ascii_reader.py @ b94889a

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since b94889a was d0ccd80f, checked in by Piotr Rozyczko <rozyczko@…>, 8 years ago
Fixes #658: ASCII reader files less than 5 lines long get thrown out.
Property mode set to `100644`
File size: 9.9 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.sascalc.dataloader.data_info import Data1D
19
20	# Check whether we have a converter available
21	has_converter = True
22	try:
23	from sas.sascalc.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	:return: Data1D object, or None
53
54	:raise RuntimeError: when the file can't be opened
55	:raise ValueError: when the length of the data vectors are inconsistent
56	"""
57	if os.path.isfile(path):
58	basename = os.path.basename(path)
59	_, extension = os.path.splitext(basename)
60	if self.allow_all or extension.lower() in self.ext:
61	try:
62	# Read in binary mode since GRASP frequently has no-ascii
63	# characters that breaks the open operation
64	input_f = open(path,'rb')
65	except:
66	raise RuntimeError, "ascii_reader: cannot open %s" % path
67	buff = input_f.read()
68	lines = buff.splitlines()
69
70	# Arrays for data storage
71	tx = numpy.zeros(0)
72	ty = numpy.zeros(0)
73	tdy = numpy.zeros(0)
74	tdx = numpy.zeros(0)
75
76	# The first good line of data will define whether
77	# we have 2-column or 3-column ascii
78	has_error_dx = None
79	has_error_dy = None
80
81	#Initialize counters for data lines and header lines.
82	is_data = False
83	# More than "5" lines of data is considered as actual
84	# data unless that is the only data
85	min_data_pts = 5
86	# To count # of current data candidate lines
87	candidate_lines = 0
88	# To count total # of previous data candidate lines
89	candidate_lines_previous = 0
90	#minimum required number of columns of data
91	lentoks = 2
92	for line in lines:
93	toks = self.splitline(line)
94	# To remember the # of columns in the current line of data
95	new_lentoks = len(toks)
96	try:
97	if new_lentoks == 1 and not is_data:
98	## If only one item in list, no longer data
99	raise ValueError
100	elif new_lentoks == 0:
101	## If the line is blank, skip and continue on
102	## In case of breaks within data sets.
103	continue
104	elif new_lentoks != lentoks and is_data:
105	## If a footer is found, break the loop and save the data
106	break
107	elif new_lentoks != lentoks and not is_data:
108	## If header lines are numerical
109	candidate_lines = 0
110	candidate_lines_previous = 0
111
112	#Make sure that all columns are numbers.
113	for colnum in range(len(toks)):
114	# Any non-floating point values throw ValueError
115	float(toks[colnum])
116
117	candidate_lines += 1
118	_x = float(toks[0])
119	_y = float(toks[1])
120	_dx = None
121	_dy = None
122
123	#If 5 or more lines, this is considering the set data
124	if candidate_lines >= min_data_pts:
125	is_data = True
126
127	# If a 3rd row is present, consider it dy
128	if new_lentoks > 2:
129	_dy = float(toks[2])
130	has_error_dy = False if _dy == None else True
131
132	# If a 4th row is present, consider it dx
133	if new_lentoks > 3:
134	_dx = float(toks[3])
135	has_error_dx = False if _dx == None else True
136
137	# Delete the previously stored lines of data candidates if
138	# the list is not data
139	if candidate_lines == 1 and -1 < candidate_lines_previous < min_data_pts and \
140	is_data == False:
141	try:
142	tx = numpy.zeros(0)
143	ty = numpy.zeros(0)
144	tdy = numpy.zeros(0)
145	tdx = numpy.zeros(0)
146	except:
147	pass
148
149	if has_error_dy == True:
150	tdy = numpy.append(tdy, _dy)
151	if has_error_dx == True:
152	tdx = numpy.append(tdx, _dx)
153	tx = numpy.append(tx, _x)
154	ty = numpy.append(ty, _y)
155
156	#To remember the # of columns on the current line
157	# for the next line of data
158	lentoks = new_lentoks
159	candidate_lines_previous = candidate_lines
160	except ValueError:
161	# It is data and meet non - number, then stop reading
162	if is_data == True:
163	break
164	lentoks = 2
165	has_error_dx = None
166	has_error_dy = None
167	#Reset # of lines of data candidates
168	candidate_lines = 0
169	except:
170	pass
171
172	input_f.close()
173	if not is_data:
174	return None
175	# Sanity check
176	if has_error_dy == True and not len(ty) == len(tdy):
177	msg = "ascii_reader: y and dy have different length"
178	raise RuntimeError, msg
179	if has_error_dx == True and not len(tx) == len(tdx):
180	msg = "ascii_reader: y and dy have different length"
181	raise RuntimeError, msg
182	# If the data length is zero, consider this as
183	# though we were not able to read the file.
184	if len(tx) == 0:
185	raise RuntimeError, "ascii_reader: could not load file"
186
187	#Let's re-order the data to make cal.
188	# curve look better some cases
189	ind = numpy.lexsort((ty, tx))
190	x = numpy.zeros(len(tx))
191	y = numpy.zeros(len(ty))
192	dy = numpy.zeros(len(tdy))
193	dx = numpy.zeros(len(tdx))
194	output = Data1D(x, y, dy=dy, dx=dx)
195	self.filename = output.filename = basename
196
197	for i in ind:
198	x[i] = tx[ind[i]]
199	y[i] = ty[ind[i]]
200	if has_error_dy == True:
201	dy[i] = tdy[ind[i]]
202	if has_error_dx == True:
203	dx[i] = tdx[ind[i]]
204	# Zeros in dx, dy
205	if has_error_dx:
206	dx[dx == 0] = _ZERO
207	if has_error_dy:
208	dy[dy == 0] = _ZERO
209	#Data
210	output.x = x[x != 0]
211	output.y = y[x != 0]
212	output.dy = dy[x != 0] if has_error_dy == True\
213	else numpy.zeros(len(output.y))
214	output.dx = dx[x != 0] if has_error_dx == True\
215	else numpy.zeros(len(output.x))
216
217	output.xaxis("\\rm{Q}", 'A^{-1}')
218	output.yaxis("\\rm{Intensity}", "cm^{-1}")
219
220	# Store loading process information
221	output.meta_data['loader'] = self.type_name
222	if len(output.x) < 1:
223	raise RuntimeError, "%s is empty" % path
224	return output
225
226	else:
227	raise RuntimeError, "%s is not a file" % path
228	return None
229
230	def splitline(self, line):
231	"""
232	Splits a line into pieces based on common delimeters
233	:param line: A single line of text
234	:return: list of values
235	"""
236	# Initial try for CSV (split on ,)
237	toks = line.split(',')
238	# Now try SCSV (split on ;)
239	if len(toks) < 2:
240	toks = line.split(';')
241	# Now go for whitespace
242	if len(toks) < 2:
243	toks = line.split()
244	return toks

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source: sasview/src/sas/sascalc/dataloader/readers/ascii_reader.py @ b94889a

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