abs_reader.py @ 3f89c0e

ticket-1094-headless

Last change on this file since 3f89c0e was d96744de, checked in by Jeff Krzywon <jkrzywon@…>, 6 years ago
Fix for loading USANS data in ABS reader including fixes to unit tests.
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	x_index = 4
51	self.reset_data_list(len(lines))
52	self.current_datainfo.detector.append(detector)
53	self.current_datainfo.filename = filepath
54
55	is_info = False
56	is_center = False
57	is_data_started = False
58
59	base_q_unit = '1/A'
60	base_i_unit = '1/cm'
61	data_conv_q = Converter(base_q_unit)
62	data_conv_i = Converter(base_i_unit)
63
64	for line in lines:
65	# Information line 1
66	if line.find(".bt5") > 0:
67	x_index = 0
68	if is_info:
69	is_info = False
70	line_toks = line.split()
71
72	# Wavelength in Angstrom
73	try:
74	value = float(line_toks[1])
75	if self.current_datainfo.source.wavelength_unit != 'A':
76	conv = Converter('A')
77	self.current_datainfo.source.wavelength = conv(value,
78	units=self.current_datainfo.source.wavelength_unit)
79	else:
80	self.current_datainfo.source.wavelength = value
81	except KeyError:
82	msg = "ABSReader cannot read wavelength from %s" % filepath
83	self.current_datainfo.errors.append(msg)
84
85	# Detector distance in meters
86	try:
87	value = float(line_toks[3])
88	if detector.distance_unit != 'm':
89	conv = Converter('m')
90	detector.distance = conv(value,
91	units=detector.distance_unit)
92	else:
93	detector.distance = value
94	except Exception:
95	msg = "ABSReader cannot read SDD from %s" % filepath
96	self.current_datainfo.errors.append(msg)
97
98	# Transmission
99	try:
100	self.current_datainfo.sample.transmission = \
101	float(line_toks[4])
102	except ValueError:
103	# Transmission isn't always in the header
104	pass
105
106	# Sample thickness in mm
107	try:
108	# ABS writer adds 'C' with no space to the end of the
109	# thickness column. Remove it if it is there before
110	# converting the thickness.
111	if line_toks[5][-1] not in '012345679.':
112	value = float(line_toks[5][:-1])
113	else:
114	value = float(line_toks[5])
115	if self.current_datainfo.sample.thickness_unit != 'cm':
116	conv = Converter('cm')
117	self.current_datainfo.sample.thickness = conv(value,
118	units=self.current_datainfo.sample.thickness_unit)
119	else:
120	self.current_datainfo.sample.thickness = value
121	except ValueError:
122	# Thickness is not a mandatory entry
123	pass
124
125	# MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP
126	if line.count("LAMBDA") > 0:
127	is_info = True
128
129	# Find center info line
130	if is_center:
131	is_center = False
132	line_toks = line.split()
133	# Center in bin number
134	center_x = float(line_toks[0])
135	center_y = float(line_toks[1])
136
137	# Bin size
138	if detector.pixel_size_unit != 'mm':
139	conv = Converter('mm')
140	detector.pixel_size.x = conv(5.08,
141	units=detector.pixel_size_unit)
142	detector.pixel_size.y = conv(5.08,
143	units=detector.pixel_size_unit)
144	else:
145	detector.pixel_size.x = 5.08
146	detector.pixel_size.y = 5.08
147
148	# Store beam center in distance units
149	# Det 640 x 640 mm
150	if detector.beam_center_unit != 'mm':
151	conv = Converter('mm')
152	detector.beam_center.x = conv(center_x * 5.08,
153	units=detector.beam_center_unit)
154	detector.beam_center.y = conv(center_y * 5.08,
155	units=detector.beam_center_unit)
156	else:
157	detector.beam_center.x = center_x * 5.08
158	detector.beam_center.y = center_y * 5.08
159
160	# Detector type
161	try:
162	detector.name = line_toks[7]
163	except:
164	# Detector name is not a mandatory entry
165	pass
166
167	# BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP
168	if line.count("BCENT") > 0:
169	is_center = True
170
171	# Parse the data
172	if is_data_started:
173	toks = line.split()
174
175	try:
176	_x = float(toks[x_index])
177	_y = float(toks[1])
178	_dy = float(toks[2])
179	_dx = float(toks[3])
180
181	if data_conv_q is not None:
182	_x = data_conv_q(_x, units=base_q_unit)
183	_dx = data_conv_q(_dx, units=base_q_unit)
184
185	if data_conv_i is not None:
186	_y = data_conv_i(_y, units=base_i_unit)
187	_dy = data_conv_i(_dy, units=base_i_unit)
188
189	self.current_dataset.x[data_line] = _x
190	self.current_dataset.y[data_line] = _y
191	self.current_dataset.dy[data_line] = _dy
192	if _dx > 0:
193	self.current_dataset.dx[data_line] = _dx
194	else:
195	if data_line == 0:
196	self.current_dataset.dx = None
197	self.current_dataset.dxl = np.zeros(len(lines))
198	self.current_dataset.dxw = np.zeros(len(lines))
199	self.current_dataset.dxl[data_line] = abs(_dx)
200	self.current_dataset.dxw[data_line] = 0
201	data_line += 1
202
203	except ValueError:
204	# Could not read this data line. If we are here
205	# it is because we are in the data section. Just
206	# skip it.
207	pass
208
209	# SANS Data:
210	# The 6 columns are \| Q (1/A) \| I(Q) (1/cm) \| std. dev.
211	# I(Q) (1/cm) \| sigmaQ \| meanQ \| ShadowFactor\|
212	# USANS Data:
213	# EMP LEVEL: <value> ; BKG LEVEL: <value>
214	if line.startswith("The 6 columns") or line.startswith("EMP LEVEL"):
215	is_data_started = True
216
217	self.remove_empty_q_values()
218
219	# Sanity check
220	if not len(self.current_dataset.y) == len(self.current_dataset.dy):
221	self.set_all_to_none()
222	msg = "abs_reader: y and dy have different length"
223	raise ValueError(msg)
224	# If the data length is zero, consider this as
225	# though we were not able to read the file.
226	if len(self.current_dataset.x) == 0:
227	self.set_all_to_none()
228	raise ValueError("ascii_reader: could not load file")
229
230	self.current_dataset = self.set_default_1d_units(self.current_dataset)
231	if data_conv_q is not None:
232	self.current_dataset.xaxis("\\rm{Q}", base_q_unit)
233	if data_conv_i is not None:
234	self.current_dataset.yaxis("\\rm{Intensity}", base_i_unit)
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 @ 3f89c0e

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