abs_reader.py @ a8ced02

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 a8ced02 was 148ad64, checked in by Jae Cho <jhjcho@…>, 16 years ago
Added a flexibility to read whole different formats of abs files (w/wo header).
Property mode set to `100644`
File size: 12.1 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, Detector
14
15	has_converter = True
16	try:
17	from data_util.nxsunit import Converter
18	except:
19	has_converter = False
20
21	class Reader:
22	"""
23	Class to load IGOR reduced .ABS files
24	"""
25	## File type
26	type = ["IGOR 1D files (.abs)\|.abs"]
27	## List of allowed extensions
28	ext=['.abs', '.ABS']
29
30	def read(self, path):
31	"""
32	Load data file
33
34	@param path: file path
35	@return: Data1D object, or None
36	@raise RuntimeError: when the file can't be opened
37	@raise ValueError: when the length of the data vectors are inconsistent
38	"""
39	if os.path.isfile(path):
40	basename = os.path.basename(path)
41	root, extension = os.path.splitext(basename)
42	if extension.lower() in self.ext:
43	try:
44	input_f = open(path,'r')
45	except :
46	raise RuntimeError, "abs_reader: cannot open %s" % path
47	buff = input_f.read()
48	lines = buff.split('\n')
49	x = numpy.zeros(0)
50	y = numpy.zeros(0)
51	dy = numpy.zeros(0)
52	dx = numpy.zeros(0)
53	output = Data1D(x, y, dy=dy, dx=dx)
54	detector = Detector()
55	output.detector.append(detector)
56	output.filename = basename
57
58	is_info = False
59	is_center = False
60	is_data_started = False
61	right_line_is = -2
62	line_n = 0
63	col = 0
64
65	data_conv_q = None
66	data_conv_i = None
67
68	if has_converter == True and output.x_unit != '1/A':
69	data_conv_q = Converter('1/A')
70	# Test it
71	data_conv_q(1.0, output.x_unit)
72
73	if has_converter == True and output.y_unit != '1/cm':
74	data_conv_i = Converter('1/cm')
75	# Test it
76	data_conv_i(1.0, output.y_unit)
77
78	for line in lines:
79	#print "line",line
80	# Information line 1
81	if is_info==True:
82	is_info = False
83	line_toks = line.split()
84
85	# Wavelength in Angstrom
86	try:
87	value = float(line_toks[1])
88	if has_converter==True and output.source.wavelength_unit != 'A':
89	conv = Converter('A')
90	output.source.wavelength = conv(value, units=output.source.wavelength_unit)
91	else:
92	output.source.wavelength = value
93	except:
94	pass
95	#raise ValueError,"IgorReader: can't read this file, missing wavelength"
96
97	# Distance in meters
98	try:
99	value = float(line_toks[3])
100	if has_converter==True and detector.distance_unit != 'm':
101	conv = Converter('m')
102	detector.distance = conv(value, units=detector.distance_unit)
103	else:
104	detector.distance = value
105	except:
106	pass
107	#raise ValueError,"IgorReader: can't read this file, missing distance"
108
109	# Transmission
110	try:
111	output.sample.transmission = float(line_toks[4])
112	except:
113	# Transmission is not a mandatory entry
114	pass
115
116	# Thickness in mm
117	try:
118	value = float(line_toks[5])
119	if has_converter==True and output.sample.thickness_unit != 'cm':
120	conv = Converter('cm')
121	output.sample.thickness = conv(value, units=output.sample.thickness_unit)
122	else:
123	output.sample.thickness = value
124	except:
125	# Thickness is not a mandatory entry
126	pass
127
128	#MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP
129	if line.count("LAMBDA")>0:
130	is_info = True
131
132	# Find center info line
133	if is_center==True:
134	is_center = False
135	line_toks = line.split()
136	# Center in bin number
137	center_x = float(line_toks[0])
138	center_y = float(line_toks[1])
139
140	# Bin size
141	if has_converter==True and detector.pixel_size_unit != 'mm':
142	conv = Converter('mm')
143	detector.pixel_size.x = conv(5.0, units=detector.pixel_size_unit)
144	detector.pixel_size.y = conv(5.0, units=detector.pixel_size_unit)
145	else:
146	detector.pixel_size.x = 5.0
147	detector.pixel_size.y = 5.0
148
149	# Store beam center in distance units
150	# Det 640 x 640 mm
151	if has_converter==True and detector.beam_center_unit != 'mm':
152	conv = Converter('mm')
153	detector.beam_center.x = conv(center_x*5.0, units=detector.beam_center_unit)
154	detector.beam_center.y = conv(center_y*5.0, units=detector.beam_center_unit)
155	else:
156	detector.beam_center.x = center_x*5.0
157	detector.beam_center.y = center_y*5.0
158
159	# Detector type
160	try:
161	detector.name = line_toks[7]
162	except:
163	# Detector name is not a mandatory entry
164	pass
165
166	#BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP
167	if line.count("BCENT")>0:
168	is_center = True
169
170	# Parse the data
171	# Specify one line of data
172	if len(lines)<2:
173	colnum = 6
174	else:
175	colnum = len(line.split())
176
177	#If # of row = # of data points
178	if colnum == 0:
179	rangeiter = 0
180	#If # of row = 1
181	else:
182	rangeiter=numpy.ceil(len(line.split())/colnum)
183
184	#If all data is in one line, chop the line by every 6 columns and read x, y, dy, dx data
185	for col in range(0,rangeiter):
186	#The 6 columns are \| Q (1/A) \| I(Q) (1/cm) \| std. dev. I(Q) (1/cm) \| sigmaQ \| meanQ \| ShadowFactor\|
187	#Check the file format whether or not it read all header lines and if it has a header
188	if line.count("The 6 columns")>0 or (output.source.wavelength==None):
189	#if it has a full header
190	if line.count("The 6 columns")>0:
191	right_line_is = line_n
192	#If no header in the file
193	else:
194	right_line_is = 0
195	is_data_started = True
196
197
198	# If on the of data, not header, read data
199	if is_data_started==True and right_line_is >= 0: #and line_n > right_line_is
200	#print "col",col
201	toks = line.split()
202	try:
203
204	if float(toks[col*6+0]) > 1:
205	continue
206	else:
207	not_data_line = False
208
209	_x = float(toks[col*6+0])
210	_y = float(toks[col*6+1])
211	_dy = float(toks[col*6+2])
212	_dx = float(toks[col*6+3])
213
214
215	if data_conv_q is not None:
216	_x = data_conv_q(_x, units=output.x_unit)
217	_dx = data_conv_i(_dx, units=output.x_unit)
218
219	if data_conv_i is not None:
220	_y = data_conv_i(_y, units=output.y_unit)
221	_dy = data_conv_i(_dy, units=output.y_unit)
222
223	x =numpy.append(x, _x)
224	y = numpy.append(y, _y)
225	dy = numpy.append(dy, _dy)
226	dx = numpy.append(dx, _dx)
227
228	except:
229	# Could not read this data line. If we are here
230	# it is because we are in the data section. Just
231	# skip it.
232	pass
233
234	line_n = line_n +1
235	# Sanity check
236	if not len(y) == len(dy):
237	raise ValueError, "abs_reader: y and dy have different length"
238	if not len(x) == len(dx):
239	raise ValueError, "abs_reader: x and dx have different length"
240
241	# If the data length is zero, consider this as
242	# though we were not able to read the file.
243	if len(x)==0:
244	raise ValueError, "ascii_reader: could not load file"
245
246	output.x = x
247	output.y = y
248	output.dy = dy
249	output.dx = dx
250	if data_conv_q is not None:
251	output.xaxis("\\rm{Q}", output.x_unit)
252	else:
253	output.xaxis("\\rm{Q}", 'A^{-1}')
254	if data_conv_i is not None:
255	output.yaxis("\\{I(Q)}", output.y_unit)
256	else:
257	output.yaxis("\\rm{I(Q)}","cm^{-1}")
258	#print " x,y,dx,dy", output.x,output.y,output.dy,output.dx
259	return output
260	else:
261	raise RuntimeError, "%s is not a file" % path
262	return None
263
264	if __name__ == "__main__":
265	reader = Reader()
266	#print reader.read("../test/jan08002.ABS")
267
268
269

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source: sasview/DataLoader/readers/abs_reader.py @ a8ced02

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