cansas_reader.py @ 51af54b

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 51af54b was 51af54b, checked in by Jeff Krzywon <jeffery.krzywon@…>, 10 years ago
Fixing project save/load and changed up an poorly worded error message.
Property mode set to `100644`
File size: 45.0 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 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	if not issubclass(datainfo.__class__, Data1D):
538	raise RuntimeError, "The cansas writer expects a Data1D instance"
539
540	# Get PIs and create root element
541	pis = self.return_processing_instructions()
542	if len(pis) > 0:
543	pi_tree = self.create_tree(pis[0])
544	i = 1
545	for i in range(1,len(pis) - 1):
546	pi_tree = self.append(pis[i], pi_tree)
547	pi_string = self.to_string(pi_tree)
548	else:
549	pi_string = ""
550
551	# Define namespaces and create SASroot object
552	xsi = "http://www.w3.org/2001/XMLSchema-instance"
553	version = self.cansas_version
554	ns = CANSAS_NS.get(version).get("ns")
555	if version == "1.1":
556	url = "http://www.cansas.org/formats/1.1/"
557	else:
558	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
559	schema_location = "{0} {1}cansas1d.xsd".format(ns, url)
560	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
561	"version" : version}
562	nsmap = {'xsi' : xsi, None: ns}
563
564	main_node = self.create_element("{" + ns + "}SASroot", \
565	attrib = attrib, \
566	nsmap = nsmap)
567
568	# Create ElementTree, append SASroot and apply processing instructions
569	base_string = pi_string + self.to_string(main_node)
570	base_element = self.create_element_from_string(base_string)
571	doc = self.create_tree(base_element)
572
573	# Create SASentry Element
574	entry_node = self.create_element("SASentry")
575	root = doc.getroot()
576	root.append(entry_node)
577
578	# Add Title to SASentry
579	self.write_node(entry_node, "Title", datainfo.title)
580
581	# Add Run to SASentry
582	if datainfo.run == None or datainfo.run == []:
583	RUN_NAME_DEFAULT = "None"
584	datainfo.run.append(RUN_NAME_DEFAULT)
585	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
586	for item in datainfo.run:
587	runname = {}
588	if item in datainfo.run_name and \
589	len(str(datainfo.run_name[item])) > 1:
590	runname = {'name': datainfo.run_name[item]}
591	self.write_node(entry_node, "Run", item, runname)
592
593	# Data info
594	node = self.create_element("SASdata")
595	self.append(node, entry_node)
596
597	for i in range(len(datainfo.x)):
598	pt = self.create_element("Idata")
599	node.append(pt)
600	self.write_node(pt, "Q", datainfo.x[i], {'unit': datainfo.x_unit})
601	if len(datainfo.y) >= i:
602	self.write_node(pt, "I", datainfo.y[i],
603	{'unit': datainfo.y_unit})
604	if datainfo.dy != None and len(datainfo.dy) > i:
605	self.write_node(pt, "Idev", datainfo.dy[i],
606	{'unit': datainfo.y_unit})
607	if datainfo.dx != None and len(datainfo.dx) > i:
608	self.write_node(pt, "Qdev", datainfo.dx[i],
609	{'unit': datainfo.x_unit})
610	if datainfo.dxw != None and len(datainfo.dxw) > i:
611	self.write_node(pt, "dQw", datainfo.dxw[i],
612	{'unit': datainfo.x_unit})
613	if datainfo.dxl != None and len(datainfo.dxl) > i:
614	self.write_node(pt, "dQl", datainfo.dxl[i],
615	{'unit': datainfo.x_unit})
616
617	# Transmission Spectrum Info
618	for i in range(len(datainfo.trans_spectrum)):
619	spectrum = datainfo.trans_spectrum[i]
620	node = self.create_element("SAStransmission_spectrum",
621	{"name" : spectrum.name})
622	self.append(node, entry_node)
623	if isinstance(spectrum.timestamp, datetime.datetime):
624	node.setAttribute("timestamp", spectrum.timestamp)
625	for i in range(len(spectrum.wavelength)):
626	pt = self.create_element("Tdata")
627	node.append(pt)
628	self.write_node(pt, "Lambda", spectrum.wavelength[i],
629	{'unit': spectrum.wavelength_unit})
630	self.write_node(pt, "T", spectrum.transmission[i],
631	{'unit': spectrum.transmission_unit})
632	if spectrum.transmission_deviation != None \
633	and len(spectrum.transmission_deviation) >= i:
634	self.write_node(pt, "Tdev", \
635	spectrum.transmission_deviation[i], \
636	{'unit': spectrum.transmission_deviation_unit})
637
638	# Sample info
639	sample = self.create_element("SASsample")
640	if datainfo.sample.name is not None:
641	self.write_attribute(sample,
642	"name",
643	str(datainfo.sample.name))
644	self.append(sample, entry_node)
645	self.write_node(sample, "ID", str(datainfo.sample.ID))
646	self.write_node(sample, "thickness", datainfo.sample.thickness,
647	{"unit": datainfo.sample.thickness_unit})
648	self.write_node(sample, "transmission", datainfo.sample.transmission)
649	self.write_node(sample, "temperature", datainfo.sample.temperature,
650	{"unit": datainfo.sample.temperature_unit})
651
652	pos = self.create_element("position")
653	written = self.write_node(pos,
654	"x",
655	datainfo.sample.position.x,
656	{"unit": datainfo.sample.position_unit})
657	written = written \| self.write_node(pos,
658	"y",
659	datainfo.sample.position.y,
660	{"unit": datainfo.sample.position_unit})
661	written = written \| self.write_node(pos,
662	"z",
663	datainfo.sample.position.z,
664	{"unit": datainfo.sample.position_unit})
665	if written == True:
666	self.append(pos, sample)
667
668	ori = self.create_element("orientation")
669	written = self.write_node(ori, "roll",
670	datainfo.sample.orientation.x,
671	{"unit": datainfo.sample.orientation_unit})
672	written = written \| self.write_node(ori, "pitch",
673	datainfo.sample.orientation.y,
674	{"unit": datainfo.sample.orientation_unit})
675	written = written \| self.write_node(ori, "yaw",
676	datainfo.sample.orientation.z,
677	{"unit": datainfo.sample.orientation_unit})
678	if written == True:
679	self.append(ori, sample)
680
681	for item in datainfo.sample.details:
682	self.write_node(sample, "details", item)
683
684	# Instrument info
685	instr = self.create_element("SASinstrument")
686	self.append(instr, entry_node)
687
688	self.write_node(instr, "name", datainfo.instrument)
689
690	# Source
691	source = self.create_element("SASsource")
692	if datainfo.source.name is not None:
693	self.write_attribute(source,
694	"name",
695	str(datainfo.source.name))
696	self.append(source, instr)
697	if datainfo.source.radiation == None or datainfo.source.radiation == '':
698	datainfo.source.radiation = "neutron"
699	self.write_node(source, "radiation", datainfo.source.radiation)
700
701	size = self.create_element("beam_size")
702	if datainfo.source.beam_size_name is not None:
703	self.write_attribute(size,
704	"name",
705	str(datainfo.source.beam_size_name))
706	written = self.write_node(size, "x", datainfo.source.beam_size.x,
707	{"unit": datainfo.source.beam_size_unit})
708	written = written \| self.write_node(size, "y",
709	datainfo.source.beam_size.y,
710	{"unit": datainfo.source.beam_size_unit})
711	written = written \| self.write_node(size, "z",
712	datainfo.source.beam_size.z,
713	{"unit": datainfo.source.beam_size_unit})
714	if written == True:
715	self.append(size, source)
716
717	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
718	self.write_node(source, "wavelength",
719	datainfo.source.wavelength,
720	{"unit": datainfo.source.wavelength_unit})
721	self.write_node(source, "wavelength_min",
722	datainfo.source.wavelength_min,
723	{"unit": datainfo.source.wavelength_min_unit})
724	self.write_node(source, "wavelength_max",
725	datainfo.source.wavelength_max,
726	{"unit": datainfo.source.wavelength_max_unit})
727	self.write_node(source, "wavelength_spread",
728	datainfo.source.wavelength_spread,
729	{"unit": datainfo.source.wavelength_spread_unit})
730
731	# Collimation
732	if datainfo.collimation == [] or datainfo.collimation == None:
733	coll = Collimation()
734	datainfo.collimation.append(coll)
735	for item in datainfo.collimation:
736	coll = self.create_element("SAScollimation")
737	if item.name is not None:
738	self.write_attribute(coll, "name", str(item.name))
739	self.append(coll, instr)
740
741	self.write_node(coll, "length", item.length,
742	{"unit": item.length_unit})
743
744	for apert in item.aperture:
745	ap = self.create_element("aperture")
746	if apert.name is not None:
747	self.write_attribute(ap, "name", str(apert.name))
748	if apert.type is not None:
749	self.write_attribute(ap, "type", str(apert.type))
750	self.append(ap, coll)
751
752	size = self.create_element("size")
753	if apert.size_name is not None:
754	self.write_attribute(size,
755	"name",
756	str(apert.size_name))
757	written = self.write_node(size, "x", apert.size.x,
758	{"unit": apert.size_unit})
759	written = written \| self.write_node(size, "y", apert.size.y,
760	{"unit": apert.size_unit})
761	written = written \| self.write_node(size, "z", apert.size.z,
762	{"unit": apert.size_unit})
763	if written == True:
764	self.append(size, ap)
765
766	self.write_node(ap, "distance", apert.distance,
767	{"unit": apert.distance_unit})
768
769	# Detectors
770	if datainfo.detector == None or datainfo.detector == []:
771	det = Detector()
772	det.name = ""
773	datainfo.detector.append(det)
774
775	for item in datainfo.detector:
776	det = self.create_element("SASdetector")
777	written = self.write_node(det, "name", item.name)
778	written = written \| self.write_node(det, "SDD", item.distance,
779	{"unit": item.distance_unit})
780	if written == True:
781	self.append(det, instr)
782
783	off = self.create_element("offset")
784	written = self.write_node(off, "x", item.offset.x,
785	{"unit": item.offset_unit})
786	written = written \| self.write_node(off, "y", item.offset.y,
787	{"unit": item.offset_unit})
788	written = written \| self.write_node(off, "z", item.offset.z,
789	{"unit": item.offset_unit})
790	if written == True:
791	self.append(off, det)
792
793	ori = self.create_element("orientation")
794	written = self.write_node(ori, "roll", item.orientation.x,
795	{"unit": item.orientation_unit})
796	written = written \| self.write_node(ori, "pitch",
797	item.orientation.y,
798	{"unit": item.orientation_unit})
799	written = written \| self.write_node(ori, "yaw",
800	item.orientation.z,
801	{"unit": item.orientation_unit})
802	if written == True:
803	self.append(ori, det)
804
805	center = self.create_element("beam_center")
806	written = self.write_node(center, "x", item.beam_center.x,
807	{"unit": item.beam_center_unit})
808	written = written \| self.write_node(center, "y",
809	item.beam_center.y,
810	{"unit": item.beam_center_unit})
811	written = written \| self.write_node(center, "z",
812	item.beam_center.z,
813	{"unit": item.beam_center_unit})
814	if written == True:
815	self.append(center, det)
816
817	pix = self.create_element("pixel_size")
818	written = self.write_node(pix, "x", item.pixel_size.x,
819	{"unit": item.pixel_size_unit})
820	written = written \| self.write_node(pix, "y", item.pixel_size.y,
821	{"unit": item.pixel_size_unit})
822	written = written \| self.write_node(pix, "z", item.pixel_size.z,
823	{"unit": item.pixel_size_unit})
824	written = written \| self.write_node(det, "slit_length",
825	item.slit_length,
826	{"unit": item.slit_length_unit})
827	if written == True:
828	self.append(pix, det)
829
830	# Processes info
831	for item in datainfo.process:
832	node = self.create_element("SASprocess")
833	self.append(node, entry_node)
834
835	self.write_node(node, "name", item.name)
836	self.write_node(node, "date", item.date)
837	self.write_node(node, "description", item.description)
838	for term in item.term:
839	value = term['value']
840	del term['value']
841	self.write_node(node, "term", value, term)
842	for note in item.notes:
843	self.write_node(node, "SASprocessnote", note)
844	if len(item.notes) == 0:
845	self.write_node(node, "SASprocessnote", "")
846
847	# Note info
848	if len(datainfo.notes) == 0:
849	node = self.create_element("SASnote")
850	self.append(node, entry_node)
851	else:
852	for item in datainfo.notes:
853	node = self.create_element("SASnote")
854	self.write_text(node, item)
855	self.append(node, entry_node)
856
857
858	# Return the document, and the SASentry node associated with
859	# the data we just wrote
860	# If the calling function was not the cansas reader, return a minidom
861	# object rather than an lxml object.
862	frm = inspect.stack()[1]
863	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
864	mod_name = mod_name.replace(".py", "")
865	mod = mod_name.split("sans/")
866	mod_name = mod[1]
867	if mod_name != "dataloader/readers/cansas_reader":
868	string = self.to_string(doc, pp=False)
869	doc = parseString(string)
870	node_name = entry_node.tag
871	node_list = doc.getElementsByTagName(node_name)
872	entry_node = node_list.item(0)
873
874	return doc, entry_node
875
876
877	def write_node(self, parent, name, value, attr=None):
878	"""
879	:param doc: document DOM
880	:param parent: parent node
881	:param name: tag of the element
882	:param value: value of the child text node
883	:param attr: attribute dictionary
884
885	:return: True if something was appended, otherwise False
886	"""
887	if value is not None:
888	parent = self.ebuilder(parent, name, value, attr)
889	return True
890	return False
891
892
893	def write(self, filename, datainfo):
894	"""
895	Write the content of a Data1D as a CanSAS XML file
896
897	:param filename: name of the file to write
898	:param datainfo: Data1D object
899	"""
900	# Create XML document
901	doc, _ = self._to_xml_doc(datainfo)
902	# Write the file
903	fd = open(filename, 'w')
904	if self.encoding == None:
905	self.encoding = "UTF-8"
906	doc.write(fd, encoding=self.encoding,
907	pretty_print=True, xml_declaration=True)
908	fd.close()
909
910
911	# DO NOT REMOVE - used in saving and loading panel states.
912	def _store_float(self, location, node, variable, storage, optional=True):
913	"""
914	Get the content of a xpath location and store
915	the result. Check that the units are compatible
916	with the destination. The value is expected to
917	be a float.
918
919	The xpath location might or might not exist.
920	If it does not exist, nothing is done
921
922	:param location: xpath location to fetch
923	:param node: node to read the data from
924	:param variable: name of the data member to store it in [string]
925	:param storage: data object that has the 'variable' data member
926	:param optional: if True, no exception will be raised
927	if unit conversion can't be done
928
929	:raise ValueError: raised when the units are not recognized
930	"""
931	entry = get_content(location, node)
932	try:
933	value = float(entry.text)
934	except:
935	value = None
936
937	if value is not None:
938	# If the entry has units, check to see that they are
939	# compatible with what we currently have in the data object
940	units = entry.get('unit')
941	if units is not None:
942	toks = variable.split('.')
943	local_unit = None
944	exec "local_unit = storage.%s_unit" % toks[0]
945	if local_unit != None and units.lower() != local_unit.lower():
946	if HAS_CONVERTER == True:
947	try:
948	conv = Converter(units)
949	exec "storage.%s = %g" % (variable,
950	conv(value, units=local_unit))
951	except:
952	exc_type, exc_value, exc_traceback = sys.exc_info()
953	err_mess = "CanSAS reader: could not convert"
954	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
955	% (variable, units, local_unit, exc_value)
956	self.errors.append(err_mess)
957	if optional:
958	logging.info(err_mess)
959	else:
960	raise ValueError, err_mess
961	else:
962	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
963	% (variable, units)
964	err_mess += " expecting [%s]" % local_unit
965	self.errors.append(err_mess)
966	if optional:
967	logging.info(err_mess)
968	else:
969	raise ValueError, err_mess
970	else:
971	exec "storage.%s = value" % variable
972	else:
973	exec "storage.%s = value" % variable
974
975
976	# DO NOT REMOVE - used in saving and loading panel states.
977	def _store_content(self, location, node, variable, storage):
978	"""
979	Get the content of a xpath location and store
980	the result. The value is treated as a string.
981
982	The xpath location might or might not exist.
983	If it does not exist, nothing is done
984
985	:param location: xpath location to fetch
986	:param node: node to read the data from
987	:param variable: name of the data member to store it in [string]
988	:param storage: data object that has the 'variable' data member
989
990	:return: return a list of errors
991	"""
992	entry = get_content(location, node)
993	if entry is not None and entry.text is not None:
994	exec "storage.%s = entry.text.strip()" % variable

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SasView

source: sasview/src/sans/dataloader/readers/cansas_reader.py @ 51af54b

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