cansas_reader.py @ 63d773c

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 63d773c was 63d773c, checked in by Adam Washington <adam.washington@…>, 7 years ago

Add yacceptance

Needed to correspond to zacceptance for 2D sesans

Property mode set to 100644

File size: 70.8 KB

Line
1	"""
2	CanSAS data reader - new recursive cansas_version.
3	"""
4	############################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#If you use DANSE applications to do scientific research that leads to
9	#publication, we ask that you acknowledge the use of the software with the
10	#following sentence:
11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
12	#copyright 2008,2009 University of Tennessee
13	#############################################################################
14
15	import logging
16	import numpy as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
23	plottable_1D, plottable_2D
24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
25	Detector, Process, Aperture
26	from sas.sascalc.dataloader.data_info import \
27	combine_data_info_with_plottable as combine_data
28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
31
32	# The following 2 imports ARE used. Do not remove either.
33	import xml.dom.minidom
34	from xml.dom.minidom import parseString
35
36	logger = logging.getLogger(__name__)
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 == 'yacceptance':
295	self.current_datainfo.sample.yacceptance = (data_point, unit)
296	elif tagname == 'zacceptance':
297	self.current_datainfo.sample.zacceptance = (data_point, unit)
298
299	# I and Qx, Qy - 2D data
300	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
301	self.current_dataset.yaxis("Intensity", unit)
302	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
303	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
304	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
305	elif tagname == 'Qx':
306	self.current_dataset.xaxis("Qx", unit)
307	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qy':
309	self.current_dataset.yaxis("Qy", unit)
310	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qxdev':
312	self.current_dataset.xaxis("Qxdev", unit)
313	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qydev':
315	self.current_dataset.yaxis("Qydev", unit)
316	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Mask':
318	inter = [item == "1" for item in data_point.split(",")]
319	self.current_dataset.mask = np.asarray(inter, dtype=bool)
320
321	# Sample Information
322	elif tagname == 'ID' and self.parent_class == 'SASsample':
323	self.current_datainfo.sample.ID = data_point
324	elif tagname == 'Title' and self.parent_class == 'SASsample':
325	self.current_datainfo.sample.name = data_point
326	elif tagname == 'thickness' and self.parent_class == 'SASsample':
327	self.current_datainfo.sample.thickness = data_point
328	self.current_datainfo.sample.thickness_unit = unit
329	elif tagname == 'transmission' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.transmission = data_point
331	elif tagname == 'temperature' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.temperature = data_point
333	self.current_datainfo.sample.temperature_unit = unit
334	elif tagname == 'details' and self.parent_class == 'SASsample':
335	self.current_datainfo.sample.details.append(data_point)
336	elif tagname == 'x' and self.parent_class == 'position':
337	self.current_datainfo.sample.position.x = data_point
338	self.current_datainfo.sample.position_unit = unit
339	elif tagname == 'y' and self.parent_class == 'position':
340	self.current_datainfo.sample.position.y = data_point
341	self.current_datainfo.sample.position_unit = unit
342	elif tagname == 'z' and self.parent_class == 'position':
343	self.current_datainfo.sample.position.z = data_point
344	self.current_datainfo.sample.position_unit = unit
345	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
346	self.current_datainfo.sample.orientation.x = data_point
347	self.current_datainfo.sample.orientation_unit = unit
348	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
349	self.current_datainfo.sample.orientation.y = data_point
350	self.current_datainfo.sample.orientation_unit = unit
351	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
352	self.current_datainfo.sample.orientation.z = data_point
353	self.current_datainfo.sample.orientation_unit = unit
354
355	# Instrumental Information
356	elif tagname == 'name' and self.parent_class == 'SASinstrument':
357	self.current_datainfo.instrument = data_point
358	# Detector Information
359	elif tagname == 'name' and self.parent_class == 'SASdetector':
360	self.detector.name = data_point
361	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
362	self.detector.distance = data_point
363	self.detector.distance_unit = unit
364	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
365	self.detector.slit_length = data_point
366	self.detector.slit_length_unit = unit
367	elif tagname == 'x' and self.parent_class == 'offset':
368	self.detector.offset.x = data_point
369	self.detector.offset_unit = unit
370	elif tagname == 'y' and self.parent_class == 'offset':
371	self.detector.offset.y = data_point
372	self.detector.offset_unit = unit
373	elif tagname == 'z' and self.parent_class == 'offset':
374	self.detector.offset.z = data_point
375	self.detector.offset_unit = unit
376	elif tagname == 'x' and self.parent_class == 'beam_center':
377	self.detector.beam_center.x = data_point
378	self.detector.beam_center_unit = unit
379	elif tagname == 'y' and self.parent_class == 'beam_center':
380	self.detector.beam_center.y = data_point
381	self.detector.beam_center_unit = unit
382	elif tagname == 'z' and self.parent_class == 'beam_center':
383	self.detector.beam_center.z = data_point
384	self.detector.beam_center_unit = unit
385	elif tagname == 'x' and self.parent_class == 'pixel_size':
386	self.detector.pixel_size.x = data_point
387	self.detector.pixel_size_unit = unit
388	elif tagname == 'y' and self.parent_class == 'pixel_size':
389	self.detector.pixel_size.y = data_point
390	self.detector.pixel_size_unit = unit
391	elif tagname == 'z' and self.parent_class == 'pixel_size':
392	self.detector.pixel_size.z = data_point
393	self.detector.pixel_size_unit = unit
394	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
395	self.detector.orientation.x = data_point
396	self.detector.orientation_unit = unit
397	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
398	self.detector.orientation.y = data_point
399	self.detector.orientation_unit = unit
400	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
401	self.detector.orientation.z = data_point
402	self.detector.orientation_unit = unit
403	# Collimation and Aperture
404	elif tagname == 'length' and self.parent_class == 'SAScollimation':
405	self.collimation.length = data_point
406	self.collimation.length_unit = unit
407	elif tagname == 'name' and self.parent_class == 'SAScollimation':
408	self.collimation.name = data_point
409	elif tagname == 'distance' and self.parent_class == 'aperture':
410	self.aperture.distance = data_point
411	self.aperture.distance_unit = unit
412	elif tagname == 'x' and self.parent_class == 'size':
413	self.aperture.size.x = data_point
414	self.collimation.size_unit = unit
415	elif tagname == 'y' and self.parent_class == 'size':
416	self.aperture.size.y = data_point
417	self.collimation.size_unit = unit
418	elif tagname == 'z' and self.parent_class == 'size':
419	self.aperture.size.z = data_point
420	self.collimation.size_unit = unit
421
422	# Process Information
423	elif tagname == 'name' and self.parent_class == 'SASprocess':
424	self.process.name = data_point
425	elif tagname == 'description' and self.parent_class == 'SASprocess':
426	self.process.description = data_point
427	elif tagname == 'date' and self.parent_class == 'SASprocess':
428	try:
429	self.process.date = datetime.datetime.fromtimestamp(data_point)
430	except:
431	self.process.date = data_point
432	elif tagname == 'SASprocessnote':
433	self.process.notes.append(data_point)
434	elif tagname == 'term' and self.parent_class == 'SASprocess':
435	unit = attr.get("unit", "")
436	dic = {}
437	dic["name"] = name
438	dic["value"] = data_point
439	dic["unit"] = unit
440	self.process.term.append(dic)
441
442	# Transmission Spectrum
443	elif tagname == 'T' and self.parent_class == 'Tdata':
444	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
445	self.transspectrum.transmission_unit = unit
446	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
447	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
448	self.transspectrum.transmission_deviation_unit = unit
449	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
450	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
451	self.transspectrum.wavelength_unit = unit
452
453	# Source Information
454	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
455	self.current_datainfo.source.wavelength = data_point
456	self.current_datainfo.source.wavelength_unit = unit
457	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
458	self.current_datainfo.source.wavelength_min = data_point
459	self.current_datainfo.source.wavelength_min_unit = unit
460	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
461	self.current_datainfo.source.wavelength_max = data_point
462	self.current_datainfo.source.wavelength_max_unit = unit
463	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
464	self.current_datainfo.source.wavelength_spread = data_point
465	self.current_datainfo.source.wavelength_spread_unit = unit
466	elif tagname == 'x' and self.parent_class == 'beam_size':
467	self.current_datainfo.source.beam_size.x = data_point
468	self.current_datainfo.source.beam_size_unit = unit
469	elif tagname == 'y' and self.parent_class == 'beam_size':
470	self.current_datainfo.source.beam_size.y = data_point
471	self.current_datainfo.source.beam_size_unit = unit
472	elif tagname == 'z' and self.parent_class == 'pixel_size':
473	self.current_datainfo.source.data_point.z = data_point
474	self.current_datainfo.source.beam_size_unit = unit
475	elif tagname == 'radiation' and self.parent_class == 'SASsource':
476	self.current_datainfo.source.radiation = data_point
477	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.beam_shape = data_point
479
480	# Everything else goes in meta_data
481	else:
482	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
483	self.current_datainfo.meta_data[new_key] = data_point
484
485	self.names.remove(tagname_original)
486	length = 0
487	if len(self.names) > 1:
488	length = len(self.names) - 1
489	self.parent_class = self.names[length]
490	if not self._is_call_local() and not recurse:
491	self.frm = ""
492	self.add_data_set()
493	empty = None
494	return self.output[0], empty
495
496
497	def _is_call_local(self):
498	"""
499
500	"""
501	if self.frm == "":
502	inter = inspect.stack()
503	self.frm = inter[2]
504	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
505	mod_name = mod_name.replace(".py", "")
506	mod = mod_name.split("sas/")
507	mod_name = mod[1]
508	if mod_name != "sascalc/dataloader/readers/cansas_reader":
509	return False
510	return True
511
512	def is_cansas(self, ext="xml"):
513	"""
514	Checks to see if the xml file is a CanSAS file
515
516	:param ext: The file extension of the data file
517	"""
518	if self.validate_xml():
519	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
520	value = self.xmlroot.get(name)
521	if CANSAS_NS.get(self.cansas_version).get("ns") == \
522	value.rsplit(" ")[0]:
523	return True
524	if ext == "svs":
525	return True
526	raise RuntimeError
527
528	def load_file_and_schema(self, xml_file, schema_path=""):
529	"""
530	Loads the file and associates a schema, if a schema is passed in or if one already exists
531
532	:param xml_file: The xml file path sent to Reader.read
533	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
534	"""
535	base_name = xml_reader.__file__
536	base_name = base_name.replace("\\", "/")
537	base = base_name.split("/sas/")[0]
538
539	# Load in xml file and get the cansas version from the header
540	self.set_xml_file(xml_file)
541	self.cansas_version = self.xmlroot.get("version", "1.0")
542
543	# Generic values for the cansas file based on the version
544	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
545	if schema_path == "":
546	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
547	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
548
549	# Link a schema to the XML file.
550	self.set_schema(schema_path)
551
552	def add_data_set(self):
553	"""
554	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
555	private method to generate a new data set.
556
557	:param key: NeXus group name for current tree level
558	"""
559
560	if self.current_datainfo and self.current_dataset:
561	self._final_cleanup()
562	self.data = []
563	self.current_datainfo = DataInfo()
564
565	def _initialize_new_data_set(self, node=None):
566	"""
567	A private class method to generate a new 1D data object.
568	Outside methods should call add_data_set() to be sure any existing data is stored properly.
569
570	:param node: XML node to determine if 1D or 2D data
571	"""
572	x = np.array(0)
573	y = np.array(0)
574	for child in node:
575	if child.tag.replace(self.base_ns, "") == "Idata":
576	for i_child in child:
577	if i_child.tag.replace(self.base_ns, "") == "Qx":
578	self.current_dataset = plottable_2D()
579	return
580	self.current_dataset = plottable_1D(x, y)
581
582	def add_intermediate(self):
583	"""
584	This method stores any intermediate objects within the final data set after fully reading the set.
585
586	:param parent: The NXclass name for the h5py Group object that just finished being processed
587	"""
588
589	if self.parent_class == 'SASprocess':
590	self.current_datainfo.process.append(self.process)
591	self.process = Process()
592	elif self.parent_class == 'SASdetector':
593	self.current_datainfo.detector.append(self.detector)
594	self.detector = Detector()
595	elif self.parent_class == 'SAStransmission_spectrum':
596	self.current_datainfo.trans_spectrum.append(self.transspectrum)
597	self.transspectrum = TransmissionSpectrum()
598	elif self.parent_class == 'SAScollimation':
599	self.current_datainfo.collimation.append(self.collimation)
600	self.collimation = Collimation()
601	elif self.parent_class == 'aperture':
602	self.collimation.aperture.append(self.aperture)
603	self.aperture = Aperture()
604	elif self.parent_class == 'SASdata':
605	self._check_for_empty_resolution()
606	self.data.append(self.current_dataset)
607
608	def _final_cleanup(self):
609	"""
610	Final cleanup of the Data1D object to be sure it has all the
611	appropriate information needed for perspectives
612	"""
613
614	# Append errors to dataset and reset class errors
615	self.current_datainfo.errors = set()
616	for error in self.errors:
617	self.current_datainfo.errors.add(error)
618	self.errors.clear()
619
620	# Combine all plottables with datainfo and append each to output
621	# Type cast data arrays to float64 and find min/max as appropriate
622	for dataset in self.data:
623	if isinstance(dataset, plottable_1D):
624	if dataset.x is not None:
625	dataset.x = np.delete(dataset.x, [0])
626	dataset.x = dataset.x.astype(np.float64)
627	dataset.xmin = np.min(dataset.x)
628	dataset.xmax = np.max(dataset.x)
629	if dataset.y is not None:
630	dataset.y = np.delete(dataset.y, [0])
631	dataset.y = dataset.y.astype(np.float64)
632	dataset.ymin = np.min(dataset.y)
633	dataset.ymax = np.max(dataset.y)
634	if dataset.dx is not None:
635	dataset.dx = np.delete(dataset.dx, [0])
636	dataset.dx = dataset.dx.astype(np.float64)
637	if dataset.dxl is not None:
638	dataset.dxl = np.delete(dataset.dxl, [0])
639	dataset.dxl = dataset.dxl.astype(np.float64)
640	if dataset.dxw is not None:
641	dataset.dxw = np.delete(dataset.dxw, [0])
642	dataset.dxw = dataset.dxw.astype(np.float64)
643	if dataset.dy is not None:
644	dataset.dy = np.delete(dataset.dy, [0])
645	dataset.dy = dataset.dy.astype(np.float64)
646	np.trim_zeros(dataset.x)
647	np.trim_zeros(dataset.y)
648	np.trim_zeros(dataset.dy)
649	elif isinstance(dataset, plottable_2D):
650	dataset.data = dataset.data.astype(np.float64)
651	dataset.qx_data = dataset.qx_data.astype(np.float64)
652	dataset.xmin = np.min(dataset.qx_data)
653	dataset.xmax = np.max(dataset.qx_data)
654	dataset.qy_data = dataset.qy_data.astype(np.float64)
655	dataset.ymin = np.min(dataset.qy_data)
656	dataset.ymax = np.max(dataset.qy_data)
657	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
658	+ dataset.qy_data * dataset.qy_data)
659	if dataset.err_data is not None:
660	dataset.err_data = dataset.err_data.astype(np.float64)
661	if dataset.dqx_data is not None:
662	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
663	if dataset.dqy_data is not None:
664	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
665	if dataset.mask is not None:
666	dataset.mask = dataset.mask.astype(dtype=bool)
667
668	if len(dataset.shape) == 2:
669	n_rows, n_cols = dataset.shape
670	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
671	dataset.x_bins = dataset.qx_data[:int(n_cols)]
672	dataset.data = dataset.data.flatten()
673	else:
674	dataset.y_bins = []
675	dataset.x_bins = []
676	dataset.data = dataset.data.flatten()
677
678	final_dataset = combine_data(dataset, self.current_datainfo)
679	self.output.append(final_dataset)
680
681	def _create_unique_key(self, dictionary, name, numb=0):
682	"""
683	Create a unique key value for any dictionary to prevent overwriting
684	Recurse until a unique key value is found.
685
686	:param dictionary: A dictionary with any number of entries
687	:param name: The index of the item to be added to dictionary
688	:param numb: The number to be appended to the name, starts at 0
689	"""
690	if dictionary.get(name) is not None:
691	numb += 1
692	name = name.split("_")[0]
693	name += "_{0}".format(numb)
694	name = self._create_unique_key(dictionary, name, numb)
695	return name
696
697	def _get_node_value(self, node, tagname):
698	"""
699	Get the value of a node and any applicable units
700
701	:param node: The XML node to get the value of
702	:param tagname: The tagname of the node
703	"""
704	#Get the text from the node and convert all whitespace to spaces
705	units = ''
706	node_value = node.text
707	if node_value is not None:
708	node_value = ' '.join(node_value.split())
709	else:
710	node_value = ""
711
712	# If the value is a float, compile with units.
713	if self.ns_list.ns_datatype == "float":
714	# If an empty value is given, set as zero.
715	if node_value is None or node_value.isspace() \
716	or node_value.lower() == "nan":
717	node_value = "0.0"
718	#Convert the value to the base units
719	node_value, units = self._unit_conversion(node, tagname, node_value)
720
721	# If the value is a timestamp, convert to a datetime object
722	elif self.ns_list.ns_datatype == "timestamp":
723	if node_value is None or node_value.isspace():
724	pass
725	else:
726	try:
727	node_value = \
728	datetime.datetime.fromtimestamp(node_value)
729	except ValueError:
730	node_value = None
731	return node_value, units
732
733	def _unit_conversion(self, node, tagname, node_value):
734	"""
735	A unit converter method used to convert the data included in the file
736	to the default units listed in data_info
737
738	:param node: XML node
739	:param tagname: name of the node
740	:param node_value: The value of the current dom node
741	"""
742	attr = node.attrib
743	value_unit = ''
744	err_msg = None
745	default_unit = None
746	if not isinstance(node_value, float):
747	node_value = float(node_value)
748	if 'unit' in attr and attr.get('unit') is not None:
749	try:
750	local_unit = attr['unit']
751	unitname = self.ns_list.current_level.get("unit", "")
752	if "SASdetector" in self.names:
753	save_in = "detector"
754	elif "aperture" in self.names:
755	save_in = "aperture"
756	elif "SAScollimation" in self.names:
757	save_in = "collimation"
758	elif "SAStransmission_spectrum" in self.names:
759	save_in = "transspectrum"
760	elif "SASdata" in self.names:
761	x = np.zeros(1)
762	y = np.zeros(1)
763	self.current_data1d = Data1D(x, y)
764	save_in = "current_data1d"
765	elif "SASsource" in self.names:
766	save_in = "current_datainfo.source"
767	elif "SASsample" in self.names:
768	save_in = "current_datainfo.sample"
769	elif "SASprocess" in self.names:
770	save_in = "process"
771	else:
772	save_in = "current_datainfo"
773	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
774	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
775	and local_unit.lower() != "none":
776	if HAS_CONVERTER == True:
777	# Check local units - bad units raise KeyError
778	data_conv_q = Converter(local_unit)
779	value_unit = default_unit
780	node_value = data_conv_q(node_value, units=default_unit)
781	else:
782	value_unit = local_unit
783	err_msg = "Unit converter is not available.\n"
784	else:
785	value_unit = local_unit
786	except KeyError:
787	err_msg = "CanSAS reader: unexpected "
788	err_msg += "\"{0}\" unit [{1}]; "
789	err_msg = err_msg.format(tagname, local_unit)
790	err_msg += "expecting [{0}]".format(default_unit)
791	value_unit = local_unit
792	except:
793	err_msg = "CanSAS reader: unknown error converting "
794	err_msg += "\"{0}\" unit [{1}]"
795	err_msg = err_msg.format(tagname, local_unit)
796	value_unit = local_unit
797	elif 'unit' in attr:
798	value_unit = attr['unit']
799	if err_msg:
800	self.errors.add(err_msg)
801	return node_value, value_unit
802
803	def _check_for_empty_data(self):
804	"""
805	Creates an empty data set if no data is passed to the reader
806
807	:param data1d: presumably a Data1D object
808	"""
809	if self.current_dataset == None:
810	x_vals = np.empty(0)
811	y_vals = np.empty(0)
812	dx_vals = np.empty(0)
813	dy_vals = np.empty(0)
814	dxl = np.empty(0)
815	dxw = np.empty(0)
816	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
817	self.current_dataset.dxl = dxl
818	self.current_dataset.dxw = dxw
819
820	def _check_for_empty_resolution(self):
821	"""
822	A method to check all resolution data sets are the same size as I and Q
823	"""
824	if isinstance(self.current_dataset, plottable_1D):
825	dql_exists = False
826	dqw_exists = False
827	dq_exists = False
828	di_exists = False
829	if self.current_dataset.dxl is not None:
830	dql_exists = True
831	if self.current_dataset.dxw is not None:
832	dqw_exists = True
833	if self.current_dataset.dx is not None:
834	dq_exists = True
835	if self.current_dataset.dy is not None:
836	di_exists = True
837	if dqw_exists and not dql_exists:
838	array_size = self.current_dataset.dxw.size - 1
839	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
840	np.zeros([array_size]))
841	elif dql_exists and not dqw_exists:
842	array_size = self.current_dataset.dxl.size - 1
843	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
844	np.zeros([array_size]))
845	elif not dql_exists and not dqw_exists and not dq_exists:
846	array_size = self.current_dataset.x.size - 1
847	self.current_dataset.dx = np.append(self.current_dataset.dx,
848	np.zeros([array_size]))
849	if not di_exists:
850	array_size = self.current_dataset.y.size - 1
851	self.current_dataset.dy = np.append(self.current_dataset.dy,
852	np.zeros([array_size]))
853	elif isinstance(self.current_dataset, plottable_2D):
854	dqx_exists = False
855	dqy_exists = False
856	di_exists = False
857	mask_exists = False
858	if self.current_dataset.dqx_data is not None:
859	dqx_exists = True
860	if self.current_dataset.dqy_data is not None:
861	dqy_exists = True
862	if self.current_dataset.err_data is not None:
863	di_exists = True
864	if self.current_dataset.mask is not None:
865	mask_exists = True
866	if not dqy_exists:
867	array_size = self.current_dataset.qy_data.size - 1
868	self.current_dataset.dqy_data = np.append(
869	self.current_dataset.dqy_data, np.zeros([array_size]))
870	if not dqx_exists:
871	array_size = self.current_dataset.qx_data.size - 1
872	self.current_dataset.dqx_data = np.append(
873	self.current_dataset.dqx_data, np.zeros([array_size]))
874	if not di_exists:
875	array_size = self.current_dataset.data.size - 1
876	self.current_dataset.err_data = np.append(
877	self.current_dataset.err_data, np.zeros([array_size]))
878	if not mask_exists:
879	array_size = self.current_dataset.data.size - 1
880	self.current_dataset.mask = np.append(
881	self.current_dataset.mask,
882	np.ones([array_size] ,dtype=bool))
883
884	####### All methods below are for writing CanSAS XML files #######
885
886	def write(self, filename, datainfo):
887	"""
888	Write the content of a Data1D as a CanSAS XML file
889
890	:param filename: name of the file to write
891	:param datainfo: Data1D object
892	"""
893	# Create XML document
894	doc, _ = self._to_xml_doc(datainfo)
895	# Write the file
896	file_ref = open(filename, 'w')
897	if self.encoding == None:
898	self.encoding = "UTF-8"
899	doc.write(file_ref, encoding=self.encoding,
900	pretty_print=True, xml_declaration=True)
901	file_ref.close()
902
903	def _to_xml_doc(self, datainfo):
904	"""
905	Create an XML document to contain the content of a Data1D
906
907	:param datainfo: Data1D object
908	"""
909	is_2d = False
910	if issubclass(datainfo.__class__, Data2D):
911	is_2d = True
912
913	# Get PIs and create root element
914	pi_string = self._get_pi_string()
915	# Define namespaces and create SASroot object
916	main_node = self._create_main_node()
917	# Create ElementTree, append SASroot and apply processing instructions
918	base_string = pi_string + self.to_string(main_node)
919	base_element = self.create_element_from_string(base_string)
920	doc = self.create_tree(base_element)
921	# Create SASentry Element
922	entry_node = self.create_element("SASentry")
923	root = doc.getroot()
924	root.append(entry_node)
925
926	# Add Title to SASentry
927	self.write_node(entry_node, "Title", datainfo.title)
928	# Add Run to SASentry
929	self._write_run_names(datainfo, entry_node)
930	# Add Data info to SASEntry
931	if is_2d:
932	self._write_data_2d(datainfo, entry_node)
933	else:
934	self._write_data(datainfo, entry_node)
935	# Transmission Spectrum Info
936	# TODO: fix the writer to linearize all data, including T_spectrum
937	# self._write_trans_spectrum(datainfo, entry_node)
938	# Sample info
939	self._write_sample_info(datainfo, entry_node)
940	# Instrument info
941	instr = self._write_instrument(datainfo, entry_node)
942	# Source
943	self._write_source(datainfo, instr)
944	# Collimation
945	self._write_collimation(datainfo, instr)
946	# Detectors
947	self._write_detectors(datainfo, instr)
948	# Processes info
949	self._write_process_notes(datainfo, entry_node)
950	# Note info
951	self._write_notes(datainfo, entry_node)
952	# Return the document, and the SASentry node associated with
953	# the data we just wrote
954	# If the calling function was not the cansas reader, return a minidom
955	# object rather than an lxml object.
956	self.frm = inspect.stack()[1]
957	doc, entry_node = self._check_origin(entry_node, doc)
958	return doc, entry_node
959
960	def write_node(self, parent, name, value, attr=None):
961	"""
962	:param doc: document DOM
963	:param parent: parent node
964	:param name: tag of the element
965	:param value: value of the child text node
966	:param attr: attribute dictionary
967
968	:return: True if something was appended, otherwise False
969	"""
970	if value is not None:
971	parent = self.ebuilder(parent, name, value, attr)
972	return True
973	return False
974
975	def _get_pi_string(self):
976	"""
977	Creates the processing instructions header for writing to file
978	"""
979	pis = self.return_processing_instructions()
980	if len(pis) > 0:
981	pi_tree = self.create_tree(pis[0])
982	i = 1
983	for i in range(1, len(pis) - 1):
984	pi_tree = self.append(pis[i], pi_tree)
985	pi_string = self.to_string(pi_tree)
986	else:
987	pi_string = ""
988	return pi_string
989
990	def _create_main_node(self):
991	"""
992	Creates the primary xml header used when writing to file
993	"""
994	xsi = "http://www.w3.org/2001/XMLSchema-instance"
995	version = self.cansas_version
996	n_s = CANSAS_NS.get(version).get("ns")
997	if version == "1.1":
998	url = "http://www.cansas.org/formats/1.1/"
999	else:
1000	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
1001	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1002	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1003	"version" : version}
1004	nsmap = {'xsi' : xsi, None: n_s}
1005
1006	main_node = self.create_element("{" + n_s + "}SASroot",
1007	attrib=attrib, nsmap=nsmap)
1008	return main_node
1009
1010	def _write_run_names(self, datainfo, entry_node):
1011	"""
1012	Writes the run names to the XML file
1013
1014	:param datainfo: The Data1D object the information is coming from
1015	:param entry_node: lxml node ElementTree object to be appended to
1016	"""
1017	if datainfo.run == None or datainfo.run == []:
1018	datainfo.run.append(RUN_NAME_DEFAULT)
1019	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1020	for item in datainfo.run:
1021	runname = {}
1022	if item in datainfo.run_name and \
1023	len(str(datainfo.run_name[item])) > 1:
1024	runname = {'name': datainfo.run_name[item]}
1025	self.write_node(entry_node, "Run", item, runname)
1026
1027	def _write_data(self, datainfo, entry_node):
1028	"""
1029	Writes 1D I and Q data to the XML file
1030
1031	:param datainfo: The Data1D object the information is coming from
1032	:param entry_node: lxml node ElementTree object to be appended to
1033	"""
1034	node = self.create_element("SASdata")
1035	self.append(node, entry_node)
1036
1037	for i in range(len(datainfo.x)):
1038	point = self.create_element("Idata")
1039	node.append(point)
1040	self.write_node(point, "Q", datainfo.x[i],
1041	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1042	if len(datainfo.y) >= i:
1043	self.write_node(point, "I", datainfo.y[i],
1044	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1045	if datainfo.dy is not None and len(datainfo.dy) > i:
1046	self.write_node(point, "Idev", datainfo.dy[i],
1047	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1048	if datainfo.dx is not None and len(datainfo.dx) > i:
1049	self.write_node(point, "Qdev", datainfo.dx[i],
1050	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1051	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1052	self.write_node(point, "dQw", datainfo.dxw[i],
1053	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1054	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1055	self.write_node(point, "dQl", datainfo.dxl[i],
1056	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1057	if datainfo.isSesans:
1058	sesans = self.create_element("Sesans")
1059	sesans.text = str(datainfo.isSesans)
1060	node.append(sesans)
1061	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
1062	{'unit': datainfo.sample.yacceptance[1]})
1063	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1064	{'unit': datainfo.sample.zacceptance[1]})
1065
1066
1067	def _write_data_2d(self, datainfo, entry_node):
1068	"""
1069	Writes 2D data to the XML file
1070
1071	:param datainfo: The Data2D object the information is coming from
1072	:param entry_node: lxml node ElementTree object to be appended to
1073	"""
1074	attr = {}
1075	if datainfo.data.shape:
1076	attr["x_bins"] = str(len(datainfo.x_bins))
1077	attr["y_bins"] = str(len(datainfo.y_bins))
1078	node = self.create_element("SASdata", attr)
1079	self.append(node, entry_node)
1080
1081	point = self.create_element("Idata")
1082	node.append(point)
1083	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1084	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1085	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1086
1087	self.write_node(point, "Qx", qx,
1088	{'unit': datainfo._xunit})
1089	self.write_node(point, "Qy", qy,
1090	{'unit': datainfo._yunit})
1091	self.write_node(point, "I", intensity,
1092	{'unit': datainfo._zunit})
1093	if datainfo.err_data is not None:
1094	err = ','.join([str(datainfo.err_data[i]) for i in
1095	xrange(len(datainfo.err_data))])
1096	self.write_node(point, "Idev", err,
1097	{'unit': datainfo._zunit})
1098	if datainfo.dqy_data is not None:
1099	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1100	xrange(len(datainfo.dqy_data))])
1101	self.write_node(point, "Qydev", dqy,
1102	{'unit': datainfo._yunit})
1103	if datainfo.dqx_data is not None:
1104	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1105	xrange(len(datainfo.dqx_data))])
1106	self.write_node(point, "Qxdev", dqx,
1107	{'unit': datainfo._xunit})
1108	if datainfo.mask is not None:
1109	mask = ','.join(
1110	["1" if datainfo.mask[i] else "0"
1111	for i in xrange(len(datainfo.mask))])
1112	self.write_node(point, "Mask", mask)
1113
1114	def _write_trans_spectrum(self, datainfo, entry_node):
1115	"""
1116	Writes the transmission spectrum data to the XML file
1117
1118	:param datainfo: The Data1D object the information is coming from
1119	:param entry_node: lxml node ElementTree object to be appended to
1120	"""
1121	for i in range(len(datainfo.trans_spectrum)):
1122	spectrum = datainfo.trans_spectrum[i]
1123	node = self.create_element("SAStransmission_spectrum",
1124	{"name" : spectrum.name})
1125	self.append(node, entry_node)
1126	if isinstance(spectrum.timestamp, datetime.datetime):
1127	node.setAttribute("timestamp", spectrum.timestamp)
1128	for i in range(len(spectrum.wavelength)):
1129	point = self.create_element("Tdata")
1130	node.append(point)
1131	self.write_node(point, "Lambda", spectrum.wavelength[i],
1132	{'unit': spectrum.wavelength_unit})
1133	self.write_node(point, "T", spectrum.transmission[i],
1134	{'unit': spectrum.transmission_unit})
1135	if spectrum.transmission_deviation != None \
1136	and len(spectrum.transmission_deviation) >= i:
1137	self.write_node(point, "Tdev",
1138	spectrum.transmission_deviation[i],
1139	{'unit':
1140	spectrum.transmission_deviation_unit})
1141
1142	def _write_sample_info(self, datainfo, entry_node):
1143	"""
1144	Writes the sample information to the XML file
1145
1146	:param datainfo: The Data1D object the information is coming from
1147	:param entry_node: lxml node ElementTree object to be appended to
1148	"""
1149	sample = self.create_element("SASsample")
1150	if datainfo.sample.name is not None:
1151	self.write_attribute(sample, "name",
1152	str(datainfo.sample.name))
1153	self.append(sample, entry_node)
1154	self.write_node(sample, "ID", str(datainfo.sample.ID))
1155	self.write_node(sample, "thickness", datainfo.sample.thickness,
1156	{"unit": datainfo.sample.thickness_unit})
1157	self.write_node(sample, "transmission", datainfo.sample.transmission)
1158	self.write_node(sample, "temperature", datainfo.sample.temperature,
1159	{"unit": datainfo.sample.temperature_unit})
1160
1161	pos = self.create_element("position")
1162	written = self.write_node(pos,
1163	"x",
1164	datainfo.sample.position.x,
1165	{"unit": datainfo.sample.position_unit})
1166	written = written \| self.write_node( \
1167	pos, "y", datainfo.sample.position.y,
1168	{"unit": datainfo.sample.position_unit})
1169	written = written \| self.write_node( \
1170	pos, "z", datainfo.sample.position.z,
1171	{"unit": datainfo.sample.position_unit})
1172	if written == True:
1173	self.append(pos, sample)
1174
1175	ori = self.create_element("orientation")
1176	written = self.write_node(ori, "roll",
1177	datainfo.sample.orientation.x,
1178	{"unit": datainfo.sample.orientation_unit})
1179	written = written \| self.write_node( \
1180	ori, "pitch", datainfo.sample.orientation.y,
1181	{"unit": datainfo.sample.orientation_unit})
1182	written = written \| self.write_node( \
1183	ori, "yaw", datainfo.sample.orientation.z,
1184	{"unit": datainfo.sample.orientation_unit})
1185	if written == True:
1186	self.append(ori, sample)
1187
1188	for item in datainfo.sample.details:
1189	self.write_node(sample, "details", item)
1190
1191	def _write_instrument(self, datainfo, entry_node):
1192	"""
1193	Writes the instrumental information to the XML file
1194
1195	:param datainfo: The Data1D object the information is coming from
1196	:param entry_node: lxml node ElementTree object to be appended to
1197	"""
1198	instr = self.create_element("SASinstrument")
1199	self.append(instr, entry_node)
1200	self.write_node(instr, "name", datainfo.instrument)
1201	return instr
1202
1203	def _write_source(self, datainfo, instr):
1204	"""
1205	Writes the source information to the XML file
1206
1207	:param datainfo: The Data1D object the information is coming from
1208	:param instr: instrument node to be appended to
1209	"""
1210	source = self.create_element("SASsource")
1211	if datainfo.source.name is not None:
1212	self.write_attribute(source, "name",
1213	str(datainfo.source.name))
1214	self.append(source, instr)
1215	if datainfo.source.radiation == None or datainfo.source.radiation == '':
1216	datainfo.source.radiation = "neutron"
1217	self.write_node(source, "radiation", datainfo.source.radiation)
1218
1219	size = self.create_element("beam_size")
1220	if datainfo.source.beam_size_name is not None:
1221	self.write_attribute(size, "name",
1222	str(datainfo.source.beam_size_name))
1223	written = self.write_node( \
1224	size, "x", datainfo.source.beam_size.x,
1225	{"unit": datainfo.source.beam_size_unit})
1226	written = written \| self.write_node( \
1227	size, "y", datainfo.source.beam_size.y,
1228	{"unit": datainfo.source.beam_size_unit})
1229	written = written \| self.write_node( \
1230	size, "z", datainfo.source.beam_size.z,
1231	{"unit": datainfo.source.beam_size_unit})
1232	if written == True:
1233	self.append(size, source)
1234
1235	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1236	self.write_node(source, "wavelength",
1237	datainfo.source.wavelength,
1238	{"unit": datainfo.source.wavelength_unit})
1239	self.write_node(source, "wavelength_min",
1240	datainfo.source.wavelength_min,
1241	{"unit": datainfo.source.wavelength_min_unit})
1242	self.write_node(source, "wavelength_max",
1243	datainfo.source.wavelength_max,
1244	{"unit": datainfo.source.wavelength_max_unit})
1245	self.write_node(source, "wavelength_spread",
1246	datainfo.source.wavelength_spread,
1247	{"unit": datainfo.source.wavelength_spread_unit})
1248
1249	def _write_collimation(self, datainfo, instr):
1250	"""
1251	Writes the collimation information to the XML file
1252
1253	:param datainfo: The Data1D object the information is coming from
1254	:param instr: lxml node ElementTree object to be appended to
1255	"""
1256	if datainfo.collimation == [] or datainfo.collimation == None:
1257	coll = Collimation()
1258	datainfo.collimation.append(coll)
1259	for item in datainfo.collimation:
1260	coll = self.create_element("SAScollimation")
1261	if item.name is not None:
1262	self.write_attribute(coll, "name", str(item.name))
1263	self.append(coll, instr)
1264
1265	self.write_node(coll, "length", item.length,
1266	{"unit": item.length_unit})
1267
1268	for aperture in item.aperture:
1269	apert = self.create_element("aperture")
1270	if aperture.name is not None:
1271	self.write_attribute(apert, "name", str(aperture.name))
1272	if aperture.type is not None:
1273	self.write_attribute(apert, "type", str(aperture.type))
1274	self.append(apert, coll)
1275
1276	size = self.create_element("size")
1277	if aperture.size_name is not None:
1278	self.write_attribute(size, "name",
1279	str(aperture.size_name))
1280	written = self.write_node(size, "x", aperture.size.x,
1281	{"unit": aperture.size_unit})
1282	written = written \| self.write_node( \
1283	size, "y", aperture.size.y,
1284	{"unit": aperture.size_unit})
1285	written = written \| self.write_node( \
1286	size, "z", aperture.size.z,
1287	{"unit": aperture.size_unit})
1288	if written == True:
1289	self.append(size, apert)
1290
1291	self.write_node(apert, "distance", aperture.distance,
1292	{"unit": aperture.distance_unit})
1293
1294	def _write_detectors(self, datainfo, instr):
1295	"""
1296	Writes the detector information to the XML file
1297
1298	:param datainfo: The Data1D object the information is coming from
1299	:param inst: lxml instrument node to be appended to
1300	"""
1301	if datainfo.detector == None or datainfo.detector == []:
1302	det = Detector()
1303	det.name = ""
1304	datainfo.detector.append(det)
1305
1306	for item in datainfo.detector:
1307	det = self.create_element("SASdetector")
1308	written = self.write_node(det, "name", item.name)
1309	written = written \| self.write_node(det, "SDD", item.distance,
1310	{"unit": item.distance_unit})
1311	if written == True:
1312	self.append(det, instr)
1313
1314	off = self.create_element("offset")
1315	written = self.write_node(off, "x", item.offset.x,
1316	{"unit": item.offset_unit})
1317	written = written \| self.write_node(off, "y", item.offset.y,
1318	{"unit": item.offset_unit})
1319	written = written \| self.write_node(off, "z", item.offset.z,
1320	{"unit": item.offset_unit})
1321	if written == True:
1322	self.append(off, det)
1323
1324	ori = self.create_element("orientation")
1325	written = self.write_node(ori, "roll", item.orientation.x,
1326	{"unit": item.orientation_unit})
1327	written = written \| self.write_node(ori, "pitch",
1328	item.orientation.y,
1329	{"unit": item.orientation_unit})
1330	written = written \| self.write_node(ori, "yaw",
1331	item.orientation.z,
1332	{"unit": item.orientation_unit})
1333	if written == True:
1334	self.append(ori, det)
1335
1336	center = self.create_element("beam_center")
1337	written = self.write_node(center, "x", item.beam_center.x,
1338	{"unit": item.beam_center_unit})
1339	written = written \| self.write_node(center, "y",
1340	item.beam_center.y,
1341	{"unit": item.beam_center_unit})
1342	written = written \| self.write_node(center, "z",
1343	item.beam_center.z,
1344	{"unit": item.beam_center_unit})
1345	if written == True:
1346	self.append(center, det)
1347
1348	pix = self.create_element("pixel_size")
1349	written = self.write_node(pix, "x", item.pixel_size.x,
1350	{"unit": item.pixel_size_unit})
1351	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1352	{"unit": item.pixel_size_unit})
1353	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1354	{"unit": item.pixel_size_unit})
1355	if written == True:
1356	self.append(pix, det)
1357	self.write_node(det, "slit_length", item.slit_length,
1358	{"unit": item.slit_length_unit})
1359
1360
1361	def _write_process_notes(self, datainfo, entry_node):
1362	"""
1363	Writes the process notes to the XML file
1364
1365	:param datainfo: The Data1D object the information is coming from
1366	:param entry_node: lxml node ElementTree object to be appended to
1367
1368	"""
1369	for item in datainfo.process:
1370	node = self.create_element("SASprocess")
1371	self.append(node, entry_node)
1372	self.write_node(node, "name", item.name)
1373	self.write_node(node, "date", item.date)
1374	self.write_node(node, "description", item.description)
1375	for term in item.term:
1376	if isinstance(term, list):
1377	value = term['value']
1378	del term['value']
1379	elif isinstance(term, dict):
1380	value = term.get("value")
1381	del term['value']
1382	else:
1383	value = term
1384	self.write_node(node, "term", value, term)
1385	for note in item.notes:
1386	self.write_node(node, "SASprocessnote", note)
1387	if len(item.notes) == 0:
1388	self.write_node(node, "SASprocessnote", "")
1389
1390	def _write_notes(self, datainfo, entry_node):
1391	"""
1392	Writes the notes to the XML file and creates an empty note if none
1393	exist
1394
1395	:param datainfo: The Data1D object the information is coming from
1396	:param entry_node: lxml node ElementTree object to be appended to
1397
1398	"""
1399	if len(datainfo.notes) == 0:
1400	node = self.create_element("SASnote")
1401	self.append(node, entry_node)
1402	else:
1403	for item in datainfo.notes:
1404	node = self.create_element("SASnote")
1405	self.write_text(node, item)
1406	self.append(node, entry_node)
1407
1408	def _check_origin(self, entry_node, doc):
1409	"""
1410	Return the document, and the SASentry node associated with
1411	the data we just wrote.
1412	If the calling function was not the cansas reader, return a minidom
1413	object rather than an lxml object.
1414
1415	:param entry_node: lxml node ElementTree object to be appended to
1416	:param doc: entire xml tree
1417	"""
1418	if not self.frm:
1419	self.frm = inspect.stack()[1]
1420	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1421	mod_name = mod_name.replace(".py", "")
1422	mod = mod_name.split("sas/")
1423	mod_name = mod[1]
1424	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1425	string = self.to_string(doc, pretty_print=False)
1426	doc = parseString(string)
1427	node_name = entry_node.tag
1428	node_list = doc.getElementsByTagName(node_name)
1429	entry_node = node_list.item(0)
1430	return doc, entry_node
1431
1432	# DO NOT REMOVE - used in saving and loading panel states.
1433	def _store_float(self, location, node, variable, storage, optional=True):
1434	"""
1435	Get the content of a xpath location and store
1436	the result. Check that the units are compatible
1437	with the destination. The value is expected to
1438	be a float.
1439
1440	The xpath location might or might not exist.
1441	If it does not exist, nothing is done
1442
1443	:param location: xpath location to fetch
1444	:param node: node to read the data from
1445	:param variable: name of the data member to store it in [string]
1446	:param storage: data object that has the 'variable' data member
1447	:param optional: if True, no exception will be raised
1448	if unit conversion can't be done
1449
1450	:raise ValueError: raised when the units are not recognized
1451	"""
1452	entry = get_content(location, node)
1453	try:
1454	value = float(entry.text)
1455	except:
1456	value = None
1457
1458	if value is not None:
1459	# If the entry has units, check to see that they are
1460	# compatible with what we currently have in the data object
1461	units = entry.get('unit')
1462	if units is not None:
1463	toks = variable.split('.')
1464	local_unit = None
1465	exec "local_unit = storage.%s_unit" % toks[0]
1466	if local_unit != None and units.lower() != local_unit.lower():
1467	if HAS_CONVERTER == True:
1468	try:
1469	conv = Converter(units)
1470	exec "storage.%s = %g" % \
1471	(variable, conv(value, units=local_unit))
1472	except:
1473	_, exc_value, _ = sys.exc_info()
1474	err_mess = "CanSAS reader: could not convert"
1475	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1476	% (variable, units, local_unit, exc_value)
1477	self.errors.add(err_mess)
1478	if optional:
1479	logger.info(err_mess)
1480	else:
1481	raise ValueError, err_mess
1482	else:
1483	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1484	% (variable, units)
1485	err_mess += " expecting [%s]" % local_unit
1486	self.errors.add(err_mess)
1487	if optional:
1488	logger.info(err_mess)
1489	else:
1490	raise ValueError, err_mess
1491	else:
1492	exec "storage.%s = value" % variable
1493	else:
1494	exec "storage.%s = value" % variable
1495
1496	# DO NOT REMOVE - used in saving and loading panel states.
1497	def _store_content(self, location, node, variable, storage):
1498	"""
1499	Get the content of a xpath location and store
1500	the result. The value is treated as a string.
1501
1502	The xpath location might or might not exist.
1503	If it does not exist, nothing is done
1504
1505	:param location: xpath location to fetch
1506	:param node: node to read the data from
1507	:param variable: name of the data member to store it in [string]
1508	:param storage: data object that has the 'variable' data member
1509
1510	:return: return a list of errors
1511	"""
1512	entry = get_content(location, node)
1513	if entry is not None and entry.text is not None:
1514	exec "storage.%s = entry.text.strip()" % variable
1515
1516
1517	# DO NOT REMOVE Called by outside packages:
1518	# sas.sasgui.perspectives.invariant.invariant_state
1519	# sas.sasgui.perspectives.fitting.pagestate
1520	def get_content(location, node):
1521	"""
1522	Get the first instance of the content of a xpath location.
1523
1524	:param location: xpath location
1525	:param node: node to start at
1526
1527	:return: Element, or None
1528	"""
1529	nodes = node.xpath(location,
1530	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1531	if len(nodes) > 0:
1532	return nodes[0]
1533	else:
1534	return None
1535
1536	# DO NOT REMOVE Called by outside packages:
1537	# sas.sasgui.perspectives.fitting.pagestate
1538	def write_node(doc, parent, name, value, attr=None):
1539	"""
1540	:param doc: document DOM
1541	:param parent: parent node
1542	:param name: tag of the element
1543	:param value: value of the child text node
1544	:param attr: attribute dictionary
1545
1546	:return: True if something was appended, otherwise False
1547	"""
1548	if attr is None:
1549	attr = {}
1550	if value is not None:
1551	node = doc.createElement(name)
1552	node.appendChild(doc.createTextNode(str(value)))
1553	for item in attr:
1554	node.setAttribute(item, attr[item])
1555	parent.appendChild(node)
1556	return True
1557	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 63d773c

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