danse_reader.py @ b63dc6e

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Last change on this file since b63dc6e was 0997158f, checked in by Gervaise Alina <gervyh@…>, 15 years ago
working on documentation
Property mode set to `100644`
File size: 10.4 KB

Rev	Line
[11a0319]	1
[b99ac227]	2
[0997158f]	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	#############################################################################
[b99ac227]	13
[0997158f]	14	"""
	15	DANSE/SANS file reader
[b99ac227]	16	"""
	17
[11a0319]	18	import math
[99d1af6]	19	import os
[11a0319]	20	import copy
	21	import numpy
[8d6440f]	22	import logging
[99d1af6]	23	from DataLoader.data_info import Data2D, Detector
[eadf1f9]	24	from DataLoader.manipulations import reader2D_converter
[99d1af6]	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
[16d8e5f]	32
[bb03739]	33	class Reader:
[11a0319]	34	"""
[0997158f]	35	Example data manipulation
[11a0319]	36	"""
	37	## File type
[28caa03]	38	type_name = "DANSE"
	39	## Wildcards
[11a0319]	40	type = ["DANSE files (.sans)\|.sans"]
	41	## Extension
[b99ac227]	42	ext = ['.sans', '.SANS']
[11a0319]	43
	44	def read(self, filename=None):
	45	"""
[0997158f]	46	Open and read the data in a file
	47	@param file: path of the file
[11a0319]	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:
[8d6440f]	56	try:
	57	datafile = open(filename, 'r')
	58	except :
	59	raise RuntimeError,"danse_reader cannot open %s"%(filename)
[11a0319]	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
[99d1af6]	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
[ca10d8e]	91	if has_converter == True and output.Q_unit != '1/A':
	92	data_conv_q = Converter('1/A')
[99d1af6]	93	# Test it
	94	data_conv_q(1.0, output.Q_unit)
	95
[ca10d8e]	96	if has_converter == True and output.I_unit != '1/cm':
	97	data_conv_i = Converter('1/cm')
[99d1af6]	98	# Test it
	99	data_conv_i(1.0, output.I_unit)
	100
[11a0319]	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])
[99d1af6]	110	if toks[0]=="WAVELENGTH":
	111	wavelength = float(toks[1])
[11a0319]	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])
[99d1af6]	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)
[11a0319]	145	data.append(val)
	146	error.append(err)
	147	except:
[8d6440f]	148	logging.info("Skipping line:%s,%s" %( data_str,sys.exc_value))
[11a0319]	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
[4fe4394]	159	theta = pixel / distance / 100.0
	160	stepq = 4.0math.pi/wavelength math.sin(theta/2.0)
[11a0319]	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)
[99d1af6]	164
[ca10d8e]	165	if has_converter == True and output.Q_unit != '1/A':
[99d1af6]	166	qx = data_conv_q(qx, units=output.Q_unit)
	167
[11a0319]	168	x_vals.append(qx)
[ca10d8e]	169	if xmin==None or qx<xmin:
[11a0319]	170	xmin = qx
[ca10d8e]	171	if xmax==None or qx>xmax:
[11a0319]	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)
[99d1af6]	179
[ca10d8e]	180	if has_converter == True and output.Q_unit != '1/A':
[99d1af6]	181	qy = data_conv_q(qy, units=output.Q_unit)
	182
[11a0319]	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
[99d1af6]	189	# Store the data in the 2D array
[b99ac227]	190	itot = 0
	191	i_x = 0
	192	i_y = -1
	193
[11a0319]	194	for i_pt in range(len(data)):
	195	try:
[99d1af6]	196	value = float(data[i_pt])
[11a0319]	197	except:
[99d1af6]	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))
[11a0319]	201
	202	# Get bin number
[b99ac227]	203	if math.fmod(i_pt, size_x)==0:
[11a0319]	204	i_x = 0
	205	i_y += 1
	206	else:
	207	i_x += 1
	208
[b99ac227]	209	output.data[i_y][i_x] = value
	210	#output.data[size_y-1-i_y][i_x] = value
[11a0319]	211	if fversion>1.0:
[b99ac227]	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]
[11a0319]	214
[99d1af6]	215
[0997158f]	216	# Store all data
[99d1af6]	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)
[4fe4394]	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
[ca10d8e]	246	if has_converter == True and output.Q_unit != '1/A':
[99d1af6]	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:
[eeaabb1]	262	output.xaxis("\\rm{Q_{x}}", output.Q_unit)
	263	output.yaxis("\\rm{Q_{y}}", output.Q_unit)
[99d1af6]	264	else:
[eeaabb1]	265	output.xaxis("\\rm{Q_{x}}", 'A^{-1}')
	266	output.yaxis("\\rm{Q_{y}}", 'A^{-1}')
[99d1af6]	267
	268	if data_conv_i is not None:
[0e2aa40]	269	output.zaxis("\\rm{Intensity}", output.I_unit)
[99d1af6]	270	else:
[0e2aa40]	271	output.zaxis("\\rm{Intensity}","cm^{-1}")
[16d8e5f]	272
	273	if not fversion>=1.0:
[c125e0c]	274	raise ValueError,"Danse_reader can't read this file %s"%filename
[11a0319]	275	else:
[8d6440f]	276	logging.info("Danse_reader Reading %s \n"%filename)
[fe78c7b]	277
	278	# Store loading process information
	279	output.meta_data['loader'] = self.type_name
[eadf1f9]	280	output = reader2D_converter(output)
[fe78c7b]	281	return output
[11a0319]	282
	283	return None
[99d1af6]	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 @ b63dc6e

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