return_processing_instructions()
803	if len(pis) > 0:
804	pi_tree = self.create_tree(pis[0])
805	i = 1
806	for i in range(1, len(pis) - 1):
807	pi_tree = self.append(pis[i], pi_tree)
808	pi_string = self.to_string(pi_tree)
809	else:
810	pi_string = ""
811	return pi_string
812
813	def _create_main_node(self):
814	"""
815	Creates the primary xml header used when writing to file
816	"""
817	xsi = "http://www.w3.org/2001/XMLSchema-instance"
818	version = self.cansas_version
819	n_s = CANSAS_NS.get(version).get("ns")
820	if version == "1.1":
821	url = "http://www.cansas.org/formats/1.1/"
822	else:
823	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
824	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
825	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
826	"version" : version}
827	nsmap = {'xsi' : xsi, None: n_s}
828
829	main_node = self.create_element("{" + n_s + "}SASroot",
830	attrib=attrib, nsmap=nsmap)
831	return main_node
832
833	def _write_run_names(self, datainfo, entry_node):
834	"""
835	Writes the run names to the XML file
836
837	:param datainfo: The Data1D object the information is coming from
838	:param entry_node: lxml node ElementTree object to be appended to
839	"""
840	if datainfo.run is None or datainfo.run == []:
841	datainfo.run.append(RUN_NAME_DEFAULT)
842	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
843	for item in datainfo.run:
844	runname = {}
845	if item in datainfo.run_name and \
846	len(str(datainfo.run_name[item])) > 1:
847	runname = {'name': datainfo.run_name[item]}
848	self.write_node(entry_node, "Run", item, runname)
849
850	def _write_data(self, datainfo, entry_node):
851	"""
852	Writes 1D I and Q data to the XML file
853
854	:param datainfo: The Data1D object the information is coming from
855	:param entry_node: lxml node ElementTree object to be appended to
856	"""
857	node = self.create_element("SASdata")
858	self.append(node, entry_node)
859
860	for i in range(len(datainfo.x)):
861	point = self.create_element("Idata")
862	node.append(point)
863	self.write_node(point, "Q", datainfo.x[i],
864	{'unit': datainfo.x_unit})
865	if len(datainfo.y) >= i:
866	self.write_node(point, "I", datainfo.y[i],
867	{'unit': datainfo.y_unit})
868	if datainfo.dy is not None and len(datainfo.dy) > i:
869	self.write_node(point, "Idev", datainfo.dy[i],
870	{'unit': datainfo.y_unit})
871	if datainfo.dx is not None and len(datainfo.dx) > i:
872	self.write_node(point, "Qdev", datainfo.dx[i],
873	{'unit': datainfo.x_unit})
874	if datainfo.dxw is not None and len(datainfo.dxw) > i:
875	self.write_node(point, "dQw", datainfo.dxw[i],
876	{'unit': datainfo.x_unit})
877	if datainfo.dxl is not None and len(datainfo.dxl) > i:
878	self.write_node(point, "dQl", datainfo.dxl[i],
879	{'unit': datainfo.x_unit})
880	if datainfo.isSesans:
881	sesans_attrib = {'x_axis': datainfo._xaxis,
882	'y_axis': datainfo._yaxis,
883	'x_unit': datainfo.x_unit,
884	'y_unit': datainfo.y_unit}
885	sesans = self.create_element("Sesans", attrib=sesans_attrib)
886	sesans.text = str(datainfo.isSesans)
887	entry_node.append(sesans)
888	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
889	{'unit': datainfo.sample.yacceptance[1]})
890	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
891	{'unit': datainfo.sample.zacceptance[1]})
892
893
894	def _write_data_2d(self, datainfo, entry_node):
895	"""
896	Writes 2D data to the XML file
897
898	:param datainfo: The Data2D object the information is coming from
899	:param entry_node: lxml node ElementTree object to be appended to
900	"""
901	attr = {}
902	if datainfo.data.shape:
903	attr["x_bins"] = str(len(datainfo.x_bins))
904	attr["y_bins"] = str(len(datainfo.y_bins))
905	node = self.create_element("SASdata", attr)
906	self.append(node, entry_node)
907
908	point = self.create_element("Idata")
909	node.append(point)
910	qx = ','.join(str(v) for v in datainfo.qx_data)
911	qy = ','.join(str(v) for v in datainfo.qy_data)
912	intensity = ','.join(str(v) for v in datainfo.data)
913
914	self.write_node(point, "Qx", qx,
915	{'unit': datainfo._xunit})
916	self.write_node(point, "Qy", qy,
917	{'unit': datainfo._yunit})
918	self.write_node(point, "I", intensity,
919	{'unit': datainfo._zunit})
920	if datainfo.err_data is not None:
921	err = ','.join(str(v) for v in datainfo.err_data)
922	self.write_node(point, "Idev", err,
923	{'unit': datainfo._zunit})
924	if datainfo.dqy_data is not None:
925	dqy = ','.join(str(v) for v in datainfo.dqy_data)
926	self.write_node(point, "Qydev", dqy,
927	{'unit': datainfo._yunit})
928	if datainfo.dqx_data is not None:
929	dqx = ','.join(str(v) for v in datainfo.dqx_data)
930	self.write_node(point, "Qxdev", dqx,
931	{'unit': datainfo._xunit})
932	if datainfo.mask is not None:
933	mask = ','.join("1" if v else "0" for v in datainfo.mask)
934	self.write_node(point, "Mask", mask)
935
936	def _write_trans_spectrum(self, datainfo, entry_node):
937	"""
938	Writes the transmission spectrum data to the XML file
939
940	:param datainfo: The Data1D object the information is coming from
941	:param entry_node: lxml node ElementTree object to be appended to
942	"""
943	for i in range(len(datainfo.trans_spectrum)):
944	spectrum = datainfo.trans_spectrum[i]
945	node = self.create_element("SAStransmission_spectrum",
946	{"name" : spectrum.name})
947	self.append(node, entry_node)
948	if isinstance(spectrum.timestamp, datetime.datetime):
949	node.setAttribute("timestamp", spectrum.timestamp)
950	for i in range(len(spectrum.wavelength)):
951	point = self.create_element("Tdata")
952	node.append(point)
953	self.write_node(point, "Lambda", spectrum.wavelength[i],
954	{'unit': spectrum.wavelength_unit})
955	self.write_node(point, "T", spectrum.transmission[i],
956	{'unit': spectrum.transmission_unit})
957	if spectrum.transmission_deviation is not None \
958	and len(spectrum.transmission_deviation) >= i:
959	self.write_node(point, "Tdev",
960	spectrum.transmission_deviation[i],
961	{'unit':
962	spectrum.transmission_deviation_unit})
963
964	def _write_sample_info(self, datainfo, entry_node):
965	"""
966	Writes the sample information to the XML file
967
968	:param datainfo: The Data1D object the information is coming from
969	:param entry_node: lxml node ElementTree object to be appended to
970	"""
971	sample = self.create_element("SASsample")
972	if datainfo.sample.name is not None:
973	self.write_attribute(sample, "name",
974	str(datainfo.sample.name))
975	self.append(sample, entry_node)
976	self.write_node(sample, "ID", str(datainfo.sample.ID))
977	self.write_node(sample, "thickness", datainfo.sample.thickness,
978	{"unit": datainfo.sample.thickness_unit})
979	self.write_node(sample, "transmission", datainfo.sample.transmission)
980	self.write_node(sample, "temperature", datainfo.sample.temperature,
981	{"unit": datainfo.sample.temperature_unit})
982
983	pos = self.create_element("position")
984	written = self.write_node(pos,
985	"x",
986	datainfo.sample.position.x,
987	{"unit": datainfo.sample.position_unit})
988	written = written \| self.write_node( \
989	pos, "y", datainfo.sample.position.y,
990	{"unit": datainfo.sample.position_unit})
991	written = written \| self.write_node( \
992	pos, "z", datainfo.sample.position.z,
993	{"unit": datainfo.sample.position_unit})
994	if written == True:
995	self.append(pos, sample)
996
997	ori = self.create_element("orientation")
998	written = self.write_node(ori, "roll",
999	datainfo.sample.orientation.x,
1000	{"unit": datainfo.sample.orientation_unit})
1001	written = written \| self.write_node( \
1002	ori, "pitch", datainfo.sample.orientation.y,
1003	{"unit": datainfo.sample.orientation_unit})
1004	written = written \| self.write_node( \
1005	ori, "yaw", datainfo.sample.orientation.z,
1006	{"unit": datainfo.sample.orientation_unit})
1007	if written == True:
1008	self.append(ori, sample)
1009
1010	for item in datainfo.sample.details:
1011	self.write_node(sample, "details", item)
1012
1013	def _write_instrument(self, datainfo, entry_node):
1014	"""
1015	Writes the instrumental information to the XML file
1016
1017	:param datainfo: The Data1D object the information is coming from
1018	:param entry_node: lxml node ElementTree object to be appended to
1019	"""
1020	instr = self.create_element("SASinstrument")
1021	self.append(instr, entry_node)
1022	self.write_node(instr, "name", datainfo.instrument)
1023	return instr
1024
1025	def _write_source(self, datainfo, instr):
1026	"""
1027	Writes the source information to the XML file
1028
1029	:param datainfo: The Data1D object the information is coming from
1030	:param instr: instrument node to be appended to
1031	"""
1032	source = self.create_element("SASsource")
1033	if datainfo.source.name is not None:
1034	self.write_attribute(source, "name",
1035	str(datainfo.source.name))
1036	self.append(source, instr)
1037	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1038	datainfo.source.radiation = "neutron"
1039	self.write_node(source, "radiation", datainfo.source.radiation)
1040
1041	size = self.create_element("beam_size")
1042	if datainfo.source.beam_size_name is not None:
1043	self.write_attribute(size, "name",
1044	str(datainfo.source.beam_size_name))
1045	written = self.write_node( \
1046	size, "x", datainfo.source.beam_size.x,
1047	{"unit": datainfo.source.beam_size_unit})
1048	written = written \| self.write_node( \
1049	size, "y", datainfo.source.beam_size.y,
1050	{"unit": datainfo.source.beam_size_unit})
1051	written = written \| self.write_node( \
1052	size, "z", datainfo.source.beam_size.z,
1053	{"unit": datainfo.source.beam_size_unit})
1054	if written == True:
1055	self.append(size, source)
1056
1057	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1058	self.write_node(source, "wavelength",
1059	datainfo.source.wavelength,
1060	{"unit": datainfo.source.wavelength_unit})
1061	self.write_node(source, "wavelength_min",
1062	datainfo.source.wavelength_min,
1063	{"unit": datainfo.source.wavelength_min_unit})
1064	self.write_node(source, "wavelength_max",
1065	datainfo.source.wavelength_max,
1066	{"unit": datainfo.source.wavelength_max_unit})
1067	self.write_node(source, "wavelength_spread",
1068	datainfo.source.wavelength_spread,
1069	{"unit": datainfo.source.wavelength_spread_unit})
1070
1071	def _write_collimation(self, datainfo, instr):
1072	"""
1073	Writes the collimation information to the XML file
1074
1075	:param datainfo: The Data1D object the information is coming from
1076	:param instr: lxml node ElementTree object to be appended to
1077	"""
1078	if datainfo.collimation == [] or datainfo.collimation is None:
1079	coll = Collimation()
1080	datainfo.collimation.append(coll)
1081	for item in datainfo.collimation:
1082	coll = self.create_element("SAScollimation")
1083	if item.name is not None:
1084	self.write_attribute(coll, "name", str(item.name))
1085	self.append(coll, instr)
1086
1087	self.write_node(coll, "length", item.length,
1088	{"unit": item.length_unit})
1089
1090	for aperture in item.aperture:
1091	apert = self.create_element("aperture")
1092	if aperture.name is not None:
1093	self.write_attribute(apert, "name", str(aperture.name))
1094	if aperture.type is not None:
1095	self.write_attribute(apert, "type", str(aperture.type))
1096	self.append(apert, coll)
1097
1098	size = self.create_element("size")
1099	if aperture.size_name is not None:
1100	self.write_attribute(size, "name",
1101	str(aperture.size_name))
1102	written = self.write_node(size, "x", aperture.size.x,
1103	{"unit": aperture.size_unit})
1104	written = written \| self.write_node( \
1105	size, "y", aperture.size.y,
1106	{"unit": aperture.size_unit})
1107	written = written \| self.write_node( \
1108	size, "z", aperture.size.z,
1109	{"unit": aperture.size_unit})
1110	if written == True:
1111	self.append(size, apert)
1112
1113	self.write_node(apert, "distance", aperture.distance,
1114	{"unit": aperture.distance_unit})
1115
1116	def _write_detectors(self, datainfo, instr):
1117	"""
1118	Writes the detector information to the XML file
1119
1120	:param datainfo: The Data1D object the information is coming from
1121	:param inst: lxml instrument node to be appended to
1122	"""
1123	if datainfo.detector is None or datainfo.detector == []:
1124	det = Detector()
1125	det.name = ""
1126	datainfo.detector.append(det)
1127
1128	for item in datainfo.detector:
1129	det = self.create_element("SASdetector")
1130	written = self.write_node(det, "name", item.name)
1131	written = written \| self.write_node(det, "SDD", item.distance,
1132	{"unit": item.distance_unit})
1133	if written == True:
1134	self.append(det, instr)
1135
1136	off = self.create_element("offset")
1137	written = self.write_node(off, "x", item.offset.x,
1138	{"unit": item.offset_unit})
1139	written = written \| self.write_node(off, "y", item.offset.y,
1140	{"unit": item.offset_unit})
1141	written = written \| self.write_node(off, "z", item.offset.z,
1142	{"unit": item.offset_unit})
1143	if written == True:
1144	self.append(off, det)
1145
1146	ori = self.create_element("orientation")
1147	written = self.write_node(ori, "roll", item.orientation.x,
1148	{"unit": item.orientation_unit})
1149	written = written \| self.write_node(ori, "pitch",
1150	item.orientation.y,
1151	{"unit": item.orientation_unit})
1152	written = written \| self.write_node(ori, "yaw",
1153	item.orientation.z,
1154	{"unit": item.orientation_unit})
1155	if written == True:
1156	self.append(ori, det)
1157
1158	center = self.create_element("beam_center")
1159	written = self.write_node(center, "x", item.beam_center.x,
1160	{"unit": item.beam_center_unit})
1161	written = written \| self.write_node(center, "y",
1162	item.beam_center.y,
1163	{"unit": item.beam_center_unit})
1164	written = written \| self.write_node(center, "z",
1165	item.beam_center.z,
1166	{"unit": item.beam_center_unit})
1167	if written == True:
1168	self.append(center, det)
1169
1170	pix = self.create_element("pixel_size")
1171	written = self.write_node(pix, "x", item.pixel_size.x,
1172	{"unit": item.pixel_size_unit})
1173	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1174	{"unit": item.pixel_size_unit})
1175	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1176	{"unit": item.pixel_size_unit})
1177	if written == True:
1178	self.append(pix, det)
1179	self.write_node(det, "slit_length", item.slit_length,
1180	{"unit": item.slit_length_unit})
1181
1182
1183	def _write_process_notes(self, datainfo, entry_node):
1184	"""
1185	Writes the process notes to the XML file
1186
1187	:param datainfo: The Data1D object the information is coming from
1188	:param entry_node: lxml node ElementTree object to be appended to
1189
1190	"""
1191	for item in datainfo.process:
1192	node = self.create_element("SASprocess")
1193	self.append(node, entry_node)
1194	self.write_node(node, "name", item.name)
1195	self.write_node(node, "date", item.date)
1196	self.write_node(node, "description", item.description)
1197	for term in item.term:
1198	if isinstance(term, list):
1199	value = term['value']
1200	del term['value']
1201	elif isinstance(term, dict):
1202	value = term.get("value")
1203	del term['value']
1204	else:
1205	value = term
1206	self.write_node(node, "term", value, term)
1207	for note in item.notes:
1208	self.write_node(node, "SASprocessnote", note)
1209	if len(item.notes) == 0:
1210	self.write_node(node, "SASprocessnote", "")
1211
1212	def _write_notes(self, datainfo, entry_node):
1213	"""
1214	Writes the notes to the XML file and creates an empty note if none
1215	exist
1216
1217	:param datainfo: The Data1D object the information is coming from
1218	:param entry_node: lxml node ElementTree object to be appended to
1219
1220	"""
1221	if len(datainfo.notes) == 0:
1222	node = self.create_element("SASnote")
1223	self.append(node, entry_node)
1224	else:
1225	for item in datainfo.notes:
1226	node = self.create_element("SASnote")
1227	self.write_text(node, item)
1228	self.append(node, entry_node)
1229
1230	def _check_origin(self, entry_node, doc):
1231	"""
1232	Return the document, and the SASentry node associated with
1233	the data we just wrote.
1234	If the calling function was not the cansas reader, return a minidom
1235	object rather than an lxml object.
1236
1237	:param entry_node: lxml node ElementTree object to be appended to
1238	:param doc: entire xml tree
1239	"""
1240	if not self.frm:
1241	self.frm = inspect.stack()[1]
1242	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1243	mod_name = mod_name.replace(".py", "")
1244	mod = mod_name.split("sas/")
1245	mod_name = mod[1]
1246	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1247	string = self.to_string(doc, pretty_print=False)
1248	doc = parseString(string)
1249	node_name = entry_node.tag
1250	node_list = doc.getElementsByTagName(node_name)
1251	entry_node = node_list.item(0)
1252	return doc, entry_node
1253
1254	# DO NOT REMOVE - used in saving and loading panel states.
1255	def _store_float(self, location, node, variable, storage, optional=True):
1256	"""
1257	Get the content of a xpath location and store
1258	the result. Check that the units are compatible
1259	with the destination. The value is expected to
1260	be a float.
1261
1262	The xpath location might or might not exist.
1263	If it does not exist, nothing is done
1264
1265	:param location: xpath location to fetch
1266	:param node: node to read the data from
1267	:param variable: name of the data member to store it in [string]
1268	:param storage: data object that has the 'variable' data member
1269	:param optional: if True, no exception will be raised
1270	if unit conversion can't be done
1271
1272	:raise ValueError: raised when the units are not recognized
1273	"""
1274	entry = get_content(location, node)
1275	try:
1276	value = float(entry.text)
1277	except ValueError:
1278	value = None
1279
1280	if value is not None:
1281	# If the entry has units, check to see that they are
1282	# compatible with what we currently have in the data object
1283	units = entry.get('unit')
1284	if units is not None:
1285	toks = variable.split('.')
1286	# TODO: why split() when accessing unit, but not when setting value?
1287	local_unit = getattr(storage, toks[0]+"_unit")
1288	if local_unit is not None and units.lower() != local_unit.lower():
1289	if HAS_CONVERTER == True:
1290	try:
1291	conv = Converter(units)
1292	setattrchain(storage, variable, conv(value, units=local_unit))
1293	except Exception:
1294	_, exc_value, _ = sys.exc_info()
1295	err_mess = "CanSAS reader: could not convert"
1296	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1297	% (variable, units, local_unit, exc_value)
1298	self.errors.add(err_mess)
1299	if optional:
1300	logger.info(err_mess)
1301	else:
1302	raise ValueError(err_mess)
1303	else:
1304	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1305	% (variable, units)
1306	err_mess += " expecting [%s]" % local_unit
1307	self.errors.add(err_mess)
1308	if optional:
1309	logger.info(err_mess)
1310	else:
1311	raise ValueError(err_mess)
1312	else:
1313	setattrchain(storage, variable, value)
1314	else:
1315	setattrchain(storage, variable, value)
1316
1317	# DO NOT REMOVE - used in saving and loading panel states.
1318	def _store_content(self, location, node, variable, storage):
1319	"""
1320	Get the content of a xpath location and store
1321	the result. The value is treated as a string.
1322
1323	The xpath location might or might not exist.
1324	If it does not exist, nothing is done
1325
1326	:param location: xpath location to fetch
1327	:param node: node to read the data from
1328	:param variable: name of the data member to store it in [string]
1329	:param storage: data object that has the 'variable' data member
1330
1331	:return: return a list of errors
1332	"""
1333	entry = get_content(location, node)
1334	if entry is not None and entry.text is not None:
1335	exec("storage.%s = entry.text.strip()" % variable)
1336
1337	# DO NOT REMOVE Called by outside packages:
1338	# sas.sasgui.perspectives.invariant.invariant_state
1339	# sas.sasgui.perspectives.fitting.pagestate
1340	def get_content(location, node):
1341	"""
1342	Get the first instance of the content of a xpath location.
1343
1344	:param location: xpath location
1345	:param node: node to start at
1346
1347	:return: Element, or None
1348	"""
1349	nodes = node.xpath(location,
1350	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1351	if len(nodes) > 0:
1352	return nodes[0]
1353	else:
1354	return None
1355
1356	# DO NOT REMOVE Called by outside packages:
1357	# sas.sasgui.perspectives.fitting.pagestate
1358	def write_node(doc, parent, name, value, attr=None):
1359	"""
1360	:param doc: document DOM
1361	:param parent: parent node
1362	:param name: tag of the element
1363	:param value: value of the child text node
1364	:param attr: attribute dictionary
1365
1366	:return: True if something was appended, otherwise False
1367	"""
1368	if attr is None:
1369	attr = {}
1370	if value is not None:
1371	node = doc.createElement(name)
1372	node.appendChild(doc.createTextNode(str(value)))
1373	for item in attr:
1374	node.setAttribute(item, attr[item])
1375	parent.appendChild(node)
1376	return True
1377	return False
1378
1379	def getattrchain(obj, chain, default=None):
1380	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
1381	for part in chain.split('.'):
1382	if hasattr(obj, part):
1383	obj = getattr(obj, part, None)
1384	else:
1385	return default
1386	return obj
1387
1388	def setattrchain(obj, chain, value):
1389	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
1390	parts = list(chain.split('.'))
1391	for part in parts[-1]:
1392	obj = getattr(obj, part, None)
1393	if obj is None:
1394	raise ValueError("missing parent object "+part)
1395	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ f00072f

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