ascii_reader.py @ f5cce4a

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 f5cce4a was 83b81b8, checked in by Jae Cho <jhjcho@…>, 12 years ago
a little better data error control
Property mode set to `100644`
File size: 15.4 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 sans.dataloader.data_info import Data1D
19
20	# Check whether we have a converter available
21	has_converter = True
22	try:
23	from 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	toks = line.split(',')
127	if len(toks) < 2:
128	toks = line.split()
129	try:
130	#Make sure that all columns are numbers.
131	for colnum in range(len(toks)):
132	float(toks[colnum])
133
134	_x = float(toks[0])
135	_y = float(toks[1])
136
137	#Reset the header line counters
138	if j == j1:
139	j = 0
140	j1 = 0
141
142	if i > 1:
143	is_data = True
144
145	if data_conv_q is not None:
146	_x = data_conv_q(_x, units=output.x_unit)
147
148	if data_conv_i is not None:
149	_y = data_conv_i(_y, units=output.y_unit)
150
151	# If we have an extra token, check
152	# whether it can be interpreted as a
153	# third column.
154	_dy = None
155	if len(toks) > 2:
156	try:
157	_dy = float(toks[2])
158
159	if data_conv_i is not None:
160	_dy = data_conv_i(_dy, units=output.y_unit)
161
162	except:
163	# The third column is not a float, skip it.
164	pass
165
166	# If we haven't set the 3rd column
167	# flag, set it now.
168	if has_error_dy == None:
169	has_error_dy = False if _dy == None else True
170
171	#Check for dx
172	_dx = None
173	if len(toks) > 3:
174	try:
175	_dx = float(toks[3])
176
177	if data_conv_i is not None:
178	_dx = data_conv_i(_dx, units=output.x_unit)
179
180	except:
181	# The 4th column is not a float, skip it.
182	pass
183
184	# If we haven't set the 3rd column
185	# flag, set it now.
186	if has_error_dx == None:
187	has_error_dx = False if _dx == None else True
188
189	#After talked with PB, we decided to take care of only
190	# 4 columns of data for now.
191	#number of columns in the current line
192	#To remember the # of columns in the current
193	#line of data
194	new_lentoks = len(toks)
195
196	#If the previous columns not equal to the current,
197	#mark the previous as non-data and reset the dependents.
198	if lentoks != new_lentoks:
199	if is_data == True:
200	break
201	else:
202	i = -1
203	i1 = 0
204	j = -1
205	j1 = -1
206
207	#Delete the previously stored lines of data candidates
208	# if is not data.
209	if i < 0 and -1 < i1 < mum_data_lines and \
210	is_data == False:
211	try:
212	x = numpy.zeros(0)
213	y = numpy.zeros(0)
214	except:
215	pass
216
217	x = numpy.append(x, _x)
218	y = numpy.append(y, _y)
219
220	if has_error_dy == True:
221	#Delete the previously stored lines of
222	# data candidates if is not data.
223	if i < 0 and -1 < i1 < mum_data_lines and \
224	is_data == False:
225	try:
226	dy = numpy.zeros(0)
227	except:
228	pass
229	dy = numpy.append(dy, _dy)
230
231	if has_error_dx == True:
232	#Delete the previously stored lines of
233	# data candidates if is not data.
234	if i < 0 and -1 < i1 < mum_data_lines and \
235	is_data == False:
236	try:
237	dx = numpy.zeros(0)
238	except:
239	pass
240	dx = numpy.append(dx, _dx)
241
242	#Same for temp.
243	#Delete the previously stored lines of data candidates
244	# if is not data.
245	if i < 0 and -1 < i1 < mum_data_lines and\
246	is_data == False:
247	try:
248	tx = numpy.zeros(0)
249	ty = numpy.zeros(0)
250	except:
251	pass
252
253	tx = numpy.append(tx, _x)
254	ty = numpy.append(ty, _y)
255
256	if has_error_dy == True:
257	#Delete the previously stored lines of
258	# data candidates if is not data.
259	if i < 0 and -1 < i1 < mum_data_lines and \
260	is_data == False:
261	try:
262	tdy = numpy.zeros(0)
263	except:
264	pass
265	tdy = numpy.append(tdy, _dy)
266	if has_error_dx == True:
267	#Delete the previously stored lines of
268	# data candidates if is not data.
269	if i < 0 and -1 < i1 < mum_data_lines and \
270	is_data == False:
271	try:
272	tdx = numpy.zeros(0)
273	except:
274	pass
275	tdx = numpy.append(tdx, _dx)
276
277	#reset i1 and flag lentoks for the next
278	if lentoks < new_lentoks:
279	if is_data == False:
280	i1 = -1
281	#To remember the # of columns on the current line
282	# for the next line of data
283	lentoks = len(toks)
284
285	#Reset # of header lines and counts #
286	# of data candidate lines
287	if j == 0 and j1 == 0:
288	i1 = i + 1
289	i += 1
290	except:
291
292	# It is data and meet non - number, then stop reading
293	if is_data == True:
294	break
295	lentoks = 2
296	#Counting # of header lines
297	j += 1
298	if j == j1 + 1:
299	j1 = j
300	else:
301	j = -1
302	#Reset # of lines of data candidates
303	i = -1
304
305	# Couldn't parse this line, skip it
306	pass
307
308	input_f.close()
309	# Sanity check
310	if has_error_dy == True and not len(y) == len(dy):
311	msg = "ascii_reader: y and dy have different length"
312	raise RuntimeError, msg
313	if has_error_dx == True and not len(x) == len(dx):
314	msg = "ascii_reader: y and dy have different length"
315	raise RuntimeError, msg
316	# If the data length is zero, consider this as
317	# though we were not able to read the file.
318	if len(x) == 0:
319	raise RuntimeError, "ascii_reader: could not load file"
320
321	#Let's re-order the data to make cal.
322	# curve look better some cases
323	ind = numpy.lexsort((ty, tx))
324	for i in ind:
325	x[i] = tx[ind[i]]
326	y[i] = ty[ind[i]]
327	if has_error_dy == True:
328	dy[i] = tdy[ind[i]]
329	if has_error_dx == True:
330	dx[i] = tdx[ind[i]]
331	# Zeros in dx, dy
332	if has_error_dx:
333	dx[dx == 0] = _ZERO
334	if has_error_dy:
335	dy[dy == 0] = _ZERO
336	#Data
337	output.x = x[x != 0]
338	output.y = y[x != 0]
339	output.dy = dy[x != 0] if has_error_dy == True\
340	else numpy.zeros(len(output.y))
341	output.dx = dx[x != 0] if has_error_dx == True\
342	else numpy.zeros(len(output.x))
343
344	if data_conv_q is not None:
345	output.xaxis("\\rm{Q}", output.x_unit)
346	else:
347	output.xaxis("\\rm{Q}", 'A^{-1}')
348	if data_conv_i is not None:
349	output.yaxis("\\rm{Intensity}", output.y_unit)
350	else:
351	output.yaxis("\\rm{Intensity}", "cm^{-1}")
352
353	# Store loading process information
354	output.meta_data['loader'] = self.type_name
355	if len(output.x) < 1:
356	raise RuntimeError, "%s is empty" % path
357	return output
358
359	else:
360	raise RuntimeError, "%s is not a file" % path
361	return None

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source: sasview/sansdataloader/src/sans/dataloader/readers/ascii_reader.py @ f5cce4a

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