cansas_reader.py @ af08e55

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 af08e55 was af08e55, checked in by krzywon, 7 years ago
Saving and loading of 2D data within projects and fit save states is working. This works alongside saving and loading 1D fits withint the same .svs file. #827
Property mode set to `100644`
File size: 69.0 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	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	data_point, unit = self._get_node_value(node, tagname)
247
248	# If this is a dataset, store the data appropriately
249	if tagname == 'Run':
250	self.current_datainfo.run_name[data_point] = name
251	self.current_datainfo.run.append(data_point)
252	elif tagname == 'Title':
253	self.current_datainfo.title = data_point
254	elif tagname == 'SASnote':
255	self.current_datainfo.notes.append(data_point)
256
257	# I and Q - 1D data
258	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
259	self.current_dataset.yaxis("Intensity", unit)
260	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
261	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
262	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
263	elif tagname == 'Q':
264	self.current_dataset.xaxis("Q", unit)
265	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
266	elif tagname == 'Qdev':
267	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
268	elif tagname == 'dQw':
269	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
270	elif tagname == 'dQl':
271	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
272	elif tagname == 'Qmean':
273	pass
274	elif tagname == 'Shadowfactor':
275	pass
276	# I and Qx, Qy - 2D data
277	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
278	self.current_dataset.yaxis("Intensity", unit)
279	self.current_dataset.data = np.append(self.current_dataset.data, data_point)
280	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
281	self.current_dataset.err_data = np.append(self.current_dataset.err_data, data_point)
282	elif tagname == 'Qx':
283	self.current_dataset.xaxis("Qx", unit)
284	self.current_dataset.qx_data = np.append(self.current_dataset.qx_data, data_point)
285	elif tagname == 'Qy':
286	self.current_dataset.yaxis("Qy", unit)
287	self.current_dataset.qy_data = np.append(self.current_dataset.qy_data, data_point)
288	elif tagname == 'Qxdev':
289	self.current_dataset.xaxis("Qxdev", unit)
290	self.current_dataset.dqx_data = np.append(self.current_dataset.dqx_data, data_point)
291	elif tagname == 'Qydev':
292	self.current_dataset.yaxis("Qydev", unit)
293	self.current_dataset.dqy_data = np.append(self.current_dataset.dqy_data, data_point)
294	elif tagname == 'Mask':
295	self.current_dataset.mask = np.append(self.current_dataset.mask, bool(data_point))
296
297	# Sample Information
298	elif tagname == 'ID' and self.parent_class == 'SASsample':
299	self.current_datainfo.sample.ID = data_point
300	elif tagname == 'Title' and self.parent_class == 'SASsample':
301	self.current_datainfo.sample.name = data_point
302	elif tagname == 'thickness' and self.parent_class == 'SASsample':
303	self.current_datainfo.sample.thickness = data_point
304	self.current_datainfo.sample.thickness_unit = unit
305	elif tagname == 'transmission' and self.parent_class == 'SASsample':
306	self.current_datainfo.sample.transmission = data_point
307	elif tagname == 'temperature' and self.parent_class == 'SASsample':
308	self.current_datainfo.sample.temperature = data_point
309	self.current_datainfo.sample.temperature_unit = unit
310	elif tagname == 'details' and self.parent_class == 'SASsample':
311	self.current_datainfo.sample.details.append(data_point)
312	elif tagname == 'x' and self.parent_class == 'position':
313	self.current_datainfo.sample.position.x = data_point
314	self.current_datainfo.sample.position_unit = unit
315	elif tagname == 'y' and self.parent_class == 'position':
316	self.current_datainfo.sample.position.y = data_point
317	self.current_datainfo.sample.position_unit = unit
318	elif tagname == 'z' and self.parent_class == 'position':
319	self.current_datainfo.sample.position.z = data_point
320	self.current_datainfo.sample.position_unit = unit
321	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
322	self.current_datainfo.sample.orientation.x = data_point
323	self.current_datainfo.sample.orientation_unit = unit
324	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
325	self.current_datainfo.sample.orientation.y = data_point
326	self.current_datainfo.sample.orientation_unit = unit
327	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
328	self.current_datainfo.sample.orientation.z = data_point
329	self.current_datainfo.sample.orientation_unit = unit
330
331	# Instrumental Information
332	elif tagname == 'name' and self.parent_class == 'SASinstrument':
333	self.current_datainfo.instrument = data_point
334	# Detector Information
335	elif tagname == 'name' and self.parent_class == 'SASdetector':
336	self.detector.name = data_point
337	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
338	self.detector.distance = data_point
339	self.detector.distance_unit = unit
340	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
341	self.detector.slit_length = data_point
342	self.detector.slit_length_unit = unit
343	elif tagname == 'x' and self.parent_class == 'offset':
344	self.detector.offset.x = data_point
345	self.detector.offset_unit = unit
346	elif tagname == 'y' and self.parent_class == 'offset':
347	self.detector.offset.y = data_point
348	self.detector.offset_unit = unit
349	elif tagname == 'z' and self.parent_class == 'offset':
350	self.detector.offset.z = data_point
351	self.detector.offset_unit = unit
352	elif tagname == 'x' and self.parent_class == 'beam_center':
353	self.detector.beam_center.x = data_point
354	self.detector.beam_center_unit = unit
355	elif tagname == 'y' and self.parent_class == 'beam_center':
356	self.detector.beam_center.y = data_point
357	self.detector.beam_center_unit = unit
358	elif tagname == 'z' and self.parent_class == 'beam_center':
359	self.detector.beam_center.z = data_point
360	self.detector.beam_center_unit = unit
361	elif tagname == 'x' and self.parent_class == 'pixel_size':
362	self.detector.pixel_size.x = data_point
363	self.detector.pixel_size_unit = unit
364	elif tagname == 'y' and self.parent_class == 'pixel_size':
365	self.detector.pixel_size.y = data_point
366	self.detector.pixel_size_unit = unit
367	elif tagname == 'z' and self.parent_class == 'pixel_size':
368	self.detector.pixel_size.z = data_point
369	self.detector.pixel_size_unit = unit
370	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
371	self.detector.orientation.x = data_point
372	self.detector.orientation_unit = unit
373	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
374	self.detector.orientation.y = data_point
375	self.detector.orientation_unit = unit
376	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
377	self.detector.orientation.z = data_point
378	self.detector.orientation_unit = unit
379	# Collimation and Aperture
380	elif tagname == 'length' and self.parent_class == 'SAScollimation':
381	self.collimation.length = data_point
382	self.collimation.length_unit = unit
383	elif tagname == 'name' and self.parent_class == 'SAScollimation':
384	self.collimation.name = data_point
385	elif tagname == 'distance' and self.parent_class == 'aperture':
386	self.aperture.distance = data_point
387	self.aperture.distance_unit = unit
388	elif tagname == 'x' and self.parent_class == 'size':
389	self.aperture.size.x = data_point
390	self.collimation.size_unit = unit
391	elif tagname == 'y' and self.parent_class == 'size':
392	self.aperture.size.y = data_point
393	self.collimation.size_unit = unit
394	elif tagname == 'z' and self.parent_class == 'size':
395	self.aperture.size.z = data_point
396	self.collimation.size_unit = unit
397
398	# Process Information
399	elif tagname == 'name' and self.parent_class == 'SASprocess':
400	self.process.name = data_point
401	elif tagname == 'description' and self.parent_class == 'SASprocess':
402	self.process.description = data_point
403	elif tagname == 'date' and self.parent_class == 'SASprocess':
404	try:
405	self.process.date = datetime.datetime.fromtimestamp(data_point)
406	except:
407	self.process.date = data_point
408	elif tagname == 'SASprocessnote':
409	self.process.notes.append(data_point)
410	elif tagname == 'term' and self.parent_class == 'SASprocess':
411	unit = attr.get("unit", "")
412	dic = {}
413	dic["name"] = name
414	dic["value"] = data_point
415	dic["unit"] = unit
416	self.process.term.append(dic)
417
418	# Transmission Spectrum
419	elif tagname == 'T' and self.parent_class == 'Tdata':
420	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
421	self.transspectrum.transmission_unit = unit
422	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
423	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
424	self.transspectrum.transmission_deviation_unit = unit
425	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
426	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
427	self.transspectrum.wavelength_unit = unit
428
429	# Source Information
430	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
431	self.current_datainfo.source.wavelength = data_point
432	self.current_datainfo.source.wavelength_unit = unit
433	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
434	self.current_datainfo.source.wavelength_min = data_point
435	self.current_datainfo.source.wavelength_min_unit = unit
436	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
437	self.current_datainfo.source.wavelength_max = data_point
438	self.current_datainfo.source.wavelength_max_unit = unit
439	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
440	self.current_datainfo.source.wavelength_spread = data_point
441	self.current_datainfo.source.wavelength_spread_unit = unit
442	elif tagname == 'x' and self.parent_class == 'beam_size':
443	self.current_datainfo.source.beam_size.x = data_point
444	self.current_datainfo.source.beam_size_unit = unit
445	elif tagname == 'y' and self.parent_class == 'beam_size':
446	self.current_datainfo.source.beam_size.y = data_point
447	self.current_datainfo.source.beam_size_unit = unit
448	elif tagname == 'z' and self.parent_class == 'pixel_size':
449	self.current_datainfo.source.data_point.z = data_point
450	self.current_datainfo.source.beam_size_unit = unit
451	elif tagname == 'radiation' and self.parent_class == 'SASsource':
452	self.current_datainfo.source.radiation = data_point
453	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
454	self.current_datainfo.source.beam_shape = data_point
455
456	# Everything else goes in meta_data
457	else:
458	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
459	self.current_datainfo.meta_data[new_key] = data_point
460
461	self.names.remove(tagname_original)
462	length = 0
463	if len(self.names) > 1:
464	length = len(self.names) - 1
465	self.parent_class = self.names[length]
466	if not self._is_call_local() and not recurse:
467	self.frm = ""
468	self.add_data_set()
469	empty = None
470	return self.output[0], empty
471
472
473	def _is_call_local(self):
474	"""
475
476	"""
477	if self.frm == "":
478	inter = inspect.stack()
479	self.frm = inter[2]
480	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
481	mod_name = mod_name.replace(".py", "")
482	mod = mod_name.split("sas/")
483	mod_name = mod[1]
484	if mod_name != "sascalc/dataloader/readers/cansas_reader":
485	return False
486	return True
487
488	def is_cansas(self, ext="xml"):
489	"""
490	Checks to see if the xml file is a CanSAS file
491
492	:param ext: The file extension of the data file
493	"""
494	if self.validate_xml():
495	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
496	value = self.xmlroot.get(name)
497	if CANSAS_NS.get(self.cansas_version).get("ns") == \
498	value.rsplit(" ")[0]:
499	return True
500	if ext == "svs":
501	return True
502	raise RuntimeError
503
504	def load_file_and_schema(self, xml_file, schema_path=""):
505	"""
506	Loads the file and associates a schema, if a schema is passed in or if one already exists
507
508	:param xml_file: The xml file path sent to Reader.read
509	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
510	"""
511	base_name = xml_reader.__file__
512	base_name = base_name.replace("\\", "/")
513	base = base_name.split("/sas/")[0]
514
515	# Load in xml file and get the cansas version from the header
516	self.set_xml_file(xml_file)
517	self.cansas_version = self.xmlroot.get("version", "1.0")
518
519	# Generic values for the cansas file based on the version
520	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
521	if schema_path == "":
522	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
523	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
524
525	# Link a schema to the XML file.
526	self.set_schema(schema_path)
527
528	def add_data_set(self):
529	"""
530	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
531	private method to generate a new data set.
532
533	:param key: NeXus group name for current tree level
534	"""
535
536	if self.current_datainfo and self.current_dataset:
537	self._final_cleanup()
538	self.data = []
539	self.current_datainfo = DataInfo()
540
541	def _initialize_new_data_set(self, node=None):
542	"""
543	A private class method to generate a new 1D data object.
544	Outside methods should call add_data_set() to be sure any existing data is stored properly.
545
546	:param node: XML node to determine if 1D or 2D data
547	"""
548	x = np.array(0)
549	y = np.array(0)
550	for child in node:
551	if child.tag.replace(self.base_ns, "") == "Idata":
552	for i_child in child:
553	if i_child.tag.replace(self.base_ns, "") == "Qx":
554	self.current_dataset = plottable_2D()
555	return
556	self.current_dataset = plottable_1D(x, y)
557
558	def add_intermediate(self):
559	"""
560	This method stores any intermediate objects within the final data set after fully reading the set.
561
562	:param parent: The NXclass name for the h5py Group object that just finished being processed
563	"""
564
565	if self.parent_class == 'SASprocess':
566	self.current_datainfo.process.append(self.process)
567	self.process = Process()
568	elif self.parent_class == 'SASdetector':
569	self.current_datainfo.detector.append(self.detector)
570	self.detector = Detector()
571	elif self.parent_class == 'SAStransmission_spectrum':
572	self.current_datainfo.trans_spectrum.append(self.transspectrum)
573	self.transspectrum = TransmissionSpectrum()
574	elif self.parent_class == 'SAScollimation':
575	self.current_datainfo.collimation.append(self.collimation)
576	self.collimation = Collimation()
577	elif self.parent_class == 'aperture':
578	self.collimation.aperture.append(self.aperture)
579	self.aperture = Aperture()
580	elif self.parent_class == 'SASdata':
581	self._check_for_empty_resolution()
582	self.data.append(self.current_dataset)
583
584	def _final_cleanup(self):
585	"""
586	Final cleanup of the Data1D object to be sure it has all the
587	appropriate information needed for perspectives
588	"""
589
590	# Append errors to dataset and reset class errors
591	self.current_datainfo.errors = set()
592	for error in self.errors:
593	self.current_datainfo.errors.add(error)
594	self.errors.clear()
595
596	# Combine all plottables with datainfo and append each to output
597	# Type cast data arrays to float64 and find min/max as appropriate
598	for dataset in self.data:
599	if isinstance(dataset, plottable_1D):
600	if dataset.x is not None:
601	dataset.x = np.delete(dataset.x, [0])
602	dataset.x = dataset.x.astype(np.float64)
603	dataset.xmin = np.min(dataset.x)
604	dataset.xmax = np.max(dataset.x)
605	if dataset.y is not None:
606	dataset.y = np.delete(dataset.y, [0])
607	dataset.y = dataset.y.astype(np.float64)
608	dataset.ymin = np.min(dataset.y)
609	dataset.ymax = np.max(dataset.y)
610	if dataset.dx is not None:
611	dataset.dx = np.delete(dataset.dx, [0])
612	dataset.dx = dataset.dx.astype(np.float64)
613	if dataset.dxl is not None:
614	dataset.dxl = np.delete(dataset.dxl, [0])
615	dataset.dxl = dataset.dxl.astype(np.float64)
616	if dataset.dxw is not None:
617	dataset.dxw = np.delete(dataset.dxw, [0])
618	dataset.dxw = dataset.dxw.astype(np.float64)
619	if dataset.dy is not None:
620	dataset.dy = np.delete(dataset.dy, [0])
621	dataset.dy = dataset.dy.astype(np.float64)
622	np.trim_zeros(dataset.x)
623	np.trim_zeros(dataset.y)
624	np.trim_zeros(dataset.dy)
625	elif isinstance(dataset, plottable_2D):
626	dataset.data = np.delete(dataset.data, [0])
627	dataset.data = dataset.data.astype(np.float64)
628	dataset.qx_data = np.delete(dataset.qx_data, [0])
629	dataset.qx_data = dataset.qx_data.astype(np.float64)
630	dataset.xmin = np.min(dataset.qx_data)
631	dataset.xmax = np.max(dataset.qx_data)
632	dataset.qy_data = np.delete(dataset.qy_data, [0])
633	dataset.qy_data = dataset.qy_data.astype(np.float64)
634	dataset.ymin = np.min(dataset.qy_data)
635	dataset.ymax = np.max(dataset.qy_data)
636	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
637	+ dataset.qy_data * dataset.qy_data)
638	if dataset.err_data is not None:
639	dataset.err_data = np.delete(dataset.err_data, [0])
640	dataset.err_data = dataset.err_data.astype(np.float64)
641	if dataset.dqx_data is not None:
642	dataset.dqx_data = np.delete(dataset.dqx_data, [0])
643	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
644	if dataset.dqy_data is not None:
645	dataset.dqy_data = np.delete(dataset.dqy_data, [0])
646	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
647	if dataset.mask is not None:
648	dataset.mask = np.delete(dataset.mask, [0])
649	dataset.mask = dataset.mask.astype(dtype=bool)
650
651	if len(dataset.shape) == 2:
652	n_rows, n_cols = dataset.shape
653	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
654	dataset.x_bins = dataset.qx_data[:int(n_cols)]
655	dataset.data = dataset.data.flatten()
656	else:
657	dataset.y_bins = []
658	dataset.x_bins = []
659	dataset.data = dataset.data.flatten()
660
661	final_dataset = combine_data(dataset, self.current_datainfo)
662	self.output.append(final_dataset)
663
664	def _create_unique_key(self, dictionary, name, numb=0):
665	"""
666	Create a unique key value for any dictionary to prevent overwriting
667	Recurse until a unique key value is found.
668
669	:param dictionary: A dictionary with any number of entries
670	:param name: The index of the item to be added to dictionary
671	:param numb: The number to be appended to the name, starts at 0
672	"""
673	if dictionary.get(name) is not None:
674	numb += 1
675	name = name.split("_")[0]
676	name += "_{0}".format(numb)
677	name = self._create_unique_key(dictionary, name, numb)
678	return name
679
680	def _get_node_value(self, node, tagname):
681	"""
682	Get the value of a node and any applicable units
683
684	:param node: The XML node to get the value of
685	:param tagname: The tagname of the node
686	"""
687	#Get the text from the node and convert all whitespace to spaces
688	units = ''
689	node_value = node.text
690	if node_value is not None:
691	node_value = ' '.join(node_value.split())
692	else:
693	node_value = ""
694
695	# If the value is a float, compile with units.
696	if self.ns_list.ns_datatype == "float":
697	# If an empty value is given, set as zero.
698	if node_value is None or node_value.isspace() \
699	or node_value.lower() == "nan":
700	node_value = "0.0"
701	#Convert the value to the base units
702	node_value, units = self._unit_conversion(node, tagname, node_value)
703
704	# If the value is a timestamp, convert to a datetime object
705	elif self.ns_list.ns_datatype == "timestamp":
706	if node_value is None or node_value.isspace():
707	pass
708	else:
709	try:
710	node_value = \
711	datetime.datetime.fromtimestamp(node_value)
712	except ValueError:
713	node_value = None
714	return node_value, units
715
716	def _unit_conversion(self, node, tagname, node_value):
717	"""
718	A unit converter method used to convert the data included in the file
719	to the default units listed in data_info
720
721	:param node: XML node
722	:param tagname: name of the node
723	:param node_value: The value of the current dom node
724	"""
725	attr = node.attrib
726	value_unit = ''
727	err_msg = None
728	default_unit = None
729	if not isinstance(node_value, float):
730	node_value = float(node_value)
731	if 'unit' in attr and attr.get('unit') is not None:
732	try:
733	local_unit = attr['unit']
734	unitname = self.ns_list.current_level.get("unit", "")
735	if "SASdetector" in self.names:
736	save_in = "detector"
737	elif "aperture" in self.names:
738	save_in = "aperture"
739	elif "SAScollimation" in self.names:
740	save_in = "collimation"
741	elif "SAStransmission_spectrum" in self.names:
742	save_in = "transspectrum"
743	elif "SASdata" in self.names:
744	x = np.zeros(1)
745	y = np.zeros(1)
746	self.current_data1d = Data1D(x, y)
747	save_in = "current_data1d"
748	elif "SASsource" in self.names:
749	save_in = "current_datainfo.source"
750	elif "SASsample" in self.names:
751	save_in = "current_datainfo.sample"
752	elif "SASprocess" in self.names:
753	save_in = "process"
754	else:
755	save_in = "current_datainfo"
756	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
757	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
758	and local_unit.lower() != "none":
759	if HAS_CONVERTER == True:
760	# Check local units - bad units raise KeyError
761	data_conv_q = Converter(local_unit)
762	value_unit = default_unit
763	node_value = data_conv_q(node_value, units=default_unit)
764	else:
765	value_unit = local_unit
766	err_msg = "Unit converter is not available.\n"
767	else:
768	value_unit = local_unit
769	except KeyError:
770	err_msg = "CanSAS reader: unexpected "
771	err_msg += "\"{0}\" unit [{1}]; "
772	err_msg = err_msg.format(tagname, local_unit)
773	err_msg += "expecting [{0}]".format(default_unit)
774	value_unit = local_unit
775	except:
776	err_msg = "CanSAS reader: unknown error converting "
777	err_msg += "\"{0}\" unit [{1}]"
778	err_msg = err_msg.format(tagname, local_unit)
779	value_unit = local_unit
780	elif 'unit' in attr:
781	value_unit = attr['unit']
782	if err_msg:
783	self.errors.add(err_msg)
784	return node_value, value_unit
785
786	def _check_for_empty_data(self):
787	"""
788	Creates an empty data set if no data is passed to the reader
789
790	:param data1d: presumably a Data1D object
791	"""
792	if self.current_dataset == None:
793	x_vals = np.empty(0)
794	y_vals = np.empty(0)
795	dx_vals = np.empty(0)
796	dy_vals = np.empty(0)
797	dxl = np.empty(0)
798	dxw = np.empty(0)
799	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
800	self.current_dataset.dxl = dxl
801	self.current_dataset.dxw = dxw
802
803	def _check_for_empty_resolution(self):
804	"""
805	A method to check all resolution data sets are the same size as I and Q
806	"""
807	if isinstance(self.current_dataset, plottable_1D):
808	dql_exists = False
809	dqw_exists = False
810	dq_exists = False
811	di_exists = False
812	if self.current_dataset.dxl is not None:
813	dql_exists = True
814	if self.current_dataset.dxw is not None:
815	dqw_exists = True
816	if self.current_dataset.dx is not None:
817	dq_exists = True
818	if self.current_dataset.dy is not None:
819	di_exists = True
820	if dqw_exists and not dql_exists:
821	array_size = self.current_dataset.dxw.size - 1
822	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
823	np.zeros([array_size]))
824	elif dql_exists and not dqw_exists:
825	array_size = self.current_dataset.dxl.size - 1
826	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
827	np.zeros([array_size]))
828	elif not dql_exists and not dqw_exists and not dq_exists:
829	array_size = self.current_dataset.x.size - 1
830	self.current_dataset.dx = np.append(self.current_dataset.dx,
831	np.zeros([array_size]))
832	if not di_exists:
833	array_size = self.current_dataset.y.size - 1
834	self.current_dataset.dy = np.append(self.current_dataset.dy,
835	np.zeros([array_size]))
836	elif isinstance(self.current_dataset, plottable_2D):
837	dqx_exists = False
838	dqy_exists = False
839	di_exists = False
840	mask_exists = False
841	if self.current_dataset.dqx_data is not None:
842	dqx_exists = True
843	if self.current_dataset.dqy_data is not None:
844	dqy_exists = True
845	if self.current_dataset.err_data is not None:
846	di_exists = True
847	if self.current_dataset.mask is not None:
848	mask_exists = True
849	if not dqy_exists:
850	array_size = self.current_dataset.qy_data.size - 1
851	self.current_dataset.dqy_data = np.append(
852	self.current_dataset.dqy_data, np.zeros([array_size]))
853	if not dqx_exists:
854	array_size = self.current_dataset.qx_data.size - 1
855	self.current_dataset.dqx_data = np.append(
856	self.current_dataset.dqx_data, np.zeros([array_size]))
857	if not di_exists:
858	array_size = self.current_dataset.data.size - 1
859	self.current_dataset.err_data = np.append(
860	self.current_dataset.err_data, np.zeros([array_size]))
861	if not mask_exists:
862	array_size = self.current_dataset.data.size - 1
863	self.current_dataset.mask = np.append(
864	self.current_dataset.mask,
865	np.ones([array_size] ,dtype=bool))
866
867	####### All methods below are for writing CanSAS XML files #######
868
869	def write(self, filename, datainfo):
870	"""
871	Write the content of a Data1D as a CanSAS XML file
872
873	:param filename: name of the file to write
874	:param datainfo: Data1D object
875	"""
876	# Create XML document
877	doc, _ = self._to_xml_doc(datainfo)
878	# Write the file
879	file_ref = open(filename, 'w')
880	if self.encoding == None:
881	self.encoding = "UTF-8"
882	doc.write(file_ref, encoding=self.encoding,
883	pretty_print=True, xml_declaration=True)
884	file_ref.close()
885
886	def _to_xml_doc(self, datainfo):
887	"""
888	Create an XML document to contain the content of a Data1D
889
890	:param datainfo: Data1D object
891	"""
892	is_2d = False
893	if issubclass(datainfo.__class__, Data2D):
894	is_2d = True
895
896	# Get PIs and create root element
897	pi_string = self._get_pi_string()
898	# Define namespaces and create SASroot object
899	main_node = self._create_main_node()
900	# Create ElementTree, append SASroot and apply processing instructions
901	base_string = pi_string + self.to_string(main_node)
902	base_element = self.create_element_from_string(base_string)
903	doc = self.create_tree(base_element)
904	# Create SASentry Element
905	entry_node = self.create_element("SASentry")
906	root = doc.getroot()
907	root.append(entry_node)
908
909	# Add Title to SASentry
910	self.write_node(entry_node, "Title", datainfo.title)
911	# Add Run to SASentry
912	self._write_run_names(datainfo, entry_node)
913	# Add Data info to SASEntry
914	if is_2d:
915	self._write_data_2d(datainfo, entry_node)
916	else:
917	self._write_data(datainfo, entry_node)
918	# Transmission Spectrum Info
919	self._write_trans_spectrum(datainfo, entry_node)
920	# Sample info
921	self._write_sample_info(datainfo, entry_node)
922	# Instrument info
923	instr = self._write_instrument(datainfo, entry_node)
924	# Source
925	self._write_source(datainfo, instr)
926	# Collimation
927	self._write_collimation(datainfo, instr)
928	# Detectors
929	self._write_detectors(datainfo, instr)
930	# Processes info
931	self._write_process_notes(datainfo, entry_node)
932	# Note info
933	self._write_notes(datainfo, entry_node)
934	# Return the document, and the SASentry node associated with
935	# the data we just wrote
936	# If the calling function was not the cansas reader, return a minidom
937	# object rather than an lxml object.
938	self.frm = inspect.stack()[1]
939	doc, entry_node = self._check_origin(entry_node, doc)
940	return doc, entry_node
941
942	def write_node(self, parent, name, value, attr=None):
943	"""
944	:param doc: document DOM
945	:param parent: parent node
946	:param name: tag of the element
947	:param value: value of the child text node
948	:param attr: attribute dictionary
949
950	:return: True if something was appended, otherwise False
951	"""
952	if value is not None:
953	parent = self.ebuilder(parent, name, value, attr)
954	return True
955	return False
956
957	def _get_pi_string(self):
958	"""
959	Creates the processing instructions header for writing to file
960	"""
961	pis = self.return_processing_instructions()
962	if len(pis) > 0:
963	pi_tree = self.create_tree(pis[0])
964	i = 1
965	for i in range(1, len(pis) - 1):
966	pi_tree = self.append(pis[i], pi_tree)
967	pi_string = self.to_string(pi_tree)
968	else:
969	pi_string = ""
970	return pi_string
971
972	def _create_main_node(self):
973	"""
974	Creates the primary xml header used when writing to file
975	"""
976	xsi = "http://www.w3.org/2001/XMLSchema-instance"
977	version = self.cansas_version
978	n_s = CANSAS_NS.get(version).get("ns")
979	if version == "1.1":
980	url = "http://www.cansas.org/formats/1.1/"
981	else:
982	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
983	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
984	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
985	"version" : version}
986	nsmap = {'xsi' : xsi, None: n_s}
987
988	main_node = self.create_element("{" + n_s + "}SASroot",
989	attrib=attrib, nsmap=nsmap)
990	return main_node
991
992	def _write_run_names(self, datainfo, entry_node):
993	"""
994	Writes the run names to the XML file
995
996	:param datainfo: The Data1D object the information is coming from
997	:param entry_node: lxml node ElementTree object to be appended to
998	"""
999	if datainfo.run == None or datainfo.run == []:
1000	datainfo.run.append(RUN_NAME_DEFAULT)
1001	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1002	for item in datainfo.run:
1003	runname = {}
1004	if item in datainfo.run_name and \
1005	len(str(datainfo.run_name[item])) > 1:
1006	runname = {'name': datainfo.run_name[item]}
1007	self.write_node(entry_node, "Run", item, runname)
1008
1009	def _write_data(self, datainfo, entry_node):
1010	"""
1011	Writes 1D I and Q data to the XML file
1012
1013	:param datainfo: The Data1D object the information is coming from
1014	:param entry_node: lxml node ElementTree object to be appended to
1015	"""
1016	node = self.create_element("SASdata")
1017	self.append(node, entry_node)
1018
1019	for i in range(len(datainfo.x)):
1020	point = self.create_element("Idata")
1021	node.append(point)
1022	self.write_node(point, "Q", datainfo.x[i],
1023	{'unit': datainfo.x_unit})
1024	if len(datainfo.y) >= i:
1025	self.write_node(point, "I", datainfo.y[i],
1026	{'unit': datainfo.y_unit})
1027	if datainfo.dy is not None and len(datainfo.dy) > i:
1028	self.write_node(point, "Idev", datainfo.dy[i],
1029	{'unit': datainfo.y_unit})
1030	if datainfo.dx is not None and len(datainfo.dx) > i:
1031	self.write_node(point, "Qdev", datainfo.dx[i],
1032	{'unit': datainfo.x_unit})
1033	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1034	self.write_node(point, "dQw", datainfo.dxw[i],
1035	{'unit': datainfo.x_unit})
1036	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1037	self.write_node(point, "dQl", datainfo.dxl[i],
1038	{'unit': datainfo.x_unit})
1039
1040	def _write_data_2d(self, datainfo, entry_node):
1041	"""
1042	Writes 2D data to the XML file
1043
1044	:param datainfo: The Data2D object the information is coming from
1045	:param entry_node: lxml node ElementTree object to be appended to
1046	"""
1047	node = self.create_element("SASdata")
1048	attr = {}
1049	if datainfo.data.shape:
1050	attr["x_bins"] = len(datainfo.x_bins)
1051	attr["y_bins"] = len(datainfo.y_bins)
1052	self.append(node, entry_node)
1053
1054	for i in range(len(datainfo.data)):
1055	point = self.create_element("Idata")
1056	node.append(point)
1057	self.write_node(point, "Qx", datainfo.qx_data[i],
1058	{'unit': datainfo._xunit})
1059	self.write_node(point, "Qy", datainfo.qy_data[i],
1060	{'unit': datainfo._yunit})
1061	self.write_node(point, "I", datainfo.data[i],
1062	{'unit': datainfo._zunit})
1063	if datainfo.err_data is not None and len(datainfo.err_data) > i:
1064	self.write_node(point, "Idev", datainfo.err_data[i],
1065	{'unit': datainfo._zunit})
1066	if datainfo.dqy_data is not None and len(datainfo.dqy_data) > i:
1067	self.write_node(point, "Qydev", datainfo.dqy_data[i],
1068	{'unit': datainfo._yunit})
1069	if datainfo.dqx_data is not None and len(datainfo.dqx_data) > i:
1070	self.write_node(point, "Qxdev", datainfo.dqx_data[i],
1071	{'unit': datainfo._xunit})
1072	if datainfo.mask is not None and len(datainfo.mask) > i:
1073	self.write_node(point, "Mask", datainfo.mask[i])
1074
1075	def _write_trans_spectrum(self, datainfo, entry_node):
1076	"""
1077	Writes the transmission spectrum data to the XML file
1078
1079	:param datainfo: The Data1D object the information is coming from
1080	:param entry_node: lxml node ElementTree object to be appended to
1081	"""
1082	for i in range(len(datainfo.trans_spectrum)):
1083	spectrum = datainfo.trans_spectrum[i]
1084	node = self.create_element("SAStransmission_spectrum",
1085	{"name" : spectrum.name})
1086	self.append(node, entry_node)
1087	if isinstance(spectrum.timestamp, datetime.datetime):
1088	node.setAttribute("timestamp", spectrum.timestamp)
1089	for i in range(len(spectrum.wavelength)):
1090	point = self.create_element("Tdata")
1091	node.append(point)
1092	self.write_node(point, "Lambda", spectrum.wavelength[i],
1093	{'unit': spectrum.wavelength_unit})
1094	self.write_node(point, "T", spectrum.transmission[i],
1095	{'unit': spectrum.transmission_unit})
1096	if spectrum.transmission_deviation != None \
1097	and len(spectrum.transmission_deviation) >= i:
1098	self.write_node(point, "Tdev",
1099	spectrum.transmission_deviation[i],
1100	{'unit':
1101	spectrum.transmission_deviation_unit})
1102
1103	def _write_sample_info(self, datainfo, entry_node):
1104	"""
1105	Writes the sample information to the XML file
1106
1107	:param datainfo: The Data1D object the information is coming from
1108	:param entry_node: lxml node ElementTree object to be appended to
1109	"""
1110	sample = self.create_element("SASsample")
1111	if datainfo.sample.name is not None:
1112	self.write_attribute(sample, "name",
1113	str(datainfo.sample.name))
1114	self.append(sample, entry_node)
1115	self.write_node(sample, "ID", str(datainfo.sample.ID))
1116	self.write_node(sample, "thickness", datainfo.sample.thickness,
1117	{"unit": datainfo.sample.thickness_unit})
1118	self.write_node(sample, "transmission", datainfo.sample.transmission)
1119	self.write_node(sample, "temperature", datainfo.sample.temperature,
1120	{"unit": datainfo.sample.temperature_unit})
1121
1122	pos = self.create_element("position")
1123	written = self.write_node(pos,
1124	"x",
1125	datainfo.sample.position.x,
1126	{"unit": datainfo.sample.position_unit})
1127	written = written \| self.write_node( \
1128	pos, "y", datainfo.sample.position.y,
1129	{"unit": datainfo.sample.position_unit})
1130	written = written \| self.write_node( \
1131	pos, "z", datainfo.sample.position.z,
1132	{"unit": datainfo.sample.position_unit})
1133	if written == True:
1134	self.append(pos, sample)
1135
1136	ori = self.create_element("orientation")
1137	written = self.write_node(ori, "roll",
1138	datainfo.sample.orientation.x,
1139	{"unit": datainfo.sample.orientation_unit})
1140	written = written \| self.write_node( \
1141	ori, "pitch", datainfo.sample.orientation.y,
1142	{"unit": datainfo.sample.orientation_unit})
1143	written = written \| self.write_node( \
1144	ori, "yaw", datainfo.sample.orientation.z,
1145	{"unit": datainfo.sample.orientation_unit})
1146	if written == True:
1147	self.append(ori, sample)
1148
1149	for item in datainfo.sample.details:
1150	self.write_node(sample, "details", item)
1151
1152	def _write_instrument(self, datainfo, entry_node):
1153	"""
1154	Writes the instrumental information to the XML file
1155
1156	:param datainfo: The Data1D object the information is coming from
1157	:param entry_node: lxml node ElementTree object to be appended to
1158	"""
1159	instr = self.create_element("SASinstrument")
1160	self.append(instr, entry_node)
1161	self.write_node(instr, "name", datainfo.instrument)
1162	return instr
1163
1164	def _write_source(self, datainfo, instr):
1165	"""
1166	Writes the source information to the XML file
1167
1168	:param datainfo: The Data1D object the information is coming from
1169	:param instr: instrument node to be appended to
1170	"""
1171	source = self.create_element("SASsource")
1172	if datainfo.source.name is not None:
1173	self.write_attribute(source, "name",
1174	str(datainfo.source.name))
1175	self.append(source, instr)
1176	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1177	datainfo.source.radiation = "neutron"
1178	self.write_node(source, "radiation", datainfo.source.radiation)
1179
1180	size = self.create_element("beam_size")
1181	if datainfo.source.beam_size_name is not None:
1182	self.write_attribute(size, "name",
1183	str(datainfo.source.beam_size_name))
1184	written = self.write_node( \
1185	size, "x", datainfo.source.beam_size.x,
1186	{"unit": datainfo.source.beam_size_unit})
1187	written = written \| self.write_node( \
1188	size, "y", datainfo.source.beam_size.y,
1189	{"unit": datainfo.source.beam_size_unit})
1190	written = written \| self.write_node( \
1191	size, "z", datainfo.source.beam_size.z,
1192	{"unit": datainfo.source.beam_size_unit})
1193	if written == True:
1194	self.append(size, source)
1195
1196	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1197	self.write_node(source, "wavelength",
1198	datainfo.source.wavelength,
1199	{"unit": datainfo.source.wavelength_unit})
1200	self.write_node(source, "wavelength_min",
1201	datainfo.source.wavelength_min,
1202	{"unit": datainfo.source.wavelength_min_unit})
1203	self.write_node(source, "wavelength_max",
1204	datainfo.source.wavelength_max,
1205	{"unit": datainfo.source.wavelength_max_unit})
1206	self.write_node(source, "wavelength_spread",
1207	datainfo.source.wavelength_spread,
1208	{"unit": datainfo.source.wavelength_spread_unit})
1209
1210	def _write_collimation(self, datainfo, instr):
1211	"""
1212	Writes the collimation information to the XML file
1213
1214	:param datainfo: The Data1D object the information is coming from
1215	:param instr: lxml node ElementTree object to be appended to
1216	"""
1217	if datainfo.collimation == [] or datainfo.collimation == None:
1218	coll = Collimation()
1219	datainfo.collimation.append(coll)
1220	for item in datainfo.collimation:
1221	coll = self.create_element("SAScollimation")
1222	if item.name is not None:
1223	self.write_attribute(coll, "name", str(item.name))
1224	self.append(coll, instr)
1225
1226	self.write_node(coll, "length", item.length,
1227	{"unit": item.length_unit})
1228
1229	for aperture in item.aperture:
1230	apert = self.create_element("aperture")
1231	if aperture.name is not None:
1232	self.write_attribute(apert, "name", str(aperture.name))
1233	if aperture.type is not None:
1234	self.write_attribute(apert, "type", str(aperture.type))
1235	self.append(apert, coll)
1236
1237	size = self.create_element("size")
1238	if aperture.size_name is not None:
1239	self.write_attribute(size, "name",
1240	str(aperture.size_name))
1241	written = self.write_node(size, "x", aperture.size.x,
1242	{"unit": aperture.size_unit})
1243	written = written \| self.write_node( \
1244	size, "y", aperture.size.y,
1245	{"unit": aperture.size_unit})
1246	written = written \| self.write_node( \
1247	size, "z", aperture.size.z,
1248	{"unit": aperture.size_unit})
1249	if written == True:
1250	self.append(size, apert)
1251
1252	self.write_node(apert, "distance", aperture.distance,
1253	{"unit": aperture.distance_unit})
1254
1255	def _write_detectors(self, datainfo, instr):
1256	"""
1257	Writes the detector information to the XML file
1258
1259	:param datainfo: The Data1D object the information is coming from
1260	:param inst: lxml instrument node to be appended to
1261	"""
1262	if datainfo.detector == None or datainfo.detector == []:
1263	det = Detector()
1264	det.name = ""
1265	datainfo.detector.append(det)
1266
1267	for item in datainfo.detector:
1268	det = self.create_element("SASdetector")
1269	written = self.write_node(det, "name", item.name)
1270	written = written \| self.write_node(det, "SDD", item.distance,
1271	{"unit": item.distance_unit})
1272	if written == True:
1273	self.append(det, instr)
1274
1275	off = self.create_element("offset")
1276	written = self.write_node(off, "x", item.offset.x,
1277	{"unit": item.offset_unit})
1278	written = written \| self.write_node(off, "y", item.offset.y,
1279	{"unit": item.offset_unit})
1280	written = written \| self.write_node(off, "z", item.offset.z,
1281	{"unit": item.offset_unit})
1282	if written == True:
1283	self.append(off, det)
1284
1285	ori = self.create_element("orientation")
1286	written = self.write_node(ori, "roll", item.orientation.x,
1287	{"unit": item.orientation_unit})
1288	written = written \| self.write_node(ori, "pitch",
1289	item.orientation.y,
1290	{"unit": item.orientation_unit})
1291	written = written \| self.write_node(ori, "yaw",
1292	item.orientation.z,
1293	{"unit": item.orientation_unit})
1294	if written == True:
1295	self.append(ori, det)
1296
1297	center = self.create_element("beam_center")
1298	written = self.write_node(center, "x", item.beam_center.x,
1299	{"unit": item.beam_center_unit})
1300	written = written \| self.write_node(center, "y",
1301	item.beam_center.y,
1302	{"unit": item.beam_center_unit})
1303	written = written \| self.write_node(center, "z",
1304	item.beam_center.z,
1305	{"unit": item.beam_center_unit})
1306	if written == True:
1307	self.append(center, det)
1308
1309	pix = self.create_element("pixel_size")
1310	written = self.write_node(pix, "x", item.pixel_size.x,
1311	{"unit": item.pixel_size_unit})
1312	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1313	{"unit": item.pixel_size_unit})
1314	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1315	{"unit": item.pixel_size_unit})
1316	if written == True:
1317	self.append(pix, det)
1318	self.write_node(det, "slit_length", item.slit_length,
1319	{"unit": item.slit_length_unit})
1320
1321
1322	def _write_process_notes(self, datainfo, entry_node):
1323	"""
1324	Writes the process notes to the XML file
1325
1326	:param datainfo: The Data1D object the information is coming from
1327	:param entry_node: lxml node ElementTree object to be appended to
1328
1329	"""
1330	for item in datainfo.process:
1331	node = self.create_element("SASprocess")
1332	self.append(node, entry_node)
1333	self.write_node(node, "name", item.name)
1334	self.write_node(node, "date", item.date)
1335	self.write_node(node, "description", item.description)
1336	for term in item.term:
1337	if isinstance(term, list):
1338	value = term['value']
1339	del term['value']
1340	elif isinstance(term, dict):
1341	value = term.get("value")
1342	del term['value']
1343	else:
1344	value = term
1345	self.write_node(node, "term", value, term)
1346	for note in item.notes:
1347	self.write_node(node, "SASprocessnote", note)
1348	if len(item.notes) == 0:
1349	self.write_node(node, "SASprocessnote", "")
1350
1351	def _write_notes(self, datainfo, entry_node):
1352	"""
1353	Writes the notes to the XML file and creates an empty note if none
1354	exist
1355
1356	:param datainfo: The Data1D object the information is coming from
1357	:param entry_node: lxml node ElementTree object to be appended to
1358
1359	"""
1360	if len(datainfo.notes) == 0:
1361	node = self.create_element("SASnote")
1362	self.append(node, entry_node)
1363	else:
1364	for item in datainfo.notes:
1365	node = self.create_element("SASnote")
1366	self.write_text(node, item)
1367	self.append(node, entry_node)
1368
1369	def _check_origin(self, entry_node, doc):
1370	"""
1371	Return the document, and the SASentry node associated with
1372	the data we just wrote.
1373	If the calling function was not the cansas reader, return a minidom
1374	object rather than an lxml object.
1375
1376	:param entry_node: lxml node ElementTree object to be appended to
1377	:param doc: entire xml tree
1378	"""
1379	if not self.frm:
1380	self.frm = inspect.stack()[1]
1381	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1382	mod_name = mod_name.replace(".py", "")
1383	mod = mod_name.split("sas/")
1384	mod_name = mod[1]
1385	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1386	string = self.to_string(doc, pretty_print=False)
1387	doc = parseString(string)
1388	node_name = entry_node.tag
1389	node_list = doc.getElementsByTagName(node_name)
1390	entry_node = node_list.item(0)
1391	return doc, entry_node
1392
1393	# DO NOT REMOVE - used in saving and loading panel states.
1394	def _store_float(self, location, node, variable, storage, optional=True):
1395	"""
1396	Get the content of a xpath location and store
1397	the result. Check that the units are compatible
1398	with the destination. The value is expected to
1399	be a float.
1400
1401	The xpath location might or might not exist.
1402	If it does not exist, nothing is done
1403
1404	:param location: xpath location to fetch
1405	:param node: node to read the data from
1406	:param variable: name of the data member to store it in [string]
1407	:param storage: data object that has the 'variable' data member
1408	:param optional: if True, no exception will be raised
1409	if unit conversion can't be done
1410
1411	:raise ValueError: raised when the units are not recognized
1412	"""
1413	entry = get_content(location, node)
1414	try:
1415	value = float(entry.text)
1416	except:
1417	value = None
1418
1419	if value is not None:
1420	# If the entry has units, check to see that they are
1421	# compatible with what we currently have in the data object
1422	units = entry.get('unit')
1423	if units is not None:
1424	toks = variable.split('.')
1425	local_unit = None
1426	exec "local_unit = storage.%s_unit" % toks[0]
1427	if local_unit != None and units.lower() != local_unit.lower():
1428	if HAS_CONVERTER == True:
1429	try:
1430	conv = Converter(units)
1431	exec "storage.%s = %g" % \
1432	(variable, conv(value, units=local_unit))
1433	except:
1434	_, exc_value, _ = sys.exc_info()
1435	err_mess = "CanSAS reader: could not convert"
1436	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1437	% (variable, units, local_unit, exc_value)
1438	self.errors.add(err_mess)
1439	if optional:
1440	logging.info(err_mess)
1441	else:
1442	raise ValueError, err_mess
1443	else:
1444	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1445	% (variable, units)
1446	err_mess += " expecting [%s]" % local_unit
1447	self.errors.add(err_mess)
1448	if optional:
1449	logging.info(err_mess)
1450	else:
1451	raise ValueError, err_mess
1452	else:
1453	exec "storage.%s = value" % variable
1454	else:
1455	exec "storage.%s = value" % variable
1456
1457	# DO NOT REMOVE - used in saving and loading panel states.
1458	def _store_content(self, location, node, variable, storage):
1459	"""
1460	Get the content of a xpath location and store
1461	the result. The value is treated as a string.
1462
1463	The xpath location might or might not exist.
1464	If it does not exist, nothing is done
1465
1466	:param location: xpath location to fetch
1467	:param node: node to read the data from
1468	:param variable: name of the data member to store it in [string]
1469	:param storage: data object that has the 'variable' data member
1470
1471	:return: return a list of errors
1472	"""
1473	entry = get_content(location, node)
1474	if entry is not None and entry.text is not None:
1475	exec "storage.%s = entry.text.strip()" % variable
1476
1477
1478	# DO NOT REMOVE Called by outside packages:
1479	# sas.sasgui.perspectives.invariant.invariant_state
1480	# sas.sasgui.perspectives.fitting.pagestate
1481	def get_content(location, node):
1482	"""
1483	Get the first instance of the content of a xpath location.
1484
1485	:param location: xpath location
1486	:param node: node to start at
1487
1488	:return: Element, or None
1489	"""
1490	nodes = node.xpath(location,
1491	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1492	if len(nodes) > 0:
1493	return nodes[0]
1494	else:
1495	return None
1496
1497	# DO NOT REMOVE Called by outside packages:
1498	# sas.sasgui.perspectives.fitting.pagestate
1499	def write_node(doc, parent, name, value, attr=None):
1500	"""
1501	:param doc: document DOM
1502	:param parent: parent node
1503	:param name: tag of the element
1504	:param value: value of the child text node
1505	:param attr: attribute dictionary
1506
1507	:return: True if something was appended, otherwise False
1508	"""
1509	if attr is None:
1510	attr = {}
1511	if value is not None:
1512	node = doc.createElement(name)
1513	node.appendChild(doc.createTextNode(str(value)))
1514	for item in attr:
1515	node.setAttribute(item, attr[item])
1516	parent.appendChild(node)
1517	return True
1518	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ af08e55

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