cansas_reader.py @ 278ddee

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 278ddee was 278ddee, checked in by krzywon, 7 years ago

Merge branch 'master' into ticket-876

# Conflicts:
# src/sas/sascalc/dataloader/readers/ascii_reader.py
# src/sas/sascalc/dataloader/readers/xml_reader.py

Property mode set to 100644

File size: 71.1 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	from sas.sascalc.dataloader.loader_exceptions import FileContentsException
32
33	# The following 2 imports ARE used. Do not remove either.
34	import xml.dom.minidom
35	from xml.dom.minidom import parseString
36
37	logger = logging.getLogger(__name__)
38
39	PREPROCESS = "xmlpreprocess"
40	ENCODING = "encoding"
41	RUN_NAME_DEFAULT = "None"
42	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
43	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
44	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
45	"as much of the data as possible.\n\n"
46	HAS_CONVERTER = True
47	try:
48	from sas.sascalc.data_util.nxsunit import Converter
49	except ImportError:
50	HAS_CONVERTER = False
51
52	CONSTANTS = CansasConstants()
53	CANSAS_FORMAT = CONSTANTS.format
54	CANSAS_NS = CONSTANTS.names
55	ALLOW_ALL = True
56
57	class Reader(XMLreader):
58	"""
59	Class to load cansas 1D XML files
60
61	:Dependencies:
62	The CanSAS reader requires PyXML 0.8.4 or later.
63	"""
64	# CanSAS version - defaults to version 1.0
65	cansas_version = "1.0"
66	base_ns = "{cansas1d/1.0}"
67	cansas_defaults = None
68	type_name = "canSAS"
69	invalid = True
70	frm = ""
71	# Log messages and errors
72	logging = None
73	errors = set()
74	# Namespace hierarchy for current xml_file object
75	names = None
76	ns_list = None
77	# Temporary storage location for loading multiple data sets in a single file
78	current_datainfo = None
79	current_dataset = None
80	current_data1d = None
81	data = None
82	# List of data1D objects to be sent back to SasView
83	output = None
84	# Wildcards
85	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
86	# List of allowed extensions
87	ext = ['.xml', '.XML', '.svs', '.SVS']
88	# Flag to bypass extension check
89	allow_all = True
90
91	def reset_state(self):
92	"""
93	Resets the class state to a base case when loading a new data file so previous
94	data files do not appear a second time
95	"""
96	self.current_datainfo = None
97	self.current_dataset = None
98	self.current_data1d = None
99	self.data = []
100	self.process = Process()
101	self.transspectrum = TransmissionSpectrum()
102	self.aperture = Aperture()
103	self.collimation = Collimation()
104	self.detector = Detector()
105	self.names = []
106	self.cansas_defaults = {}
107	self.output = []
108	self.ns_list = None
109	self.logging = []
110	self.encoding = None
111
112	def read(self, xml_file, schema_path="", invalid=True):
113	"""
114	Validate and read in an xml_file file in the canSAS format.
115
116	:param xml_file: A canSAS file path in proper XML format
117	:param schema_path: A file path to an XML schema to validate the xml_file against
118	"""
119	# For every file loaded, reset everything to a base state
120	self.reset_state()
121	self.invalid = invalid
122	# Check that the file exists
123	if os.path.isfile(xml_file):
124	basename, extension = os.path.splitext(os.path.basename(xml_file))
125	# If the file type is not allowed, return nothing
126	if extension in self.ext or self.allow_all:
127	# Get the file location of
128	self.load_file_and_schema(xml_file, schema_path)
129	self.add_data_set()
130	# Try to load the file, but raise an error if unable to.
131	# Check the file matches the XML schema
132	try:
133	self.is_cansas(extension)
134	self.invalid = False
135	# Get each SASentry from XML file and add it to a list.
136	entry_list = self.xmlroot.xpath(
137	'/ns:SASroot/ns:SASentry',
138	namespaces={'ns': self.cansas_defaults.get("ns")})
139	self.names.append("SASentry")
140
141	# Get all preprocessing events and encoding
142	self.set_processing_instructions()
143
144	# Parse each <SASentry> item
145	for entry in entry_list:
146	# Create a new DataInfo object for every <SASentry>
147
148	# Set the file name and then parse the entry.
149	self.current_datainfo.filename = basename + extension
150	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
151	self.current_datainfo.meta_data[PREPROCESS] = \
152	self.processing_instructions
153
154	# Parse the XML SASentry
155	self._parse_entry(entry)
156	# Combine datasets with datainfo
157	self.add_data_set()
158	except RuntimeError:
159	# If the file does not match the schema, raise this error
160	invalid_xml = self.find_invalid_xml()
161	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
162	self.errors.add(invalid_xml)
163	# Try again with an invalid CanSAS schema, that requires only a data set in each
164	base_name = xml_reader.__file__
165	base_name = base_name.replace("\\", "/")
166	base = base_name.split("/sas/")[0]
167	if self.cansas_version == "1.1":
168	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
169	else:
170	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
171	self.set_schema(invalid_schema)
172	try:
173	if self.invalid:
174	if self.is_cansas():
175	self.output = self.read(xml_file, invalid_schema, False)
176	else:
177	raise RuntimeError
178	else:
179	raise RuntimeError
180	except RuntimeError:
181	x = np.zeros(1)
182	y = np.zeros(1)
183	self.current_data1d = Data1D(x,y)
184	self.current_data1d.errors = self.errors
185	return [self.current_data1d]
186	else:
187	self.output.append("Not a valid file path.")
188	# Return a list of parsed entries that dataloader can manage
189	return self.output
190
191	def _parse_entry(self, dom, recurse=False):
192	"""
193	Parse a SASEntry - new recursive method for parsing the dom of
194	the CanSAS data format. This will allow multiple data files
195	and extra nodes to be read in simultaneously.
196
197	:param dom: dom object with a namespace base of names
198	"""
199
200	if not self._is_call_local() and not recurse:
201	self.reset_state()
202	self.add_data_set()
203	self.names.append("SASentry")
204	self.parent_class = "SASentry"
205	self._check_for_empty_data()
206	self.base_ns = "{0}{1}{2}".format("{", \
207	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
208
209	# Go through each child in the parent element
210	for node in dom:
211	attr = node.attrib
212	name = attr.get("name", "")
213	type = attr.get("type", "")
214	# Get the element name and set the current names level
215	tagname = node.tag.replace(self.base_ns, "")
216	tagname_original = tagname
217	# Skip this iteration when loading in save state information
218	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
219	continue
220
221	# Get where to store content
222	self.names.append(tagname_original)
223	self.ns_list = CONSTANTS.iterate_namespace(self.names)
224	# If the element is a child element, recurse
225	if len(node.getchildren()) > 0:
226	self.parent_class = tagname_original
227	if tagname == 'SASdata':
228	self._initialize_new_data_set(node)
229	if isinstance(self.current_dataset, plottable_2D):
230	x_bins = attr.get("x_bins", "")
231	y_bins = attr.get("y_bins", "")
232	if x_bins is not "" and y_bins is not "":
233	self.current_dataset.shape = (x_bins, y_bins)
234	else:
235	self.current_dataset.shape = ()
236	# Recursion step to access data within the group
237	self._parse_entry(node, True)
238	if tagname == "SASsample":
239	self.current_datainfo.sample.name = name
240	elif tagname == "beam_size":
241	self.current_datainfo.source.beam_size_name = name
242	elif tagname == "SAScollimation":
243	self.collimation.name = name
244	elif tagname == "aperture":
245	self.aperture.name = name
246	self.aperture.type = type
247	self.add_intermediate()
248	else:
249	if isinstance(self.current_dataset, plottable_2D):
250	data_point = node.text
251	unit = attr.get('unit', '')
252	else:
253	data_point, unit = self._get_node_value(node, tagname)
254
255	# If this is a dataset, store the data appropriately
256	if tagname == 'Run':
257	self.current_datainfo.run_name[data_point] = name
258	self.current_datainfo.run.append(data_point)
259	elif tagname == 'Title':
260	self.current_datainfo.title = data_point
261	elif tagname == 'SASnote':
262	self.current_datainfo.notes.append(data_point)
263
264	# I and Q - 1D data
265	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
266	unit_list = unit.split("\|")
267	if len(unit_list) > 1:
268	self.current_dataset.yaxis(unit_list[0].strip(),
269	unit_list[1].strip())
270	else:
271	self.current_dataset.yaxis("Intensity", unit)
272	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
273	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
274	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
275	elif tagname == 'Q':
276	unit_list = unit.split("\|")
277	if len(unit_list) > 1:
278	self.current_dataset.xaxis(unit_list[0].strip(),
279	unit_list[1].strip())
280	else:
281	self.current_dataset.xaxis("Q", unit)
282	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
283	elif tagname == 'Qdev':
284	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
285	elif tagname == 'dQw':
286	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
287	elif tagname == 'dQl':
288	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
289	elif tagname == 'Qmean':
290	pass
291	elif tagname == 'Shadowfactor':
292	pass
293	elif tagname == 'Sesans':
294	self.current_datainfo.isSesans = bool(data_point)
295	elif tagname == 'yacceptance':
296	self.current_datainfo.sample.yacceptance = (data_point, unit)
297	elif tagname == 'zacceptance':
298	self.current_datainfo.sample.zacceptance = (data_point, unit)
299
300	# I and Qx, Qy - 2D data
301	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
302	self.current_dataset.yaxis("Intensity", unit)
303	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
304	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
305	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
306	elif tagname == 'Qx':
307	self.current_dataset.xaxis("Qx", unit)
308	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
309	elif tagname == 'Qy':
310	self.current_dataset.yaxis("Qy", unit)
311	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
312	elif tagname == 'Qxdev':
313	self.current_dataset.xaxis("Qxdev", unit)
314	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
315	elif tagname == 'Qydev':
316	self.current_dataset.yaxis("Qydev", unit)
317	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
318	elif tagname == 'Mask':
319	inter = [item == "1" for item in data_point.split(",")]
320	self.current_dataset.mask = np.asarray(inter, dtype=bool)
321
322	# Sample Information
323	elif tagname == 'ID' and self.parent_class == 'SASsample':
324	self.current_datainfo.sample.ID = data_point
325	elif tagname == 'Title' and self.parent_class == 'SASsample':
326	self.current_datainfo.sample.name = data_point
327	elif tagname == 'thickness' and self.parent_class == 'SASsample':
328	self.current_datainfo.sample.thickness = data_point
329	self.current_datainfo.sample.thickness_unit = unit
330	elif tagname == 'transmission' and self.parent_class == 'SASsample':
331	self.current_datainfo.sample.transmission = data_point
332	elif tagname == 'temperature' and self.parent_class == 'SASsample':
333	self.current_datainfo.sample.temperature = data_point
334	self.current_datainfo.sample.temperature_unit = unit
335	elif tagname == 'details' and self.parent_class == 'SASsample':
336	self.current_datainfo.sample.details.append(data_point)
337	elif tagname == 'x' and self.parent_class == 'position':
338	self.current_datainfo.sample.position.x = data_point
339	self.current_datainfo.sample.position_unit = unit
340	elif tagname == 'y' and self.parent_class == 'position':
341	self.current_datainfo.sample.position.y = data_point
342	self.current_datainfo.sample.position_unit = unit
343	elif tagname == 'z' and self.parent_class == 'position':
344	self.current_datainfo.sample.position.z = data_point
345	self.current_datainfo.sample.position_unit = unit
346	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
347	self.current_datainfo.sample.orientation.x = data_point
348	self.current_datainfo.sample.orientation_unit = unit
349	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
350	self.current_datainfo.sample.orientation.y = data_point
351	self.current_datainfo.sample.orientation_unit = unit
352	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
353	self.current_datainfo.sample.orientation.z = data_point
354	self.current_datainfo.sample.orientation_unit = unit
355
356	# Instrumental Information
357	elif tagname == 'name' and self.parent_class == 'SASinstrument':
358	self.current_datainfo.instrument = data_point
359	# Detector Information
360	elif tagname == 'name' and self.parent_class == 'SASdetector':
361	self.detector.name = data_point
362	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
363	self.detector.distance = data_point
364	self.detector.distance_unit = unit
365	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
366	self.detector.slit_length = data_point
367	self.detector.slit_length_unit = unit
368	elif tagname == 'x' and self.parent_class == 'offset':
369	self.detector.offset.x = data_point
370	self.detector.offset_unit = unit
371	elif tagname == 'y' and self.parent_class == 'offset':
372	self.detector.offset.y = data_point
373	self.detector.offset_unit = unit
374	elif tagname == 'z' and self.parent_class == 'offset':
375	self.detector.offset.z = data_point
376	self.detector.offset_unit = unit
377	elif tagname == 'x' and self.parent_class == 'beam_center':
378	self.detector.beam_center.x = data_point
379	self.detector.beam_center_unit = unit
380	elif tagname == 'y' and self.parent_class == 'beam_center':
381	self.detector.beam_center.y = data_point
382	self.detector.beam_center_unit = unit
383	elif tagname == 'z' and self.parent_class == 'beam_center':
384	self.detector.beam_center.z = data_point
385	self.detector.beam_center_unit = unit
386	elif tagname == 'x' and self.parent_class == 'pixel_size':
387	self.detector.pixel_size.x = data_point
388	self.detector.pixel_size_unit = unit
389	elif tagname == 'y' and self.parent_class == 'pixel_size':
390	self.detector.pixel_size.y = data_point
391	self.detector.pixel_size_unit = unit
392	elif tagname == 'z' and self.parent_class == 'pixel_size':
393	self.detector.pixel_size.z = data_point
394	self.detector.pixel_size_unit = unit
395	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
396	self.detector.orientation.x = data_point
397	self.detector.orientation_unit = unit
398	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
399	self.detector.orientation.y = data_point
400	self.detector.orientation_unit = unit
401	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
402	self.detector.orientation.z = data_point
403	self.detector.orientation_unit = unit
404	# Collimation and Aperture
405	elif tagname == 'length' and self.parent_class == 'SAScollimation':
406	self.collimation.length = data_point
407	self.collimation.length_unit = unit
408	elif tagname == 'name' and self.parent_class == 'SAScollimation':
409	self.collimation.name = data_point
410	elif tagname == 'distance' and self.parent_class == 'aperture':
411	self.aperture.distance = data_point
412	self.aperture.distance_unit = unit
413	elif tagname == 'x' and self.parent_class == 'size':
414	self.aperture.size.x = data_point
415	self.collimation.size_unit = unit
416	elif tagname == 'y' and self.parent_class == 'size':
417	self.aperture.size.y = data_point
418	self.collimation.size_unit = unit
419	elif tagname == 'z' and self.parent_class == 'size':
420	self.aperture.size.z = data_point
421	self.collimation.size_unit = unit
422
423	# Process Information
424	elif tagname == 'name' and self.parent_class == 'SASprocess':
425	self.process.name = data_point
426	elif tagname == 'description' and self.parent_class == 'SASprocess':
427	self.process.description = data_point
428	elif tagname == 'date' and self.parent_class == 'SASprocess':
429	try:
430	self.process.date = datetime.datetime.fromtimestamp(data_point)
431	except:
432	self.process.date = data_point
433	elif tagname == 'SASprocessnote':
434	self.process.notes.append(data_point)
435	elif tagname == 'term' and self.parent_class == 'SASprocess':
436	unit = attr.get("unit", "")
437	dic = {}
438	dic["name"] = name
439	dic["value"] = data_point
440	dic["unit"] = unit
441	self.process.term.append(dic)
442
443	# Transmission Spectrum
444	elif tagname == 'T' and self.parent_class == 'Tdata':
445	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
446	self.transspectrum.transmission_unit = unit
447	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
448	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
449	self.transspectrum.transmission_deviation_unit = unit
450	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
451	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
452	self.transspectrum.wavelength_unit = unit
453
454	# Source Information
455	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
456	self.current_datainfo.source.wavelength = data_point
457	self.current_datainfo.source.wavelength_unit = unit
458	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
459	self.current_datainfo.source.wavelength_min = data_point
460	self.current_datainfo.source.wavelength_min_unit = unit
461	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
462	self.current_datainfo.source.wavelength_max = data_point
463	self.current_datainfo.source.wavelength_max_unit = unit
464	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
465	self.current_datainfo.source.wavelength_spread = data_point
466	self.current_datainfo.source.wavelength_spread_unit = unit
467	elif tagname == 'x' and self.parent_class == 'beam_size':
468	self.current_datainfo.source.beam_size.x = data_point
469	self.current_datainfo.source.beam_size_unit = unit
470	elif tagname == 'y' and self.parent_class == 'beam_size':
471	self.current_datainfo.source.beam_size.y = data_point
472	self.current_datainfo.source.beam_size_unit = unit
473	elif tagname == 'z' and self.parent_class == 'pixel_size':
474	self.current_datainfo.source.data_point.z = data_point
475	self.current_datainfo.source.beam_size_unit = unit
476	elif tagname == 'radiation' and self.parent_class == 'SASsource':
477	self.current_datainfo.source.radiation = data_point
478	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
479	self.current_datainfo.source.beam_shape = data_point
480
481	# Everything else goes in meta_data
482	else:
483	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
484	self.current_datainfo.meta_data[new_key] = data_point
485
486	self.names.remove(tagname_original)
487	length = 0
488	if len(self.names) > 1:
489	length = len(self.names) - 1
490	self.parent_class = self.names[length]
491	if not self._is_call_local() and not recurse:
492	self.frm = ""
493	self.add_data_set()
494	empty = None
495	return self.output[0], empty
496
497
498	def _is_call_local(self):
499	"""
500
501	"""
502	if self.frm == "":
503	inter = inspect.stack()
504	self.frm = inter[2]
505	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
506	mod_name = mod_name.replace(".py", "")
507	mod = mod_name.split("sas/")
508	mod_name = mod[1]
509	if mod_name != "sascalc/dataloader/readers/cansas_reader":
510	return False
511	return True
512
513	def is_cansas(self, ext="xml"):
514	"""
515	Checks to see if the xml file is a CanSAS file
516
517	:param ext: The file extension of the data file
518	"""
519	if self.validate_xml():
520	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
521	value = self.xmlroot.get(name)
522	if CANSAS_NS.get(self.cansas_version).get("ns") == \
523	value.rsplit(" ")[0]:
524	return True
525	if ext == "svs":
526	return True
527	raise RuntimeError
528
529	def load_file_and_schema(self, xml_file, schema_path=""):
530	"""
531	Loads the file and associates a schema, if a schema is passed in or if one already exists
532
533	:param xml_file: The xml file path sent to Reader.read
534	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
535	"""
536	base_name = xml_reader.__file__
537	base_name = base_name.replace("\\", "/")
538	base = base_name.split("/sas/")[0]
539
540	# Load in xml file and get the cansas version from the header
541	from lxml import etree
542	try:
543	self.set_xml_file(xml_file)
544	except etree.XMLSyntaxError:
545	msg = "Cansas cannot load this file"
546	raise FileContentsException, msg
547	self.cansas_version = self.xmlroot.get("version", "1.0")
548
549	# Generic values for the cansas file based on the version
550	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
551	if schema_path == "":
552	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
553	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
554
555	# Link a schema to the XML file.
556	self.set_schema(schema_path)
557
558	def add_data_set(self):
559	"""
560	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
561	private method to generate a new data set.
562
563	:param key: NeXus group name for current tree level
564	"""
565
566	if self.current_datainfo and self.current_dataset:
567	self._final_cleanup()
568	self.data = []
569	self.current_datainfo = DataInfo()
570
571	def _initialize_new_data_set(self, node=None):
572	"""
573	A private class method to generate a new 1D data object.
574	Outside methods should call add_data_set() to be sure any existing data is stored properly.
575
576	:param node: XML node to determine if 1D or 2D data
577	"""
578	x = np.array(0)
579	y = np.array(0)
580	for child in node:
581	if child.tag.replace(self.base_ns, "") == "Idata":
582	for i_child in child:
583	if i_child.tag.replace(self.base_ns, "") == "Qx":
584	self.current_dataset = plottable_2D()
585	return
586	self.current_dataset = plottable_1D(x, y)
587
588	def add_intermediate(self):
589	"""
590	This method stores any intermediate objects within the final data set after fully reading the set.
591
592	:param parent: The NXclass name for the h5py Group object that just finished being processed
593	"""
594
595	if self.parent_class == 'SASprocess':
596	self.current_datainfo.process.append(self.process)
597	self.process = Process()
598	elif self.parent_class == 'SASdetector':
599	self.current_datainfo.detector.append(self.detector)
600	self.detector = Detector()
601	elif self.parent_class == 'SAStransmission_spectrum':
602	self.current_datainfo.trans_spectrum.append(self.transspectrum)
603	self.transspectrum = TransmissionSpectrum()
604	elif self.parent_class == 'SAScollimation':
605	self.current_datainfo.collimation.append(self.collimation)
606	self.collimation = Collimation()
607	elif self.parent_class == 'aperture':
608	self.collimation.aperture.append(self.aperture)
609	self.aperture = Aperture()
610	elif self.parent_class == 'SASdata':
611	self._check_for_empty_resolution()
612	self.data.append(self.current_dataset)
613
614	def _final_cleanup(self):
615	"""
616	Final cleanup of the Data1D object to be sure it has all the
617	appropriate information needed for perspectives
618	"""
619
620	# Append errors to dataset and reset class errors
621	self.current_datainfo.errors = set()
622	for error in self.errors:
623	self.current_datainfo.errors.add(error)
624	self.errors.clear()
625
626	# Combine all plottables with datainfo and append each to output
627	# Type cast data arrays to float64 and find min/max as appropriate
628	for dataset in self.data:
629	if isinstance(dataset, plottable_1D):
630	if dataset.x is not None:
631	dataset.x = np.delete(dataset.x, [0])
632	dataset.x = dataset.x.astype(np.float64)
633	dataset.xmin = np.min(dataset.x)
634	dataset.xmax = np.max(dataset.x)
635	if dataset.y is not None:
636	dataset.y = np.delete(dataset.y, [0])
637	dataset.y = dataset.y.astype(np.float64)
638	dataset.ymin = np.min(dataset.y)
639	dataset.ymax = np.max(dataset.y)
640	if dataset.dx is not None:
641	dataset.dx = np.delete(dataset.dx, [0])
642	dataset.dx = dataset.dx.astype(np.float64)
643	if dataset.dxl is not None:
644	dataset.dxl = np.delete(dataset.dxl, [0])
645	dataset.dxl = dataset.dxl.astype(np.float64)
646	if dataset.dxw is not None:
647	dataset.dxw = np.delete(dataset.dxw, [0])
648	dataset.dxw = dataset.dxw.astype(np.float64)
649	if dataset.dy is not None:
650	dataset.dy = np.delete(dataset.dy, [0])
651	dataset.dy = dataset.dy.astype(np.float64)
652	np.trim_zeros(dataset.x)
653	np.trim_zeros(dataset.y)
654	np.trim_zeros(dataset.dy)
655	elif isinstance(dataset, plottable_2D):
656	dataset.data = dataset.data.astype(np.float64)
657	dataset.qx_data = dataset.qx_data.astype(np.float64)
658	dataset.xmin = np.min(dataset.qx_data)
659	dataset.xmax = np.max(dataset.qx_data)
660	dataset.qy_data = dataset.qy_data.astype(np.float64)
661	dataset.ymin = np.min(dataset.qy_data)
662	dataset.ymax = np.max(dataset.qy_data)
663	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
664	+ dataset.qy_data * dataset.qy_data)
665	if dataset.err_data is not None:
666	dataset.err_data = dataset.err_data.astype(np.float64)
667	if dataset.dqx_data is not None:
668	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
669	if dataset.dqy_data is not None:
670	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
671	if dataset.mask is not None:
672	dataset.mask = dataset.mask.astype(dtype=bool)
673
674	if len(dataset.shape) == 2:
675	n_rows, n_cols = dataset.shape
676	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
677	dataset.x_bins = dataset.qx_data[:int(n_cols)]
678	dataset.data = dataset.data.flatten()
679	else:
680	dataset.y_bins = []
681	dataset.x_bins = []
682	dataset.data = dataset.data.flatten()
683
684	final_dataset = combine_data(dataset, self.current_datainfo)
685	self.output.append(final_dataset)
686
687	def _create_unique_key(self, dictionary, name, numb=0):
688	"""
689	Create a unique key value for any dictionary to prevent overwriting
690	Recurse until a unique key value is found.
691
692	:param dictionary: A dictionary with any number of entries
693	:param name: The index of the item to be added to dictionary
694	:param numb: The number to be appended to the name, starts at 0
695	"""
696	if dictionary.get(name) is not None:
697	numb += 1
698	name = name.split("_")[0]
699	name += "_{0}".format(numb)
700	name = self._create_unique_key(dictionary, name, numb)
701	return name
702
703	def _get_node_value(self, node, tagname):
704	"""
705	Get the value of a node and any applicable units
706
707	:param node: The XML node to get the value of
708	:param tagname: The tagname of the node
709	"""
710	#Get the text from the node and convert all whitespace to spaces
711	units = ''
712	node_value = node.text
713	if node_value is not None:
714	node_value = ' '.join(node_value.split())
715	else:
716	node_value = ""
717
718	# If the value is a float, compile with units.
719	if self.ns_list.ns_datatype == "float":
720	# If an empty value is given, set as zero.
721	if node_value is None or node_value.isspace() \
722	or node_value.lower() == "nan":
723	node_value = "0.0"
724	#Convert the value to the base units
725	node_value, units = self._unit_conversion(node, tagname, node_value)
726
727	# If the value is a timestamp, convert to a datetime object
728	elif self.ns_list.ns_datatype == "timestamp":
729	if node_value is None or node_value.isspace():
730	pass
731	else:
732	try:
733	node_value = \
734	datetime.datetime.fromtimestamp(node_value)
735	except ValueError:
736	node_value = None
737	return node_value, units
738
739	def _unit_conversion(self, node, tagname, node_value):
740	"""
741	A unit converter method used to convert the data included in the file
742	to the default units listed in data_info
743
744	:param node: XML node
745	:param tagname: name of the node
746	:param node_value: The value of the current dom node
747	"""
748	attr = node.attrib
749	value_unit = ''
750	err_msg = None
751	default_unit = None
752	if not isinstance(node_value, float):
753	node_value = float(node_value)
754	if 'unit' in attr and attr.get('unit') is not None:
755	try:
756	local_unit = attr['unit']
757	unitname = self.ns_list.current_level.get("unit", "")
758	if "SASdetector" in self.names:
759	save_in = "detector"
760	elif "aperture" in self.names:
761	save_in = "aperture"
762	elif "SAScollimation" in self.names:
763	save_in = "collimation"
764	elif "SAStransmission_spectrum" in self.names:
765	save_in = "transspectrum"
766	elif "SASdata" in self.names:
767	x = np.zeros(1)
768	y = np.zeros(1)
769	self.current_data1d = Data1D(x, y)
770	save_in = "current_data1d"
771	elif "SASsource" in self.names:
772	save_in = "current_datainfo.source"
773	elif "SASsample" in self.names:
774	save_in = "current_datainfo.sample"
775	elif "SASprocess" in self.names:
776	save_in = "process"
777	else:
778	save_in = "current_datainfo"
779	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
780	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
781	and local_unit.lower() != "none":
782	if HAS_CONVERTER == True:
783	# Check local units - bad units raise KeyError
784	data_conv_q = Converter(local_unit)
785	value_unit = default_unit
786	node_value = data_conv_q(node_value, units=default_unit)
787	else:
788	value_unit = local_unit
789	err_msg = "Unit converter is not available.\n"
790	else:
791	value_unit = local_unit
792	except KeyError:
793	err_msg = "CanSAS reader: unexpected "
794	err_msg += "\"{0}\" unit [{1}]; "
795	err_msg = err_msg.format(tagname, local_unit)
796	err_msg += "expecting [{0}]".format(default_unit)
797	value_unit = local_unit
798	except:
799	err_msg = "CanSAS reader: unknown error converting "
800	err_msg += "\"{0}\" unit [{1}]"
801	err_msg = err_msg.format(tagname, local_unit)
802	value_unit = local_unit
803	elif 'unit' in attr:
804	value_unit = attr['unit']
805	if err_msg:
806	self.errors.add(err_msg)
807	return node_value, value_unit
808
809	def _check_for_empty_data(self):
810	"""
811	Creates an empty data set if no data is passed to the reader
812
813	:param data1d: presumably a Data1D object
814	"""
815	if self.current_dataset is None:
816	x_vals = np.empty(0)
817	y_vals = np.empty(0)
818	dx_vals = np.empty(0)
819	dy_vals = np.empty(0)
820	dxl = np.empty(0)
821	dxw = np.empty(0)
822	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
823	self.current_dataset.dxl = dxl
824	self.current_dataset.dxw = dxw
825
826	def _check_for_empty_resolution(self):
827	"""
828	A method to check all resolution data sets are the same size as I and Q
829	"""
830	if isinstance(self.current_dataset, plottable_1D):
831	dql_exists = False
832	dqw_exists = False
833	dq_exists = False
834	di_exists = False
835	if self.current_dataset.dxl is not None:
836	dql_exists = True
837	if self.current_dataset.dxw is not None:
838	dqw_exists = True
839	if self.current_dataset.dx is not None:
840	dq_exists = True
841	if self.current_dataset.dy is not None:
842	di_exists = True
843	if dqw_exists and not dql_exists:
844	array_size = self.current_dataset.dxw.size - 1
845	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
846	np.zeros([array_size]))
847	elif dql_exists and not dqw_exists:
848	array_size = self.current_dataset.dxl.size - 1
849	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
850	np.zeros([array_size]))
851	elif not dql_exists and not dqw_exists and not dq_exists:
852	array_size = self.current_dataset.x.size - 1
853	self.current_dataset.dx = np.append(self.current_dataset.dx,
854	np.zeros([array_size]))
855	if not di_exists:
856	array_size = self.current_dataset.y.size - 1
857	self.current_dataset.dy = np.append(self.current_dataset.dy,
858	np.zeros([array_size]))
859	elif isinstance(self.current_dataset, plottable_2D):
860	dqx_exists = False
861	dqy_exists = False
862	di_exists = False
863	mask_exists = False
864	if self.current_dataset.dqx_data is not None:
865	dqx_exists = True
866	if self.current_dataset.dqy_data is not None:
867	dqy_exists = True
868	if self.current_dataset.err_data is not None:
869	di_exists = True
870	if self.current_dataset.mask is not None:
871	mask_exists = True
872	if not dqy_exists:
873	array_size = self.current_dataset.qy_data.size - 1
874	self.current_dataset.dqy_data = np.append(
875	self.current_dataset.dqy_data, np.zeros([array_size]))
876	if not dqx_exists:
877	array_size = self.current_dataset.qx_data.size - 1
878	self.current_dataset.dqx_data = np.append(
879	self.current_dataset.dqx_data, np.zeros([array_size]))
880	if not di_exists:
881	array_size = self.current_dataset.data.size - 1
882	self.current_dataset.err_data = np.append(
883	self.current_dataset.err_data, np.zeros([array_size]))
884	if not mask_exists:
885	array_size = self.current_dataset.data.size - 1
886	self.current_dataset.mask = np.append(
887	self.current_dataset.mask,
888	np.ones([array_size] ,dtype=bool))
889
890	####### All methods below are for writing CanSAS XML files #######
891
892	def write(self, filename, datainfo):
893	"""
894	Write the content of a Data1D as a CanSAS XML file
895
896	:param filename: name of the file to write
897	:param datainfo: Data1D object
898	"""
899	# Create XML document
900	doc, _ = self._to_xml_doc(datainfo)
901	# Write the file
902	file_ref = open(filename, 'w')
903	if self.encoding is None:
904	self.encoding = "UTF-8"
905	doc.write(file_ref, encoding=self.encoding,
906	pretty_print=True, xml_declaration=True)
907	file_ref.close()
908
909	def _to_xml_doc(self, datainfo):
910	"""
911	Create an XML document to contain the content of a Data1D
912
913	:param datainfo: Data1D object
914	"""
915	is_2d = False
916	if issubclass(datainfo.__class__, Data2D):
917	is_2d = True
918
919	# Get PIs and create root element
920	pi_string = self._get_pi_string()
921	# Define namespaces and create SASroot object
922	main_node = self._create_main_node()
923	# Create ElementTree, append SASroot and apply processing instructions
924	base_string = pi_string + self.to_string(main_node)
925	base_element = self.create_element_from_string(base_string)
926	doc = self.create_tree(base_element)
927	# Create SASentry Element
928	entry_node = self.create_element("SASentry")
929	root = doc.getroot()
930	root.append(entry_node)
931
932	# Add Title to SASentry
933	self.write_node(entry_node, "Title", datainfo.title)
934	# Add Run to SASentry
935	self._write_run_names(datainfo, entry_node)
936	# Add Data info to SASEntry
937	if is_2d:
938	self._write_data_2d(datainfo, entry_node)
939	else:
940	self._write_data(datainfo, entry_node)
941	# Transmission Spectrum Info
942	# TODO: fix the writer to linearize all data, including T_spectrum
943	# self._write_trans_spectrum(datainfo, entry_node)
944	# Sample info
945	self._write_sample_info(datainfo, entry_node)
946	# Instrument info
947	instr = self._write_instrument(datainfo, entry_node)
948	# Source
949	self._write_source(datainfo, instr)
950	# Collimation
951	self._write_collimation(datainfo, instr)
952	# Detectors
953	self._write_detectors(datainfo, instr)
954	# Processes info
955	self._write_process_notes(datainfo, entry_node)
956	# Note info
957	self._write_notes(datainfo, entry_node)
958	# Return the document, and the SASentry node associated with
959	# the data we just wrote
960	# If the calling function was not the cansas reader, return a minidom
961	# object rather than an lxml object.
962	self.frm = inspect.stack()[1]
963	doc, entry_node = self._check_origin(entry_node, doc)
964	return doc, entry_node
965
966	def write_node(self, parent, name, value, attr=None):
967	"""
968	:param doc: document DOM
969	:param parent: parent node
970	:param name: tag of the element
971	:param value: value of the child text node
972	:param attr: attribute dictionary
973
974	:return: True if something was appended, otherwise False
975	"""
976	if value is not None:
977	parent = self.ebuilder(parent, name, value, attr)
978	return True
979	return False
980
981	def _get_pi_string(self):
982	"""
983	Creates the processing instructions header for writing to file
984	"""
985	pis = self.return_processing_instructions()
986	if len(pis) > 0:
987	pi_tree = self.create_tree(pis[0])
988	i = 1
989	for i in range(1, len(pis) - 1):
990	pi_tree = self.append(pis[i], pi_tree)
991	pi_string = self.to_string(pi_tree)
992	else:
993	pi_string = ""
994	return pi_string
995
996	def _create_main_node(self):
997	"""
998	Creates the primary xml header used when writing to file
999	"""
1000	xsi = "http://www.w3.org/2001/XMLSchema-instance"
1001	version = self.cansas_version
1002	n_s = CANSAS_NS.get(version).get("ns")
1003	if version == "1.1":
1004	url = "http://www.cansas.org/formats/1.1/"
1005	else:
1006	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
1007	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1008	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1009	"version" : version}
1010	nsmap = {'xsi' : xsi, None: n_s}
1011
1012	main_node = self.create_element("{" + n_s + "}SASroot",
1013	attrib=attrib, nsmap=nsmap)
1014	return main_node
1015
1016	def _write_run_names(self, datainfo, entry_node):
1017	"""
1018	Writes the run names to the XML file
1019
1020	:param datainfo: The Data1D object the information is coming from
1021	:param entry_node: lxml node ElementTree object to be appended to
1022	"""
1023	if datainfo.run is None or datainfo.run == []:
1024	datainfo.run.append(RUN_NAME_DEFAULT)
1025	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1026	for item in datainfo.run:
1027	runname = {}
1028	if item in datainfo.run_name and \
1029	len(str(datainfo.run_name[item])) > 1:
1030	runname = {'name': datainfo.run_name[item]}
1031	self.write_node(entry_node, "Run", item, runname)
1032
1033	def _write_data(self, datainfo, entry_node):
1034	"""
1035	Writes 1D I and Q data to the XML file
1036
1037	:param datainfo: The Data1D object the information is coming from
1038	:param entry_node: lxml node ElementTree object to be appended to
1039	"""
1040	node = self.create_element("SASdata")
1041	self.append(node, entry_node)
1042
1043	for i in range(len(datainfo.x)):
1044	point = self.create_element("Idata")
1045	node.append(point)
1046	self.write_node(point, "Q", datainfo.x[i],
1047	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1048	if len(datainfo.y) >= i:
1049	self.write_node(point, "I", datainfo.y[i],
1050	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1051	if datainfo.dy is not None and len(datainfo.dy) > i:
1052	self.write_node(point, "Idev", datainfo.dy[i],
1053	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1054	if datainfo.dx is not None and len(datainfo.dx) > i:
1055	self.write_node(point, "Qdev", datainfo.dx[i],
1056	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1057	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1058	self.write_node(point, "dQw", datainfo.dxw[i],
1059	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1060	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1061	self.write_node(point, "dQl", datainfo.dxl[i],
1062	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1063	if datainfo.isSesans:
1064	sesans = self.create_element("Sesans")
1065	sesans.text = str(datainfo.isSesans)
1066	node.append(sesans)
1067	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
1068	{'unit': datainfo.sample.yacceptance[1]})
1069	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1070	{'unit': datainfo.sample.zacceptance[1]})
1071
1072
1073	def _write_data_2d(self, datainfo, entry_node):
1074	"""
1075	Writes 2D data to the XML file
1076
1077	:param datainfo: The Data2D object the information is coming from
1078	:param entry_node: lxml node ElementTree object to be appended to
1079	"""
1080	attr = {}
1081	if datainfo.data.shape:
1082	attr["x_bins"] = str(len(datainfo.x_bins))
1083	attr["y_bins"] = str(len(datainfo.y_bins))
1084	node = self.create_element("SASdata", attr)
1085	self.append(node, entry_node)
1086
1087	point = self.create_element("Idata")
1088	node.append(point)
1089	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1090	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1091	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1092
1093	self.write_node(point, "Qx", qx,
1094	{'unit': datainfo._xunit})
1095	self.write_node(point, "Qy", qy,
1096	{'unit': datainfo._yunit})
1097	self.write_node(point, "I", intensity,
1098	{'unit': datainfo._zunit})
1099	if datainfo.err_data is not None:
1100	err = ','.join([str(datainfo.err_data[i]) for i in
1101	xrange(len(datainfo.err_data))])
1102	self.write_node(point, "Idev", err,
1103	{'unit': datainfo._zunit})
1104	if datainfo.dqy_data is not None:
1105	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1106	xrange(len(datainfo.dqy_data))])
1107	self.write_node(point, "Qydev", dqy,
1108	{'unit': datainfo._yunit})
1109	if datainfo.dqx_data is not None:
1110	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1111	xrange(len(datainfo.dqx_data))])
1112	self.write_node(point, "Qxdev", dqx,
1113	{'unit': datainfo._xunit})
1114	if datainfo.mask is not None:
1115	mask = ','.join(
1116	["1" if datainfo.mask[i] else "0"
1117	for i in xrange(len(datainfo.mask))])
1118	self.write_node(point, "Mask", mask)
1119
1120	def _write_trans_spectrum(self, datainfo, entry_node):
1121	"""
1122	Writes the transmission spectrum data to the XML file
1123
1124	:param datainfo: The Data1D object the information is coming from
1125	:param entry_node: lxml node ElementTree object to be appended to
1126	"""
1127	for i in range(len(datainfo.trans_spectrum)):
1128	spectrum = datainfo.trans_spectrum[i]
1129	node = self.create_element("SAStransmission_spectrum",
1130	{"name" : spectrum.name})
1131	self.append(node, entry_node)
1132	if isinstance(spectrum.timestamp, datetime.datetime):
1133	node.setAttribute("timestamp", spectrum.timestamp)
1134	for i in range(len(spectrum.wavelength)):
1135	point = self.create_element("Tdata")
1136	node.append(point)
1137	self.write_node(point, "Lambda", spectrum.wavelength[i],
1138	{'unit': spectrum.wavelength_unit})
1139	self.write_node(point, "T", spectrum.transmission[i],
1140	{'unit': spectrum.transmission_unit})
1141	if spectrum.transmission_deviation is not None \
1142	and len(spectrum.transmission_deviation) >= i:
1143	self.write_node(point, "Tdev",
1144	spectrum.transmission_deviation[i],
1145	{'unit':
1146	spectrum.transmission_deviation_unit})
1147
1148	def _write_sample_info(self, datainfo, entry_node):
1149	"""
1150	Writes the sample information to the XML file
1151
1152	:param datainfo: The Data1D object the information is coming from
1153	:param entry_node: lxml node ElementTree object to be appended to
1154	"""
1155	sample = self.create_element("SASsample")
1156	if datainfo.sample.name is not None:
1157	self.write_attribute(sample, "name",
1158	str(datainfo.sample.name))
1159	self.append(sample, entry_node)
1160	self.write_node(sample, "ID", str(datainfo.sample.ID))
1161	self.write_node(sample, "thickness", datainfo.sample.thickness,
1162	{"unit": datainfo.sample.thickness_unit})
1163	self.write_node(sample, "transmission", datainfo.sample.transmission)
1164	self.write_node(sample, "temperature", datainfo.sample.temperature,
1165	{"unit": datainfo.sample.temperature_unit})
1166
1167	pos = self.create_element("position")
1168	written = self.write_node(pos,
1169	"x",
1170	datainfo.sample.position.x,
1171	{"unit": datainfo.sample.position_unit})
1172	written = written \| self.write_node( \
1173	pos, "y", datainfo.sample.position.y,
1174	{"unit": datainfo.sample.position_unit})
1175	written = written \| self.write_node( \
1176	pos, "z", datainfo.sample.position.z,
1177	{"unit": datainfo.sample.position_unit})
1178	if written == True:
1179	self.append(pos, sample)
1180
1181	ori = self.create_element("orientation")
1182	written = self.write_node(ori, "roll",
1183	datainfo.sample.orientation.x,
1184	{"unit": datainfo.sample.orientation_unit})
1185	written = written \| self.write_node( \
1186	ori, "pitch", datainfo.sample.orientation.y,
1187	{"unit": datainfo.sample.orientation_unit})
1188	written = written \| self.write_node( \
1189	ori, "yaw", datainfo.sample.orientation.z,
1190	{"unit": datainfo.sample.orientation_unit})
1191	if written == True:
1192	self.append(ori, sample)
1193
1194	for item in datainfo.sample.details:
1195	self.write_node(sample, "details", item)
1196
1197	def _write_instrument(self, datainfo, entry_node):
1198	"""
1199	Writes the instrumental information to the XML file
1200
1201	:param datainfo: The Data1D object the information is coming from
1202	:param entry_node: lxml node ElementTree object to be appended to
1203	"""
1204	instr = self.create_element("SASinstrument")
1205	self.append(instr, entry_node)
1206	self.write_node(instr, "name", datainfo.instrument)
1207	return instr
1208
1209	def _write_source(self, datainfo, instr):
1210	"""
1211	Writes the source information to the XML file
1212
1213	:param datainfo: The Data1D object the information is coming from
1214	:param instr: instrument node to be appended to
1215	"""
1216	source = self.create_element("SASsource")
1217	if datainfo.source.name is not None:
1218	self.write_attribute(source, "name",
1219	str(datainfo.source.name))
1220	self.append(source, instr)
1221	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1222	datainfo.source.radiation = "neutron"
1223	self.write_node(source, "radiation", datainfo.source.radiation)
1224
1225	size = self.create_element("beam_size")
1226	if datainfo.source.beam_size_name is not None:
1227	self.write_attribute(size, "name",
1228	str(datainfo.source.beam_size_name))
1229	written = self.write_node( \
1230	size, "x", datainfo.source.beam_size.x,
1231	{"unit": datainfo.source.beam_size_unit})
1232	written = written \| self.write_node( \
1233	size, "y", datainfo.source.beam_size.y,
1234	{"unit": datainfo.source.beam_size_unit})
1235	written = written \| self.write_node( \
1236	size, "z", datainfo.source.beam_size.z,
1237	{"unit": datainfo.source.beam_size_unit})
1238	if written == True:
1239	self.append(size, source)
1240
1241	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1242	self.write_node(source, "wavelength",
1243	datainfo.source.wavelength,
1244	{"unit": datainfo.source.wavelength_unit})
1245	self.write_node(source, "wavelength_min",
1246	datainfo.source.wavelength_min,
1247	{"unit": datainfo.source.wavelength_min_unit})
1248	self.write_node(source, "wavelength_max",
1249	datainfo.source.wavelength_max,
1250	{"unit": datainfo.source.wavelength_max_unit})
1251	self.write_node(source, "wavelength_spread",
1252	datainfo.source.wavelength_spread,
1253	{"unit": datainfo.source.wavelength_spread_unit})
1254
1255	def _write_collimation(self, datainfo, instr):
1256	"""
1257	Writes the collimation information to the XML file
1258
1259	:param datainfo: The Data1D object the information is coming from
1260	:param instr: lxml node ElementTree object to be appended to
1261	"""
1262	if datainfo.collimation == [] or datainfo.collimation is None:
1263	coll = Collimation()
1264	datainfo.collimation.append(coll)
1265	for item in datainfo.collimation:
1266	coll = self.create_element("SAScollimation")
1267	if item.name is not None:
1268	self.write_attribute(coll, "name", str(item.name))
1269	self.append(coll, instr)
1270
1271	self.write_node(coll, "length", item.length,
1272	{"unit": item.length_unit})
1273
1274	for aperture in item.aperture:
1275	apert = self.create_element("aperture")
1276	if aperture.name is not None:
1277	self.write_attribute(apert, "name", str(aperture.name))
1278	if aperture.type is not None:
1279	self.write_attribute(apert, "type", str(aperture.type))
1280	self.append(apert, coll)
1281
1282	size = self.create_element("size")
1283	if aperture.size_name is not None:
1284	self.write_attribute(size, "name",
1285	str(aperture.size_name))
1286	written = self.write_node(size, "x", aperture.size.x,
1287	{"unit": aperture.size_unit})
1288	written = written \| self.write_node( \
1289	size, "y", aperture.size.y,
1290	{"unit": aperture.size_unit})
1291	written = written \| self.write_node( \
1292	size, "z", aperture.size.z,
1293	{"unit": aperture.size_unit})
1294	if written == True:
1295	self.append(size, apert)
1296
1297	self.write_node(apert, "distance", aperture.distance,
1298	{"unit": aperture.distance_unit})
1299
1300	def _write_detectors(self, datainfo, instr):
1301	"""
1302	Writes the detector information to the XML file
1303
1304	:param datainfo: The Data1D object the information is coming from
1305	:param inst: lxml instrument node to be appended to
1306	"""
1307	if datainfo.detector is None or datainfo.detector == []:
1308	det = Detector()
1309	det.name = ""
1310	datainfo.detector.append(det)
1311
1312	for item in datainfo.detector:
1313	det = self.create_element("SASdetector")
1314	written = self.write_node(det, "name", item.name)
1315	written = written \| self.write_node(det, "SDD", item.distance,
1316	{"unit": item.distance_unit})
1317	if written == True:
1318	self.append(det, instr)
1319
1320	off = self.create_element("offset")
1321	written = self.write_node(off, "x", item.offset.x,
1322	{"unit": item.offset_unit})
1323	written = written \| self.write_node(off, "y", item.offset.y,
1324	{"unit": item.offset_unit})
1325	written = written \| self.write_node(off, "z", item.offset.z,
1326	{"unit": item.offset_unit})
1327	if written == True:
1328	self.append(off, det)
1329
1330	ori = self.create_element("orientation")
1331	written = self.write_node(ori, "roll", item.orientation.x,
1332	{"unit": item.orientation_unit})
1333	written = written \| self.write_node(ori, "pitch",
1334	item.orientation.y,
1335	{"unit": item.orientation_unit})
1336	written = written \| self.write_node(ori, "yaw",
1337	item.orientation.z,
1338	{"unit": item.orientation_unit})
1339	if written == True:
1340	self.append(ori, det)
1341
1342	center = self.create_element("beam_center")
1343	written = self.write_node(center, "x", item.beam_center.x,
1344	{"unit": item.beam_center_unit})
1345	written = written \| self.write_node(center, "y",
1346	item.beam_center.y,
1347	{"unit": item.beam_center_unit})
1348	written = written \| self.write_node(center, "z",
1349	item.beam_center.z,
1350	{"unit": item.beam_center_unit})
1351	if written == True:
1352	self.append(center, det)
1353
1354	pix = self.create_element("pixel_size")
1355	written = self.write_node(pix, "x", item.pixel_size.x,
1356	{"unit": item.pixel_size_unit})
1357	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1358	{"unit": item.pixel_size_unit})
1359	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1360	{"unit": item.pixel_size_unit})
1361	if written == True:
1362	self.append(pix, det)
1363	self.write_node(det, "slit_length", item.slit_length,
1364	{"unit": item.slit_length_unit})
1365
1366
1367	def _write_process_notes(self, datainfo, entry_node):
1368	"""
1369	Writes the process notes to the XML file
1370
1371	:param datainfo: The Data1D object the information is coming from
1372	:param entry_node: lxml node ElementTree object to be appended to
1373
1374	"""
1375	for item in datainfo.process:
1376	node = self.create_element("SASprocess")
1377	self.append(node, entry_node)
1378	self.write_node(node, "name", item.name)
1379	self.write_node(node, "date", item.date)
1380	self.write_node(node, "description", item.description)
1381	for term in item.term:
1382	if isinstance(term, list):
1383	value = term['value']
1384	del term['value']
1385	elif isinstance(term, dict):
1386	value = term.get("value")
1387	del term['value']
1388	else:
1389	value = term
1390	self.write_node(node, "term", value, term)
1391	for note in item.notes:
1392	self.write_node(node, "SASprocessnote", note)
1393	if len(item.notes) == 0:
1394	self.write_node(node, "SASprocessnote", "")
1395
1396	def _write_notes(self, datainfo, entry_node):
1397	"""
1398	Writes the notes to the XML file and creates an empty note if none
1399	exist
1400
1401	:param datainfo: The Data1D object the information is coming from
1402	:param entry_node: lxml node ElementTree object to be appended to
1403
1404	"""
1405	if len(datainfo.notes) == 0:
1406	node = self.create_element("SASnote")
1407	self.append(node, entry_node)
1408	else:
1409	for item in datainfo.notes:
1410	node = self.create_element("SASnote")
1411	self.write_text(node, item)
1412	self.append(node, entry_node)
1413
1414	def _check_origin(self, entry_node, doc):
1415	"""
1416	Return the document, and the SASentry node associated with
1417	the data we just wrote.
1418	If the calling function was not the cansas reader, return a minidom
1419	object rather than an lxml object.
1420
1421	:param entry_node: lxml node ElementTree object to be appended to
1422	:param doc: entire xml tree
1423	"""
1424	if not self.frm:
1425	self.frm = inspect.stack()[1]
1426	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1427	mod_name = mod_name.replace(".py", "")
1428	mod = mod_name.split("sas/")
1429	mod_name = mod[1]
1430	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1431	string = self.to_string(doc, pretty_print=False)
1432	doc = parseString(string)
1433	node_name = entry_node.tag
1434	node_list = doc.getElementsByTagName(node_name)
1435	entry_node = node_list.item(0)
1436	return doc, entry_node
1437
1438	# DO NOT REMOVE - used in saving and loading panel states.
1439	def _store_float(self, location, node, variable, storage, optional=True):
1440	"""
1441	Get the content of a xpath location and store
1442	the result. Check that the units are compatible
1443	with the destination. The value is expected to
1444	be a float.
1445
1446	The xpath location might or might not exist.
1447	If it does not exist, nothing is done
1448
1449	:param location: xpath location to fetch
1450	:param node: node to read the data from
1451	:param variable: name of the data member to store it in [string]
1452	:param storage: data object that has the 'variable' data member
1453	:param optional: if True, no exception will be raised
1454	if unit conversion can't be done
1455
1456	:raise ValueError: raised when the units are not recognized
1457	"""
1458	entry = get_content(location, node)
1459	try:
1460	value = float(entry.text)
1461	except:
1462	value = None
1463
1464	if value is not None:
1465	# If the entry has units, check to see that they are
1466	# compatible with what we currently have in the data object
1467	units = entry.get('unit')
1468	if units is not None:
1469	toks = variable.split('.')
1470	local_unit = None
1471	exec "local_unit = storage.%s_unit" % toks[0]
1472	if local_unit is not None and units.lower() != local_unit.lower():
1473	if HAS_CONVERTER == True:
1474	try:
1475	conv = Converter(units)
1476	exec "storage.%s = %g" % \
1477	(variable, conv(value, units=local_unit))
1478	except:
1479	_, exc_value, _ = sys.exc_info()
1480	err_mess = "CanSAS reader: could not convert"
1481	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1482	% (variable, units, local_unit, exc_value)
1483	self.errors.add(err_mess)
1484	if optional:
1485	logger.info(err_mess)
1486	else:
1487	raise ValueError, err_mess
1488	else:
1489	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1490	% (variable, units)
1491	err_mess += " expecting [%s]" % local_unit
1492	self.errors.add(err_mess)
1493	if optional:
1494	logger.info(err_mess)
1495	else:
1496	raise ValueError, err_mess
1497	else:
1498	exec "storage.%s = value" % variable
1499	else:
1500	exec "storage.%s = value" % variable
1501
1502	# DO NOT REMOVE - used in saving and loading panel states.
1503	def _store_content(self, location, node, variable, storage):
1504	"""
1505	Get the content of a xpath location and store
1506	the result. The value is treated as a string.
1507
1508	The xpath location might or might not exist.
1509	If it does not exist, nothing is done
1510
1511	:param location: xpath location to fetch
1512	:param node: node to read the data from
1513	:param variable: name of the data member to store it in [string]
1514	:param storage: data object that has the 'variable' data member
1515
1516	:return: return a list of errors
1517	"""
1518	entry = get_content(location, node)
1519	if entry is not None and entry.text is not None:
1520	exec "storage.%s = entry.text.strip()" % variable
1521
1522
1523	# DO NOT REMOVE Called by outside packages:
1524	# sas.sasgui.perspectives.invariant.invariant_state
1525	# sas.sasgui.perspectives.fitting.pagestate
1526	def get_content(location, node):
1527	"""
1528	Get the first instance of the content of a xpath location.
1529
1530	:param location: xpath location
1531	:param node: node to start at
1532
1533	:return: Element, or None
1534	"""
1535	nodes = node.xpath(location,
1536	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1537	if len(nodes) > 0:
1538	return nodes[0]
1539	else:
1540	return None
1541
1542	# DO NOT REMOVE Called by outside packages:
1543	# sas.sasgui.perspectives.fitting.pagestate
1544	def write_node(doc, parent, name, value, attr=None):
1545	"""
1546	:param doc: document DOM
1547	:param parent: parent node
1548	:param name: tag of the element
1549	:param value: value of the child text node
1550	:param attr: attribute dictionary
1551
1552	:return: True if something was appended, otherwise False
1553	"""
1554	if attr is None:
1555	attr = {}
1556	if value is not None:
1557	node = doc.createElement(name)
1558	node.appendChild(doc.createTextNode(str(value)))
1559	for item in attr:
1560	node.setAttribute(item, attr[item])
1561	parent.appendChild(node)
1562	return True
1563	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 278ddee

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