cansas_reader.py @ 3d6c010

Last change on this file since 3d6c010 was 3d6c010, checked in by Tim Snow <tim.snow@…>, 8 years ago
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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
32	# The following 2 imports ARE used. Do not remove either.
33	import xml.dom.minidom
34	from xml.dom.minidom import parseString
35
36	PREPROCESS = "xmlpreprocess"
37	ENCODING = "encoding"
38	RUN_NAME_DEFAULT = "None"
39	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
40	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
41	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
42	"as much of the data as possible.\n\n"
43	HAS_CONVERTER = True
44	try:
45	from sas.sascalc.data_util.nxsunit import Converter
46	except ImportError:
47	HAS_CONVERTER = False
48
49	CONSTANTS = CansasConstants()
50	CANSAS_FORMAT = CONSTANTS.format
51	CANSAS_NS = CONSTANTS.names
52	ALLOW_ALL = True
53
54	class Reader(XMLreader):
55	"""
56	Class to load cansas 1D XML files
57
58	:Dependencies:
59	The CanSAS reader requires PyXML 0.8.4 or later.
60	"""
61	# CanSAS version - defaults to version 1.0
62	cansas_version = "1.0"
63	base_ns = "{cansas1d/1.0}"
64	cansas_defaults = None
65	type_name = "canSAS"
66	invalid = True
67	frm = ""
68	# Log messages and errors
69	logging = None
70	errors = set()
71	# Namespace hierarchy for current xml_file object
72	names = None
73	ns_list = None
74	# Temporary storage location for loading multiple data sets in a single file
75	current_datainfo = None
76	current_dataset = None
77	current_data1d = None
78	data = None
79	# List of data1D objects to be sent back to SasView
80	output = None
81	# Wildcards
82	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
83	# List of allowed extensions
84	ext = ['.xml', '.XML', '.svs', '.SVS']
85	# Flag to bypass extension check
86	allow_all = True
87
88	def reset_state(self):
89	"""
90	Resets the class state to a base case when loading a new data file so previous
91	data files do not appear a second time
92	"""
93	self.current_datainfo = None
94	self.current_dataset = None
95	self.current_data1d = None
96	self.data = []
97	self.process = Process()
98	self.transspectrum = TransmissionSpectrum()
99	self.aperture = Aperture()
100	self.collimation = Collimation()
101	self.detector = Detector()
102	self.names = []
103	self.cansas_defaults = {}
104	self.output = []
105	self.ns_list = None
106	self.logging = []
107	self.encoding = None
108
109	def read(self, xml_file, schema_path="", invalid=True):
110	"""
111	Validate and read in an xml_file file in the canSAS format.
112
113	:param xml_file: A canSAS file path in proper XML format
114	:param schema_path: A file path to an XML schema to validate the xml_file against
115	"""
116	# For every file loaded, reset everything to a base state
117	self.reset_state()
118	self.invalid = invalid
119	# Check that the file exists
120	if os.path.isfile(xml_file):
121	basename, extension = os.path.splitext(os.path.basename(xml_file))
122	# If the file type is not allowed, return nothing
123	if extension in self.ext or self.allow_all:
124	# Get the file location of
125	self.load_file_and_schema(xml_file, schema_path)
126	self.add_data_set()
127	# Try to load the file, but raise an error if unable to.
128	# Check the file matches the XML schema
129	try:
130	self.is_cansas(extension)
131	self.invalid = False
132	# Get each SASentry from XML file and add it to a list.
133	entry_list = self.xmlroot.xpath(
134	'/ns:SASroot/ns:SASentry',
135	namespaces={'ns': self.cansas_defaults.get("ns")})
136	self.names.append("SASentry")
137
138	# Get all preprocessing events and encoding
139	self.set_processing_instructions()
140
141	# Parse each <SASentry> item
142	for entry in entry_list:
143	# Create a new DataInfo object for every <SASentry>
144
145	# Set the file name and then parse the entry.
146	self.current_datainfo.filename = basename + extension
147	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
148	self.current_datainfo.meta_data[PREPROCESS] = \
149	self.processing_instructions
150
151	# Parse the XML SASentry
152	self._parse_entry(entry)
153	# Combine datasets with datainfo
154	self.add_data_set()
155	except RuntimeError:
156	# If the file does not match the schema, raise this error
157	invalid_xml = self.find_invalid_xml()
158	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
159	self.errors.add(invalid_xml)
160	# Try again with an invalid CanSAS schema, that requires only a data set in each
161	base_name = xml_reader.__file__
162	base_name = base_name.replace("\\", "/")
163	base = base_name.split("/sas/")[0]
164	if self.cansas_version == "1.1":
165	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
166	else:
167	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
168	self.set_schema(invalid_schema)
169	try:
170	if self.invalid:
171	if self.is_cansas():
172	self.output = self.read(xml_file, invalid_schema, False)
173	else:
174	raise RuntimeError
175	else:
176	raise RuntimeError
177	except RuntimeError:
178	x = np.zeros(1)
179	y = np.zeros(1)
180	self.current_data1d = Data1D(x,y)
181	self.current_data1d.errors = self.errors
182	return [self.current_data1d]
183	else:
184	self.output.append("Not a valid file path.")
185	# Return a list of parsed entries that dataloader can manage
186	return self.output
187
188	def _parse_entry(self, dom, recurse=False):
189	"""
190	Parse a SASEntry - new recursive method for parsing the dom of
191	the CanSAS data format. This will allow multiple data files
192	and extra nodes to be read in simultaneously.
193
194	:param dom: dom object with a namespace base of names
195	"""
196
197	if not self._is_call_local() and not recurse:
198	self.reset_state()
199	self.add_data_set()
200	self.names.append("SASentry")
201	self.parent_class = "SASentry"
202	self._check_for_empty_data()
203	self.base_ns = "{0}{1}{2}".format("{", \
204	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
205
206	# Go through each child in the parent element
207	for node in dom:
208	attr = node.attrib
209	name = attr.get("name", "")
210	type = attr.get("type", "")
211	unit = attr.get("unit", "")
212	# Get the element name and set the current names level
213	tagname = node.tag.replace(self.base_ns, "")
214	tagname_original = tagname
215	# Skip this iteration when loading in save state information
216	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
217	continue
218
219	# Get where to store content
220	self.names.append(tagname_original)
221	self.ns_list = CONSTANTS.iterate_namespace(self.names)
222	# If the element is a child element, recurse
223	if len(node.getchildren()) > 0:
224	self.parent_class = tagname_original
225	if tagname == 'SASdata':
226	self._initialize_new_data_set(node)
227	if isinstance(self.current_dataset, plottable_2D):
228	x_bins = attr.get("x_bins", "")
229	y_bins = attr.get("y_bins", "")
230	if x_bins is not "" and y_bins is not "":
231	self.current_dataset.shape = (x_bins, y_bins)
232	else:
233	self.current_dataset.shape = ()
234	# Recursion step to access data within the group
235	self._parse_entry(node, True)
236	if tagname == "SASsample":
237	self.current_datainfo.sample.name = name
238	elif tagname == "beam_size":
239	self.current_datainfo.source.beam_size_name = name
240	elif tagname == "SAScollimation":
241	self.collimation.name = name
242	elif tagname == "aperture":
243	self.aperture.name = name
244	self.aperture.type = type
245	self.add_intermediate()
246	else:
247	if isinstance(self.current_dataset, plottable_2D):
248	data_point = node.text
249	unit = attr.get('unit', '')
250	else:
251	data_point, unit = self._get_node_value(node)
252
253	# If this is a dataset, store the data appropriately
254	if tagname == 'Run':
255	self.current_datainfo.run_name[data_point] = name
256	self.current_datainfo.run.append(data_point)
257	elif tagname == 'Title':
258	self.current_datainfo.title = data_point
259	elif tagname == 'SASnote':
260	self.current_datainfo.notes.append(data_point)
261
262	# I and Q - 1D data
263	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
264	unit_list = unit.split("\|")
265	if len(unit_list) > 1:
266	self.current_dataset.yaxis(unit_list[0].strip(),
267	unit_list[1].strip())
268	else:
269	self.current_dataset.yaxis("Intensity", unit)
270	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
271	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
272	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
273	elif tagname == 'Q':
274	unit_list = unit.split("\|")
275	if len(unit_list) > 1:
276	self.current_dataset.xaxis(unit_list[0].strip(),
277	unit_list[1].strip())
278	else:
279	self.current_dataset.xaxis("Q", unit)
280	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
281	elif tagname == 'Qdev':
282	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
283	elif tagname == 'dQw':
284	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
285	elif tagname == 'dQl':
286	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
287	elif tagname == 'Qmean':
288	pass
289	elif tagname == 'Shadowfactor':
290	pass
291	elif tagname == 'Sesans':
292	self.current_datainfo.isSesans = bool(data_point)
293	elif tagname == 'zacceptance':
294	self.current_datainfo.sample.zacceptance = (data_point, unit)
295
296	# I and Qx, Qy - 2D data
297	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
298	self.current_dataset.yaxis("Intensity", unit)
299	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
300	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
301	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
302	elif tagname == 'Qx':
303	self.current_dataset.xaxis("Qx", unit)
304	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qy':
306	self.current_dataset.yaxis("Qy", unit)
307	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qxdev':
309	self.current_dataset.xaxis("Qxdev", unit)
310	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qydev':
312	self.current_dataset.yaxis("Qydev", unit)
313	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Mask':
315	inter = [item == "1" for item in data_point.split(",")]
316	self.current_dataset.mask = np.asarray(inter, dtype=bool)
317
318	# Sample Information
319	elif tagname == 'ID' and self.parent_class == 'SASsample':
320	self.current_datainfo.sample.ID = data_point
321	elif tagname == 'Title' and self.parent_class == 'SASsample':
322	self.current_datainfo.sample.name = data_point
323	elif tagname == 'thickness' and self.parent_class == 'SASsample':
324	self.current_datainfo.sample.thickness = data_point
325	self.current_datainfo.sample.thickness_unit = unit
326	elif tagname == 'transmission' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.transmission = data_point
328	elif tagname == 'temperature' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.temperature = data_point
330	self.current_datainfo.sample.temperature_unit = unit
331	elif tagname == 'details' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.details.append(data_point)
333	elif tagname == 'x' and self.parent_class == 'position':
334	self.current_datainfo.sample.position.x = data_point
335	self.current_datainfo.sample.position_unit = unit
336	elif tagname == 'y' and self.parent_class == 'position':
337	self.current_datainfo.sample.position.y = data_point
338	self.current_datainfo.sample.position_unit = unit
339	elif tagname == 'z' and self.parent_class == 'position':
340	self.current_datainfo.sample.position.z = data_point
341	self.current_datainfo.sample.position_unit = unit
342	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
343	self.current_datainfo.sample.orientation.x = data_point
344	self.current_datainfo.sample.orientation_unit = unit
345	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
346	self.current_datainfo.sample.orientation.y = data_point
347	self.current_datainfo.sample.orientation_unit = unit
348	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
349	self.current_datainfo.sample.orientation.z = data_point
350	self.current_datainfo.sample.orientation_unit = unit
351
352	# Instrumental Information
353	elif tagname == 'name' and self.parent_class == 'SASinstrument':
354	self.current_datainfo.instrument = data_point
355	# Detector Information
356	elif tagname == 'name' and self.parent_class == 'SASdetector':
357	self.detector.name = data_point
358	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
359	self.detector.distance = data_point
360	self.detector.distance_unit = unit
361	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
362	self.detector.slit_length = data_point
363	self.detector.slit_length_unit = unit
364	elif tagname == 'x' and self.parent_class == 'offset':
365	self.detector.offset.x = data_point
366	self.detector.offset_unit = unit
367	elif tagname == 'y' and self.parent_class == 'offset':
368	self.detector.offset.y = data_point
369	self.detector.offset_unit = unit
370	elif tagname == 'z' and self.parent_class == 'offset':
371	self.detector.offset.z = data_point
372	self.detector.offset_unit = unit
373	elif tagname == 'x' and self.parent_class == 'beam_center':
374	self.detector.beam_center.x = data_point
375	self.detector.beam_center_unit = unit
376	elif tagname == 'y' and self.parent_class == 'beam_center':
377	self.detector.beam_center.y = data_point
378	self.detector.beam_center_unit = unit
379	elif tagname == 'z' and self.parent_class == 'beam_center':
380	self.detector.beam_center.z = data_point
381	self.detector.beam_center_unit = unit
382	elif tagname == 'x' and self.parent_class == 'pixel_size':
383	self.detector.pixel_size.x = data_point
384	self.detector.pixel_size_unit = unit
385	elif tagname == 'y' and self.parent_class == 'pixel_size':
386	self.detector.pixel_size.y = data_point
387	self.detector.pixel_size_unit = unit
388	elif tagname == 'z' and self.parent_class == 'pixel_size':
389	self.detector.pixel_size.z = data_point
390	self.detector.pixel_size_unit = unit
391	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
392	self.detector.orientation.x = data_point
393	self.detector.orientation_unit = unit
394	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
395	self.detector.orientation.y = data_point
396	self.detector.orientation_unit = unit
397	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
398	self.detector.orientation.z = data_point
399	self.detector.orientation_unit = unit
400	# Collimation and Aperture
401	elif tagname == 'length' and self.parent_class == 'SAScollimation':
402	self.collimation.length = data_point
403	self.collimation.length_unit = unit
404	elif tagname == 'name' and self.parent_class == 'SAScollimation':
405	self.collimation.name = data_point
406	elif tagname == 'distance' and self.parent_class == 'aperture':
407	self.aperture.distance = data_point
408	self.aperture.distance_unit = unit
409	elif tagname == 'x' and self.parent_class == 'size':
410	self.aperture.size.x = data_point
411	self.collimation.size_unit = unit
412	elif tagname == 'y' and self.parent_class == 'size':
413	self.aperture.size.y = data_point
414	self.collimation.size_unit = unit
415	elif tagname == 'z' and self.parent_class == 'size':
416	self.aperture.size.z = data_point
417	self.collimation.size_unit = unit
418
419	# Process Information
420	elif tagname == 'name' and self.parent_class == 'SASprocess':
421	self.process.name = data_point
422	elif tagname == 'description' and self.parent_class == 'SASprocess':
423	self.process.description = data_point
424	elif tagname == 'date' and self.parent_class == 'SASprocess':
425	try:
426	self.process.date = datetime.datetime.fromtimestamp(data_point)
427	except:
428	self.process.date = data_point
429	elif tagname == 'SASprocessnote':
430	self.process.notes.append(data_point)
431	elif tagname == 'term' and self.parent_class == 'SASprocess':
432	unit = attr.get("unit", "")
433	dic = {}
434	dic["name"] = name
435	dic["value"] = data_point
436	dic["unit"] = unit
437	self.process.term.append(dic)
438
439	# Transmission Spectrum
440	elif tagname == 'T' and self.parent_class == 'Tdata':
441	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
442	self.transspectrum.transmission_unit = unit
443	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
444	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
445	self.transspectrum.transmission_deviation_unit = unit
446	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
447	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
448	self.transspectrum.wavelength_unit = unit
449
450	# Source Information
451	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
452	self.current_datainfo.source.wavelength = data_point
453	self.current_datainfo.source.wavelength_unit = unit
454	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
455	self.current_datainfo.source.wavelength_min = data_point
456	self.current_datainfo.source.wavelength_min_unit = unit
457	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
458	self.current_datainfo.source.wavelength_max = data_point
459	self.current_datainfo.source.wavelength_max_unit = unit
460	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
461	self.current_datainfo.source.wavelength_spread = data_point
462	self.current_datainfo.source.wavelength_spread_unit = unit
463	elif tagname == 'x' and self.parent_class == 'beam_size':
464	self.current_datainfo.source.beam_size.x = data_point
465	self.current_datainfo.source.beam_size_unit = unit
466	elif tagname == 'y' and self.parent_class == 'beam_size':
467	self.current_datainfo.source.beam_size.y = data_point
468	self.current_datainfo.source.beam_size_unit = unit
469	elif tagname == 'z' and self.parent_class == 'pixel_size':
470	self.current_datainfo.source.data_point.z = data_point
471	self.current_datainfo.source.beam_size_unit = unit
472	elif tagname == 'radiation' and self.parent_class == 'SASsource':
473	self.current_datainfo.source.radiation = data_point
474	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
475	self.current_datainfo.source.beam_shape = data_point
476
477	# Everything else goes in meta_data
478	else:
479	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
480	self.current_datainfo.meta_data[new_key] = data_point
481
482	self.names.remove(tagname_original)
483	length = 0
484	if len(self.names) > 1:
485	length = len(self.names) - 1
486	self.parent_class = self.names[length]
487	if not self._is_call_local() and not recurse:
488	self.frm = ""
489	self.add_data_set()
490	empty = None
491	return self.output[0], empty
492
493
494	def _is_call_local(self):
495	"""
496
497	"""
498	if self.frm == "":
499	inter = inspect.stack()
500	self.frm = inter[2]
501	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
502	mod_name = mod_name.replace(".py", "")
503	mod = mod_name.split("sas/")
504	mod_name = mod[1]
505	if mod_name != "sascalc/dataloader/readers/cansas_reader":
506	return False
507	return True
508
509	def is_cansas(self, ext="xml"):
510	"""
511	Checks to see if the xml file is a CanSAS file
512
513	:param ext: The file extension of the data file
514	"""
515	if self.validate_xml():
516	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
517	value = self.xmlroot.get(name)
518	if CANSAS_NS.get(self.cansas_version).get("ns") == \
519	value.rsplit(" ")[0]:
520	return True
521	if ext == "svs":
522	return True
523	raise RuntimeError
524
525	def load_file_and_schema(self, xml_file, schema_path=""):
526	"""
527	Loads the file and associates a schema, if a schema is passed in or if one already exists
528
529	:param xml_file: The xml file path sent to Reader.read
530	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
531	"""
532	base_name = xml_reader.__file__
533	base_name = base_name.replace("\\", "/")
534	base = base_name.split("/sas/")[0]
535
536	# Load in xml file and get the cansas version from the header
537	self.set_xml_file(xml_file)
538	self.cansas_version = self.xmlroot.get("version", "1.0")
539
540	# Generic values for the cansas file based on the version
541	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
542	if schema_path == "":
543	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
544	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
545
546	# Link a schema to the XML file.
547	self.set_schema(schema_path)
548
549	def add_data_set(self):
550	"""
551	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
552	private method to generate a new data set.
553
554	:param key: NeXus group name for current tree level
555	"""
556
557	if self.current_datainfo and self.current_dataset:
558	self._final_cleanup()
559	self.data = []
560	self.current_datainfo = DataInfo()
561
562	def _initialize_new_data_set(self, node=None):
563	"""
564	A private class method to generate a new 1D data object.
565	Outside methods should call add_data_set() to be sure any existing data is stored properly.
566
567	:param node: XML node to determine if 1D or 2D data
568	"""
569	x = np.array(0)
570	y = np.array(0)
571	for child in node:
572	if child.tag.replace(self.base_ns, "") == "Idata":
573	for i_child in child:
574	if i_child.tag.replace(self.base_ns, "") == "Qx":
575	self.current_dataset = plottable_2D()
576	return
577	self.current_dataset = plottable_1D(x, y)
578
579	def add_intermediate(self):
580	"""
581	This method stores any intermediate objects within the final data set after fully reading the set.
582
583	:param parent: The NXclass name for the h5py Group object that just finished being processed
584	"""
585
586	if self.parent_class == 'SASprocess':
587	self.current_datainfo.process.append(self.process)
588	self.process = Process()
589	elif self.parent_class == 'SASdetector':
590	self.current_datainfo.detector.append(self.detector)
591	self.detector = Detector()
592	elif self.parent_class == 'SAStransmission_spectrum':
593	self.current_datainfo.trans_spectrum.append(self.transspectrum)
594	self.transspectrum = TransmissionSpectrum()
595	elif self.parent_class == 'SAScollimation':
596	self.current_datainfo.collimation.append(self.collimation)
597	self.collimation = Collimation()
598	elif self.parent_class == 'aperture':
599	self.collimation.aperture.append(self.aperture)
600	self.aperture = Aperture()
601	elif self.parent_class == 'SASdata':
602	self._check_for_empty_resolution()
603	self.data.append(self.current_dataset)
604
605	def _final_cleanup(self):
606	"""
607	Final cleanup of the Data1D object to be sure it has all the
608	appropriate information needed for perspectives
609	"""
610
611	# Append errors to dataset and reset class errors
612	self.current_datainfo.errors = set()
613	for error in self.errors:
614	self.current_datainfo.errors.add(error)
615	self.errors.clear()
616
617	# Combine all plottables with datainfo and append each to output
618	# Type cast data arrays to float64 and find min/max as appropriate
619	for dataset in self.data:
620	if isinstance(dataset, plottable_1D):
621	if dataset.x is not None:
622	dataset.x = np.delete(dataset.x, [0])
623	dataset.x = dataset.x.astype(np.float64)
624	dataset.xmin = np.min(dataset.x)
625	dataset.xmax = np.max(dataset.x)
626	if dataset.y is not None:
627	dataset.y = np.delete(dataset.y, [0])
628	dataset.y = dataset.y.astype(np.float64)
629	dataset.ymin = np.min(dataset.y)
630	dataset.ymax = np.max(dataset.y)
631	if dataset.dx is not None:
632	dataset.dx = np.delete(dataset.dx, [0])
633	dataset.dx = dataset.dx.astype(np.float64)
634	if dataset.dxl is not None:
635	dataset.dxl = np.delete(dataset.dxl, [0])
636	dataset.dxl = dataset.dxl.astype(np.float64)
637	if dataset.dxw is not None:
638	dataset.dxw = np.delete(dataset.dxw, [0])
639	dataset.dxw = dataset.dxw.astype(np.float64)
640	if dataset.dy is not None:
641	dataset.dy = np.delete(dataset.dy, [0])
642	dataset.dy = dataset.dy.astype(np.float64)
643	np.trim_zeros(dataset.x)
644	np.trim_zeros(dataset.y)
645	np.trim_zeros(dataset.dy)
646	elif isinstance(dataset, plottable_2D):
647	dataset.data = dataset.data.astype(np.float64)
648	dataset.qx_data = dataset.qx_data.astype(np.float64)
649	dataset.xmin = np.min(dataset.qx_data)
650	dataset.xmax = np.max(dataset.qx_data)
651	dataset.qy_data = dataset.qy_data.astype(np.float64)
652	dataset.ymin = np.min(dataset.qy_data)
653	dataset.ymax = np.max(dataset.qy_data)
654	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
655	+ dataset.qy_data * dataset.qy_data)
656	if dataset.err_data is not None:
657	dataset.err_data = dataset.err_data.astype(np.float64)
658	if dataset.dqx_data is not None:
659	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
660	if dataset.dqy_data is not None:
661	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
662	if dataset.mask is not None:
663	dataset.mask = dataset.mask.astype(dtype=bool)
664
665	if len(dataset.shape) == 2:
666	n_rows, n_cols = dataset.shape
667	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
668	dataset.x_bins = dataset.qx_data[:int(n_cols)]
669	dataset.data = dataset.data.flatten()
670	else:
671	dataset.y_bins = []
672	dataset.x_bins = []
673	dataset.data = dataset.data.flatten()
674
675	final_dataset = combine_data(dataset, self.current_datainfo)
676	self.output.append(final_dataset)
677
678	def _create_unique_key(self, dictionary, name, numb=0):
679	"""
680	Create a unique key value for any dictionary to prevent overwriting
681	Recurse until a unique key value is found.
682
683	:param dictionary: A dictionary with any number of entries
684	:param name: The index of the item to be added to dictionary
685	:param numb: The number to be appended to the name, starts at 0
686	"""
687	if dictionary.get(name) is not None:
688	numb += 1
689	name = name.split("_")[0]
690	name += "_{0}".format(numb)
691	name = self._create_unique_key(dictionary, name, numb)
692	return name
693
694	def _get_node_value_from_text(self, node, node_text):
695	"""
696	Get the value of a node and any applicable units
697
698	:param node: The XML node to get the value of
699	:param tagname: The tagname of the node
700	"""
701	units = ""
702	# If the value is a float, compile with units.
703	if self.ns_list.ns_datatype == "float":
704	# If an empty value is given, set as zero.
705	if node_text is None or node_text.isspace() \
706	or node_text.lower() == "nan":
707	node_text = "0.0"
708	# Convert the value to the base units
709	tag = node.tag.replace(self.base_ns, "")
710	node_text, units = self._unit_conversion(node, tag, node_text)
711
712	# If the value is a timestamp, convert to a datetime object
713	elif self.ns_list.ns_datatype == "timestamp":
714	if node_text is None or node_text.isspace():
715	pass
716	else:
717	try:
718	node_text = \
719	datetime.datetime.fromtimestamp(node_text)
720	except ValueError:
721	node_text = None
722	return node_text, units
723
724	def _get_node_value(self, node):
725	"""
726	Get the value of a node and any applicable units
727
728	:param node: The XML node to get the value of
729	:param tagname: The tagname of the node
730	"""
731	#Get the text from the node and convert all whitespace to spaces
732	units = ''
733	node_value = node.text
734	if node_value is not None:
735	node_value = ' '.join(node_value.split())
736	else:
737	node_value = ""
738	node_value, units = self._get_node_value_from_text(node, node_value)
739	return node_value, units
740
741	def _unit_conversion(self, node, tagname, node_value):
742	"""
743	A unit converter method used to convert the data included in the file
744	to the default units listed in data_info
745
746	:param node: XML node
747	:param tagname: name of the node
748	:param node_value: The value of the current dom node
749	"""
750	attr = node.attrib
751	value_unit = ''
752	err_msg = None
753	default_unit = None
754	if not isinstance(node_value, float):
755	node_value = float(node_value)
756	if 'unit' in attr and attr.get('unit') is not None:
757	try:
758	local_unit = attr['unit']
759	unitname = self.ns_list.current_level.get("unit", "")
760	if "SASdetector" in self.names:
761	save_in = "detector"
762	elif "aperture" in self.names:
763	save_in = "aperture"
764	elif "SAScollimation" in self.names:
765	save_in = "collimation"
766	elif "SAStransmission_spectrum" in self.names:
767	save_in = "transspectrum"
768	elif "SASdata" in self.names:
769	x = np.zeros(1)
770	y = np.zeros(1)
771	self.current_data1d = Data1D(x, y)
772	save_in = "current_data1d"
773	elif "SASsource" in self.names:
774	save_in = "current_datainfo.source"
775	elif "SASsample" in self.names:
776	save_in = "current_datainfo.sample"
777	elif "SASprocess" in self.names:
778	save_in = "process"
779	else:
780	save_in = "current_datainfo"
781	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
782	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
783	and local_unit.lower() != "none":
784	if HAS_CONVERTER == True:
785	# Check local units - bad units raise KeyError
786	data_conv_q = Converter(local_unit)
787	value_unit = default_unit
788	node_value = data_conv_q(node_value, units=default_unit)
789	else:
790	value_unit = local_unit
791	err_msg = "Unit converter is not available.\n"
792	else:
793	value_unit = local_unit
794	except KeyError:
795	err_msg = "CanSAS reader: unexpected "
796	err_msg += "\"{0}\" unit [{1}]; "
797	err_msg = err_msg.format(tagname, local_unit)
798	err_msg += "expecting [{0}]".format(default_unit)
799	value_unit = local_unit
800	except:
801	err_msg = "CanSAS reader: unknown error converting "
802	err_msg += "\"{0}\" unit [{1}]"
803	err_msg = err_msg.format(tagname, local_unit)
804	value_unit = local_unit
805	elif 'unit' in attr:
806	value_unit = attr['unit']
807	if err_msg:
808	self.errors.add(err_msg)
809	return node_value, value_unit
810
811	def _check_for_empty_data(self):
812	"""
813	Creates an empty data set if no data is passed to the reader
814
815	:param data1d: presumably a Data1D object
816	"""
817	if self.current_dataset == None:
818	x_vals = np.empty(0)
819	y_vals = np.empty(0)
820	dx_vals = np.empty(0)
821	dy_vals = np.empty(0)
822	dxl = np.empty(0)
823	dxw = np.empty(0)
824	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
825	self.current_dataset.dxl = dxl
826	self.current_dataset.dxw = dxw
827
828	def _check_for_empty_resolution(self):
829	"""
830	A method to check all resolution data sets are the same size as I and Q
831	"""
832	if isinstance(self.current_dataset, plottable_1D):
833	dql_exists = False
834	dqw_exists = False
835	dq_exists = False
836	di_exists = False
837	if self.current_dataset.dxl is not None:
838	dql_exists = True
839	if self.current_dataset.dxw is not None:
840	dqw_exists = True
841	if self.current_dataset.dx is not None:
842	dq_exists = True
843	if self.current_dataset.dy is not None:
844	di_exists = True
845	if dqw_exists and not dql_exists:
846	array_size = self.current_dataset.dxw.size - 1
847	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
848	np.zeros([array_size]))
849	elif dql_exists and not dqw_exists:
850	array_size = self.current_dataset.dxl.size - 1
851	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
852	np.zeros([array_size]))
853	elif not dql_exists and not dqw_exists and not dq_exists:
854	array_size = self.current_dataset.x.size - 1
855	self.current_dataset.dx = np.append(self.current_dataset.dx,
856	np.zeros([array_size]))
857	if not di_exists:
858	array_size = self.current_dataset.y.size - 1
859	self.current_dataset.dy = np.append(self.current_dataset.dy,
860	np.zeros([array_size]))
861	elif isinstance(self.current_dataset, plottable_2D):
862	dqx_exists = False
863	dqy_exists = False
864	di_exists = False
865	mask_exists = False
866	if self.current_dataset.dqx_data is not None:
867	dqx_exists = True
868	if self.current_dataset.dqy_data is not None:
869	dqy_exists = True
870	if self.current_dataset.err_data is not None:
871	di_exists = True
872	if self.current_dataset.mask is not None:
873	mask_exists = True
874	if not dqy_exists:
875	array_size = self.current_dataset.qy_data.size - 1
876	self.current_dataset.dqy_data = np.append(
877	self.current_dataset.dqy_data, np.zeros([array_size]))
878	if not dqx_exists:
879	array_size = self.current_dataset.qx_data.size - 1
880	self.current_dataset.dqx_data = np.append(
881	self.current_dataset.dqx_data, np.zeros([array_size]))
882	if not di_exists:
883	array_size = self.current_dataset.data.size - 1
884	self.current_dataset.err_data = np.append(
885	self.current_dataset.err_data, np.zeros([array_size]))
886	if not mask_exists:
887	array_size = self.current_dataset.data.size - 1
888	self.current_dataset.mask = np.append(
889	self.current_dataset.mask,
890	np.ones([array_size] ,dtype=bool))
891
892	####### All methods below are for writing CanSAS XML files #######
893
894	def write(self, filename, datainfo):
895	"""
896	Write the content of a Data1D as a CanSAS XML file
897
898	:param filename: name of the file to write
899	:param datainfo: Data1D object
900	"""
901	# Create XML document
902	doc, _ = self._to_xml_doc(datainfo)
903	# Write the file
904	file_ref = open(filename, 'w')
905	if self.encoding == None:
906	self.encoding = "UTF-8"
907	doc.write(file_ref, encoding=self.encoding,
908	pretty_print=True, xml_declaration=True)
909	file_ref.close()
910
911	def _to_xml_doc(self, datainfo):
912	"""
913	Create an XML document to contain the content of a Data1D
914
915	:param datainfo: Data1D object
916	"""
917	is_2d = False
918	if issubclass(datainfo.__class__, Data2D):
919	is_2d = True
920
921	# Get PIs and create root element
922	pi_string = self._get_pi_string()
923	# Define namespaces and create SASroot object
924	main_node = self._create_main_node()
925	# Create ElementTree, append SASroot and apply processing instructions
926	base_string = pi_string + self.to_string(main_node)
927	base_element = self.create_element_from_string(base_string)
928	doc = self.create_tree(base_element)
929	# Create SASentry Element
930	entry_node = self.create_element("SASentry")
931	root = doc.getroot()
932	root.append(entry_node)
933
934	# Add Title to SASentry
935	self.write_node(entry_node, "Title", datainfo.title)
936	# Add Run to SASentry
937	self._write_run_names(datainfo, entry_node)
938	# Add Data info to SASEntry
939	if is_2d:
940	self._write_data_2d(datainfo, entry_node)
941	else:
942	if self._check_root():
943	self._write_data(datainfo, entry_node)
944	else:
945	self._write_data_linearized(datainfo, entry_node)
946	# Transmission Spectrum Info
947	# TODO: fix the writer to linearize all data, including T_spectrum
948	# self._write_trans_spectrum(datainfo, entry_node)
949	# Sample info
950	self._write_sample_info(datainfo, entry_node)
951	# Instrument info
952	instr = self._write_instrument(datainfo, entry_node)
953	# Source
954	self._write_source(datainfo, instr)
955	# Collimation
956	self._write_collimation(datainfo, instr)
957	# Detectors
958	self._write_detectors(datainfo, instr)
959	# Processes info
960	self._write_process_notes(datainfo, entry_node)
961	# Note info
962	self._write_notes(datainfo, entry_node)
963	# Return the document, and the SASentry node associated with
964	# the data we just wrote
965	# If the calling function was not the cansas reader, return a minidom
966	# object rather than an lxml object.
967	self.frm = inspect.stack()[1]
968	doc, entry_node = self._check_origin(entry_node, doc)
969	return doc, entry_node
970
971	def write_node(self, parent, name, value, attr=None):
972	"""
973	:param doc: document DOM
974	:param parent: parent node
975	:param name: tag of the element
976	:param value: value of the child text node
977	:param attr: attribute dictionary
978
979	:return: True if something was appended, otherwise False
980	"""
981	if value is not None:
982	parent = self.ebuilder(parent, name, value, attr)
983	return True
984	return False
985
986	def _get_pi_string(self):
987	"""
988	Creates the processing instructions header for writing to file
989	"""
990	pis = self.return_processing_instructions()
991	if len(pis) > 0:
992	pi_tree = self.create_tree(pis[0])
993	i = 1
994	for i in range(1, len(pis) - 1):
995	pi_tree = self.append(pis[i], pi_tree)
996	pi_string = self.to_string(pi_tree)
997	else:
998	pi_string = ""
999	return pi_string
1000
1001	def _create_main_node(self):
1002	"""
1003	Creates the primary xml header used when writing to file
1004	"""
1005	xsi = "http://www.w3.org/2001/XMLSchema-instance"
1006	version = self.cansas_version
1007	n_s = CANSAS_NS.get(version).get("ns")
1008	if version == "1.1":
1009	url = "http://www.cansas.org/formats/1.1/"
1010	else:
1011	url = "http://www.cansas.org/formats/1.0/"
1012	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1013	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1014	"version" : version}
1015	nsmap = {'xsi' : xsi, None: n_s}
1016
1017	main_node = self.create_element("{" + n_s + "}SASroot",
1018	attrib=attrib, nsmap=nsmap)
1019	return main_node
1020
1021	def _write_run_names(self, datainfo, entry_node):
1022	"""
1023	Writes the run names to the XML file
1024
1025	:param datainfo: The Data1D object the information is coming from
1026	:param entry_node: lxml node ElementTree object to be appended to
1027	"""
1028	if datainfo.run == None or datainfo.run == []:
1029	datainfo.run.append(RUN_NAME_DEFAULT)
1030	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1031	for item in datainfo.run:
1032	runname = {}
1033	if item in datainfo.run_name and \
1034	len(str(datainfo.run_name[item])) > 1:
1035	runname = {'name': datainfo.run_name[item]}
1036	self.write_node(entry_node, "Run", item, runname)
1037
1038	def _write_data(self, datainfo, entry_node):
1039	"""
1040	Writes 1D I and Q data to the XML file
1041
1042	:param datainfo: The Data1D object the information is coming from
1043	:param entry_node: lxml node ElementTree object to be appended to
1044	"""
1045	node = self.create_element("SASdata")
1046	self.append(node, entry_node)
1047
1048	for i in range(len(datainfo.x)):
1049	point = self.create_element("Idata")
1050	node.append(point)
1051	self.write_node(point, "Q", datainfo.x[i],
1052	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1053	if len(datainfo.y) >= i:
1054	self.write_node(point, "I", datainfo.y[i],
1055	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1056	if datainfo.dy is not None and len(datainfo.dy) > i:
1057	self.write_node(point, "Idev", datainfo.dy[i],
1058	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1059	if datainfo.dx is not None and len(datainfo.dx) > i:
1060	self.write_node(point, "Qdev", datainfo.dx[i],
1061	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1062	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1063	self.write_node(point, "dQw", datainfo.dxw[i],
1064	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1065	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1066	self.write_node(point, "dQl", datainfo.dxl[i],
1067	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1068	if datainfo.isSesans:
1069	sesans = self.create_element("Sesans")
1070	sesans.text = str(datainfo.isSesans)
1071	node.append(sesans)
1072	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1073	{'unit': datainfo.sample.zacceptance[1]})
1074
1075
1076	def _write_data_2d(self, datainfo, entry_node):
1077	"""
1078	Writes 2D data to the XML file
1079
1080	:param datainfo: The Data2D object the information is coming from
1081	:param entry_node: lxml node ElementTree object to be appended to
1082	"""
1083	attr = {}
1084	if datainfo.data.shape:
1085	attr["x_bins"] = str(len(datainfo.x_bins))
1086	attr["y_bins"] = str(len(datainfo.y_bins))
1087	node = self.create_element("SASdata", attr)
1088	self.append(node, entry_node)
1089
1090	point = self.create_element("Idata")
1091	node.append(point)
1092	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1093	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1094	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1095
1096	self.write_node(point, "Qx", qx,
1097	{'unit': datainfo._xunit})
1098	self.write_node(point, "Qy", qy,
1099	{'unit': datainfo._yunit})
1100	self.write_node(point, "I", intensity,
1101	{'unit': datainfo._zunit})
1102	if datainfo.err_data is not None:
1103	err = ','.join([str(datainfo.err_data[i]) for i in
1104	xrange(len(datainfo.err_data))])
1105	self.write_node(point, "Idev", err,
1106	{'unit': datainfo._zunit})
1107	if datainfo.dqy_data is not None:
1108	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1109	xrange(len(datainfo.dqy_data))])
1110	self.write_node(point, "Qydev", dqy,
1111	{'unit': datainfo._yunit})
1112	if datainfo.dqx_data is not None:
1113	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1114	xrange(len(datainfo.dqx_data))])
1115	self.write_node(point, "Qxdev", dqx,
1116	{'unit': datainfo._xunit})
1117	if datainfo.mask is not None:
1118	mask = ','.join(
1119	["1" if datainfo.mask[i] else "0"
1120	for i in xrange(len(datainfo.mask))])
1121	self.write_node(point, "Mask", mask)
1122
1123	def _write_trans_spectrum(self, datainfo, entry_node):
1124	"""
1125	Writes the transmission spectrum data to the XML file
1126
1127	:param datainfo: The Data1D object the information is coming from
1128	:param entry_node: lxml node ElementTree object to be appended to
1129	"""
1130	for i in range(len(datainfo.trans_spectrum)):
1131	spectrum = datainfo.trans_spectrum[i]
1132	node = self.create_element("SAStransmission_spectrum",
1133	{"name" : spectrum.name})
1134	self.append(node, entry_node)
1135	if isinstance(spectrum.timestamp, datetime.datetime):
1136	node.setAttribute("timestamp", spectrum.timestamp)
1137	for i in range(len(spectrum.wavelength)):
1138	point = self.create_element("Tdata")
1139	node.append(point)
1140	self.write_node(point, "Lambda", spectrum.wavelength[i],
1141	{'unit': spectrum.wavelength_unit})
1142	self.write_node(point, "T", spectrum.transmission[i],
1143	{'unit': spectrum.transmission_unit})
1144	if spectrum.transmission_deviation != None \
1145	and len(spectrum.transmission_deviation) >= i:
1146	self.write_node(point, "Tdev",
1147	spectrum.transmission_deviation[i],
1148	{'unit':
1149	spectrum.transmission_deviation_unit})
1150
1151	def _write_sample_info(self, datainfo, entry_node):
1152	"""
1153	Writes the sample information to the XML file
1154
1155	:param datainfo: The Data1D object the information is coming from
1156	:param entry_node: lxml node ElementTree object to be appended to
1157	"""
1158	sample = self.create_element("SASsample")
1159	if datainfo.sample.name is not None:
1160	self.write_attribute(sample, "name",
1161	str(datainfo.sample.name))
1162	self.append(sample, entry_node)
1163	self.write_node(sample, "ID", str(datainfo.sample.ID))
1164	self.write_node(sample, "thickness", datainfo.sample.thickness,
1165	{"unit": datainfo.sample.thickness_unit})
1166	self.write_node(sample, "transmission", datainfo.sample.transmission)
1167	self.write_node(sample, "temperature", datainfo.sample.temperature,
1168	{"unit": datainfo.sample.temperature_unit})
1169
1170	pos = self.create_element("position")
1171	written = self.write_node(pos,
1172	"x",
1173	datainfo.sample.position.x,
1174	{"unit": datainfo.sample.position_unit})
1175	written = written \| self.write_node( \
1176	pos, "y", datainfo.sample.position.y,
1177	{"unit": datainfo.sample.position_unit})
1178	written = written \| self.write_node( \
1179	pos, "z", datainfo.sample.position.z,
1180	{"unit": datainfo.sample.position_unit})
1181	if written == True:
1182	self.append(pos, sample)
1183
1184	ori = self.create_element("orientation")
1185	written = self.write_node(ori, "roll",
1186	datainfo.sample.orientation.x,
1187	{"unit": datainfo.sample.orientation_unit})
1188	written = written \| self.write_node( \
1189	ori, "pitch", datainfo.sample.orientation.y,
1190	{"unit": datainfo.sample.orientation_unit})
1191	written = written \| self.write_node( \
1192	ori, "yaw", datainfo.sample.orientation.z,
1193	{"unit": datainfo.sample.orientation_unit})
1194	if written == True:
1195	self.append(ori, sample)
1196
1197	for item in datainfo.sample.details:
1198	self.write_node(sample, "details", item)
1199
1200	def _write_instrument(self, datainfo, entry_node):
1201	"""
1202	Writes the instrumental information to the XML file
1203
1204	:param datainfo: The Data1D object the information is coming from
1205	:param entry_node: lxml node ElementTree object to be appended to
1206	"""
1207	instr = self.create_element("SASinstrument")
1208	self.append(instr, entry_node)
1209	self.write_node(instr, "name", datainfo.instrument)
1210	return instr
1211
1212	def _write_source(self, datainfo, instr):
1213	"""
1214	Writes the source information to the XML file
1215
1216	:param datainfo: The Data1D object the information is coming from
1217	:param instr: instrument node to be appended to
1218	"""
1219	source = self.create_element("SASsource")
1220	if datainfo.source.name is not None:
1221	self.write_attribute(source, "name",
1222	str(datainfo.source.name))
1223	self.append(source, instr)
1224	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1225	datainfo.source.radiation = "neutron"
1226	self.write_node(source, "radiation", datainfo.source.radiation)
1227
1228	size = self.create_element("beam_size")
1229	if datainfo.source.beam_size_name is not None:
1230	self.write_attribute(size, "name",
1231	str(datainfo.source.beam_size_name))
1232	written = self.write_node( \
1233	size, "x", datainfo.source.beam_size.x,
1234	{"unit": datainfo.source.beam_size_unit})
1235	written = written \| self.write_node( \
1236	size, "y", datainfo.source.beam_size.y,
1237	{"unit": datainfo.source.beam_size_unit})
1238	written = written \| self.write_node( \
1239	size, "z", datainfo.source.beam_size.z,
1240	{"unit": datainfo.source.beam_size_unit})
1241	if written == True:
1242	self.append(size, source)
1243
1244	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1245	self.write_node(source, "wavelength",
1246	datainfo.source.wavelength,
1247	{"unit": datainfo.source.wavelength_unit})
1248	self.write_node(source, "wavelength_min",
1249	datainfo.source.wavelength_min,
1250	{"unit": datainfo.source.wavelength_min_unit})
1251	self.write_node(source, "wavelength_max",
1252	datainfo.source.wavelength_max,
1253	{"unit": datainfo.source.wavelength_max_unit})
1254	self.write_node(source, "wavelength_spread",
1255	datainfo.source.wavelength_spread,
1256	{"unit": datainfo.source.wavelength_spread_unit})
1257
1258	def _write_collimation(self, datainfo, instr):
1259	"""
1260	Writes the collimation information to the XML file
1261
1262	:param datainfo: The Data1D object the information is coming from
1263	:param instr: lxml node ElementTree object to be appended to
1264	"""
1265	if datainfo.collimation == [] or datainfo.collimation == None:
1266	coll = Collimation()
1267	datainfo.collimation.append(coll)
1268	for item in datainfo.collimation:
1269	coll = self.create_element("SAScollimation")
1270	if item.name is not None:
1271	self.write_attribute(coll, "name", str(item.name))
1272	self.append(coll, instr)
1273
1274	self.write_node(coll, "length", item.length,
1275	{"unit": item.length_unit})
1276
1277	for aperture in item.aperture:
1278	apert = self.create_element("aperture")
1279	if aperture.name is not None:
1280	self.write_attribute(apert, "name", str(aperture.name))
1281	if aperture.type is not None:
1282	self.write_attribute(apert, "type", str(aperture.type))
1283	self.append(apert, coll)
1284
1285	size = self.create_element("size")
1286	if aperture.size_name is not None:
1287	self.write_attribute(size, "name",
1288	str(aperture.size_name))
1289	written = self.write_node(size, "x", aperture.size.x,
1290	{"unit": aperture.size_unit})
1291	written = written \| self.write_node( \
1292	size, "y", aperture.size.y,
1293	{"unit": aperture.size_unit})
1294	written = written \| self.write_node( \
1295	size, "z", aperture.size.z,
1296	{"unit": aperture.size_unit})
1297	if written == True:
1298	self.append(size, apert)
1299
1300	self.write_node(apert, "distance", aperture.distance,
1301	{"unit": aperture.distance_unit})
1302
1303	def _write_detectors(self, datainfo, instr):
1304	"""
1305	Writes the detector information to the XML file
1306
1307	:param datainfo: The Data1D object the information is coming from
1308	:param inst: lxml instrument node to be appended to
1309	"""
1310	if datainfo.detector == None or datainfo.detector == []:
1311	det = Detector()
1312	det.name = ""
1313	datainfo.detector.append(det)
1314
1315	for item in datainfo.detector:
1316	det = self.create_element("SASdetector")
1317	written = self.write_node(det, "name", item.name)
1318	written = written \| self.write_node(det, "SDD", item.distance,
1319	{"unit": item.distance_unit})
1320	if written == True:
1321	self.append(det, instr)
1322
1323	off = self.create_element("offset")
1324	written = self.write_node(off, "x", item.offset.x,
1325	{"unit": item.offset_unit})
1326	written = written \| self.write_node(off, "y", item.offset.y,
1327	{"unit": item.offset_unit})
1328	written = written \| self.write_node(off, "z", item.offset.z,
1329	{"unit": item.offset_unit})
1330	if written == True:
1331	self.append(off, det)
1332
1333	ori = self.create_element("orientation")
1334	written = self.write_node(ori, "roll", item.orientation.x,
1335	{"unit": item.orientation_unit})
1336	written = written \| self.write_node(ori, "pitch",
1337	item.orientation.y,
1338	{"unit": item.orientation_unit})
1339	written = written \| self.write_node(ori, "yaw",
1340	item.orientation.z,
1341	{"unit": item.orientation_unit})
1342	if written == True:
1343	self.append(ori, det)
1344
1345	center = self.create_element("beam_center")
1346	written = self.write_node(center, "x", item.beam_center.x,
1347	{"unit": item.beam_center_unit})
1348	written = written \| self.write_node(center, "y",
1349	item.beam_center.y,
1350	{"unit": item.beam_center_unit})
1351	written = written \| self.write_node(center, "z",
1352	item.beam_center.z,
1353	{"unit": item.beam_center_unit})
1354	if written == True:
1355	self.append(center, det)
1356
1357	pix = self.create_element("pixel_size")
1358	written = self.write_node(pix, "x", item.pixel_size.x,
1359	{"unit": item.pixel_size_unit})
1360	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1361	{"unit": item.pixel_size_unit})
1362	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1363	{"unit": item.pixel_size_unit})
1364	if written == True:
1365	self.append(pix, det)
1366	self.write_node(det, "slit_length", item.slit_length,
1367	{"unit": item.slit_length_unit})
1368
1369	def _write_process_notes(self, datainfo, entry_node):
1370	"""
1371	Writes the process notes to the XML file
1372
1373	:param datainfo: The Data1D object the information is coming from
1374	:param entry_node: lxml node ElementTree object to be appended to
1375
1376	"""
1377	for item in datainfo.process:
1378	node = self.create_element("SASprocess")
1379	self.append(node, entry_node)
1380	self.write_node(node, "name", item.name)
1381	self.write_node(node, "date", item.date)
1382	self.write_node(node, "description", item.description)
1383	for term in item.term:
1384	if isinstance(term, list):
1385	value = term['value']
1386	del term['value']
1387	elif isinstance(term, dict):
1388	value = term.get("value")
1389	del term['value']
1390	else:
1391	value = term
1392	self.write_node(node, "term", value, term)
1393	for note in item.notes:
1394	self.write_node(node, "SASprocessnote", note)
1395	if len(item.notes) == 0:
1396	self.write_node(node, "SASprocessnote", "")
1397
1398	def _write_notes(self, datainfo, entry_node):
1399	"""
1400	Writes the notes to the XML file and creates an empty note if none
1401	exist
1402
1403	:param datainfo: The Data1D object the information is coming from
1404	:param entry_node: lxml node ElementTree object to be appended to
1405
1406	"""
1407	if len(datainfo.notes) == 0:
1408	node = self.create_element("SASnote")
1409	self.append(node, entry_node)
1410	else:
1411	for item in datainfo.notes:
1412	node = self.create_element("SASnote")
1413	self.write_text(node, item)
1414	self.append(node, entry_node)
1415
1416	def _check_root(self):
1417	"""
1418	Return the document, and the SASentry node associated with
1419	the data we just wrote.
1420	If the calling function was not the cansas reader, return a minidom
1421	object rather than an lxml object.
1422
1423	:param entry_node: lxml node ElementTree object to be appended to
1424	:param doc: entire xml tree
1425	"""
1426	if not self.frm:
1427	self.frm = inspect.stack()[2]
1428	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1429	mod_name = mod_name.replace(".py", "")
1430	mod = mod_name.split("sas/")
1431	mod_name = mod[1]
1432	return mod_name == "sascalc/dataloader/readers/cansas_reader"
1433
1434	def _check_origin(self, entry_node, doc):
1435	"""
1436	Return the document, and the SASentry node associated with
1437	the data we just wrote.
1438	If the calling function was not the cansas reader, return a minidom
1439	object rather than an lxml object.
1440
1441	:param entry_node: lxml node ElementTree object to be appended to
1442	:param doc: entire xml tree
1443	"""
1444	if not self._check_root():
1445	string = self.to_string(doc, pretty_print=False)
1446	doc = parseString(string)
1447	node_name = entry_node.tag
1448	node_list = doc.getElementsByTagName(node_name)
1449	entry_node = node_list.item(0)
1450	return doc, entry_node
1451
1452	# DO NOT REMOVE - used in saving and loading panel states.
1453	def _store_float(self, location, node, variable, storage, optional=True):
1454	"""
1455	Get the content of a xpath location and store
1456	the result. Check that the units are compatible
1457	with the destination. The value is expected to
1458	be a float.
1459
1460	The xpath location might or might not exist.
1461	If it does not exist, nothing is done
1462
1463	:param location: xpath location to fetch
1464	:param node: node to read the data from
1465	:param variable: name of the data member to store it in [string]
1466	:param storage: data object that has the 'variable' data member
1467	:param optional: if True, no exception will be raised
1468	if unit conversion can't be done
1469
1470	:raise ValueError: raised when the units are not recognized
1471	"""
1472	entry = get_content(location, node)
1473	try:
1474	value = float(entry.text)
1475	except:
1476	value = None
1477
1478	if value is not None:
1479	# If the entry has units, check to see that they are
1480	# compatible with what we currently have in the data object
1481	units = entry.get('unit')
1482	if units is not None:
1483	toks = variable.split('.')
1484	local_unit = None
1485	exec "local_unit = storage.%s_unit" % toks[0]
1486	if local_unit != None and units.lower() != local_unit.lower():
1487	if HAS_CONVERTER == True:
1488	try:
1489	conv = Converter(units)
1490	exec "storage.%s = %g" % \
1491	(variable, conv(value, units=local_unit))
1492	except:
1493	_, exc_value, _ = sys.exc_info()
1494	err_mess = "CanSAS reader: could not convert"
1495	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1496	% (variable, units, local_unit, exc_value)
1497	self.errors.add(err_mess)
1498	if optional:
1499	logging.info(err_mess)
1500	else:
1501	raise ValueError, err_mess
1502	else:
1503	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1504	% (variable, units)
1505	err_mess += " expecting [%s]" % local_unit
1506	self.errors.add(err_mess)
1507	if optional:
1508	logging.info(err_mess)
1509	else:
1510	raise ValueError, err_mess
1511	else:
1512	exec "storage.%s = value" % variable
1513	else:
1514	exec "storage.%s = value" % variable
1515
1516	# DO NOT REMOVE - used in saving and loading panel states.
1517	def _store_content(self, location, node, variable, storage):
1518	"""
1519	Get the content of a xpath location and store
1520	the result. The value is treated as a string.
1521
1522	The xpath location might or might not exist.
1523	If it does not exist, nothing is done
1524
1525	:param location: xpath location to fetch
1526	:param node: node to read the data from
1527	:param variable: name of the data member to store it in [string]
1528	:param storage: data object that has the 'variable' data member
1529
1530	:return: return a list of errors
1531	"""
1532	entry = get_content(location, node)
1533	if entry is not None and entry.text is not None:
1534	exec "storage.%s = entry.text.strip()" % variable
1535
1536
1537	# DO NOT REMOVE Called by outside packages:
1538	# sas.sasgui.perspectives.invariant.invariant_state
1539	# sas.sasgui.perspectives.fitting.pagestate
1540	def get_content(location, node):
1541	"""
1542	Get the first instance of the content of a xpath location.
1543
1544	:param location: xpath location
1545	:param node: node to start at
1546
1547	:return: Element, or None
1548	"""
1549	nodes = node.xpath(location,
1550	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1551	if len(nodes) > 0:
1552	return nodes[0]
1553	else:
1554	return None
1555
1556	# DO NOT REMOVE Called by outside packages:
1557	# sas.sasgui.perspectives.fitting.pagestate
1558	def write_node(doc, parent, name, value, attr=None):
1559	"""
1560	:param doc: document DOM
1561	:param parent: parent node
1562	:param name: tag of the element
1563	:param value: value of the child text node
1564	:param attr: attribute dictionary
1565
1566	:return: True if something was appended, otherwise False
1567	"""
1568	if attr is None:
1569	attr = {}
1570	if value is not None:
1571	node = doc.createElement(name)
1572	node.appendChild(doc.createTextNode(str(value)))
1573	for item in attr:
1574	node.setAttribute(item, attr[item])
1575	parent.appendChild(node)
1576	return True
1577	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 3d6c010

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