cansas_reader.py @ 9efdb29

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 9efdb29 was 9efdb29, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
further python3 conversion cleanup for cansas
Property mode set to `100644`
File size: 62.9 KB

Line
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
37	CONSTANTS = CansasConstants()
38	CANSAS_FORMAT = CONSTANTS.format
39	CANSAS_NS = CONSTANTS.names
40	ALLOW_ALL = True
41
42	class Reader(XMLreader):
43	cansas_version = "1.0"
44	base_ns = "{cansas1d/1.0}"
45	cansas_defaults = None
46	type_name = "canSAS"
47	invalid = True
48	frm = ""
49	# Log messages and errors
50	logging = None
51	errors = set()
52	# Namespace hierarchy for current xml_file object
53	names = None
54	ns_list = None
55	# Temporary storage location for loading multiple data sets in a single file
56	current_data1d = None
57	data = None
58	# Wildcards
59	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
60	# List of allowed extensions
61	ext = ['.xml', '.XML', '.svs', '.SVS']
62	# Flag to bypass extension check
63	allow_all = True
64
65	def reset_state(self):
66	"""
67	Resets the class state to a base case when loading a new data file so previous
68	data files do not appear a second time
69	"""
70	self.current_datainfo = None
71	self.current_dataset = None
72	self.current_data1d = None
73	self.data = []
74	self.process = Process()
75	self.transspectrum = TransmissionSpectrum()
76	self.aperture = Aperture()
77	self.collimation = Collimation()
78	self.detector = Detector()
79	self.names = []
80	self.cansas_defaults = {}
81	self.output = []
82	self.ns_list = None
83	self.logging = []
84	self.encoding = None
85
86	def read(self, xml_file, schema_path="", invalid=True):
87	if schema_path != "" or invalid != True:
88	# read has been called from self.get_file_contents because xml file doens't conform to schema
89	_, self.extension = os.path.splitext(os.path.basename(xml_file))
90	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
91
92	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
93	return super(XMLreader, self).read(xml_file)
94
95	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
96	# Reset everything since we're loading a new file
97	self.reset_state()
98	self.invalid = invalid
99	if xml_file is None:
100	xml_file = self.f_open.name
101	# We don't sure f_open since lxml handles opnening/closing files
102	if not self.f_open.closed:
103	self.f_open.close()
104
105	basename, _ = os.path.splitext(os.path.basename(xml_file))
106
107	try:
108	# Raises FileContentsException
109	self.load_file_and_schema(xml_file, schema_path)
110	self.current_datainfo = DataInfo()
111	# Raises FileContentsException if file doesn't meet CanSAS schema
112	self.is_cansas(self.extension)
113	self.invalid = False # If we reach this point then file must be valid CanSAS
114
115	# Parse each SASentry
116	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
117	'ns': self.cansas_defaults.get("ns")
118	})
119	# Look for a SASentry
120	self.names.append("SASentry")
121	self.set_processing_instructions()
122
123	for entry in entry_list:
124	self.current_datainfo.filename = basename + self.extension
125	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
126	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
127	self._parse_entry(entry)
128	self.data_cleanup()
129	except FileContentsException as fc_exc:
130	# File doesn't meet schema - try loading with a less strict schema
131	base_name = xml_reader.__file__
132	base_name = base_name.replace("\\", "/")
133	base = base_name.split("/sas/")[0]
134	if self.cansas_version == "1.1":
135	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
136	else:
137	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
138	self.set_schema(invalid_schema)
139	if self.invalid:
140	try:
141	# Load data with less strict schema
142	self.read(xml_file, invalid_schema, False)
143
144	# File can still be read but doesn't match schema, so raise exception
145	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
146	invalid_xml = self.find_invalid_xml()
147	if invalid_xml != "":
148	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
149	raise DataReaderException(invalid_xml) # Handled by base class
150	except FileContentsException as fc_exc:
151	msg = "CanSAS Reader could not load the file {}".format(xml_file)
152	if fc_exc.message is not None: # Propagate error messages from earlier
153	msg = fc_exc.message
154	if not self.extension in self.ext: # If the file has no associated loader
155	raise DefaultReaderException(msg)
156	raise FileContentsException(msg)
157	pass
158	else:
159	raise fc_exc
160	except Exception as e: # Convert all other exceptions to FileContentsExceptions
161	raise FileContentsException(str(e))
162
163
164	def load_file_and_schema(self, xml_file, schema_path=""):
165	base_name = xml_reader.__file__
166	base_name = base_name.replace("\\", "/")
167	base = base_name.split("/sas/")[0]
168
169	# Try and parse the XML file
170	try:
171	self.set_xml_file(xml_file)
172	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
173	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
174	raise FileContentsException(msg)
175
176	self.cansas_version = self.xmlroot.get("version", "1.0")
177	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
178
179	if schema_path == "":
180	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
181	base, self.cansas_defaults.get("schema").replace("\\", "/")
182	)
183	self.set_schema(schema_path)
184
185	def is_cansas(self, ext="xml"):
186	"""
187	Checks to see if the XML file is a CanSAS file
188
189	:param ext: The file extension of the data file
190	:raises FileContentsException: Raised if XML file isn't valid CanSAS
191	"""
192	if self.validate_xml(): # Check file is valid XML
193	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
194	value = self.xmlroot.get(name)
195	# Check schema CanSAS version matches file CanSAS version
196	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
197	return True
198	if ext == "svs":
199	return True # Why is this required?
200	# If we get to this point then file isn't valid CanSAS
201	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
202	raise FileContentsException("The file is not valid CanSAS")
203
204	def _parse_entry(self, dom, recurse=False):
205	if not self._is_call_local() and not recurse:
206	self.reset_state()
207	self.data = []
208	self.current_datainfo = DataInfo()
209	self.names.append("SASentry")
210	self.parent_class = "SASentry"
211	# Create an empty dataset if no data has been passed to the reader
212	if self.current_dataset is None:
213	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
214	np.empty(0), np.empty(0))
215	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
216
217	# Loop through each child in the parent element
218	for node in dom:
219	attr = node.attrib
220	name = attr.get("name", "")
221	type = attr.get("type", "")
222	# Get the element name and set the current names level
223	tagname = node.tag.replace(self.base_ns, "")
224	tagname_original = tagname
225	# Skip this iteration when loading in save state information
226	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
227	continue
228	# Get where to store content
229	self.names.append(tagname_original)
230	self.ns_list = CONSTANTS.iterate_namespace(self.names)
231	# If the element is a child element, recurse
232	if len(node.getchildren()) > 0:
233	self.parent_class = tagname_original
234	if tagname == 'SASdata':
235	self._initialize_new_data_set(node)
236	if isinstance(self.current_dataset, plottable_2D):
237	x_bins = attr.get("x_bins", "")
238	y_bins = attr.get("y_bins", "")
239	if x_bins is not "" and y_bins is not "":
240	self.current_dataset.shape = (x_bins, y_bins)
241	else:
242	self.current_dataset.shape = ()
243	# Recurse to access data within the group
244	self._parse_entry(node, recurse=True)
245	if tagname == "SASsample":
246	self.current_datainfo.sample.name = name
247	elif tagname == "beam_size":
248	self.current_datainfo.source.beam_size_name = name
249	elif tagname == "SAScollimation":
250	self.collimation.name = name
251	elif tagname == "aperture":
252	self.aperture.name = name
253	self.aperture.type = type
254	self._add_intermediate()
255	else:
256	if isinstance(self.current_dataset, plottable_2D):
257	data_point = node.text
258	unit = attr.get('unit', '')
259	else:
260	data_point, unit = self._get_node_value(node, tagname)
261
262	# If this is a dataset, store the data appropriately
263	if tagname == 'Run':
264	self.current_datainfo.run_name[data_point] = name
265	self.current_datainfo.run.append(data_point)
266	elif tagname == 'Title':
267	self.current_datainfo.title = data_point
268	elif tagname == 'SASnote':
269	self.current_datainfo.notes.append(data_point)
270
271	# I and Q points
272	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
273	self.current_dataset.yaxis("Intensity", unit)
274	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
275	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
276	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
277	elif tagname == 'Q':
278	self.current_dataset.xaxis("Q", unit)
279	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
280	elif tagname == 'Qdev':
281	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
282	elif tagname == 'dQw':
283	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
284	elif tagname == 'dQl':
285	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
286	elif tagname == 'Qmean':
287	pass
288	elif tagname == 'Shadowfactor':
289	pass
290	elif tagname == 'Sesans':
291	self.current_datainfo.isSesans = bool(data_point)
292	self.current_dataset.xaxis(attr.get('x_axis'),
293	attr.get('x_unit'))
294	self.current_dataset.yaxis(attr.get('y_axis'),
295	attr.get('y_unit'))
296	elif tagname == 'yacceptance':
297	self.current_datainfo.sample.yacceptance = (data_point, unit)
298	elif tagname == 'zacceptance':
299	self.current_datainfo.sample.zacceptance = (data_point, unit)
300
301	# I and Qx, Qy - 2D data
302	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
303	self.current_dataset.yaxis("Intensity", unit)
304	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
306	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
307	elif tagname == 'Qx':
308	self.current_dataset.xaxis("Qx", unit)
309	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
310	elif tagname == 'Qy':
311	self.current_dataset.yaxis("Qy", unit)
312	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
313	elif tagname == 'Qxdev':
314	self.current_dataset.xaxis("Qxdev", unit)
315	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
316	elif tagname == 'Qydev':
317	self.current_dataset.yaxis("Qydev", unit)
318	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
319	elif tagname == 'Mask':
320	inter = [item == "1" for item in data_point.split(",")]
321	self.current_dataset.mask = np.asarray(inter, dtype=bool)
322
323	# Sample Information
324	elif tagname == 'ID' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.ID = data_point
326	elif tagname == 'Title' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.name = data_point
328	elif tagname == 'thickness' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.thickness = data_point
330	self.current_datainfo.sample.thickness_unit = unit
331	elif tagname == 'transmission' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.transmission = data_point
333	elif tagname == 'temperature' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.temperature = data_point
335	self.current_datainfo.sample.temperature_unit = unit
336	elif tagname == 'details' and self.parent_class == 'SASsample':
337	self.current_datainfo.sample.details.append(data_point)
338	elif tagname == 'x' and self.parent_class == 'position':
339	self.current_datainfo.sample.position.x = data_point
340	self.current_datainfo.sample.position_unit = unit
341	elif tagname == 'y' and self.parent_class == 'position':
342	self.current_datainfo.sample.position.y = data_point
343	self.current_datainfo.sample.position_unit = unit
344	elif tagname == 'z' and self.parent_class == 'position':
345	self.current_datainfo.sample.position.z = data_point
346	self.current_datainfo.sample.position_unit = unit
347	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
348	self.current_datainfo.sample.orientation.x = data_point
349	self.current_datainfo.sample.orientation_unit = unit
350	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
351	self.current_datainfo.sample.orientation.y = data_point
352	self.current_datainfo.sample.orientation_unit = unit
353	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
354	self.current_datainfo.sample.orientation.z = data_point
355	self.current_datainfo.sample.orientation_unit = unit
356
357	# Instrumental Information
358	elif tagname == 'name' and self.parent_class == 'SASinstrument':
359	self.current_datainfo.instrument = data_point
360
361	# Detector Information
362	elif tagname == 'name' and self.parent_class == 'SASdetector':
363	self.detector.name = data_point
364	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
365	self.detector.distance = data_point
366	self.detector.distance_unit = unit
367	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
368	self.detector.slit_length = data_point
369	self.detector.slit_length_unit = unit
370	elif tagname == 'x' and self.parent_class == 'offset':
371	self.detector.offset.x = data_point
372	self.detector.offset_unit = unit
373	elif tagname == 'y' and self.parent_class == 'offset':
374	self.detector.offset.y = data_point
375	self.detector.offset_unit = unit
376	elif tagname == 'z' and self.parent_class == 'offset':
377	self.detector.offset.z = data_point
378	self.detector.offset_unit = unit
379	elif tagname == 'x' and self.parent_class == 'beam_center':
380	self.detector.beam_center.x = data_point
381	self.detector.beam_center_unit = unit
382	elif tagname == 'y' and self.parent_class == 'beam_center':
383	self.detector.beam_center.y = data_point
384	self.detector.beam_center_unit = unit
385	elif tagname == 'z' and self.parent_class == 'beam_center':
386	self.detector.beam_center.z = data_point
387	self.detector.beam_center_unit = unit
388	elif tagname == 'x' and self.parent_class == 'pixel_size':
389	self.detector.pixel_size.x = data_point
390	self.detector.pixel_size_unit = unit
391	elif tagname == 'y' and self.parent_class == 'pixel_size':
392	self.detector.pixel_size.y = data_point
393	self.detector.pixel_size_unit = unit
394	elif tagname == 'z' and self.parent_class == 'pixel_size':
395	self.detector.pixel_size.z = data_point
396	self.detector.pixel_size_unit = unit
397	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
398	self.detector.orientation.x = data_point
399	self.detector.orientation_unit = unit
400	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
401	self.detector.orientation.y = data_point
402	self.detector.orientation_unit = unit
403	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
404	self.detector.orientation.z = data_point
405	self.detector.orientation_unit = unit
406
407	# Collimation and Aperture
408	elif tagname == 'length' and self.parent_class == 'SAScollimation':
409	self.collimation.length = data_point
410	self.collimation.length_unit = unit
411	elif tagname == 'name' and self.parent_class == 'SAScollimation':
412	self.collimation.name = data_point
413	elif tagname == 'distance' and self.parent_class == 'aperture':
414	self.aperture.distance = data_point
415	self.aperture.distance_unit = unit
416	elif tagname == 'x' and self.parent_class == 'size':
417	self.aperture.size.x = data_point
418	self.collimation.size_unit = unit
419	elif tagname == 'y' and self.parent_class == 'size':
420	self.aperture.size.y = data_point
421	self.collimation.size_unit = unit
422	elif tagname == 'z' and self.parent_class == 'size':
423	self.aperture.size.z = data_point
424	self.collimation.size_unit = unit
425
426	# Process Information
427	elif tagname == 'name' and self.parent_class == 'SASprocess':
428	self.process.name = data_point
429	elif tagname == 'description' and self.parent_class == 'SASprocess':
430	self.process.description = data_point
431	elif tagname == 'date' and self.parent_class == 'SASprocess':
432	try:
433	self.process.date = datetime.datetime.fromtimestamp(data_point)
434	except:
435	self.process.date = data_point
436	elif tagname == 'SASprocessnote':
437	self.process.notes.append(data_point)
438	elif tagname == 'term' and self.parent_class == 'SASprocess':
439	unit = attr.get("unit", "")
440	dic = { "name": name, "value": data_point, "unit": unit }
441	self.process.term.append(dic)
442
443	# Transmission Spectrum
444	elif tagname == 'T' and self.parent_class == 'Tdata':
445	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
446	self.transspectrum.transmission_unit = unit
447	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
448	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
449	self.transspectrum.transmission_deviation_unit = unit
450	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
451	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
452	self.transspectrum.wavelength_unit = unit
453
454	# Source Information
455	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
456	self.current_datainfo.source.wavelength = data_point
457	self.current_datainfo.source.wavelength_unit = unit
458	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
459	self.current_datainfo.source.wavelength_min = data_point
460	self.current_datainfo.source.wavelength_min_unit = unit
461	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
462	self.current_datainfo.source.wavelength_max = data_point
463	self.current_datainfo.source.wavelength_max_unit = unit
464	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
465	self.current_datainfo.source.wavelength_spread = data_point
466	self.current_datainfo.source.wavelength_spread_unit = unit
467	elif tagname == 'x' and self.parent_class == 'beam_size':
468	self.current_datainfo.source.beam_size.x = data_point
469	self.current_datainfo.source.beam_size_unit = unit
470	elif tagname == 'y' and self.parent_class == 'beam_size':
471	self.current_datainfo.source.beam_size.y = data_point
472	self.current_datainfo.source.beam_size_unit = unit
473	elif tagname == 'z' and self.parent_class == 'pixel_size':
474	self.current_datainfo.source.data_point.z = data_point
475	self.current_datainfo.source.beam_size_unit = unit
476	elif tagname == 'radiation' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.radiation = data_point
478	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
479	self.current_datainfo.source.beam_shape = data_point
480
481	# Everything else goes in meta_data
482	else:
483	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
484	self.current_datainfo.meta_data[new_key] = data_point
485
486	self.names.remove(tagname_original)
487	length = 0
488	if len(self.names) > 1:
489	length = len(self.names) - 1
490	self.parent_class = self.names[length]
491	if not self._is_call_local() and not recurse:
492	self.frm = ""
493	self.current_datainfo.errors = set()
494	for error in self.errors:
495	self.current_datainfo.errors.add(error)
496	self.data_cleanup()
497	self.sort_one_d_data()
498	self.sort_two_d_data()
499	self.reset_data_list()
500	empty = None
501	return self.output[0], empty
502
503	def data_cleanup(self):
504	"""
505	Clean up the data sets and refresh everything
506	:return: None
507	"""
508	has_error_dx = self.current_dataset.dx is not None
509	has_error_dxl = self.current_dataset.dxl is not None
510	has_error_dxw = self.current_dataset.dxw is not None
511	has_error_dy = self.current_dataset.dy is not None
512	self.remove_empty_q_values(has_error_dx=has_error_dx,
513	has_error_dxl=has_error_dxl,
514	has_error_dxw=has_error_dxw,
515	has_error_dy=has_error_dy)
516	self.send_to_output() # Combine datasets with DataInfo
517	self.current_datainfo = DataInfo() # Reset DataInfo
518
519	def _is_call_local(self):
520	if self.frm == "":
521	inter = inspect.stack()
522	self.frm = inter[2]
523	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
524	mod_name = mod_name.replace(".py", "")
525	mod = mod_name.split("sas/")
526	mod_name = mod[1]
527	if mod_name != "sascalc/dataloader/readers/cansas_reader":
528	return False
529	return True
530
531	def _add_intermediate(self):
532	"""
533	This method stores any intermediate objects within the final data set after fully reading the set.
534	"""
535	if self.parent_class == 'SASprocess':
536	self.current_datainfo.process.append(self.process)
537	self.process = Process()
538	elif self.parent_class == 'SASdetector':
539	self.current_datainfo.detector.append(self.detector)
540	self.detector = Detector()
541	elif self.parent_class == 'SAStransmission_spectrum':
542	self.current_datainfo.trans_spectrum.append(self.transspectrum)
543	self.transspectrum = TransmissionSpectrum()
544	elif self.parent_class == 'SAScollimation':
545	self.current_datainfo.collimation.append(self.collimation)
546	self.collimation = Collimation()
547	elif self.parent_class == 'aperture':
548	self.collimation.aperture.append(self.aperture)
549	self.aperture = Aperture()
550	elif self.parent_class == 'SASdata':
551	self._check_for_empty_resolution()
552	self.data.append(self.current_dataset)
553
554	def _get_node_value(self, node, tagname):
555	"""
556	Get the value of a node and any applicable units
557
558	:param node: The XML node to get the value of
559	:param tagname: The tagname of the node
560	"""
561	#Get the text from the node and convert all whitespace to spaces
562	units = ''
563	node_value = node.text
564	if node_value is not None:
565	node_value = ' '.join(node_value.split())
566	else:
567	node_value = ""
568
569	# If the value is a float, compile with units.
570	if self.ns_list.ns_datatype == "float":
571	# If an empty value is given, set as zero.
572	if node_value is None or node_value.isspace() \
573	or node_value.lower() == "nan":
574	node_value = "0.0"
575	#Convert the value to the base units
576	node_value, units = self._unit_conversion(node, tagname, node_value)
577
578	# If the value is a timestamp, convert to a datetime object
579	elif self.ns_list.ns_datatype == "timestamp":
580	if node_value is None or node_value.isspace():
581	pass
582	else:
583	try:
584	node_value = \
585	datetime.datetime.fromtimestamp(node_value)
586	except ValueError:
587	node_value = None
588	return node_value, units
589
590	def _unit_conversion(self, node, tagname, node_value):
591	"""
592	A unit converter method used to convert the data included in the file
593	to the default units listed in data_info
594
595	:param node: XML node
596	:param tagname: name of the node
597	:param node_value: The value of the current dom node
598	"""
599	attr = node.attrib
600	value_unit = ''
601	err_msg = None
602	default_unit = None
603	if not isinstance(node_value, float):
604	node_value = float(node_value)
605	if 'unit' in attr and attr.get('unit') is not None:
606	try:
607	local_unit = attr['unit']
608	unitname = self.ns_list.current_level.get("unit", "")
609	if "SASdetector" in self.names:
610	save_in = "detector"
611	elif "aperture" in self.names:
612	save_in = "aperture"
613	elif "SAScollimation" in self.names:
614	save_in = "collimation"
615	elif "SAStransmission_spectrum" in self.names:
616	save_in = "transspectrum"
617	elif "SASdata" in self.names:
618	x = np.zeros(1)
619	y = np.zeros(1)
620	self.current_data1d = Data1D(x, y)
621	save_in = "current_data1d"
622	elif "SASsource" in self.names:
623	save_in = "current_datainfo.source"
624	elif "SASsample" in self.names:
625	save_in = "current_datainfo.sample"
626	elif "SASprocess" in self.names:
627	save_in = "process"
628	else:
629	save_in = "current_datainfo"
630	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
631	if (local_unit and default_unit
632	and local_unit.lower() != default_unit.lower()
633	and local_unit.lower() != "none"):
634	# Check local units - bad units raise KeyError
635	#print("loading", tagname, node_value, local_unit, default_unit)
636	data_conv_q = Converter(local_unit)
637	value_unit = default_unit
638	node_value = data_conv_q(node_value, units=default_unit)
639	else:
640	value_unit = local_unit
641	except KeyError:
642	# Do not throw an error for loading Sesans data in cansas xml
643	# This is a temporary fix.
644	if local_unit != "A" and local_unit != 'pol':
645	err_msg = "CanSAS reader: unexpected "
646	err_msg += "\"{0}\" unit [{1}]; "
647	err_msg = err_msg.format(tagname, local_unit)
648	err_msg += "expecting [{0}]".format(default_unit)
649	value_unit = local_unit
650	except Exception:
651	err_msg = "CanSAS reader: unknown error converting "
652	err_msg += "\"{0}\" unit [{1}]"
653	err_msg = err_msg.format(tagname, local_unit)
654	value_unit = local_unit
655	elif 'unit' in attr:
656	value_unit = attr['unit']
657	if err_msg:
658	self.errors.add(err_msg)
659	return node_value, value_unit
660
661	def _check_for_empty_resolution(self):
662	"""
663	a method to check all resolution data sets are the same size as I and q
664	"""
665	dql_exists = False
666	dqw_exists = False
667	dq_exists = False
668	di_exists = False
669	if self.current_dataset.dxl is not None:
670	dql_exists = True
671	if self.current_dataset.dxw is not None:
672	dqw_exists = True
673	if self.current_dataset.dx is not None:
674	dq_exists = True
675	if self.current_dataset.dy is not None:
676	di_exists = True
677	if dqw_exists and not dql_exists:
678	array_size = self.current_dataset.dxw.size
679	self.current_dataset.dxl = np.zeros(array_size)
680	elif dql_exists and not dqw_exists:
681	array_size = self.current_dataset.dxl.size
682	self.current_dataset.dxw = np.zeros(array_size)
683	elif not dql_exists and not dqw_exists and not dq_exists:
684	array_size = self.current_dataset.x.size
685	self.current_dataset.dx = np.append(self.current_dataset.dx,
686	np.zeros([array_size]))
687	if not di_exists:
688	array_size = self.current_dataset.y.size
689	self.current_dataset.dy = np.append(self.current_dataset.dy,
690	np.zeros([array_size]))
691
692	def _initialize_new_data_set(self, node=None):
693	if node is not None:
694	for child in node:
695	if child.tag.replace(self.base_ns, "") == "Idata":
696	for i_child in child:
697	if i_child.tag.replace(self.base_ns, "") == "Qx":
698	self.current_dataset = plottable_2D()
699	return
700	self.current_dataset = plottable_1D(np.array(0), np.array(0))
701
702	## Writing Methods
703	def write(self, filename, datainfo):
704	"""
705	Write the content of a Data1D as a CanSAS XML file
706
707	:param filename: name of the file to write
708	:param datainfo: Data1D object
709	"""
710	# Create XML document
711	doc, _ = self._to_xml_doc(datainfo)
712	# Write the file
713	file_ref = open(filename, 'wb')
714	if self.encoding is None:
715	self.encoding = "UTF-8"
716	doc.write(file_ref, encoding=self.encoding,
717	pretty_print=True, xml_declaration=True)
718	file_ref.close()
719
720	def _to_xml_doc(self, datainfo):
721	"""
722	Create an XML document to contain the content of a Data1D
723
724	:param datainfo: Data1D object
725	"""
726	is_2d = False
727	if issubclass(datainfo.__class__, Data2D):
728	is_2d = True
729
730	# Get PIs and create root element
731	pi_string = self._get_pi_string()
732	# Define namespaces and create SASroot object
733	main_node = self._create_main_node()
734	# Create ElementTree, append SASroot and apply processing instructions
735	base_string = pi_string + self.to_string(main_node)
736	base_element = self.create_element_from_string(base_string)
737	doc = self.create_tree(base_element)
738	# Create SASentry Element
739	entry_node = self.create_element("SASentry")
740	root = doc.getroot()
741	root.append(entry_node)
742
743	# Add Title to SASentry
744	self.write_node(entry_node, "Title", datainfo.title)
745	# Add Run to SASentry
746	self._write_run_names(datainfo, entry_node)
747	# Add Data info to SASEntry
748	if is_2d:
749	self._write_data_2d(datainfo, entry_node)
750	else:
751	self._write_data(datainfo, entry_node)
752	# Transmission Spectrum Info
753	# TODO: fix the writer to linearize all data, including T_spectrum
754	# self._write_trans_spectrum(datainfo, entry_node)
755	# Sample info
756	self._write_sample_info(datainfo, entry_node)
757	# Instrument info
758	instr = self._write_instrument(datainfo, entry_node)
759	# Source
760	self._write_source(datainfo, instr)
761	# Collimation
762	self._write_collimation(datainfo, instr)
763	# Detectors
764	self._write_detectors(datainfo, instr)
765	# Processes info
766	self._write_process_notes(datainfo, entry_node)
767	# Note info
768	self._write_notes(datainfo, entry_node)
769	# Return the document, and the SASentry node associated with
770	# the data we just wrote
771	# If the calling function was not the cansas reader, return a minidom
772	# object rather than an lxml object.
773	self.frm = inspect.stack()[1]
774	doc, entry_node = self._check_origin(entry_node, doc)
775	return doc, entry_node
776
777	def write_node(self, parent, name, value, attr=None):
778	"""
779	:param doc: document DOM
780	:param parent: parent node
781	:param name: tag of the element
782	:param value: value of the child text node
783	:param attr: attribute dictionary
784
785	:return: True if something was appended, otherwise False
786	"""
787	if value is not None:
788	parent = self.ebuilder(parent, name, value, attr)
789	return True
790	return False
791
792	def _get_pi_string(self):
793	"""
794	Creates the processing instructions header for writing to file
795	"""
796	pis = self.return_processing_instructions()
797	if len(pis) > 0:
798	pi_tree = self.create_tree(pis[0])
799	i = 1
800	for i in range(1, len(pis) - 1):
801	pi_tree = self.append(pis[i], pi_tree)
802	pi_string = self.to_string(pi_tree)
803	else:
804	pi_string = ""
805	return pi_string
806
807	def _create_main_node(self):
808	"""
809	Creates the primary xml header used when writing to file
810	"""
811	xsi = "http://www.w3.org/2001/XMLSchema-instance"
812	version = self.cansas_version
813	n_s = CANSAS_NS.get(version).get("ns")
814	if version == "1.1":
815	url = "http://www.cansas.org/formats/1.1/"
816	else:
817	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
818	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
819	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
820	"version" : version}
821	nsmap = {'xsi' : xsi, None: n_s}
822
823	main_node = self.create_element("{" + n_s + "}SASroot",
824	attrib=attrib, nsmap=nsmap)
825	return main_node
826
827	def _write_run_names(self, datainfo, entry_node):
828	"""
829	Writes the run names to the XML file
830
831	:param datainfo: The Data1D object the information is coming from
832	:param entry_node: lxml node ElementTree object to be appended to
833	"""
834	if datainfo.run is None or datainfo.run == []:
835	datainfo.run.append(RUN_NAME_DEFAULT)
836	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
837	for item in datainfo.run:
838	runname = {}
839	if item in datainfo.run_name and \
840	len(str(datainfo.run_name[item])) > 1:
841	runname = {'name': datainfo.run_name[item]}
842	self.write_node(entry_node, "Run", item, runname)
843
844	def _write_data(self, datainfo, entry_node):
845	"""
846	Writes 1D I and Q data to the XML file
847
848	:param datainfo: The Data1D object the information is coming from
849	:param entry_node: lxml node ElementTree object to be appended to
850	"""
851	node = self.create_element("SASdata")
852	self.append(node, entry_node)
853
854	for i in range(len(datainfo.x)):
855	point = self.create_element("Idata")
856	node.append(point)
857	self.write_node(point, "Q", datainfo.x[i],
858	{'unit': datainfo.x_unit})
859	if len(datainfo.y) >= i:
860	self.write_node(point, "I", datainfo.y[i],
861	{'unit': datainfo.y_unit})
862	if datainfo.dy is not None and len(datainfo.dy) > i:
863	self.write_node(point, "Idev", datainfo.dy[i],
864	{'unit': datainfo.y_unit})
865	if datainfo.dx is not None and len(datainfo.dx) > i:
866	self.write_node(point, "Qdev", datainfo.dx[i],
867	{'unit': datainfo.x_unit})
868	if datainfo.dxw is not None and len(datainfo.dxw) > i:
869	self.write_node(point, "dQw", datainfo.dxw[i],
870	{'unit': datainfo.x_unit})
871	if datainfo.dxl is not None and len(datainfo.dxl) > i:
872	self.write_node(point, "dQl", datainfo.dxl[i],
873	{'unit': datainfo.x_unit})
874	if datainfo.isSesans:
875	sesans_attrib = {'x_axis': datainfo._xaxis,
876	'y_axis': datainfo._yaxis,
877	'x_unit': datainfo.x_unit,
878	'y_unit': datainfo.y_unit}
879	sesans = self.create_element("Sesans", attrib=sesans_attrib)
880	sesans.text = str(datainfo.isSesans)
881	entry_node.append(sesans)
882	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
883	{'unit': datainfo.sample.yacceptance[1]})
884	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
885	{'unit': datainfo.sample.zacceptance[1]})
886
887
888	def _write_data_2d(self, datainfo, entry_node):
889	"""
890	Writes 2D data to the XML file
891
892	:param datainfo: The Data2D object the information is coming from
893	:param entry_node: lxml node ElementTree object to be appended to
894	"""
895	attr = {}
896	if datainfo.data.shape:
897	attr["x_bins"] = str(len(datainfo.x_bins))
898	attr["y_bins"] = str(len(datainfo.y_bins))
899	node = self.create_element("SASdata", attr)
900	self.append(node, entry_node)
901
902	point = self.create_element("Idata")
903	node.append(point)
904	qx = ','.join(str(v) for v in datainfo.qx_data)
905	qy = ','.join(str(v) for v in datainfo.qy_data)
906	intensity = ','.join(str(v) for v in datainfo.data)
907
908	self.write_node(point, "Qx", qx,
909	{'unit': datainfo._xunit})
910	self.write_node(point, "Qy", qy,
911	{'unit': datainfo._yunit})
912	self.write_node(point, "I", intensity,
913	{'unit': datainfo._zunit})
914	if datainfo.err_data is not None:
915	err = ','.join(str(v) for v in datainfo.err_data)
916	self.write_node(point, "Idev", err,
917	{'unit': datainfo._zunit})
918	if datainfo.dqy_data is not None:
919	dqy = ','.join(str(v) for v in datainfo.dqy_data)
920	self.write_node(point, "Qydev", dqy,
921	{'unit': datainfo._yunit})
922	if datainfo.dqx_data is not None:
923	dqx = ','.join(str(v) for v in datainfo.dqx_data)
924	self.write_node(point, "Qxdev", dqx,
925	{'unit': datainfo._xunit})
926	if datainfo.mask is not None:
927	mask = ','.join("1" if v else "0" for v in 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 ValueError:
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	# TODO: why split() when accessing unit, but not when setting value?
1281	local_unit = getattr(storage, toks[0]+"_unit")
1282	if local_unit is not None and units.lower() != local_unit.lower():
1283	try:
1284	conv = Converter(units)
1285	setattrchain(storage, variable, conv(value, units=local_unit))
1286	except Exception:
1287	_, exc_value, _ = sys.exc_info()
1288	err_mess = "CanSAS reader: could not convert"
1289	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1290	% (variable, units, local_unit, exc_value)
1291	self.errors.add(err_mess)
1292	if optional:
1293	logger.info(err_mess)
1294	else:
1295	raise ValueError(err_mess)
1296	else:
1297	setattrchain(storage, variable, value)
1298	else:
1299	setattrchain(storage, variable, value)
1300
1301	# DO NOT REMOVE - used in saving and loading panel states.
1302	def _store_content(self, location, node, variable, storage):
1303	"""
1304	Get the content of a xpath location and store
1305	the result. The value is treated as a string.
1306
1307	The xpath location might or might not exist.
1308	If it does not exist, nothing is done
1309
1310	:param location: xpath location to fetch
1311	:param node: node to read the data from
1312	:param variable: name of the data member to store it in [string]
1313	:param storage: data object that has the 'variable' data member
1314
1315	:return: return a list of errors
1316	"""
1317	entry = get_content(location, node)
1318	if entry is not None and entry.text is not None:
1319	setattrchain(storage, variable, entry.text.strip())
1320
1321	# DO NOT REMOVE Called by outside packages:
1322	# sas.sasgui.perspectives.invariant.invariant_state
1323	# sas.sasgui.perspectives.fitting.pagestate
1324	def get_content(location, node):
1325	"""
1326	Get the first instance of the content of a xpath location.
1327
1328	:param location: xpath location
1329	:param node: node to start at
1330
1331	:return: Element, or None
1332	"""
1333	nodes = node.xpath(location,
1334	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1335	if len(nodes) > 0:
1336	return nodes[0]
1337	else:
1338	return None
1339
1340	# DO NOT REMOVE Called by outside packages:
1341	# sas.sasgui.perspectives.fitting.pagestate
1342	def write_node(doc, parent, name, value, attr=None):
1343	"""
1344	:param doc: document DOM
1345	:param parent: parent node
1346	:param name: tag of the element
1347	:param value: value of the child text node
1348	:param attr: attribute dictionary
1349
1350	:return: True if something was appended, otherwise False
1351	"""
1352	if attr is None:
1353	attr = {}
1354	if value is not None:
1355	node = doc.createElement(name)
1356	node.appendChild(doc.createTextNode(str(value)))
1357	for item in attr:
1358	node.setAttribute(item, attr[item])
1359	parent.appendChild(node)
1360	return True
1361	return False
1362
1363	def getattrchain(obj, chain, default=None):
1364	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
1365	for part in chain.split('.'):
1366	if hasattr(obj, part):
1367	obj = getattr(obj, part, None)
1368	else:
1369	return default
1370	return obj
1371
1372	def setattrchain(obj, chain, value):
1373	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
1374	parts = list(chain.split('.'))
1375	for part in parts[-1]:
1376	obj = getattr(obj, part, None)
1377	if obj is None:
1378	raise ValueError("missing parent object "+part)
1379	setattr(obj, value)

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

SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 9efdb29

Download in other formats: