cansas_reader.py @ a2573fc

Last change on this file since a2573fc was a2573fc, checked in by Tim Snow <tim.snow@…>, 8 years ago

Sorted out conflicts after merging

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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
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
272	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
273	print data_point
274
275	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
276	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
277
278	elif tagname == 'Q':
279	unit_list = unit.split("\|")
280	if len(unit_list) > 1:
281	self.current_dataset.xaxis(unit_list[0].strip(),
282	unit_list[1].strip())
283	else:
284	self.current_dataset.xaxis("Q", unit)
285	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
286	elif tagname == 'Qdev':
287	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
288	elif tagname == 'dQw':
289	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
290	elif tagname == 'dQl':
291	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
292	elif tagname == 'Qmean':
293	pass
294	elif tagname == 'Shadowfactor':
295	pass
296	elif tagname == 'Sesans':
297	self.current_datainfo.isSesans = bool(data_point)
298	elif tagname == 'zacceptance':
299	self.current_datainfo.sample.zacceptance = (data_point, unit)
300
301	# I and Qx, Qy - 2D data
302	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
303	self.current_dataset.yaxis("Intensity", unit)
304	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
306	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
307	elif tagname == 'Qx':
308	self.current_dataset.xaxis("Qx", unit)
309	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
310	elif tagname == 'Qy':
311	self.current_dataset.yaxis("Qy", unit)
312	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
313	elif tagname == 'Qxdev':
314	self.current_dataset.xaxis("Qxdev", unit)
315	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
316	elif tagname == 'Qydev':
317	self.current_dataset.yaxis("Qydev", unit)
318	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
319	elif tagname == 'Mask':
320	inter = [item == "1" for item in data_point.split(",")]
321	self.current_dataset.mask = np.asarray(inter, dtype=bool)
322
323	# Sample Information
324	elif tagname == 'ID' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.ID = data_point
326	elif tagname == 'Title' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.name = data_point
328	elif tagname == 'thickness' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.thickness = data_point
330	self.current_datainfo.sample.thickness_unit = unit
331	elif tagname == 'transmission' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.transmission = data_point
333	elif tagname == 'temperature' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.temperature = data_point
335	self.current_datainfo.sample.temperature_unit = unit
336	elif tagname == 'details' and self.parent_class == 'SASsample':
337	self.current_datainfo.sample.details.append(data_point)
338	elif tagname == 'x' and self.parent_class == 'position':
339	self.current_datainfo.sample.position.x = data_point
340	self.current_datainfo.sample.position_unit = unit
341	elif tagname == 'y' and self.parent_class == 'position':
342	self.current_datainfo.sample.position.y = data_point
343	self.current_datainfo.sample.position_unit = unit
344	elif tagname == 'z' and self.parent_class == 'position':
345	self.current_datainfo.sample.position.z = data_point
346	self.current_datainfo.sample.position_unit = unit
347	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
348	self.current_datainfo.sample.orientation.x = data_point
349	self.current_datainfo.sample.orientation_unit = unit
350	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
351	self.current_datainfo.sample.orientation.y = data_point
352	self.current_datainfo.sample.orientation_unit = unit
353	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
354	self.current_datainfo.sample.orientation.z = data_point
355	self.current_datainfo.sample.orientation_unit = unit
356
357	# Instrumental Information
358	elif tagname == 'name' and self.parent_class == 'SASinstrument':
359	self.current_datainfo.instrument = data_point
360	# Detector Information
361	elif tagname == 'name' and self.parent_class == 'SASdetector':
362	self.detector.name = data_point
363	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
364	self.detector.distance = data_point
365	self.detector.distance_unit = unit
366	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
367	self.detector.slit_length = data_point
368	self.detector.slit_length_unit = unit
369	elif tagname == 'x' and self.parent_class == 'offset':
370	self.detector.offset.x = data_point
371	self.detector.offset_unit = unit
372	elif tagname == 'y' and self.parent_class == 'offset':
373	self.detector.offset.y = data_point
374	self.detector.offset_unit = unit
375	elif tagname == 'z' and self.parent_class == 'offset':
376	self.detector.offset.z = data_point
377	self.detector.offset_unit = unit
378	elif tagname == 'x' and self.parent_class == 'beam_center':
379	self.detector.beam_center.x = data_point
380	self.detector.beam_center_unit = unit
381	elif tagname == 'y' and self.parent_class == 'beam_center':
382	self.detector.beam_center.y = data_point
383	self.detector.beam_center_unit = unit
384	elif tagname == 'z' and self.parent_class == 'beam_center':
385	self.detector.beam_center.z = data_point
386	self.detector.beam_center_unit = unit
387	elif tagname == 'x' and self.parent_class == 'pixel_size':
388	self.detector.pixel_size.x = data_point
389	self.detector.pixel_size_unit = unit
390	elif tagname == 'y' and self.parent_class == 'pixel_size':
391	self.detector.pixel_size.y = data_point
392	self.detector.pixel_size_unit = unit
393	elif tagname == 'z' and self.parent_class == 'pixel_size':
394	self.detector.pixel_size.z = data_point
395	self.detector.pixel_size_unit = unit
396	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
397	self.detector.orientation.x = data_point
398	self.detector.orientation_unit = unit
399	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
400	self.detector.orientation.y = data_point
401	self.detector.orientation_unit = unit
402	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
403	self.detector.orientation.z = data_point
404	self.detector.orientation_unit = unit
405	# Collimation and Aperture
406	elif tagname == 'length' and self.parent_class == 'SAScollimation':
407	self.collimation.length = data_point
408	self.collimation.length_unit = unit
409	elif tagname == 'name' and self.parent_class == 'SAScollimation':
410	self.collimation.name = data_point
411	elif tagname == 'distance' and self.parent_class == 'aperture':
412	self.aperture.distance = data_point
413	self.aperture.distance_unit = unit
414	elif tagname == 'x' and self.parent_class == 'size':
415	self.aperture.size.x = data_point
416	self.collimation.size_unit = unit
417	elif tagname == 'y' and self.parent_class == 'size':
418	self.aperture.size.y = data_point
419	self.collimation.size_unit = unit
420	elif tagname == 'z' and self.parent_class == 'size':
421	self.aperture.size.z = data_point
422	self.collimation.size_unit = unit
423
424	# Process Information
425	elif tagname == 'name' and self.parent_class == 'SASprocess':
426	self.process.name = data_point
427	elif tagname == 'description' and self.parent_class == 'SASprocess':
428	self.process.description = data_point
429	elif tagname == 'date' and self.parent_class == 'SASprocess':
430	try:
431	self.process.date = datetime.datetime.fromtimestamp(data_point)
432	except:
433	self.process.date = data_point
434	elif tagname == 'SASprocessnote':
435	self.process.notes.append(data_point)
436	elif tagname == 'term' and self.parent_class == 'SASprocess':
437	unit = attr.get("unit", "")
438	dic = {}
439	dic["name"] = name
440	dic["value"] = data_point
441	dic["unit"] = unit
442	self.process.term.append(dic)
443
444	# Transmission Spectrum
445	elif tagname == 'T' and self.parent_class == 'Tdata':
446	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
447	self.transspectrum.transmission_unit = unit
448	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
449	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
450	self.transspectrum.transmission_deviation_unit = unit
451	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
452	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
453	self.transspectrum.wavelength_unit = unit
454
455	# Source Information
456	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
457	self.current_datainfo.source.wavelength = data_point
458	self.current_datainfo.source.wavelength_unit = unit
459	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
460	self.current_datainfo.source.wavelength_min = data_point
461	self.current_datainfo.source.wavelength_min_unit = unit
462	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
463	self.current_datainfo.source.wavelength_max = data_point
464	self.current_datainfo.source.wavelength_max_unit = unit
465	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
466	self.current_datainfo.source.wavelength_spread = data_point
467	self.current_datainfo.source.wavelength_spread_unit = unit
468	elif tagname == 'x' and self.parent_class == 'beam_size':
469	self.current_datainfo.source.beam_size.x = data_point
470	self.current_datainfo.source.beam_size_unit = unit
471	elif tagname == 'y' and self.parent_class == 'beam_size':
472	self.current_datainfo.source.beam_size.y = data_point
473	self.current_datainfo.source.beam_size_unit = unit
474	elif tagname == 'z' and self.parent_class == 'pixel_size':
475	self.current_datainfo.source.data_point.z = data_point
476	self.current_datainfo.source.beam_size_unit = unit
477	elif tagname == 'radiation' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.radiation = data_point
479	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
480	self.current_datainfo.source.beam_shape = data_point
481
482	# Everything else goes in meta_data
483	else:
484	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
485	self.current_datainfo.meta_data[new_key] = data_point
486
487	self.names.remove(tagname_original)
488	length = 0
489	if len(self.names) > 1:
490	length = len(self.names) - 1
491	self.parent_class = self.names[length]
492	if not self._is_call_local() and not recurse:
493	self.frm = ""
494	self.add_data_set()
495	empty = None
496	return self.output[0], empty
497
498
499	def _is_call_local(self):
500	"""
501
502	"""
503	if self.frm == "":
504	inter = inspect.stack()
505	self.frm = inter[2]
506	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
507	mod_name = mod_name.replace(".py", "")
508	mod = mod_name.split("sas/")
509	mod_name = mod[1]
510	if mod_name != "sascalc/dataloader/readers/cansas_reader":
511	return False
512	return True
513
514	def is_cansas(self, ext="xml"):
515	"""
516	Checks to see if the xml file is a CanSAS file
517
518	:param ext: The file extension of the data file
519	"""
520	if self.validate_xml():
521	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
522	value = self.xmlroot.get(name)
523	if CANSAS_NS.get(self.cansas_version).get("ns") == \
524	value.rsplit(" ")[0]:
525	return True
526	if ext == "svs":
527	return True
528	raise RuntimeError
529
530	def load_file_and_schema(self, xml_file, schema_path=""):
531	"""
532	Loads the file and associates a schema, if a schema is passed in or if one already exists
533
534	:param xml_file: The xml file path sent to Reader.read
535	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
536	"""
537	base_name = xml_reader.__file__
538	base_name = base_name.replace("\\", "/")
539	base = base_name.split("/sas/")[0]
540
541	# Load in xml file and get the cansas version from the header
542	self.set_xml_file(xml_file)
543	self.cansas_version = self.xmlroot.get("version", "1.0")
544
545	# Generic values for the cansas file based on the version
546	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
547	if schema_path == "":
548	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
549	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
550
551	# Link a schema to the XML file.
552	self.set_schema(schema_path)
553
554	def add_data_set(self):
555	"""
556	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
557	private method to generate a new data set.
558
559	:param key: NeXus group name for current tree level
560	"""
561
562	if self.current_datainfo and self.current_dataset:
563	self._final_cleanup()
564	self.data = []
565	self.current_datainfo = DataInfo()
566
567	def _initialize_new_data_set(self, node=None):
568	"""
569	A private class method to generate a new 1D data object.
570	Outside methods should call add_data_set() to be sure any existing data is stored properly.
571
572	:param node: XML node to determine if 1D or 2D data
573	"""
574	x = np.array(0)
575	y = np.array(0)
576	for child in node:
577	if child.tag.replace(self.base_ns, "") == "Idata":
578	for i_child in child:
579	if i_child.tag.replace(self.base_ns, "") == "Qx":
580	self.current_dataset = plottable_2D()
581	return
582	self.current_dataset = plottable_1D(x, y)
583
584	def add_intermediate(self):
585	"""
586	This method stores any intermediate objects within the final data set after fully reading the set.
587
588	:param parent: The NXclass name for the h5py Group object that just finished being processed
589	"""
590
591	if self.parent_class == 'SASprocess':
592	self.current_datainfo.process.append(self.process)
593	self.process = Process()
594	elif self.parent_class == 'SASdetector':
595	self.current_datainfo.detector.append(self.detector)
596	self.detector = Detector()
597	elif self.parent_class == 'SAStransmission_spectrum':
598	self.current_datainfo.trans_spectrum.append(self.transspectrum)
599	self.transspectrum = TransmissionSpectrum()
600	elif self.parent_class == 'SAScollimation':
601	self.current_datainfo.collimation.append(self.collimation)
602	self.collimation = Collimation()
603	elif self.parent_class == 'aperture':
604	self.collimation.aperture.append(self.aperture)
605	self.aperture = Aperture()
606	elif self.parent_class == 'SASdata':
607	self._check_for_empty_resolution()
608	self.data.append(self.current_dataset)
609
610	def _final_cleanup(self):
611	"""
612	Final cleanup of the Data1D object to be sure it has all the
613	appropriate information needed for perspectives
614	"""
615
616	# Append errors to dataset and reset class errors
617	self.current_datainfo.errors = set()
618	for error in self.errors:
619	self.current_datainfo.errors.add(error)
620	self.errors.clear()
621
622	# Combine all plottables with datainfo and append each to output
623	# Type cast data arrays to float64 and find min/max as appropriate
624	for dataset in self.data:
625	if isinstance(dataset, plottable_1D):
626	if dataset.x is not None:
627	dataset.x = np.delete(dataset.x, [0])
628	dataset.x = dataset.x.astype(np.float64)
629	dataset.xmin = np.min(dataset.x)
630	dataset.xmax = np.max(dataset.x)
631	if dataset.y is not None:
632	dataset.y = np.delete(dataset.y, [0])
633	dataset.y = dataset.y.astype(np.float64)
634	dataset.ymin = np.min(dataset.y)
635	dataset.ymax = np.max(dataset.y)
636	if dataset.dx is not None:
637	dataset.dx = np.delete(dataset.dx, [0])
638	dataset.dx = dataset.dx.astype(np.float64)
639	if dataset.dxl is not None:
640	dataset.dxl = np.delete(dataset.dxl, [0])
641	dataset.dxl = dataset.dxl.astype(np.float64)
642	if dataset.dxw is not None:
643	dataset.dxw = np.delete(dataset.dxw, [0])
644	dataset.dxw = dataset.dxw.astype(np.float64)
645	if dataset.dy is not None:
646	dataset.dy = np.delete(dataset.dy, [0])
647	dataset.dy = dataset.dy.astype(np.float64)
648	np.trim_zeros(dataset.x)
649	np.trim_zeros(dataset.y)
650	np.trim_zeros(dataset.dy)
651	elif isinstance(dataset, plottable_2D):
652	dataset.data = dataset.data.astype(np.float64)
653	dataset.qx_data = dataset.qx_data.astype(np.float64)
654	dataset.xmin = np.min(dataset.qx_data)
655	dataset.xmax = np.max(dataset.qx_data)
656	dataset.qy_data = dataset.qy_data.astype(np.float64)
657	dataset.ymin = np.min(dataset.qy_data)
658	dataset.ymax = np.max(dataset.qy_data)
659	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
660	+ dataset.qy_data * dataset.qy_data)
661	if dataset.err_data is not None:
662	dataset.err_data = dataset.err_data.astype(np.float64)
663	if dataset.dqx_data is not None:
664	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
665	if dataset.dqy_data is not None:
666	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
667	if dataset.mask is not None:
668	dataset.mask = dataset.mask.astype(dtype=bool)
669
670	if len(dataset.shape) == 2:
671	n_rows, n_cols = dataset.shape
672	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
673	dataset.x_bins = dataset.qx_data[:int(n_cols)]
674	dataset.data = dataset.data.flatten()
675	else:
676	dataset.y_bins = []
677	dataset.x_bins = []
678	dataset.data = dataset.data.flatten()
679
680	final_dataset = combine_data(dataset, self.current_datainfo)
681	self.output.append(final_dataset)
682
683	def _create_unique_key(self, dictionary, name, numb=0):
684	"""
685	Create a unique key value for any dictionary to prevent overwriting
686	Recurse until a unique key value is found.
687
688	:param dictionary: A dictionary with any number of entries
689	:param name: The index of the item to be added to dictionary
690	:param numb: The number to be appended to the name, starts at 0
691	"""
692	if dictionary.get(name) is not None:
693	numb += 1
694	name = name.split("_")[0]
695	name += "_{0}".format(numb)
696	name = self._create_unique_key(dictionary, name, numb)
697	return name
698
699	def _get_node_value_from_text(self, node, node_text):
700	"""
701	Get the value of a node and any applicable units
702
703	:param node: The XML node to get the value of
704	:param tagname: The tagname of the node
705	"""
706	units = ""
707	# If the value is a float, compile with units.
708	if self.ns_list.ns_datatype == "float":
709	# If an empty value is given, set as zero.
710	if node_text is None or node_text.isspace() \
711	or node_text.lower() == "nan":
712	node_text = "0.0"
713	# Convert the value to the base units
714	tag = node.tag.replace(self.base_ns, "")
715	node_text, units = self._unit_conversion(node, tag, node_text)
716
717	# If the value is a timestamp, convert to a datetime object
718	elif self.ns_list.ns_datatype == "timestamp":
719	if node_text is None or node_text.isspace():
720	pass
721	else:
722	try:
723	node_text = \
724	datetime.datetime.fromtimestamp(node_text)
725	except ValueError:
726	node_text = None
727	return node_text, units
728
729	def _get_node_value(self, node):
730	"""
731	Get the value of a node and any applicable units
732
733	:param node: The XML node to get the value of
734	:param tagname: The tagname of the node
735	"""
736	#Get the text from the node and convert all whitespace to spaces
737	units = ''
738	node_value = node.text
739	if node_value is not None:
740	node_value = ' '.join(node_value.split())
741	else:
742	node_value = ""
743	node_value, units = self._get_node_value_from_text(node, node_value)
744	return node_value, units
745
746	def _unit_conversion(self, node, tagname, node_value):
747	"""
748	A unit converter method used to convert the data included in the file
749	to the default units listed in data_info
750
751	:param node: XML node
752	:param tagname: name of the node
753	:param node_value: The value of the current dom node
754	"""
755	attr = node.attrib
756	value_unit = ''
757	err_msg = None
758	default_unit = None
759	if not isinstance(node_value, float):
760	node_value = float(node_value)
761	if 'unit' in attr and attr.get('unit') is not None:
762	try:
763	local_unit = attr['unit']
764	unitname = self.ns_list.current_level.get("unit", "")
765	if "SASdetector" in self.names:
766	save_in = "detector"
767	elif "aperture" in self.names:
768	save_in = "aperture"
769	elif "SAScollimation" in self.names:
770	save_in = "collimation"
771	elif "SAStransmission_spectrum" in self.names:
772	save_in = "transspectrum"
773	elif "SASdata" in self.names:
774	x = np.zeros(1)
775	y = np.zeros(1)
776	self.current_data1d = Data1D(x, y)
777	save_in = "current_data1d"
778	elif "SASsource" in self.names:
779	save_in = "current_datainfo.source"
780	elif "SASsample" in self.names:
781	save_in = "current_datainfo.sample"
782	elif "SASprocess" in self.names:
783	save_in = "process"
784	else:
785	save_in = "current_datainfo"
786	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
787	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
788	and local_unit.lower() != "none":
789	if HAS_CONVERTER == True:
790	# Check local units - bad units raise KeyError
791	data_conv_q = Converter(local_unit)
792	value_unit = default_unit
793	node_value = data_conv_q(node_value, units=default_unit)
794	else:
795	value_unit = local_unit
796	err_msg = "Unit converter is not available.\n"
797	else:
798	value_unit = local_unit
799	except KeyError:
800	err_msg = "CanSAS reader: unexpected "
801	err_msg += "\"{0}\" unit [{1}]; "
802	err_msg = err_msg.format(tagname, local_unit)
803	err_msg += "expecting [{0}]".format(default_unit)
804	value_unit = local_unit
805	except:
806	err_msg = "CanSAS reader: unknown error converting "
807	err_msg += "\"{0}\" unit [{1}]"
808	err_msg = err_msg.format(tagname, local_unit)
809	value_unit = local_unit
810	elif 'unit' in attr:
811	value_unit = attr['unit']
812	if err_msg:
813	self.errors.add(err_msg)
814	return node_value, value_unit
815
816	def _check_for_empty_data(self):
817	"""
818	Creates an empty data set if no data is passed to the reader
819
820	:param data1d: presumably a Data1D object
821	"""
822	if self.current_dataset == None:
823	x_vals = np.empty(0)
824	y_vals = np.empty(0)
825	dx_vals = np.empty(0)
826	dy_vals = np.empty(0)
827	dxl = np.empty(0)
828	dxw = np.empty(0)
829	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
830	self.current_dataset.dxl = dxl
831	self.current_dataset.dxw = dxw
832
833	def _check_for_empty_resolution(self):
834	"""
835	A method to check all resolution data sets are the same size as I and Q
836	"""
837	if isinstance(self.current_dataset, plottable_1D):
838	dql_exists = False
839	dqw_exists = False
840	dq_exists = False
841	di_exists = False
842	if self.current_dataset.dxl is not None:
843	dql_exists = True
844	if self.current_dataset.dxw is not None:
845	dqw_exists = True
846	if self.current_dataset.dx is not None:
847	dq_exists = True
848	if self.current_dataset.dy is not None:
849	di_exists = True
850	if dqw_exists and not dql_exists:
851	array_size = self.current_dataset.dxw.size - 1
852	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
853	np.zeros([array_size]))
854	elif dql_exists and not dqw_exists:
855	array_size = self.current_dataset.dxl.size - 1
856	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
857	np.zeros([array_size]))
858	elif not dql_exists and not dqw_exists and not dq_exists:
859	array_size = self.current_dataset.x.size - 1
860	self.current_dataset.dx = np.append(self.current_dataset.dx,
861	np.zeros([array_size]))
862	if not di_exists:
863	array_size = self.current_dataset.y.size - 1
864	self.current_dataset.dy = np.append(self.current_dataset.dy,
865	np.zeros([array_size]))
866	elif isinstance(self.current_dataset, plottable_2D):
867	dqx_exists = False
868	dqy_exists = False
869	di_exists = False
870	mask_exists = False
871	if self.current_dataset.dqx_data is not None:
872	dqx_exists = True
873	if self.current_dataset.dqy_data is not None:
874	dqy_exists = True
875	if self.current_dataset.err_data is not None:
876	di_exists = True
877	if self.current_dataset.mask is not None:
878	mask_exists = True
879	if not dqy_exists:
880	array_size = self.current_dataset.qy_data.size - 1
881	self.current_dataset.dqy_data = np.append(
882	self.current_dataset.dqy_data, np.zeros([array_size]))
883	if not dqx_exists:
884	array_size = self.current_dataset.qx_data.size - 1
885	self.current_dataset.dqx_data = np.append(
886	self.current_dataset.dqx_data, np.zeros([array_size]))
887	if not di_exists:
888	array_size = self.current_dataset.data.size - 1
889	self.current_dataset.err_data = np.append(
890	self.current_dataset.err_data, np.zeros([array_size]))
891	if not mask_exists:
892	array_size = self.current_dataset.data.size - 1
893	self.current_dataset.mask = np.append(
894	self.current_dataset.mask,
895	np.ones([array_size] ,dtype=bool))
896
897	####### All methods below are for writing CanSAS XML files #######
898
899	def write(self, filename, datainfo):
900	"""
901	Write the content of a Data1D as a CanSAS XML file
902
903	:param filename: name of the file to write
904	:param datainfo: Data1D object
905	"""
906	# Create XML document
907	doc, _ = self._to_xml_doc(datainfo)
908	# Write the file
909	file_ref = open(filename, 'w')
910	if self.encoding == None:
911	self.encoding = "UTF-8"
912	doc.write(file_ref, encoding=self.encoding,
913	pretty_print=True, xml_declaration=True)
914	file_ref.close()
915
916	def _to_xml_doc(self, datainfo):
917	"""
918	Create an XML document to contain the content of a Data1D
919
920	:param datainfo: Data1D object
921	"""
922	is_2d = False
923	if issubclass(datainfo.__class__, Data2D):
924	is_2d = True
925
926	# Get PIs and create root element
927	pi_string = self._get_pi_string()
928	# Define namespaces and create SASroot object
929	main_node = self._create_main_node()
930	# Create ElementTree, append SASroot and apply processing instructions
931	base_string = pi_string + self.to_string(main_node)
932	base_element = self.create_element_from_string(base_string)
933	doc = self.create_tree(base_element)
934	# Create SASentry Element
935	entry_node = self.create_element("SASentry")
936	root = doc.getroot()
937	root.append(entry_node)
938
939	# Add Title to SASentry
940	self.write_node(entry_node, "Title", datainfo.title)
941	# Add Run to SASentry
942	self._write_run_names(datainfo, entry_node)
943	# Add Data info to SASEntry
944	if is_2d:
945	self._write_data_2d(datainfo, entry_node)
946	else:
947	if self._check_root():
948	self._write_data(datainfo, entry_node)
949	else:
950	self._write_data_linearized(datainfo, entry_node)
951	# Transmission Spectrum Info
952	# TODO: fix the writer to linearize all data, including T_spectrum
953	# self._write_trans_spectrum(datainfo, entry_node)
954	# Sample info
955	self._write_sample_info(datainfo, entry_node)
956	# Instrument info
957	instr = self._write_instrument(datainfo, entry_node)
958	# Source
959	self._write_source(datainfo, instr)
960	# Collimation
961	self._write_collimation(datainfo, instr)
962	# Detectors
963	self._write_detectors(datainfo, instr)
964	# Processes info
965	self._write_process_notes(datainfo, entry_node)
966	# Note info
967	self._write_notes(datainfo, entry_node)
968	# Return the document, and the SASentry node associated with
969	# the data we just wrote
970	# If the calling function was not the cansas reader, return a minidom
971	# object rather than an lxml object.
972	self.frm = inspect.stack()[1]
973	doc, entry_node = self._check_origin(entry_node, doc)
974	return doc, entry_node
975
976	def write_node(self, parent, name, value, attr=None):
977	"""
978	:param doc: document DOM
979	:param parent: parent node
980	:param name: tag of the element
981	:param value: value of the child text node
982	:param attr: attribute dictionary
983
984	:return: True if something was appended, otherwise False
985	"""
986	if value is not None:
987	parent = self.ebuilder(parent, name, value, attr)
988	return True
989	return False
990
991	def _get_pi_string(self):
992	"""
993	Creates the processing instructions header for writing to file
994	"""
995	pis = self.return_processing_instructions()
996	if len(pis) > 0:
997	pi_tree = self.create_tree(pis[0])
998	i = 1
999	for i in range(1, len(pis) - 1):
1000	pi_tree = self.append(pis[i], pi_tree)
1001	pi_string = self.to_string(pi_tree)
1002	else:
1003	pi_string = ""
1004	return pi_string
1005
1006	def _create_main_node(self):
1007	"""
1008	Creates the primary xml header used when writing to file
1009	"""
1010	xsi = "http://www.w3.org/2001/XMLSchema-instance"
1011	version = self.cansas_version
1012	n_s = CANSAS_NS.get(version).get("ns")
1013	if version == "1.1":
1014	url = "http://www.cansas.org/formats/1.1/"
1015	else:
1016	url = "http://www.cansas.org/formats/1.0/"
1017	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1018	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1019	"version" : version}
1020	nsmap = {'xsi' : xsi, None: n_s}
1021
1022	main_node = self.create_element("{" + n_s + "}SASroot",
1023	attrib=attrib, nsmap=nsmap)
1024	return main_node
1025
1026	def _write_run_names(self, datainfo, entry_node):
1027	"""
1028	Writes the run names to the XML file
1029
1030	:param datainfo: The Data1D object the information is coming from
1031	:param entry_node: lxml node ElementTree object to be appended to
1032	"""
1033	if datainfo.run == None or datainfo.run == []:
1034	datainfo.run.append(RUN_NAME_DEFAULT)
1035	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1036	for item in datainfo.run:
1037	runname = {}
1038	if item in datainfo.run_name and \
1039	len(str(datainfo.run_name[item])) > 1:
1040	runname = {'name': datainfo.run_name[item]}
1041	self.write_node(entry_node, "Run", item, runname)
1042
1043	def _write_data(self, datainfo, entry_node):
1044	"""
1045	Writes 1D I and Q data to the XML file
1046
1047	:param datainfo: The Data1D object the information is coming from
1048	:param entry_node: lxml node ElementTree object to be appended to
1049	"""
1050	node = self.create_element("SASdata")
1051	self.append(node, entry_node)
1052
1053	for i in range(len(datainfo.x)):
1054	point = self.create_element("Idata")
1055	node.append(point)
1056	self.write_node(point, "Q", datainfo.x[i],
1057	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1058	if len(datainfo.y) >= i:
1059	self.write_node(point, "I", datainfo.y[i],
1060	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1061	if datainfo.dy is not None and len(datainfo.dy) > i:
1062	self.write_node(point, "Idev", datainfo.dy[i],
1063	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1064	if datainfo.dx is not None and len(datainfo.dx) > i:
1065	self.write_node(point, "Qdev", datainfo.dx[i],
1066	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1067	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1068	self.write_node(point, "dQw", datainfo.dxw[i],
1069	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1070	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1071	self.write_node(point, "dQl", datainfo.dxl[i],
1072	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1073	if datainfo.isSesans:
1074	sesans = self.create_element("Sesans")
1075	sesans.text = str(datainfo.isSesans)
1076	node.append(sesans)
1077	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1078	{'unit': datainfo.sample.zacceptance[1]})
1079
1080
1081	def _write_data_2d(self, datainfo, entry_node):
1082	"""
1083	Writes 2D data to the XML file
1084
1085	:param datainfo: The Data2D object the information is coming from
1086	:param entry_node: lxml node ElementTree object to be appended to
1087	"""
1088	attr = {}
1089	if datainfo.data.shape:
1090	attr["x_bins"] = str(len(datainfo.x_bins))
1091	attr["y_bins"] = str(len(datainfo.y_bins))
1092	node = self.create_element("SASdata", attr)
1093	self.append(node, entry_node)
1094
1095	point = self.create_element("Idata")
1096	node.append(point)
1097	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1098	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1099	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1100
1101	self.write_node(point, "Qx", qx,
1102	{'unit': datainfo._xunit})
1103	self.write_node(point, "Qy", qy,
1104	{'unit': datainfo._yunit})
1105	self.write_node(point, "I", intensity,
1106	{'unit': datainfo._zunit})
1107	if datainfo.err_data is not None:
1108	err = ','.join([str(datainfo.err_data[i]) for i in
1109	xrange(len(datainfo.err_data))])
1110	self.write_node(point, "Idev", err,
1111	{'unit': datainfo._zunit})
1112	if datainfo.dqy_data is not None:
1113	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1114	xrange(len(datainfo.dqy_data))])
1115	self.write_node(point, "Qydev", dqy,
1116	{'unit': datainfo._yunit})
1117	if datainfo.dqx_data is not None:
1118	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1119	xrange(len(datainfo.dqx_data))])
1120	self.write_node(point, "Qxdev", dqx,
1121	{'unit': datainfo._xunit})
1122	if datainfo.mask is not None:
1123	mask = ','.join(
1124	["1" if datainfo.mask[i] else "0"
1125	for i in xrange(len(datainfo.mask))])
1126	self.write_node(point, "Mask", mask)
1127
1128	def _write_trans_spectrum(self, datainfo, entry_node):
1129	"""
1130	Writes the transmission spectrum data to the XML file
1131
1132	:param datainfo: The Data1D object the information is coming from
1133	:param entry_node: lxml node ElementTree object to be appended to
1134	"""
1135	for i in range(len(datainfo.trans_spectrum)):
1136	spectrum = datainfo.trans_spectrum[i]
1137	node = self.create_element("SAStransmission_spectrum",
1138	{"name" : spectrum.name})
1139	self.append(node, entry_node)
1140	if isinstance(spectrum.timestamp, datetime.datetime):
1141	node.setAttribute("timestamp", spectrum.timestamp)
1142	for i in range(len(spectrum.wavelength)):
1143	point = self.create_element("Tdata")
1144	node.append(point)
1145	self.write_node(point, "Lambda", spectrum.wavelength[i],
1146	{'unit': spectrum.wavelength_unit})
1147	self.write_node(point, "T", spectrum.transmission[i],
1148	{'unit': spectrum.transmission_unit})
1149	if spectrum.transmission_deviation != None \
1150	and len(spectrum.transmission_deviation) >= i:
1151	self.write_node(point, "Tdev",
1152	spectrum.transmission_deviation[i],
1153	{'unit':
1154	spectrum.transmission_deviation_unit})
1155
1156	def _write_sample_info(self, datainfo, entry_node):
1157	"""
1158	Writes the sample information to the XML file
1159
1160	:param datainfo: The Data1D object the information is coming from
1161	:param entry_node: lxml node ElementTree object to be appended to
1162	"""
1163	sample = self.create_element("SASsample")
1164	if datainfo.sample.name is not None:
1165	self.write_attribute(sample, "name",
1166	str(datainfo.sample.name))
1167	self.append(sample, entry_node)
1168	self.write_node(sample, "ID", str(datainfo.sample.ID))
1169	self.write_node(sample, "thickness", datainfo.sample.thickness,
1170	{"unit": datainfo.sample.thickness_unit})
1171	self.write_node(sample, "transmission", datainfo.sample.transmission)
1172	self.write_node(sample, "temperature", datainfo.sample.temperature,
1173	{"unit": datainfo.sample.temperature_unit})
1174
1175	pos = self.create_element("position")
1176	written = self.write_node(pos,
1177	"x",
1178	datainfo.sample.position.x,
1179	{"unit": datainfo.sample.position_unit})
1180	written = written \| self.write_node( \
1181	pos, "y", datainfo.sample.position.y,
1182	{"unit": datainfo.sample.position_unit})
1183	written = written \| self.write_node( \
1184	pos, "z", datainfo.sample.position.z,
1185	{"unit": datainfo.sample.position_unit})
1186	if written == True:
1187	self.append(pos, sample)
1188
1189	ori = self.create_element("orientation")
1190	written = self.write_node(ori, "roll",
1191	datainfo.sample.orientation.x,
1192	{"unit": datainfo.sample.orientation_unit})
1193	written = written \| self.write_node( \
1194	ori, "pitch", datainfo.sample.orientation.y,
1195	{"unit": datainfo.sample.orientation_unit})
1196	written = written \| self.write_node( \
1197	ori, "yaw", datainfo.sample.orientation.z,
1198	{"unit": datainfo.sample.orientation_unit})
1199	if written == True:
1200	self.append(ori, sample)
1201
1202	for item in datainfo.sample.details:
1203	self.write_node(sample, "details", item)
1204
1205	def _write_instrument(self, datainfo, entry_node):
1206	"""
1207	Writes the instrumental information to the XML file
1208
1209	:param datainfo: The Data1D object the information is coming from
1210	:param entry_node: lxml node ElementTree object to be appended to
1211	"""
1212	instr = self.create_element("SASinstrument")
1213	self.append(instr, entry_node)
1214	self.write_node(instr, "name", datainfo.instrument)
1215	return instr
1216
1217	def _write_source(self, datainfo, instr):
1218	"""
1219	Writes the source information to the XML file
1220
1221	:param datainfo: The Data1D object the information is coming from
1222	:param instr: instrument node to be appended to
1223	"""
1224	source = self.create_element("SASsource")
1225	if datainfo.source.name is not None:
1226	self.write_attribute(source, "name",
1227	str(datainfo.source.name))
1228	self.append(source, instr)
1229	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1230	datainfo.source.radiation = "neutron"
1231	self.write_node(source, "radiation", datainfo.source.radiation)
1232
1233	size = self.create_element("beam_size")
1234	if datainfo.source.beam_size_name is not None:
1235	self.write_attribute(size, "name",
1236	str(datainfo.source.beam_size_name))
1237	written = self.write_node( \
1238	size, "x", datainfo.source.beam_size.x,
1239	{"unit": datainfo.source.beam_size_unit})
1240	written = written \| self.write_node( \
1241	size, "y", datainfo.source.beam_size.y,
1242	{"unit": datainfo.source.beam_size_unit})
1243	written = written \| self.write_node( \
1244	size, "z", datainfo.source.beam_size.z,
1245	{"unit": datainfo.source.beam_size_unit})
1246	if written == True:
1247	self.append(size, source)
1248
1249	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1250	self.write_node(source, "wavelength",
1251	datainfo.source.wavelength,
1252	{"unit": datainfo.source.wavelength_unit})
1253	self.write_node(source, "wavelength_min",
1254	datainfo.source.wavelength_min,
1255	{"unit": datainfo.source.wavelength_min_unit})
1256	self.write_node(source, "wavelength_max",
1257	datainfo.source.wavelength_max,
1258	{"unit": datainfo.source.wavelength_max_unit})
1259	self.write_node(source, "wavelength_spread",
1260	datainfo.source.wavelength_spread,
1261	{"unit": datainfo.source.wavelength_spread_unit})
1262
1263	def _write_collimation(self, datainfo, instr):
1264	"""
1265	Writes the collimation information to the XML file
1266
1267	:param datainfo: The Data1D object the information is coming from
1268	:param instr: lxml node ElementTree object to be appended to
1269	"""
1270	if datainfo.collimation == [] or datainfo.collimation == None:
1271	coll = Collimation()
1272	datainfo.collimation.append(coll)
1273	for item in datainfo.collimation:
1274	coll = self.create_element("SAScollimation")
1275	if item.name is not None:
1276	self.write_attribute(coll, "name", str(item.name))
1277	self.append(coll, instr)
1278
1279	self.write_node(coll, "length", item.length,
1280	{"unit": item.length_unit})
1281
1282	for aperture in item.aperture:
1283	apert = self.create_element("aperture")
1284	if aperture.name is not None:
1285	self.write_attribute(apert, "name", str(aperture.name))
1286	if aperture.type is not None:
1287	self.write_attribute(apert, "type", str(aperture.type))
1288	self.append(apert, coll)
1289
1290	size = self.create_element("size")
1291	if aperture.size_name is not None:
1292	self.write_attribute(size, "name",
1293	str(aperture.size_name))
1294	written = self.write_node(size, "x", aperture.size.x,
1295	{"unit": aperture.size_unit})
1296	written = written \| self.write_node( \
1297	size, "y", aperture.size.y,
1298	{"unit": aperture.size_unit})
1299	written = written \| self.write_node( \
1300	size, "z", aperture.size.z,
1301	{"unit": aperture.size_unit})
1302	if written == True:
1303	self.append(size, apert)
1304
1305	self.write_node(apert, "distance", aperture.distance,
1306	{"unit": aperture.distance_unit})
1307
1308	def _write_detectors(self, datainfo, instr):
1309	"""
1310	Writes the detector information to the XML file
1311
1312	:param datainfo: The Data1D object the information is coming from
1313	:param inst: lxml instrument node to be appended to
1314	"""
1315	if datainfo.detector == None or datainfo.detector == []:
1316	det = Detector()
1317	det.name = ""
1318	datainfo.detector.append(det)
1319
1320	for item in datainfo.detector:
1321	det = self.create_element("SASdetector")
1322	written = self.write_node(det, "name", item.name)
1323	written = written \| self.write_node(det, "SDD", item.distance,
1324	{"unit": item.distance_unit})
1325	if written == True:
1326	self.append(det, instr)
1327
1328	off = self.create_element("offset")
1329	written = self.write_node(off, "x", item.offset.x,
1330	{"unit": item.offset_unit})
1331	written = written \| self.write_node(off, "y", item.offset.y,
1332	{"unit": item.offset_unit})
1333	written = written \| self.write_node(off, "z", item.offset.z,
1334	{"unit": item.offset_unit})
1335	if written == True:
1336	self.append(off, det)
1337
1338	ori = self.create_element("orientation")
1339	written = self.write_node(ori, "roll", item.orientation.x,
1340	{"unit": item.orientation_unit})
1341	written = written \| self.write_node(ori, "pitch",
1342	item.orientation.y,
1343	{"unit": item.orientation_unit})
1344	written = written \| self.write_node(ori, "yaw",
1345	item.orientation.z,
1346	{"unit": item.orientation_unit})
1347	if written == True:
1348	self.append(ori, det)
1349
1350	center = self.create_element("beam_center")
1351	written = self.write_node(center, "x", item.beam_center.x,
1352	{"unit": item.beam_center_unit})
1353	written = written \| self.write_node(center, "y",
1354	item.beam_center.y,
1355	{"unit": item.beam_center_unit})
1356	written = written \| self.write_node(center, "z",
1357	item.beam_center.z,
1358	{"unit": item.beam_center_unit})
1359	if written == True:
1360	self.append(center, det)
1361
1362	pix = self.create_element("pixel_size")
1363	written = self.write_node(pix, "x", item.pixel_size.x,
1364	{"unit": item.pixel_size_unit})
1365	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1366	{"unit": item.pixel_size_unit})
1367	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1368	{"unit": item.pixel_size_unit})
1369	if written == True:
1370	self.append(pix, det)
1371	self.write_node(det, "slit_length", item.slit_length,
1372	{"unit": item.slit_length_unit})
1373
1374	def _write_process_notes(self, datainfo, entry_node):
1375	"""
1376	Writes the process notes to the XML file
1377
1378	:param datainfo: The Data1D object the information is coming from
1379	:param entry_node: lxml node ElementTree object to be appended to
1380
1381	"""
1382	for item in datainfo.process:
1383	node = self.create_element("SASprocess")
1384	self.append(node, entry_node)
1385	self.write_node(node, "name", item.name)
1386	self.write_node(node, "date", item.date)
1387	self.write_node(node, "description", item.description)
1388	for term in item.term:
1389	if isinstance(term, list):
1390	value = term['value']
1391	del term['value']
1392	elif isinstance(term, dict):
1393	value = term.get("value")
1394	del term['value']
1395	else:
1396	value = term
1397	self.write_node(node, "term", value, term)
1398	for note in item.notes:
1399	self.write_node(node, "SASprocessnote", note)
1400	if len(item.notes) == 0:
1401	self.write_node(node, "SASprocessnote", "")
1402
1403	def _write_notes(self, datainfo, entry_node):
1404	"""
1405	Writes the notes to the XML file and creates an empty note if none
1406	exist
1407
1408	:param datainfo: The Data1D object the information is coming from
1409	:param entry_node: lxml node ElementTree object to be appended to
1410
1411	"""
1412	if len(datainfo.notes) == 0:
1413	node = self.create_element("SASnote")
1414	self.append(node, entry_node)
1415	else:
1416	for item in datainfo.notes:
1417	node = self.create_element("SASnote")
1418	self.write_text(node, item)
1419	self.append(node, entry_node)
1420
1421	def _check_root(self):
1422	"""
1423	Return the document, and the SASentry node associated with
1424	the data we just wrote.
1425	If the calling function was not the cansas reader, return a minidom
1426	object rather than an lxml object.
1427
1428	:param entry_node: lxml node ElementTree object to be appended to
1429	:param doc: entire xml tree
1430	"""
1431	if not self.frm:
1432	self.frm = inspect.stack()[2]
1433	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1434	mod_name = mod_name.replace(".py", "")
1435	mod = mod_name.split("sas/")
1436	mod_name = mod[1]
1437	return mod_name == "sascalc/dataloader/readers/cansas_reader"
1438
1439	def _check_origin(self, entry_node, doc):
1440	"""
1441	Return the document, and the SASentry node associated with
1442	the data we just wrote.
1443	If the calling function was not the cansas reader, return a minidom
1444	object rather than an lxml object.
1445
1446	:param entry_node: lxml node ElementTree object to be appended to
1447	:param doc: entire xml tree
1448	"""
1449	if not self._check_root():
1450	string = self.to_string(doc, pretty_print=False)
1451	doc = parseString(string)
1452	node_name = entry_node.tag
1453	node_list = doc.getElementsByTagName(node_name)
1454	entry_node = node_list.item(0)
1455	return doc, entry_node
1456
1457	# DO NOT REMOVE - used in saving and loading panel states.
1458	def _store_float(self, location, node, variable, storage, optional=True):
1459	"""
1460	Get the content of a xpath location and store
1461	the result. Check that the units are compatible
1462	with the destination. The value is expected to
1463	be a float.
1464
1465	The xpath location might or might not exist.
1466	If it does not exist, nothing is done
1467
1468	:param location: xpath location to fetch
1469	:param node: node to read the data from
1470	:param variable: name of the data member to store it in [string]
1471	:param storage: data object that has the 'variable' data member
1472	:param optional: if True, no exception will be raised
1473	if unit conversion can't be done
1474
1475	:raise ValueError: raised when the units are not recognized
1476	"""
1477	entry = get_content(location, node)
1478	try:
1479	value = float(entry.text)
1480	except:
1481	value = None
1482
1483	if value is not None:
1484	# If the entry has units, check to see that they are
1485	# compatible with what we currently have in the data object
1486	units = entry.get('unit')
1487	if units is not None:
1488	toks = variable.split('.')
1489	local_unit = None
1490	exec "local_unit = storage.%s_unit" % toks[0]
1491	if local_unit != None and units.lower() != local_unit.lower():
1492	if HAS_CONVERTER == True:
1493	try:
1494	conv = Converter(units)
1495	exec "storage.%s = %g" % \
1496	(variable, conv(value, units=local_unit))
1497	except:
1498	_, exc_value, _ = sys.exc_info()
1499	err_mess = "CanSAS reader: could not convert"
1500	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1501	% (variable, units, local_unit, exc_value)
1502	self.errors.add(err_mess)
1503	if optional:
1504	logging.info(err_mess)
1505	else:
1506	raise ValueError, err_mess
1507	else:
1508	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1509	% (variable, units)
1510	err_mess += " expecting [%s]" % local_unit
1511	self.errors.add(err_mess)
1512	if optional:
1513	logging.info(err_mess)
1514	else:
1515	raise ValueError, err_mess
1516	else:
1517	exec "storage.%s = value" % variable
1518	else:
1519	exec "storage.%s = value" % variable
1520
1521	# DO NOT REMOVE - used in saving and loading panel states.
1522	def _store_content(self, location, node, variable, storage):
1523	"""
1524	Get the content of a xpath location and store
1525	the result. The value is treated as a string.
1526
1527	The xpath location might or might not exist.
1528	If it does not exist, nothing is done
1529
1530	:param location: xpath location to fetch
1531	:param node: node to read the data from
1532	:param variable: name of the data member to store it in [string]
1533	:param storage: data object that has the 'variable' data member
1534
1535	:return: return a list of errors
1536	"""
1537	entry = get_content(location, node)
1538	if entry is not None and entry.text is not None:
1539	exec "storage.%s = entry.text.strip()" % variable
1540
1541
1542	# DO NOT REMOVE Called by outside packages:
1543	# sas.sasgui.perspectives.invariant.invariant_state
1544	# sas.sasgui.perspectives.fitting.pagestate
1545	def get_content(location, node):
1546	"""
1547	Get the first instance of the content of a xpath location.
1548
1549	:param location: xpath location
1550	:param node: node to start at
1551
1552	:return: Element, or None
1553	"""
1554	nodes = node.xpath(location,
1555	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1556	if len(nodes) > 0:
1557	return nodes[0]
1558	else:
1559	return None
1560
1561	# DO NOT REMOVE Called by outside packages:
1562	# sas.sasgui.perspectives.fitting.pagestate
1563	def write_node(doc, parent, name, value, attr=None):
1564	"""
1565	:param doc: document DOM
1566	:param parent: parent node
1567	:param name: tag of the element
1568	:param value: value of the child text node
1569	:param attr: attribute dictionary
1570
1571	:return: True if something was appended, otherwise False
1572	"""
1573	if attr is None:
1574	attr = {}
1575	if value is not None:
1576	node = doc.createElement(name)
1577	node.appendChild(doc.createTextNode(str(value)))
1578	for item in attr:
1579	node.setAttribute(item, attr[item])
1580	parent.appendChild(node)
1581	return True
1582	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ a2573fc

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