danse_reader.py @ d619341

Last change on this file since d619341 was b699768, checked in by Piotr Rozyczko <piotr.rozyczko@…>, 9 years ago
Initial commit of the refactored SasCalc? module.
Property mode set to `100644`
File size: 10.4 KB

Line
1	"""
2	DANSE/SANS file 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	import math
15	import os
16	import sys
17	import numpy
18	import logging
19	from sas.sascalc.dataloader.data_info import Data2D, Detector
20	from sas.sascalc.dataloader.manipulations import reader2D_converter
21
22	# Look for unit converter
23	has_converter = True
24	try:
25	from sas.sascalc.data_util.nxsunit import Converter
26	except:
27	has_converter = False
28
29
30	class Reader:
31	"""
32	Example data manipulation
33	"""
34	## File type
35	type_name = "DANSE"
36	## Wildcards
37	type = ["DANSE files (.sans)\|.sans"]
38	## Extension
39	ext = ['.sans', '.SANS']
40
41	def read(self, filename=None):
42	"""
43	Open and read the data in a file
44	@param file: path of the file
45	"""
46
47	read_it = False
48	for item in self.ext:
49	if filename.lower().find(item) >= 0:
50	read_it = True
51
52	if read_it:
53	try:
54	datafile = open(filename, 'r')
55	except:
56	raise RuntimeError,"danse_reader cannot open %s" % (filename)
57
58	# defaults
59	# wavelength in Angstrom
60	wavelength = 10.0
61	# Distance in meter
62	distance = 11.0
63	# Pixel number of center in x
64	center_x = 65
65	# Pixel number of center in y
66	center_y = 65
67	# Pixel size [mm]
68	pixel = 5.0
69	# Size in x, in pixels
70	size_x = 128
71	# Size in y, in pixels
72	size_y = 128
73	# Format version
74	fversion = 1.0
75
76	output = Data2D()
77	output.filename = os.path.basename(filename)
78	detector = Detector()
79	output.detector.append(detector)
80
81	output.data = numpy.zeros([size_x,size_y])
82	output.err_data = numpy.zeros([size_x, size_y])
83
84	data_conv_q = None
85	data_conv_i = None
86
87	if has_converter == True and output.Q_unit != '1/A':
88	data_conv_q = Converter('1/A')
89	# Test it
90	data_conv_q(1.0, output.Q_unit)
91
92	if has_converter == True and output.I_unit != '1/cm':
93	data_conv_i = Converter('1/cm')
94	# Test it
95	data_conv_i(1.0, output.I_unit)
96
97	read_on = True
98	while read_on:
99	line = datafile.readline()
100	if line.find("DATA:") >= 0:
101	read_on = False
102	break
103	toks = line.split(':')
104	if toks[0] == "FORMATVERSION":
105	fversion = float(toks[1])
106	if toks[0] == "WAVELENGTH":
107	wavelength = float(toks[1])
108	elif toks[0] == "DISTANCE":
109	distance = float(toks[1])
110	elif toks[0] == "CENTER_X":
111	center_x = float(toks[1])
112	elif toks[0] == "CENTER_Y":
113	center_y = float(toks[1])
114	elif toks[0] == "PIXELSIZE":
115	pixel = float(toks[1])
116	elif toks[0] == "SIZE_X":
117	size_x = int(toks[1])
118	elif toks[0] == "SIZE_Y":
119	size_y = int(toks[1])
120
121	# Read the data
122	data = []
123	error = []
124	if fversion == 1.0:
125	data_str = datafile.readline()
126	data = data_str.split(' ')
127	else:
128	read_on = True
129	while read_on:
130	data_str = datafile.readline()
131	if len(data_str) == 0:
132	read_on = False
133	else:
134	toks = data_str.split()
135	try:
136	val = float(toks[0])
137	err = float(toks[1])
138	if data_conv_i is not None:
139	val = data_conv_i(val, units=output._yunit)
140	err = data_conv_i(err, units=output._yunit)
141	data.append(val)
142	error.append(err)
143	except:
144	logging.info("Skipping line:%s,%s" %(data_str,
145	sys.exc_value))
146
147	# Initialize
148	x_vals = []
149	y_vals = []
150	ymin = None
151	ymax = None
152	xmin = None
153	xmax = None
154
155	# Qx and Qy vectors
156	theta = pixel / distance / 100.0
157	stepq = 4.0 * math.pi / wavelength * math.sin(theta / 2.0)
158	for i_x in range(size_x):
159	theta = (i_x - center_x + 1) * pixel / distance / 100.0
160	qx = 4.0 * math.pi / wavelength * math.sin(theta / 2.0)
161
162	if has_converter == True and output.Q_unit != '1/A':
163	qx = data_conv_q(qx, units=output.Q_unit)
164
165	x_vals.append(qx)
166	if xmin == None or qx < xmin:
167	xmin = qx
168	if xmax == None or qx > xmax:
169	xmax = qx
170
171	ymin = None
172	ymax = None
173	for i_y in range(size_y):
174	theta = (i_y - center_y + 1) * pixel / distance / 100.0
175	qy = 4.0 * math.pi / wavelength * math.sin(theta/2.0)
176
177	if has_converter == True and output.Q_unit != '1/A':
178	qy = data_conv_q(qy, units=output.Q_unit)
179
180	y_vals.append(qy)
181	if ymin == None or qy < ymin:
182	ymin = qy
183	if ymax == None or qy > ymax:
184	ymax = qy
185
186	# Store the data in the 2D array
187	i_x = 0
188	i_y = -1
189
190	for i_pt in range(len(data)):
191	try:
192	value = float(data[i_pt])
193	except:
194	# For version 1.0, the data were still
195	# stored as strings at this point.
196	msg = "Skipping entry (v1.0):%s,%s" % (str(data[i_pt]),
197	sys.exc_value)
198	logging.info(msg)
199
200	# Get bin number
201	if math.fmod(i_pt, size_x) == 0:
202	i_x = 0
203	i_y += 1
204	else:
205	i_x += 1
206
207	output.data[i_y][i_x] = value
208	if fversion>1.0:
209	output.err_data[i_y][i_x] = error[i_pt]
210
211	# Store all data
212	# Store wavelength
213	if has_converter == True and output.source.wavelength_unit != 'A':
214	conv = Converter('A')
215	wavelength = conv(wavelength,
216	units=output.source.wavelength_unit)
217	output.source.wavelength = wavelength
218
219	# Store distance
220	if has_converter == True and detector.distance_unit != 'm':
221	conv = Converter('m')
222	distance = conv(distance, units=detector.distance_unit)
223	detector.distance = distance
224
225	# Store pixel size
226	if has_converter == True and detector.pixel_size_unit != 'mm':
227	conv = Converter('mm')
228	pixel = conv(pixel, units=detector.pixel_size_unit)
229	detector.pixel_size.x = pixel
230	detector.pixel_size.y = pixel
231
232	# Store beam center in distance units
233	detector.beam_center.x = center_x * pixel
234	detector.beam_center.y = center_y * pixel
235
236	# Store limits of the image (2D array)
237	xmin = xmin - stepq / 2.0
238	xmax = xmax + stepq / 2.0
239	ymin = ymin - stepq /2.0
240	ymax = ymax + stepq / 2.0
241
242	if has_converter == True and output.Q_unit != '1/A':
243	xmin = data_conv_q(xmin, units=output.Q_unit)
244	xmax = data_conv_q(xmax, units=output.Q_unit)
245	ymin = data_conv_q(ymin, units=output.Q_unit)
246	ymax = data_conv_q(ymax, units=output.Q_unit)
247	output.xmin = xmin
248	output.xmax = xmax
249	output.ymin = ymin
250	output.ymax = ymax
251
252	# Store x and y axis bin centers
253	output.x_bins = x_vals
254	output.y_bins = y_vals
255
256	# Units
257	if data_conv_q is not None:
258	output.xaxis("\\rm{Q_{x}}", output.Q_unit)
259	output.yaxis("\\rm{Q_{y}}", output.Q_unit)
260	else:
261	output.xaxis("\\rm{Q_{x}}", 'A^{-1}')
262	output.yaxis("\\rm{Q_{y}}", 'A^{-1}')
263
264	if data_conv_i is not None:
265	output.zaxis("\\rm{Intensity}", output.I_unit)
266	else:
267	output.zaxis("\\rm{Intensity}", "cm^{-1}")
268
269	if not fversion >= 1.0:
270	msg = "Danse_reader can't read this file %s" % filename
271	raise ValueError, msg
272	else:
273	logging.info("Danse_reader Reading %s \n" % filename)
274
275	# Store loading process information
276	output.meta_data['loader'] = self.type_name
277	output = reader2D_converter(output)
278	return output
279
280	return None

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source: sasview/src/sas/sascalc/dataloader/readers/danse_reader.py @ d619341

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