abs_reader.py @ a16cbb0

Last change on this file since a16cbb0 was e3775c6, checked in by krzywon, 7 years ago
Use startswith instead of count for line matching in ABS reader.
Property mode set to `100644`
File size: 9.2 KB

Line
1	"""
2	IGOR 1D data 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	# See the license text in license.txt
9	# copyright 2008, University of Tennessee
10	######################################################################
11
12	import logging
13
14	import numpy as np
15
16	from sas.sascalc.data_util.nxsunit import Converter
17	from ..file_reader_base_class import FileReader
18	from ..data_info import DataInfo, plottable_1D, Data1D, Detector
19	from ..loader_exceptions import FileContentsException, DefaultReaderException
20
21	logger = logging.getLogger(__name__)
22
23
24	class Reader(FileReader):
25	"""
26	Class to load IGOR reduced .ABS files
27	"""
28	# File type
29	type_name = "IGOR 1D"
30	# Wildcards
31	type = ["IGOR 1D files (.abs)\|.abs", "IGOR 1D USANS files (.cor)\|.cor"]
32	# List of allowed extensions
33	ext = ['.abs', '.cor']
34
35	def get_file_contents(self):
36	"""
37	Get the contents of the file
38
39	:raise RuntimeError: when the file can't be opened
40	:raise ValueError: when the length of the data vectors are inconsistent
41	"""
42	buff = self.readall()
43	filepath = self.f_open.name
44	lines = buff.splitlines()
45	self.output = []
46	self.current_datainfo = DataInfo()
47	self.current_datainfo.filename = filepath
48	detector = Detector()
49	data_line = 0
50	self.reset_data_list(len(lines))
51	self.current_datainfo.detector.append(detector)
52	self.current_datainfo.filename = filepath
53
54	is_info = False
55	is_center = False
56	is_data_started = False
57
58	base_q_unit = '1/A'
59	base_i_unit = '1/cm'
60	data_conv_q = Converter(base_q_unit)
61	data_conv_i = Converter(base_i_unit)
62
63	for line in lines:
64	# Information line 1
65	if is_info:
66	is_info = False
67	line_toks = line.split()
68
69	# Wavelength in Angstrom
70	try:
71	value = float(line_toks[1])
72	if self.current_datainfo.source.wavelength_unit != 'A':
73	conv = Converter('A')
74	self.current_datainfo.source.wavelength = conv(value,
75	units=self.current_datainfo.source.wavelength_unit)
76	else:
77	self.current_datainfo.source.wavelength = value
78	except KeyError:
79	msg = "ABSReader cannot read wavelength from %s" % filepath
80	self.current_datainfo.errors.append(msg)
81
82	# Detector distance in meters
83	try:
84	value = float(line_toks[3])
85	if detector.distance_unit != 'm':
86	conv = Converter('m')
87	detector.distance = conv(value,
88	units=detector.distance_unit)
89	else:
90	detector.distance = value
91	except Exception:
92	msg = "ABSReader cannot read SDD from %s" % filepath
93	self.current_datainfo.errors.append(msg)
94
95	# Transmission
96	try:
97	self.current_datainfo.sample.transmission = \
98	float(line_toks[4])
99	except ValueError:
100	# Transmission isn't always in the header
101	pass
102
103	# Sample thickness in mm
104	try:
105	# ABS writer adds 'C' with no space to the end of the
106	# thickness column. Remove it if it is there before
107	# converting the thickness.
108	if line_toks[5][-1] not in '012345679.':
109	value = float(line_toks[5][:-1])
110	else:
111	value = float(line_toks[5])
112	if self.current_datainfo.sample.thickness_unit != 'cm':
113	conv = Converter('cm')
114	self.current_datainfo.sample.thickness = conv(value,
115	units=self.current_datainfo.sample.thickness_unit)
116	else:
117	self.current_datainfo.sample.thickness = value
118	except ValueError:
119	# Thickness is not a mandatory entry
120	pass
121
122	# MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP
123	if line.count("LAMBDA") > 0:
124	is_info = True
125
126	# Find center info line
127	if is_center:
128	is_center = False
129	line_toks = line.split()
130	# Center in bin number
131	center_x = float(line_toks[0])
132	center_y = float(line_toks[1])
133
134	# Bin size
135	if detector.pixel_size_unit != 'mm':
136	conv = Converter('mm')
137	detector.pixel_size.x = conv(5.08,
138	units=detector.pixel_size_unit)
139	detector.pixel_size.y = conv(5.08,
140	units=detector.pixel_size_unit)
141	else:
142	detector.pixel_size.x = 5.08
143	detector.pixel_size.y = 5.08
144
145	# Store beam center in distance units
146	# Det 640 x 640 mm
147	if detector.beam_center_unit != 'mm':
148	conv = Converter('mm')
149	detector.beam_center.x = conv(center_x * 5.08,
150	units=detector.beam_center_unit)
151	detector.beam_center.y = conv(center_y * 5.08,
152	units=detector.beam_center_unit)
153	else:
154	detector.beam_center.x = center_x * 5.08
155	detector.beam_center.y = center_y * 5.08
156
157	# Detector type
158	try:
159	detector.name = line_toks[7]
160	except:
161	# Detector name is not a mandatory entry
162	pass
163
164	# BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP
165	if line.count("BCENT") > 0:
166	is_center = True
167
168	# Parse the data
169	if is_data_started:
170	toks = line.split()
171
172	try:
173	_x = float(toks[0])
174	_y = float(toks[1])
175	_dy = float(toks[2])
176	_dx = float(toks[3])
177
178	if data_conv_q is not None:
179	_x = data_conv_q(_x, units=base_q_unit)
180	_dx = data_conv_q(_dx, units=base_q_unit)
181
182	if data_conv_i is not None:
183	_y = data_conv_i(_y, units=base_i_unit)
184	_dy = data_conv_i(_dy, units=base_i_unit)
185
186	self.current_dataset.x[data_line] = _x
187	self.current_dataset.y[data_line] = _y
188	self.current_dataset.dy[data_line] = _dy
189	if _dx > 0:
190	self.current_dataset.dx[data_line] = _dx
191	else:
192	if data_line == 0:
193	self.current_dataset.dx = None
194	self.current_dataset.dxl = np.zeros(len(lines))
195	self.current_dataset.dxw = np.zeros(len(lines))
196	self.current_dataset.dxl[data_line] = abs(_dx)
197	self.current_dataset.dxw[data_line] = 0
198	data_line += 1
199
200	except ValueError:
201	# Could not read this data line. If we are here
202	# it is because we are in the data section. Just
203	# skip it.
204	pass
205
206	# SANS Data:
207	# The 6 columns are \| Q (1/A) \| I(Q) (1/cm) \| std. dev.
208	# I(Q) (1/cm) \| sigmaQ \| meanQ \| ShadowFactor\|
209	# USANS Data:
210	# EMP LEVEL: <value> ; BKG LEVEL: <value>
211	if line.startswith("The 6 columns") or line.startswith("EMP LEVEL"):
212	is_data_started = True
213
214	self.remove_empty_q_values()
215
216	# Sanity check
217	if not len(self.current_dataset.y) == len(self.current_dataset.dy):
218	self.set_all_to_none()
219	msg = "abs_reader: y and dy have different length"
220	raise ValueError(msg)
221	# If the data length is zero, consider this as
222	# though we were not able to read the file.
223	if len(self.current_dataset.x) == 0:
224	self.set_all_to_none()
225	raise ValueError("ascii_reader: could not load file")
226
227	if data_conv_q is not None:
228	self.current_dataset.xaxis("\\rm{Q}", base_q_unit)
229	else:
230	self.current_dataset.xaxis("\\rm{Q}", 'A^{-1}')
231	if data_conv_i is not None:
232	self.current_dataset.yaxis("\\rm{Intensity}", base_i_unit)
233	else:
234	self.current_dataset.yaxis("\\rm{Intensity}", "cm^{-1}")
235
236	# Store loading process information
237	self.current_datainfo.meta_data['loader'] = self.type_name
238	self.send_to_output()

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source: sasview/src/sas/sascalc/dataloader/readers/abs_reader.py @ a16cbb0

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