cansas_reader.py @ 6a455cd3

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 6a455cd3 was 6a455cd3, checked in by krzywon, 7 years ago

Merge branch 'master' into 4_1_issues

# Conflicts:
# docs/sphinx-docs/source/conf.py
# src/sas/sascalc/dataloader/readers/cansas_reader.py
# src/sas/sasgui/guiframe/documentation_window.py
# src/sas/sasgui/perspectives/fitting/models.py

Property mode set to 100644

File size: 70.9 KB

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

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 6a455cd3

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