danse_reader.py @ 023c8e2

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Last change on this file since 023c8e2 was 0997158f, checked in by Gervaise Alina <gervyh@…>, 14 years ago
working on documentation
Property mode set to `100644`
File size: 10.4 KB

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2
3	############################################################################
4	#This software was developed by the University of Tennessee as part of the
5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
6	#project funded by the US National Science Foundation.
7	#If you use DANSE applications to do scientific research that leads to
8	#publication, we ask that you acknowledge the use of the software with the
9	#following sentence:
10	#This work benefited from DANSE software developed under NSF award DMR-0520547.
11	#copyright 2008, University of Tennessee
12	#############################################################################
13
14	"""
15	DANSE/SANS file reader
16	"""
17
18	import math
19	import os
20	import copy
21	import numpy
22	import logging
23	from DataLoader.data_info import Data2D, Detector
24	from DataLoader.manipulations import reader2D_converter
25
26	# Look for unit converter
27	has_converter = True
28	try:
29	from data_util.nxsunit import Converter
30	except:
31	has_converter = False
32
33	class Reader:
34	"""
35	Example data manipulation
36	"""
37	## File type
38	type_name = "DANSE"
39	## Wildcards
40	type = ["DANSE files (.sans)\|.sans"]
41	## Extension
42	ext = ['.sans', '.SANS']
43
44	def read(self, filename=None):
45	"""
46	Open and read the data in a file
47	@param file: path of the file
48	"""
49
50	read_it = False
51	for item in self.ext:
52	if filename.lower().find(item)>=0:
53	read_it = True
54
55	if read_it:
56	try:
57	datafile = open(filename, 'r')
58	except :
59	raise RuntimeError,"danse_reader cannot open %s"%(filename)
60
61
62	# defaults
63	# wavelength in Angstrom
64	wavelength = 10.0
65	# Distance in meter
66	distance = 11.0
67	# Pixel number of center in x
68	center_x = 65
69	# Pixel number of center in y
70	center_y = 65
71	# Pixel size [mm]
72	pixel = 5.0
73	# Size in x, in pixels
74	size_x = 128
75	# Size in y, in pixels
76	size_y = 128
77	# Format version
78	fversion = 1.0
79
80	output = Data2D()
81	output.filename = os.path.basename(filename)
82	detector = Detector()
83	output.detector.append(detector)
84
85	output.data = numpy.zeros([size_x,size_y])
86	output.err_data = numpy.zeros([size_x,size_y])
87
88	data_conv_q = None
89	data_conv_i = None
90
91	if has_converter == True and output.Q_unit != '1/A':
92	data_conv_q = Converter('1/A')
93	# Test it
94	data_conv_q(1.0, output.Q_unit)
95
96	if has_converter == True and output.I_unit != '1/cm':
97	data_conv_i = Converter('1/cm')
98	# Test it
99	data_conv_i(1.0, output.I_unit)
100
101	read_on = True
102	while read_on:
103	line = datafile.readline()
104	if line.find("DATA:")>=0:
105	read_on = False
106	break
107	toks = line.split(':')
108	if toks[0]=="FORMATVERSION":
109	fversion = float(toks[1])
110	if toks[0]=="WAVELENGTH":
111	wavelength = float(toks[1])
112	elif toks[0]=="DISTANCE":
113	distance = float(toks[1])
114	elif toks[0]=="CENTER_X":
115	center_x = float(toks[1])
116	elif toks[0]=="CENTER_Y":
117	center_y = float(toks[1])
118	elif toks[0]=="PIXELSIZE":
119	pixel = float(toks[1])
120	elif toks[0]=="SIZE_X":
121	size_x = int(toks[1])
122	elif toks[0]=="SIZE_Y":
123	size_y = int(toks[1])
124
125	# Read the data
126	data = []
127	error = []
128	if fversion==1.0:
129	data_str = datafile.readline()
130	data = data_str.split(' ')
131	else:
132	read_on = True
133	while read_on:
134	data_str = datafile.readline()
135	if len(data_str)==0:
136	read_on = False
137	else:
138	toks = data_str.split()
139	try:
140	val = float(toks[0])
141	err = float(toks[1])
142	if data_conv_i is not None:
143	val = data_conv_i(val, units=output.y_unit)
144	err = data_conv_i(err, units=output.y_unit)
145	data.append(val)
146	error.append(err)
147	except:
148	logging.info("Skipping line:%s,%s" %( data_str,sys.exc_value))
149
150	# Initialize
151	x_vals = []
152	y_vals = []
153	ymin = None
154	ymax = None
155	xmin = None
156	xmax = None
157
158	# Qx and Qy vectors
159	theta = pixel / distance / 100.0
160	stepq = 4.0math.pi/wavelength math.sin(theta/2.0)
161	for i_x in range(size_x):
162	theta = (i_x-center_x+1)*pixel / distance / 100.0
163	qx = 4.0math.pi/wavelength math.sin(theta/2.0)
164
165	if has_converter == True and output.Q_unit != '1/A':
166	qx = data_conv_q(qx, units=output.Q_unit)
167
168	x_vals.append(qx)
169	if xmin==None or qx<xmin:
170	xmin = qx
171	if xmax==None or qx>xmax:
172	xmax = qx
173
174	ymin = None
175	ymax = None
176	for i_y in range(size_y):
177	theta = (i_y-center_y+1)*pixel / distance / 100.0
178	qy = 4.0math.pi/wavelength math.sin(theta/2.0)
179
180	if has_converter == True and output.Q_unit != '1/A':
181	qy = data_conv_q(qy, units=output.Q_unit)
182
183	y_vals.append(qy)
184	if ymin==None or qy<ymin:
185	ymin = qy
186	if ymax==None or qy>ymax:
187	ymax = qy
188
189	# Store the data in the 2D array
190	itot = 0
191	i_x = 0
192	i_y = -1
193
194	for i_pt in range(len(data)):
195	try:
196	value = float(data[i_pt])
197	except:
198	# For version 1.0, the data were still
199	# stored as strings at this point.
200	logging.info("Skipping entry (v1.0):%s,%s" %(str(data[i_pt]), sys.exc_value))
201
202	# Get bin number
203	if math.fmod(i_pt, size_x)==0:
204	i_x = 0
205	i_y += 1
206	else:
207	i_x += 1
208
209	output.data[i_y][i_x] = value
210	#output.data[size_y-1-i_y][i_x] = value
211	if fversion>1.0:
212	output.err_data[i_y][i_x] = error[i_pt]
213	#output.err_data[size_y-1-i_y][i_x] = error[i_pt]
214
215
216	# Store all data
217	# Store wavelength
218	if has_converter==True and output.source.wavelength_unit != 'A':
219	conv = Converter('A')
220	wavelength = conv(wavelength, units=output.source.wavelength_unit)
221	output.source.wavelength = wavelength
222
223	# Store distance
224	if has_converter==True and detector.distance_unit != 'm':
225	conv = Converter('m')
226	distance = conv(distance, units=detector.distance_unit)
227	detector.distance = distance
228
229	# Store pixel size
230	if has_converter==True and detector.pixel_size_unit != 'mm':
231	conv = Converter('mm')
232	pixel = conv(pixel, units=detector.pixel_size_unit)
233	detector.pixel_size.x = pixel
234	detector.pixel_size.y = pixel
235
236	# Store beam center in distance units
237	detector.beam_center.x = center_x*pixel
238	detector.beam_center.y = center_y*pixel
239
240	# Store limits of the image (2D array)
241	xmin =xmin-stepq/2.0
242	xmax =xmax+stepq/2.0
243	ymin =ymin-stepq/2.0
244	ymax =ymax+stepq/2.0
245
246	if has_converter == True and output.Q_unit != '1/A':
247	xmin = data_conv_q(xmin, units=output.Q_unit)
248	xmax = data_conv_q(xmax, units=output.Q_unit)
249	ymin = data_conv_q(ymin, units=output.Q_unit)
250	ymax = data_conv_q(ymax, units=output.Q_unit)
251	output.xmin = xmin
252	output.xmax = xmax
253	output.ymin = ymin
254	output.ymax = ymax
255
256	# Store x and y axis bin centers
257	output.x_bins = x_vals
258	output.y_bins = y_vals
259
260	# Units
261	if data_conv_q is not None:
262	output.xaxis("\\rm{Q_{x}}", output.Q_unit)
263	output.yaxis("\\rm{Q_{y}}", output.Q_unit)
264	else:
265	output.xaxis("\\rm{Q_{x}}", 'A^{-1}')
266	output.yaxis("\\rm{Q_{y}}", 'A^{-1}')
267
268	if data_conv_i is not None:
269	output.zaxis("\\rm{Intensity}", output.I_unit)
270	else:
271	output.zaxis("\\rm{Intensity}","cm^{-1}")
272
273	if not fversion>=1.0:
274	raise ValueError,"Danse_reader can't read this file %s"%filename
275	else:
276	logging.info("Danse_reader Reading %s \n"%filename)
277
278	# Store loading process information
279	output.meta_data['loader'] = self.type_name
280	output = reader2D_converter(output)
281	return output
282
283	return None
284
285	if __name__ == "__main__":
286	reader = Reader()
287	print reader.read("../test/MP_New.sans")
288

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source: sasview/DataLoader/readers/danse_reader.py @ 023c8e2

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