ascii_reader.py @ 296f290

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 296f290 was 79492222, checked in by krzywon, 10 years ago
Changed the file and folder names to remove all SANS references.
Property mode set to `100644`
File size: 15.6 KB

Line
1	"""
2	ASCII reader
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, University of Tennessee
13	#############################################################################
14
15
16	import numpy
17	import os
18	from sas.dataloader.data_info import Data1D
19
20	# Check whether we have a converter available
21	has_converter = True
22	try:
23	from sas.data_util.nxsunit import Converter
24	except:
25	has_converter = False
26	_ZERO = 1e-16
27
28
29	class Reader:
30	"""
31	Class to load ascii files (2, 3 or 4 columns).
32	"""
33	## File type
34	type_name = "ASCII"
35
36	## Wildcards
37	type = ["ASCII files (.txt)\|.txt",
38	"ASCII files (.dat)\|.dat",
39	"ASCII files (.abs)\|.abs",
40	"CSV files (.csv)\|.csv"]
41	## List of allowed extensions
42	ext = ['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS', 'csv', 'CSV']
43
44	## Flag to bypass extension check
45	allow_all = True
46
47	def read(self, path):
48	"""
49	Load data file
50
51	:param path: file path
52
53	:return: Data1D object, or None
54
55	:raise RuntimeError: when the file can't be opened
56	:raise ValueError: when the length of the data vectors are inconsistent
57	"""
58	if os.path.isfile(path):
59	basename = os.path.basename(path)
60	_, extension = os.path.splitext(basename)
61	if self.allow_all or extension.lower() in self.ext:
62	try:
63	# Read in binary mode since GRASP frequently has no-ascii
64	# characters that brakes the open operation
65	input_f = open(path,'rb')
66	except:
67	raise RuntimeError, "ascii_reader: cannot open %s" % path
68	buff = input_f.read()
69	lines = buff.split('\n')
70
71	#Jae could not find python universal line spliter:
72	#keep the below for now
73	# some ascii data has \r line separator,
74	# try it when the data is on only one long line
75	if len(lines) < 2 :
76	lines = buff.split('\r')
77
78	x = numpy.zeros(0)
79	y = numpy.zeros(0)
80	dy = numpy.zeros(0)
81	dx = numpy.zeros(0)
82
83	#temp. space to sort data
84	tx = numpy.zeros(0)
85	ty = numpy.zeros(0)
86	tdy = numpy.zeros(0)
87	tdx = numpy.zeros(0)
88
89	output = Data1D(x, y, dy=dy, dx=dx)
90	self.filename = output.filename = basename
91
92	data_conv_q = None
93	data_conv_i = None
94
95	if has_converter == True and output.x_unit != '1/A':
96	data_conv_q = Converter('1/A')
97	# Test it
98	data_conv_q(1.0, output.x_unit)
99
100	if has_converter == True and output.y_unit != '1/cm':
101	data_conv_i = Converter('1/cm')
102	# Test it
103	data_conv_i(1.0, output.y_unit)
104
105	# The first good line of data will define whether
106	# we have 2-column or 3-column ascii
107	has_error_dx = None
108	has_error_dy = None
109
110	#Initialize counters for data lines and header lines.
111	is_data = False # Has more than 5 lines
112	# More than "5" lines of data is considered as actual
113	# data unless that is the only data
114	mum_data_lines = 5
115	# To count # of current data candidate lines
116	i = -1
117	# To count total # of previous data candidate lines
118	i1 = -1
119	# To count # of header lines
120	j = -1
121	# Helps to count # of header lines
122	j1 = -1
123	#minimum required number of columns of data; ( <= 4).
124	lentoks = 2
125	for line in lines:
126	# Initial try for CSV (split on ,)
127	toks = line.split(',')
128	# Now try SCSV (split on ;)
129	if len(toks) < 2:
130	toks = line.split(';')
131	# Now go for whitespace
132	if len(toks) < 2:
133	toks = line.split()
134	try:
135	#Make sure that all columns are numbers.
136	for colnum in range(len(toks)):
137	float(toks[colnum])
138
139	_x = float(toks[0])
140	_y = float(toks[1])
141
142	#Reset the header line counters
143	if j == j1:
144	j = 0
145	j1 = 0
146
147	if i > 1:
148	is_data = True
149
150	if data_conv_q is not None:
151	_x = data_conv_q(_x, units=output.x_unit)
152
153	if data_conv_i is not None:
154	_y = data_conv_i(_y, units=output.y_unit)
155
156	# If we have an extra token, check
157	# whether it can be interpreted as a
158	# third column.
159	_dy = None
160	if len(toks) > 2:
161	try:
162	_dy = float(toks[2])
163
164	if data_conv_i is not None:
165	_dy = data_conv_i(_dy, units=output.y_unit)
166
167	except:
168	# The third column is not a float, skip it.
169	pass
170
171	# If we haven't set the 3rd column
172	# flag, set it now.
173	if has_error_dy == None:
174	has_error_dy = False if _dy == None else True
175
176	#Check for dx
177	_dx = None
178	if len(toks) > 3:
179	try:
180	_dx = float(toks[3])
181
182	if data_conv_i is not None:
183	_dx = data_conv_i(_dx, units=output.x_unit)
184
185	except:
186	# The 4th column is not a float, skip it.
187	pass
188
189	# If we haven't set the 3rd column
190	# flag, set it now.
191	if has_error_dx == None:
192	has_error_dx = False if _dx == None else True
193
194	#After talked with PB, we decided to take care of only
195	# 4 columns of data for now.
196	#number of columns in the current line
197	#To remember the # of columns in the current
198	#line of data
199	new_lentoks = len(toks)
200
201	#If the previous columns not equal to the current,
202	#mark the previous as non-data and reset the dependents.
203	if lentoks != new_lentoks:
204	if is_data == True:
205	break
206	else:
207	i = -1
208	i1 = 0
209	j = -1
210	j1 = -1
211
212	#Delete the previously stored lines of data candidates
213	# if is not data.
214	if i < 0 and -1 < i1 < mum_data_lines and \
215	is_data == False:
216	try:
217	x = numpy.zeros(0)
218	y = numpy.zeros(0)
219	except:
220	pass
221
222	x = numpy.append(x, _x)
223	y = numpy.append(y, _y)
224
225	if has_error_dy == True:
226	#Delete the previously stored lines of
227	# data candidates if is not data.
228	if i < 0 and -1 < i1 < mum_data_lines and \
229	is_data == False:
230	try:
231	dy = numpy.zeros(0)
232	except:
233	pass
234	dy = numpy.append(dy, _dy)
235
236	if has_error_dx == True:
237	#Delete the previously stored lines of
238	# data candidates if is not data.
239	if i < 0 and -1 < i1 < mum_data_lines and \
240	is_data == False:
241	try:
242	dx = numpy.zeros(0)
243	except:
244	pass
245	dx = numpy.append(dx, _dx)
246
247	#Same for temp.
248	#Delete the previously stored lines of data candidates
249	# if is not data.
250	if i < 0 and -1 < i1 < mum_data_lines and\
251	is_data == False:
252	try:
253	tx = numpy.zeros(0)
254	ty = numpy.zeros(0)
255	except:
256	pass
257
258	tx = numpy.append(tx, _x)
259	ty = numpy.append(ty, _y)
260
261	if has_error_dy == True:
262	#Delete the previously stored lines of
263	# data candidates if is not data.
264	if i < 0 and -1 < i1 < mum_data_lines and \
265	is_data == False:
266	try:
267	tdy = numpy.zeros(0)
268	except:
269	pass
270	tdy = numpy.append(tdy, _dy)
271	if has_error_dx == True:
272	#Delete the previously stored lines of
273	# data candidates if is not data.
274	if i < 0 and -1 < i1 < mum_data_lines and \
275	is_data == False:
276	try:
277	tdx = numpy.zeros(0)
278	except:
279	pass
280	tdx = numpy.append(tdx, _dx)
281
282	#reset i1 and flag lentoks for the next
283	if lentoks < new_lentoks:
284	if is_data == False:
285	i1 = -1
286	#To remember the # of columns on the current line
287	# for the next line of data
288	lentoks = len(toks)
289
290	#Reset # of header lines and counts #
291	# of data candidate lines
292	if j == 0 and j1 == 0:
293	i1 = i + 1
294	i += 1
295	except:
296
297	# It is data and meet non - number, then stop reading
298	if is_data == True:
299	break
300	lentoks = 2
301	#Counting # of header lines
302	j += 1
303	if j == j1 + 1:
304	j1 = j
305	else:
306	j = -1
307	#Reset # of lines of data candidates
308	i = -1
309
310	# Couldn't parse this line, skip it
311	pass
312
313	input_f.close()
314	# Sanity check
315	if has_error_dy == True and not len(y) == len(dy):
316	msg = "ascii_reader: y and dy have different length"
317	raise RuntimeError, msg
318	if has_error_dx == True and not len(x) == len(dx):
319	msg = "ascii_reader: y and dy have different length"
320	raise RuntimeError, msg
321	# If the data length is zero, consider this as
322	# though we were not able to read the file.
323	if len(x) == 0:
324	raise RuntimeError, "ascii_reader: could not load file"
325
326	#Let's re-order the data to make cal.
327	# curve look better some cases
328	ind = numpy.lexsort((ty, tx))
329	for i in ind:
330	x[i] = tx[ind[i]]
331	y[i] = ty[ind[i]]
332	if has_error_dy == True:
333	dy[i] = tdy[ind[i]]
334	if has_error_dx == True:
335	dx[i] = tdx[ind[i]]
336	# Zeros in dx, dy
337	if has_error_dx:
338	dx[dx == 0] = _ZERO
339	if has_error_dy:
340	dy[dy == 0] = _ZERO
341	#Data
342	output.x = x[x != 0]
343	output.y = y[x != 0]
344	output.dy = dy[x != 0] if has_error_dy == True\
345	else numpy.zeros(len(output.y))
346	output.dx = dx[x != 0] if has_error_dx == True\
347	else numpy.zeros(len(output.x))
348
349	if data_conv_q is not None:
350	output.xaxis("\\rm{Q}", output.x_unit)
351	else:
352	output.xaxis("\\rm{Q}", 'A^{-1}')
353	if data_conv_i is not None:
354	output.yaxis("\\rm{Intensity}", output.y_unit)
355	else:
356	output.yaxis("\\rm{Intensity}", "cm^{-1}")
357
358	# Store loading process information
359	output.meta_data['loader'] = self.type_name
360	if len(output.x) < 1:
361	raise RuntimeError, "%s is empty" % path
362	return output
363
364	else:
365	raise RuntimeError, "%s is not a file" % path
366	return None

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source: sasview/src/sas/dataloader/readers/ascii_reader.py @ 296f290

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