cansas_reader.py @ 92a2ecd

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 92a2ecd was 92a2ecd, checked in by Jeff Krzywon <jeffery.krzywon@…>, 11 years ago
Save and load project files seems fixed now. I haven't tested individual analysis windows yet.
Property mode set to `100644`
File size: 44.7 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
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sans.dataloader.data_info import Data1D
23	from sans.dataloader.data_info import Collimation
24	from sans.dataloader.data_info import TransmissionSpectrum
25	from sans.dataloader.data_info import Detector
26	from sans.dataloader.data_info import Process
27	from sans.dataloader.data_info import Aperture
28	# Both imports used. Do not remove either.
29	from xml.dom.minidom import parseString
30	import sans.dataloader.readers.xml_reader as xml_reader
31	from sans.dataloader.readers.xml_reader import XMLreader
32	from sans.dataloader.readers.cansas_constants import CansasConstants
33
34	_ZERO = 1e-16
35	PREPROCESS = "xmlpreprocess"
36	ENCODING = "encoding"
37	HAS_CONVERTER = True
38	try:
39	from sans.data_util.nxsunit import Converter
40	except:
41	HAS_CONVERTER = False
42
43	CONSTANTS = CansasConstants()
44	CANSAS_FORMAT = CONSTANTS.format
45	CANSAS_NS = CONSTANTS.names
46	ALLOW_ALL = True
47
48
49	# minidom used in functions called by outside classes
50	import xml.dom.minidom
51	# DO NOT REMOVE
52	# Called by outside packages:
53	# sans.perspectives.invariant.invariant_state
54	# sans.perspectives.fitting.pagestate
55	def get_content(location, node):
56	"""
57	Get the first instance of the content of a xpath location.
58
59	:param location: xpath location
60	:param node: node to start at
61
62	:return: Element, or None
63	"""
64	nodes = node.xpath(location,
65	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
66
67	if len(nodes) > 0:
68	return nodes[0]
69	else:
70	return None
71
72
73	# DO NOT REMOVE
74	# Called by outside packages:
75	# sans.perspectives.fitting.pagestate
76	def write_node(doc, parent, name, value, attr={}):
77	"""
78	:param doc: document DOM
79	:param parent: parent node
80	:param name: tag of the element
81	:param value: value of the child text node
82	:param attr: attribute dictionary
83
84	:return: True if something was appended, otherwise False
85	"""
86	if value is not None:
87	node = doc.createElement(name)
88	node.appendChild(doc.createTextNode(str(value)))
89	for item in attr:
90	node.setAttribute(item, attr[item])
91	parent.appendChild(node)
92	return True
93	return False
94
95
96	class Reader(XMLreader):
97	"""
98	Class to load cansas 1D XML files
99
100	:Dependencies:
101	The CanSAS reader requires PyXML 0.8.4 or later.
102	"""
103	##CanSAS version - defaults to version 1.0
104	cansas_version = "1.0"
105
106	logging = []
107	errors = []
108
109	type_name = "canSAS"
110	## Wildcards
111	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
112	## List of allowed extensions
113	ext = ['.xml', '.XML', '.svs', '.SVS']
114
115	## Flag to bypass extension check
116	allow_all = True
117
118	def __init__(self):
119	## List of errors
120	self.errors = []
121
122	def is_cansas(self, ext="xml"):
123	"""
124	Checks to see if the xml file is a CanSAS file
125	"""
126	if self.validate_xml():
127	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
128	value = self.xmlroot.get(name)
129	if CANSAS_NS.get(self.cansas_version).get("ns") == \
130	value.rsplit(" ")[0]:
131	return True
132	if ext == "svs":
133	return True
134	return False
135
136	def read(self, xml):
137	"""
138	Validate and read in an xml file in the canSAS format.
139
140	:param xml: A canSAS file path in proper XML format
141	"""
142	# X - Q value; Y - Intensity (Abs)
143	x_vals = numpy.empty(0)
144	y_vals = numpy.empty(0)
145	dx_vals = numpy.empty(0)
146	dy_vals = numpy.empty(0)
147	dxl = numpy.empty(0)
148	dxw = numpy.empty(0)
149
150	# output - Final list of Data1D objects
151	output = []
152	# ns - Namespace hierarchy for current xml object
153	ns_list = []
154
155	# Check that the file exists
156	if os.path.isfile(xml):
157	basename = os.path.basename(xml)
158	_, extension = os.path.splitext(basename)
159	# If the file type is not allowed, return nothing
160	if extension in self.ext or self.allow_all:
161	# Get the file location of
162	base_name = xml_reader.__file__
163	base_name = base_name.replace("\\","/")
164	base = base_name.split("/sans/")[0]
165
166	# Load in xml file and get the cansas version from the header
167	self.set_xml_file(xml)
168	root = self.xmlroot
169	if root is None:
170	root = {}
171	self.cansas_version = root.get("version", "1.0")
172
173	# Generic values for the cansas file based on the version
174	cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
175	schema_path = "{0}/sans/dataloader/readers/schema/{1}".format\
176	(base, cansas_defaults.get("schema")).replace("\\", "/")
177
178	# Link a schema to the XML file.
179	self.set_schema(schema_path)
180
181	# Try to load the file, but raise an error if unable to.
182	# Check the file matches the XML schema
183	try:
184	if self.is_cansas(extension):
185	# Get each SASentry from XML file and add it to a list.
186	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
187	namespaces={'ns': cansas_defaults.get("ns")})
188	ns_list.append("SASentry")
189
190	# If multiple files, modify the name for each is unique
191	multiple_files = len(entry_list) - 1
192	increment = 0
193	name = basename
194	# Parse each SASentry item
195	for entry in entry_list:
196	# Define a new Data1D object with zeroes for
197	# x_vals and y_vals
198	data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
199	data1d.dxl = dxl
200	data1d.dxw = dxw
201
202	# If more than one SASentry, increment each in order
203	if multiple_files:
204	name += "_{0}".format(increment)
205	increment += 1
206
207	# Set the Data1D name and then parse the entry.
208	# The entry is appended to a list of entry values
209	data1d.filename = name
210	data1d.meta_data["loader"] = "CanSAS 1D"
211
212	# Get all preprocessing events and encoding
213	self.set_processing_instructions()
214	data1d.meta_data[PREPROCESS] = \
215	self.processing_instructions
216
217	# Parse the XML file
218	return_value, extras = \
219	self._parse_entry(entry, ns_list, data1d)
220	del extras[:]
221
222	# Final cleanup
223	# Remove empty nodes, verify array sizes are correct
224	for error in self.errors:
225	return_value.errors.append(error)
226	del self.errors[:]
227	numpy.trim_zeros(return_value.x)
228	numpy.trim_zeros(return_value.y)
229	numpy.trim_zeros(return_value.dy)
230	size_dx = return_value.dx.size
231	size_dxl = return_value.dxl.size
232	size_dxw = return_value.dxw.size
233	if size_dxl == 0 and size_dxw == 0:
234	return_value.dxl = None
235	return_value.dxw = None
236	numpy.trim_zeros(return_value.dx)
237	elif size_dx == 0:
238	return_value.dx = None
239	size_dx = size_dxl
240	numpy.trim_zeros(return_value.dxl)
241	numpy.trim_zeros(return_value.dxw)
242	output.append(return_value)
243	else:
244	value = self.find_invalid_xml()
245	output.append("Invalid XML at: {0}".format(value))
246	except:
247	# If the file does not match the schema, raise this error
248	raise RuntimeError, "%s cannot be read" % xml
249	return output
250	# Return a list of parsed entries that dataloader can manage
251	return None
252
253	def _create_unique_key(self, dictionary, name, numb = 0):
254	"""
255	Create a unique key value for any dictionary to prevent overwriting
256	Recurses until a unique key value is found.
257
258	:param dictionary: A dictionary with any number of entries
259	:param name: The index of the item to be added to dictionary
260	:param numb: The number to be appended to the name, starts at 0
261	"""
262	if dictionary.get(name) is not None:
263	numb += 1
264	name = name.split("_")[0]
265	name += "_{0}".format(numb)
266	name = self._create_unique_key(dictionary, name, numb)
267	return name
268
269
270	def _unit_conversion(self, new_current_level, attr, data1d, \
271	tagname, node_value, optional = True):
272	"""
273	A unit converter method used to convert the data included in the file
274	to the default units listed in data_info
275
276	:param new_current_level: cansas_constants level as returned by
277	iterate_namespace
278	:param attr: The attributes of the node
279	:param data1d: Where the values will be saved
280	:param node_value: The value of the current dom node
281	:param optional: Boolean that says if the units are required
282	"""
283	value_unit = ''
284	if 'unit' in attr and new_current_level.get('unit') is not None:
285	try:
286	if isinstance(node_value, float) is False:
287	exec("node_value = float({0})".format(node_value))
288	default_unit = None
289	unitname = new_current_level.get("unit")
290	exec "default_unit = data1d.{0}".format(unitname)
291	local_unit = attr['unit']
292	if local_unit.lower() != default_unit.lower() and \
293	local_unit is not None and local_unit.lower() != "none" and\
294	default_unit is not None:
295	if HAS_CONVERTER == True:
296	try:
297	## Check local units - bad units raise KeyError
298	Converter(local_unit)
299	data_conv_q = Converter(attr['unit'])
300	value_unit = default_unit
301	exec "node_value = data_conv_q(node_value, units=data1d.{0})".format(unitname)
302	except KeyError as e:
303	err_msg = "CanSAS reader: could not convert "
304	err_msg += "{0} unit {1}; ".format(tagname, local_unit)
305	intermediate = "err_msg += \"expecting [{1}] {2}\".format(data1d.{0}, sys.exc_info()[1])".format(unitname, "{0}", "{1}")
306	exec intermediate
307	self.errors.append(err_msg)
308	raise ValueError(err_msg)
309	return
310	except:
311	err_msg = \
312	"CanSAS reader: could not convert the units"
313	self.errors.append(err_msg)
314	return
315	else:
316	value_unit = local_unit
317	err_msg = "CanSAS reader: unrecognized %s unit [%s];"\
318	% (node_value, default_unit)
319	err_msg += " expecting [%s]" % local_unit
320	self.errors.append(err_msg)
321	raise ValueError, err_msg
322	return
323	else:
324	value_unit = local_unit
325	except:
326	err_msg = "CanSAS reader: could not convert "
327	err_msg += "Q unit [%s]; " % attr['unit'],
328	exec "err_msg += \"expecting [%s]\n %s\" % (data1d.{0}, sys.exc_info()[1])".format(unitname)
329	self.errors.append(err_msg)
330	raise ValueError, err_msg
331	return
332	elif 'unit' in attr:
333	value_unit = attr['unit']
334	node_value = "float({0})".format(node_value)
335	return node_value, value_unit
336
337	def _parse_entry(self, dom, names=["SASentry"], data1d=None, extras=[]):
338	"""
339	Parse a SASEntry - new recursive method for parsing the dom of
340	the CanSAS data format. This will allow multiple data files
341	and extra nodes to be read in simultaneously.
342
343	:param dom: dom object with a namespace base of names
344	:param names: A list of element names that lead up to the dom object
345	:param data1d: The data1d object that will be modified
346	:param extras: Any values that should go into meta_data when data1d
347	is not a Data1D object
348	"""
349
350	# A portion of every namespace entry
351	if data1d == None:
352	x_vals = numpy.empty(0)
353	y_vals = numpy.empty(0)
354	dx_vals = numpy.empty(0)
355	dy_vals = numpy.empty(0)
356	dxl = numpy.empty(0)
357	dxw = numpy.empty(0)
358	data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
359	data1d.dxl = dxl
360	data1d.dxw = dxw
361
362	base_ns = "{0}{1}{2}".format("{", \
363	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
364	unit = ''
365	tagname = ''
366	tagname_original = ''
367
368	# Go through each child in the parent element
369	for node in dom:
370	try:
371	# Get the element name and set the current names level
372	tagname = node.tag.replace(base_ns, "")
373	tagname_original = tagname
374	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or\
375	tagname == "invariant":
376	continue
377	names.append(tagname)
378	attr = node.attrib
379	children = node.getchildren()
380	if len(children) == 0:
381	children = None
382	save_data1d = data1d
383
384	# Look for special cases
385	if tagname == "SASdetector":
386	data1d = Detector()
387	elif tagname == "SAScollimation":
388	data1d = Collimation()
389	elif tagname == "SAStransmission_spectrum":
390	data1d = TransmissionSpectrum()
391	elif tagname == "SASprocess":
392	data1d = Process()
393	for child in node:
394	if child.tag.replace(base_ns, "") == "term":
395	term_attr = {}
396	for attr in child.keys():
397	term_attr[attr] = \
398	' '.join(child.get(attr).split())
399	if child.text is not None:
400	term_attr['value'] = \
401	' '.join(child.text.split())
402	data1d.term.append(term_attr)
403	elif tagname == "aperture":
404	data1d = Aperture()
405	if tagname == "Idata" and children is not None:
406	dql = 0
407	dqw = 0
408	for child in children:
409	tag = child.tag.replace(base_ns, "")
410	if tag == "dQl":
411	dql = 1
412	if tag == "dQw":
413	dqw = 1
414	if dqw == 1 and dql == 0:
415	data1d.dxl = numpy.append(data1d.dxl, 0.0)
416	elif dql == 1 and dqw == 0:
417	data1d.dxw = numpy.append(data1d.dxw, 0.0)
418
419	# Get where to store content
420	cs_values = CONSTANTS.iterate_namespace(names)
421	# If the element is a child element, recurse
422	if children is not None:
423	# Returned value is new Data1D object with all previous and
424	# new values in it.
425	data1d, extras = self._parse_entry(node,
426	names, data1d, extras)
427
428	#Get the information from the node
429	node_value = node.text
430	if node_value == "":
431	node_value = None
432	if node_value is not None:
433	node_value = ' '.join(node_value.split())
434
435	# If the value is a float, compile with units.
436	if cs_values.ns_datatype == "float":
437	# If an empty value is given, store as zero.
438	if node_value is None or node_value.isspace() \
439	or node_value.lower() == "nan":
440	node_value = "0.0"
441	node_value, unit = self._unit_conversion(\
442	cs_values.current_level, attr, data1d, \
443	tagname, node_value, cs_values.ns_optional)
444	# If the value is a timestamp, convert to a datetime object
445	elif cs_values.ns_datatype == "timestamp":
446	if node_value is None or node_value.isspace():
447	pass
448	else:
449	try:
450	node_value = \
451	datetime.datetime.fromtimestamp(node_value)
452	except ValueError:
453	node_value = None
454	# If appending to a dictionary (meta_data \| run_name)
455	# make sure the key is unique
456	if cs_values.ns_variable == "{0}.meta_data[\"{2}\"] = \"{1}\"":
457	# If we are within a Process, Detector, Collimation or
458	# Aperture instance, pull out old data1d
459	tagname = self._create_unique_key(data1d.meta_data, \
460	tagname, 0)
461	if isinstance(data1d, Data1D) == False:
462	store_me = cs_values.ns_variable.format("data1d", \
463	node_value, tagname)
464	extras.append(store_me)
465	cs_values.ns_variable = None
466	if cs_values.ns_variable == "{0}.run_name[\"{2}\"] = \"{1}\"":
467	tagname = self._create_unique_key(data1d.run_name, \
468	tagname, 0)
469
470	# Check for Data1D object and any extra commands to save
471	if isinstance(data1d, Data1D):
472	for item in extras:
473	exec item
474	# Don't bother saving empty information unless it is a float
475	if cs_values.ns_variable is not None and \
476	node_value is not None and \
477	node_value.isspace() == False:
478	# Format a string and then execute it.
479	store_me = cs_values.ns_variable.format("data1d", \
480	node_value, tagname)
481	exec store_me
482	# Get attributes and process them
483	if attr is not None:
484	for key in node.keys():
485	try:
486	cansas_attrib = \
487	cs_values.current_level.get("attributes").get(key)
488	attrib_variable = cansas_attrib.get("variable")
489	if key == 'unit' and unit != '':
490	attrib_value = unit
491	else:
492	attrib_value = node.attrib[key]
493	store_attr = attrib_variable.format("data1d", \
494	attrib_value, key)
495	exec store_attr
496	except AttributeError as e:
497	pass
498
499	except TypeError as e:
500	pass
501	except Exception as e:
502	exc_type, exc_obj, exc_tb = sys.exc_info()
503	fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
504	print(e, exc_type, fname, exc_tb.tb_lineno, tagname, exc_obj)
505	finally:
506	# Save special cases in original data1d object
507	# then restore the data1d
508	if tagname_original == "SASdetector":
509	save_data1d.detector.append(data1d)
510	elif tagname_original == "SAScollimation":
511	save_data1d.collimation.append(data1d)
512	elif tagname == "SAStransmission_spectrum":
513	save_data1d.trans_spectrum.append(data1d)
514	elif tagname_original == "SASprocess":
515	save_data1d.process.append(data1d)
516	elif tagname_original == "aperture":
517	save_data1d.aperture.append(data1d)
518	else:
519	save_data1d = data1d
520	if tagname_original == "fitting_plug_in" or \
521	tagname_original == "invariant" or \
522	tagname_original == "pr_inversion":
523	pass
524	else:
525	data1d = save_data1d
526	# Remove tagname from names to restore original base
527	names.remove(tagname_original)
528	return data1d, extras
529
530
531	def _to_xml_doc(self, datainfo):
532	"""
533	Create an XML document to contain the content of a Data1D
534
535	:param datainfo: Data1D object
536	"""
537
538	if not issubclass(datainfo.__class__, Data1D):
539	raise RuntimeError, "The cansas writer expects a Data1D instance"
540
541	# Get PIs and create root element
542	pis = self.return_processing_instructions()
543	if len(pis) > 0:
544	pi_tree = self.create_tree(pis[0])
545	i = 1
546	for i in range(1,len(pis) - 1):
547	pi_tree = self.append(pis[i], pi_tree)
548	pi_string = self.to_string(pi_tree)
549	else:
550	pi_string = ""
551
552	# Define namespaces and create SASroot object
553	xsi = "http://www.w3.org/2001/XMLSchema-instance"
554	version = self.cansas_version
555	ns = CANSAS_NS.get(version).get("ns")
556	if version == "1.1":
557	url = "http://www.cansas.org/formats/1.1/"
558	else:
559	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
560	schema_location = "{0} {1}cansas1d.xsd".format(ns, url)
561	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
562	"version" : version}
563	nsmap = {'xsi' : xsi, None: ns}
564
565	main_node = self.create_element("{" + ns + "}SASroot", \
566	attrib = attrib, \
567	nsmap = nsmap)
568
569	# Create ElementTree, append SASroot and apply processing instructions
570	base_string = pi_string + self.to_string(main_node)
571	base_element = self.create_element_from_string(base_string)
572	doc = self.create_tree(base_element)
573
574	# Create SASentry Element
575	entry_node = self.create_element("SASentry")
576	root = doc.getroot()
577	root.append(entry_node)
578
579	# Add Title to SASentry
580	self.write_node(entry_node, "Title", datainfo.title)
581
582	# Add Run to SASentry
583	if datainfo.run == None or datainfo.run == []:
584	RUN_NAME_DEFAULT = "None"
585	datainfo.run.append(RUN_NAME_DEFAULT)
586	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
587	for item in datainfo.run:
588	runname = {}
589	if item in datainfo.run_name and \
590	len(str(datainfo.run_name[item])) > 1:
591	runname = {'name': datainfo.run_name[item]}
592	self.write_node(entry_node, "Run", item, runname)
593
594	# Data info
595	node = self.create_element("SASdata")
596	self.append(node, entry_node)
597
598	for i in range(len(datainfo.x)):
599	pt = self.create_element("Idata")
600	node.append(pt)
601	self.write_node(pt, "Q", datainfo.x[i], {'unit': datainfo.x_unit})
602	if len(datainfo.y) >= i:
603	self.write_node(pt, "I", datainfo.y[i],
604	{'unit': datainfo.y_unit})
605	if datainfo.dy != None and len(datainfo.dy) > i:
606	self.write_node(pt, "Idev", datainfo.dy[i],
607	{'unit': datainfo.y_unit})
608	if datainfo.dx != None and len(datainfo.dx) > i:
609	self.write_node(pt, "Qdev", datainfo.dx[i],
610	{'unit': datainfo.x_unit})
611	if datainfo.dxw != None and len(datainfo.dxw) > i:
612	self.write_node(pt, "dQw", datainfo.dxw[i],
613	{'unit': datainfo.x_unit})
614	if datainfo.dxl != None and len(datainfo.dxl) > i:
615	self.write_node(pt, "dQl", datainfo.dxl[i],
616	{'unit': datainfo.x_unit})
617
618	# Transmission Spectrum Info
619	for i in range(len(datainfo.trans_spectrum)):
620	spectrum = datainfo.trans_spectrum[i]
621	node = self.create_element("SAStransmission_spectrum",
622	{"name" : spectrum.name})
623	self.append(node, entry_node)
624	if isinstance(spectrum.timestamp, datetime.datetime):
625	node.setAttribute("timestamp", spectrum.timestamp)
626	for i in range(len(spectrum.wavelength)):
627	pt = self.create_element("Tdata")
628	node.append(pt)
629	self.write_node(pt, "Lambda", spectrum.wavelength[i],
630	{'unit': spectrum.wavelength_unit})
631	self.write_node(pt, "T", spectrum.transmission[i],
632	{'unit': spectrum.transmission_unit})
633	if spectrum.transmission_deviation != None \
634	and len(spectrum.transmission_deviation) >= i:
635	self.write_node(pt, "Tdev", \
636	spectrum.transmission_deviation[i], \
637	{'unit': spectrum.transmission_deviation_unit})
638
639	# Sample info
640	sample = self.create_element("SASsample")
641	if datainfo.sample.name is not None:
642	self.write_attribute(sample,
643	"name",
644	str(datainfo.sample.name))
645	self.append(sample, entry_node)
646	self.write_node(sample, "ID", str(datainfo.sample.ID))
647	self.write_node(sample, "thickness", datainfo.sample.thickness,
648	{"unit": datainfo.sample.thickness_unit})
649	self.write_node(sample, "transmission", datainfo.sample.transmission)
650	self.write_node(sample, "temperature", datainfo.sample.temperature,
651	{"unit": datainfo.sample.temperature_unit})
652
653	pos = self.create_element("position")
654	written = self.write_node(pos,
655	"x",
656	datainfo.sample.position.x,
657	{"unit": datainfo.sample.position_unit})
658	written = written \| self.write_node(pos,
659	"y",
660	datainfo.sample.position.y,
661	{"unit": datainfo.sample.position_unit})
662	written = written \| self.write_node(pos,
663	"z",
664	datainfo.sample.position.z,
665	{"unit": datainfo.sample.position_unit})
666	if written == True:
667	self.append(pos, sample)
668
669	ori = self.create_element("orientation")
670	written = self.write_node(ori, "roll",
671	datainfo.sample.orientation.x,
672	{"unit": datainfo.sample.orientation_unit})
673	written = written \| self.write_node(ori, "pitch",
674	datainfo.sample.orientation.y,
675	{"unit": datainfo.sample.orientation_unit})
676	written = written \| self.write_node(ori, "yaw",
677	datainfo.sample.orientation.z,
678	{"unit": datainfo.sample.orientation_unit})
679	if written == True:
680	self.append(ori, sample)
681
682	for item in datainfo.sample.details:
683	self.write_node(sample, "details", item)
684
685	# Instrument info
686	instr = self.create_element("SASinstrument")
687	self.append(instr, entry_node)
688
689	self.write_node(instr, "name", datainfo.instrument)
690
691	# Source
692	source = self.create_element("SASsource")
693	if datainfo.source.name is not None:
694	self.write_attribute(source,
695	"name",
696	str(datainfo.source.name))
697	self.append(source, instr)
698	if datainfo.source.radiation == None or datainfo.source.radiation == '':
699	datainfo.source.radiation = "neutron"
700	self.write_node(source, "radiation", datainfo.source.radiation)
701
702	size = self.create_element("beam_size")
703	if datainfo.source.beam_size_name is not None:
704	self.write_attribute(size,
705	"name",
706	str(datainfo.source.beam_size_name))
707	written = self.write_node(size, "x", datainfo.source.beam_size.x,
708	{"unit": datainfo.source.beam_size_unit})
709	written = written \| self.write_node(size, "y",
710	datainfo.source.beam_size.y,
711	{"unit": datainfo.source.beam_size_unit})
712	written = written \| self.write_node(size, "z",
713	datainfo.source.beam_size.z,
714	{"unit": datainfo.source.beam_size_unit})
715	if written == True:
716	self.append(size, source)
717
718	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
719	self.write_node(source, "wavelength",
720	datainfo.source.wavelength,
721	{"unit": datainfo.source.wavelength_unit})
722	self.write_node(source, "wavelength_min",
723	datainfo.source.wavelength_min,
724	{"unit": datainfo.source.wavelength_min_unit})
725	self.write_node(source, "wavelength_max",
726	datainfo.source.wavelength_max,
727	{"unit": datainfo.source.wavelength_max_unit})
728	self.write_node(source, "wavelength_spread",
729	datainfo.source.wavelength_spread,
730	{"unit": datainfo.source.wavelength_spread_unit})
731
732	# Collimation
733	if datainfo.collimation == [] or datainfo.collimation == None:
734	coll = Collimation()
735	datainfo.collimation.append(coll)
736	for item in datainfo.collimation:
737	coll = self.create_element("SAScollimation")
738	if item.name is not None:
739	self.write_attribute(coll, "name", str(item.name))
740	self.append(coll, instr)
741
742	self.write_node(coll, "length", item.length,
743	{"unit": item.length_unit})
744
745	for apert in item.aperture:
746	ap = self.create_element("aperture")
747	if apert.name is not None:
748	self.write_attribute(ap, "name", str(apert.name))
749	if apert.type is not None:
750	self.write_attribute(ap, "type", str(apert.type))
751	self.append(ap, coll)
752
753	size = self.create_element("size")
754	if apert.size_name is not None:
755	self.write_attribute(size,
756	"name",
757	str(apert.size_name))
758	written = self.write_node(size, "x", apert.size.x,
759	{"unit": apert.size_unit})
760	written = written \| self.write_node(size, "y", apert.size.y,
761	{"unit": apert.size_unit})
762	written = written \| self.write_node(size, "z", apert.size.z,
763	{"unit": apert.size_unit})
764	if written == True:
765	self.append(size, ap)
766
767	self.write_node(ap, "distance", apert.distance,
768	{"unit": apert.distance_unit})
769
770	# Detectors
771	if datainfo.detector == None or datainfo.detector == []:
772	det = Detector()
773	det.name = ""
774	datainfo.detector.append(det)
775
776	for item in datainfo.detector:
777	det = self.create_element("SASdetector")
778	written = self.write_node(det, "name", item.name)
779	written = written \| self.write_node(det, "SDD", item.distance,
780	{"unit": item.distance_unit})
781	if written == True:
782	self.append(det, instr)
783
784	off = self.create_element("offset")
785	written = self.write_node(off, "x", item.offset.x,
786	{"unit": item.offset_unit})
787	written = written \| self.write_node(off, "y", item.offset.y,
788	{"unit": item.offset_unit})
789	written = written \| self.write_node(off, "z", item.offset.z,
790	{"unit": item.offset_unit})
791	if written == True:
792	self.append(off, det)
793
794	ori = self.create_element("orientation")
795	written = self.write_node(ori, "roll", item.orientation.x,
796	{"unit": item.orientation_unit})
797	written = written \| self.write_node(ori, "pitch",
798	item.orientation.y,
799	{"unit": item.orientation_unit})
800	written = written \| self.write_node(ori, "yaw",
801	item.orientation.z,
802	{"unit": item.orientation_unit})
803	if written == True:
804	self.append(ori, det)
805
806	center = self.create_element("beam_center")
807	written = self.write_node(center, "x", item.beam_center.x,
808	{"unit": item.beam_center_unit})
809	written = written \| self.write_node(center, "y",
810	item.beam_center.y,
811	{"unit": item.beam_center_unit})
812	written = written \| self.write_node(center, "z",
813	item.beam_center.z,
814	{"unit": item.beam_center_unit})
815	if written == True:
816	self.append(center, det)
817
818	pix = self.create_element("pixel_size")
819	written = self.write_node(pix, "x", item.pixel_size.x,
820	{"unit": item.pixel_size_unit})
821	written = written \| self.write_node(pix, "y", item.pixel_size.y,
822	{"unit": item.pixel_size_unit})
823	written = written \| self.write_node(pix, "z", item.pixel_size.z,
824	{"unit": item.pixel_size_unit})
825	written = written \| self.write_node(det, "slit_length",
826	item.slit_length,
827	{"unit": item.slit_length_unit})
828	if written == True:
829	self.append(pix, det)
830
831	# Processes info
832	for item in datainfo.process:
833	node = self.create_element("SASprocess")
834	self.append(node, entry_node)
835
836	self.write_node(node, "name", item.name)
837	self.write_node(node, "date", item.date)
838	self.write_node(node, "description", item.description)
839	for term in item.term:
840	value = term['value']
841	del term['value']
842	self.write_node(node, "term", value, term)
843	for note in item.notes:
844	self.write_node(node, "SASprocessnote", note)
845	if len(item.notes) == 0:
846	self.write_node(node, "SASprocessnote", "")
847
848	# Note info
849	if len(datainfo.notes) == 0:
850	node = self.create_element("SASnote")
851	self.append(node, entry_node)
852	else:
853	for item in datainfo.notes:
854	node = self.create_element("SASnote")
855	self.write_text(node, item)
856	self.append(node, entry_node)
857
858
859	# Return the document, and the SASentry node associated with
860	# the data we just wrote
861
862	frm = inspect.stack()[1]
863	mod = inspect.getmodule(frm[0])
864	mod_name = mod.__name__
865	if mod_name != "sans.dataloader.readers.cansas_reader":
866	string = self.to_string(doc, pp=True)
867	doc = parseString(string)
868	node_name = entry_node.tag
869	node_list = doc.getElementsByTagName(node_name)
870	entry_node = node_list.item(0)
871
872	return doc, entry_node
873
874
875	def write_node(self, parent, name, value, attr=None):
876	"""
877	:param doc: document DOM
878	:param parent: parent node
879	:param name: tag of the element
880	:param value: value of the child text node
881	:param attr: attribute dictionary
882
883	:return: True if something was appended, otherwise False
884	"""
885	if value is not None:
886	parent = self.ebuilder(parent, name, value, attr)
887	return True
888	return False
889
890
891	def write(self, filename, datainfo):
892	"""
893	Write the content of a Data1D as a CanSAS XML file
894
895	:param filename: name of the file to write
896	:param datainfo: Data1D object
897	"""
898	# Create XML document
899	doc, _ = self._to_xml_doc(datainfo)
900	# Write the file
901	fd = open(filename, 'w')
902	if self.encoding == None:
903	self.encoding = "UTF-8"
904	doc.write(fd, encoding=self.encoding,
905	pretty_print=True, xml_declaration=True)
906	fd.close()
907
908
909	# DO NOT REMOVE - used in saving and loading panel states.
910	def _store_float(self, location, node, variable, storage, optional=True):
911	"""
912	Get the content of a xpath location and store
913	the result. Check that the units are compatible
914	with the destination. The value is expected to
915	be a float.
916
917	The xpath location might or might not exist.
918	If it does not exist, nothing is done
919
920	:param location: xpath location to fetch
921	:param node: node to read the data from
922	:param variable: name of the data member to store it in [string]
923	:param storage: data object that has the 'variable' data member
924	:param optional: if True, no exception will be raised
925	if unit conversion can't be done
926
927	:raise ValueError: raised when the units are not recognized
928	"""
929	entry = get_content(location, node)
930	try:
931	value = float(entry.text)
932	except:
933	value = None
934
935	if value is not None:
936	# If the entry has units, check to see that they are
937	# compatible with what we currently have in the data object
938	units = entry.get('unit')
939	if units is not None:
940	toks = variable.split('.')
941	local_unit = None
942	exec "local_unit = storage.%s_unit" % toks[0]
943	if local_unit != None and units.lower() != local_unit.lower():
944	if HAS_CONVERTER == True:
945	try:
946	conv = Converter(units)
947	exec "storage.%s = %g" % (variable,
948	conv(value, units=local_unit))
949	except:
950	err_mess = "CanSAS reader: could not convert"
951	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
952	% (variable, units, local_unit, sys.exc_value)
953	self.errors.append(err_mess)
954	if optional:
955	logging.info(err_mess)
956	else:
957	raise ValueError, err_mess
958	else:
959	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
960	% (variable, units)
961	err_mess += " expecting [%s]" % local_unit
962	self.errors.append(err_mess)
963	if optional:
964	logging.info(err_mess)
965	else:
966	raise ValueError, err_mess
967	else:
968	exec "storage.%s = value" % variable
969	else:
970	exec "storage.%s = value" % variable
971
972
973	# DO NOT REMOVE - used in saving and loading panel states.
974	def _store_content(self, location, node, variable, storage):
975	"""
976	Get the content of a xpath location and store
977	the result. The value is treated as a string.
978
979	The xpath location might or might not exist.
980	If it does not exist, nothing is done
981
982	:param location: xpath location to fetch
983	:param node: node to read the data from
984	:param variable: name of the data member to store it in [string]
985	:param storage: data object that has the 'variable' data member
986
987	:return: return a list of errors
988	"""
989	entry = get_content(location, node)
990	if entry is not None and entry.text is not None:
991	exec "storage.%s = entry.text.strip()" % variable

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SasView

source: sasview/src/sans/dataloader/readers/cansas_reader.py @ 92a2ecd

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