cansas_reader.py @ b5e9ce26

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since b5e9ce26 was b5e9ce26, checked in by GitHub <noreply@…>, 7 years ago
Merge branch 'master' into sesans41
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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	# Get the element name and set the current names level
212	tagname = node.tag.replace(self.base_ns, "")
213	tagname_original = tagname
214	# Skip this iteration when loading in save state information
215	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
216	continue
217
218	# Get where to store content
219	self.names.append(tagname_original)
220	self.ns_list = CONSTANTS.iterate_namespace(self.names)
221	# If the element is a child element, recurse
222	if len(node.getchildren()) > 0:
223	self.parent_class = tagname_original
224	if tagname == 'SASdata':
225	self._initialize_new_data_set(node)
226	if isinstance(self.current_dataset, plottable_2D):
227	x_bins = attr.get("x_bins", "")
228	y_bins = attr.get("y_bins", "")
229	if x_bins is not "" and y_bins is not "":
230	self.current_dataset.shape = (x_bins, y_bins)
231	else:
232	self.current_dataset.shape = ()
233	# Recursion step to access data within the group
234	self._parse_entry(node, True)
235	if tagname == "SASsample":
236	self.current_datainfo.sample.name = name
237	elif tagname == "beam_size":
238	self.current_datainfo.source.beam_size_name = name
239	elif tagname == "SAScollimation":
240	self.collimation.name = name
241	elif tagname == "aperture":
242	self.aperture.name = name
243	self.aperture.type = type
244	self.add_intermediate()
245	else:
246	if isinstance(self.current_dataset, plottable_2D):
247	data_point = node.text
248	unit = attr.get('unit', '')
249	else:
250	data_point, unit = self._get_node_value(node, tagname)
251
252	# If this is a dataset, store the data appropriately
253	if tagname == 'Run':
254	self.current_datainfo.run_name[data_point] = name
255	self.current_datainfo.run.append(data_point)
256	elif tagname == 'Title':
257	self.current_datainfo.title = data_point
258	elif tagname == 'SASnote':
259	self.current_datainfo.notes.append(data_point)
260
261	# I and Q - 1D data
262	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
263	unit_list = unit.split(" \| ")
264	if len(unit_list) > 1:
265	self.current_dataset.yaxis(unit_list[0], unit_list[1])
266	else:
267	self.current_dataset.yaxis("Intensity", unit)
268	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
269	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
270	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
271	elif tagname == 'Q':
272	unit_list = unit.split(" \| ")
273	if len(unit_list) > 1:
274	self.current_dataset.xaxis(unit_list[0], unit_list[1])
275	else:
276	self.current_dataset.xaxis("Q", unit)
277	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
278	elif tagname == 'Qdev':
279	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
280	elif tagname == 'dQw':
281	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
282	elif tagname == 'dQl':
283	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
284	elif tagname == 'Qmean':
285	pass
286	elif tagname == 'Shadowfactor':
287	pass
288	elif tagname == 'Sesans':
289	self.current_datainfo.isSesans = bool(data_point)
290	elif tagname == 'zacceptance':
291	self.current_datainfo.sample.zacceptance = (data_point, unit)
292
293	# I and Qx, Qy - 2D data
294	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
295	self.current_dataset.yaxis("Intensity", unit)
296	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
297	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
298	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
299	elif tagname == 'Qx':
300	self.current_dataset.xaxis("Qx", unit)
301	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
302	elif tagname == 'Qy':
303	self.current_dataset.yaxis("Qy", unit)
304	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qxdev':
306	self.current_dataset.xaxis("Qxdev", unit)
307	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qydev':
309	self.current_dataset.yaxis("Qydev", unit)
310	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Mask':
312	inter = [item == "1" for item in data_point.split(",")]
313	self.current_dataset.mask = np.asarray(inter, dtype=bool)
314
315	# Sample Information
316	elif tagname == 'ID' and self.parent_class == 'SASsample':
317	self.current_datainfo.sample.ID = data_point
318	elif tagname == 'Title' and self.parent_class == 'SASsample':
319	self.current_datainfo.sample.name = data_point
320	elif tagname == 'thickness' and self.parent_class == 'SASsample':
321	self.current_datainfo.sample.thickness = data_point
322	self.current_datainfo.sample.thickness_unit = unit
323	elif tagname == 'transmission' and self.parent_class == 'SASsample':
324	self.current_datainfo.sample.transmission = data_point
325	elif tagname == 'temperature' and self.parent_class == 'SASsample':
326	self.current_datainfo.sample.temperature = data_point
327	self.current_datainfo.sample.temperature_unit = unit
328	elif tagname == 'details' and self.parent_class == 'SASsample':
329	self.current_datainfo.sample.details.append(data_point)
330	elif tagname == 'x' and self.parent_class == 'position':
331	self.current_datainfo.sample.position.x = data_point
332	self.current_datainfo.sample.position_unit = unit
333	elif tagname == 'y' and self.parent_class == 'position':
334	self.current_datainfo.sample.position.y = data_point
335	self.current_datainfo.sample.position_unit = unit
336	elif tagname == 'z' and self.parent_class == 'position':
337	self.current_datainfo.sample.position.z = data_point
338	self.current_datainfo.sample.position_unit = unit
339	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
340	self.current_datainfo.sample.orientation.x = data_point
341	self.current_datainfo.sample.orientation_unit = unit
342	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
343	self.current_datainfo.sample.orientation.y = data_point
344	self.current_datainfo.sample.orientation_unit = unit
345	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
346	self.current_datainfo.sample.orientation.z = data_point
347	self.current_datainfo.sample.orientation_unit = unit
348
349	# Instrumental Information
350	elif tagname == 'name' and self.parent_class == 'SASinstrument':
351	self.current_datainfo.instrument = data_point
352	# Detector Information
353	elif tagname == 'name' and self.parent_class == 'SASdetector':
354	self.detector.name = data_point
355	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
356	self.detector.distance = data_point
357	self.detector.distance_unit = unit
358	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
359	self.detector.slit_length = data_point
360	self.detector.slit_length_unit = unit
361	elif tagname == 'x' and self.parent_class == 'offset':
362	self.detector.offset.x = data_point
363	self.detector.offset_unit = unit
364	elif tagname == 'y' and self.parent_class == 'offset':
365	self.detector.offset.y = data_point
366	self.detector.offset_unit = unit
367	elif tagname == 'z' and self.parent_class == 'offset':
368	self.detector.offset.z = data_point
369	self.detector.offset_unit = unit
370	elif tagname == 'x' and self.parent_class == 'beam_center':
371	self.detector.beam_center.x = data_point
372	self.detector.beam_center_unit = unit
373	elif tagname == 'y' and self.parent_class == 'beam_center':
374	self.detector.beam_center.y = data_point
375	self.detector.beam_center_unit = unit
376	elif tagname == 'z' and self.parent_class == 'beam_center':
377	self.detector.beam_center.z = data_point
378	self.detector.beam_center_unit = unit
379	elif tagname == 'x' and self.parent_class == 'pixel_size':
380	self.detector.pixel_size.x = data_point
381	self.detector.pixel_size_unit = unit
382	elif tagname == 'y' and self.parent_class == 'pixel_size':
383	self.detector.pixel_size.y = data_point
384	self.detector.pixel_size_unit = unit
385	elif tagname == 'z' and self.parent_class == 'pixel_size':
386	self.detector.pixel_size.z = data_point
387	self.detector.pixel_size_unit = unit
388	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
389	self.detector.orientation.x = data_point
390	self.detector.orientation_unit = unit
391	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
392	self.detector.orientation.y = data_point
393	self.detector.orientation_unit = unit
394	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
395	self.detector.orientation.z = data_point
396	self.detector.orientation_unit = unit
397	# Collimation and Aperture
398	elif tagname == 'length' and self.parent_class == 'SAScollimation':
399	self.collimation.length = data_point
400	self.collimation.length_unit = unit
401	elif tagname == 'name' and self.parent_class == 'SAScollimation':
402	self.collimation.name = data_point
403	elif tagname == 'distance' and self.parent_class == 'aperture':
404	self.aperture.distance = data_point
405	self.aperture.distance_unit = unit
406	elif tagname == 'x' and self.parent_class == 'size':
407	self.aperture.size.x = data_point
408	self.collimation.size_unit = unit
409	elif tagname == 'y' and self.parent_class == 'size':
410	self.aperture.size.y = data_point
411	self.collimation.size_unit = unit
412	elif tagname == 'z' and self.parent_class == 'size':
413	self.aperture.size.z = data_point
414	self.collimation.size_unit = unit
415
416	# Process Information
417	elif tagname == 'name' and self.parent_class == 'SASprocess':
418	self.process.name = data_point
419	elif tagname == 'description' and self.parent_class == 'SASprocess':
420	self.process.description = data_point
421	elif tagname == 'date' and self.parent_class == 'SASprocess':
422	try:
423	self.process.date = datetime.datetime.fromtimestamp(data_point)
424	except:
425	self.process.date = data_point
426	elif tagname == 'SASprocessnote':
427	self.process.notes.append(data_point)
428	elif tagname == 'term' and self.parent_class == 'SASprocess':
429	unit = attr.get("unit", "")
430	dic = {}
431	dic["name"] = name
432	dic["value"] = data_point
433	dic["unit"] = unit
434	self.process.term.append(dic)
435
436	# Transmission Spectrum
437	elif tagname == 'T' and self.parent_class == 'Tdata':
438	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
439	self.transspectrum.transmission_unit = unit
440	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
441	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
442	self.transspectrum.transmission_deviation_unit = unit
443	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
444	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
445	self.transspectrum.wavelength_unit = unit
446
447	# Source Information
448	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
449	self.current_datainfo.source.wavelength = data_point
450	self.current_datainfo.source.wavelength_unit = unit
451	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
452	self.current_datainfo.source.wavelength_min = data_point
453	self.current_datainfo.source.wavelength_min_unit = unit
454	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
455	self.current_datainfo.source.wavelength_max = data_point
456	self.current_datainfo.source.wavelength_max_unit = unit
457	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
458	self.current_datainfo.source.wavelength_spread = data_point
459	self.current_datainfo.source.wavelength_spread_unit = unit
460	elif tagname == 'x' and self.parent_class == 'beam_size':
461	self.current_datainfo.source.beam_size.x = data_point
462	self.current_datainfo.source.beam_size_unit = unit
463	elif tagname == 'y' and self.parent_class == 'beam_size':
464	self.current_datainfo.source.beam_size.y = data_point
465	self.current_datainfo.source.beam_size_unit = unit
466	elif tagname == 'z' and self.parent_class == 'pixel_size':
467	self.current_datainfo.source.data_point.z = data_point
468	self.current_datainfo.source.beam_size_unit = unit
469	elif tagname == 'radiation' and self.parent_class == 'SASsource':
470	self.current_datainfo.source.radiation = data_point
471	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
472	self.current_datainfo.source.beam_shape = data_point
473
474	# Everything else goes in meta_data
475	else:
476	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
477	self.current_datainfo.meta_data[new_key] = data_point
478
479	self.names.remove(tagname_original)
480	length = 0
481	if len(self.names) > 1:
482	length = len(self.names) - 1
483	self.parent_class = self.names[length]
484	if not self._is_call_local() and not recurse:
485	self.frm = ""
486	self.add_data_set()
487	empty = None
488	return self.output[0], empty
489
490
491	def _is_call_local(self):
492	"""
493
494	"""
495	if self.frm == "":
496	inter = inspect.stack()
497	self.frm = inter[2]
498	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
499	mod_name = mod_name.replace(".py", "")
500	mod = mod_name.split("sas/")
501	mod_name = mod[1]
502	if mod_name != "sascalc/dataloader/readers/cansas_reader":
503	return False
504	return True
505
506	def is_cansas(self, ext="xml"):
507	"""
508	Checks to see if the xml file is a CanSAS file
509
510	:param ext: The file extension of the data file
511	"""
512	if self.validate_xml():
513	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
514	value = self.xmlroot.get(name)
515	if CANSAS_NS.get(self.cansas_version).get("ns") == \
516	value.rsplit(" ")[0]:
517	return True
518	if ext == "svs":
519	return True
520	raise RuntimeError
521
522	def load_file_and_schema(self, xml_file, schema_path=""):
523	"""
524	Loads the file and associates a schema, if a schema is passed in or if one already exists
525
526	:param xml_file: The xml file path sent to Reader.read
527	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
528	"""
529	base_name = xml_reader.__file__
530	base_name = base_name.replace("\\", "/")
531	base = base_name.split("/sas/")[0]
532
533	# Load in xml file and get the cansas version from the header
534	self.set_xml_file(xml_file)
535	self.cansas_version = self.xmlroot.get("version", "1.0")
536
537	# Generic values for the cansas file based on the version
538	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
539	if schema_path == "":
540	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
541	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
542
543	# Link a schema to the XML file.
544	self.set_schema(schema_path)
545
546	def add_data_set(self):
547	"""
548	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
549	private method to generate a new data set.
550
551	:param key: NeXus group name for current tree level
552	"""
553
554	if self.current_datainfo and self.current_dataset:
555	self._final_cleanup()
556	self.data = []
557	self.current_datainfo = DataInfo()
558
559	def _initialize_new_data_set(self, node=None):
560	"""
561	A private class method to generate a new 1D data object.
562	Outside methods should call add_data_set() to be sure any existing data is stored properly.
563
564	:param node: XML node to determine if 1D or 2D data
565	"""
566	x = np.array(0)
567	y = np.array(0)
568	for child in node:
569	if child.tag.replace(self.base_ns, "") == "Idata":
570	for i_child in child:
571	if i_child.tag.replace(self.base_ns, "") == "Qx":
572	self.current_dataset = plottable_2D()
573	return
574	self.current_dataset = plottable_1D(x, y)
575
576	def add_intermediate(self):
577	"""
578	This method stores any intermediate objects within the final data set after fully reading the set.
579
580	:param parent: The NXclass name for the h5py Group object that just finished being processed
581	"""
582
583	if self.parent_class == 'SASprocess':
584	self.current_datainfo.process.append(self.process)
585	self.process = Process()
586	elif self.parent_class == 'SASdetector':
587	self.current_datainfo.detector.append(self.detector)
588	self.detector = Detector()
589	elif self.parent_class == 'SAStransmission_spectrum':
590	self.current_datainfo.trans_spectrum.append(self.transspectrum)
591	self.transspectrum = TransmissionSpectrum()
592	elif self.parent_class == 'SAScollimation':
593	self.current_datainfo.collimation.append(self.collimation)
594	self.collimation = Collimation()
595	elif self.parent_class == 'aperture':
596	self.collimation.aperture.append(self.aperture)
597	self.aperture = Aperture()
598	elif self.parent_class == 'SASdata':
599	self._check_for_empty_resolution()
600	self.data.append(self.current_dataset)
601
602	def _final_cleanup(self):
603	"""
604	Final cleanup of the Data1D object to be sure it has all the
605	appropriate information needed for perspectives
606	"""
607
608	# Append errors to dataset and reset class errors
609	self.current_datainfo.errors = set()
610	for error in self.errors:
611	self.current_datainfo.errors.add(error)
612	self.errors.clear()
613
614	# Combine all plottables with datainfo and append each to output
615	# Type cast data arrays to float64 and find min/max as appropriate
616	for dataset in self.data:
617	if isinstance(dataset, plottable_1D):
618	if dataset.x is not None:
619	dataset.x = np.delete(dataset.x, [0])
620	dataset.x = dataset.x.astype(np.float64)
621	dataset.xmin = np.min(dataset.x)
622	dataset.xmax = np.max(dataset.x)
623	if dataset.y is not None:
624	dataset.y = np.delete(dataset.y, [0])
625	dataset.y = dataset.y.astype(np.float64)
626	dataset.ymin = np.min(dataset.y)
627	dataset.ymax = np.max(dataset.y)
628	if dataset.dx is not None:
629	dataset.dx = np.delete(dataset.dx, [0])
630	dataset.dx = dataset.dx.astype(np.float64)
631	if dataset.dxl is not None:
632	dataset.dxl = np.delete(dataset.dxl, [0])
633	dataset.dxl = dataset.dxl.astype(np.float64)
634	if dataset.dxw is not None:
635	dataset.dxw = np.delete(dataset.dxw, [0])
636	dataset.dxw = dataset.dxw.astype(np.float64)
637	if dataset.dy is not None:
638	dataset.dy = np.delete(dataset.dy, [0])
639	dataset.dy = dataset.dy.astype(np.float64)
640	np.trim_zeros(dataset.x)
641	np.trim_zeros(dataset.y)
642	np.trim_zeros(dataset.dy)
643	elif isinstance(dataset, plottable_2D):
644	dataset.data = dataset.data.astype(np.float64)
645	dataset.qx_data = dataset.qx_data.astype(np.float64)
646	dataset.xmin = np.min(dataset.qx_data)
647	dataset.xmax = np.max(dataset.qx_data)
648	dataset.qy_data = dataset.qy_data.astype(np.float64)
649	dataset.ymin = np.min(dataset.qy_data)
650	dataset.ymax = np.max(dataset.qy_data)
651	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
652	+ dataset.qy_data * dataset.qy_data)
653	if dataset.err_data is not None:
654	dataset.err_data = dataset.err_data.astype(np.float64)
655	if dataset.dqx_data is not None:
656	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
657	if dataset.dqy_data is not None:
658	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
659	if dataset.mask is not None:
660	dataset.mask = dataset.mask.astype(dtype=bool)
661
662	if len(dataset.shape) == 2:
663	n_rows, n_cols = dataset.shape
664	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
665	dataset.x_bins = dataset.qx_data[:int(n_cols)]
666	dataset.data = dataset.data.flatten()
667	else:
668	dataset.y_bins = []
669	dataset.x_bins = []
670	dataset.data = dataset.data.flatten()
671
672	final_dataset = combine_data(dataset, self.current_datainfo)
673	self.output.append(final_dataset)
674
675	def _create_unique_key(self, dictionary, name, numb=0):
676	"""
677	Create a unique key value for any dictionary to prevent overwriting
678	Recurse until a unique key value is found.
679
680	:param dictionary: A dictionary with any number of entries
681	:param name: The index of the item to be added to dictionary
682	:param numb: The number to be appended to the name, starts at 0
683	"""
684	if dictionary.get(name) is not None:
685	numb += 1
686	name = name.split("_")[0]
687	name += "_{0}".format(numb)
688	name = self._create_unique_key(dictionary, name, numb)
689	return name
690
691	def _get_node_value(self, node, tagname):
692	"""
693	Get the value of a node and any applicable units
694
695	:param node: The XML node to get the value of
696	:param tagname: The tagname of the node
697	"""
698	#Get the text from the node and convert all whitespace to spaces
699	units = ''
700	node_value = node.text
701	if node_value is not None:
702	node_value = ' '.join(node_value.split())
703	else:
704	node_value = ""
705
706	# If the value is a float, compile with units.
707	if self.ns_list.ns_datatype == "float":
708	# If an empty value is given, set as zero.
709	if node_value is None or node_value.isspace() \
710	or node_value.lower() == "nan":
711	node_value = "0.0"
712	#Convert the value to the base units
713	node_value, units = self._unit_conversion(node, tagname, node_value)
714
715	# If the value is a timestamp, convert to a datetime object
716	elif self.ns_list.ns_datatype == "timestamp":
717	if node_value is None or node_value.isspace():
718	pass
719	else:
720	try:
721	node_value = \
722	datetime.datetime.fromtimestamp(node_value)
723	except ValueError:
724	node_value = None
725	return node_value, units
726
727	def _unit_conversion(self, node, tagname, node_value):
728	"""
729	A unit converter method used to convert the data included in the file
730	to the default units listed in data_info
731
732	:param node: XML node
733	:param tagname: name of the node
734	:param node_value: The value of the current dom node
735	"""
736	attr = node.attrib
737	value_unit = ''
738	err_msg = None
739	default_unit = None
740	if not isinstance(node_value, float):
741	node_value = float(node_value)
742	if 'unit' in attr and attr.get('unit') is not None:
743	try:
744	local_unit = attr['unit']
745	unitname = self.ns_list.current_level.get("unit", "")
746	if "SASdetector" in self.names:
747	save_in = "detector"
748	elif "aperture" in self.names:
749	save_in = "aperture"
750	elif "SAScollimation" in self.names:
751	save_in = "collimation"
752	elif "SAStransmission_spectrum" in self.names:
753	save_in = "transspectrum"
754	elif "SASdata" in self.names:
755	x = np.zeros(1)
756	y = np.zeros(1)
757	self.current_data1d = Data1D(x, y)
758	save_in = "current_data1d"
759	elif "SASsource" in self.names:
760	save_in = "current_datainfo.source"
761	elif "SASsample" in self.names:
762	save_in = "current_datainfo.sample"
763	elif "SASprocess" in self.names:
764	save_in = "process"
765	else:
766	save_in = "current_datainfo"
767	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
768	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
769	and local_unit.lower() != "none":
770	if HAS_CONVERTER == True:
771	# Check local units - bad units raise KeyError
772	data_conv_q = Converter(local_unit)
773	value_unit = default_unit
774	node_value = data_conv_q(node_value, units=default_unit)
775	else:
776	value_unit = local_unit
777	err_msg = "Unit converter is not available.\n"
778	else:
779	value_unit = local_unit
780	except KeyError:
781	err_msg = "CanSAS reader: unexpected "
782	err_msg += "\"{0}\" unit [{1}]; "
783	err_msg = err_msg.format(tagname, local_unit)
784	err_msg += "expecting [{0}]".format(default_unit)
785	value_unit = local_unit
786	except:
787	err_msg = "CanSAS reader: unknown error converting "
788	err_msg += "\"{0}\" unit [{1}]"
789	err_msg = err_msg.format(tagname, local_unit)
790	value_unit = local_unit
791	elif 'unit' in attr:
792	value_unit = attr['unit']
793	if err_msg:
794	self.errors.add(err_msg)
795	return node_value, value_unit
796
797	def _check_for_empty_data(self):
798	"""
799	Creates an empty data set if no data is passed to the reader
800
801	:param data1d: presumably a Data1D object
802	"""
803	if self.current_dataset == None:
804	x_vals = np.empty(0)
805	y_vals = np.empty(0)
806	dx_vals = np.empty(0)
807	dy_vals = np.empty(0)
808	dxl = np.empty(0)
809	dxw = np.empty(0)
810	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
811	self.current_dataset.dxl = dxl
812	self.current_dataset.dxw = dxw
813
814	def _check_for_empty_resolution(self):
815	"""
816	A method to check all resolution data sets are the same size as I and Q
817	"""
818	if isinstance(self.current_dataset, plottable_1D):
819	dql_exists = False
820	dqw_exists = False
821	dq_exists = False
822	di_exists = False
823	if self.current_dataset.dxl is not None:
824	dql_exists = True
825	if self.current_dataset.dxw is not None:
826	dqw_exists = True
827	if self.current_dataset.dx is not None:
828	dq_exists = True
829	if self.current_dataset.dy is not None:
830	di_exists = True
831	if dqw_exists and not dql_exists:
832	array_size = self.current_dataset.dxw.size - 1
833	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
834	np.zeros([array_size]))
835	elif dql_exists and not dqw_exists:
836	array_size = self.current_dataset.dxl.size - 1
837	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
838	np.zeros([array_size]))
839	elif not dql_exists and not dqw_exists and not dq_exists:
840	array_size = self.current_dataset.x.size - 1
841	self.current_dataset.dx = np.append(self.current_dataset.dx,
842	np.zeros([array_size]))
843	if not di_exists:
844	array_size = self.current_dataset.y.size - 1
845	self.current_dataset.dy = np.append(self.current_dataset.dy,
846	np.zeros([array_size]))
847	elif isinstance(self.current_dataset, plottable_2D):
848	dqx_exists = False
849	dqy_exists = False
850	di_exists = False
851	mask_exists = False
852	if self.current_dataset.dqx_data is not None:
853	dqx_exists = True
854	if self.current_dataset.dqy_data is not None:
855	dqy_exists = True
856	if self.current_dataset.err_data is not None:
857	di_exists = True
858	if self.current_dataset.mask is not None:
859	mask_exists = True
860	if not dqy_exists:
861	array_size = self.current_dataset.qy_data.size - 1
862	self.current_dataset.dqy_data = np.append(
863	self.current_dataset.dqy_data, np.zeros([array_size]))
864	if not dqx_exists:
865	array_size = self.current_dataset.qx_data.size - 1
866	self.current_dataset.dqx_data = np.append(
867	self.current_dataset.dqx_data, np.zeros([array_size]))
868	if not di_exists:
869	array_size = self.current_dataset.data.size - 1
870	self.current_dataset.err_data = np.append(
871	self.current_dataset.err_data, np.zeros([array_size]))
872	if not mask_exists:
873	array_size = self.current_dataset.data.size - 1
874	self.current_dataset.mask = np.append(
875	self.current_dataset.mask,
876	np.ones([array_size] ,dtype=bool))
877
878	####### All methods below are for writing CanSAS XML files #######
879
880	def write(self, filename, datainfo):
881	"""
882	Write the content of a Data1D as a CanSAS XML file
883
884	:param filename: name of the file to write
885	:param datainfo: Data1D object
886	"""
887	# Create XML document
888	doc, _ = self._to_xml_doc(datainfo)
889	# Write the file
890	file_ref = open(filename, 'w')
891	if self.encoding == None:
892	self.encoding = "UTF-8"
893	doc.write(file_ref, encoding=self.encoding,
894	pretty_print=True, xml_declaration=True)
895	file_ref.close()
896
897	def _to_xml_doc(self, datainfo):
898	"""
899	Create an XML document to contain the content of a Data1D
900
901	:param datainfo: Data1D object
902	"""
903	is_2d = False
904	if issubclass(datainfo.__class__, Data2D):
905	is_2d = True
906
907	# Get PIs and create root element
908	pi_string = self._get_pi_string()
909	# Define namespaces and create SASroot object
910	main_node = self._create_main_node()
911	# Create ElementTree, append SASroot and apply processing instructions
912	base_string = pi_string + self.to_string(main_node)
913	base_element = self.create_element_from_string(base_string)
914	doc = self.create_tree(base_element)
915	# Create SASentry Element
916	entry_node = self.create_element("SASentry")
917	root = doc.getroot()
918	root.append(entry_node)
919
920	# Add Title to SASentry
921	self.write_node(entry_node, "Title", datainfo.title)
922	# Add Run to SASentry
923	self._write_run_names(datainfo, entry_node)
924	# Add Data info to SASEntry
925	if is_2d:
926	self._write_data_2d(datainfo, entry_node)
927	else:
928	self._write_data(datainfo, entry_node)
929	# Transmission Spectrum Info
930	self._write_trans_spectrum(datainfo, entry_node)
931	# Sample info
932	self._write_sample_info(datainfo, entry_node)
933	# Instrument info
934	instr = self._write_instrument(datainfo, entry_node)
935	# Source
936	self._write_source(datainfo, instr)
937	# Collimation
938	self._write_collimation(datainfo, instr)
939	# Detectors
940	self._write_detectors(datainfo, instr)
941	# Processes info
942	self._write_process_notes(datainfo, entry_node)
943	# Note info
944	self._write_notes(datainfo, entry_node)
945	# Return the document, and the SASentry node associated with
946	# the data we just wrote
947	# If the calling function was not the cansas reader, return a minidom
948	# object rather than an lxml object.
949	self.frm = inspect.stack()[1]
950	doc, entry_node = self._check_origin(entry_node, doc)
951	return doc, entry_node
952
953	def write_node(self, parent, name, value, attr=None):
954	"""
955	:param doc: document DOM
956	:param parent: parent node
957	:param name: tag of the element
958	:param value: value of the child text node
959	:param attr: attribute dictionary
960
961	:return: True if something was appended, otherwise False
962	"""
963	if value is not None:
964	parent = self.ebuilder(parent, name, value, attr)
965	return True
966	return False
967
968	def _get_pi_string(self):
969	"""
970	Creates the processing instructions header for writing to file
971	"""
972	pis = self.return_processing_instructions()
973	if len(pis) > 0:
974	pi_tree = self.create_tree(pis[0])
975	i = 1
976	for i in range(1, len(pis) - 1):
977	pi_tree = self.append(pis[i], pi_tree)
978	pi_string = self.to_string(pi_tree)
979	else:
980	pi_string = ""
981	return pi_string
982
983	def _create_main_node(self):
984	"""
985	Creates the primary xml header used when writing to file
986	"""
987	xsi = "http://www.w3.org/2001/XMLSchema-instance"
988	version = self.cansas_version
989	n_s = CANSAS_NS.get(version).get("ns")
990	if version == "1.1":
991	url = "http://www.cansas.org/formats/1.1/"
992	else:
993	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
994	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
995	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
996	"version" : version}
997	nsmap = {'xsi' : xsi, None: n_s}
998
999	main_node = self.create_element("{" + n_s + "}SASroot",
1000	attrib=attrib, nsmap=nsmap)
1001	return main_node
1002
1003	def _write_run_names(self, datainfo, entry_node):
1004	"""
1005	Writes the run names to the XML file
1006
1007	:param datainfo: The Data1D object the information is coming from
1008	:param entry_node: lxml node ElementTree object to be appended to
1009	"""
1010	if datainfo.run == None or datainfo.run == []:
1011	datainfo.run.append(RUN_NAME_DEFAULT)
1012	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1013	for item in datainfo.run:
1014	runname = {}
1015	if item in datainfo.run_name and \
1016	len(str(datainfo.run_name[item])) > 1:
1017	runname = {'name': datainfo.run_name[item]}
1018	self.write_node(entry_node, "Run", item, runname)
1019
1020	def _write_data(self, datainfo, entry_node):
1021	"""
1022	Writes 1D I and Q data to the XML file
1023
1024	:param datainfo: The Data1D object the information is coming from
1025	:param entry_node: lxml node ElementTree object to be appended to
1026	"""
1027	node = self.create_element("SASdata")
1028	self.append(node, entry_node)
1029
1030	for i in range(len(datainfo.x)):
1031	point = self.create_element("Idata")
1032	node.append(point)
1033	self.write_node(point, "Q", datainfo.x[i],
1034	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1035	if len(datainfo.y) >= i:
1036	self.write_node(point, "I", datainfo.y[i],
1037	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1038	if datainfo.dy is not None and len(datainfo.dy) > i:
1039	self.write_node(point, "Idev", datainfo.dy[i],
1040	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1041	if datainfo.dx is not None and len(datainfo.dx) > i:
1042	self.write_node(point, "Qdev", datainfo.dx[i],
1043	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1044	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1045	self.write_node(point, "dQw", datainfo.dxw[i],
1046	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1047	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1048	self.write_node(point, "dQl", datainfo.dxl[i],
1049	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1050	if datainfo.isSesans:
1051	sesans = self.create_element("Sesans")
1052	sesans.text = str(datainfo.isSesans)
1053	node.append(sesans)
1054	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1055	{'unit': datainfo.sample.zacceptance[1]})
1056
1057
1058	def _write_data_2d(self, datainfo, entry_node):
1059	"""
1060	Writes 2D data to the XML file
1061
1062	:param datainfo: The Data2D object the information is coming from
1063	:param entry_node: lxml node ElementTree object to be appended to
1064	"""
1065	attr = {}
1066	if datainfo.data.shape:
1067	attr["x_bins"] = str(len(datainfo.x_bins))
1068	attr["y_bins"] = str(len(datainfo.y_bins))
1069	node = self.create_element("SASdata", attr)
1070	self.append(node, entry_node)
1071
1072	point = self.create_element("Idata")
1073	node.append(point)
1074	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1075	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1076	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1077
1078	self.write_node(point, "Qx", qx,
1079	{'unit': datainfo._xunit})
1080	self.write_node(point, "Qy", qy,
1081	{'unit': datainfo._yunit})
1082	self.write_node(point, "I", intensity,
1083	{'unit': datainfo._zunit})
1084	if datainfo.err_data is not None:
1085	err = ','.join([str(datainfo.err_data[i]) for i in
1086	xrange(len(datainfo.err_data))])
1087	self.write_node(point, "Idev", err,
1088	{'unit': datainfo._zunit})
1089	if datainfo.dqy_data is not None:
1090	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1091	xrange(len(datainfo.dqy_data))])
1092	self.write_node(point, "Qydev", dqy,
1093	{'unit': datainfo._yunit})
1094	if datainfo.dqx_data is not None:
1095	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1096	xrange(len(datainfo.dqx_data))])
1097	self.write_node(point, "Qxdev", dqx,
1098	{'unit': datainfo._xunit})
1099	if datainfo.mask is not None:
1100	mask = ','.join(
1101	["1" if datainfo.mask[i] else "0"
1102	for i in xrange(len(datainfo.mask))])
1103	self.write_node(point, "Mask", mask)
1104
1105	def _write_trans_spectrum(self, datainfo, entry_node):
1106	"""
1107	Writes the transmission spectrum data to the XML file
1108
1109	:param datainfo: The Data1D object the information is coming from
1110	:param entry_node: lxml node ElementTree object to be appended to
1111	"""
1112	for i in range(len(datainfo.trans_spectrum)):
1113	spectrum = datainfo.trans_spectrum[i]
1114	node = self.create_element("SAStransmission_spectrum",
1115	{"name" : spectrum.name})
1116	self.append(node, entry_node)
1117	if isinstance(spectrum.timestamp, datetime.datetime):
1118	node.setAttribute("timestamp", spectrum.timestamp)
1119	for i in range(len(spectrum.wavelength)):
1120	point = self.create_element("Tdata")
1121	node.append(point)
1122	self.write_node(point, "Lambda", spectrum.wavelength[i],
1123	{'unit': spectrum.wavelength_unit})
1124	self.write_node(point, "T", spectrum.transmission[i],
1125	{'unit': spectrum.transmission_unit})
1126	if spectrum.transmission_deviation != None \
1127	and len(spectrum.transmission_deviation) >= i:
1128	self.write_node(point, "Tdev",
1129	spectrum.transmission_deviation[i],
1130	{'unit':
1131	spectrum.transmission_deviation_unit})
1132
1133	def _write_sample_info(self, datainfo, entry_node):
1134	"""
1135	Writes the sample information to the XML file
1136
1137	:param datainfo: The Data1D object the information is coming from
1138	:param entry_node: lxml node ElementTree object to be appended to
1139	"""
1140	sample = self.create_element("SASsample")
1141	if datainfo.sample.name is not None:
1142	self.write_attribute(sample, "name",
1143	str(datainfo.sample.name))
1144	self.append(sample, entry_node)
1145	self.write_node(sample, "ID", str(datainfo.sample.ID))
1146	self.write_node(sample, "thickness", datainfo.sample.thickness,
1147	{"unit": datainfo.sample.thickness_unit})
1148	self.write_node(sample, "transmission", datainfo.sample.transmission)
1149	self.write_node(sample, "temperature", datainfo.sample.temperature,
1150	{"unit": datainfo.sample.temperature_unit})
1151
1152	pos = self.create_element("position")
1153	written = self.write_node(pos,
1154	"x",
1155	datainfo.sample.position.x,
1156	{"unit": datainfo.sample.position_unit})
1157	written = written \| self.write_node( \
1158	pos, "y", datainfo.sample.position.y,
1159	{"unit": datainfo.sample.position_unit})
1160	written = written \| self.write_node( \
1161	pos, "z", datainfo.sample.position.z,
1162	{"unit": datainfo.sample.position_unit})
1163	if written == True:
1164	self.append(pos, sample)
1165
1166	ori = self.create_element("orientation")
1167	written = self.write_node(ori, "roll",
1168	datainfo.sample.orientation.x,
1169	{"unit": datainfo.sample.orientation_unit})
1170	written = written \| self.write_node( \
1171	ori, "pitch", datainfo.sample.orientation.y,
1172	{"unit": datainfo.sample.orientation_unit})
1173	written = written \| self.write_node( \
1174	ori, "yaw", datainfo.sample.orientation.z,
1175	{"unit": datainfo.sample.orientation_unit})
1176	if written == True:
1177	self.append(ori, sample)
1178
1179	for item in datainfo.sample.details:
1180	self.write_node(sample, "details", item)
1181
1182	def _write_instrument(self, datainfo, entry_node):
1183	"""
1184	Writes the instrumental information to the XML file
1185
1186	:param datainfo: The Data1D object the information is coming from
1187	:param entry_node: lxml node ElementTree object to be appended to
1188	"""
1189	instr = self.create_element("SASinstrument")
1190	self.append(instr, entry_node)
1191	self.write_node(instr, "name", datainfo.instrument)
1192	return instr
1193
1194	def _write_source(self, datainfo, instr):
1195	"""
1196	Writes the source information to the XML file
1197
1198	:param datainfo: The Data1D object the information is coming from
1199	:param instr: instrument node to be appended to
1200	"""
1201	source = self.create_element("SASsource")
1202	if datainfo.source.name is not None:
1203	self.write_attribute(source, "name",
1204	str(datainfo.source.name))
1205	self.append(source, instr)
1206	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1207	datainfo.source.radiation = "neutron"
1208	self.write_node(source, "radiation", datainfo.source.radiation)
1209
1210	size = self.create_element("beam_size")
1211	if datainfo.source.beam_size_name is not None:
1212	self.write_attribute(size, "name",
1213	str(datainfo.source.beam_size_name))
1214	written = self.write_node( \
1215	size, "x", datainfo.source.beam_size.x,
1216	{"unit": datainfo.source.beam_size_unit})
1217	written = written \| self.write_node( \
1218	size, "y", datainfo.source.beam_size.y,
1219	{"unit": datainfo.source.beam_size_unit})
1220	written = written \| self.write_node( \
1221	size, "z", datainfo.source.beam_size.z,
1222	{"unit": datainfo.source.beam_size_unit})
1223	if written == True:
1224	self.append(size, source)
1225
1226	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1227	self.write_node(source, "wavelength",
1228	datainfo.source.wavelength,
1229	{"unit": datainfo.source.wavelength_unit})
1230	self.write_node(source, "wavelength_min",
1231	datainfo.source.wavelength_min,
1232	{"unit": datainfo.source.wavelength_min_unit})
1233	self.write_node(source, "wavelength_max",
1234	datainfo.source.wavelength_max,
1235	{"unit": datainfo.source.wavelength_max_unit})
1236	self.write_node(source, "wavelength_spread",
1237	datainfo.source.wavelength_spread,
1238	{"unit": datainfo.source.wavelength_spread_unit})
1239
1240	def _write_collimation(self, datainfo, instr):
1241	"""
1242	Writes the collimation information to the XML file
1243
1244	:param datainfo: The Data1D object the information is coming from
1245	:param instr: lxml node ElementTree object to be appended to
1246	"""
1247	if datainfo.collimation == [] or datainfo.collimation == None:
1248	coll = Collimation()
1249	datainfo.collimation.append(coll)
1250	for item in datainfo.collimation:
1251	coll = self.create_element("SAScollimation")
1252	if item.name is not None:
1253	self.write_attribute(coll, "name", str(item.name))
1254	self.append(coll, instr)
1255
1256	self.write_node(coll, "length", item.length,
1257	{"unit": item.length_unit})
1258
1259	for aperture in item.aperture:
1260	apert = self.create_element("aperture")
1261	if aperture.name is not None:
1262	self.write_attribute(apert, "name", str(aperture.name))
1263	if aperture.type is not None:
1264	self.write_attribute(apert, "type", str(aperture.type))
1265	self.append(apert, coll)
1266
1267	size = self.create_element("size")
1268	if aperture.size_name is not None:
1269	self.write_attribute(size, "name",
1270	str(aperture.size_name))
1271	written = self.write_node(size, "x", aperture.size.x,
1272	{"unit": aperture.size_unit})
1273	written = written \| self.write_node( \
1274	size, "y", aperture.size.y,
1275	{"unit": aperture.size_unit})
1276	written = written \| self.write_node( \
1277	size, "z", aperture.size.z,
1278	{"unit": aperture.size_unit})
1279	if written == True:
1280	self.append(size, apert)
1281
1282	self.write_node(apert, "distance", aperture.distance,
1283	{"unit": aperture.distance_unit})
1284
1285	def _write_detectors(self, datainfo, instr):
1286	"""
1287	Writes the detector information to the XML file
1288
1289	:param datainfo: The Data1D object the information is coming from
1290	:param inst: lxml instrument node to be appended to
1291	"""
1292	if datainfo.detector == None or datainfo.detector == []:
1293	det = Detector()
1294	det.name = ""
1295	datainfo.detector.append(det)
1296
1297	for item in datainfo.detector:
1298	det = self.create_element("SASdetector")
1299	written = self.write_node(det, "name", item.name)
1300	written = written \| self.write_node(det, "SDD", item.distance,
1301	{"unit": item.distance_unit})
1302	if written == True:
1303	self.append(det, instr)
1304
1305	off = self.create_element("offset")
1306	written = self.write_node(off, "x", item.offset.x,
1307	{"unit": item.offset_unit})
1308	written = written \| self.write_node(off, "y", item.offset.y,
1309	{"unit": item.offset_unit})
1310	written = written \| self.write_node(off, "z", item.offset.z,
1311	{"unit": item.offset_unit})
1312	if written == True:
1313	self.append(off, det)
1314
1315	ori = self.create_element("orientation")
1316	written = self.write_node(ori, "roll", item.orientation.x,
1317	{"unit": item.orientation_unit})
1318	written = written \| self.write_node(ori, "pitch",
1319	item.orientation.y,
1320	{"unit": item.orientation_unit})
1321	written = written \| self.write_node(ori, "yaw",
1322	item.orientation.z,
1323	{"unit": item.orientation_unit})
1324	if written == True:
1325	self.append(ori, det)
1326
1327	center = self.create_element("beam_center")
1328	written = self.write_node(center, "x", item.beam_center.x,
1329	{"unit": item.beam_center_unit})
1330	written = written \| self.write_node(center, "y",
1331	item.beam_center.y,
1332	{"unit": item.beam_center_unit})
1333	written = written \| self.write_node(center, "z",
1334	item.beam_center.z,
1335	{"unit": item.beam_center_unit})
1336	if written == True:
1337	self.append(center, det)
1338
1339	pix = self.create_element("pixel_size")
1340	written = self.write_node(pix, "x", item.pixel_size.x,
1341	{"unit": item.pixel_size_unit})
1342	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1343	{"unit": item.pixel_size_unit})
1344	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1345	{"unit": item.pixel_size_unit})
1346	if written == True:
1347	self.append(pix, det)
1348	self.write_node(det, "slit_length", item.slit_length,
1349	{"unit": item.slit_length_unit})
1350
1351
1352	def _write_process_notes(self, datainfo, entry_node):
1353	"""
1354	Writes the process notes to the XML file
1355
1356	:param datainfo: The Data1D object the information is coming from
1357	:param entry_node: lxml node ElementTree object to be appended to
1358
1359	"""
1360	for item in datainfo.process:
1361	node = self.create_element("SASprocess")
1362	self.append(node, entry_node)
1363	self.write_node(node, "name", item.name)
1364	self.write_node(node, "date", item.date)
1365	self.write_node(node, "description", item.description)
1366	for term in item.term:
1367	if isinstance(term, list):
1368	value = term['value']
1369	del term['value']
1370	elif isinstance(term, dict):
1371	value = term.get("value")
1372	del term['value']
1373	else:
1374	value = term
1375	self.write_node(node, "term", value, term)
1376	for note in item.notes:
1377	self.write_node(node, "SASprocessnote", note)
1378	if len(item.notes) == 0:
1379	self.write_node(node, "SASprocessnote", "")
1380
1381	def _write_notes(self, datainfo, entry_node):
1382	"""
1383	Writes the notes to the XML file and creates an empty note if none
1384	exist
1385
1386	:param datainfo: The Data1D object the information is coming from
1387	:param entry_node: lxml node ElementTree object to be appended to
1388
1389	"""
1390	if len(datainfo.notes) == 0:
1391	node = self.create_element("SASnote")
1392	self.append(node, entry_node)
1393	else:
1394	for item in datainfo.notes:
1395	node = self.create_element("SASnote")
1396	self.write_text(node, item)
1397	self.append(node, entry_node)
1398
1399	def _check_origin(self, entry_node, doc):
1400	"""
1401	Return the document, and the SASentry node associated with
1402	the data we just wrote.
1403	If the calling function was not the cansas reader, return a minidom
1404	object rather than an lxml object.
1405
1406	:param entry_node: lxml node ElementTree object to be appended to
1407	:param doc: entire xml tree
1408	"""
1409	if not self.frm:
1410	self.frm = inspect.stack()[1]
1411	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1412	mod_name = mod_name.replace(".py", "")
1413	mod = mod_name.split("sas/")
1414	mod_name = mod[1]
1415	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1416	string = self.to_string(doc, pretty_print=False)
1417	doc = parseString(string)
1418	node_name = entry_node.tag
1419	node_list = doc.getElementsByTagName(node_name)
1420	entry_node = node_list.item(0)
1421	return doc, entry_node
1422
1423	# DO NOT REMOVE - used in saving and loading panel states.
1424	def _store_float(self, location, node, variable, storage, optional=True):
1425	"""
1426	Get the content of a xpath location and store
1427	the result. Check that the units are compatible
1428	with the destination. The value is expected to
1429	be a float.
1430
1431	The xpath location might or might not exist.
1432	If it does not exist, nothing is done
1433
1434	:param location: xpath location to fetch
1435	:param node: node to read the data from
1436	:param variable: name of the data member to store it in [string]
1437	:param storage: data object that has the 'variable' data member
1438	:param optional: if True, no exception will be raised
1439	if unit conversion can't be done
1440
1441	:raise ValueError: raised when the units are not recognized
1442	"""
1443	entry = get_content(location, node)
1444	try:
1445	value = float(entry.text)
1446	except:
1447	value = None
1448
1449	if value is not None:
1450	# If the entry has units, check to see that they are
1451	# compatible with what we currently have in the data object
1452	units = entry.get('unit')
1453	if units is not None:
1454	toks = variable.split('.')
1455	local_unit = None
1456	exec "local_unit = storage.%s_unit" % toks[0]
1457	if local_unit != None and units.lower() != local_unit.lower():
1458	if HAS_CONVERTER == True:
1459	try:
1460	conv = Converter(units)
1461	exec "storage.%s = %g" % \
1462	(variable, conv(value, units=local_unit))
1463	except:
1464	_, exc_value, _ = sys.exc_info()
1465	err_mess = "CanSAS reader: could not convert"
1466	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1467	% (variable, units, local_unit, exc_value)
1468	self.errors.add(err_mess)
1469	if optional:
1470	logging.info(err_mess)
1471	else:
1472	raise ValueError, err_mess
1473	else:
1474	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1475	% (variable, units)
1476	err_mess += " expecting [%s]" % local_unit
1477	self.errors.add(err_mess)
1478	if optional:
1479	logging.info(err_mess)
1480	else:
1481	raise ValueError, err_mess
1482	else:
1483	exec "storage.%s = value" % variable
1484	else:
1485	exec "storage.%s = value" % variable
1486
1487	# DO NOT REMOVE - used in saving and loading panel states.
1488	def _store_content(self, location, node, variable, storage):
1489	"""
1490	Get the content of a xpath location and store
1491	the result. The value is treated as a string.
1492
1493	The xpath location might or might not exist.
1494	If it does not exist, nothing is done
1495
1496	:param location: xpath location to fetch
1497	:param node: node to read the data from
1498	:param variable: name of the data member to store it in [string]
1499	:param storage: data object that has the 'variable' data member
1500
1501	:return: return a list of errors
1502	"""
1503	entry = get_content(location, node)
1504	if entry is not None and entry.text is not None:
1505	exec "storage.%s = entry.text.strip()" % variable
1506
1507
1508	# DO NOT REMOVE Called by outside packages:
1509	# sas.sasgui.perspectives.invariant.invariant_state
1510	# sas.sasgui.perspectives.fitting.pagestate
1511	def get_content(location, node):
1512	"""
1513	Get the first instance of the content of a xpath location.
1514
1515	:param location: xpath location
1516	:param node: node to start at
1517
1518	:return: Element, or None
1519	"""
1520	nodes = node.xpath(location,
1521	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1522	if len(nodes) > 0:
1523	return nodes[0]
1524	else:
1525	return None
1526
1527	# DO NOT REMOVE Called by outside packages:
1528	# sas.sasgui.perspectives.fitting.pagestate
1529	def write_node(doc, parent, name, value, attr=None):
1530	"""
1531	:param doc: document DOM
1532	:param parent: parent node
1533	:param name: tag of the element
1534	:param value: value of the child text node
1535	:param attr: attribute dictionary
1536
1537	:return: True if something was appended, otherwise False
1538	"""
1539	if attr is None:
1540	attr = {}
1541	if value is not None:
1542	node = doc.createElement(name)
1543	node.appendChild(doc.createTextNode(str(value)))
1544	for item in attr:
1545	node.setAttribute(item, attr[item])
1546	parent.appendChild(node)
1547	return True
1548	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ b5e9ce26

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