cansas_reader.py @ 0615d54

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 0615d54 was 0615d54, checked in by lewis, 7 years ago
Correctly set error message in CanSAS XML reader
Property mode set to `100644`
File size: 62.9 KB

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

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 0615d54

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