cansas_reader.py @ cb05bfd

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 cb05bfd was bcabf4e, checked in by krzywon, 8 years ago
2D masking loaded properly and mask is now saved as 1s and 0s as per CanSAS specification.
Property mode set to `100644`
File size: 69.2 KB

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

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ cb05bfd

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