cansas_reader.py @ bc570f4

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since bc570f4 was bc570f4, checked in by lewis, 7 years ago
Refactor CanSASReader/XMLReader to use FileReader? class
Property mode set to `100644`
File size: 71.7 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 as np
17	import os
18	import sys
19	import datetime
20	import inspect
21	# For saving individual sections of data
22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
23	plottable_1D, plottable_2D
24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
25	Detector, Process, Aperture
26	from sas.sascalc.dataloader.data_info import \
27	combine_data_info_with_plottable as combine_data
28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
31	from sas.sascalc.dataloader.loader_exceptions import FileContentsException, \
32	DefaultReaderException, DataReaderException
33
34	# The following 2 imports ARE used. Do not remove either.
35	import xml.dom.minidom
36	from xml.dom.minidom import parseString
37
38	logger = logging.getLogger(__name__)
39
40	PREPROCESS = "xmlpreprocess"
41	ENCODING = "encoding"
42	RUN_NAME_DEFAULT = "None"
43	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
44	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
45	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
46	"as much of the data as possible.\n\n"
47	HAS_CONVERTER = True
48	try:
49	from sas.sascalc.data_util.nxsunit import Converter
50	except ImportError:
51	HAS_CONVERTER = False
52
53	CONSTANTS = CansasConstants()
54	CANSAS_FORMAT = CONSTANTS.format
55	CANSAS_NS = CONSTANTS.names
56	ALLOW_ALL = True
57
58	class Reader(XMLreader):
59	"""
60	Class to load cansas 1D XML files
61
62	:Dependencies:
63	The CanSAS reader requires PyXML 0.8.4 or later.
64	"""
65	# CanSAS version - defaults to version 1.0
66	cansas_version = "1.0"
67	base_ns = "{cansas1d/1.0}"
68	cansas_defaults = None
69	type_name = "canSAS"
70	invalid = True
71	frm = ""
72	# Log messages and errors
73	logging = None
74	errors = set()
75	# Namespace hierarchy for current xml_file object
76	names = None
77	ns_list = None
78	# Temporary storage location for loading multiple data sets in a single file
79	current_data1d = None
80	data = None
81	# Wildcards
82	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
83	# List of allowed extensions
84	ext = ['.xml', '.XML', '.svs', '.SVS']
85	# Flag to bypass extension check
86	allow_all = True
87
88	def reset_state(self):
89	"""
90	Resets the class state to a base case when loading a new data file so previous
91	data files do not appear a second time
92	"""
93	self.current_datainfo = None
94	self.current_dataset = None
95	self.current_data1d = None
96	self.data = []
97	self.process = Process()
98	self.transspectrum = TransmissionSpectrum()
99	self.aperture = Aperture()
100	self.collimation = Collimation()
101	self.detector = Detector()
102	self.names = []
103	self.cansas_defaults = {}
104	self.output = []
105	self.ns_list = None
106	self.logging = []
107	self.encoding = None
108
109	def read(self, xml_file, schema_path="", invalid=True):
110	if schema_path != "" or invalid != True:
111	# read has been called from self.get_file_contents because xml file doens't conform to schema
112	_, self.extension = os.path.splitext(os.path.basename(xml_file))
113	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
114
115	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
116	return super(XMLreader, self).read(xml_file)
117
118	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
119	"""
120	Validate and read in an xml_file file in the canSAS format.
121
122	:param xml_file: A canSAS file path in proper XML format
123	:param schema_path: A file path to an XML schema to validate the xml_file against
124	"""
125	# For every file loaded, reset everything to a base state
126	self.reset_state()
127	self.invalid = invalid
128	# We don't use f_open since libxml handles opening/closing files
129	if xml_file is None:
130	xml_file = self.f_open.name
131	if not self.f_open.closed:
132	self.f_open.close()
133	basename, _ = os.path.splitext(os.path.basename(xml_file))
134	try:
135	# Get the file location of
136	self.load_file_and_schema(xml_file, schema_path)
137	self.add_data_set()
138	# Try to load the file, but raise an error if unable to.
139	# Check the file matches the XML schema
140	self.is_cansas(self.extension) # Raises FileContentsException if not CanSAS
141	self.invalid = False
142	# Get each SASentry from XML file and add it to a list.
143	entry_list = self.xmlroot.xpath(
144	'/ns:SASroot/ns:SASentry',
145	namespaces={'ns': self.cansas_defaults.get("ns")})
146	self.names.append("SASentry")
147
148	# Get all preprocessing events and encoding
149	self.set_processing_instructions()
150
151	# Parse each <SASentry> item
152	for entry in entry_list:
153	# Create a new DataInfo object for every <SASentry>
154
155	# Set the file name and then parse the entry.
156	self.current_datainfo.filename = basename + self.extension
157	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
158	self.current_datainfo.meta_data[PREPROCESS] = \
159	self.processing_instructions
160
161	# Parse the XML SASentry
162	self._parse_entry(entry)
163	# Combine datasets with datainfo
164	self.add_data_set()
165	except FileContentsException as fc_exc:
166	try:
167	# Try again with an invalid CanSAS schema, that requires only a data set in each
168	base_name = xml_reader.__file__
169	base_name = base_name.replace("\\", "/")
170	base = base_name.split("/sas/")[0]
171	if self.cansas_version == "1.1":
172	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
173	else:
174	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
175	self.set_schema(invalid_schema)
176	if self.invalid:
177	self.output = self.read(xml_file, invalid_schema, False)
178	# If the file does not match the schema, but can still be read, raise this error
179	self.load_file_and_schema(xml_file) # Relaod valid schema so we can find errors
180	invalid_xml = self.find_invalid_xml()
181	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
182	raise DataReaderException(invalid_xml)
183	else:
184	raise fc_exc
185	except FileContentsException as fc_exc:
186	msg = "CanSAS Reader could not load the file {}".format(xml_file)
187	if not self.extension in self.ext: # If the file has no associated loader
188	raise DefaultReaderException(msg)
189	if fc_exc.message is not None: # Propagate error messages from earlier
190	msg = fc_exc.message
191	raise FileContentsException(msg)
192	except DataReaderException as dr_exc: # Handled by file_reader_base_class
193	raise dr_exc
194	except Exception as e: # Convert any other exceptions to FileContentsExceptions
195	raise FileContentsException(e.message)
196	# Return a list of parsed entries that dataloader can manage
197	return self.output
198
199	def _parse_entry(self, dom, recurse=False):
200	"""
201	Parse a SASEntry - new recursive method for parsing the dom of
202	the CanSAS data format. This will allow multiple data files
203	and extra nodes to be read in simultaneously.
204
205	:param dom: dom object with a namespace base of names
206	"""
207
208	if not self._is_call_local() and not recurse:
209	self.reset_state()
210	self.add_data_set()
211	self.names.append("SASentry")
212	self.parent_class = "SASentry"
213	self._check_for_empty_data()
214	self.base_ns = "{0}{1}{2}".format("{", \
215	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
216
217	# Go through each child in the parent element
218	for node in dom:
219	attr = node.attrib
220	name = attr.get("name", "")
221	type = attr.get("type", "")
222	# Get the element name and set the current names level
223	tagname = node.tag.replace(self.base_ns, "")
224	tagname_original = tagname
225	# Skip this iteration when loading in save state information
226	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
227	continue
228
229	# Get where to store content
230	self.names.append(tagname_original)
231	self.ns_list = CONSTANTS.iterate_namespace(self.names)
232	# If the element is a child element, recurse
233	if len(node.getchildren()) > 0:
234	self.parent_class = tagname_original
235	if tagname == 'SASdata':
236	self._initialize_new_data_set(node)
237	if isinstance(self.current_dataset, plottable_2D):
238	x_bins = attr.get("x_bins", "")
239	y_bins = attr.get("y_bins", "")
240	if x_bins is not "" and y_bins is not "":
241	self.current_dataset.shape = (x_bins, y_bins)
242	else:
243	self.current_dataset.shape = ()
244	# Recursion step to access data within the group
245	self._parse_entry(node, True)
246	if tagname == "SASsample":
247	self.current_datainfo.sample.name = name
248	elif tagname == "beam_size":
249	self.current_datainfo.source.beam_size_name = name
250	elif tagname == "SAScollimation":
251	self.collimation.name = name
252	elif tagname == "aperture":
253	self.aperture.name = name
254	self.aperture.type = type
255	self.add_intermediate()
256	else:
257	if isinstance(self.current_dataset, plottable_2D):
258	data_point = node.text
259	unit = attr.get('unit', '')
260	else:
261	data_point, unit = self._get_node_value(node, tagname)
262
263	# If this is a dataset, store the data appropriately
264	if tagname == 'Run':
265	self.current_datainfo.run_name[data_point] = name
266	self.current_datainfo.run.append(data_point)
267	elif tagname == 'Title':
268	self.current_datainfo.title = data_point
269	elif tagname == 'SASnote':
270	self.current_datainfo.notes.append(data_point)
271
272	# I and Q - 1D data
273	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
274	unit_list = unit.split("\|")
275	if len(unit_list) > 1:
276	self.current_dataset.yaxis(unit_list[0].strip(),
277	unit_list[1].strip())
278	else:
279	self.current_dataset.yaxis("Intensity", unit)
280	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
281	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
282	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
283	elif tagname == 'Q':
284	unit_list = unit.split("\|")
285	if len(unit_list) > 1:
286	self.current_dataset.xaxis(unit_list[0].strip(),
287	unit_list[1].strip())
288	else:
289	self.current_dataset.xaxis("Q", unit)
290	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
291	elif tagname == 'Qdev':
292	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
293	elif tagname == 'dQw':
294	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
295	elif tagname == 'dQl':
296	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
297	elif tagname == 'Qmean':
298	pass
299	elif tagname == 'Shadowfactor':
300	pass
301	elif tagname == 'Sesans':
302	self.current_datainfo.isSesans = bool(data_point)
303	elif tagname == 'yacceptance':
304	self.current_datainfo.sample.yacceptance = (data_point, unit)
305	elif tagname == 'zacceptance':
306	self.current_datainfo.sample.zacceptance = (data_point, unit)
307
308	# I and Qx, Qy - 2D data
309	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
310	self.current_dataset.yaxis("Intensity", unit)
311	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
312	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
313	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qx':
315	self.current_dataset.xaxis("Qx", unit)
316	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Qy':
318	self.current_dataset.yaxis("Qy", unit)
319	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
320	elif tagname == 'Qxdev':
321	self.current_dataset.xaxis("Qxdev", unit)
322	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
323	elif tagname == 'Qydev':
324	self.current_dataset.yaxis("Qydev", unit)
325	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
326	elif tagname == 'Mask':
327	inter = [item == "1" for item in data_point.split(",")]
328	self.current_dataset.mask = np.asarray(inter, dtype=bool)
329
330	# Sample Information
331	elif tagname == 'ID' and self.parent_class == 'SASsample':
332	self.current_datainfo.sample.ID = data_point
333	elif tagname == 'Title' and self.parent_class == 'SASsample':
334	self.current_datainfo.sample.name = data_point
335	elif tagname == 'thickness' and self.parent_class == 'SASsample':
336	self.current_datainfo.sample.thickness = data_point
337	self.current_datainfo.sample.thickness_unit = unit
338	elif tagname == 'transmission' and self.parent_class == 'SASsample':
339	self.current_datainfo.sample.transmission = data_point
340	elif tagname == 'temperature' and self.parent_class == 'SASsample':
341	self.current_datainfo.sample.temperature = data_point
342	self.current_datainfo.sample.temperature_unit = unit
343	elif tagname == 'details' and self.parent_class == 'SASsample':
344	self.current_datainfo.sample.details.append(data_point)
345	elif tagname == 'x' and self.parent_class == 'position':
346	self.current_datainfo.sample.position.x = data_point
347	self.current_datainfo.sample.position_unit = unit
348	elif tagname == 'y' and self.parent_class == 'position':
349	self.current_datainfo.sample.position.y = data_point
350	self.current_datainfo.sample.position_unit = unit
351	elif tagname == 'z' and self.parent_class == 'position':
352	self.current_datainfo.sample.position.z = data_point
353	self.current_datainfo.sample.position_unit = unit
354	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
355	self.current_datainfo.sample.orientation.x = data_point
356	self.current_datainfo.sample.orientation_unit = unit
357	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
358	self.current_datainfo.sample.orientation.y = data_point
359	self.current_datainfo.sample.orientation_unit = unit
360	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
361	self.current_datainfo.sample.orientation.z = data_point
362	self.current_datainfo.sample.orientation_unit = unit
363
364	# Instrumental Information
365	elif tagname == 'name' and self.parent_class == 'SASinstrument':
366	self.current_datainfo.instrument = data_point
367	# Detector Information
368	elif tagname == 'name' and self.parent_class == 'SASdetector':
369	self.detector.name = data_point
370	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
371	self.detector.distance = data_point
372	self.detector.distance_unit = unit
373	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
374	self.detector.slit_length = data_point
375	self.detector.slit_length_unit = unit
376	elif tagname == 'x' and self.parent_class == 'offset':
377	self.detector.offset.x = data_point
378	self.detector.offset_unit = unit
379	elif tagname == 'y' and self.parent_class == 'offset':
380	self.detector.offset.y = data_point
381	self.detector.offset_unit = unit
382	elif tagname == 'z' and self.parent_class == 'offset':
383	self.detector.offset.z = data_point
384	self.detector.offset_unit = unit
385	elif tagname == 'x' and self.parent_class == 'beam_center':
386	self.detector.beam_center.x = data_point
387	self.detector.beam_center_unit = unit
388	elif tagname == 'y' and self.parent_class == 'beam_center':
389	self.detector.beam_center.y = data_point
390	self.detector.beam_center_unit = unit
391	elif tagname == 'z' and self.parent_class == 'beam_center':
392	self.detector.beam_center.z = data_point
393	self.detector.beam_center_unit = unit
394	elif tagname == 'x' and self.parent_class == 'pixel_size':
395	self.detector.pixel_size.x = data_point
396	self.detector.pixel_size_unit = unit
397	elif tagname == 'y' and self.parent_class == 'pixel_size':
398	self.detector.pixel_size.y = data_point
399	self.detector.pixel_size_unit = unit
400	elif tagname == 'z' and self.parent_class == 'pixel_size':
401	self.detector.pixel_size.z = data_point
402	self.detector.pixel_size_unit = unit
403	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
404	self.detector.orientation.x = data_point
405	self.detector.orientation_unit = unit
406	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
407	self.detector.orientation.y = data_point
408	self.detector.orientation_unit = unit
409	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
410	self.detector.orientation.z = data_point
411	self.detector.orientation_unit = unit
412	# Collimation and Aperture
413	elif tagname == 'length' and self.parent_class == 'SAScollimation':
414	self.collimation.length = data_point
415	self.collimation.length_unit = unit
416	elif tagname == 'name' and self.parent_class == 'SAScollimation':
417	self.collimation.name = data_point
418	elif tagname == 'distance' and self.parent_class == 'aperture':
419	self.aperture.distance = data_point
420	self.aperture.distance_unit = unit
421	elif tagname == 'x' and self.parent_class == 'size':
422	self.aperture.size.x = data_point
423	self.collimation.size_unit = unit
424	elif tagname == 'y' and self.parent_class == 'size':
425	self.aperture.size.y = data_point
426	self.collimation.size_unit = unit
427	elif tagname == 'z' and self.parent_class == 'size':
428	self.aperture.size.z = data_point
429	self.collimation.size_unit = unit
430
431	# Process Information
432	elif tagname == 'name' and self.parent_class == 'SASprocess':
433	self.process.name = data_point
434	elif tagname == 'description' and self.parent_class == 'SASprocess':
435	self.process.description = data_point
436	elif tagname == 'date' and self.parent_class == 'SASprocess':
437	try:
438	self.process.date = datetime.datetime.fromtimestamp(data_point)
439	except:
440	self.process.date = data_point
441	elif tagname == 'SASprocessnote':
442	self.process.notes.append(data_point)
443	elif tagname == 'term' and self.parent_class == 'SASprocess':
444	unit = attr.get("unit", "")
445	dic = {}
446	dic["name"] = name
447	dic["value"] = data_point
448	dic["unit"] = unit
449	self.process.term.append(dic)
450
451	# Transmission Spectrum
452	elif tagname == 'T' and self.parent_class == 'Tdata':
453	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
454	self.transspectrum.transmission_unit = unit
455	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
456	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
457	self.transspectrum.transmission_deviation_unit = unit
458	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
459	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
460	self.transspectrum.wavelength_unit = unit
461
462	# Source Information
463	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
464	self.current_datainfo.source.wavelength = data_point
465	self.current_datainfo.source.wavelength_unit = unit
466	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
467	self.current_datainfo.source.wavelength_min = data_point
468	self.current_datainfo.source.wavelength_min_unit = unit
469	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
470	self.current_datainfo.source.wavelength_max = data_point
471	self.current_datainfo.source.wavelength_max_unit = unit
472	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
473	self.current_datainfo.source.wavelength_spread = data_point
474	self.current_datainfo.source.wavelength_spread_unit = unit
475	elif tagname == 'x' and self.parent_class == 'beam_size':
476	self.current_datainfo.source.beam_size.x = data_point
477	self.current_datainfo.source.beam_size_unit = unit
478	elif tagname == 'y' and self.parent_class == 'beam_size':
479	self.current_datainfo.source.beam_size.y = data_point
480	self.current_datainfo.source.beam_size_unit = unit
481	elif tagname == 'z' and self.parent_class == 'pixel_size':
482	self.current_datainfo.source.data_point.z = data_point
483	self.current_datainfo.source.beam_size_unit = unit
484	elif tagname == 'radiation' and self.parent_class == 'SASsource':
485	self.current_datainfo.source.radiation = data_point
486	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
487	self.current_datainfo.source.beam_shape = data_point
488
489	# Everything else goes in meta_data
490	else:
491	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
492	self.current_datainfo.meta_data[new_key] = data_point
493
494	self.names.remove(tagname_original)
495	length = 0
496	if len(self.names) > 1:
497	length = len(self.names) - 1
498	self.parent_class = self.names[length]
499	if not self._is_call_local() and not recurse:
500	self.frm = ""
501	self.add_data_set()
502	empty = None
503	return self.output[0], empty
504
505
506	def _is_call_local(self):
507	"""
508
509	"""
510	if self.frm == "":
511	inter = inspect.stack()
512	self.frm = inter[2]
513	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
514	mod_name = mod_name.replace(".py", "")
515	mod = mod_name.split("sas/")
516	mod_name = mod[1]
517	if mod_name != "sascalc/dataloader/readers/cansas_reader":
518	return False
519	return True
520
521	def is_cansas(self, ext="xml"):
522	"""
523	Checks to see if the xml file is a CanSAS file
524
525	:param ext: The file extension of the data file
526	"""
527	if self.validate_xml():
528	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
529	value = self.xmlroot.get(name)
530	if CANSAS_NS.get(self.cansas_version).get("ns") == \
531	value.rsplit(" ")[0]:
532	return True
533	if ext == "svs":
534	return True
535	raise FileContentsException("Not valid CanSAS")
536
537	def load_file_and_schema(self, xml_file, schema_path=""):
538	"""
539	Loads the file and associates a schema, if a schema is passed in or if one already exists
540
541	:param xml_file: The xml file path sent to Reader.read
542	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
543	"""
544	base_name = xml_reader.__file__
545	base_name = base_name.replace("\\", "/")
546	base = base_name.split("/sas/")[0]
547
548	# Load in xml file and get the cansas version from the header
549	from lxml import etree
550	try:
551	self.set_xml_file(xml_file)
552	except etree.XMLSyntaxError:
553	msg = "Cansas cannot load {}.\n Invalid XML syntax.".format(xml_file)
554	raise FileContentsException(msg)
555	self.cansas_version = self.xmlroot.get("version", "1.0")
556
557	# Generic values for the cansas file based on the version
558	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
559	if schema_path == "":
560	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
561	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
562
563	# Link a schema to the XML file.
564	self.set_schema(schema_path)
565
566	def add_data_set(self):
567	"""
568	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
569	private method to generate a new data set.
570
571	:param key: NeXus group name for current tree level
572	"""
573
574	if self.current_datainfo and self.current_dataset:
575	self._final_cleanup()
576	self.data = []
577	self.current_datainfo = DataInfo()
578
579	def _initialize_new_data_set(self, node=None):
580	"""
581	A private class method to generate a new 1D data object.
582	Outside methods should call add_data_set() to be sure any existing data is stored properly.
583
584	:param node: XML node to determine if 1D or 2D data
585	"""
586	x = np.array(0)
587	y = np.array(0)
588	for child in node:
589	if child.tag.replace(self.base_ns, "") == "Idata":
590	for i_child in child:
591	if i_child.tag.replace(self.base_ns, "") == "Qx":
592	self.current_dataset = plottable_2D()
593	return
594	self.current_dataset = plottable_1D(x, y)
595
596	def add_intermediate(self):
597	"""
598	This method stores any intermediate objects within the final data set after fully reading the set.
599
600	:param parent: The NXclass name for the h5py Group object that just finished being processed
601	"""
602
603	if self.parent_class == 'SASprocess':
604	self.current_datainfo.process.append(self.process)
605	self.process = Process()
606	elif self.parent_class == 'SASdetector':
607	self.current_datainfo.detector.append(self.detector)
608	self.detector = Detector()
609	elif self.parent_class == 'SAStransmission_spectrum':
610	self.current_datainfo.trans_spectrum.append(self.transspectrum)
611	self.transspectrum = TransmissionSpectrum()
612	elif self.parent_class == 'SAScollimation':
613	self.current_datainfo.collimation.append(self.collimation)
614	self.collimation = Collimation()
615	elif self.parent_class == 'aperture':
616	self.collimation.aperture.append(self.aperture)
617	self.aperture = Aperture()
618	elif self.parent_class == 'SASdata':
619	self._check_for_empty_resolution()
620	self.data.append(self.current_dataset)
621
622	def _final_cleanup(self):
623	"""
624	Final cleanup of the Data1D object to be sure it has all the
625	appropriate information needed for perspectives
626	"""
627
628	# Append errors to dataset and reset class errors
629	self.current_datainfo.errors = set()
630	for error in self.errors:
631	self.current_datainfo.errors.add(error)
632	self.errors.clear()
633
634	# Combine all plottables with datainfo and append each to output
635	# Type cast data arrays to float64 and find min/max as appropriate
636	for dataset in self.data:
637	if isinstance(dataset, plottable_1D):
638	if dataset.x is not None:
639	dataset.x = np.delete(dataset.x, [0])
640	dataset.x = dataset.x.astype(np.float64)
641	dataset.xmin = np.min(dataset.x)
642	dataset.xmax = np.max(dataset.x)
643	if dataset.y is not None:
644	dataset.y = np.delete(dataset.y, [0])
645	dataset.y = dataset.y.astype(np.float64)
646	dataset.ymin = np.min(dataset.y)
647	dataset.ymax = np.max(dataset.y)
648	if dataset.dx is not None:
649	dataset.dx = np.delete(dataset.dx, [0])
650	dataset.dx = dataset.dx.astype(np.float64)
651	if dataset.dxl is not None:
652	dataset.dxl = np.delete(dataset.dxl, [0])
653	dataset.dxl = dataset.dxl.astype(np.float64)
654	if dataset.dxw is not None:
655	dataset.dxw = np.delete(dataset.dxw, [0])
656	dataset.dxw = dataset.dxw.astype(np.float64)
657	if dataset.dy is not None:
658	dataset.dy = np.delete(dataset.dy, [0])
659	dataset.dy = dataset.dy.astype(np.float64)
660	np.trim_zeros(dataset.x)
661	np.trim_zeros(dataset.y)
662	np.trim_zeros(dataset.dy)
663	elif isinstance(dataset, plottable_2D):
664	dataset.data = dataset.data.astype(np.float64)
665	dataset.qx_data = dataset.qx_data.astype(np.float64)
666	dataset.xmin = np.min(dataset.qx_data)
667	dataset.xmax = np.max(dataset.qx_data)
668	dataset.qy_data = dataset.qy_data.astype(np.float64)
669	dataset.ymin = np.min(dataset.qy_data)
670	dataset.ymax = np.max(dataset.qy_data)
671	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
672	+ dataset.qy_data * dataset.qy_data)
673	if dataset.err_data is not None:
674	dataset.err_data = dataset.err_data.astype(np.float64)
675	if dataset.dqx_data is not None:
676	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
677	if dataset.dqy_data is not None:
678	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
679	if dataset.mask is not None:
680	dataset.mask = dataset.mask.astype(dtype=bool)
681
682	if len(dataset.shape) == 2:
683	n_rows, n_cols = dataset.shape
684	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
685	dataset.x_bins = dataset.qx_data[:int(n_cols)]
686	dataset.data = dataset.data.flatten()
687	else:
688	dataset.y_bins = []
689	dataset.x_bins = []
690	dataset.data = dataset.data.flatten()
691
692	final_dataset = combine_data(dataset, self.current_datainfo)
693	self.output.append(final_dataset)
694
695	def _create_unique_key(self, dictionary, name, numb=0):
696	"""
697	Create a unique key value for any dictionary to prevent overwriting
698	Recurse until a unique key value is found.
699
700	:param dictionary: A dictionary with any number of entries
701	:param name: The index of the item to be added to dictionary
702	:param numb: The number to be appended to the name, starts at 0
703	"""
704	if dictionary.get(name) is not None:
705	numb += 1
706	name = name.split("_")[0]
707	name += "_{0}".format(numb)
708	name = self._create_unique_key(dictionary, name, numb)
709	return name
710
711	def _get_node_value(self, node, tagname):
712	"""
713	Get the value of a node and any applicable units
714
715	:param node: The XML node to get the value of
716	:param tagname: The tagname of the node
717	"""
718	#Get the text from the node and convert all whitespace to spaces
719	units = ''
720	node_value = node.text
721	if node_value is not None:
722	node_value = ' '.join(node_value.split())
723	else:
724	node_value = ""
725
726	# If the value is a float, compile with units.
727	if self.ns_list.ns_datatype == "float":
728	# If an empty value is given, set as zero.
729	if node_value is None or node_value.isspace() \
730	or node_value.lower() == "nan":
731	node_value = "0.0"
732	#Convert the value to the base units
733	node_value, units = self._unit_conversion(node, tagname, node_value)
734
735	# If the value is a timestamp, convert to a datetime object
736	elif self.ns_list.ns_datatype == "timestamp":
737	if node_value is None or node_value.isspace():
738	pass
739	else:
740	try:
741	node_value = \
742	datetime.datetime.fromtimestamp(node_value)
743	except ValueError:
744	node_value = None
745	return node_value, units
746
747	def _unit_conversion(self, node, tagname, node_value):
748	"""
749	A unit converter method used to convert the data included in the file
750	to the default units listed in data_info
751
752	:param node: XML node
753	:param tagname: name of the node
754	:param node_value: The value of the current dom node
755	"""
756	attr = node.attrib
757	value_unit = ''
758	err_msg = None
759	default_unit = None
760	if not isinstance(node_value, float):
761	node_value = float(node_value)
762	if 'unit' in attr and attr.get('unit') is not None:
763	try:
764	local_unit = attr['unit']
765	unitname = self.ns_list.current_level.get("unit", "")
766	if "SASdetector" in self.names:
767	save_in = "detector"
768	elif "aperture" in self.names:
769	save_in = "aperture"
770	elif "SAScollimation" in self.names:
771	save_in = "collimation"
772	elif "SAStransmission_spectrum" in self.names:
773	save_in = "transspectrum"
774	elif "SASdata" in self.names:
775	x = np.zeros(1)
776	y = np.zeros(1)
777	self.current_data1d = Data1D(x, y)
778	save_in = "current_data1d"
779	elif "SASsource" in self.names:
780	save_in = "current_datainfo.source"
781	elif "SASsample" in self.names:
782	save_in = "current_datainfo.sample"
783	elif "SASprocess" in self.names:
784	save_in = "process"
785	else:
786	save_in = "current_datainfo"
787	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
788	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
789	and local_unit.lower() != "none":
790	if HAS_CONVERTER == True:
791	# Check local units - bad units raise KeyError
792	data_conv_q = Converter(local_unit)
793	value_unit = default_unit
794	node_value = data_conv_q(node_value, units=default_unit)
795	else:
796	value_unit = local_unit
797	err_msg = "Unit converter is not available.\n"
798	else:
799	value_unit = local_unit
800	except KeyError:
801	err_msg = "CanSAS reader: unexpected "
802	err_msg += "\"{0}\" unit [{1}]; "
803	err_msg = err_msg.format(tagname, local_unit)
804	err_msg += "expecting [{0}]".format(default_unit)
805	value_unit = local_unit
806	except:
807	err_msg = "CanSAS reader: unknown error converting "
808	err_msg += "\"{0}\" unit [{1}]"
809	err_msg = err_msg.format(tagname, local_unit)
810	value_unit = local_unit
811	elif 'unit' in attr:
812	value_unit = attr['unit']
813	if err_msg:
814	self.errors.add(err_msg)
815	return node_value, value_unit
816
817	def _check_for_empty_data(self):
818	"""
819	Creates an empty data set if no data is passed to the reader
820
821	:param data1d: presumably a Data1D object
822	"""
823	if self.current_dataset is None:
824	x_vals = np.empty(0)
825	y_vals = np.empty(0)
826	dx_vals = np.empty(0)
827	dy_vals = np.empty(0)
828	dxl = np.empty(0)
829	dxw = np.empty(0)
830	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
831	self.current_dataset.dxl = dxl
832	self.current_dataset.dxw = dxw
833
834	def _check_for_empty_resolution(self):
835	"""
836	A method to check all resolution data sets are the same size as I and Q
837	"""
838	if isinstance(self.current_dataset, plottable_1D):
839	dql_exists = False
840	dqw_exists = False
841	dq_exists = False
842	di_exists = False
843	if self.current_dataset.dxl is not None:
844	dql_exists = True
845	if self.current_dataset.dxw is not None:
846	dqw_exists = True
847	if self.current_dataset.dx is not None:
848	dq_exists = True
849	if self.current_dataset.dy is not None:
850	di_exists = True
851	if dqw_exists and not dql_exists:
852	array_size = self.current_dataset.dxw.size - 1
853	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
854	np.zeros([array_size]))
855	elif dql_exists and not dqw_exists:
856	array_size = self.current_dataset.dxl.size - 1
857	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
858	np.zeros([array_size]))
859	elif not dql_exists and not dqw_exists and not dq_exists:
860	array_size = self.current_dataset.x.size - 1
861	self.current_dataset.dx = np.append(self.current_dataset.dx,
862	np.zeros([array_size]))
863	if not di_exists:
864	array_size = self.current_dataset.y.size - 1
865	self.current_dataset.dy = np.append(self.current_dataset.dy,
866	np.zeros([array_size]))
867	elif isinstance(self.current_dataset, plottable_2D):
868	dqx_exists = False
869	dqy_exists = False
870	di_exists = False
871	mask_exists = False
872	if self.current_dataset.dqx_data is not None:
873	dqx_exists = True
874	if self.current_dataset.dqy_data is not None:
875	dqy_exists = True
876	if self.current_dataset.err_data is not None:
877	di_exists = True
878	if self.current_dataset.mask is not None:
879	mask_exists = True
880	if not dqy_exists:
881	array_size = self.current_dataset.qy_data.size - 1
882	self.current_dataset.dqy_data = np.append(
883	self.current_dataset.dqy_data, np.zeros([array_size]))
884	if not dqx_exists:
885	array_size = self.current_dataset.qx_data.size - 1
886	self.current_dataset.dqx_data = np.append(
887	self.current_dataset.dqx_data, np.zeros([array_size]))
888	if not di_exists:
889	array_size = self.current_dataset.data.size - 1
890	self.current_dataset.err_data = np.append(
891	self.current_dataset.err_data, np.zeros([array_size]))
892	if not mask_exists:
893	array_size = self.current_dataset.data.size - 1
894	self.current_dataset.mask = np.append(
895	self.current_dataset.mask,
896	np.ones([array_size] ,dtype=bool))
897
898	####### All methods below are for writing CanSAS XML files #######
899
900	def write(self, filename, datainfo):
901	"""
902	Write the content of a Data1D as a CanSAS XML file
903
904	:param filename: name of the file to write
905	:param datainfo: Data1D object
906	"""
907	# Create XML document
908	doc, _ = self._to_xml_doc(datainfo)
909	# Write the file
910	file_ref = open(filename, 'w')
911	if self.encoding is None:
912	self.encoding = "UTF-8"
913	doc.write(file_ref, encoding=self.encoding,
914	pretty_print=True, xml_declaration=True)
915	file_ref.close()
916
917	def _to_xml_doc(self, datainfo):
918	"""
919	Create an XML document to contain the content of a Data1D
920
921	:param datainfo: Data1D object
922	"""
923	is_2d = False
924	if issubclass(datainfo.__class__, Data2D):
925	is_2d = True
926
927	# Get PIs and create root element
928	pi_string = self._get_pi_string()
929	# Define namespaces and create SASroot object
930	main_node = self._create_main_node()
931	# Create ElementTree, append SASroot and apply processing instructions
932	base_string = pi_string + self.to_string(main_node)
933	base_element = self.create_element_from_string(base_string)
934	doc = self.create_tree(base_element)
935	# Create SASentry Element
936	entry_node = self.create_element("SASentry")
937	root = doc.getroot()
938	root.append(entry_node)
939
940	# Add Title to SASentry
941	self.write_node(entry_node, "Title", datainfo.title)
942	# Add Run to SASentry
943	self._write_run_names(datainfo, entry_node)
944	# Add Data info to SASEntry
945	if is_2d:
946	self._write_data_2d(datainfo, entry_node)
947	else:
948	self._write_data(datainfo, entry_node)
949	# Transmission Spectrum Info
950	# TODO: fix the writer to linearize all data, including T_spectrum
951	# self._write_trans_spectrum(datainfo, entry_node)
952	# Sample info
953	self._write_sample_info(datainfo, entry_node)
954	# Instrument info
955	instr = self._write_instrument(datainfo, entry_node)
956	# Source
957	self._write_source(datainfo, instr)
958	# Collimation
959	self._write_collimation(datainfo, instr)
960	# Detectors
961	self._write_detectors(datainfo, instr)
962	# Processes info
963	self._write_process_notes(datainfo, entry_node)
964	# Note info
965	self._write_notes(datainfo, entry_node)
966	# Return the document, and the SASentry node associated with
967	# the data we just wrote
968	# If the calling function was not the cansas reader, return a minidom
969	# object rather than an lxml object.
970	self.frm = inspect.stack()[1]
971	doc, entry_node = self._check_origin(entry_node, doc)
972	return doc, entry_node
973
974	def write_node(self, parent, name, value, attr=None):
975	"""
976	:param doc: document DOM
977	:param parent: parent node
978	:param name: tag of the element
979	:param value: value of the child text node
980	:param attr: attribute dictionary
981
982	:return: True if something was appended, otherwise False
983	"""
984	if value is not None:
985	parent = self.ebuilder(parent, name, value, attr)
986	return True
987	return False
988
989	def _get_pi_string(self):
990	"""
991	Creates the processing instructions header for writing to file
992	"""
993	pis = self.return_processing_instructions()
994	if len(pis) > 0:
995	pi_tree = self.create_tree(pis[0])
996	i = 1
997	for i in range(1, len(pis) - 1):
998	pi_tree = self.append(pis[i], pi_tree)
999	pi_string = self.to_string(pi_tree)
1000	else:
1001	pi_string = ""
1002	return pi_string
1003
1004	def _create_main_node(self):
1005	"""
1006	Creates the primary xml header used when writing to file
1007	"""
1008	xsi = "http://www.w3.org/2001/XMLSchema-instance"
1009	version = self.cansas_version
1010	n_s = CANSAS_NS.get(version).get("ns")
1011	if version == "1.1":
1012	url = "http://www.cansas.org/formats/1.1/"
1013	else:
1014	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
1015	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
1016	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
1017	"version" : version}
1018	nsmap = {'xsi' : xsi, None: n_s}
1019
1020	main_node = self.create_element("{" + n_s + "}SASroot",
1021	attrib=attrib, nsmap=nsmap)
1022	return main_node
1023
1024	def _write_run_names(self, datainfo, entry_node):
1025	"""
1026	Writes the run names to the XML file
1027
1028	:param datainfo: The Data1D object the information is coming from
1029	:param entry_node: lxml node ElementTree object to be appended to
1030	"""
1031	if datainfo.run is None or datainfo.run == []:
1032	datainfo.run.append(RUN_NAME_DEFAULT)
1033	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
1034	for item in datainfo.run:
1035	runname = {}
1036	if item in datainfo.run_name and \
1037	len(str(datainfo.run_name[item])) > 1:
1038	runname = {'name': datainfo.run_name[item]}
1039	self.write_node(entry_node, "Run", item, runname)
1040
1041	def _write_data(self, datainfo, entry_node):
1042	"""
1043	Writes 1D I and Q data to the XML file
1044
1045	:param datainfo: The Data1D object the information is coming from
1046	:param entry_node: lxml node ElementTree object to be appended to
1047	"""
1048	node = self.create_element("SASdata")
1049	self.append(node, entry_node)
1050
1051	for i in range(len(datainfo.x)):
1052	point = self.create_element("Idata")
1053	node.append(point)
1054	self.write_node(point, "Q", datainfo.x[i],
1055	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1056	if len(datainfo.y) >= i:
1057	self.write_node(point, "I", datainfo.y[i],
1058	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1059	if datainfo.dy is not None and len(datainfo.dy) > i:
1060	self.write_node(point, "Idev", datainfo.dy[i],
1061	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
1062	if datainfo.dx is not None and len(datainfo.dx) > i:
1063	self.write_node(point, "Qdev", datainfo.dx[i],
1064	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1065	if datainfo.dxw is not None and len(datainfo.dxw) > i:
1066	self.write_node(point, "dQw", datainfo.dxw[i],
1067	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1068	if datainfo.dxl is not None and len(datainfo.dxl) > i:
1069	self.write_node(point, "dQl", datainfo.dxl[i],
1070	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
1071	if datainfo.isSesans:
1072	sesans = self.create_element("Sesans")
1073	sesans.text = str(datainfo.isSesans)
1074	node.append(sesans)
1075	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
1076	{'unit': datainfo.sample.yacceptance[1]})
1077	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
1078	{'unit': datainfo.sample.zacceptance[1]})
1079
1080
1081	def _write_data_2d(self, datainfo, entry_node):
1082	"""
1083	Writes 2D data to the XML file
1084
1085	:param datainfo: The Data2D object the information is coming from
1086	:param entry_node: lxml node ElementTree object to be appended to
1087	"""
1088	attr = {}
1089	if datainfo.data.shape:
1090	attr["x_bins"] = str(len(datainfo.x_bins))
1091	attr["y_bins"] = str(len(datainfo.y_bins))
1092	node = self.create_element("SASdata", attr)
1093	self.append(node, entry_node)
1094
1095	point = self.create_element("Idata")
1096	node.append(point)
1097	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
1098	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
1099	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
1100
1101	self.write_node(point, "Qx", qx,
1102	{'unit': datainfo._xunit})
1103	self.write_node(point, "Qy", qy,
1104	{'unit': datainfo._yunit})
1105	self.write_node(point, "I", intensity,
1106	{'unit': datainfo._zunit})
1107	if datainfo.err_data is not None:
1108	err = ','.join([str(datainfo.err_data[i]) for i in
1109	xrange(len(datainfo.err_data))])
1110	self.write_node(point, "Idev", err,
1111	{'unit': datainfo._zunit})
1112	if datainfo.dqy_data is not None:
1113	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
1114	xrange(len(datainfo.dqy_data))])
1115	self.write_node(point, "Qydev", dqy,
1116	{'unit': datainfo._yunit})
1117	if datainfo.dqx_data is not None:
1118	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
1119	xrange(len(datainfo.dqx_data))])
1120	self.write_node(point, "Qxdev", dqx,
1121	{'unit': datainfo._xunit})
1122	if datainfo.mask is not None:
1123	mask = ','.join(
1124	["1" if datainfo.mask[i] else "0"
1125	for i in xrange(len(datainfo.mask))])
1126	self.write_node(point, "Mask", mask)
1127
1128	def _write_trans_spectrum(self, datainfo, entry_node):
1129	"""
1130	Writes the transmission spectrum data to the XML file
1131
1132	:param datainfo: The Data1D object the information is coming from
1133	:param entry_node: lxml node ElementTree object to be appended to
1134	"""
1135	for i in range(len(datainfo.trans_spectrum)):
1136	spectrum = datainfo.trans_spectrum[i]
1137	node = self.create_element("SAStransmission_spectrum",
1138	{"name" : spectrum.name})
1139	self.append(node, entry_node)
1140	if isinstance(spectrum.timestamp, datetime.datetime):
1141	node.setAttribute("timestamp", spectrum.timestamp)
1142	for i in range(len(spectrum.wavelength)):
1143	point = self.create_element("Tdata")
1144	node.append(point)
1145	self.write_node(point, "Lambda", spectrum.wavelength[i],
1146	{'unit': spectrum.wavelength_unit})
1147	self.write_node(point, "T", spectrum.transmission[i],
1148	{'unit': spectrum.transmission_unit})
1149	if spectrum.transmission_deviation is not None \
1150	and len(spectrum.transmission_deviation) >= i:
1151	self.write_node(point, "Tdev",
1152	spectrum.transmission_deviation[i],
1153	{'unit':
1154	spectrum.transmission_deviation_unit})
1155
1156	def _write_sample_info(self, datainfo, entry_node):
1157	"""
1158	Writes the sample information to the XML file
1159
1160	:param datainfo: The Data1D object the information is coming from
1161	:param entry_node: lxml node ElementTree object to be appended to
1162	"""
1163	sample = self.create_element("SASsample")
1164	if datainfo.sample.name is not None:
1165	self.write_attribute(sample, "name",
1166	str(datainfo.sample.name))
1167	self.append(sample, entry_node)
1168	self.write_node(sample, "ID", str(datainfo.sample.ID))
1169	self.write_node(sample, "thickness", datainfo.sample.thickness,
1170	{"unit": datainfo.sample.thickness_unit})
1171	self.write_node(sample, "transmission", datainfo.sample.transmission)
1172	self.write_node(sample, "temperature", datainfo.sample.temperature,
1173	{"unit": datainfo.sample.temperature_unit})
1174
1175	pos = self.create_element("position")
1176	written = self.write_node(pos,
1177	"x",
1178	datainfo.sample.position.x,
1179	{"unit": datainfo.sample.position_unit})
1180	written = written \| self.write_node( \
1181	pos, "y", datainfo.sample.position.y,
1182	{"unit": datainfo.sample.position_unit})
1183	written = written \| self.write_node( \
1184	pos, "z", datainfo.sample.position.z,
1185	{"unit": datainfo.sample.position_unit})
1186	if written == True:
1187	self.append(pos, sample)
1188
1189	ori = self.create_element("orientation")
1190	written = self.write_node(ori, "roll",
1191	datainfo.sample.orientation.x,
1192	{"unit": datainfo.sample.orientation_unit})
1193	written = written \| self.write_node( \
1194	ori, "pitch", datainfo.sample.orientation.y,
1195	{"unit": datainfo.sample.orientation_unit})
1196	written = written \| self.write_node( \
1197	ori, "yaw", datainfo.sample.orientation.z,
1198	{"unit": datainfo.sample.orientation_unit})
1199	if written == True:
1200	self.append(ori, sample)
1201
1202	for item in datainfo.sample.details:
1203	self.write_node(sample, "details", item)
1204
1205	def _write_instrument(self, datainfo, entry_node):
1206	"""
1207	Writes the instrumental information to the XML file
1208
1209	:param datainfo: The Data1D object the information is coming from
1210	:param entry_node: lxml node ElementTree object to be appended to
1211	"""
1212	instr = self.create_element("SASinstrument")
1213	self.append(instr, entry_node)
1214	self.write_node(instr, "name", datainfo.instrument)
1215	return instr
1216
1217	def _write_source(self, datainfo, instr):
1218	"""
1219	Writes the source information to the XML file
1220
1221	:param datainfo: The Data1D object the information is coming from
1222	:param instr: instrument node to be appended to
1223	"""
1224	source = self.create_element("SASsource")
1225	if datainfo.source.name is not None:
1226	self.write_attribute(source, "name",
1227	str(datainfo.source.name))
1228	self.append(source, instr)
1229	if datainfo.source.radiation is None or datainfo.source.radiation == '':
1230	datainfo.source.radiation = "neutron"
1231	self.write_node(source, "radiation", datainfo.source.radiation)
1232
1233	size = self.create_element("beam_size")
1234	if datainfo.source.beam_size_name is not None:
1235	self.write_attribute(size, "name",
1236	str(datainfo.source.beam_size_name))
1237	written = self.write_node( \
1238	size, "x", datainfo.source.beam_size.x,
1239	{"unit": datainfo.source.beam_size_unit})
1240	written = written \| self.write_node( \
1241	size, "y", datainfo.source.beam_size.y,
1242	{"unit": datainfo.source.beam_size_unit})
1243	written = written \| self.write_node( \
1244	size, "z", datainfo.source.beam_size.z,
1245	{"unit": datainfo.source.beam_size_unit})
1246	if written == True:
1247	self.append(size, source)
1248
1249	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1250	self.write_node(source, "wavelength",
1251	datainfo.source.wavelength,
1252	{"unit": datainfo.source.wavelength_unit})
1253	self.write_node(source, "wavelength_min",
1254	datainfo.source.wavelength_min,
1255	{"unit": datainfo.source.wavelength_min_unit})
1256	self.write_node(source, "wavelength_max",
1257	datainfo.source.wavelength_max,
1258	{"unit": datainfo.source.wavelength_max_unit})
1259	self.write_node(source, "wavelength_spread",
1260	datainfo.source.wavelength_spread,
1261	{"unit": datainfo.source.wavelength_spread_unit})
1262
1263	def _write_collimation(self, datainfo, instr):
1264	"""
1265	Writes the collimation information to the XML file
1266
1267	:param datainfo: The Data1D object the information is coming from
1268	:param instr: lxml node ElementTree object to be appended to
1269	"""
1270	if datainfo.collimation == [] or datainfo.collimation is None:
1271	coll = Collimation()
1272	datainfo.collimation.append(coll)
1273	for item in datainfo.collimation:
1274	coll = self.create_element("SAScollimation")
1275	if item.name is not None:
1276	self.write_attribute(coll, "name", str(item.name))
1277	self.append(coll, instr)
1278
1279	self.write_node(coll, "length", item.length,
1280	{"unit": item.length_unit})
1281
1282	for aperture in item.aperture:
1283	apert = self.create_element("aperture")
1284	if aperture.name is not None:
1285	self.write_attribute(apert, "name", str(aperture.name))
1286	if aperture.type is not None:
1287	self.write_attribute(apert, "type", str(aperture.type))
1288	self.append(apert, coll)
1289
1290	size = self.create_element("size")
1291	if aperture.size_name is not None:
1292	self.write_attribute(size, "name",
1293	str(aperture.size_name))
1294	written = self.write_node(size, "x", aperture.size.x,
1295	{"unit": aperture.size_unit})
1296	written = written \| self.write_node( \
1297	size, "y", aperture.size.y,
1298	{"unit": aperture.size_unit})
1299	written = written \| self.write_node( \
1300	size, "z", aperture.size.z,
1301	{"unit": aperture.size_unit})
1302	if written == True:
1303	self.append(size, apert)
1304
1305	self.write_node(apert, "distance", aperture.distance,
1306	{"unit": aperture.distance_unit})
1307
1308	def _write_detectors(self, datainfo, instr):
1309	"""
1310	Writes the detector information to the XML file
1311
1312	:param datainfo: The Data1D object the information is coming from
1313	:param inst: lxml instrument node to be appended to
1314	"""
1315	if datainfo.detector is None or datainfo.detector == []:
1316	det = Detector()
1317	det.name = ""
1318	datainfo.detector.append(det)
1319
1320	for item in datainfo.detector:
1321	det = self.create_element("SASdetector")
1322	written = self.write_node(det, "name", item.name)
1323	written = written \| self.write_node(det, "SDD", item.distance,
1324	{"unit": item.distance_unit})
1325	if written == True:
1326	self.append(det, instr)
1327
1328	off = self.create_element("offset")
1329	written = self.write_node(off, "x", item.offset.x,
1330	{"unit": item.offset_unit})
1331	written = written \| self.write_node(off, "y", item.offset.y,
1332	{"unit": item.offset_unit})
1333	written = written \| self.write_node(off, "z", item.offset.z,
1334	{"unit": item.offset_unit})
1335	if written == True:
1336	self.append(off, det)
1337
1338	ori = self.create_element("orientation")
1339	written = self.write_node(ori, "roll", item.orientation.x,
1340	{"unit": item.orientation_unit})
1341	written = written \| self.write_node(ori, "pitch",
1342	item.orientation.y,
1343	{"unit": item.orientation_unit})
1344	written = written \| self.write_node(ori, "yaw",
1345	item.orientation.z,
1346	{"unit": item.orientation_unit})
1347	if written == True:
1348	self.append(ori, det)
1349
1350	center = self.create_element("beam_center")
1351	written = self.write_node(center, "x", item.beam_center.x,
1352	{"unit": item.beam_center_unit})
1353	written = written \| self.write_node(center, "y",
1354	item.beam_center.y,
1355	{"unit": item.beam_center_unit})
1356	written = written \| self.write_node(center, "z",
1357	item.beam_center.z,
1358	{"unit": item.beam_center_unit})
1359	if written == True:
1360	self.append(center, det)
1361
1362	pix = self.create_element("pixel_size")
1363	written = self.write_node(pix, "x", item.pixel_size.x,
1364	{"unit": item.pixel_size_unit})
1365	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1366	{"unit": item.pixel_size_unit})
1367	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1368	{"unit": item.pixel_size_unit})
1369	if written == True:
1370	self.append(pix, det)
1371	self.write_node(det, "slit_length", item.slit_length,
1372	{"unit": item.slit_length_unit})
1373
1374
1375	def _write_process_notes(self, datainfo, entry_node):
1376	"""
1377	Writes the process notes to the XML file
1378
1379	:param datainfo: The Data1D object the information is coming from
1380	:param entry_node: lxml node ElementTree object to be appended to
1381
1382	"""
1383	for item in datainfo.process:
1384	node = self.create_element("SASprocess")
1385	self.append(node, entry_node)
1386	self.write_node(node, "name", item.name)
1387	self.write_node(node, "date", item.date)
1388	self.write_node(node, "description", item.description)
1389	for term in item.term:
1390	if isinstance(term, list):
1391	value = term['value']
1392	del term['value']
1393	elif isinstance(term, dict):
1394	value = term.get("value")
1395	del term['value']
1396	else:
1397	value = term
1398	self.write_node(node, "term", value, term)
1399	for note in item.notes:
1400	self.write_node(node, "SASprocessnote", note)
1401	if len(item.notes) == 0:
1402	self.write_node(node, "SASprocessnote", "")
1403
1404	def _write_notes(self, datainfo, entry_node):
1405	"""
1406	Writes the notes to the XML file and creates an empty note if none
1407	exist
1408
1409	:param datainfo: The Data1D object the information is coming from
1410	:param entry_node: lxml node ElementTree object to be appended to
1411
1412	"""
1413	if len(datainfo.notes) == 0:
1414	node = self.create_element("SASnote")
1415	self.append(node, entry_node)
1416	else:
1417	for item in datainfo.notes:
1418	node = self.create_element("SASnote")
1419	self.write_text(node, item)
1420	self.append(node, entry_node)
1421
1422	def _check_origin(self, entry_node, doc):
1423	"""
1424	Return the document, and the SASentry node associated with
1425	the data we just wrote.
1426	If the calling function was not the cansas reader, return a minidom
1427	object rather than an lxml object.
1428
1429	:param entry_node: lxml node ElementTree object to be appended to
1430	:param doc: entire xml tree
1431	"""
1432	if not self.frm:
1433	self.frm = inspect.stack()[1]
1434	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1435	mod_name = mod_name.replace(".py", "")
1436	mod = mod_name.split("sas/")
1437	mod_name = mod[1]
1438	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1439	string = self.to_string(doc, pretty_print=False)
1440	doc = parseString(string)
1441	node_name = entry_node.tag
1442	node_list = doc.getElementsByTagName(node_name)
1443	entry_node = node_list.item(0)
1444	return doc, entry_node
1445
1446	# DO NOT REMOVE - used in saving and loading panel states.
1447	def _store_float(self, location, node, variable, storage, optional=True):
1448	"""
1449	Get the content of a xpath location and store
1450	the result. Check that the units are compatible
1451	with the destination. The value is expected to
1452	be a float.
1453
1454	The xpath location might or might not exist.
1455	If it does not exist, nothing is done
1456
1457	:param location: xpath location to fetch
1458	:param node: node to read the data from
1459	:param variable: name of the data member to store it in [string]
1460	:param storage: data object that has the 'variable' data member
1461	:param optional: if True, no exception will be raised
1462	if unit conversion can't be done
1463
1464	:raise ValueError: raised when the units are not recognized
1465	"""
1466	entry = get_content(location, node)
1467	try:
1468	value = float(entry.text)
1469	except:
1470	value = None
1471
1472	if value is not None:
1473	# If the entry has units, check to see that they are
1474	# compatible with what we currently have in the data object
1475	units = entry.get('unit')
1476	if units is not None:
1477	toks = variable.split('.')
1478	local_unit = None
1479	exec "local_unit = storage.%s_unit" % toks[0]
1480	if local_unit is not None and units.lower() != local_unit.lower():
1481	if HAS_CONVERTER == True:
1482	try:
1483	conv = Converter(units)
1484	exec "storage.%s = %g" % \
1485	(variable, conv(value, units=local_unit))
1486	except:
1487	_, exc_value, _ = sys.exc_info()
1488	err_mess = "CanSAS reader: could not convert"
1489	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1490	% (variable, units, local_unit, exc_value)
1491	self.errors.add(err_mess)
1492	if optional:
1493	logger.info(err_mess)
1494	else:
1495	raise ValueError, err_mess
1496	else:
1497	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
1498	% (variable, units)
1499	err_mess += " expecting [%s]" % local_unit
1500	self.errors.add(err_mess)
1501	if optional:
1502	logger.info(err_mess)
1503	else:
1504	raise ValueError, err_mess
1505	else:
1506	exec "storage.%s = value" % variable
1507	else:
1508	exec "storage.%s = value" % variable
1509
1510	# DO NOT REMOVE - used in saving and loading panel states.
1511	def _store_content(self, location, node, variable, storage):
1512	"""
1513	Get the content of a xpath location and store
1514	the result. The value is treated as a string.
1515
1516	The xpath location might or might not exist.
1517	If it does not exist, nothing is done
1518
1519	:param location: xpath location to fetch
1520	:param node: node to read the data from
1521	:param variable: name of the data member to store it in [string]
1522	:param storage: data object that has the 'variable' data member
1523
1524	:return: return a list of errors
1525	"""
1526	entry = get_content(location, node)
1527	if entry is not None and entry.text is not None:
1528	exec "storage.%s = entry.text.strip()" % variable
1529
1530
1531	# DO NOT REMOVE Called by outside packages:
1532	# sas.sasgui.perspectives.invariant.invariant_state
1533	# sas.sasgui.perspectives.fitting.pagestate
1534	def get_content(location, node):
1535	"""
1536	Get the first instance of the content of a xpath location.
1537
1538	:param location: xpath location
1539	:param node: node to start at
1540
1541	:return: Element, or None
1542	"""
1543	nodes = node.xpath(location,
1544	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1545	if len(nodes) > 0:
1546	return nodes[0]
1547	else:
1548	return None
1549
1550	# DO NOT REMOVE Called by outside packages:
1551	# sas.sasgui.perspectives.fitting.pagestate
1552	def write_node(doc, parent, name, value, attr=None):
1553	"""
1554	:param doc: document DOM
1555	:param parent: parent node
1556	:param name: tag of the element
1557	:param value: value of the child text node
1558	:param attr: attribute dictionary
1559
1560	:return: True if something was appended, otherwise False
1561	"""
1562	if attr is None:
1563	attr = {}
1564	if value is not None:
1565	node = doc.createElement(name)
1566	node.appendChild(doc.createTextNode(str(value)))
1567	for item in attr:
1568	node.setAttribute(item, attr[item])
1569	parent.appendChild(node)
1570	return True
1571	return False

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ bc570f4

Download in other formats: