cansas_reader.py @ 3ece5dd

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 3ece5dd was 3ece5dd, checked in by lewis, 7 years ago
Raise and catch correct exceptions in CanSAS XML reader
Property mode set to `100644`
File size: 71.1 KB

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1	"""
2	CanSAS data reader - new recursive cansas_version.
3	"""
4	############################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#If you use DANSE applications to do scientific research that leads to
9	#publication, we ask that you acknowledge the use of the software with the
10	#following sentence:
11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
12	#copyright 2008,2009 University of Tennessee
13	#############################################################################
14
15	import logging
16	import numpy as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
23	plottable_1D, plottable_2D
24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
25	Detector, Process, Aperture
26	from sas.sascalc.dataloader.data_info import \
27	combine_data_info_with_plottable as combine_data
28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
31	from sas.sascalc.dataloader.loader_exceptions import FileContentsException, \
32	DefaultReaderException, DataReaderException
33
34	# The following 2 imports ARE used. Do not remove either.
35	import xml.dom.minidom
36	from xml.dom.minidom import parseString
37
38	logger = logging.getLogger(__name__)
39
40	PREPROCESS = "xmlpreprocess"
41	ENCODING = "encoding"
42	RUN_NAME_DEFAULT = "None"
43	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
44	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
45	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
46	"as much of the data as possible.\n\n"
47	HAS_CONVERTER = True
48	try:
49	from sas.sascalc.data_util.nxsunit import Converter
50	except ImportError:
51	HAS_CONVERTER = False
52
53	CONSTANTS = CansasConstants()
54	CANSAS_FORMAT = CONSTANTS.format
55	CANSAS_NS = CONSTANTS.names
56	ALLOW_ALL = True
57
58	class Reader(XMLreader):
59	"""
60	Class to load cansas 1D XML files
61
62	:Dependencies:
63	The CanSAS reader requires PyXML 0.8.4 or later.
64	"""
65	# CanSAS version - defaults to version 1.0
66	cansas_version = "1.0"
67	base_ns = "{cansas1d/1.0}"
68	cansas_defaults = None
69	type_name = "canSAS"
70	invalid = True
71	frm = ""
72	# Log messages and errors
73	logging = None
74	errors = set()
75	# Namespace hierarchy for current xml_file object
76	names = None
77	ns_list = None
78	# Temporary storage location for loading multiple data sets in a single file
79	current_datainfo = None
80	current_dataset = None
81	current_data1d = None
82	data = None
83	# List of data1D objects to be sent back to SasView
84	output = None
85	# Wildcards
86	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
87	# List of allowed extensions
88	ext = ['.xml', '.XML', '.svs', '.SVS']
89	# Flag to bypass extension check
90	allow_all = True
91
92	def reset_state(self):
93	"""
94	Resets the class state to a base case when loading a new data file so previous
95	data files do not appear a second time
96	"""
97	self.current_datainfo = None
98	self.current_dataset = None
99	self.current_data1d = None
100	self.data = []
101	self.process = Process()
102	self.transspectrum = TransmissionSpectrum()
103	self.aperture = Aperture()
104	self.collimation = Collimation()
105	self.detector = Detector()
106	self.names = []
107	self.cansas_defaults = {}
108	self.output = []
109	self.ns_list = None
110	self.logging = []
111	self.encoding = None
112
113	def read(self, xml_file, schema_path="", invalid=True):
114	"""
115	Validate and read in an xml_file file in the canSAS format.
116
117	:param xml_file: A canSAS file path in proper XML format
118	:param schema_path: A file path to an XML schema to validate the xml_file against
119	"""
120	# For every file loaded, reset everything to a base state
121	self.reset_state()
122	self.invalid = invalid
123	# Check that the file exists
124	if os.path.isfile(xml_file):
125	basename, extension = os.path.splitext(os.path.basename(xml_file))
126	try:
127	# Get the file location of
128	self.load_file_and_schema(xml_file, schema_path)
129	self.add_data_set()
130	# Try to load the file, but raise an error if unable to.
131	# Check the file matches the XML schema
132	self.is_cansas(extension) # Raises FileContentsException if not CanSAS
133	self.invalid = False
134	# Get each SASentry from XML file and add it to a list.
135	entry_list = self.xmlroot.xpath(
136	'/ns:SASroot/ns:SASentry',
137	namespaces={'ns': self.cansas_defaults.get("ns")})
138	self.names.append("SASentry")
139
140	# Get all preprocessing events and encoding
141	self.set_processing_instructions()
142
143	# Parse each <SASentry> item
144	for entry in entry_list:
145	# Create a new DataInfo object for every <SASentry>
146
147	# Set the file name and then parse the entry.
148	self.current_datainfo.filename = basename + extension
149	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
150	self.current_datainfo.meta_data[PREPROCESS] = \
151	self.processing_instructions
152
153	# Parse the XML SASentry
154	self._parse_entry(entry)
155	# Combine datasets with datainfo
156	self.add_data_set()
157	except FileContentsException as fc_exc:
158	try:
159	# If the file does not match the schema, raise this error
160	invalid_xml = self.find_invalid_xml()
161	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
162	self.errors.add(invalid_xml)
163	# Try again with an invalid CanSAS schema, that requires only a data set in each
164	base_name = xml_reader.__file__
165	base_name = base_name.replace("\\", "/")
166	base = base_name.split("/sas/")[0]
167	if self.cansas_version == "1.1":
168	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
169	else:
170	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
171	self.set_schema(invalid_schema)
172	if self.invalid:
173	self.output = self.read(xml_file, invalid_schema, False)
174	else:
175	raise fc_exc
176	except FileContentsException as fc_exc:
177	msg = "CanSAS Reader could not load the file {}".format(xml_file)
178	if not extension in self.ext:
179	raise DefaultReaderException(msg)
180	if fc_exc.message is not None:
181	msg = fc_exc.message
182	raise FileContentsException(msg)
183	except Exception as e:
184	raise FileContentsException(e.message)
185	else:
186	self.output.append("Not a valid file path.")
187	# Return a list of parsed entries that dataloader can manage
188	return self.output
189
190	def _parse_entry(self, dom, recurse=False):
191	"""
192	Parse a SASEntry - new recursive method for parsing the dom of
193	the CanSAS data format. This will allow multiple data files
194	and extra nodes to be read in simultaneously.
195
196	:param dom: dom object with a namespace base of names
197	"""
198
199	if not self._is_call_local() and not recurse:
200	self.reset_state()
201	self.add_data_set()
202	self.names.append("SASentry")
203	self.parent_class = "SASentry"
204	self._check_for_empty_data()
205	self.base_ns = "{0}{1}{2}".format("{", \
206	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
207
208	# Go through each child in the parent element
209	for node in dom:
210	attr = node.attrib
211	name = attr.get("name", "")
212	type = attr.get("type", "")
213	# Get the element name and set the current names level
214	tagname = node.tag.replace(self.base_ns, "")
215	tagname_original = tagname
216	# Skip this iteration when loading in save state information
217	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
218	continue
219
220	# Get where to store content
221	self.names.append(tagname_original)
222	self.ns_list = CONSTANTS.iterate_namespace(self.names)
223	# If the element is a child element, recurse
224	if len(node.getchildren()) > 0:
225	self.parent_class = tagname_original
226	if tagname == 'SASdata':
227	self._initialize_new_data_set(node)
228	if isinstance(self.current_dataset, plottable_2D):
229	x_bins = attr.get("x_bins", "")
230	y_bins = attr.get("y_bins", "")
231	if x_bins is not "" and y_bins is not "":
232	self.current_dataset.shape = (x_bins, y_bins)
233	else:
234	self.current_dataset.shape = ()
235	# Recursion step to access data within the group
236	self._parse_entry(node, True)
237	if tagname == "SASsample":
238	self.current_datainfo.sample.name = name
239	elif tagname == "beam_size":
240	self.current_datainfo.source.beam_size_name = name
241	elif tagname == "SAScollimation":
242	self.collimation.name = name
243	elif tagname == "aperture":
244	self.aperture.name = name
245	self.aperture.type = type
246	self.add_intermediate()
247	else:
248	if isinstance(self.current_dataset, plottable_2D):
249	data_point = node.text
250	unit = attr.get('unit', '')
251	else:
252	data_point, unit = self._get_node_value(node, tagname)
253
254	# If this is a dataset, store the data appropriately
255	if tagname == 'Run':
256	self.current_datainfo.run_name[data_point] = name
257	self.current_datainfo.run.append(data_point)
258	elif tagname == 'Title':
259	self.current_datainfo.title = data_point
260	elif tagname == 'SASnote':
261	self.current_datainfo.notes.append(data_point)
262
263	# I and Q - 1D data
264	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
265	unit_list = unit.split("\|")
266	if len(unit_list) > 1:
267	self.current_dataset.yaxis(unit_list[0].strip(),
268	unit_list[1].strip())
269	else:
270	self.current_dataset.yaxis("Intensity", unit)
271	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
272	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
273	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
274	elif tagname == 'Q':
275	unit_list = unit.split("\|")
276	if len(unit_list) > 1:
277	self.current_dataset.xaxis(unit_list[0].strip(),
278	unit_list[1].strip())
279	else:
280	self.current_dataset.xaxis("Q", unit)
281	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
282	elif tagname == 'Qdev':
283	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
284	elif tagname == 'dQw':
285	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
286	elif tagname == 'dQl':
287	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
288	elif tagname == 'Qmean':
289	pass
290	elif tagname == 'Shadowfactor':
291	pass
292	elif tagname == 'Sesans':
293	self.current_datainfo.isSesans = bool(data_point)
294	elif tagname == 'yacceptance':
295	self.current_datainfo.sample.yacceptance = (data_point, unit)
296	elif tagname == 'zacceptance':
297	self.current_datainfo.sample.zacceptance = (data_point, unit)
298
299	# I and Qx, Qy - 2D data
300	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
301	self.current_dataset.yaxis("Intensity", unit)
302	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
303	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
304	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qx':
306	self.current_dataset.xaxis("Qx", unit)
307	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qy':
309	self.current_dataset.yaxis("Qy", unit)
310	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qxdev':
312	self.current_dataset.xaxis("Qxdev", unit)
313	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qydev':
315	self.current_dataset.yaxis("Qydev", unit)
316	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Mask':
318	inter = [item == "1" for item in data_point.split(",")]
319	self.current_dataset.mask = np.asarray(inter, dtype=bool)
320
321	# Sample Information
322	elif tagname == 'ID' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.ID = data_point
324	elif tagname == 'Title' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.name = data_point
326	elif tagname == 'thickness' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.thickness = data_point
328	self.current_datainfo.sample.thickness_unit = unit
329	elif tagname == 'transmission' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.transmission = data_point
331	elif tagname == 'temperature' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.temperature = data_point
333	self.current_datainfo.sample.temperature_unit = unit
334	elif tagname == 'details' and self.parent_class == 'SASsample':
335	self.current_datainfo.sample.details.append(data_point)
336	elif tagname == 'x' and self.parent_class == 'position':
337	self.current_datainfo.sample.position.x = data_point
338	self.current_datainfo.sample.position_unit = unit
339	elif tagname == 'y' and self.parent_class == 'position':
340	self.current_datainfo.sample.position.y = data_point
341	self.current_datainfo.sample.position_unit = unit
342	elif tagname == 'z' and self.parent_class == 'position':
343	self.current_datainfo.sample.position.z = data_point
344	self.current_datainfo.sample.position_unit = unit
345	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
346	self.current_datainfo.sample.orientation.x = data_point
347	self.current_datainfo.sample.orientation_unit = unit
348	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
349	self.current_datainfo.sample.orientation.y = data_point
350	self.current_datainfo.sample.orientation_unit = unit
351	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
352	self.current_datainfo.sample.orientation.z = data_point
353	self.current_datainfo.sample.orientation_unit = unit
354
355	# Instrumental Information
356	elif tagname == 'name' and self.parent_class == 'SASinstrument':
357	self.current_datainfo.instrument = data_point
358	# Detector Information
359	elif tagname == 'name' and self.parent_class == 'SASdetector':
360	self.detector.name = data_point
361	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
362	self.detector.distance = data_point
363	self.detector.distance_unit = unit
364	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
365	self.detector.slit_length = data_point
366	self.detector.slit_length_unit = unit
367	elif tagname == 'x' and self.parent_class == 'offset':
368	self.detector.offset.x = data_point
369	self.detector.offset_unit = unit
370	elif tagname == 'y' and self.parent_class == 'offset':
371	self.detector.offset.y = data_point
372	self.detector.offset_unit = unit
373	elif tagname == 'z' and self.parent_class == 'offset':
374	self.detector.offset.z = data_point
375	self.detector.offset_unit = unit
376	elif tagname == 'x' and self.parent_class == 'beam_center':
377	self.detector.beam_center.x = data_point
378	self.detector.beam_center_unit = unit
379	elif tagname == 'y' and self.parent_class == 'beam_center':
380	self.detector.beam_center.y = data_point
381	self.detector.beam_center_unit = unit
382	elif tagname == 'z' and self.parent_class == 'beam_center':
383	self.detector.beam_center.z = data_point
384	self.detector.beam_center_unit = unit
385	elif tagname == 'x' and self.parent_class == 'pixel_size':
386	self.detector.pixel_size.x = data_point
387	self.detector.pixel_size_unit = unit
388	elif tagname == 'y' and self.parent_class == 'pixel_size':
389	self.detector.pixel_size.y = data_point
390	self.detector.pixel_size_unit = unit
391	elif tagname == 'z' and self.parent_class == 'pixel_size':
392	self.detector.pixel_size.z = data_point
393	self.detector.pixel_size_unit = unit
394	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
395	self.detector.orientation.x = data_point
396	self.detector.orientation_unit = unit
397	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
398	self.detector.orientation.y = data_point
399	self.detector.orientation_unit = unit
400	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
401	self.detector.orientation.z = data_point
402	self.detector.orientation_unit = unit
403	# Collimation and Aperture
404	elif tagname == 'length' and self.parent_class == 'SAScollimation':
405	self.collimation.length = data_point
406	self.collimation.length_unit = unit
407	elif tagname == 'name' and self.parent_class == 'SAScollimation':
408	self.collimation.name = data_point
409	elif tagname == 'distance' and self.parent_class == 'aperture':
410	self.aperture.distance = data_point
411	self.aperture.distance_unit = unit
412	elif tagname == 'x' and self.parent_class == 'size':
413	self.aperture.size.x = data_point
414	self.collimation.size_unit = unit
415	elif tagname == 'y' and self.parent_class == 'size':
416	self.aperture.size.y = data_point
417	self.collimation.size_unit = unit
418	elif tagname == 'z' and self.parent_class == 'size':
419	self.aperture.size.z = data_point
420	self.collimation.size_unit = unit
421
422	# Process Information
423	elif tagname == 'name' and self.parent_class == 'SASprocess':
424	self.process.name = data_point
425	elif tagname == 'description' and self.parent_class == 'SASprocess':
426	self.process.description = data_point
427	elif tagname == 'date' and self.parent_class == 'SASprocess':
428	try:
429	self.process.date = datetime.datetime.fromtimestamp(data_point)
430	except:
431	self.process.date = data_point
432	elif tagname == 'SASprocessnote':
433	self.process.notes.append(data_point)
434	elif tagname == 'term' and self.parent_class == 'SASprocess':
435	unit = attr.get("unit", "")
436	dic = {}
437	dic["name"] = name
438	dic["value"] = data_point
439	dic["unit"] = unit
440	self.process.term.append(dic)
441
442	# Transmission Spectrum
443	elif tagname == 'T' and self.parent_class == 'Tdata':
444	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
445	self.transspectrum.transmission_unit = unit
446	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
447	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
448	self.transspectrum.transmission_deviation_unit = unit
449	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
450	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
451	self.transspectrum.wavelength_unit = unit
452
453	# Source Information
454	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
455	self.current_datainfo.source.wavelength = data_point
456	self.current_datainfo.source.wavelength_unit = unit
457	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
458	self.current_datainfo.source.wavelength_min = data_point
459	self.current_datainfo.source.wavelength_min_unit = unit
460	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
461	self.current_datainfo.source.wavelength_max = data_point
462	self.current_datainfo.source.wavelength_max_unit = unit
463	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
464	self.current_datainfo.source.wavelength_spread = data_point
465	self.current_datainfo.source.wavelength_spread_unit = unit
466	elif tagname == 'x' and self.parent_class == 'beam_size':
467	self.current_datainfo.source.beam_size.x = data_point
468	self.current_datainfo.source.beam_size_unit = unit
469	elif tagname == 'y' and self.parent_class == 'beam_size':
470	self.current_datainfo.source.beam_size.y = data_point
471	self.current_datainfo.source.beam_size_unit = unit
472	elif tagname == 'z' and self.parent_class == 'pixel_size':
473	self.current_datainfo.source.data_point.z = data_point
474	self.current_datainfo.source.beam_size_unit = unit
475	elif tagname == 'radiation' and self.parent_class == 'SASsource':
476	self.current_datainfo.source.radiation = data_point
477	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.beam_shape = data_point
479
480	# Everything else goes in meta_data
481	else:
482	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
483	self.current_datainfo.meta_data[new_key] = data_point
484
485	self.names.remove(tagname_original)
486	length = 0
487	if len(self.names) > 1:
488	length = len(self.names) - 1
489	self.parent_class = self.names[length]
490	if not self._is_call_local() and not recurse:
491	self.frm = ""
492	self.add_data_set()
493	empty = None
494	return self.output[0], empty
495
496
497	def _is_call_local(self):
498	"""
499
500	"""
501	if self.frm == "":
502	inter = inspect.stack()
503	self.frm = inter[2]
504	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
505	mod_name = mod_name.replace(".py", "")
506	mod = mod_name.split("sas/")
507	mod_name = mod[1]
508	if mod_name != "sascalc/dataloader/readers/cansas_reader":
509	return False
510	return True
511
512	def is_cansas(self, ext="xml"):
513	"""
514	Checks to see if the xml file is a CanSAS file
515
516	:param ext: The file extension of the data file
517	"""
518	if self.validate_xml():
519	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
520	value = self.xmlroot.get(name)
521	if CANSAS_NS.get(self.cansas_version).get("ns") == \
522	value.rsplit(" ")[0]:
523	return True
524	if ext == "svs":
525	return True
526	raise FileContentsException("Not valid CanSAS")
527
528	def load_file_and_schema(self, xml_file, schema_path=""):
529	"""
530	Loads the file and associates a schema, if a schema is passed in or if one already exists
531
532	:param xml_file: The xml file path sent to Reader.read
533	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
534	"""
535	base_name = xml_reader.__file__
536	base_name = base_name.replace("\\", "/")
537	base = base_name.split("/sas/")[0]
538
539	# Load in xml file and get the cansas version from the header
540	from lxml import etree
541	try:
542	self.set_xml_file(xml_file)
543	except etree.XMLSyntaxError:
544	msg = "Cansas cannot load {}.\n Invalid XML syntax.".format(xml_file)
545	raise FileContentsException(msg)
546	self.cansas_version = self.xmlroot.get("version", "1.0")
547
548	# Generic values for the cansas file based on the version
549	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
550	if schema_path == "":
551	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
552	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
553
554	# Link a schema to the XML file.
555	self.set_schema(schema_path)
556
557	def add_data_set(self):
558	"""
559	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
560	private method to generate a new data set.
561
562	:param key: NeXus group name for current tree level
563	"""
564
565	if self.current_datainfo and self.current_dataset:
566	self._final_cleanup()
567	self.data = []
568	self.current_datainfo = DataInfo()
569
570	def _initialize_new_data_set(self, node=None):
571	"""
572	A private class method to generate a new 1D data object.
573	Outside methods should call add_data_set() to be sure any existing data is stored properly.
574
575	:param node: XML node to determine if 1D or 2D data
576	"""
577	x = np.array(0)
578	y = np.array(0)
579	for child in node:
580	if child.tag.replace(self.base_ns, "") == "Idata":
581	for i_child in child:
582	if i_child.tag.replace(self.base_ns, "") == "Qx":
583	self.current_dataset = plottable_2D()
584	return
585	self.current_dataset = plottable_1D(x, y)
586
587	def add_intermediate(self):
588	"""
589	This method stores any intermediate objects within the final data set after fully reading the set.
590
591	:param parent: The NXclass name for the h5py Group object that just finished being processed
592	"""
593
594	if self.parent_class == 'SASprocess':
595	self.current_datainfo.process.append(self.process)
596	self.process = Process()
597	elif self.parent_class == 'SASdetector':
598	self.current_datainfo.detector.append(self.detector)
599	self.detector = Detector()
600	elif self.parent_class == 'SAStransmission_spectrum':
601	self.current_datainfo.trans_spectrum.append(self.transspectrum)
602	self.transspectrum = TransmissionSpectrum()
603	elif self.parent_class == 'SAScollimation':
604	self.current_datainfo.collimation.append(self.collimation)
605	self.collimation = Collimation()
606	elif self.parent_class == 'aperture':
607	self.collimation.aperture.append(self.aperture)
608	self.aperture = Aperture()
609	elif self.parent_class == 'SASdata':
610	self._check_for_empty_resolution()
611	self.data.append(self.current_dataset)
612
613	def _final_cleanup(self):
614	"""
615	Final cleanup of the Data1D object to be sure it has all the
616	appropriate information needed for perspectives
617	"""
618
619	# Append errors to dataset and reset class errors
620	self.current_datainfo.errors = set()
621	for error in self.errors:
622	self.current_datainfo.errors.add(error)
623	self.errors.clear()
624
625	# Combine all plottables with datainfo and append each to output
626	# Type cast data arrays to float64 and find min/max as appropriate
627	for dataset in self.data:
628	if isinstance(dataset, plottable_1D):
629	if dataset.x is not None:
630	dataset.x = np.delete(dataset.x, [0])
631	dataset.x = dataset.x.astype(np.float64)
632	dataset.xmin = np.min(dataset.x)
633	dataset.xmax = np.max(dataset.x)
634	if dataset.y is not None:
635	dataset.y = np.delete(dataset.y, [0])
636	dataset.y = dataset.y.astype(np.float64)
637	dataset.ymin = np.min(dataset.y)
638	dataset.ymax = np.max(dataset.y)
639	if dataset.dx is not None:
640	dataset.dx = np.delete(dataset.dx, [0])
641	dataset.dx = dataset.dx.astype(np.float64)
642	if dataset.dxl is not None:
643	dataset.dxl = np.delete(dataset.dxl, [0])
644	dataset.dxl = dataset.dxl.astype(np.float64)
645	if dataset.dxw is not None:
646	dataset.dxw = np.delete(dataset.dxw, [0])
647	dataset.dxw = dataset.dxw.astype(np.float64)
648	if dataset.dy is not None:
649	dataset.dy = np.delete(dataset.dy, [0])
650	dataset.dy = dataset.dy.astype(np.float64)
651	np.trim_zeros(dataset.x)
652	np.trim_zeros(dataset.y)
653	np.trim_zeros(dataset.dy)
654	elif isinstance(dataset, plottable_2D):
655	dataset.data = dataset.data.astype(np.float64)
656	dataset.qx_data = dataset.qx_data.astype(np.float64)
657	dataset.xmin = np.min(dataset.qx_data)
658	dataset.xmax = np.max(dataset.qx_data)
659	dataset.qy_data = dataset.qy_data.astype(np.float64)
660	dataset.ymin = np.min(dataset.qy_data)
661	dataset.ymax = np.max(dataset.qy_data)
662	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
663	+ dataset.qy_data * dataset.qy_data)
664	if dataset.err_data is not None:
665	dataset.err_data = dataset.err_data.astype(np.float64)
666	if dataset.dqx_data is not None:
667	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
668	if dataset.dqy_data is not None:
669	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
670	if dataset.mask is not None:
671	dataset.mask = dataset.mask.astype(dtype=bool)
672
673	if len(dataset.shape) == 2:
674	n_rows, n_cols = dataset.shape
675	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
676	dataset.x_bins = dataset.qx_data[:int(n_cols)]
677	dataset.data = dataset.data.flatten()
678	else:
679	dataset.y_bins = []
680	dataset.x_bins = []
681	dataset.data = dataset.data.flatten()
682
683	final_dataset = combine_data(dataset, self.current_datainfo)
684	self.output.append(final_dataset)
685
686	def _create_unique_key(self, dictionary, name, numb=0):
687	"""
688	Create a unique key value for any dictionary to prevent overwriting
689	Recurse until a unique key value is found.
690
691	:param dictionary: A dictionary with any number of entries
692	:param name: The index of the item to be added to dictionary
693	:param numb: The number to be appended to the name, starts at 0
694	"""
695	if dictionary.get(name) is not None:
696	numb += 1
697	name = name.split("_")[0]
698	name += "_{0}".format(numb)
699	name = self._create_unique_key(dictionary, name, numb)
700	return name
701
702	def _get_node_value(self, node, tagname):
703	"""
704	Get the value of a node and any applicable units
705
706	:param node: The XML node to get the value of
707	:param tagname: The tagname of the node
708	"""
709	#Get the text from the node and convert all whitespace to spaces
710	units = ''
711	node_value = node.text
712	if node_value is not None:
713	node_value = ' '.join(node_value.split())
714	else:
715	node_value = ""
716
717	# If the value is a float, compile with units.
718	if self.ns_list.ns_datatype == "float":
719	# If an empty value is given, set as zero.
720	if node_value is None or node_value.isspace() \
721	or node_value.lower() == "nan":
722	node_value = "0.0"
723	#Convert the value to the base units
724	node_value, units = self._unit_conversion(node, tagname, node_value)
725
726	# If the value is a timestamp, convert to a datetime object
727	elif self.ns_list.ns_datatype == "timestamp":
728	if node_value is None or node_value.isspace():
729	pass
730	else:
731	try:
732	node_value = \
733	datetime.datetime.fromtimestamp(node_value)
734	except ValueError:
735	node_value = None
736	return node_value, units
737
738	def _unit_conversion(self, node, tagname, node_value):
739	"""
740	A unit converter method used to convert the data included in the file
741	to the default units listed in data_info
742
743	:param node: XML node
744	:param tagname: name of the node
745	:param node_value: The value of the current dom node
746	"""
747	attr = node.attrib
748	value_unit = ''
749	err_msg = None
750	default_unit = None
751	if not isinstance(node_value, float):
752	node_value = float(node_value)
753	if 'unit' in attr and attr.get('unit') is not None:
754	try:
755	local_unit = attr['unit']
756	unitname = self.ns_list.current_level.get("unit", "")
757	if "SASdetector" in self.names:
758	save_in = "detector"
759	elif "aperture" in self.names:
760	save_in = "aperture"
761	elif "SAScollimation" in self.names:
762	save_in = "collimation"
763	elif "SAStransmission_spectrum" in self.names:
764	save_in = "transspectrum"
765	elif "SASdata" in self.names:
766	x = np.zeros(1)
767	y = np.zeros(1)
768	self.current_data1d = Data1D(x, y)
769	save_in = "current_data1d"
770	elif "SASsource" in self.names:
771	save_in = "current_datainfo.source"
772	elif "SASsample" in self.names:
773	save_in = "current_datainfo.sample"
774	elif "SASprocess" in self.names:
775	save_in = "process"
776	else:
777	save_in = "current_datainfo"
778	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
779	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
780	and local_unit.lower() != "none":
781	if HAS_CONVERTER == True:
782	# Check local units - bad units raise KeyError
783	data_conv_q = Converter(local_unit)
784	value_unit = default_unit
785	node_value = data_conv_q(node_value, units=default_unit)
786	else:
787	value_unit = local_unit
788	err_msg = "Unit converter is not available.\n"
789	else:
790	value_unit = local_unit
791	except KeyError:
792	err_msg = "CanSAS reader: unexpected "
793	err_msg += "\"{0}\" unit [{1}]; "
794	err_msg = err_msg.format(tagname, local_unit)
795	err_msg += "expecting [{0}]".format(default_unit)
796	value_unit = local_unit
797	except:
798	err_msg = "CanSAS reader: unknown error converting "
799	err_msg += "\"{0}\" unit [{1}]"
800	err_msg = err_msg.format(tagname, local_unit)
801	value_unit = local_unit
802	elif 'unit' in attr:
803	value_unit = attr['unit']
804	if err_msg:
805	self.errors.add(err_msg)
806	return node_value, value_unit
807
808	def _check_for_empty_data(self):
809	"""
810	Creates an empty data set if no data is passed to the reader
811
812	:param data1d: presumably a Data1D object
813	"""
814	if self.current_dataset is None:
815	x_vals = np.empty(0)
816	y_vals = np.empty(0)
817	dx_vals = np.empty(0)
818	dy_vals = np.empty(0)
819	dxl = np.empty(0)
820	dxw = np.empty(0)
821	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
822	self.current_dataset.dxl = dxl
823	self.current_dataset.dxw = dxw
824
825	def _check_for_empty_resolution(self):
826	"""
827	A method to check all resolution data sets are the same size as I and Q
828	"""
829	if isinstance(self.current_dataset, plottable_1D):
830	dql_exists = False
831	dqw_exists = False
832	dq_exists = False
833	di_exists = False
834	if self.current_dataset.dxl is not None:
835	dql_exists = True
836	if self.current_dataset.dxw is not None:
837	dqw_exists = True
838	if self.current_dataset.dx is not None:
839	dq_exists = True
840	if self.current_dataset.dy is not None:
841	di_exists = True
842	if dqw_exists and not dql_exists:
843	array_size = self.current_dataset.dxw.size - 1
844	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
845	np.zeros([array_size]))
846	elif dql_exists and not dqw_exists:
847	array_size = self.current_dataset.dxl.size - 1
848	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
849	np.zeros([array_size]))
850	elif not dql_exists and not dqw_exists and not dq_exists:
851	array_size = self.current_dataset.x.size - 1
852	self.current_dataset.dx = np.append(self.current_dataset.dx,
853	np.zeros([array_size]))
854	if not di_exists:
855	array_size = self.current_dataset.y.size - 1
856	self.current_dataset.dy = np.append(self.current_dataset.dy,
857	np.zeros([array_size]))
858	elif isinstance(self.current_dataset, plottable_2D):
859	dqx_exists = False
860	dqy_exists = False
861	di_exists = False
862	mask_exists = False
863	if self.current_dataset.dqx_data is not None:
864	dqx_exists = True
865	if self.current_dataset.dqy_data is not None:
866	dqy_exists = True
867	if self.current_dataset.err_data is not None:
868	di_exists = True
869	if self.current_dataset.mask is not None:
870	mask_exists = True
871	if not dqy_exists:
872	array_size = self.current_dataset.qy_data.size - 1
873	self.current_dataset.dqy_data = np.append(
874	self.current_dataset.dqy_data, np.zeros([array_size]))
875	if not dqx_exists:
876	array_size = self.current_dataset.qx_data.size - 1
877	self.current_dataset.dqx_data = np.append(
878	self.current_dataset.dqx_data, np.zeros([array_size]))
879	if not di_exists:
880	array_size = self.current_dataset.data.size - 1
881	self.current_dataset.err_data = np.append(
882	self.current_dataset.err_data, np.zeros([array_size]))
883	if not mask_exists:
884	array_size = self.current_dataset.data.size - 1
885	self.current_dataset.mask = np.append(
886	self.current_dataset.mask,
887	np.ones([array_size] ,dtype=bool))
888
889	####### All methods below are for writing CanSAS XML files #######
890
891	def write(self, filename, datainfo):
892	"""
893	Write the content of a Data1D as a CanSAS XML file
894
895	:param filename: name of the file to write
896	:param datainfo: Data1D object
897	"""
898	# Create XML document
899	doc, _ = self._to_xml_doc(datainfo)
900	# Write the file
901	file_ref = open(filename, 'w')
902	if self.encoding is None:
903	self.encoding = "UTF-8"
904	doc.write(file_ref, encoding=self.encoding,
905	pretty_print=True, xml_declaration=True)
906	file_ref.close()
907
908	def _to_xml_doc(self, datainfo):
909	"""
910	Create an XML document to contain the content of a Data1D
911
912	:param datainfo: Data1D object
913	"""
914	is_2d = False
915	if issubclass(datainfo.__class__, Data2D):
916	is_2d = True
917
918	# Get PIs and create root element
919	pi_string = self._get_pi_string()
920	# Define namespaces and create SASroot object
921	main_node = self._create_main_node()
922	# Create ElementTree, append SASroot and apply processing instructions
923	base_string = pi_string + self.to_string(main_node)
924	base_element = self.create_element_from_string(base_string)
925	doc = self.create_tree(base_element)
926	# Create SASentry Element
927	entry_node = self.create_element("SASentry")
928	root = doc.getroot()
929	root.append(entry_node)
930
931	# Add Title to SASentry
932	self.write_node(entry_node, "Title", datainfo.title)
933	# Add Run to SASentry
934	self._write_run_names(datainfo, entry_node)
935	# Add Data info to SASEntry
936	if is_2d:
937	self._write_data_2d(datainfo, entry_node)
938	else:
939	self._write_data(datainfo, entry_node)
940	# Transmission Spectrum Info
941	# TODO: fix the writer to linearize all data, including T_spectrum
942	# self._write_trans_spectrum(datainfo, entry_node)
943	# Sample info
944	self._write_sample_info(datainfo, entry_node)
945	# Instrument info
946	instr = self._write_instrument(datainfo, entry_node)
947	# Source
948	self._write_source(datainfo, instr)
949	# Collimation
950	self._write_collimation(datainfo, instr)
951	# Detectors
952	self._write_detectors(datainfo, instr)
953	# Processes info
954	self._write_process_notes(datainfo, entry_node)
955	# Note info
956	self._write_notes(datainfo, entry_node)
957	# Return the document, and the SASentry node associated with
958	# the data we just wrote
959	# If the calling function was not the cansas reader, return a minidom
960	# object rather than an lxml object.
961	self.frm = inspect.stack()[1]
962	doc, entry_node = self._check_origin(entry_node, doc)
963	return doc, entry_node
964
965	def write_node(self, parent, name, value, attr=None):
966	"""
967	:param doc: document DOM
968	:param parent: parent node
969	:param name: tag of the element
970	:param value: value of the child text node
971	:param attr: attribute dictionary
972
973	:return: True if something was appended, otherwise False
974	"""
975	if value is not None:
976	parent = self.ebuilder(parent, name, value, attr)
977	return True
978	return False
979
980	def _get_pi_string(self):
981	"""
982	Creates the processing instructions header for writing to file
983	"""
984	pis = self.return_processing_instructions()
985	if len(pis) > 0:
986	pi_tree = self.create_tree(pis[0])
987	i = 1
988	for i in range(1, len(pis) - 1):
989	pi_tree = self.append(pis[i], pi_tree)
990	pi_string = self.to_string(pi_tree)
991	else:
992	pi_string = ""
993	return pi_string
994
995	def _create_main_node(self):
996	"""
997	Creates the primary xml header used when writing to file
998	"""
999	xsi = "http://www.w3.org/2001/XMLSchema-instance"
1000	version = self.cansas_version
1001	n_s = CANSAS_NS.get(version).get("ns")
1002	if version == "1.1":
1003	url = "http://www.cansas.org/formats/1.1/"
1004	else:
1005	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
1006	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1007	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1008	"version" : version}
1009	nsmap = {'xsi' : xsi, None: n_s}
1010
1011	main_node = self.create_element("{" + n_s + "}SASroot",
1012	attrib=attrib, nsmap=nsmap)
1013	return main_node
1014
1015	def _write_run_names(self, datainfo, entry_node):
1016	"""
1017	Writes the run names to the XML file
1018
1019	:param datainfo: The Data1D object the information is coming from
1020	:param entry_node: lxml node ElementTree object to be appended to
1021	"""
1022	if datainfo.run is None or datainfo.run == []:
1023	datainfo.run.append(RUN_NAME_DEFAULT)
1024	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1025	for item in datainfo.run:
1026	runname = {}
1027	if item in datainfo.run_name and \
1028	len(str(datainfo.run_name[item])) > 1:
1029	runname = {'name': datainfo.run_name[item]}
1030	self.write_node(entry_node, "Run", item, runname)
1031
1032	def _write_data(self, datainfo, entry_node):
1033	"""
1034	Writes 1D I and Q data to the XML file
1035
1036	:param datainfo: The Data1D object the information is coming from
1037	:param entry_node: lxml node ElementTree object to be appended to
1038	"""
1039	node = self.create_element("SASdata")
1040	self.append(node, entry_node)
1041
1042	for i in range(len(datainfo.x)):
1043	point = self.create_element("Idata")
1044	node.append(point)
1045	self.write_node(point, "Q", datainfo.x[i],
1046	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1047	if len(datainfo.y) >= i:
1048	self.write_node(point, "I", datainfo.y[i],
1049	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1050	if datainfo.dy is not None and len(datainfo.dy) > i:
1051	self.write_node(point, "Idev", datainfo.dy[i],
1052	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1053	if datainfo.dx is not None and len(datainfo.dx) > i:
1054	self.write_node(point, "Qdev", datainfo.dx[i],
1055	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1056	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1057	self.write_node(point, "dQw", datainfo.dxw[i],
1058	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1059	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1060	self.write_node(point, "dQl", datainfo.dxl[i],
1061	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1062	if datainfo.isSesans:
1063	sesans = self.create_element("Sesans")
1064	sesans.text = str(datainfo.isSesans)
1065	node.append(sesans)
1066	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
1067	{'unit': datainfo.sample.yacceptance[1]})
1068	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1069	{'unit': datainfo.sample.zacceptance[1]})
1070
1071
1072	def _write_data_2d(self, datainfo, entry_node):
1073	"""
1074	Writes 2D data to the XML file
1075
1076	:param datainfo: The Data2D object the information is coming from
1077	:param entry_node: lxml node ElementTree object to be appended to
1078	"""
1079	attr = {}
1080	if datainfo.data.shape:
1081	attr["x_bins"] = str(len(datainfo.x_bins))
1082	attr["y_bins"] = str(len(datainfo.y_bins))
1083	node = self.create_element("SASdata", attr)
1084	self.append(node, entry_node)
1085
1086	point = self.create_element("Idata")
1087	node.append(point)
1088	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1089	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1090	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1091
1092	self.write_node(point, "Qx", qx,
1093	{'unit': datainfo._xunit})
1094	self.write_node(point, "Qy", qy,
1095	{'unit': datainfo._yunit})
1096	self.write_node(point, "I", intensity,
1097	{'unit': datainfo._zunit})
1098	if datainfo.err_data is not None:
1099	err = ','.join([str(datainfo.err_data[i]) for i in
1100	xrange(len(datainfo.err_data))])
1101	self.write_node(point, "Idev", err,
1102	{'unit': datainfo._zunit})
1103	if datainfo.dqy_data is not None:
1104	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1105	xrange(len(datainfo.dqy_data))])
1106	self.write_node(point, "Qydev", dqy,
1107	{'unit': datainfo._yunit})
1108	if datainfo.dqx_data is not None:
1109	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1110	xrange(len(datainfo.dqx_data))])
1111	self.write_node(point, "Qxdev", dqx,
1112	{'unit': datainfo._xunit})
1113	if datainfo.mask is not None:
1114	mask = ','.join(
1115	["1" if datainfo.mask[i] else "0"
1116	for i in xrange(len(datainfo.mask))])
1117	self.write_node(point, "Mask", mask)
1118
1119	def _write_trans_spectrum(self, datainfo, entry_node):
1120	"""
1121	Writes the transmission spectrum data to the XML file
1122
1123	:param datainfo: The Data1D object the information is coming from
1124	:param entry_node: lxml node ElementTree object to be appended to
1125	"""
1126	for i in range(len(datainfo.trans_spectrum)):
1127	spectrum = datainfo.trans_spectrum[i]
1128	node = self.create_element("SAStransmission_spectrum",
1129	{"name" : spectrum.name})
1130	self.append(node, entry_node)
1131	if isinstance(spectrum.timestamp, datetime.datetime):
1132	node.setAttribute("timestamp", spectrum.timestamp)
1133	for i in range(len(spectrum.wavelength)):
1134	point = self.create_element("Tdata")
1135	node.append(point)
1136	self.write_node(point, "Lambda", spectrum.wavelength[i],
1137	{'unit': spectrum.wavelength_unit})
1138	self.write_node(point, "T", spectrum.transmission[i],
1139	{'unit': spectrum.transmission_unit})
1140	if spectrum.transmission_deviation is not None \
1141	and len(spectrum.transmission_deviation) >= i:
1142	self.write_node(point, "Tdev",
1143	spectrum.transmission_deviation[i],
1144	{'unit':
1145	spectrum.transmission_deviation_unit})
1146
1147	def _write_sample_info(self, datainfo, entry_node):
1148	"""
1149	Writes the sample information to the XML file
1150
1151	:param datainfo: The Data1D object the information is coming from
1152	:param entry_node: lxml node ElementTree object to be appended to
1153	"""
1154	sample = self.create_element("SASsample")
1155	if datainfo.sample.name is not None:
1156	self.write_attribute(sample, "name",
1157	str(datainfo.sample.name))
1158	self.append(sample, entry_node)
1159	self.write_node(sample, "ID", str(datainfo.sample.ID))
1160	self.write_node(sample, "thickness", datainfo.sample.thickness,
1161	{"unit": datainfo.sample.thickness_unit})
1162	self.write_node(sample, "transmission", datainfo.sample.transmission)
1163	self.write_node(sample, "temperature", datainfo.sample.temperature,
1164	{"unit": datainfo.sample.temperature_unit})
1165
1166	pos = self.create_element("position")
1167	written = self.write_node(pos,
1168	"x",
1169	datainfo.sample.position.x,
1170	{"unit": datainfo.sample.position_unit})
1171	written = written \| self.write_node( \
1172	pos, "y", datainfo.sample.position.y,
1173	{"unit": datainfo.sample.position_unit})
1174	written = written \| self.write_node( \
1175	pos, "z", datainfo.sample.position.z,
1176	{"unit": datainfo.sample.position_unit})
1177	if written == True:
1178	self.append(pos, sample)
1179
1180	ori = self.create_element("orientation")
1181	written = self.write_node(ori, "roll",
1182	datainfo.sample.orientation.x,
1183	{"unit": datainfo.sample.orientation_unit})
1184	written = written \| self.write_node( \
1185	ori, "pitch", datainfo.sample.orientation.y,
1186	{"unit": datainfo.sample.orientation_unit})
1187	written = written \| self.write_node( \
1188	ori, "yaw", datainfo.sample.orientation.z,
1189	{"unit": datainfo.sample.orientation_unit})
1190	if written == True:
1191	self.append(ori, sample)
1192
1193	for item in datainfo.sample.details:
1194	self.write_node(sample, "details", item)
1195
1196	def _write_instrument(self, datainfo, entry_node):
1197	"""
1198	Writes the instrumental information to the XML file
1199
1200	:param datainfo: The Data1D object the information is coming from
1201	:param entry_node: lxml node ElementTree object to be appended to
1202	"""
1203	instr = self.create_element("SASinstrument")
1204	self.append(instr, entry_node)
1205	self.write_node(instr, "name", datainfo.instrument)
1206	return instr
1207
1208	def _write_source(self, datainfo, instr):
1209	"""
1210	Writes the source information to the XML file
1211
1212	:param datainfo: The Data1D object the information is coming from
1213	:param instr: instrument node to be appended to
1214	"""
1215	source = self.create_element("SASsource")
1216	if datainfo.source.name is not None:
1217	self.write_attribute(source, "name",
1218	str(datainfo.source.name))
1219	self.append(source, instr)
1220	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1221	datainfo.source.radiation = "neutron"
1222	self.write_node(source, "radiation", datainfo.source.radiation)
1223
1224	size = self.create_element("beam_size")
1225	if datainfo.source.beam_size_name is not None:
1226	self.write_attribute(size, "name",
1227	str(datainfo.source.beam_size_name))
1228	written = self.write_node( \
1229	size, "x", datainfo.source.beam_size.x,
1230	{"unit": datainfo.source.beam_size_unit})
1231	written = written \| self.write_node( \
1232	size, "y", datainfo.source.beam_size.y,
1233	{"unit": datainfo.source.beam_size_unit})
1234	written = written \| self.write_node( \
1235	size, "z", datainfo.source.beam_size.z,
1236	{"unit": datainfo.source.beam_size_unit})
1237	if written == True:
1238	self.append(size, source)
1239
1240	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1241	self.write_node(source, "wavelength",
1242	datainfo.source.wavelength,
1243	{"unit": datainfo.source.wavelength_unit})
1244	self.write_node(source, "wavelength_min",
1245	datainfo.source.wavelength_min,
1246	{"unit": datainfo.source.wavelength_min_unit})
1247	self.write_node(source, "wavelength_max",
1248	datainfo.source.wavelength_max,
1249	{"unit": datainfo.source.wavelength_max_unit})
1250	self.write_node(source, "wavelength_spread",
1251	datainfo.source.wavelength_spread,
1252	{"unit": datainfo.source.wavelength_spread_unit})
1253
1254	def _write_collimation(self, datainfo, instr):
1255	"""
1256	Writes the collimation information to the XML file
1257
1258	:param datainfo: The Data1D object the information is coming from
1259	:param instr: lxml node ElementTree object to be appended to
1260	"""
1261	if datainfo.collimation == [] or datainfo.collimation is None:
1262	coll = Collimation()
1263	datainfo.collimation.append(coll)
1264	for item in datainfo.collimation:
1265	coll = self.create_element("SAScollimation")
1266	if item.name is not None:
1267	self.write_attribute(coll, "name", str(item.name))
1268	self.append(coll, instr)
1269
1270	self.write_node(coll, "length", item.length,
1271	{"unit": item.length_unit})
1272
1273	for aperture in item.aperture:
1274	apert = self.create_element("aperture")
1275	if aperture.name is not None:
1276	self.write_attribute(apert, "name", str(aperture.name))
1277	if aperture.type is not None:
1278	self.write_attribute(apert, "type", str(aperture.type))
1279	self.append(apert, coll)
1280
1281	size = self.create_element("size")
1282	if aperture.size_name is not None:
1283	self.write_attribute(size, "name",
1284	str(aperture.size_name))
1285	written = self.write_node(size, "x", aperture.size.x,
1286	{"unit": aperture.size_unit})
1287	written = written \| self.write_node( \
1288	size, "y", aperture.size.y,
1289	{"unit": aperture.size_unit})
1290	written = written \| self.write_node( \
1291	size, "z", aperture.size.z,
1292	{"unit": aperture.size_unit})
1293	if written == True:
1294	self.append(size, apert)
1295
1296	self.write_node(apert, "distance", aperture.distance,
1297	{"unit": aperture.distance_unit})
1298
1299	def _write_detectors(self, datainfo, instr):
1300	"""
1301	Writes the detector information to the XML file
1302
1303	:param datainfo: The Data1D object the information is coming from
1304	:param inst: lxml instrument node to be appended to
1305	"""
1306	if datainfo.detector is None or datainfo.detector == []:
1307	det = Detector()
1308	det.name = ""
1309	datainfo.detector.append(det)
1310
1311	for item in datainfo.detector:
1312	det = self.create_element("SASdetector")
1313	written = self.write_node(det, "name", item.name)
1314	written = written \| self.write_node(det, "SDD", item.distance,
1315	{"unit": item.distance_unit})
1316	if written == True:
1317	self.append(det, instr)
1318
1319	off = self.create_element("offset")
1320	written = self.write_node(off, "x", item.offset.x,
1321	{"unit": item.offset_unit})
1322	written = written \| self.write_node(off, "y", item.offset.y,
1323	{"unit": item.offset_unit})
1324	written = written \| self.write_node(off, "z", item.offset.z,
1325	{"unit": item.offset_unit})
1326	if written == True:
1327	self.append(off, det)
1328
1329	ori = self.create_element("orientation")
1330	written = self.write_node(ori, "roll", item.orientation.x,
1331	{"unit": item.orientation_unit})
1332	written = written \| self.write_node(ori, "pitch",
1333	item.orientation.y,
1334	{"unit": item.orientation_unit})
1335	written = written \| self.write_node(ori, "yaw",
1336	item.orientation.z,
1337	{"unit": item.orientation_unit})
1338	if written == True:
1339	self.append(ori, det)
1340
1341	center = self.create_element("beam_center")
1342	written = self.write_node(center, "x", item.beam_center.x,
1343	{"unit": item.beam_center_unit})
1344	written = written \| self.write_node(center, "y",
1345	item.beam_center.y,
1346	{"unit": item.beam_center_unit})
1347	written = written \| self.write_node(center, "z",
1348	item.beam_center.z,
1349	{"unit": item.beam_center_unit})
1350	if written == True:
1351	self.append(center, det)
1352
1353	pix = self.create_element("pixel_size")
1354	written = self.write_node(pix, "x", item.pixel_size.x,
1355	{"unit": item.pixel_size_unit})
1356	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1357	{"unit": item.pixel_size_unit})
1358	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1359	{"unit": item.pixel_size_unit})
1360	if written == True:
1361	self.append(pix, det)
1362	self.write_node(det, "slit_length", item.slit_length,
1363	{"unit": item.slit_length_unit})
1364
1365
1366	def _write_process_notes(self, datainfo, entry_node):
1367	"""
1368	Writes the process notes to the XML file
1369
1370	:param datainfo: The Data1D object the information is coming from
1371	:param entry_node: lxml node ElementTree object to be appended to
1372
1373	"""
1374	for item in datainfo.process:
1375	node = self.create_element("SASprocess")
1376	self.append(node, entry_node)
1377	self.write_node(node, "name", item.name)
1378	self.write_node(node, "date", item.date)
1379	self.write_node(node, "description", item.description)
1380	for term in item.term:
1381	if isinstance(term, list):
1382	value = term['value']
1383	del term['value']
1384	elif isinstance(term, dict):
1385	value = term.get("value")
1386	del term['value']
1387	else:
1388	value = term
1389	self.write_node(node, "term", value, term)
1390	for note in item.notes:
1391	self.write_node(node, "SASprocessnote", note)
1392	if len(item.notes) == 0:
1393	self.write_node(node, "SASprocessnote", "")
1394
1395	def _write_notes(self, datainfo, entry_node):
1396	"""
1397	Writes the notes to the XML file and creates an empty note if none
1398	exist
1399
1400	:param datainfo: The Data1D object the information is coming from
1401	:param entry_node: lxml node ElementTree object to be appended to
1402
1403	"""
1404	if len(datainfo.notes) == 0:
1405	node = self.create_element("SASnote")
1406	self.append(node, entry_node)
1407	else:
1408	for item in datainfo.notes:
1409	node = self.create_element("SASnote")
1410	self.write_text(node, item)
1411	self.append(node, entry_node)
1412
1413	def _check_origin(self, entry_node, doc):
1414	"""
1415	Return the document, and the SASentry node associated with
1416	the data we just wrote.
1417	If the calling function was not the cansas reader, return a minidom
1418	object rather than an lxml object.
1419
1420	:param entry_node: lxml node ElementTree object to be appended to
1421	:param doc: entire xml tree
1422	"""
1423	if not self.frm:
1424	self.frm = inspect.stack()[1]
1425	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1426	mod_name = mod_name.replace(".py", "")
1427	mod = mod_name.split("sas/")
1428	mod_name = mod[1]
1429	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1430	string = self.to_string(doc, pretty_print=False)
1431	doc = parseString(string)
1432	node_name = entry_node.tag
1433	node_list = doc.getElementsByTagName(node_name)
1434	entry_node = node_list.item(0)
1435	return doc, entry_node
1436
1437	# DO NOT REMOVE - used in saving and loading panel states.
1438	def _store_float(self, location, node, variable, storage, optional=True):
1439	"""
1440	Get the content of a xpath location and store
1441	the result. Check that the units are compatible
1442	with the destination. The value is expected to
1443	be a float.
1444
1445	The xpath location might or might not exist.
1446	If it does not exist, nothing is done
1447
1448	:param location: xpath location to fetch
1449	:param node: node to read the data from
1450	:param variable: name of the data member to store it in [string]
1451	:param storage: data object that has the 'variable' data member
1452	:param optional: if True, no exception will be raised
1453	if unit conversion can't be done
1454
1455	:raise ValueError: raised when the units are not recognized
1456	"""
1457	entry = get_content(location, node)
1458	try:
1459	value = float(entry.text)
1460	except:
1461	value = None
1462
1463	if value is not None:
1464	# If the entry has units, check to see that they are
1465	# compatible with what we currently have in the data object
1466	units = entry.get('unit')
1467	if units is not None:
1468	toks = variable.split('.')
1469	local_unit = None
1470	exec "local_unit = storage.%s_unit" % toks[0]
1471	if local_unit is not None and units.lower() != local_unit.lower():
1472	if HAS_CONVERTER == True:
1473	try:
1474	conv = Converter(units)
1475	exec "storage.%s = %g" % \
1476	(variable, conv(value, units=local_unit))
1477	except:
1478	_, exc_value, _ = sys.exc_info()
1479	err_mess = "CanSAS reader: could not convert"
1480	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1481	% (variable, units, local_unit, exc_value)
1482	self.errors.add(err_mess)
1483	if optional:
1484	logger.info(err_mess)
1485	else:
1486	raise ValueError, err_mess
1487	else:
1488	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1489	% (variable, units)
1490	err_mess += " expecting [%s]" % local_unit
1491	self.errors.add(err_mess)
1492	if optional:
1493	logger.info(err_mess)
1494	else:
1495	raise ValueError, err_mess
1496	else:
1497	exec "storage.%s = value" % variable
1498	else:
1499	exec "storage.%s = value" % variable
1500
1501	# DO NOT REMOVE - used in saving and loading panel states.
1502	def _store_content(self, location, node, variable, storage):
1503	"""
1504	Get the content of a xpath location and store
1505	the result. The value is treated as a string.
1506
1507	The xpath location might or might not exist.
1508	If it does not exist, nothing is done
1509
1510	:param location: xpath location to fetch
1511	:param node: node to read the data from
1512	:param variable: name of the data member to store it in [string]
1513	:param storage: data object that has the 'variable' data member
1514
1515	:return: return a list of errors
1516	"""
1517	entry = get_content(location, node)
1518	if entry is not None and entry.text is not None:
1519	exec "storage.%s = entry.text.strip()" % variable
1520
1521
1522	# DO NOT REMOVE Called by outside packages:
1523	# sas.sasgui.perspectives.invariant.invariant_state
1524	# sas.sasgui.perspectives.fitting.pagestate
1525	def get_content(location, node):
1526	"""
1527	Get the first instance of the content of a xpath location.
1528
1529	:param location: xpath location
1530	:param node: node to start at
1531
1532	:return: Element, or None
1533	"""
1534	nodes = node.xpath(location,
1535	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1536	if len(nodes) > 0:
1537	return nodes[0]
1538	else:
1539	return None
1540
1541	# DO NOT REMOVE Called by outside packages:
1542	# sas.sasgui.perspectives.fitting.pagestate
1543	def write_node(doc, parent, name, value, attr=None):
1544	"""
1545	:param doc: document DOM
1546	:param parent: parent node
1547	:param name: tag of the element
1548	:param value: value of the child text node
1549	:param attr: attribute dictionary
1550
1551	:return: True if something was appended, otherwise False
1552	"""
1553	if attr is None:
1554	attr = {}
1555	if value is not None:
1556	node = doc.createElement(name)
1557	node.appendChild(doc.createTextNode(str(value)))
1558	for item in attr:
1559	node.setAttribute(item, attr[item])
1560	parent.appendChild(node)
1561	return True
1562	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 3ece5dd

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