cansas_reader.py @ c155a16

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

Last change on this file since c155a16 was c155a16, checked in by Ricardo Ferraz Leal <ricleal@…>, 7 years ago
Logging is now logger
Property mode set to `100644`
File size: 70.5 KB

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1	"""
2	CanSAS data reader - new recursive cansas_version.
3	"""
4	############################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#If you use DANSE applications to do scientific research that leads to
9	#publication, we ask that you acknowledge the use of the software with the
10	#following sentence:
11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
12	#copyright 2008,2009 University of Tennessee
13	#############################################################################
14
15	import logging
16	import numpy as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
23	plottable_1D, plottable_2D
24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
25	Detector, Process, Aperture
26	from sas.sascalc.dataloader.data_info import \
27	combine_data_info_with_plottable as combine_data
28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
31
32	# The following 2 imports ARE used. Do not remove either.
33	import xml.dom.minidom
34	from xml.dom.minidom import parseString
35
36	logger = logging.getLogger()
37
38	PREPROCESS = "xmlpreprocess"
39	ENCODING = "encoding"
40	RUN_NAME_DEFAULT = "None"
41	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
42	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
43	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
44	"as much of the data as possible.\n\n"
45	HAS_CONVERTER = True
46	try:
47	from sas.sascalc.data_util.nxsunit import Converter
48	except ImportError:
49	HAS_CONVERTER = False
50
51	CONSTANTS = CansasConstants()
52	CANSAS_FORMAT = CONSTANTS.format
53	CANSAS_NS = CONSTANTS.names
54	ALLOW_ALL = True
55
56	class Reader(XMLreader):
57	"""
58	Class to load cansas 1D XML files
59
60	:Dependencies:
61	The CanSAS reader requires PyXML 0.8.4 or later.
62	"""
63	# CanSAS version - defaults to version 1.0
64	cansas_version = "1.0"
65	base_ns = "{cansas1d/1.0}"
66	cansas_defaults = None
67	type_name = "canSAS"
68	invalid = True
69	frm = ""
70	# Log messages and errors
71	logging = None
72	errors = set()
73	# Namespace hierarchy for current xml_file object
74	names = None
75	ns_list = None
76	# Temporary storage location for loading multiple data sets in a single file
77	current_datainfo = None
78	current_dataset = None
79	current_data1d = None
80	data = None
81	# List of data1D objects to be sent back to SasView
82	output = None
83	# Wildcards
84	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
85	# List of allowed extensions
86	ext = ['.xml', '.XML', '.svs', '.SVS']
87	# Flag to bypass extension check
88	allow_all = True
89
90	def reset_state(self):
91	"""
92	Resets the class state to a base case when loading a new data file so previous
93	data files do not appear a second time
94	"""
95	self.current_datainfo = None
96	self.current_dataset = None
97	self.current_data1d = None
98	self.data = []
99	self.process = Process()
100	self.transspectrum = TransmissionSpectrum()
101	self.aperture = Aperture()
102	self.collimation = Collimation()
103	self.detector = Detector()
104	self.names = []
105	self.cansas_defaults = {}
106	self.output = []
107	self.ns_list = None
108	self.logging = []
109	self.encoding = None
110
111	def read(self, xml_file, schema_path="", invalid=True):
112	"""
113	Validate and read in an xml_file file in the canSAS format.
114
115	:param xml_file: A canSAS file path in proper XML format
116	:param schema_path: A file path to an XML schema to validate the xml_file against
117	"""
118	# For every file loaded, reset everything to a base state
119	self.reset_state()
120	self.invalid = invalid
121	# Check that the file exists
122	if os.path.isfile(xml_file):
123	basename, extension = os.path.splitext(os.path.basename(xml_file))
124	# If the file type is not allowed, return nothing
125	if extension in self.ext or self.allow_all:
126	# Get the file location of
127	self.load_file_and_schema(xml_file, schema_path)
128	self.add_data_set()
129	# Try to load the file, but raise an error if unable to.
130	# Check the file matches the XML schema
131	try:
132	self.is_cansas(extension)
133	self.invalid = False
134	# Get each SASentry from XML file and add it to a list.
135	entry_list = self.xmlroot.xpath(
136	'/ns:SASroot/ns:SASentry',
137	namespaces={'ns': self.cansas_defaults.get("ns")})
138	self.names.append("SASentry")
139
140	# Get all preprocessing events and encoding
141	self.set_processing_instructions()
142
143	# Parse each <SASentry> item
144	for entry in entry_list:
145	# Create a new DataInfo object for every <SASentry>
146
147	# Set the file name and then parse the entry.
148	self.current_datainfo.filename = basename + extension
149	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
150	self.current_datainfo.meta_data[PREPROCESS] = \
151	self.processing_instructions
152
153	# Parse the XML SASentry
154	self._parse_entry(entry)
155	# Combine datasets with datainfo
156	self.add_data_set()
157	except RuntimeError:
158	# If the file does not match the schema, raise this error
159	invalid_xml = self.find_invalid_xml()
160	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
161	self.errors.add(invalid_xml)
162	# Try again with an invalid CanSAS schema, that requires only a data set in each
163	base_name = xml_reader.__file__
164	base_name = base_name.replace("\\", "/")
165	base = base_name.split("/sas/")[0]
166	if self.cansas_version == "1.1":
167	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
168	else:
169	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
170	self.set_schema(invalid_schema)
171	try:
172	if self.invalid:
173	if self.is_cansas():
174	self.output = self.read(xml_file, invalid_schema, False)
175	else:
176	raise RuntimeError
177	else:
178	raise RuntimeError
179	except RuntimeError:
180	x = np.zeros(1)
181	y = np.zeros(1)
182	self.current_data1d = Data1D(x,y)
183	self.current_data1d.errors = self.errors
184	return [self.current_data1d]
185	else:
186	self.output.append("Not a valid file path.")
187	# Return a list of parsed entries that dataloader can manage
188	return self.output
189
190	def _parse_entry(self, dom, recurse=False):
191	"""
192	Parse a SASEntry - new recursive method for parsing the dom of
193	the CanSAS data format. This will allow multiple data files
194	and extra nodes to be read in simultaneously.
195
196	:param dom: dom object with a namespace base of names
197	"""
198
199	if not self._is_call_local() and not recurse:
200	self.reset_state()
201	self.add_data_set()
202	self.names.append("SASentry")
203	self.parent_class = "SASentry"
204	self._check_for_empty_data()
205	self.base_ns = "{0}{1}{2}".format("{", \
206	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
207
208	# Go through each child in the parent element
209	for node in dom:
210	attr = node.attrib
211	name = attr.get("name", "")
212	type = attr.get("type", "")
213	# Get the element name and set the current names level
214	tagname = node.tag.replace(self.base_ns, "")
215	tagname_original = tagname
216	# Skip this iteration when loading in save state information
217	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
218	continue
219
220	# Get where to store content
221	self.names.append(tagname_original)
222	self.ns_list = CONSTANTS.iterate_namespace(self.names)
223	# If the element is a child element, recurse
224	if len(node.getchildren()) > 0:
225	self.parent_class = tagname_original
226	if tagname == 'SASdata':
227	self._initialize_new_data_set(node)
228	if isinstance(self.current_dataset, plottable_2D):
229	x_bins = attr.get("x_bins", "")
230	y_bins = attr.get("y_bins", "")
231	if x_bins is not "" and y_bins is not "":
232	self.current_dataset.shape = (x_bins, y_bins)
233	else:
234	self.current_dataset.shape = ()
235	# Recursion step to access data within the group
236	self._parse_entry(node, True)
237	if tagname == "SASsample":
238	self.current_datainfo.sample.name = name
239	elif tagname == "beam_size":
240	self.current_datainfo.source.beam_size_name = name
241	elif tagname == "SAScollimation":
242	self.collimation.name = name
243	elif tagname == "aperture":
244	self.aperture.name = name
245	self.aperture.type = type
246	self.add_intermediate()
247	else:
248	if isinstance(self.current_dataset, plottable_2D):
249	data_point = node.text
250	unit = attr.get('unit', '')
251	else:
252	data_point, unit = self._get_node_value(node, tagname)
253
254	# If this is a dataset, store the data appropriately
255	if tagname == 'Run':
256	self.current_datainfo.run_name[data_point] = name
257	self.current_datainfo.run.append(data_point)
258	elif tagname == 'Title':
259	self.current_datainfo.title = data_point
260	elif tagname == 'SASnote':
261	self.current_datainfo.notes.append(data_point)
262
263	# I and Q - 1D data
264	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
265	unit_list = unit.split("\|")
266	if len(unit_list) > 1:
267	self.current_dataset.yaxis(unit_list[0].strip(),
268	unit_list[1].strip())
269	else:
270	self.current_dataset.yaxis("Intensity", unit)
271	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
272	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
273	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
274	elif tagname == 'Q':
275	unit_list = unit.split("\|")
276	if len(unit_list) > 1:
277	self.current_dataset.xaxis(unit_list[0].strip(),
278	unit_list[1].strip())
279	else:
280	self.current_dataset.xaxis("Q", unit)
281	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
282	elif tagname == 'Qdev':
283	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
284	elif tagname == 'dQw':
285	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
286	elif tagname == 'dQl':
287	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
288	elif tagname == 'Qmean':
289	pass
290	elif tagname == 'Shadowfactor':
291	pass
292	elif tagname == 'Sesans':
293	self.current_datainfo.isSesans = bool(data_point)
294	elif tagname == 'zacceptance':
295	self.current_datainfo.sample.zacceptance = (data_point, unit)
296
297	# I and Qx, Qy - 2D data
298	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
299	self.current_dataset.yaxis("Intensity", unit)
300	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
301	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
302	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
303	elif tagname == 'Qx':
304	self.current_dataset.xaxis("Qx", unit)
305	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
306	elif tagname == 'Qy':
307	self.current_dataset.yaxis("Qy", unit)
308	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
309	elif tagname == 'Qxdev':
310	self.current_dataset.xaxis("Qxdev", unit)
311	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
312	elif tagname == 'Qydev':
313	self.current_dataset.yaxis("Qydev", unit)
314	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
315	elif tagname == 'Mask':
316	inter = [item == "1" for item in data_point.split(",")]
317	self.current_dataset.mask = np.asarray(inter, dtype=bool)
318
319	# Sample Information
320	elif tagname == 'ID' and self.parent_class == 'SASsample':
321	self.current_datainfo.sample.ID = data_point
322	elif tagname == 'Title' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.name = data_point
324	elif tagname == 'thickness' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.thickness = data_point
326	self.current_datainfo.sample.thickness_unit = unit
327	elif tagname == 'transmission' and self.parent_class == 'SASsample':
328	self.current_datainfo.sample.transmission = data_point
329	elif tagname == 'temperature' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.temperature = data_point
331	self.current_datainfo.sample.temperature_unit = unit
332	elif tagname == 'details' and self.parent_class == 'SASsample':
333	self.current_datainfo.sample.details.append(data_point)
334	elif tagname == 'x' and self.parent_class == 'position':
335	self.current_datainfo.sample.position.x = data_point
336	self.current_datainfo.sample.position_unit = unit
337	elif tagname == 'y' and self.parent_class == 'position':
338	self.current_datainfo.sample.position.y = data_point
339	self.current_datainfo.sample.position_unit = unit
340	elif tagname == 'z' and self.parent_class == 'position':
341	self.current_datainfo.sample.position.z = data_point
342	self.current_datainfo.sample.position_unit = unit
343	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
344	self.current_datainfo.sample.orientation.x = data_point
345	self.current_datainfo.sample.orientation_unit = unit
346	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
347	self.current_datainfo.sample.orientation.y = data_point
348	self.current_datainfo.sample.orientation_unit = unit
349	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
350	self.current_datainfo.sample.orientation.z = data_point
351	self.current_datainfo.sample.orientation_unit = unit
352
353	# Instrumental Information
354	elif tagname == 'name' and self.parent_class == 'SASinstrument':
355	self.current_datainfo.instrument = data_point
356	# Detector Information
357	elif tagname == 'name' and self.parent_class == 'SASdetector':
358	self.detector.name = data_point
359	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
360	self.detector.distance = data_point
361	self.detector.distance_unit = unit
362	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
363	self.detector.slit_length = data_point
364	self.detector.slit_length_unit = unit
365	elif tagname == 'x' and self.parent_class == 'offset':
366	self.detector.offset.x = data_point
367	self.detector.offset_unit = unit
368	elif tagname == 'y' and self.parent_class == 'offset':
369	self.detector.offset.y = data_point
370	self.detector.offset_unit = unit
371	elif tagname == 'z' and self.parent_class == 'offset':
372	self.detector.offset.z = data_point
373	self.detector.offset_unit = unit
374	elif tagname == 'x' and self.parent_class == 'beam_center':
375	self.detector.beam_center.x = data_point
376	self.detector.beam_center_unit = unit
377	elif tagname == 'y' and self.parent_class == 'beam_center':
378	self.detector.beam_center.y = data_point
379	self.detector.beam_center_unit = unit
380	elif tagname == 'z' and self.parent_class == 'beam_center':
381	self.detector.beam_center.z = data_point
382	self.detector.beam_center_unit = unit
383	elif tagname == 'x' and self.parent_class == 'pixel_size':
384	self.detector.pixel_size.x = data_point
385	self.detector.pixel_size_unit = unit
386	elif tagname == 'y' and self.parent_class == 'pixel_size':
387	self.detector.pixel_size.y = data_point
388	self.detector.pixel_size_unit = unit
389	elif tagname == 'z' and self.parent_class == 'pixel_size':
390	self.detector.pixel_size.z = data_point
391	self.detector.pixel_size_unit = unit
392	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
393	self.detector.orientation.x = data_point
394	self.detector.orientation_unit = unit
395	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
396	self.detector.orientation.y = data_point
397	self.detector.orientation_unit = unit
398	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
399	self.detector.orientation.z = data_point
400	self.detector.orientation_unit = unit
401	# Collimation and Aperture
402	elif tagname == 'length' and self.parent_class == 'SAScollimation':
403	self.collimation.length = data_point
404	self.collimation.length_unit = unit
405	elif tagname == 'name' and self.parent_class == 'SAScollimation':
406	self.collimation.name = data_point
407	elif tagname == 'distance' and self.parent_class == 'aperture':
408	self.aperture.distance = data_point
409	self.aperture.distance_unit = unit
410	elif tagname == 'x' and self.parent_class == 'size':
411	self.aperture.size.x = data_point
412	self.collimation.size_unit = unit
413	elif tagname == 'y' and self.parent_class == 'size':
414	self.aperture.size.y = data_point
415	self.collimation.size_unit = unit
416	elif tagname == 'z' and self.parent_class == 'size':
417	self.aperture.size.z = data_point
418	self.collimation.size_unit = unit
419
420	# Process Information
421	elif tagname == 'name' and self.parent_class == 'SASprocess':
422	self.process.name = data_point
423	elif tagname == 'description' and self.parent_class == 'SASprocess':
424	self.process.description = data_point
425	elif tagname == 'date' and self.parent_class == 'SASprocess':
426	try:
427	self.process.date = datetime.datetime.fromtimestamp(data_point)
428	except:
429	self.process.date = data_point
430	elif tagname == 'SASprocessnote':
431	self.process.notes.append(data_point)
432	elif tagname == 'term' and self.parent_class == 'SASprocess':
433	unit = attr.get("unit", "")
434	dic = {}
435	dic["name"] = name
436	dic["value"] = data_point
437	dic["unit"] = unit
438	self.process.term.append(dic)
439
440	# Transmission Spectrum
441	elif tagname == 'T' and self.parent_class == 'Tdata':
442	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
443	self.transspectrum.transmission_unit = unit
444	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
445	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
446	self.transspectrum.transmission_deviation_unit = unit
447	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
448	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
449	self.transspectrum.wavelength_unit = unit
450
451	# Source Information
452	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
453	self.current_datainfo.source.wavelength = data_point
454	self.current_datainfo.source.wavelength_unit = unit
455	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
456	self.current_datainfo.source.wavelength_min = data_point
457	self.current_datainfo.source.wavelength_min_unit = unit
458	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
459	self.current_datainfo.source.wavelength_max = data_point
460	self.current_datainfo.source.wavelength_max_unit = unit
461	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
462	self.current_datainfo.source.wavelength_spread = data_point
463	self.current_datainfo.source.wavelength_spread_unit = unit
464	elif tagname == 'x' and self.parent_class == 'beam_size':
465	self.current_datainfo.source.beam_size.x = data_point
466	self.current_datainfo.source.beam_size_unit = unit
467	elif tagname == 'y' and self.parent_class == 'beam_size':
468	self.current_datainfo.source.beam_size.y = data_point
469	self.current_datainfo.source.beam_size_unit = unit
470	elif tagname == 'z' and self.parent_class == 'pixel_size':
471	self.current_datainfo.source.data_point.z = data_point
472	self.current_datainfo.source.beam_size_unit = unit
473	elif tagname == 'radiation' and self.parent_class == 'SASsource':
474	self.current_datainfo.source.radiation = data_point
475	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
476	self.current_datainfo.source.beam_shape = data_point
477
478	# Everything else goes in meta_data
479	else:
480	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
481	self.current_datainfo.meta_data[new_key] = data_point
482
483	self.names.remove(tagname_original)
484	length = 0
485	if len(self.names) > 1:
486	length = len(self.names) - 1
487	self.parent_class = self.names[length]
488	if not self._is_call_local() and not recurse:
489	self.frm = ""
490	self.add_data_set()
491	empty = None
492	return self.output[0], empty
493
494
495	def _is_call_local(self):
496	"""
497
498	"""
499	if self.frm == "":
500	inter = inspect.stack()
501	self.frm = inter[2]
502	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
503	mod_name = mod_name.replace(".py", "")
504	mod = mod_name.split("sas/")
505	mod_name = mod[1]
506	if mod_name != "sascalc/dataloader/readers/cansas_reader":
507	return False
508	return True
509
510	def is_cansas(self, ext="xml"):
511	"""
512	Checks to see if the xml file is a CanSAS file
513
514	:param ext: The file extension of the data file
515	"""
516	if self.validate_xml():
517	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
518	value = self.xmlroot.get(name)
519	if CANSAS_NS.get(self.cansas_version).get("ns") == \
520	value.rsplit(" ")[0]:
521	return True
522	if ext == "svs":
523	return True
524	raise RuntimeError
525
526	def load_file_and_schema(self, xml_file, schema_path=""):
527	"""
528	Loads the file and associates a schema, if a schema is passed in or if one already exists
529
530	:param xml_file: The xml file path sent to Reader.read
531	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
532	"""
533	base_name = xml_reader.__file__
534	base_name = base_name.replace("\\", "/")
535	base = base_name.split("/sas/")[0]
536
537	# Load in xml file and get the cansas version from the header
538	self.set_xml_file(xml_file)
539	self.cansas_version = self.xmlroot.get("version", "1.0")
540
541	# Generic values for the cansas file based on the version
542	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
543	if schema_path == "":
544	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
545	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
546
547	# Link a schema to the XML file.
548	self.set_schema(schema_path)
549
550	def add_data_set(self):
551	"""
552	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
553	private method to generate a new data set.
554
555	:param key: NeXus group name for current tree level
556	"""
557
558	if self.current_datainfo and self.current_dataset:
559	self._final_cleanup()
560	self.data = []
561	self.current_datainfo = DataInfo()
562
563	def _initialize_new_data_set(self, node=None):
564	"""
565	A private class method to generate a new 1D data object.
566	Outside methods should call add_data_set() to be sure any existing data is stored properly.
567
568	:param node: XML node to determine if 1D or 2D data
569	"""
570	x = np.array(0)
571	y = np.array(0)
572	for child in node:
573	if child.tag.replace(self.base_ns, "") == "Idata":
574	for i_child in child:
575	if i_child.tag.replace(self.base_ns, "") == "Qx":
576	self.current_dataset = plottable_2D()
577	return
578	self.current_dataset = plottable_1D(x, y)
579
580	def add_intermediate(self):
581	"""
582	This method stores any intermediate objects within the final data set after fully reading the set.
583
584	:param parent: The NXclass name for the h5py Group object that just finished being processed
585	"""
586
587	if self.parent_class == 'SASprocess':
588	self.current_datainfo.process.append(self.process)
589	self.process = Process()
590	elif self.parent_class == 'SASdetector':
591	self.current_datainfo.detector.append(self.detector)
592	self.detector = Detector()
593	elif self.parent_class == 'SAStransmission_spectrum':
594	self.current_datainfo.trans_spectrum.append(self.transspectrum)
595	self.transspectrum = TransmissionSpectrum()
596	elif self.parent_class == 'SAScollimation':
597	self.current_datainfo.collimation.append(self.collimation)
598	self.collimation = Collimation()
599	elif self.parent_class == 'aperture':
600	self.collimation.aperture.append(self.aperture)
601	self.aperture = Aperture()
602	elif self.parent_class == 'SASdata':
603	self._check_for_empty_resolution()
604	self.data.append(self.current_dataset)
605
606	def _final_cleanup(self):
607	"""
608	Final cleanup of the Data1D object to be sure it has all the
609	appropriate information needed for perspectives
610	"""
611
612	# Append errors to dataset and reset class errors
613	self.current_datainfo.errors = set()
614	for error in self.errors:
615	self.current_datainfo.errors.add(error)
616	self.errors.clear()
617
618	# Combine all plottables with datainfo and append each to output
619	# Type cast data arrays to float64 and find min/max as appropriate
620	for dataset in self.data:
621	if isinstance(dataset, plottable_1D):
622	if dataset.x is not None:
623	dataset.x = np.delete(dataset.x, [0])
624	dataset.x = dataset.x.astype(np.float64)
625	dataset.xmin = np.min(dataset.x)
626	dataset.xmax = np.max(dataset.x)
627	if dataset.y is not None:
628	dataset.y = np.delete(dataset.y, [0])
629	dataset.y = dataset.y.astype(np.float64)
630	dataset.ymin = np.min(dataset.y)
631	dataset.ymax = np.max(dataset.y)
632	if dataset.dx is not None:
633	dataset.dx = np.delete(dataset.dx, [0])
634	dataset.dx = dataset.dx.astype(np.float64)
635	if dataset.dxl is not None:
636	dataset.dxl = np.delete(dataset.dxl, [0])
637	dataset.dxl = dataset.dxl.astype(np.float64)
638	if dataset.dxw is not None:
639	dataset.dxw = np.delete(dataset.dxw, [0])
640	dataset.dxw = dataset.dxw.astype(np.float64)
641	if dataset.dy is not None:
642	dataset.dy = np.delete(dataset.dy, [0])
643	dataset.dy = dataset.dy.astype(np.float64)
644	np.trim_zeros(dataset.x)
645	np.trim_zeros(dataset.y)
646	np.trim_zeros(dataset.dy)
647	elif isinstance(dataset, plottable_2D):
648	dataset.data = dataset.data.astype(np.float64)
649	dataset.qx_data = dataset.qx_data.astype(np.float64)
650	dataset.xmin = np.min(dataset.qx_data)
651	dataset.xmax = np.max(dataset.qx_data)
652	dataset.qy_data = dataset.qy_data.astype(np.float64)
653	dataset.ymin = np.min(dataset.qy_data)
654	dataset.ymax = np.max(dataset.qy_data)
655	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
656	+ dataset.qy_data * dataset.qy_data)
657	if dataset.err_data is not None:
658	dataset.err_data = dataset.err_data.astype(np.float64)
659	if dataset.dqx_data is not None:
660	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
661	if dataset.dqy_data is not None:
662	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
663	if dataset.mask is not None:
664	dataset.mask = dataset.mask.astype(dtype=bool)
665
666	if len(dataset.shape) == 2:
667	n_rows, n_cols = dataset.shape
668	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
669	dataset.x_bins = dataset.qx_data[:int(n_cols)]
670	dataset.data = dataset.data.flatten()
671	else:
672	dataset.y_bins = []
673	dataset.x_bins = []
674	dataset.data = dataset.data.flatten()
675
676	final_dataset = combine_data(dataset, self.current_datainfo)
677	self.output.append(final_dataset)
678
679	def _create_unique_key(self, dictionary, name, numb=0):
680	"""
681	Create a unique key value for any dictionary to prevent overwriting
682	Recurse until a unique key value is found.
683
684	:param dictionary: A dictionary with any number of entries
685	:param name: The index of the item to be added to dictionary
686	:param numb: The number to be appended to the name, starts at 0
687	"""
688	if dictionary.get(name) is not None:
689	numb += 1
690	name = name.split("_")[0]
691	name += "_{0}".format(numb)
692	name = self._create_unique_key(dictionary, name, numb)
693	return name
694
695	def _get_node_value(self, node, tagname):
696	"""
697	Get the value of a node and any applicable units
698
699	:param node: The XML node to get the value of
700	:param tagname: The tagname of the node
701	"""
702	#Get the text from the node and convert all whitespace to spaces
703	units = ''
704	node_value = node.text
705	if node_value is not None:
706	node_value = ' '.join(node_value.split())
707	else:
708	node_value = ""
709
710	# If the value is a float, compile with units.
711	if self.ns_list.ns_datatype == "float":
712	# If an empty value is given, set as zero.
713	if node_value is None or node_value.isspace() \
714	or node_value.lower() == "nan":
715	node_value = "0.0"
716	#Convert the value to the base units
717	node_value, units = self._unit_conversion(node, tagname, node_value)
718
719	# If the value is a timestamp, convert to a datetime object
720	elif self.ns_list.ns_datatype == "timestamp":
721	if node_value is None or node_value.isspace():
722	pass
723	else:
724	try:
725	node_value = \
726	datetime.datetime.fromtimestamp(node_value)
727	except ValueError:
728	node_value = None
729	return node_value, units
730
731	def _unit_conversion(self, node, tagname, node_value):
732	"""
733	A unit converter method used to convert the data included in the file
734	to the default units listed in data_info
735
736	:param node: XML node
737	:param tagname: name of the node
738	:param node_value: The value of the current dom node
739	"""
740	attr = node.attrib
741	value_unit = ''
742	err_msg = None
743	default_unit = None
744	if not isinstance(node_value, float):
745	node_value = float(node_value)
746	if 'unit' in attr and attr.get('unit') is not None:
747	try:
748	local_unit = attr['unit']
749	unitname = self.ns_list.current_level.get("unit", "")
750	if "SASdetector" in self.names:
751	save_in = "detector"
752	elif "aperture" in self.names:
753	save_in = "aperture"
754	elif "SAScollimation" in self.names:
755	save_in = "collimation"
756	elif "SAStransmission_spectrum" in self.names:
757	save_in = "transspectrum"
758	elif "SASdata" in self.names:
759	x = np.zeros(1)
760	y = np.zeros(1)
761	self.current_data1d = Data1D(x, y)
762	save_in = "current_data1d"
763	elif "SASsource" in self.names:
764	save_in = "current_datainfo.source"
765	elif "SASsample" in self.names:
766	save_in = "current_datainfo.sample"
767	elif "SASprocess" in self.names:
768	save_in = "process"
769	else:
770	save_in = "current_datainfo"
771	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
772	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
773	and local_unit.lower() != "none":
774	if HAS_CONVERTER == True:
775	# Check local units - bad units raise KeyError
776	data_conv_q = Converter(local_unit)
777	value_unit = default_unit
778	node_value = data_conv_q(node_value, units=default_unit)
779	else:
780	value_unit = local_unit
781	err_msg = "Unit converter is not available.\n"
782	else:
783	value_unit = local_unit
784	except KeyError:
785	err_msg = "CanSAS reader: unexpected "
786	err_msg += "\"{0}\" unit [{1}]; "
787	err_msg = err_msg.format(tagname, local_unit)
788	err_msg += "expecting [{0}]".format(default_unit)
789	value_unit = local_unit
790	except:
791	err_msg = "CanSAS reader: unknown error converting "
792	err_msg += "\"{0}\" unit [{1}]"
793	err_msg = err_msg.format(tagname, local_unit)
794	value_unit = local_unit
795	elif 'unit' in attr:
796	value_unit = attr['unit']
797	if err_msg:
798	self.errors.add(err_msg)
799	return node_value, value_unit
800
801	def _check_for_empty_data(self):
802	"""
803	Creates an empty data set if no data is passed to the reader
804
805	:param data1d: presumably a Data1D object
806	"""
807	if self.current_dataset == None:
808	x_vals = np.empty(0)
809	y_vals = np.empty(0)
810	dx_vals = np.empty(0)
811	dy_vals = np.empty(0)
812	dxl = np.empty(0)
813	dxw = np.empty(0)
814	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
815	self.current_dataset.dxl = dxl
816	self.current_dataset.dxw = dxw
817
818	def _check_for_empty_resolution(self):
819	"""
820	A method to check all resolution data sets are the same size as I and Q
821	"""
822	if isinstance(self.current_dataset, plottable_1D):
823	dql_exists = False
824	dqw_exists = False
825	dq_exists = False
826	di_exists = False
827	if self.current_dataset.dxl is not None:
828	dql_exists = True
829	if self.current_dataset.dxw is not None:
830	dqw_exists = True
831	if self.current_dataset.dx is not None:
832	dq_exists = True
833	if self.current_dataset.dy is not None:
834	di_exists = True
835	if dqw_exists and not dql_exists:
836	array_size = self.current_dataset.dxw.size - 1
837	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
838	np.zeros([array_size]))
839	elif dql_exists and not dqw_exists:
840	array_size = self.current_dataset.dxl.size - 1
841	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
842	np.zeros([array_size]))
843	elif not dql_exists and not dqw_exists and not dq_exists:
844	array_size = self.current_dataset.x.size - 1
845	self.current_dataset.dx = np.append(self.current_dataset.dx,
846	np.zeros([array_size]))
847	if not di_exists:
848	array_size = self.current_dataset.y.size - 1
849	self.current_dataset.dy = np.append(self.current_dataset.dy,
850	np.zeros([array_size]))
851	elif isinstance(self.current_dataset, plottable_2D):
852	dqx_exists = False
853	dqy_exists = False
854	di_exists = False
855	mask_exists = False
856	if self.current_dataset.dqx_data is not None:
857	dqx_exists = True
858	if self.current_dataset.dqy_data is not None:
859	dqy_exists = True
860	if self.current_dataset.err_data is not None:
861	di_exists = True
862	if self.current_dataset.mask is not None:
863	mask_exists = True
864	if not dqy_exists:
865	array_size = self.current_dataset.qy_data.size - 1
866	self.current_dataset.dqy_data = np.append(
867	self.current_dataset.dqy_data, np.zeros([array_size]))
868	if not dqx_exists:
869	array_size = self.current_dataset.qx_data.size - 1
870	self.current_dataset.dqx_data = np.append(
871	self.current_dataset.dqx_data, np.zeros([array_size]))
872	if not di_exists:
873	array_size = self.current_dataset.data.size - 1
874	self.current_dataset.err_data = np.append(
875	self.current_dataset.err_data, np.zeros([array_size]))
876	if not mask_exists:
877	array_size = self.current_dataset.data.size - 1
878	self.current_dataset.mask = np.append(
879	self.current_dataset.mask,
880	np.ones([array_size] ,dtype=bool))
881
882	####### All methods below are for writing CanSAS XML files #######
883
884	def write(self, filename, datainfo):
885	"""
886	Write the content of a Data1D as a CanSAS XML file
887
888	:param filename: name of the file to write
889	:param datainfo: Data1D object
890	"""
891	# Create XML document
892	doc, _ = self._to_xml_doc(datainfo)
893	# Write the file
894	file_ref = open(filename, 'w')
895	if self.encoding == None:
896	self.encoding = "UTF-8"
897	doc.write(file_ref, encoding=self.encoding,
898	pretty_print=True, xml_declaration=True)
899	file_ref.close()
900
901	def _to_xml_doc(self, datainfo):
902	"""
903	Create an XML document to contain the content of a Data1D
904
905	:param datainfo: Data1D object
906	"""
907	is_2d = False
908	if issubclass(datainfo.__class__, Data2D):
909	is_2d = True
910
911	# Get PIs and create root element
912	pi_string = self._get_pi_string()
913	# Define namespaces and create SASroot object
914	main_node = self._create_main_node()
915	# Create ElementTree, append SASroot and apply processing instructions
916	base_string = pi_string + self.to_string(main_node)
917	base_element = self.create_element_from_string(base_string)
918	doc = self.create_tree(base_element)
919	# Create SASentry Element
920	entry_node = self.create_element("SASentry")
921	root = doc.getroot()
922	root.append(entry_node)
923
924	# Add Title to SASentry
925	self.write_node(entry_node, "Title", datainfo.title)
926	# Add Run to SASentry
927	self._write_run_names(datainfo, entry_node)
928	# Add Data info to SASEntry
929	if is_2d:
930	self._write_data_2d(datainfo, entry_node)
931	else:
932	self._write_data(datainfo, entry_node)
933	# Transmission Spectrum Info
934	# TODO: fix the writer to linearize all data, including T_spectrum
935	# self._write_trans_spectrum(datainfo, entry_node)
936	# Sample info
937	self._write_sample_info(datainfo, entry_node)
938	# Instrument info
939	instr = self._write_instrument(datainfo, entry_node)
940	# Source
941	self._write_source(datainfo, instr)
942	# Collimation
943	self._write_collimation(datainfo, instr)
944	# Detectors
945	self._write_detectors(datainfo, instr)
946	# Processes info
947	self._write_process_notes(datainfo, entry_node)
948	# Note info
949	self._write_notes(datainfo, entry_node)
950	# Return the document, and the SASentry node associated with
951	# the data we just wrote
952	# If the calling function was not the cansas reader, return a minidom
953	# object rather than an lxml object.
954	self.frm = inspect.stack()[1]
955	doc, entry_node = self._check_origin(entry_node, doc)
956	return doc, entry_node
957
958	def write_node(self, parent, name, value, attr=None):
959	"""
960	:param doc: document DOM
961	:param parent: parent node
962	:param name: tag of the element
963	:param value: value of the child text node
964	:param attr: attribute dictionary
965
966	:return: True if something was appended, otherwise False
967	"""
968	if value is not None:
969	parent = self.ebuilder(parent, name, value, attr)
970	return True
971	return False
972
973	def _get_pi_string(self):
974	"""
975	Creates the processing instructions header for writing to file
976	"""
977	pis = self.return_processing_instructions()
978	if len(pis) > 0:
979	pi_tree = self.create_tree(pis[0])
980	i = 1
981	for i in range(1, len(pis) - 1):
982	pi_tree = self.append(pis[i], pi_tree)
983	pi_string = self.to_string(pi_tree)
984	else:
985	pi_string = ""
986	return pi_string
987
988	def _create_main_node(self):
989	"""
990	Creates the primary xml header used when writing to file
991	"""
992	xsi = "http://www.w3.org/2001/XMLSchema-instance"
993	version = self.cansas_version
994	n_s = CANSAS_NS.get(version).get("ns")
995	if version == "1.1":
996	url = "http://www.cansas.org/formats/1.1/"
997	else:
998	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
999	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1000	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1001	"version" : version}
1002	nsmap = {'xsi' : xsi, None: n_s}
1003
1004	main_node = self.create_element("{" + n_s + "}SASroot",
1005	attrib=attrib, nsmap=nsmap)
1006	return main_node
1007
1008	def _write_run_names(self, datainfo, entry_node):
1009	"""
1010	Writes the run names to the XML file
1011
1012	:param datainfo: The Data1D object the information is coming from
1013	:param entry_node: lxml node ElementTree object to be appended to
1014	"""
1015	if datainfo.run == None or datainfo.run == []:
1016	datainfo.run.append(RUN_NAME_DEFAULT)
1017	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1018	for item in datainfo.run:
1019	runname = {}
1020	if item in datainfo.run_name and \
1021	len(str(datainfo.run_name[item])) > 1:
1022	runname = {'name': datainfo.run_name[item]}
1023	self.write_node(entry_node, "Run", item, runname)
1024
1025	def _write_data(self, datainfo, entry_node):
1026	"""
1027	Writes 1D I and Q data to the XML file
1028
1029	:param datainfo: The Data1D object the information is coming from
1030	:param entry_node: lxml node ElementTree object to be appended to
1031	"""
1032	node = self.create_element("SASdata")
1033	self.append(node, entry_node)
1034
1035	for i in range(len(datainfo.x)):
1036	point = self.create_element("Idata")
1037	node.append(point)
1038	self.write_node(point, "Q", datainfo.x[i],
1039	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1040	if len(datainfo.y) >= i:
1041	self.write_node(point, "I", datainfo.y[i],
1042	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1043	if datainfo.dy is not None and len(datainfo.dy) > i:
1044	self.write_node(point, "Idev", datainfo.dy[i],
1045	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1046	if datainfo.dx is not None and len(datainfo.dx) > i:
1047	self.write_node(point, "Qdev", datainfo.dx[i],
1048	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1049	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1050	self.write_node(point, "dQw", datainfo.dxw[i],
1051	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1052	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1053	self.write_node(point, "dQl", datainfo.dxl[i],
1054	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1055	if datainfo.isSesans:
1056	sesans = self.create_element("Sesans")
1057	sesans.text = str(datainfo.isSesans)
1058	node.append(sesans)
1059	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1060	{'unit': datainfo.sample.zacceptance[1]})
1061
1062
1063	def _write_data_2d(self, datainfo, entry_node):
1064	"""
1065	Writes 2D data to the XML file
1066
1067	:param datainfo: The Data2D object the information is coming from
1068	:param entry_node: lxml node ElementTree object to be appended to
1069	"""
1070	attr = {}
1071	if datainfo.data.shape:
1072	attr["x_bins"] = str(len(datainfo.x_bins))
1073	attr["y_bins"] = str(len(datainfo.y_bins))
1074	node = self.create_element("SASdata", attr)
1075	self.append(node, entry_node)
1076
1077	point = self.create_element("Idata")
1078	node.append(point)
1079	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1080	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1081	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1082
1083	self.write_node(point, "Qx", qx,
1084	{'unit': datainfo._xunit})
1085	self.write_node(point, "Qy", qy,
1086	{'unit': datainfo._yunit})
1087	self.write_node(point, "I", intensity,
1088	{'unit': datainfo._zunit})
1089	if datainfo.err_data is not None:
1090	err = ','.join([str(datainfo.err_data[i]) for i in
1091	xrange(len(datainfo.err_data))])
1092	self.write_node(point, "Idev", err,
1093	{'unit': datainfo._zunit})
1094	if datainfo.dqy_data is not None:
1095	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1096	xrange(len(datainfo.dqy_data))])
1097	self.write_node(point, "Qydev", dqy,
1098	{'unit': datainfo._yunit})
1099	if datainfo.dqx_data is not None:
1100	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1101	xrange(len(datainfo.dqx_data))])
1102	self.write_node(point, "Qxdev", dqx,
1103	{'unit': datainfo._xunit})
1104	if datainfo.mask is not None:
1105	mask = ','.join(
1106	["1" if datainfo.mask[i] else "0"
1107	for i in xrange(len(datainfo.mask))])
1108	self.write_node(point, "Mask", mask)
1109
1110	def _write_trans_spectrum(self, datainfo, entry_node):
1111	"""
1112	Writes the transmission spectrum data to the XML file
1113
1114	:param datainfo: The Data1D object the information is coming from
1115	:param entry_node: lxml node ElementTree object to be appended to
1116	"""
1117	for i in range(len(datainfo.trans_spectrum)):
1118	spectrum = datainfo.trans_spectrum[i]
1119	node = self.create_element("SAStransmission_spectrum",
1120	{"name" : spectrum.name})
1121	self.append(node, entry_node)
1122	if isinstance(spectrum.timestamp, datetime.datetime):
1123	node.setAttribute("timestamp", spectrum.timestamp)
1124	for i in range(len(spectrum.wavelength)):
1125	point = self.create_element("Tdata")
1126	node.append(point)
1127	self.write_node(point, "Lambda", spectrum.wavelength[i],
1128	{'unit': spectrum.wavelength_unit})
1129	self.write_node(point, "T", spectrum.transmission[i],
1130	{'unit': spectrum.transmission_unit})
1131	if spectrum.transmission_deviation != None \
1132	and len(spectrum.transmission_deviation) >= i:
1133	self.write_node(point, "Tdev",
1134	spectrum.transmission_deviation[i],
1135	{'unit':
1136	spectrum.transmission_deviation_unit})
1137
1138	def _write_sample_info(self, datainfo, entry_node):
1139	"""
1140	Writes the sample information to the XML file
1141
1142	:param datainfo: The Data1D object the information is coming from
1143	:param entry_node: lxml node ElementTree object to be appended to
1144	"""
1145	sample = self.create_element("SASsample")
1146	if datainfo.sample.name is not None:
1147	self.write_attribute(sample, "name",
1148	str(datainfo.sample.name))
1149	self.append(sample, entry_node)
1150	self.write_node(sample, "ID", str(datainfo.sample.ID))
1151	self.write_node(sample, "thickness", datainfo.sample.thickness,
1152	{"unit": datainfo.sample.thickness_unit})
1153	self.write_node(sample, "transmission", datainfo.sample.transmission)
1154	self.write_node(sample, "temperature", datainfo.sample.temperature,
1155	{"unit": datainfo.sample.temperature_unit})
1156
1157	pos = self.create_element("position")
1158	written = self.write_node(pos,
1159	"x",
1160	datainfo.sample.position.x,
1161	{"unit": datainfo.sample.position_unit})
1162	written = written \| self.write_node( \
1163	pos, "y", datainfo.sample.position.y,
1164	{"unit": datainfo.sample.position_unit})
1165	written = written \| self.write_node( \
1166	pos, "z", datainfo.sample.position.z,
1167	{"unit": datainfo.sample.position_unit})
1168	if written == True:
1169	self.append(pos, sample)
1170
1171	ori = self.create_element("orientation")
1172	written = self.write_node(ori, "roll",
1173	datainfo.sample.orientation.x,
1174	{"unit": datainfo.sample.orientation_unit})
1175	written = written \| self.write_node( \
1176	ori, "pitch", datainfo.sample.orientation.y,
1177	{"unit": datainfo.sample.orientation_unit})
1178	written = written \| self.write_node( \
1179	ori, "yaw", datainfo.sample.orientation.z,
1180	{"unit": datainfo.sample.orientation_unit})
1181	if written == True:
1182	self.append(ori, sample)
1183
1184	for item in datainfo.sample.details:
1185	self.write_node(sample, "details", item)
1186
1187	def _write_instrument(self, datainfo, entry_node):
1188	"""
1189	Writes the instrumental information to the XML file
1190
1191	:param datainfo: The Data1D object the information is coming from
1192	:param entry_node: lxml node ElementTree object to be appended to
1193	"""
1194	instr = self.create_element("SASinstrument")
1195	self.append(instr, entry_node)
1196	self.write_node(instr, "name", datainfo.instrument)
1197	return instr
1198
1199	def _write_source(self, datainfo, instr):
1200	"""
1201	Writes the source information to the XML file
1202
1203	:param datainfo: The Data1D object the information is coming from
1204	:param instr: instrument node to be appended to
1205	"""
1206	source = self.create_element("SASsource")
1207	if datainfo.source.name is not None:
1208	self.write_attribute(source, "name",
1209	str(datainfo.source.name))
1210	self.append(source, instr)
1211	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1212	datainfo.source.radiation = "neutron"
1213	self.write_node(source, "radiation", datainfo.source.radiation)
1214
1215	size = self.create_element("beam_size")
1216	if datainfo.source.beam_size_name is not None:
1217	self.write_attribute(size, "name",
1218	str(datainfo.source.beam_size_name))
1219	written = self.write_node( \
1220	size, "x", datainfo.source.beam_size.x,
1221	{"unit": datainfo.source.beam_size_unit})
1222	written = written \| self.write_node( \
1223	size, "y", datainfo.source.beam_size.y,
1224	{"unit": datainfo.source.beam_size_unit})
1225	written = written \| self.write_node( \
1226	size, "z", datainfo.source.beam_size.z,
1227	{"unit": datainfo.source.beam_size_unit})
1228	if written == True:
1229	self.append(size, source)
1230
1231	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1232	self.write_node(source, "wavelength",
1233	datainfo.source.wavelength,
1234	{"unit": datainfo.source.wavelength_unit})
1235	self.write_node(source, "wavelength_min",
1236	datainfo.source.wavelength_min,
1237	{"unit": datainfo.source.wavelength_min_unit})
1238	self.write_node(source, "wavelength_max",
1239	datainfo.source.wavelength_max,
1240	{"unit": datainfo.source.wavelength_max_unit})
1241	self.write_node(source, "wavelength_spread",
1242	datainfo.source.wavelength_spread,
1243	{"unit": datainfo.source.wavelength_spread_unit})
1244
1245	def _write_collimation(self, datainfo, instr):
1246	"""
1247	Writes the collimation information to the XML file
1248
1249	:param datainfo: The Data1D object the information is coming from
1250	:param instr: lxml node ElementTree object to be appended to
1251	"""
1252	if datainfo.collimation == [] or datainfo.collimation == None:
1253	coll = Collimation()
1254	datainfo.collimation.append(coll)
1255	for item in datainfo.collimation:
1256	coll = self.create_element("SAScollimation")
1257	if item.name is not None:
1258	self.write_attribute(coll, "name", str(item.name))
1259	self.append(coll, instr)
1260
1261	self.write_node(coll, "length", item.length,
1262	{"unit": item.length_unit})
1263
1264	for aperture in item.aperture:
1265	apert = self.create_element("aperture")
1266	if aperture.name is not None:
1267	self.write_attribute(apert, "name", str(aperture.name))
1268	if aperture.type is not None:
1269	self.write_attribute(apert, "type", str(aperture.type))
1270	self.append(apert, coll)
1271
1272	size = self.create_element("size")
1273	if aperture.size_name is not None:
1274	self.write_attribute(size, "name",
1275	str(aperture.size_name))
1276	written = self.write_node(size, "x", aperture.size.x,
1277	{"unit": aperture.size_unit})
1278	written = written \| self.write_node( \
1279	size, "y", aperture.size.y,
1280	{"unit": aperture.size_unit})
1281	written = written \| self.write_node( \
1282	size, "z", aperture.size.z,
1283	{"unit": aperture.size_unit})
1284	if written == True:
1285	self.append(size, apert)
1286
1287	self.write_node(apert, "distance", aperture.distance,
1288	{"unit": aperture.distance_unit})
1289
1290	def _write_detectors(self, datainfo, instr):
1291	"""
1292	Writes the detector information to the XML file
1293
1294	:param datainfo: The Data1D object the information is coming from
1295	:param inst: lxml instrument node to be appended to
1296	"""
1297	if datainfo.detector == None or datainfo.detector == []:
1298	det = Detector()
1299	det.name = ""
1300	datainfo.detector.append(det)
1301
1302	for item in datainfo.detector:
1303	det = self.create_element("SASdetector")
1304	written = self.write_node(det, "name", item.name)
1305	written = written \| self.write_node(det, "SDD", item.distance,
1306	{"unit": item.distance_unit})
1307	if written == True:
1308	self.append(det, instr)
1309
1310	off = self.create_element("offset")
1311	written = self.write_node(off, "x", item.offset.x,
1312	{"unit": item.offset_unit})
1313	written = written \| self.write_node(off, "y", item.offset.y,
1314	{"unit": item.offset_unit})
1315	written = written \| self.write_node(off, "z", item.offset.z,
1316	{"unit": item.offset_unit})
1317	if written == True:
1318	self.append(off, det)
1319
1320	ori = self.create_element("orientation")
1321	written = self.write_node(ori, "roll", item.orientation.x,
1322	{"unit": item.orientation_unit})
1323	written = written \| self.write_node(ori, "pitch",
1324	item.orientation.y,
1325	{"unit": item.orientation_unit})
1326	written = written \| self.write_node(ori, "yaw",
1327	item.orientation.z,
1328	{"unit": item.orientation_unit})
1329	if written == True:
1330	self.append(ori, det)
1331
1332	center = self.create_element("beam_center")
1333	written = self.write_node(center, "x", item.beam_center.x,
1334	{"unit": item.beam_center_unit})
1335	written = written \| self.write_node(center, "y",
1336	item.beam_center.y,
1337	{"unit": item.beam_center_unit})
1338	written = written \| self.write_node(center, "z",
1339	item.beam_center.z,
1340	{"unit": item.beam_center_unit})
1341	if written == True:
1342	self.append(center, det)
1343
1344	pix = self.create_element("pixel_size")
1345	written = self.write_node(pix, "x", item.pixel_size.x,
1346	{"unit": item.pixel_size_unit})
1347	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1348	{"unit": item.pixel_size_unit})
1349	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1350	{"unit": item.pixel_size_unit})
1351	if written == True:
1352	self.append(pix, det)
1353	self.write_node(det, "slit_length", item.slit_length,
1354	{"unit": item.slit_length_unit})
1355
1356
1357	def _write_process_notes(self, datainfo, entry_node):
1358	"""
1359	Writes the process notes to the XML file
1360
1361	:param datainfo: The Data1D object the information is coming from
1362	:param entry_node: lxml node ElementTree object to be appended to
1363
1364	"""
1365	for item in datainfo.process:
1366	node = self.create_element("SASprocess")
1367	self.append(node, entry_node)
1368	self.write_node(node, "name", item.name)
1369	self.write_node(node, "date", item.date)
1370	self.write_node(node, "description", item.description)
1371	for term in item.term:
1372	if isinstance(term, list):
1373	value = term['value']
1374	del term['value']
1375	elif isinstance(term, dict):
1376	value = term.get("value")
1377	del term['value']
1378	else:
1379	value = term
1380	self.write_node(node, "term", value, term)
1381	for note in item.notes:
1382	self.write_node(node, "SASprocessnote", note)
1383	if len(item.notes) == 0:
1384	self.write_node(node, "SASprocessnote", "")
1385
1386	def _write_notes(self, datainfo, entry_node):
1387	"""
1388	Writes the notes to the XML file and creates an empty note if none
1389	exist
1390
1391	:param datainfo: The Data1D object the information is coming from
1392	:param entry_node: lxml node ElementTree object to be appended to
1393
1394	"""
1395	if len(datainfo.notes) == 0:
1396	node = self.create_element("SASnote")
1397	self.append(node, entry_node)
1398	else:
1399	for item in datainfo.notes:
1400	node = self.create_element("SASnote")
1401	self.write_text(node, item)
1402	self.append(node, entry_node)
1403
1404	def _check_origin(self, entry_node, doc):
1405	"""
1406	Return the document, and the SASentry node associated with
1407	the data we just wrote.
1408	If the calling function was not the cansas reader, return a minidom
1409	object rather than an lxml object.
1410
1411	:param entry_node: lxml node ElementTree object to be appended to
1412	:param doc: entire xml tree
1413	"""
1414	if not self.frm:
1415	self.frm = inspect.stack()[1]
1416	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1417	mod_name = mod_name.replace(".py", "")
1418	mod = mod_name.split("sas/")
1419	mod_name = mod[1]
1420	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1421	string = self.to_string(doc, pretty_print=False)
1422	doc = parseString(string)
1423	node_name = entry_node.tag
1424	node_list = doc.getElementsByTagName(node_name)
1425	entry_node = node_list.item(0)
1426	return doc, entry_node
1427
1428	# DO NOT REMOVE - used in saving and loading panel states.
1429	def _store_float(self, location, node, variable, storage, optional=True):
1430	"""
1431	Get the content of a xpath location and store
1432	the result. Check that the units are compatible
1433	with the destination. The value is expected to
1434	be a float.
1435
1436	The xpath location might or might not exist.
1437	If it does not exist, nothing is done
1438
1439	:param location: xpath location to fetch
1440	:param node: node to read the data from
1441	:param variable: name of the data member to store it in [string]
1442	:param storage: data object that has the 'variable' data member
1443	:param optional: if True, no exception will be raised
1444	if unit conversion can't be done
1445
1446	:raise ValueError: raised when the units are not recognized
1447	"""
1448	entry = get_content(location, node)
1449	try:
1450	value = float(entry.text)
1451	except:
1452	value = None
1453
1454	if value is not None:
1455	# If the entry has units, check to see that they are
1456	# compatible with what we currently have in the data object
1457	units = entry.get('unit')
1458	if units is not None:
1459	toks = variable.split('.')
1460	local_unit = None
1461	exec "local_unit = storage.%s_unit" % toks[0]
1462	if local_unit != None and units.lower() != local_unit.lower():
1463	if HAS_CONVERTER == True:
1464	try:
1465	conv = Converter(units)
1466	exec "storage.%s = %g" % \
1467	(variable, conv(value, units=local_unit))
1468	except:
1469	_, exc_value, _ = sys.exc_info()
1470	err_mess = "CanSAS reader: could not convert"
1471	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1472	% (variable, units, local_unit, exc_value)
1473	self.errors.add(err_mess)
1474	if optional:
1475	logger.info(err_mess)
1476	else:
1477	raise ValueError, err_mess
1478	else:
1479	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1480	% (variable, units)
1481	err_mess += " expecting [%s]" % local_unit
1482	self.errors.add(err_mess)
1483	if optional:
1484	logger.info(err_mess)
1485	else:
1486	raise ValueError, err_mess
1487	else:
1488	exec "storage.%s = value" % variable
1489	else:
1490	exec "storage.%s = value" % variable
1491
1492	# DO NOT REMOVE - used in saving and loading panel states.
1493	def _store_content(self, location, node, variable, storage):
1494	"""
1495	Get the content of a xpath location and store
1496	the result. The value is treated as a string.
1497
1498	The xpath location might or might not exist.
1499	If it does not exist, nothing is done
1500
1501	:param location: xpath location to fetch
1502	:param node: node to read the data from
1503	:param variable: name of the data member to store it in [string]
1504	:param storage: data object that has the 'variable' data member
1505
1506	:return: return a list of errors
1507	"""
1508	entry = get_content(location, node)
1509	if entry is not None and entry.text is not None:
1510	exec "storage.%s = entry.text.strip()" % variable
1511
1512
1513	# DO NOT REMOVE Called by outside packages:
1514	# sas.sasgui.perspectives.invariant.invariant_state
1515	# sas.sasgui.perspectives.fitting.pagestate
1516	def get_content(location, node):
1517	"""
1518	Get the first instance of the content of a xpath location.
1519
1520	:param location: xpath location
1521	:param node: node to start at
1522
1523	:return: Element, or None
1524	"""
1525	nodes = node.xpath(location,
1526	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1527	if len(nodes) > 0:
1528	return nodes[0]
1529	else:
1530	return None
1531
1532	# DO NOT REMOVE Called by outside packages:
1533	# sas.sasgui.perspectives.fitting.pagestate
1534	def write_node(doc, parent, name, value, attr=None):
1535	"""
1536	:param doc: document DOM
1537	:param parent: parent node
1538	:param name: tag of the element
1539	:param value: value of the child text node
1540	:param attr: attribute dictionary
1541
1542	:return: True if something was appended, otherwise False
1543	"""
1544	if attr is None:
1545	attr = {}
1546	if value is not None:
1547	node = doc.createElement(name)
1548	node.appendChild(doc.createTextNode(str(value)))
1549	for item in attr:
1550	node.setAttribute(item, attr[item])
1551	parent.appendChild(node)
1552	return True
1553	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ c155a16

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