ascii_reader.py @ 7d8094b

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 7d8094b was 3aed0eb, checked in by Jae Cho <jhjcho@…>, 15 years ago
cleaned up mess
Property mode set to `100644`
File size: 14.2 KB

Line
1	"""
2	This software was developed by the University of Tennessee as part of the
3	Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
4	project funded by the US National Science Foundation.
5
6	See the license text in license.txt
7
8	copyright 2008, University of Tennessee
9	"""
10
11	import numpy
12	import os
13	from DataLoader.data_info import Data1D
14
15	# Check whether we have a converter available
16	has_converter = True
17	try:
18	from data_util.nxsunit import Converter
19	except:
20	has_converter = False
21
22	class Reader:
23	"""
24	Class to load ascii files (2 or 3 columns)
25	"""
26	## File type
27	type_name = "ASCII"
28
29	## Wildcards
30	type = ["ASCII files (.txt)\|.txt",
31	"ASCII files (.dat)\|.dat",
32	"ASCII files (.abs)\|.abs"]
33	## List of allowed extensions
34	ext=['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS']
35
36	def read(self, path):
37	"""
38	Load data file
39
40	@param path: file path
41	@return: Data1D object, or None
42	@raise RuntimeError: when the file can't be opened
43	@raise ValueError: when the length of the data vectors are inconsistent
44	"""
45	if os.path.isfile(path):
46	basename = os.path.basename(path)
47	root, extension = os.path.splitext(basename)
48	if extension.lower() in self.ext:
49	try:
50	input_f = open(path,'r')
51	except :
52	raise RuntimeError, "ascii_reader: cannot open %s" % path
53	buff = input_f.read()
54	lines = buff.split('\n')
55
56	#Jae could not find python universal line spliter: keep the below for now
57	# some ascii data has \r line separator, try it when it has only one line
58	if len(lines) < 2 :
59	lines = buff.split('\r')
60
61	x = numpy.zeros(0)
62	y = numpy.zeros(0)
63	dy = numpy.zeros(0)
64	dx = numpy.zeros(0)
65
66	#temp. space to sort data
67	tx = numpy.zeros(0)
68	ty = numpy.zeros(0)
69	tdy = numpy.zeros(0)
70	tdx = numpy.zeros(0)
71
72	output = Data1D(x, y, dy=dy, dx=dx)
73	self.filename = output.filename = basename
74
75	data_conv_q = None
76	data_conv_i = None
77
78	if has_converter == True and output.x_unit != '1/A':
79	data_conv_q = Converter('1/A')
80	# Test it
81	data_conv_q(1.0, output.x_unit)
82
83	if has_converter == True and output.y_unit != '1/cm':
84	data_conv_i = Converter('1/cm')
85	# Test it
86	data_conv_i(1.0, output.y_unit)
87
88
89	# The first good line of data will define whether
90	# we have 2-column or 3-column ascii
91	has_error_dx = None
92	has_error_dy = None
93
94	#Initialize counters for data lines and header lines.
95	is_data = False #Has more than 3 lines
96	mum_data_lines = 3 # More than "3" lines of data is considered as actual data unless that is the only data
97
98	i=-1 # To count # of current data candidate lines
99	i1=-1 # To count total # of previous data candidate lines
100	j=-1 # To count # of header lines
101	j1=-1 # Helps to count # of header lines
102	lentoks = 2 # minimum required number of columns of data; ( <= 4).
103
104	for line in lines:
105	toks = line.split()
106
107	try:
108
109	_x = float(toks[0])
110	_y = float(toks[1])
111
112	#Reset the header line counters
113	if j == j1:
114	j = 0
115	j1 = 0
116
117	if i > 1:
118	is_data = True
119
120	if data_conv_q is not None:
121	_x = data_conv_q(_x, units=output.x_unit)
122
123	if data_conv_i is not None:
124	_y = data_conv_i(_y, units=output.y_unit)
125
126	# If we have an extra token, check
127	# whether it can be interpreted as a
128	# third column.
129	_dy = None
130	if len(toks)>2:
131	try:
132	_dy = float(toks[2])
133
134	if data_conv_i is not None:
135	_dy = data_conv_i(_dy, units=output.y_unit)
136
137	except:
138	# The third column is not a float, skip it.
139	pass
140
141	# If we haven't set the 3rd column
142	# flag, set it now.
143	if has_error_dy == None:
144	has_error_dy = False if _dy == None else True
145
146	#Check for dx
147	_dx = None
148	if len(toks)>3:
149	try:
150	_dx = float(toks[3])
151
152	if data_conv_i is not None:
153	_dx = data_conv_i(_dx, units=output.x_unit)
154
155	except:
156	# The 4th column is not a float, skip it.
157	pass
158
159	# If we haven't set the 3rd column
160	# flag, set it now.
161	if has_error_dx == None:
162	has_error_dx = False if _dx == None else True
163
164	#After talked with PB, we decided to take care of only 4 columns of data for now.
165	#number of columns in the current line
166	if len(toks)>= 4:
167	new_lentoks = 4
168	else:
169	new_lentoks = len(toks)
170
171	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
172	if lentoks != new_lentoks :
173	if is_data == True:
174	break
175	else:
176	i = -1
177	i1 = 0
178	j = -1
179	j1 = -1
180
181
182	#Delete the previously stored lines of data candidates if is not data.
183	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
184	try:
185	x= numpy.zeros(0)
186	y= numpy.zeros(0)
187
188	except:
189	pass
190
191	x = numpy.append(x, _x)
192	y = numpy.append(y, _y)
193
194	if has_error_dy == True:
195	#Delete the previously stored lines of data candidates if is not data.
196	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
197	try:
198	dy = numpy.zeros(0)
199	except:
200	pass
201	dy = numpy.append(dy, _dy)
202
203	if has_error_dx == True:
204	#Delete the previously stored lines of data candidates if is not data.
205	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
206	try:
207	dx = numpy.zeros(0)
208	except:
209	pass
210	dx = numpy.append(dx, _dx)
211
212	#Same for temp.
213	#Delete the previously stored lines of data candidates if is not data.
214	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
215	try:
216	tx = numpy.zeros(0)
217	ty = numpy.zeros(0)
218	except:
219	pass
220
221	tx = numpy.append(tx, _x)
222	ty = numpy.append(ty, _y)
223
224	if has_error_dy == True:
225	#Delete the previously stored lines of data candidates if is not data.
226	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
227	try:
228	tdy = numpy.zeros(0)
229	except:
230	pass
231	tdy = numpy.append(tdy, _dy)
232	if has_error_dx == True:
233	#Delete the previously stored lines of data candidates if is not data.
234	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
235	try:
236	tdx = numpy.zeros(0)
237	except:
238	pass
239	tdx = numpy.append(tdx, _dx)
240
241	#reset i1 and flag lentoks for the next
242	if lentoks < new_lentoks :
243	if is_data == False:
244	i1 = -1
245	if len(toks)>= 4:
246	lentoks = 4
247	else:
248	lentoks = len(toks)
249
250	#Reset # of header lines and counts # of data candidate lines
251	if j == 0 and j1 ==0:
252	i1 = i + 1
253	i+=1
254
255	except:
256
257	# It is data and meet non - number, then stop reading
258	if is_data == True:
259	break
260	lentoks = 2
261	#Counting # of header lines
262	j+=1
263	if j == j1+1:
264	j1 = j
265	else:
266	j = -1
267	#Reset # of lines of data candidates
268	i = -1
269
270	# Couldn't parse this line, skip it
271	pass
272
273
274
275	# Sanity check
276	if has_error_dy == True and not len(y) == len(dy):
277	raise RuntimeError, "ascii_reader: y and dy have different length"
278	if has_error_dx == True and not len(x) == len(dx):
279	raise RuntimeError, "ascii_reader: y and dy have different length"
280
281	# If the data length is zero, consider this as
282	# though we were not able to read the file.
283	if len(x)==0:
284	raise RuntimeError, "ascii_reader: could not load file"
285
286	#Let's re-order the data to make cal. curve look better some cases
287	ind = numpy.lexsort((ty,tx))
288	for i in ind:
289	x[i] = tx[ind[i]]
290	y[i] = ty[ind[i]]
291	if has_error_dy == True:
292	dy[i] = tdy[ind[i]]
293	if has_error_dx == True:
294	dx[i] = tdx[ind[i]]
295
296
297	#Data
298	output.x = x
299	output.y = y
300	output.dy = dy if has_error_dy == True else None
301	output.dx = dx if has_error_dx == True else None
302
303	if data_conv_q is not None:
304	output.xaxis("\\rm{Q}", output.x_unit)
305	else:
306	output.xaxis("\\rm{Q}", 'A^{-1}')
307	if data_conv_i is not None:
308	output.yaxis("\\rm{Intensity}", output.y_unit)
309	else:
310	output.yaxis("\\rm{Intensity}","cm^{-1}")
311	return output
312
313	else:
314	raise RuntimeError, "%s is not a file" % path
315	return None
316
317	if __name__ == "__main__":
318	reader = Reader()
319	#print reader.read("../test/test_3_columns.txt")
320	print reader.read("../test/empty.txt")
321
322
323

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source: sasview/DataLoader/readers/ascii_reader.py @ 7d8094b

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