sesans_reader.py @ 600bea1

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 600bea1 was edfc8ac, checked in by jhbakker, 10 years ago
Changed Sesans x-axis title to from A to nm
Property mode set to `100644`
File size: 9.9 KB

Line
1	"""
2	SESANS reader (based on ASCII reader)
3
4	Reader for .ses or .sesans file format
5
6	Jurrian Bakker
7	"""
8	import numpy
9	import os
10	from sas.dataloader.data_info import SESANSData1D
11
12	# Check whether we have a converter available
13	has_converter = True
14	try:
15	from sas.data_util.nxsunit import Converter
16	except:
17	has_converter = False
18	_ZERO = 1e-16
19
20	class Reader:
21	"""
22	Class to load sesans files (6 columns).
23	"""
24	## File type
25	type_name = "SESANS"
26
27	## Wildcards
28	type = ["SESANS files (.ses)\|.ses",
29	"SESANS files (..sesans)\|.sesans"]
30	## List of allowed extensions
31	ext = ['.ses', '.SES', '.sesans', '.SESANS']
32
33	## Flag to bypass extension check
34	allow_all = True
35
36	def read(self, path):
37
38	# print "reader triggered"
39
40	"""
41	Load data file
42
43	:param path: file path
44
45	:return: SESANSData1D object, or None
46
47	:raise RuntimeError: when the file can't be opened
48	:raise ValueError: when the length of the data vectors are inconsistent
49	"""
50	if os.path.isfile(path):
51	basename = os.path.basename(path)
52	_, extension = os.path.splitext(basename)
53	if self.allow_all or extension.lower() in self.ext:
54	try:
55	# Read in binary mode since GRASP frequently has no-ascii
56	# characters that brakes the open operation
57	input_f = open(path,'rb')
58	except:
59	raise RuntimeError, "sesans_reader: cannot open %s" % path
60	buff = input_f.read()
61	# print buff
62	lines = buff.splitlines()
63	# print lines
64	#Jae could not find python universal line spliter:
65	#keep the below for now
66	# some ascii data has \r line separator,
67	# try it when the data is on only one long line
68	# if len(lines) < 2 :
69	# lines = buff.split('\r')
70
71	x = numpy.zeros(0)
72	y = numpy.zeros(0)
73	dy = numpy.zeros(0)
74	lam = numpy.zeros(0)
75	dlam = numpy.zeros(0)
76	dx = numpy.zeros(0)
77
78	#temp. space to sort data
79	tx = numpy.zeros(0)
80	ty = numpy.zeros(0)
81	tdy = numpy.zeros(0)
82	tlam = numpy.zeros(0)
83	tdlam = numpy.zeros(0)
84	tdx = numpy.zeros(0)
85	# print "all good"
86	output = SESANSData1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam)
87	# print output
88	self.filename = output.filename = basename
89
90
91	data_conv_z = None
92	data_conv_P = None
93	# print "passing"
94	if has_converter == True and output.x_unit != 'A':
95	data_conv_z = Converter('nm')
96	# Test it
97	data_conv_z(1.0, output.x_unit)
98	# print data_conv_z
99	# print data_conv_z(1.0, output.x_unit)
100	if has_converter == True and output.y_unit != ' ':
101	data_conv_P = Converter('a.u.')
102	# Test it
103	data_conv_P(1.0, output.y_unit)
104	# print data_conv_P
105	# print data_conv_P(1.0, output.y_unit)
106	# The first good line of data will define whether
107	# we have 2-column or 3-column ascii
108	# print output.x_unit
109	# print output.y_unit
110
111	# print "past output"
112
113	# has_error_dx = None
114	# has_error_dy = None
115
116	# #Initialize counters for data lines and header lines.
117	# is_data = False # Has more than 5 lines
118	# # More than "5" lines of data is considered as actual
119	# # data unless that is the only data
120	# mum_data_lines = 5
121	# # To count # of current data candidate lines
122	# i = -1
123	# # To count total # of previous data candidate lines
124	# i1 = -1
125	# # To count # of header lines
126	# j = -1
127	# # Helps to count # of header lines
128	# j1 = -1
129	# #minimum required number of columns of data; ( <= 4).
130	# lentoks = 2
131	paramnames=[]
132	paramvals=[]
133	zvals=[]
134	dzvals=[]
135	lamvals=[]
136	dlamvals=[]
137	Pvals=[]
138	dPvals=[]
139	# print x
140	# print zvals
141	for line in lines:
142	# Initial try for CSV (split on ,)
143	# print line
144	line=line.strip()
145	# print line
146	toks = line.split('\t')
147	# print toks
148	if len(toks)==2:
149	paramnames.append(toks[0])
150	# print paramnames
151	paramvals.append(toks[1])
152	# print paramvals
153	if len(toks)>5:
154	zvals.append(toks[0])
155	dzvals.append(toks[1])
156	lamvals.append(toks[2])
157	dlamvals.append(toks[3])
158	Pvals.append(toks[4])
159	dPvals.append(toks[5])
160	else:
161	continue
162	# print varheaders
163	# print paramnames
164	# print paramvals
165	# print zvals
166	# print len(zvals)
167
168	x=[]
169	y=[]
170	lam=[]
171	dx=[]
172	dy=[]
173	dlam=[]
174	varheader=[zvals[0],dzvals[0],lamvals[0],dlamvals[0],Pvals[0],dPvals[0]]
175	# print varheader
176	valrange=range(len(zvals)-1)
177	# print valrange
178	for i in valrange:
179	x.append(float(zvals[i+1]))
180	y.append(float(Pvals[i+1]))
181	lam.append(float(lamvals[i+1]))
182	dy.append(float(dPvals[i+1]))
183	dx.append(float(dzvals[i+1]))
184	dlam.append(float(dlamvals[i+1]))
185
186	x,y,lam,dy,dx,dlam = [
187	numpy.asarray(v, 'double')
188	for v in (x,y,lam,dy,dx,dlam)
189	]
190
191	# print x
192	# print y
193	# print dx
194	# print dy
195	# print len(x)
196	# print len(y)
197	# print len(dx)
198	# print len(dy)
199
200
201	input_f.close()
202	# Sanity check
203	# if has_error_dy == True and not len(y) == len(dy):
204	# msg = "sesans_reader: y and dy have different length"
205	# raise RuntimeError, msg
206	# if has_error_dx == True and not len(x) == len(dx):
207	# msg = "sesans_reader: y and dy have different length"
208	# raise RuntimeError, msg
209	# # If the data length is zero, consider this as
210	# # though we were not able to read the file.
211	# if len(x) == 0:
212	# raise RuntimeError, "sesans_reader: could not load file"
213	# print "alive"
214	#Let's re-order the data to make cal.
215	# curve look better some cases
216	# ind = numpy.lexsort((ty, tx))
217	# for i in ind:
218	# x[i] = tx[ind[i]]
219	# y[i] = ty[ind[i]]
220	# if has_error_dy == True:
221	# dy[i] = tdy[ind[i]]
222	# if has_error_dx == True:
223	# dx[i] = tdx[ind[i]]
224	# Zeros in dx, dy
225	# if has_error_dx:
226	# dx[dx == 0] = _ZERO
227	# if has_error_dy:
228	# dy[dy == 0] = _ZERO
229	#Data
230	output.x = x #[x != 0]
231	# print output.x
232	output.y = y #[x != 0]
233	# print output.y
234	# output.dy = dy[x != 0] if has_error_dy == True\
235	# else numpy.zeros(len(output.y))
236	# output.dx = dx[x != 0] if has_error_dx == True\
237	# else numpy.zeros(len(output.x))
238	output.dy = dy
239	output.dx = dx
240	output.lam = lam
241	output.dlam = dlam
242
243
244	# print "still alive"
245	# if data_conv_z is not None:
246	# output.xaxis("\\rm{z}", output.x_unit)
247	# else:
248	# output.xaxis("\\rm{z}", 'nm')
249	# if data_conv_P is not None:
250	# output.yaxis("\\rm{P/P0}", output.y_unit)
251	# else:
252	# output.yaxis("\\rm{P/P0}", "a.u.")
253	output.xaxis("\\rm{z}", 'nm')
254	output.yaxis("\\rm{P/P0}", " ")
255	# Store loading process information
256	output.meta_data['loader'] = self.type_name
257	output.sample.thickness = float(paramvals[6])
258	output.sample.name = paramvals[1]
259	output.sample.ID = paramvals[0]
260	output.sample.zacceptance=float(paramvals[7])
261	output.vars=varheader
262
263	# print "sesans_reader end"
264
265	if len(output.x) < 1:
266	raise RuntimeError, "%s is empty" % path
267	# print output
268	# print output.lam
269	return output
270
271	else:
272	raise RuntimeError, "%s is not a file" % path
273	return None

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source: sasview/src/sas/dataloader/readers/sesans_reader.py @ 600bea1

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