cansas_reader.py @ d7ee5866

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.1.1release-4.1.2release-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since d7ee5866 was 527a190, checked in by krzywon, 8 years ago
Loading XML files saved through no longer throwing errors. see #938
Property mode set to `100644`
File size: 70.6 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	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	if invalid_xml != "":
159	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
160	self.errors.add(invalid_xml)
161	# Try again with an invalid CanSAS schema, that requires only a data set in each
162	base_name = xml_reader.__file__
163	base_name = base_name.replace("\\", "/")
164	base = base_name.split("/sas/")[0]
165	if self.cansas_version == "1.1":
166	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
167	else:
168	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
169	self.set_schema(invalid_schema)
170	try:
171	if self.invalid:
172	if self.is_cansas():
173	self.output = self.read(xml_file, invalid_schema, False)
174	else:
175	raise RuntimeError
176	else:
177	raise RuntimeError
178	except RuntimeError:
179	x = np.zeros(1)
180	y = np.zeros(1)
181	self.current_data1d = Data1D(x,y)
182	self.current_data1d.errors = self.errors
183	return [self.current_data1d]
184	else:
185	self.output.append("Not a valid file path.")
186	# Return a list of parsed entries that dataloader can manage
187	return self.output
188
189	def _parse_entry(self, dom, recurse=False):
190	"""
191	Parse a SASEntry - new recursive method for parsing the dom of
192	the CanSAS data format. This will allow multiple data files
193	and extra nodes to be read in simultaneously.
194
195	:param dom: dom object with a namespace base of names
196	"""
197
198	if not self._is_call_local() and not recurse:
199	self.reset_state()
200	self.add_data_set()
201	self.names.append("SASentry")
202	self.parent_class = "SASentry"
203	self._check_for_empty_data()
204	self.base_ns = "{0}{1}{2}".format("{", \
205	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
206
207	# Go through each child in the parent element
208	for node in dom:
209	attr = node.attrib
210	name = attr.get("name", "")
211	type = attr.get("type", "")
212	# Get the element name and set the current names level
213	tagname = node.tag.replace(self.base_ns, "")
214	tagname_original = tagname
215	# Skip this iteration when loading in save state information
216	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
217	continue
218
219	# Get where to store content
220	self.names.append(tagname_original)
221	self.ns_list = CONSTANTS.iterate_namespace(self.names)
222	# If the element is a child element, recurse
223	if len(node.getchildren()) > 0:
224	self.parent_class = tagname_original
225	if tagname == 'SASdata':
226	self._initialize_new_data_set(node)
227	if isinstance(self.current_dataset, plottable_2D):
228	x_bins = attr.get("x_bins", "")
229	y_bins = attr.get("y_bins", "")
230	if x_bins is not "" and y_bins is not "":
231	self.current_dataset.shape = (x_bins, y_bins)
232	else:
233	self.current_dataset.shape = ()
234	# Recursion step to access data within the group
235	self._parse_entry(node, True)
236	if tagname == "SASsample":
237	self.current_datainfo.sample.name = name
238	elif tagname == "beam_size":
239	self.current_datainfo.source.beam_size_name = name
240	elif tagname == "SAScollimation":
241	self.collimation.name = name
242	elif tagname == "aperture":
243	self.aperture.name = name
244	self.aperture.type = type
245	self.add_intermediate()
246	else:
247	if isinstance(self.current_dataset, plottable_2D):
248	data_point = node.text
249	unit = attr.get('unit', '')
250	else:
251	data_point, unit = self._get_node_value(node, tagname)
252
253	# If this is a dataset, store the data appropriately
254	if tagname == 'Run':
255	self.current_datainfo.run_name[data_point] = name
256	self.current_datainfo.run.append(data_point)
257	elif tagname == 'Title':
258	self.current_datainfo.title = data_point
259	elif tagname == 'SASnote':
260	self.current_datainfo.notes.append(data_point)
261
262	# I and Q - 1D data
263	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
264	self.current_dataset.yaxis("Intensity", unit)
265	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
266	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
267	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
268	elif tagname == 'Q':
269	self.current_dataset.xaxis("Q", unit)
270	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
271	elif tagname == 'Qdev':
272	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
273	elif tagname == 'dQw':
274	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
275	elif tagname == 'dQl':
276	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
277	elif tagname == 'Qmean':
278	pass
279	elif tagname == 'Shadowfactor':
280	pass
281	elif tagname == 'Sesans':
282	self.current_datainfo.isSesans = bool(data_point)
283	self.current_dataset.xaxis(attr.get('x_axis'),
284	attr.get('x_unit'))
285	self.current_dataset.yaxis(attr.get('y_axis'),
286	attr.get('y_unit'))
287	elif tagname == 'zacceptance':
288	self.current_datainfo.sample.zacceptance = (data_point, unit)
289
290	# I and Qx, Qy - 2D data
291	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
292	self.current_dataset.yaxis("Intensity", unit)
293	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
294	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
295	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
296	elif tagname == 'Qx':
297	self.current_dataset.xaxis("Qx", unit)
298	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
299	elif tagname == 'Qy':
300	self.current_dataset.yaxis("Qy", unit)
301	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
302	elif tagname == 'Qxdev':
303	self.current_dataset.xaxis("Qxdev", unit)
304	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qydev':
306	self.current_dataset.yaxis("Qydev", unit)
307	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Mask':
309	inter = [item == "1" for item in data_point.split(",")]
310	self.current_dataset.mask = np.asarray(inter, dtype=bool)
311
312	# Sample Information
313	elif tagname == 'ID' and self.parent_class == 'SASsample':
314	self.current_datainfo.sample.ID = data_point
315	elif tagname == 'Title' and self.parent_class == 'SASsample':
316	self.current_datainfo.sample.name = data_point
317	elif tagname == 'thickness' and self.parent_class == 'SASsample':
318	self.current_datainfo.sample.thickness = data_point
319	self.current_datainfo.sample.thickness_unit = unit
320	elif tagname == 'transmission' and self.parent_class == 'SASsample':
321	self.current_datainfo.sample.transmission = data_point
322	elif tagname == 'temperature' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.temperature = data_point
324	self.current_datainfo.sample.temperature_unit = unit
325	elif tagname == 'details' and self.parent_class == 'SASsample':
326	self.current_datainfo.sample.details.append(data_point)
327	elif tagname == 'x' and self.parent_class == 'position':
328	self.current_datainfo.sample.position.x = data_point
329	self.current_datainfo.sample.position_unit = unit
330	elif tagname == 'y' and self.parent_class == 'position':
331	self.current_datainfo.sample.position.y = data_point
332	self.current_datainfo.sample.position_unit = unit
333	elif tagname == 'z' and self.parent_class == 'position':
334	self.current_datainfo.sample.position.z = data_point
335	self.current_datainfo.sample.position_unit = unit
336	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
337	self.current_datainfo.sample.orientation.x = data_point
338	self.current_datainfo.sample.orientation_unit = unit
339	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
340	self.current_datainfo.sample.orientation.y = data_point
341	self.current_datainfo.sample.orientation_unit = unit
342	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
343	self.current_datainfo.sample.orientation.z = data_point
344	self.current_datainfo.sample.orientation_unit = unit
345
346	# Instrumental Information
347	elif tagname == 'name' and self.parent_class == 'SASinstrument':
348	self.current_datainfo.instrument = data_point
349	# Detector Information
350	elif tagname == 'name' and self.parent_class == 'SASdetector':
351	self.detector.name = data_point
352	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
353	self.detector.distance = data_point
354	self.detector.distance_unit = unit
355	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
356	self.detector.slit_length = data_point
357	self.detector.slit_length_unit = unit
358	elif tagname == 'x' and self.parent_class == 'offset':
359	self.detector.offset.x = data_point
360	self.detector.offset_unit = unit
361	elif tagname == 'y' and self.parent_class == 'offset':
362	self.detector.offset.y = data_point
363	self.detector.offset_unit = unit
364	elif tagname == 'z' and self.parent_class == 'offset':
365	self.detector.offset.z = data_point
366	self.detector.offset_unit = unit
367	elif tagname == 'x' and self.parent_class == 'beam_center':
368	self.detector.beam_center.x = data_point
369	self.detector.beam_center_unit = unit
370	elif tagname == 'y' and self.parent_class == 'beam_center':
371	self.detector.beam_center.y = data_point
372	self.detector.beam_center_unit = unit
373	elif tagname == 'z' and self.parent_class == 'beam_center':
374	self.detector.beam_center.z = data_point
375	self.detector.beam_center_unit = unit
376	elif tagname == 'x' and self.parent_class == 'pixel_size':
377	self.detector.pixel_size.x = data_point
378	self.detector.pixel_size_unit = unit
379	elif tagname == 'y' and self.parent_class == 'pixel_size':
380	self.detector.pixel_size.y = data_point
381	self.detector.pixel_size_unit = unit
382	elif tagname == 'z' and self.parent_class == 'pixel_size':
383	self.detector.pixel_size.z = data_point
384	self.detector.pixel_size_unit = unit
385	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
386	self.detector.orientation.x = data_point
387	self.detector.orientation_unit = unit
388	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
389	self.detector.orientation.y = data_point
390	self.detector.orientation_unit = unit
391	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
392	self.detector.orientation.z = data_point
393	self.detector.orientation_unit = unit
394	# Collimation and Aperture
395	elif tagname == 'length' and self.parent_class == 'SAScollimation':
396	self.collimation.length = data_point
397	self.collimation.length_unit = unit
398	elif tagname == 'name' and self.parent_class == 'SAScollimation':
399	self.collimation.name = data_point
400	elif tagname == 'distance' and self.parent_class == 'aperture':
401	self.aperture.distance = data_point
402	self.aperture.distance_unit = unit
403	elif tagname == 'x' and self.parent_class == 'size':
404	self.aperture.size.x = data_point
405	self.collimation.size_unit = unit
406	elif tagname == 'y' and self.parent_class == 'size':
407	self.aperture.size.y = data_point
408	self.collimation.size_unit = unit
409	elif tagname == 'z' and self.parent_class == 'size':
410	self.aperture.size.z = data_point
411	self.collimation.size_unit = unit
412
413	# Process Information
414	elif tagname == 'name' and self.parent_class == 'SASprocess':
415	self.process.name = data_point
416	elif tagname == 'description' and self.parent_class == 'SASprocess':
417	self.process.description = data_point
418	elif tagname == 'date' and self.parent_class == 'SASprocess':
419	try:
420	self.process.date = datetime.datetime.fromtimestamp(data_point)
421	except:
422	self.process.date = data_point
423	elif tagname == 'SASprocessnote':
424	self.process.notes.append(data_point)
425	elif tagname == 'term' and self.parent_class == 'SASprocess':
426	unit = attr.get("unit", "")
427	dic = {}
428	dic["name"] = name
429	dic["value"] = data_point
430	dic["unit"] = unit
431	self.process.term.append(dic)
432
433	# Transmission Spectrum
434	elif tagname == 'T' and self.parent_class == 'Tdata':
435	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
436	self.transspectrum.transmission_unit = unit
437	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
438	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
439	self.transspectrum.transmission_deviation_unit = unit
440	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
441	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
442	self.transspectrum.wavelength_unit = unit
443
444	# Source Information
445	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
446	self.current_datainfo.source.wavelength = data_point
447	self.current_datainfo.source.wavelength_unit = unit
448	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
449	self.current_datainfo.source.wavelength_min = data_point
450	self.current_datainfo.source.wavelength_min_unit = unit
451	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
452	self.current_datainfo.source.wavelength_max = data_point
453	self.current_datainfo.source.wavelength_max_unit = unit
454	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
455	self.current_datainfo.source.wavelength_spread = data_point
456	self.current_datainfo.source.wavelength_spread_unit = unit
457	elif tagname == 'x' and self.parent_class == 'beam_size':
458	self.current_datainfo.source.beam_size.x = data_point
459	self.current_datainfo.source.beam_size_unit = unit
460	elif tagname == 'y' and self.parent_class == 'beam_size':
461	self.current_datainfo.source.beam_size.y = data_point
462	self.current_datainfo.source.beam_size_unit = unit
463	elif tagname == 'z' and self.parent_class == 'pixel_size':
464	self.current_datainfo.source.data_point.z = data_point
465	self.current_datainfo.source.beam_size_unit = unit
466	elif tagname == 'radiation' and self.parent_class == 'SASsource':
467	self.current_datainfo.source.radiation = data_point
468	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
469	self.current_datainfo.source.beam_shape = data_point
470
471	# Everything else goes in meta_data
472	else:
473	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
474	self.current_datainfo.meta_data[new_key] = data_point
475
476	self.names.remove(tagname_original)
477	length = 0
478	if len(self.names) > 1:
479	length = len(self.names) - 1
480	self.parent_class = self.names[length]
481	if not self._is_call_local() and not recurse:
482	self.frm = ""
483	self.add_data_set()
484	empty = None
485	return self.output[0], empty
486
487
488	def _is_call_local(self):
489	"""
490
491	"""
492	if self.frm == "":
493	inter = inspect.stack()
494	self.frm = inter[2]
495	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
496	mod_name = mod_name.replace(".py", "")
497	mod = mod_name.split("sas/")
498	mod_name = mod[1]
499	if mod_name != "sascalc/dataloader/readers/cansas_reader":
500	return False
501	return True
502
503	def is_cansas(self, ext="xml"):
504	"""
505	Checks to see if the xml file is a CanSAS file
506
507	:param ext: The file extension of the data file
508	"""
509	if self.validate_xml():
510	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
511	value = self.xmlroot.get(name)
512	if CANSAS_NS.get(self.cansas_version).get("ns") == \
513	value.rsplit(" ")[0]:
514	return True
515	if ext == "svs":
516	return True
517	raise RuntimeError
518
519	def load_file_and_schema(self, xml_file, schema_path=""):
520	"""
521	Loads the file and associates a schema, if a schema is passed in or if one already exists
522
523	:param xml_file: The xml file path sent to Reader.read
524	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
525	"""
526	base_name = xml_reader.__file__
527	base_name = base_name.replace("\\", "/")
528	base = base_name.split("/sas/")[0]
529
530	# Load in xml file and get the cansas version from the header
531	self.set_xml_file(xml_file)
532	self.cansas_version = self.xmlroot.get("version", "1.0")
533
534	# Generic values for the cansas file based on the version
535	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
536	if schema_path == "":
537	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
538	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
539
540	# Link a schema to the XML file.
541	self.set_schema(schema_path)
542
543	def add_data_set(self):
544	"""
545	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
546	private method to generate a new data set.
547
548	:param key: NeXus group name for current tree level
549	"""
550
551	if self.current_datainfo and self.current_dataset:
552	self._final_cleanup()
553	self.data = []
554	self.current_datainfo = DataInfo()
555
556	def _initialize_new_data_set(self, node=None):
557	"""
558	A private class method to generate a new 1D data object.
559	Outside methods should call add_data_set() to be sure any existing data is stored properly.
560
561	:param node: XML node to determine if 1D or 2D data
562	"""
563	x = np.array(0)
564	y = np.array(0)
565	for child in node:
566	if child.tag.replace(self.base_ns, "") == "Idata":
567	for i_child in child:
568	if i_child.tag.replace(self.base_ns, "") == "Qx":
569	self.current_dataset = plottable_2D()
570	return
571	self.current_dataset = plottable_1D(x, y)
572
573	def add_intermediate(self):
574	"""
575	This method stores any intermediate objects within the final data set after fully reading the set.
576
577	:param parent: The NXclass name for the h5py Group object that just finished being processed
578	"""
579
580	if self.parent_class == 'SASprocess':
581	self.current_datainfo.process.append(self.process)
582	self.process = Process()
583	elif self.parent_class == 'SASdetector':
584	self.current_datainfo.detector.append(self.detector)
585	self.detector = Detector()
586	elif self.parent_class == 'SAStransmission_spectrum':
587	self.current_datainfo.trans_spectrum.append(self.transspectrum)
588	self.transspectrum = TransmissionSpectrum()
589	elif self.parent_class == 'SAScollimation':
590	self.current_datainfo.collimation.append(self.collimation)
591	self.collimation = Collimation()
592	elif self.parent_class == 'aperture':
593	self.collimation.aperture.append(self.aperture)
594	self.aperture = Aperture()
595	elif self.parent_class == 'SASdata':
596	self._check_for_empty_resolution()
597	self.data.append(self.current_dataset)
598
599	def _final_cleanup(self):
600	"""
601	Final cleanup of the Data1D object to be sure it has all the
602	appropriate information needed for perspectives
603	"""
604
605	# Append errors to dataset and reset class errors
606	self.current_datainfo.errors = set()
607	for error in self.errors:
608	self.current_datainfo.errors.add(error)
609	self.errors.clear()
610
611	# Combine all plottables with datainfo and append each to output
612	# Type cast data arrays to float64 and find min/max as appropriate
613	for dataset in self.data:
614	if isinstance(dataset, plottable_1D):
615	if dataset.x is not None:
616	dataset.x = np.delete(dataset.x, [0])
617	dataset.x = dataset.x.astype(np.float64)
618	dataset.xmin = np.min(dataset.x)
619	dataset.xmax = np.max(dataset.x)
620	if dataset.y is not None:
621	dataset.y = np.delete(dataset.y, [0])
622	dataset.y = dataset.y.astype(np.float64)
623	dataset.ymin = np.min(dataset.y)
624	dataset.ymax = np.max(dataset.y)
625	if dataset.dx is not None:
626	dataset.dx = np.delete(dataset.dx, [0])
627	dataset.dx = dataset.dx.astype(np.float64)
628	if dataset.dxl is not None:
629	dataset.dxl = np.delete(dataset.dxl, [0])
630	dataset.dxl = dataset.dxl.astype(np.float64)
631	if dataset.dxw is not None:
632	dataset.dxw = np.delete(dataset.dxw, [0])
633	dataset.dxw = dataset.dxw.astype(np.float64)
634	if dataset.dy is not None:
635	dataset.dy = np.delete(dataset.dy, [0])
636	dataset.dy = dataset.dy.astype(np.float64)
637	np.trim_zeros(dataset.x)
638	np.trim_zeros(dataset.y)
639	np.trim_zeros(dataset.dy)
640	elif isinstance(dataset, plottable_2D):
641	dataset.data = dataset.data.astype(np.float64)
642	dataset.qx_data = dataset.qx_data.astype(np.float64)
643	dataset.xmin = np.min(dataset.qx_data)
644	dataset.xmax = np.max(dataset.qx_data)
645	dataset.qy_data = dataset.qy_data.astype(np.float64)
646	dataset.ymin = np.min(dataset.qy_data)
647	dataset.ymax = np.max(dataset.qy_data)
648	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
649	+ dataset.qy_data * dataset.qy_data)
650	if dataset.err_data is not None:
651	dataset.err_data = dataset.err_data.astype(np.float64)
652	if dataset.dqx_data is not None:
653	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
654	if dataset.dqy_data is not None:
655	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
656	if dataset.mask is not None:
657	dataset.mask = dataset.mask.astype(dtype=bool)
658
659	if len(dataset.shape) == 2:
660	n_rows, n_cols = dataset.shape
661	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
662	dataset.x_bins = dataset.qx_data[:int(n_cols)]
663	dataset.data = dataset.data.flatten()
664	else:
665	dataset.y_bins = []
666	dataset.x_bins = []
667	dataset.data = dataset.data.flatten()
668
669	final_dataset = combine_data(dataset, self.current_datainfo)
670	self.output.append(final_dataset)
671
672	def _create_unique_key(self, dictionary, name, numb=0):
673	"""
674	Create a unique key value for any dictionary to prevent overwriting
675	Recurse until a unique key value is found.
676
677	:param dictionary: A dictionary with any number of entries
678	:param name: The index of the item to be added to dictionary
679	:param numb: The number to be appended to the name, starts at 0
680	"""
681	if dictionary.get(name) is not None:
682	numb += 1
683	name = name.split("_")[0]
684	name += "_{0}".format(numb)
685	name = self._create_unique_key(dictionary, name, numb)
686	return name
687
688	def _get_node_value(self, node, tagname):
689	"""
690	Get the value of a node and any applicable units
691
692	:param node: The XML node to get the value of
693	:param tagname: The tagname of the node
694	"""
695	#Get the text from the node and convert all whitespace to spaces
696	units = ''
697	node_value = node.text
698	if node_value is not None:
699	node_value = ' '.join(node_value.split())
700	else:
701	node_value = ""
702
703	# If the value is a float, compile with units.
704	if self.ns_list.ns_datatype == "float":
705	# If an empty value is given, set as zero.
706	if node_value is None or node_value.isspace() \
707	or node_value.lower() == "nan":
708	node_value = "0.0"
709	#Convert the value to the base units
710	node_value, units = self._unit_conversion(node, tagname, node_value)
711
712	# If the value is a timestamp, convert to a datetime object
713	elif self.ns_list.ns_datatype == "timestamp":
714	if node_value is None or node_value.isspace():
715	pass
716	else:
717	try:
718	node_value = \
719	datetime.datetime.fromtimestamp(node_value)
720	except ValueError:
721	node_value = None
722	return node_value, units
723
724	def _unit_conversion(self, node, tagname, node_value):
725	"""
726	A unit converter method used to convert the data included in the file
727	to the default units listed in data_info
728
729	:param node: XML node
730	:param tagname: name of the node
731	:param node_value: The value of the current dom node
732	"""
733	attr = node.attrib
734	value_unit = ''
735	err_msg = None
736	default_unit = None
737	if not isinstance(node_value, float):
738	node_value = float(node_value)
739	if 'unit' in attr and attr.get('unit') is not None:
740	try:
741	local_unit = attr['unit']
742	unitname = self.ns_list.current_level.get("unit", "")
743	if "SASdetector" in self.names:
744	save_in = "detector"
745	elif "aperture" in self.names:
746	save_in = "aperture"
747	elif "SAScollimation" in self.names:
748	save_in = "collimation"
749	elif "SAStransmission_spectrum" in self.names:
750	save_in = "transspectrum"
751	elif "SASdata" in self.names:
752	x = np.zeros(1)
753	y = np.zeros(1)
754	self.current_data1d = Data1D(x, y)
755	save_in = "current_data1d"
756	elif "SASsource" in self.names:
757	save_in = "current_datainfo.source"
758	elif "SASsample" in self.names:
759	save_in = "current_datainfo.sample"
760	elif "SASprocess" in self.names:
761	save_in = "process"
762	else:
763	save_in = "current_datainfo"
764	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
765	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
766	and local_unit.lower() != "none":
767	if HAS_CONVERTER == True:
768	# Check local units - bad units raise KeyError
769	data_conv_q = Converter(local_unit)
770	value_unit = default_unit
771	node_value = data_conv_q(node_value, units=default_unit)
772	else:
773	value_unit = local_unit
774	err_msg = "Unit converter is not available.\n"
775	else:
776	value_unit = local_unit
777	except KeyError:
778	# Do not throw an error for loading Sesans data in cansas xml
779	# This is a temporary fix.
780	if local_unit != "A" and local_unit != 'pol':
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	# TODO: fix the writer to linearize all data, including T_spectrum
931	# self._write_trans_spectrum(datainfo, entry_node)
932	# Sample info
933	self._write_sample_info(datainfo, entry_node)
934	# Instrument info
935	instr = self._write_instrument(datainfo, entry_node)
936	# Source
937	self._write_source(datainfo, instr)
938	# Collimation
939	self._write_collimation(datainfo, instr)
940	# Detectors
941	self._write_detectors(datainfo, instr)
942	# Processes info
943	self._write_process_notes(datainfo, entry_node)
944	# Note info
945	self._write_notes(datainfo, entry_node)
946	# Return the document, and the SASentry node associated with
947	# the data we just wrote
948	# If the calling function was not the cansas reader, return a minidom
949	# object rather than an lxml object.
950	self.frm = inspect.stack()[1]
951	doc, entry_node = self._check_origin(entry_node, doc)
952	return doc, entry_node
953
954	def write_node(self, parent, name, value, attr=None):
955	"""
956	:param doc: document DOM
957	:param parent: parent node
958	:param name: tag of the element
959	:param value: value of the child text node
960	:param attr: attribute dictionary
961
962	:return: True if something was appended, otherwise False
963	"""
964	if value is not None:
965	parent = self.ebuilder(parent, name, value, attr)
966	return True
967	return False
968
969	def _get_pi_string(self):
970	"""
971	Creates the processing instructions header for writing to file
972	"""
973	pis = self.return_processing_instructions()
974	if len(pis) > 0:
975	pi_tree = self.create_tree(pis[0])
976	i = 1
977	for i in range(1, len(pis) - 1):
978	pi_tree = self.append(pis[i], pi_tree)
979	pi_string = self.to_string(pi_tree)
980	else:
981	pi_string = ""
982	return pi_string
983
984	def _create_main_node(self):
985	"""
986	Creates the primary xml header used when writing to file
987	"""
988	xsi = "http://www.w3.org/2001/XMLSchema-instance"
989	version = self.cansas_version
990	n_s = CANSAS_NS.get(version).get("ns")
991	if version == "1.1":
992	url = "http://www.cansas.org/formats/1.1/"
993	else:
994	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
995	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
996	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
997	"version" : version}
998	nsmap = {'xsi' : xsi, None: n_s}
999
1000	main_node = self.create_element("{" + n_s + "}SASroot",
1001	attrib=attrib, nsmap=nsmap)
1002	return main_node
1003
1004	def _write_run_names(self, datainfo, entry_node):
1005	"""
1006	Writes the run names to the XML file
1007
1008	:param datainfo: The Data1D object the information is coming from
1009	:param entry_node: lxml node ElementTree object to be appended to
1010	"""
1011	if datainfo.run == None or datainfo.run == []:
1012	datainfo.run.append(RUN_NAME_DEFAULT)
1013	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1014	for item in datainfo.run:
1015	runname = {}
1016	if item in datainfo.run_name and \
1017	len(str(datainfo.run_name[item])) > 1:
1018	runname = {'name': datainfo.run_name[item]}
1019	self.write_node(entry_node, "Run", item, runname)
1020
1021	def _write_data(self, datainfo, entry_node):
1022	"""
1023	Writes 1D I and Q data to the XML file
1024
1025	:param datainfo: The Data1D object the information is coming from
1026	:param entry_node: lxml node ElementTree object to be appended to
1027	"""
1028	node = self.create_element("SASdata")
1029	self.append(node, entry_node)
1030
1031	for i in range(len(datainfo.x)):
1032	point = self.create_element("Idata")
1033	node.append(point)
1034	self.write_node(point, "Q", datainfo.x[i],
1035	{'unit': datainfo.x_unit})
1036	if len(datainfo.y) >= i:
1037	self.write_node(point, "I", datainfo.y[i],
1038	{'unit': datainfo.y_unit})
1039	if datainfo.dy is not None and len(datainfo.dy) > i:
1040	self.write_node(point, "Idev", datainfo.dy[i],
1041	{'unit': datainfo.y_unit})
1042	if datainfo.dx is not None and len(datainfo.dx) > i:
1043	self.write_node(point, "Qdev", datainfo.dx[i],
1044	{'unit': datainfo.x_unit})
1045	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1046	self.write_node(point, "dQw", datainfo.dxw[i],
1047	{'unit': datainfo.x_unit})
1048	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1049	self.write_node(point, "dQl", datainfo.dxl[i],
1050	{'unit': datainfo.x_unit})
1051	if datainfo.isSesans:
1052	sesans_attrib = {'x_axis': datainfo._xaxis,
1053	'y_axis': datainfo._yaxis,
1054	'x_unit': datainfo.x_unit,
1055	'y_unit': datainfo.y_unit}
1056	sesans = self.create_element("Sesans", attrib=sesans_attrib)
1057	sesans.text = str(datainfo.isSesans)
1058	entry_node.append(sesans)
1059	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
1060	{'unit': datainfo.sample.zacceptance[1]})
1061
1062
1063	def _write_data_2d(self, datainfo, entry_node):
1064	"""
1065	Writes 2D data to the XML file
1066
1067	:param datainfo: The Data2D object the information is coming from
1068	:param entry_node: lxml node ElementTree object to be appended to
1069	"""
1070	attr = {}
1071	if datainfo.data.shape:
1072	attr["x_bins"] = str(len(datainfo.x_bins))
1073	attr["y_bins"] = str(len(datainfo.y_bins))
1074	node = self.create_element("SASdata", attr)
1075	self.append(node, entry_node)
1076
1077	point = self.create_element("Idata")
1078	node.append(point)
1079	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1080	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1081	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1082
1083	self.write_node(point, "Qx", qx,
1084	{'unit': datainfo._xunit})
1085	self.write_node(point, "Qy", qy,
1086	{'unit': datainfo._yunit})
1087	self.write_node(point, "I", intensity,
1088	{'unit': datainfo._zunit})
1089	if datainfo.err_data is not None:
1090	err = ','.join([str(datainfo.err_data[i]) for i in
1091	xrange(len(datainfo.err_data))])
1092	self.write_node(point, "Idev", err,
1093	{'unit': datainfo._zunit})
1094	if datainfo.dqy_data is not None:
1095	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1096	xrange(len(datainfo.dqy_data))])
1097	self.write_node(point, "Qydev", dqy,
1098	{'unit': datainfo._yunit})
1099	if datainfo.dqx_data is not None:
1100	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1101	xrange(len(datainfo.dqx_data))])
1102	self.write_node(point, "Qxdev", dqx,
1103	{'unit': datainfo._xunit})
1104	if datainfo.mask is not None:
1105	mask = ','.join(
1106	["1" if datainfo.mask[i] else "0"
1107	for i in xrange(len(datainfo.mask))])
1108	self.write_node(point, "Mask", mask)
1109
1110	def _write_trans_spectrum(self, datainfo, entry_node):
1111	"""
1112	Writes the transmission spectrum data to the XML file
1113
1114	:param datainfo: The Data1D object the information is coming from
1115	:param entry_node: lxml node ElementTree object to be appended to
1116	"""
1117	for i in range(len(datainfo.trans_spectrum)):
1118	spectrum = datainfo.trans_spectrum[i]
1119	node = self.create_element("SAStransmission_spectrum",
1120	{"name" : spectrum.name})
1121	self.append(node, entry_node)
1122	if isinstance(spectrum.timestamp, datetime.datetime):
1123	node.setAttribute("timestamp", spectrum.timestamp)
1124	for i in range(len(spectrum.wavelength)):
1125	point = self.create_element("Tdata")
1126	node.append(point)
1127	self.write_node(point, "Lambda", spectrum.wavelength[i],
1128	{'unit': spectrum.wavelength_unit})
1129	self.write_node(point, "T", spectrum.transmission[i],
1130	{'unit': spectrum.transmission_unit})
1131	if spectrum.transmission_deviation != None \
1132	and len(spectrum.transmission_deviation) >= i:
1133	self.write_node(point, "Tdev",
1134	spectrum.transmission_deviation[i],
1135	{'unit':
1136	spectrum.transmission_deviation_unit})
1137
1138	def _write_sample_info(self, datainfo, entry_node):
1139	"""
1140	Writes the sample information to the XML file
1141
1142	:param datainfo: The Data1D object the information is coming from
1143	:param entry_node: lxml node ElementTree object to be appended to
1144	"""
1145	sample = self.create_element("SASsample")
1146	if datainfo.sample.name is not None:
1147	self.write_attribute(sample, "name",
1148	str(datainfo.sample.name))
1149	self.append(sample, entry_node)
1150	self.write_node(sample, "ID", str(datainfo.sample.ID))
1151	self.write_node(sample, "thickness", datainfo.sample.thickness,
1152	{"unit": datainfo.sample.thickness_unit})
1153	self.write_node(sample, "transmission", datainfo.sample.transmission)
1154	self.write_node(sample, "temperature", datainfo.sample.temperature,
1155	{"unit": datainfo.sample.temperature_unit})
1156
1157	pos = self.create_element("position")
1158	written = self.write_node(pos,
1159	"x",
1160	datainfo.sample.position.x,
1161	{"unit": datainfo.sample.position_unit})
1162	written = written \| self.write_node( \
1163	pos, "y", datainfo.sample.position.y,
1164	{"unit": datainfo.sample.position_unit})
1165	written = written \| self.write_node( \
1166	pos, "z", datainfo.sample.position.z,
1167	{"unit": datainfo.sample.position_unit})
1168	if written == True:
1169	self.append(pos, sample)
1170
1171	ori = self.create_element("orientation")
1172	written = self.write_node(ori, "roll",
1173	datainfo.sample.orientation.x,
1174	{"unit": datainfo.sample.orientation_unit})
1175	written = written \| self.write_node( \
1176	ori, "pitch", datainfo.sample.orientation.y,
1177	{"unit": datainfo.sample.orientation_unit})
1178	written = written \| self.write_node( \
1179	ori, "yaw", datainfo.sample.orientation.z,
1180	{"unit": datainfo.sample.orientation_unit})
1181	if written == True:
1182	self.append(ori, sample)
1183
1184	for item in datainfo.sample.details:
1185	self.write_node(sample, "details", item)
1186
1187	def _write_instrument(self, datainfo, entry_node):
1188	"""
1189	Writes the instrumental information to the XML file
1190
1191	:param datainfo: The Data1D object the information is coming from
1192	:param entry_node: lxml node ElementTree object to be appended to
1193	"""
1194	instr = self.create_element("SASinstrument")
1195	self.append(instr, entry_node)
1196	self.write_node(instr, "name", datainfo.instrument)
1197	return instr
1198
1199	def _write_source(self, datainfo, instr):
1200	"""
1201	Writes the source information to the XML file
1202
1203	:param datainfo: The Data1D object the information is coming from
1204	:param instr: instrument node to be appended to
1205	"""
1206	source = self.create_element("SASsource")
1207	if datainfo.source.name is not None:
1208	self.write_attribute(source, "name",
1209	str(datainfo.source.name))
1210	self.append(source, instr)
1211	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1212	datainfo.source.radiation = "neutron"
1213	self.write_node(source, "radiation", datainfo.source.radiation)
1214
1215	size = self.create_element("beam_size")
1216	if datainfo.source.beam_size_name is not None:
1217	self.write_attribute(size, "name",
1218	str(datainfo.source.beam_size_name))
1219	written = self.write_node( \
1220	size, "x", datainfo.source.beam_size.x,
1221	{"unit": datainfo.source.beam_size_unit})
1222	written = written \| self.write_node( \
1223	size, "y", datainfo.source.beam_size.y,
1224	{"unit": datainfo.source.beam_size_unit})
1225	written = written \| self.write_node( \
1226	size, "z", datainfo.source.beam_size.z,
1227	{"unit": datainfo.source.beam_size_unit})
1228	if written == True:
1229	self.append(size, source)
1230
1231	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1232	self.write_node(source, "wavelength",
1233	datainfo.source.wavelength,
1234	{"unit": datainfo.source.wavelength_unit})
1235	self.write_node(source, "wavelength_min",
1236	datainfo.source.wavelength_min,
1237	{"unit": datainfo.source.wavelength_min_unit})
1238	self.write_node(source, "wavelength_max",
1239	datainfo.source.wavelength_max,
1240	{"unit": datainfo.source.wavelength_max_unit})
1241	self.write_node(source, "wavelength_spread",
1242	datainfo.source.wavelength_spread,
1243	{"unit": datainfo.source.wavelength_spread_unit})
1244
1245	def _write_collimation(self, datainfo, instr):
1246	"""
1247	Writes the collimation information to the XML file
1248
1249	:param datainfo: The Data1D object the information is coming from
1250	:param instr: lxml node ElementTree object to be appended to
1251	"""
1252	if datainfo.collimation == [] or datainfo.collimation == None:
1253	coll = Collimation()
1254	datainfo.collimation.append(coll)
1255	for item in datainfo.collimation:
1256	coll = self.create_element("SAScollimation")
1257	if item.name is not None:
1258	self.write_attribute(coll, "name", str(item.name))
1259	self.append(coll, instr)
1260
1261	self.write_node(coll, "length", item.length,
1262	{"unit": item.length_unit})
1263
1264	for aperture in item.aperture:
1265	apert = self.create_element("aperture")
1266	if aperture.name is not None:
1267	self.write_attribute(apert, "name", str(aperture.name))
1268	if aperture.type is not None:
1269	self.write_attribute(apert, "type", str(aperture.type))
1270	self.append(apert, coll)
1271
1272	size = self.create_element("size")
1273	if aperture.size_name is not None:
1274	self.write_attribute(size, "name",
1275	str(aperture.size_name))
1276	written = self.write_node(size, "x", aperture.size.x,
1277	{"unit": aperture.size_unit})
1278	written = written \| self.write_node( \
1279	size, "y", aperture.size.y,
1280	{"unit": aperture.size_unit})
1281	written = written \| self.write_node( \
1282	size, "z", aperture.size.z,
1283	{"unit": aperture.size_unit})
1284	if written == True:
1285	self.append(size, apert)
1286
1287	self.write_node(apert, "distance", aperture.distance,
1288	{"unit": aperture.distance_unit})
1289
1290	def _write_detectors(self, datainfo, instr):
1291	"""
1292	Writes the detector information to the XML file
1293
1294	:param datainfo: The Data1D object the information is coming from
1295	:param inst: lxml instrument node to be appended to
1296	"""
1297	if datainfo.detector == None or datainfo.detector == []:
1298	det = Detector()
1299	det.name = ""
1300	datainfo.detector.append(det)
1301
1302	for item in datainfo.detector:
1303	det = self.create_element("SASdetector")
1304	written = self.write_node(det, "name", item.name)
1305	written = written \| self.write_node(det, "SDD", item.distance,
1306	{"unit": item.distance_unit})
1307	if written == True:
1308	self.append(det, instr)
1309
1310	off = self.create_element("offset")
1311	written = self.write_node(off, "x", item.offset.x,
1312	{"unit": item.offset_unit})
1313	written = written \| self.write_node(off, "y", item.offset.y,
1314	{"unit": item.offset_unit})
1315	written = written \| self.write_node(off, "z", item.offset.z,
1316	{"unit": item.offset_unit})
1317	if written == True:
1318	self.append(off, det)
1319
1320	ori = self.create_element("orientation")
1321	written = self.write_node(ori, "roll", item.orientation.x,
1322	{"unit": item.orientation_unit})
1323	written = written \| self.write_node(ori, "pitch",
1324	item.orientation.y,
1325	{"unit": item.orientation_unit})
1326	written = written \| self.write_node(ori, "yaw",
1327	item.orientation.z,
1328	{"unit": item.orientation_unit})
1329	if written == True:
1330	self.append(ori, det)
1331
1332	center = self.create_element("beam_center")
1333	written = self.write_node(center, "x", item.beam_center.x,
1334	{"unit": item.beam_center_unit})
1335	written = written \| self.write_node(center, "y",
1336	item.beam_center.y,
1337	{"unit": item.beam_center_unit})
1338	written = written \| self.write_node(center, "z",
1339	item.beam_center.z,
1340	{"unit": item.beam_center_unit})
1341	if written == True:
1342	self.append(center, det)
1343
1344	pix = self.create_element("pixel_size")
1345	written = self.write_node(pix, "x", item.pixel_size.x,
1346	{"unit": item.pixel_size_unit})
1347	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1348	{"unit": item.pixel_size_unit})
1349	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1350	{"unit": item.pixel_size_unit})
1351	if written == True:
1352	self.append(pix, det)
1353	self.write_node(det, "slit_length", item.slit_length,
1354	{"unit": item.slit_length_unit})
1355
1356
1357	def _write_process_notes(self, datainfo, entry_node):
1358	"""
1359	Writes the process notes to the XML file
1360
1361	:param datainfo: The Data1D object the information is coming from
1362	:param entry_node: lxml node ElementTree object to be appended to
1363
1364	"""
1365	for item in datainfo.process:
1366	node = self.create_element("SASprocess")
1367	self.append(node, entry_node)
1368	self.write_node(node, "name", item.name)
1369	self.write_node(node, "date", item.date)
1370	self.write_node(node, "description", item.description)
1371	for term in item.term:
1372	if isinstance(term, list):
1373	value = term['value']
1374	del term['value']
1375	elif isinstance(term, dict):
1376	value = term.get("value")
1377	del term['value']
1378	else:
1379	value = term
1380	self.write_node(node, "term", value, term)
1381	for note in item.notes:
1382	self.write_node(node, "SASprocessnote", note)
1383	if len(item.notes) == 0:
1384	self.write_node(node, "SASprocessnote", "")
1385
1386	def _write_notes(self, datainfo, entry_node):
1387	"""
1388	Writes the notes to the XML file and creates an empty note if none
1389	exist
1390
1391	:param datainfo: The Data1D object the information is coming from
1392	:param entry_node: lxml node ElementTree object to be appended to
1393
1394	"""
1395	if len(datainfo.notes) == 0:
1396	node = self.create_element("SASnote")
1397	self.append(node, entry_node)
1398	else:
1399	for item in datainfo.notes:
1400	node = self.create_element("SASnote")
1401	self.write_text(node, item)
1402	self.append(node, entry_node)
1403
1404	def _check_origin(self, entry_node, doc):
1405	"""
1406	Return the document, and the SASentry node associated with
1407	the data we just wrote.
1408	If the calling function was not the cansas reader, return a minidom
1409	object rather than an lxml object.
1410
1411	:param entry_node: lxml node ElementTree object to be appended to
1412	:param doc: entire xml tree
1413	"""
1414	if not self.frm:
1415	self.frm = inspect.stack()[1]
1416	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1417	mod_name = mod_name.replace(".py", "")
1418	mod = mod_name.split("sas/")
1419	mod_name = mod[1]
1420	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1421	string = self.to_string(doc, pretty_print=False)
1422	doc = parseString(string)
1423	node_name = entry_node.tag
1424	node_list = doc.getElementsByTagName(node_name)
1425	entry_node = node_list.item(0)
1426	return doc, entry_node
1427
1428	# DO NOT REMOVE - used in saving and loading panel states.
1429	def _store_float(self, location, node, variable, storage, optional=True):
1430	"""
1431	Get the content of a xpath location and store
1432	the result. Check that the units are compatible
1433	with the destination. The value is expected to
1434	be a float.
1435
1436	The xpath location might or might not exist.
1437	If it does not exist, nothing is done
1438
1439	:param location: xpath location to fetch
1440	:param node: node to read the data from
1441	:param variable: name of the data member to store it in [string]
1442	:param storage: data object that has the 'variable' data member
1443	:param optional: if True, no exception will be raised
1444	if unit conversion can't be done
1445
1446	:raise ValueError: raised when the units are not recognized
1447	"""
1448	entry = get_content(location, node)
1449	try:
1450	value = float(entry.text)
1451	except:
1452	value = None
1453
1454	if value is not None:
1455	# If the entry has units, check to see that they are
1456	# compatible with what we currently have in the data object
1457	units = entry.get('unit')
1458	if units is not None:
1459	toks = variable.split('.')
1460	local_unit = None
1461	exec "local_unit = storage.%s_unit" % toks[0]
1462	if local_unit != None and units.lower() != local_unit.lower():
1463	if HAS_CONVERTER == True:
1464	try:
1465	conv = Converter(units)
1466	exec "storage.%s = %g" % \
1467	(variable, conv(value, units=local_unit))
1468	except:
1469	_, exc_value, _ = sys.exc_info()
1470	err_mess = "CanSAS reader: could not convert"
1471	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1472	% (variable, units, local_unit, exc_value)
1473	self.errors.add(err_mess)
1474	if optional:
1475	logging.info(err_mess)
1476	else:
1477	raise ValueError, err_mess
1478	else:
1479	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1480	% (variable, units)
1481	err_mess += " expecting [%s]" % local_unit
1482	self.errors.add(err_mess)
1483	if optional:
1484	logging.info(err_mess)
1485	else:
1486	raise ValueError, err_mess
1487	else:
1488	exec "storage.%s = value" % variable
1489	else:
1490	exec "storage.%s = value" % variable
1491
1492	# DO NOT REMOVE - used in saving and loading panel states.
1493	def _store_content(self, location, node, variable, storage):
1494	"""
1495	Get the content of a xpath location and store
1496	the result. The value is treated as a string.
1497
1498	The xpath location might or might not exist.
1499	If it does not exist, nothing is done
1500
1501	:param location: xpath location to fetch
1502	:param node: node to read the data from
1503	:param variable: name of the data member to store it in [string]
1504	:param storage: data object that has the 'variable' data member
1505
1506	:return: return a list of errors
1507	"""
1508	entry = get_content(location, node)
1509	if entry is not None and entry.text is not None:
1510	exec "storage.%s = entry.text.strip()" % variable
1511
1512
1513	# DO NOT REMOVE Called by outside packages:
1514	# sas.sasgui.perspectives.invariant.invariant_state
1515	# sas.sasgui.perspectives.fitting.pagestate
1516	def get_content(location, node):
1517	"""
1518	Get the first instance of the content of a xpath location.
1519
1520	:param location: xpath location
1521	:param node: node to start at
1522
1523	:return: Element, or None
1524	"""
1525	nodes = node.xpath(location,
1526	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1527	if len(nodes) > 0:
1528	return nodes[0]
1529	else:
1530	return None
1531
1532	# DO NOT REMOVE Called by outside packages:
1533	# sas.sasgui.perspectives.fitting.pagestate
1534	def write_node(doc, parent, name, value, attr=None):
1535	"""
1536	:param doc: document DOM
1537	:param parent: parent node
1538	:param name: tag of the element
1539	:param value: value of the child text node
1540	:param attr: attribute dictionary
1541
1542	:return: True if something was appended, otherwise False
1543	"""
1544	if attr is None:
1545	attr = {}
1546	if value is not None:
1547	node = doc.createElement(name)
1548	node.appendChild(doc.createTextNode(str(value)))
1549	for item in attr:
1550	node.setAttribute(item, attr[item])
1551	parent.appendChild(node)
1552	return True
1553	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ d7ee5866

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