cansas_reader.py @ 79492222

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 79492222 was 79492222, checked in by krzywon, 9 years ago
Changed the file and folder names to remove all SANS references.
Property mode set to `100644`
File size: 53.0 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 sas.dataloader.data_info import Data1D
23	from sas.dataloader.data_info import Collimation
24	from sas.dataloader.data_info import TransmissionSpectrum
25	from sas.dataloader.data_info import Detector
26	from sas.dataloader.data_info import Process
27	from sas.dataloader.data_info import Aperture
28	# Both imports used. Do not remove either.
29	from xml.dom.minidom import parseString
30	import sas.dataloader.readers.xml_reader as xml_reader
31	from sas.dataloader.readers.xml_reader import XMLreader
32	from sas.dataloader.readers.cansas_constants import CansasConstants
33
34	_ZERO = 1e-16
35	PREPROCESS = "xmlpreprocess"
36	ENCODING = "encoding"
37	RUN_NAME_DEFAULT = "None"
38	HAS_CONVERTER = True
39	try:
40	from sas.data_util.nxsunit import Converter
41	except ImportError:
42	HAS_CONVERTER = False
43
44	CONSTANTS = CansasConstants()
45	CANSAS_FORMAT = CONSTANTS.format
46	CANSAS_NS = CONSTANTS.names
47	ALLOW_ALL = True
48
49
50	# minidom used in functions called by outside classes
51	import xml.dom.minidom
52	# DO NOT REMOVE
53	# Called by outside packages:
54	# sas.perspectives.invariant.invariant_state
55	# sas.perspectives.fitting.pagestate
56	def get_content(location, node):
57	"""
58	Get the first instance of the content of a xpath location.
59
60	:param location: xpath location
61	:param node: node to start at
62
63	:return: Element, or None
64	"""
65	nodes = node.xpath(location,
66	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
67
68	if len(nodes) > 0:
69	return nodes[0]
70	else:
71	return None
72
73
74	# DO NOT REMOVE
75	# Called by outside packages:
76	# sas.perspectives.fitting.pagestate
77	def write_node(doc, parent, name, value, attr=None):
78	"""
79	:param doc: document DOM
80	:param parent: parent node
81	:param name: tag of the element
82	:param value: value of the child text node
83	:param attr: attribute dictionary
84
85	:return: True if something was appended, otherwise False
86	"""
87	if attr is None:
88	attr = {}
89	if value is not None:
90	node = doc.createElement(name)
91	node.appendChild(doc.createTextNode(str(value)))
92	for item in attr:
93	node.setAttribute(item, attr[item])
94	parent.appendChild(node)
95	return True
96	return False
97
98
99	class Reader(XMLreader):
100	"""
101	Class to load cansas 1D XML files
102
103	:Dependencies:
104	The CanSAS reader requires PyXML 0.8.4 or later.
105	"""
106	##CanSAS version - defaults to version 1.0
107	cansas_version = "1.0"
108	base_ns = "{cansas1d/1.0}"
109
110	logging = []
111	errors = []
112
113	type_name = "canSAS"
114	## Wildcards
115	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
116	## List of allowed extensions
117	ext = ['.xml', '.XML', '.svs', '.SVS']
118
119	## Flag to bypass extension check
120	allow_all = True
121
122
123	def __init__(self):
124	## List of errors
125	self.errors = []
126	self.encoding = None
127
128
129	def is_cansas(self, ext="xml"):
130	"""
131	Checks to see if the xml file is a CanSAS file
132
133	:param ext: The file extension of the data file
134	"""
135	if self.validate_xml():
136	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
137	value = self.xmlroot.get(name)
138	if CANSAS_NS.get(self.cansas_version).get("ns") == \
139	value.rsplit(" ")[0]:
140	return True
141	if ext == "svs":
142	return True
143	return False
144
145
146	def load_file_and_schema(self, xml_file):
147	"""
148	Loads the file and associates a schema, if a known schema exists
149
150	:param xml_file: The xml file path sent to Reader.read
151	"""
152	base_name = xml_reader.__file__
153	base_name = base_name.replace("\\","/")
154	base = base_name.split("/sas/")[0]
155
156	# Load in xml file and get the cansas version from the header
157	self.set_xml_file(xml_file)
158	self.cansas_version = self.xmlroot.get("version", "1.0")
159
160	# Generic values for the cansas file based on the version
161	cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
162	schema_path = "{0}/sas/dataloader/readers/schema/{1}".format\
163	(base, cansas_defaults.get("schema")).replace("\\", "/")
164
165	# Link a schema to the XML file.
166	self.set_schema(schema_path)
167	return cansas_defaults
168
169
170	def read(self, xml_file):
171	"""
172	Validate and read in an xml_file file in the canSAS format.
173
174	:param xml_file: A canSAS file path in proper XML format
175	"""
176
177	# output - Final list of Data1D objects
178	output = []
179	# ns - Namespace hierarchy for current xml_file object
180	ns_list = []
181
182	# Check that the file exists
183	if os.path.isfile(xml_file):
184	basename = os.path.basename(xml_file)
185	_, extension = os.path.splitext(basename)
186	# If the file type is not allowed, return nothing
187	if extension in self.ext or self.allow_all:
188	# Get the file location of
189	cansas_defaults = self.load_file_and_schema(xml_file)
190
191	# Try to load the file, but raise an error if unable to.
192	# Check the file matches the XML schema
193	try:
194	if self.is_cansas(extension):
195	# Get each SASentry from XML file and add it to a list.
196	entry_list = self.xmlroot.xpath(
197	'/ns:SASroot/ns:SASentry',
198	namespaces = {'ns': cansas_defaults.get("ns")})
199	ns_list.append("SASentry")
200
201	# If multiple files, modify the name for each is unique
202	increment = 0
203	# Parse each SASentry item
204	for entry in entry_list:
205	# Define a new Data1D object with zeroes for
206	# x_vals and y_vals
207	data1d = Data1D(numpy.empty(0), numpy.empty(0), \
208	numpy.empty(0), numpy.empty(0))
209	data1d.dxl = numpy.empty(0)
210	data1d.dxw = numpy.empty(0)
211
212	# If more than one SASentry, increment each in order
213	name = basename
214	if len(entry_list) - 1 > 0:
215	name += "_{0}".format(increment)
216	increment += 1
217
218	# Set the Data1D name and then parse the entry.
219	# The entry is appended to a list of entry values
220	data1d.filename = name
221	data1d.meta_data["loader"] = "CanSAS 1D"
222
223	# Get all preprocessing events and encoding
224	self.set_processing_instructions()
225	data1d.meta_data[PREPROCESS] = \
226	self.processing_instructions
227
228	# Parse the XML file
229	return_value, extras = \
230	self._parse_entry(entry, ns_list, data1d)
231	del extras[:]
232
233	return_value = self._final_cleanup(return_value)
234	output.append(return_value)
235	else:
236	output.append("Invalid XML at: {0}".format(\
237	self.find_invalid_xml()))
238	except:
239	# If the file does not match the schema, raise this error
240	raise RuntimeError, "%s cannot be read" % xml_file
241	return output
242	# Return a list of parsed entries that dataloader can manage
243	return None
244
245
246	def _final_cleanup(self, data1d):
247	"""
248	Final cleanup of the Data1D object to be sure it has all the
249	appropriate information needed for perspectives
250
251	:param data1d: Data1D object that has been populated
252	"""
253	# Final cleanup
254	# Remove empty nodes, verify array sizes are correct
255	for error in self.errors:
256	data1d.errors.append(error)
257	del self.errors[:]
258	numpy.trim_zeros(data1d.x)
259	numpy.trim_zeros(data1d.y)
260	numpy.trim_zeros(data1d.dy)
261	size_dx = data1d.dx.size
262	size_dxl = data1d.dxl.size
263	size_dxw = data1d.dxw.size
264	if size_dxl == 0 and size_dxw == 0:
265	data1d.dxl = None
266	data1d.dxw = None
267	numpy.trim_zeros(data1d.dx)
268	elif size_dx == 0:
269	data1d.dx = None
270	size_dx = size_dxl
271	numpy.trim_zeros(data1d.dxl)
272	numpy.trim_zeros(data1d.dxw)
273	return data1d
274
275
276	def _create_unique_key(self, dictionary, name, numb = 0):
277	"""
278	Create a unique key value for any dictionary to prevent overwriting
279	Recurses until a unique key value is found.
280
281	:param dictionary: A dictionary with any number of entries
282	:param name: The index of the item to be added to dictionary
283	:param numb: The number to be appended to the name, starts at 0
284	"""
285	if dictionary.get(name) is not None:
286	numb += 1
287	name = name.split("_")[0]
288	name += "_{0}".format(numb)
289	name = self._create_unique_key(dictionary, name, numb)
290	return name
291
292
293	def _unit_conversion(self, node, new_current_level, data1d, \
294	tagname, node_value):
295	"""
296	A unit converter method used to convert the data included in the file
297	to the default units listed in data_info
298
299	:param new_current_level: cansas_constants level as returned by
300	iterate_namespace
301	:param attr: The attributes of the node
302	:param data1d: Where the values will be saved
303	:param node_value: The value of the current dom node
304	"""
305	attr = node.attrib
306	value_unit = ''
307	if 'unit' in attr and new_current_level.get('unit') is not None:
308	try:
309	if isinstance(node_value, float) is False:
310	exec("node_value = float({0})".format(node_value))
311	default_unit = None
312	unitname = new_current_level.get("unit")
313	exec "default_unit = data1d.{0}".format(unitname)
314	local_unit = attr['unit']
315	if local_unit.lower() != default_unit.lower() and \
316	local_unit is not None and local_unit.lower() != "none" \
317	and default_unit is not None:
318	if HAS_CONVERTER == True:
319	try:
320	## Check local units - bad units raise KeyError
321	Converter(local_unit)
322	data_conv_q = Converter(attr['unit'])
323	value_unit = default_unit
324	i_string = "node_value = data_conv_q"
325	i_string += "(node_value, units=data1d.{0})"
326	exec i_string.format(unitname)
327	except KeyError:
328	err_msg = "CanSAS reader: could not convert "
329	err_msg += "{0} unit {1}; "
330	err_msg = err_msg.format(tagname, local_unit)
331	intermediate = "err_msg += " + \
332	"\"expecting [{1}] {2}\"" + \
333	".format(data1d.{0}, " + \
334	"sys.exc_info()[1])"
335	exec intermediate.format(unitname, "{0}", "{1}")
336	self.errors.append(err_msg)
337	raise ValueError(err_msg)
338	except:
339	err_msg = \
340	"CanSAS reader: could not convert the units"
341	self.errors.append(err_msg)
342	return
343	else:
344	value_unit = local_unit
345	err_msg = "CanSAS reader: unrecognized %s unit [%s];"\
346	% (node_value, default_unit)
347	err_msg += " expecting [%s]" % local_unit
348	self.errors.append(err_msg)
349	raise ValueError, err_msg
350	else:
351	value_unit = local_unit
352	except:
353	err_msg = "CanSAS reader: could not convert "
354	err_msg += "Q unit [%s]; " % attr['unit']
355	intermediate = "err_msg += \"expecting [%s]\n %s\" % " + \
356	"(data1d.{0}, sys.exc_info()[1])"
357	exec intermediate.format(unitname)
358	self.errors.append(err_msg)
359	raise ValueError, err_msg
360	elif 'unit' in attr:
361	value_unit = attr['unit']
362	node_value = "float({0})".format(node_value)
363	return node_value, value_unit
364
365
366	def _check_for_empty_data(self, data1d):
367	"""
368	Creates an empty data set if no data is passed to the reader
369
370	:param data1d: presumably a Data1D object
371	"""
372	if data1d == None:
373	self.errors = []
374	x_vals = numpy.empty(0)
375	y_vals = numpy.empty(0)
376	dx_vals = numpy.empty(0)
377	dy_vals = numpy.empty(0)
378	dxl = numpy.empty(0)
379	dxw = numpy.empty(0)
380	data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
381	data1d.dxl = dxl
382	data1d.dxw = dxw
383	return data1d
384
385
386	def _handle_special_cases(self, tagname, data1d, children):
387	"""
388	Handle cases where the data type in Data1D is a dictionary or list
389
390	:param tagname: XML tagname in use
391	:param data1d: The original Data1D object
392	:param children: Child nodes of node
393	:param node: existing node with tag name 'tagname'
394	"""
395	if tagname == "SASdetector":
396	data1d = Detector()
397	elif tagname == "SAScollimation":
398	data1d = Collimation()
399	elif tagname == "SAStransmission_spectrum":
400	data1d = TransmissionSpectrum()
401	elif tagname == "SASprocess":
402	data1d = Process()
403	for child in children:
404	if child.tag.replace(self.base_ns, "") == "term":
405	term_attr = {}
406	for attr in child.keys():
407	term_attr[attr] = \
408	' '.join(child.get(attr).split())
409	if child.text is not None:
410	term_attr['value'] = \
411	' '.join(child.text.split())
412	data1d.term.append(term_attr)
413	elif tagname == "aperture":
414	data1d = Aperture()
415	if tagname == "Idata" and children is not None:
416	data1d = self._check_for_empty_resolution(data1d, children)
417	return data1d
418
419
420	def _check_for_empty_resolution(self, data1d, children):
421	"""
422	A method to check all resolution data sets are the same size as I and Q
423	"""
424	dql_exists = False
425	dqw_exists = False
426	dq_exists = False
427	di_exists = False
428	for child in children:
429	tag = child.tag.replace(self.base_ns, "")
430	if tag == "dQl":
431	dql_exists = True
432	if tag == "dQw":
433	dqw_exists = True
434	if tag == "Qdev":
435	dq_exists = True
436	if tag == "Idev":
437	di_exists = True
438	if dqw_exists and dql_exists == False:
439	data1d.dxl = numpy.append(data1d.dxl, 0.0)
440	elif dql_exists and dqw_exists == False:
441	data1d.dxw = numpy.append(data1d.dxw, 0.0)
442	elif dql_exists == False and dqw_exists == False \
443	and dq_exists == False:
444	data1d.dx = numpy.append(data1d.dx, 0.0)
445	if di_exists == False:
446	data1d.dy = numpy.append(data1d.dy, 0.0)
447	return data1d
448
449
450	def _restore_original_case(self,
451	tagname_original,
452	tagname,
453	save_data1d,
454	data1d):
455	"""
456	Save the special case data to the appropriate location and restore
457	the original Data1D object
458
459	:param tagname_original: Unmodified tagname for the node
460	:param tagname: modified tagname for the node
461	:param save_data1d: The original Data1D object
462	:param data1d: If a special case was handled, an object of that type
463	"""
464	if tagname_original == "SASdetector":
465	save_data1d.detector.append(data1d)
466	elif tagname_original == "SAScollimation":
467	save_data1d.collimation.append(data1d)
468	elif tagname == "SAStransmission_spectrum":
469	save_data1d.trans_spectrum.append(data1d)
470	elif tagname_original == "SASprocess":
471	save_data1d.process.append(data1d)
472	elif tagname_original == "aperture":
473	save_data1d.aperture.append(data1d)
474	else:
475	save_data1d = data1d
476	return save_data1d
477
478
479	def _handle_attributes(self, node, data1d, cs_values, tagname):
480	"""
481	Process all of the attributes for a node
482	"""
483	attr = node.attrib
484	if attr is not None:
485	for key in node.keys():
486	try:
487	node_value, unit = self._get_node_value(node, cs_values, \
488	data1d, tagname)
489	cansas_attrib = \
490	cs_values.current_level.get("attributes").get(key)
491	attrib_variable = cansas_attrib.get("variable")
492	if key == 'unit' and unit != '':
493	attrib_value = unit
494	else:
495	attrib_value = node.attrib[key]
496	store_attr = attrib_variable.format("data1d", \
497	attrib_value, key)
498	exec store_attr
499	except AttributeError:
500	pass
501	return data1d
502
503
504	def _get_node_value(self, node, cs_values, data1d, tagname):
505	"""
506	Get the value of a node and any applicable units
507
508	:param node: The XML node to get the value of
509	:param cs_values: A CansasConstants.CurrentLevel object
510	:param attr: The node attributes
511	:param dataid: The working object to be modified
512	:param tagname: The tagname of the node
513	"""
514	#Get the text from the node and convert all whitespace to spaces
515	units = ''
516	node_value = node.text
517	if node_value == "":
518	node_value = None
519	if node_value is not None:
520	node_value = ' '.join(node_value.split())
521
522	# If the value is a float, compile with units.
523	if cs_values.ns_datatype == "float":
524	# If an empty value is given, set as zero.
525	if node_value is None or node_value.isspace() \
526	or node_value.lower() == "nan":
527	node_value = "0.0"
528	#Convert the value to the base units
529	node_value, units = self._unit_conversion(node, \
530	cs_values.current_level, data1d, tagname, node_value)
531
532	# If the value is a timestamp, convert to a datetime object
533	elif cs_values.ns_datatype == "timestamp":
534	if node_value is None or node_value.isspace():
535	pass
536	else:
537	try:
538	node_value = \
539	datetime.datetime.fromtimestamp(node_value)
540	except ValueError:
541	node_value = None
542	return node_value, units
543
544
545	def _parse_entry(self, dom, names=None, data1d=None, extras=None):
546	"""
547	Parse a SASEntry - new recursive method for parsing the dom of
548	the CanSAS data format. This will allow multiple data files
549	and extra nodes to be read in simultaneously.
550
551	:param dom: dom object with a namespace base of names
552	:param names: A list of element names that lead up to the dom object
553	:param data1d: The data1d object that will be modified
554	:param extras: Any values that should go into meta_data when data1d
555	is not a Data1D object
556	"""
557
558	if extras is None:
559	extras = []
560	if names is None or names == []:
561	names = ["SASentry"]
562
563	data1d = self._check_for_empty_data(data1d)
564
565	self.base_ns = "{0}{1}{2}".format("{", \
566	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
567	tagname = ''
568	tagname_original = ''
569
570	# Go through each child in the parent element
571	for node in dom:
572	try:
573	# Get the element name and set the current names level
574	tagname = node.tag.replace(self.base_ns, "")
575	tagname_original = tagname
576	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or\
577	tagname == "invariant":
578	continue
579	names.append(tagname)
580	children = node.getchildren()
581	if len(children) == 0:
582	children = None
583	save_data1d = data1d
584
585	# Look for special cases
586	data1d = self._handle_special_cases(tagname, data1d, children)
587
588	# Get where to store content
589	cs_values = CONSTANTS.iterate_namespace(names)
590	# If the element is a child element, recurse
591	if children is not None:
592	# Returned value is new Data1D object with all previous and
593	# new values in it.
594	data1d, extras = self._parse_entry(node,
595	names, data1d, extras)
596
597	#Get the information from the node
598	node_value, _ = self._get_node_value(node, cs_values, \
599	data1d, tagname)
600
601	# If appending to a dictionary (meta_data \| run_name)
602	# make sure the key is unique
603	if cs_values.ns_variable == "{0}.meta_data[\"{2}\"] = \"{1}\"":
604	# If we are within a Process, Detector, Collimation or
605	# Aperture instance, pull out old data1d
606	tagname = self._create_unique_key(data1d.meta_data, \
607	tagname, 0)
608	if isinstance(data1d, Data1D) == False:
609	store_me = cs_values.ns_variable.format("data1d", \
610	node_value, tagname)
611	extras.append(store_me)
612	cs_values.ns_variable = None
613	if cs_values.ns_variable == "{0}.run_name[\"{2}\"] = \"{1}\"":
614	tagname = self._create_unique_key(data1d.run_name, \
615	tagname, 0)
616
617	# Check for Data1D object and any extra commands to save
618	if isinstance(data1d, Data1D):
619	for item in extras:
620	exec item
621	# Don't bother saving empty information unless it is a float
622	if cs_values.ns_variable is not None and \
623	node_value is not None and \
624	node_value.isspace() == False:
625	# Format a string and then execute it.
626	store_me = cs_values.ns_variable.format("data1d", \
627	node_value, tagname)
628	exec store_me
629	# Get attributes and process them
630	data1d = self._handle_attributes(node, data1d, cs_values, \
631	tagname)
632
633	except TypeError:
634	pass
635	except Exception as excep:
636	exc_type, exc_obj, exc_tb = sys.exc_info()
637	fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
638	print(excep, exc_type, fname, exc_tb.tb_lineno, \
639	tagname, exc_obj)
640	finally:
641	# Save special cases in original data1d object
642	# then restore the data1d
643	save_data1d = self._restore_original_case(tagname_original, \
644	tagname, save_data1d, data1d)
645	if tagname_original == "fitting_plug_in" or \
646	tagname_original == "invariant" or \
647	tagname_original == "pr_inversion":
648	pass
649	else:
650	data1d = save_data1d
651	# Remove tagname from names to restore original base
652	names.remove(tagname_original)
653	return data1d, extras
654
655
656	def _get_pi_string(self):
657	"""
658	Creates the processing instructions header for writing to file
659	"""
660	pis = self.return_processing_instructions()
661	if len(pis) > 0:
662	pi_tree = self.create_tree(pis[0])
663	i = 1
664	for i in range(1, len(pis) - 1):
665	pi_tree = self.append(pis[i], pi_tree)
666	pi_string = self.to_string(pi_tree)
667	else:
668	pi_string = ""
669	return pi_string
670
671
672	def _create_main_node(self):
673	"""
674	Creates the primary xml header used when writing to file
675	"""
676	xsi = "http://www.w3.org/2001/XMLSchema-instance"
677	version = self.cansas_version
678	n_s = CANSAS_NS.get(version).get("ns")
679	if version == "1.1":
680	url = "http://www.cansas.org/formats/1.1/"
681	else:
682	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
683	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
684	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
685	"version" : version}
686	nsmap = {'xsi' : xsi, None: n_s}
687
688	main_node = self.create_element("{" + n_s + "}SASroot", \
689	attrib = attrib, \
690	nsmap = nsmap)
691	return main_node
692
693
694	def _write_run_names(self, datainfo, entry_node):
695	"""
696	Writes the run names to the XML file
697
698	:param datainfo: The Data1D object the information is coming from
699	:param entry_node: lxml node ElementTree object to be appended to
700	"""
701	if datainfo.run == None or datainfo.run == []:
702	datainfo.run.append(RUN_NAME_DEFAULT)
703	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
704	for item in datainfo.run:
705	runname = {}
706	if item in datainfo.run_name and \
707	len(str(datainfo.run_name[item])) > 1:
708	runname = {'name': datainfo.run_name[item]}
709	self.write_node(entry_node, "Run", item, runname)
710
711
712	def _write_data(self, datainfo, entry_node):
713	"""
714	Writes the I and Q data to the XML file
715
716	:param datainfo: The Data1D object the information is coming from
717	:param entry_node: lxml node ElementTree object to be appended to
718	"""
719	node = self.create_element("SASdata")
720	self.append(node, entry_node)
721
722	for i in range(len(datainfo.x)):
723	point = self.create_element("Idata")
724	node.append(point)
725	self.write_node(point, "Q", datainfo.x[i], \
726	{'unit': datainfo.x_unit})
727	if len(datainfo.y) >= i:
728	self.write_node(point, "I", datainfo.y[i],
729	{'unit': datainfo.y_unit})
730	if datainfo.dy != None and len(datainfo.dy) > i:
731	self.write_node(point, "Idev", datainfo.dy[i],
732	{'unit': datainfo.y_unit})
733	if datainfo.dx != None and len(datainfo.dx) > i:
734	self.write_node(point, "Qdev", datainfo.dx[i],
735	{'unit': datainfo.x_unit})
736	if datainfo.dxw != None and len(datainfo.dxw) > i:
737	self.write_node(point, "dQw", datainfo.dxw[i],
738	{'unit': datainfo.x_unit})
739	if datainfo.dxl != None and len(datainfo.dxl) > i:
740	self.write_node(point, "dQl", datainfo.dxl[i],
741	{'unit': datainfo.x_unit})
742
743
744
745	def _write_trans_spectrum(self, datainfo, entry_node):
746	"""
747	Writes the transmission spectrum data to the XML file
748
749	:param datainfo: The Data1D object the information is coming from
750	:param entry_node: lxml node ElementTree object to be appended to
751	"""
752	for i in range(len(datainfo.trans_spectrum)):
753	spectrum = datainfo.trans_spectrum[i]
754	node = self.create_element("SAStransmission_spectrum",
755	{"name" : spectrum.name})
756	self.append(node, entry_node)
757	if isinstance(spectrum.timestamp, datetime.datetime):
758	node.setAttribute("timestamp", spectrum.timestamp)
759	for i in range(len(spectrum.wavelength)):
760	point = self.create_element("Tdata")
761	node.append(point)
762	self.write_node(point, "Lambda", spectrum.wavelength[i],
763	{'unit': spectrum.wavelength_unit})
764	self.write_node(point, "T", spectrum.transmission[i],
765	{'unit': spectrum.transmission_unit})
766	if spectrum.transmission_deviation != None \
767	and len(spectrum.transmission_deviation) >= i:
768	self.write_node(point, "Tdev", \
769	spectrum.transmission_deviation[i], \
770	{'unit': spectrum.transmission_deviation_unit})
771
772
773	def _write_sample_info(self, datainfo, entry_node):
774	"""
775	Writes the sample information to the XML file
776
777	:param datainfo: The Data1D object the information is coming from
778	:param entry_node: lxml node ElementTree object to be appended to
779	"""
780	sample = self.create_element("SASsample")
781	if datainfo.sample.name is not None:
782	self.write_attribute(sample,
783	"name",
784	str(datainfo.sample.name))
785	self.append(sample, entry_node)
786	self.write_node(sample, "ID", str(datainfo.sample.ID))
787	self.write_node(sample, "thickness", datainfo.sample.thickness,
788	{"unit": datainfo.sample.thickness_unit})
789	self.write_node(sample, "transmission", datainfo.sample.transmission)
790	self.write_node(sample, "temperature", datainfo.sample.temperature,
791	{"unit": datainfo.sample.temperature_unit})
792
793	pos = self.create_element("position")
794	written = self.write_node(pos,
795	"x",
796	datainfo.sample.position.x,
797	{"unit": datainfo.sample.position_unit})
798	written = written \| self.write_node(pos,
799	"y",
800	datainfo.sample.position.y,
801	{"unit": datainfo.sample.position_unit})
802	written = written \| self.write_node(pos,
803	"z",
804	datainfo.sample.position.z,
805	{"unit": datainfo.sample.position_unit})
806	if written == True:
807	self.append(pos, sample)
808
809	ori = self.create_element("orientation")
810	written = self.write_node(ori, "roll",
811	datainfo.sample.orientation.x,
812	{"unit": datainfo.sample.orientation_unit})
813	written = written \| self.write_node(ori, "pitch",
814	datainfo.sample.orientation.y,
815	{"unit": datainfo.sample.orientation_unit})
816	written = written \| self.write_node(ori, "yaw",
817	datainfo.sample.orientation.z,
818	{"unit": datainfo.sample.orientation_unit})
819	if written == True:
820	self.append(ori, sample)
821
822	for item in datainfo.sample.details:
823	self.write_node(sample, "details", item)
824
825
826	def _write_instrument(self, datainfo, entry_node):
827	"""
828	Writes the instrumental information to the XML file
829
830	:param datainfo: The Data1D object the information is coming from
831	:param entry_node: lxml node ElementTree object to be appended to
832	"""
833	instr = self.create_element("SASinstrument")
834	self.append(instr, entry_node)
835	self.write_node(instr, "name", datainfo.instrument)
836	return instr
837
838
839	def _write_source(self, datainfo, instr):
840	"""
841	Writes the source information to the XML file
842
843	:param datainfo: The Data1D object the information is coming from
844	:param instr: instrument node to be appended to
845	"""
846	source = self.create_element("SASsource")
847	if datainfo.source.name is not None:
848	self.write_attribute(source,
849	"name",
850	str(datainfo.source.name))
851	self.append(source, instr)
852	if datainfo.source.radiation == None or datainfo.source.radiation == '':
853	datainfo.source.radiation = "neutron"
854	self.write_node(source, "radiation", datainfo.source.radiation)
855
856	size = self.create_element("beam_size")
857	if datainfo.source.beam_size_name is not None:
858	self.write_attribute(size,
859	"name",
860	str(datainfo.source.beam_size_name))
861	written = self.write_node(size, "x", datainfo.source.beam_size.x,
862	{"unit": datainfo.source.beam_size_unit})
863	written = written \| self.write_node(size, "y",
864	datainfo.source.beam_size.y,
865	{"unit": datainfo.source.beam_size_unit})
866	written = written \| self.write_node(size, "z",
867	datainfo.source.beam_size.z,
868	{"unit": datainfo.source.beam_size_unit})
869	if written == True:
870	self.append(size, source)
871
872	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
873	self.write_node(source, "wavelength",
874	datainfo.source.wavelength,
875	{"unit": datainfo.source.wavelength_unit})
876	self.write_node(source, "wavelength_min",
877	datainfo.source.wavelength_min,
878	{"unit": datainfo.source.wavelength_min_unit})
879	self.write_node(source, "wavelength_max",
880	datainfo.source.wavelength_max,
881	{"unit": datainfo.source.wavelength_max_unit})
882	self.write_node(source, "wavelength_spread",
883	datainfo.source.wavelength_spread,
884	{"unit": datainfo.source.wavelength_spread_unit})
885
886
887	def _write_collimation(self, datainfo, instr):
888	"""
889	Writes the collimation information to the XML file
890
891	:param datainfo: The Data1D object the information is coming from
892	:param instr: lxml node ElementTree object to be appended to
893	"""
894	if datainfo.collimation == [] or datainfo.collimation == None:
895	coll = Collimation()
896	datainfo.collimation.append(coll)
897	for item in datainfo.collimation:
898	coll = self.create_element("SAScollimation")
899	if item.name is not None:
900	self.write_attribute(coll, "name", str(item.name))
901	self.append(coll, instr)
902
903	self.write_node(coll, "length", item.length,
904	{"unit": item.length_unit})
905
906	for aperture in item.aperture:
907	apert = self.create_element("aperture")
908	if aperture.name is not None:
909	self.write_attribute(apert, "name", str(aperture.name))
910	if aperture.type is not None:
911	self.write_attribute(apert, "type", str(aperture.type))
912	self.append(apert, coll)
913
914	size = self.create_element("size")
915	if aperture.size_name is not None:
916	self.write_attribute(size,
917	"name",
918	str(aperture.size_name))
919	written = self.write_node(size, "x", aperture.size.x,
920	{"unit": aperture.size_unit})
921	written = written \| self.write_node(size, "y", aperture.size.y,
922	{"unit": aperture.size_unit})
923	written = written \| self.write_node(size, "z", aperture.size.z,
924	{"unit": aperture.size_unit})
925	if written == True:
926	self.append(size, apert)
927
928	self.write_node(apert, "distance", aperture.distance,
929	{"unit": aperture.distance_unit})
930
931
932	def _write_detectors(self, datainfo, instr):
933	"""
934	Writes the detector information to the XML file
935
936	:param datainfo: The Data1D object the information is coming from
937	:param inst: lxml instrument node to be appended to
938	"""
939	if datainfo.detector == None or datainfo.detector == []:
940	det = Detector()
941	det.name = ""
942	datainfo.detector.append(det)
943
944	for item in datainfo.detector:
945	det = self.create_element("SASdetector")
946	written = self.write_node(det, "name", item.name)
947	written = written \| self.write_node(det, "SDD", item.distance,
948	{"unit": item.distance_unit})
949	if written == True:
950	self.append(det, instr)
951
952	off = self.create_element("offset")
953	written = self.write_node(off, "x", item.offset.x,
954	{"unit": item.offset_unit})
955	written = written \| self.write_node(off, "y", item.offset.y,
956	{"unit": item.offset_unit})
957	written = written \| self.write_node(off, "z", item.offset.z,
958	{"unit": item.offset_unit})
959	if written == True:
960	self.append(off, det)
961
962	ori = self.create_element("orientation")
963	written = self.write_node(ori, "roll", item.orientation.x,
964	{"unit": item.orientation_unit})
965	written = written \| self.write_node(ori, "pitch",
966	item.orientation.y,
967	{"unit": item.orientation_unit})
968	written = written \| self.write_node(ori, "yaw",
969	item.orientation.z,
970	{"unit": item.orientation_unit})
971	if written == True:
972	self.append(ori, det)
973
974	center = self.create_element("beam_center")
975	written = self.write_node(center, "x", item.beam_center.x,
976	{"unit": item.beam_center_unit})
977	written = written \| self.write_node(center, "y",
978	item.beam_center.y,
979	{"unit": item.beam_center_unit})
980	written = written \| self.write_node(center, "z",
981	item.beam_center.z,
982	{"unit": item.beam_center_unit})
983	if written == True:
984	self.append(center, det)
985
986	pix = self.create_element("pixel_size")
987	written = self.write_node(pix, "x", item.pixel_size.x,
988	{"unit": item.pixel_size_unit})
989	written = written \| self.write_node(pix, "y", item.pixel_size.y,
990	{"unit": item.pixel_size_unit})
991	written = written \| self.write_node(pix, "z", item.pixel_size.z,
992	{"unit": item.pixel_size_unit})
993	written = written \| self.write_node(det, "slit_length",
994	item.slit_length,
995	{"unit": item.slit_length_unit})
996	if written == True:
997	self.append(pix, det)
998
999
1000	def _write_process_notes(self, datainfo, entry_node):
1001	"""
1002	Writes the process notes to the XML file
1003
1004	:param datainfo: The Data1D object the information is coming from
1005	:param entry_node: lxml node ElementTree object to be appended to
1006
1007	"""
1008	for item in datainfo.process:
1009	node = self.create_element("SASprocess")
1010	self.append(node, entry_node)
1011
1012	self.write_node(node, "name", item.name)
1013	self.write_node(node, "date", item.date)
1014	self.write_node(node, "description", item.description)
1015	for term in item.term:
1016	value = term['value']
1017	del term['value']
1018	self.write_node(node, "term", value, term)
1019	for note in item.notes:
1020	self.write_node(node, "SASprocessnote", note)
1021	if len(item.notes) == 0:
1022	self.write_node(node, "SASprocessnote", "")
1023
1024
1025	def _write_notes(self, datainfo, entry_node):
1026	"""
1027	Writes the notes to the XML file and creates an empty note if none
1028	exist
1029
1030	:param datainfo: The Data1D object the information is coming from
1031	:param entry_node: lxml node ElementTree object to be appended to
1032
1033	"""
1034	if len(datainfo.notes) == 0:
1035	node = self.create_element("SASnote")
1036	self.append(node, entry_node)
1037	else:
1038	for item in datainfo.notes:
1039	node = self.create_element("SASnote")
1040	self.write_text(node, item)
1041	self.append(node, entry_node)
1042
1043
1044	def _check_origin(self, entry_node, doc):
1045	"""
1046	Return the document, and the SASentry node associated with
1047	the data we just wrote.
1048	If the calling function was not the cansas reader, return a minidom
1049	object rather than an lxml object.
1050
1051	:param entry_node: lxml node ElementTree object to be appended to
1052	:param doc: entire xml tree
1053	"""
1054	frm = inspect.stack()[1]
1055	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
1056	mod_name = mod_name.replace(".py", "")
1057	mod = mod_name.split("sas/")
1058	mod_name = mod[1]
1059	if mod_name != "dataloader/readers/cansas_reader":
1060	string = self.to_string(doc, pretty_print=False)
1061	doc = parseString(string)
1062	node_name = entry_node.tag
1063	node_list = doc.getElementsByTagName(node_name)
1064	entry_node = node_list.item(0)
1065	return entry_node
1066
1067
1068	def _to_xml_doc(self, datainfo):
1069	"""
1070	Create an XML document to contain the content of a Data1D
1071
1072	:param datainfo: Data1D object
1073	"""
1074	if not issubclass(datainfo.__class__, Data1D):
1075	raise RuntimeError, "The cansas writer expects a Data1D instance"
1076
1077	# Get PIs and create root element
1078	pi_string = self._get_pi_string()
1079
1080	# Define namespaces and create SASroot object
1081	main_node = self._create_main_node()
1082
1083	# Create ElementTree, append SASroot and apply processing instructions
1084	base_string = pi_string + self.to_string(main_node)
1085	base_element = self.create_element_from_string(base_string)
1086	doc = self.create_tree(base_element)
1087
1088	# Create SASentry Element
1089	entry_node = self.create_element("SASentry")
1090	root = doc.getroot()
1091	root.append(entry_node)
1092
1093	# Add Title to SASentry
1094	self.write_node(entry_node, "Title", datainfo.title)
1095
1096	# Add Run to SASentry
1097	self._write_run_names(datainfo, entry_node)
1098
1099	# Add Data info to SASEntry
1100	self._write_data(datainfo, entry_node)
1101
1102	# Transmission Spectrum Info
1103	self._write_trans_spectrum(datainfo, entry_node)
1104
1105	# Sample info
1106	self._write_sample_info(datainfo, entry_node)
1107
1108	# Instrument info
1109	instr = self._write_instrument(datainfo, entry_node)
1110
1111	# Source
1112	self._write_source(datainfo, instr)
1113
1114	# Collimation
1115	self._write_collimation(datainfo, instr)
1116
1117	# Detectors
1118	self._write_detectors(datainfo, instr)
1119
1120	# Processes info
1121	self._write_process_notes(datainfo, entry_node)
1122
1123	# Note info
1124	self._write_notes(datainfo, entry_node)
1125
1126	# Return the document, and the SASentry node associated with
1127	# the data we just wrote
1128	# If the calling function was not the cansas reader, return a minidom
1129	# object rather than an lxml object.
1130	entry_node = self._check_origin(entry_node, doc)
1131
1132	return doc, entry_node
1133
1134
1135	def write_node(self, parent, name, value, attr=None):
1136	"""
1137	:param doc: document DOM
1138	:param parent: parent node
1139	:param name: tag of the element
1140	:param value: value of the child text node
1141	:param attr: attribute dictionary
1142
1143	:return: True if something was appended, otherwise False
1144	"""
1145	if value is not None:
1146	parent = self.ebuilder(parent, name, value, attr)
1147	return True
1148	return False
1149
1150
1151	def write(self, filename, datainfo):
1152	"""
1153	Write the content of a Data1D as a CanSAS XML file
1154
1155	:param filename: name of the file to write
1156	:param datainfo: Data1D object
1157	"""
1158	# Create XML document
1159	doc, _ = self._to_xml_doc(datainfo)
1160	# Write the file
1161	file_ref = open(filename, 'w')
1162	if self.encoding == None:
1163	self.encoding = "UTF-8"
1164	doc.write(file_ref, encoding=self.encoding,
1165	pretty_print=True, xml_declaration=True)
1166	file_ref.close()
1167
1168
1169	# DO NOT REMOVE - used in saving and loading panel states.
1170	def _store_float(self, location, node, variable, storage, optional=True):
1171	"""
1172	Get the content of a xpath location and store
1173	the result. Check that the units are compatible
1174	with the destination. The value is expected to
1175	be a float.
1176
1177	The xpath location might or might not exist.
1178	If it does not exist, nothing is done
1179
1180	:param location: xpath location to fetch
1181	:param node: node to read the data from
1182	:param variable: name of the data member to store it in [string]
1183	:param storage: data object that has the 'variable' data member
1184	:param optional: if True, no exception will be raised
1185	if unit conversion can't be done
1186
1187	:raise ValueError: raised when the units are not recognized
1188	"""
1189	entry = get_content(location, node)
1190	try:
1191	value = float(entry.text)
1192	except:
1193	value = None
1194
1195	if value is not None:
1196	# If the entry has units, check to see that they are
1197	# compatible with what we currently have in the data object
1198	units = entry.get('unit')
1199	if units is not None:
1200	toks = variable.split('.')
1201	local_unit = None
1202	exec "local_unit = storage.%s_unit" % toks[0]
1203	if local_unit != None and units.lower() != local_unit.lower():
1204	if HAS_CONVERTER == True:
1205	try:
1206	conv = Converter(units)
1207	exec "storage.%s = %g" % (variable,
1208	conv(value, units=local_unit))
1209	except:
1210	_, exc_value, _ = sys.exc_info()
1211	err_mess = "CanSAS reader: could not convert"
1212	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1213	% (variable, units, local_unit, exc_value)
1214	self.errors.append(err_mess)
1215	if optional:
1216	logging.info(err_mess)
1217	else:
1218	raise ValueError, err_mess
1219	else:
1220	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1221	% (variable, units)
1222	err_mess += " expecting [%s]" % local_unit
1223	self.errors.append(err_mess)
1224	if optional:
1225	logging.info(err_mess)
1226	else:
1227	raise ValueError, err_mess
1228	else:
1229	exec "storage.%s = value" % variable
1230	else:
1231	exec "storage.%s = value" % variable
1232
1233
1234	# DO NOT REMOVE - used in saving and loading panel states.
1235	def _store_content(self, location, node, variable, storage):
1236	"""
1237	Get the content of a xpath location and store
1238	the result. The value is treated as a string.
1239
1240	The xpath location might or might not exist.
1241	If it does not exist, nothing is done
1242
1243	:param location: xpath location to fetch
1244	:param node: node to read the data from
1245	:param variable: name of the data member to store it in [string]
1246	:param storage: data object that has the 'variable' data member
1247
1248	:return: return a list of errors
1249	"""
1250	entry = get_content(location, node)
1251	if entry is not None and entry.text is not None:
1252	exec "storage.%s = entry.text.strip()" % variable

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SasView

source: sasview/src/sas/dataloader/readers/cansas_reader.py @ 79492222

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