red2d_reader.py @ e56869f

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since e56869f was c7c5ef8, checked in by Jae Cho <jhjcho@…>, 15 years ago
Added file.close() after reading
Property mode set to `100644`
File size: 11.0 KB

Rev	Line
[3cd95c8]	1	"""
	2	TXT/IGOR 2D Q Map file reader
	3	"""
	4
	5	"""
	6	This software was developed by the University of Tennessee as part of the
	7	Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	8	project funded by the US National Science Foundation.
	9
	10	If you use DANSE applications to do scientific research that leads to
	11	publication, we ask that you acknowledge the use of the software with the
	12	following sentence:
	13
	14	"This work benefited from DANSE software developed under NSF award DMR-0520547."
	15
	16	copyright 2008, University of Tennessee
	17	"""
	18
	19	import os, sys
	20	import numpy
	21	import math, logging
	22	from DataLoader.data_info import Data2D, Detector
	23
	24	# Look for unit converter
	25	has_converter = True
	26	try:
	27	from data_util.nxsunit import Converter
	28	except:
	29	has_converter = False
	30
	31	class Reader:
	32	""" Simple data reader for Igor data files """
	33	## File type
	34	type_name = "IGOR/DAT 2D Q_map"
	35	## Wildcards
	36	type = ["IGOR/DAT 2D file in Q_map (.dat)\|.DAT"]
	37	## Extension
	38	ext=['.DAT', '.dat']
	39
	40	def read(self,filename=None):
	41	""" Read file """
	42	if not os.path.isfile(filename):
	43	raise ValueError, \
	44	"Specified file %s is not a regular file" % filename
	45
	46	# Read file
	47	f = open(filename,'r')
	48	buf = f.read()
	49
	50	# Instantiate data object
	51	output = Data2D()
	52	output.filename = os.path.basename(filename)
	53	detector = Detector()
	54	if len(output.detector)>0: print str(output.detector[0])
	55	output.detector.append(detector)
	56
	57	# Get content
	58	dataStarted = False
	59
	60	## Defaults
	61	lines = buf.split('\n')
	62	itot = 0
	63	x = []
	64	y = []
	65
	66	ncounts = 0
	67
	68	wavelength = None
	69	distance = None
	70	transmission = None
	71
	72	pixel_x = None
	73	pixel_y = None
	74
	75	i_x = 0
	76	i_y = -1
	77	pixels = 0
	78
	79	isInfo = False
	80	isCenter = False
	81
	82	data_conv_q = None
	83	data_conv_i = None
	84
	85	# Set units: This is the unit assumed for Q and I in the data file.
	86	if has_converter == True and output.Q_unit != '1/A':
	87	data_conv_q = Converter('1/A')
	88	# Test it
	89	data_conv_q(1.0, output.Q_unit)
	90
	91	if has_converter == True and output.I_unit != '1/cm':
	92	data_conv_i = Converter('1/cm')
	93	# Test it
	94	data_conv_i(1.0, output.I_unit)
	95
	96	#Set the space for data
	97	data = numpy.zeros(0)
	98	qx_data = numpy.zeros(0)
	99	qy_data = numpy.zeros(0)
	100	q_data = numpy.zeros(0)
	101	dqx_data = numpy.zeros(0)
	102	dqy_data = numpy.zeros(0)
	103	mask = numpy.zeros(0,dtype=bool)
	104
	105	#Read Header and 2D data
	106	for line in lines:
	107	## Reading the header applies only to IGOR/NIST 2D q_map data files
	108	# Find setup info line
	109	if isInfo:
	110	isInfo = False
	111	line_toks = line.split()
	112	# Wavelength in Angstrom
	113	try:
	114	wavelength = float(line_toks[1])
	115	# Units
	116	if has_converter==True and output.source.wavelength_unit != 'A':
	117	conv = Converter('A')
	118	wavelength = conv(wavelength, units=output.source.wavelength_unit)
	119	except:
	120	#Not required
	121	pass
	122	# Distance in mm
	123	try:
	124	distance = float(line_toks[3])
	125	# Units
	126	if has_converter==True and detector.distance_unit != 'm':
	127	conv = Converter('m')
	128	distance = conv(distance, units=detector.distance_unit)
	129	except:
	130	#Not required
	131	pass
	132
	133	# Distance in meters
	134	try:
	135	transmission = float(line_toks[4])
	136	except:
	137	#Not required
	138	pass
	139
	140	if line.count("LAMBDA")>0:
	141	isInfo = True
	142
	143	# Find center info line
	144	if isCenter:
	145	isCenter = False
	146	line_toks = line.split()
	147	# Center in bin number
	148	center_x = float(line_toks[0])
	149	center_y = float(line_toks[1])
	150
	151	if line.count("BCENT")>0:
	152	isCenter = True
	153
	154	# Find data start
	155	if line.count("Data columns") or line.count("ASCII data")>0:
	156	dataStarted = True
	157	continue
	158
	159	## Read and get data.
	160	if dataStarted == True:
	161	line_toks = line.split()
	162	if len(line_toks) == 0:
	163	#empty line
	164	continue
[32e8c78]	165	elif len(line_toks) < 3:
[3cd95c8]	166	#Q-map 2d require 3 or more columns of data
	167	raise ValueError,"Igor_Qmap_Reader: Can't read this file: Not a proper file format"
	168
	169	# defaults
	170	dqx_value = None
	171	dqy_value = None
	172	qz_value = None
	173	mask_value = 0
	174
	175	##Read and get data values
	176	qx_value = float(line_toks[0])
	177	qy_value = float(line_toks[1])
	178	value = float(line_toks[2])
	179
	180	try:
	181	#Read qz_value if exist on 4th column
	182	qz_value = float(line_toks[3])
	183	except:
	184	# Found a non-float entry, skip it: Not required.
	185	pass
	186	try:
	187	#Read qz_value if exist on 5th column
	188	dqx_value = float(line_toks[4])
	189	except:
	190	# Found a non-float entry, skip it: Not required.
	191	pass
	192	try:
	193	#Read qz_value if exist on 6th column
	194	dqy_value = float(line_toks[5])
	195	except:
	196	# Found a non-float entry, skip it: Not required.
	197	pass
	198	try:
	199	#Read beam block mask if exist on 7th column
	200	mask_value = float(line_toks[6])
	201	except:
	202	# Found a non-float entry, skip it
	203	pass
	204
	205	# get data
	206	data = numpy.append(data, value)
	207	qx_data = numpy.append(qx_data, qx_value)
	208	qy_data = numpy.append(qy_data, qy_value)
	209
	210	# optional data
	211	if dqx_value != None and numpy.isfinite(dqx_value):
	212	dqx_data = numpy.append(dqx_data, dqx_value)
	213	if dqy_value != None and numpy.isfinite(dqy_value):
	214	dqy_data = numpy.append(dqy_data, dqy_value)
	215
	216	# default data
	217	if qz_value == None or not numpy.isfinite(qz_value):
	218	qz_value = 0
[32e8c78]	219	if not numpy.isfinite(mask_value):
[3cd95c8]	220	mask_value = 1
	221	q_data = numpy.append(q_data,numpy.sqrt(qx_value2+qy_value2+qz_value**2))
[32e8c78]	222	# Note: For convenience, mask = False stands for masked, while mask = True for unmasked
[3cd95c8]	223	mask = numpy.append(mask,(mask_value>=1))
	224
[c7c5ef8]	225	f.close()
[32e8c78]	226	# If all mask elements are False, put all True
	227	if not mask.any(): mask[mask==False] = True
	228
[3cd95c8]	229	# Store limits of the image in q space
	230	xmin = numpy.min(qx_data)
	231	xmax = numpy.max(qx_data)
	232	ymin = numpy.min(qy_data)
	233	ymax = numpy.max(qy_data)
	234
	235	# units
	236	if has_converter == True and output.Q_unit != '1/A':
	237	xmin = data_conv_q(xmin, units=output.Q_unit)
	238	xmax = data_conv_q(xmax, units=output.Q_unit)
	239	ymin = data_conv_q(ymin, units=output.Q_unit)
	240	ymax = data_conv_q(ymax, units=output.Q_unit)
	241
	242	## calculate the range of the qx and qy_data
	243	x_size = math.fabs(xmax - xmin)
	244	y_size = math.fabs(ymax - ymin)
	245
	246	# calculate the number of pixels in the each axes
	247	npix_y = math.floor(math.sqrt(len(data)))
	248	npix_x = math.floor(len(data)/npix_y)
	249
	250	# calculate the size of bins
	251	xstep = x_size/(npix_x-1)
	252	ystep = y_size/(npix_y-1)
	253
	254	# store x and y axis bin centers in q space
	255	x_bins = numpy.arange(xmin,xmax+xstep,xstep)
	256	y_bins = numpy.arange(ymin,ymax+ystep,ystep)
	257
	258	# get the limits of q values
	259	xmin = xmin - xstep/2
	260	xmax = xmax + xstep/2
	261	ymin = ymin - ystep/2
	262	ymax = ymax + ystep/2
	263
	264	#Store data in outputs
	265	#TODO: Check the lengths
	266	output.data = data
	267	output.err_data = numpy.sqrt(numpy.abs(data))
	268	output.qx_data = qx_data
	269	output.qy_data = qy_data
	270	output.q_data = q_data
	271	output.mask = mask
	272
	273	output.x_bins = x_bins
	274	output.y_bins = y_bins
	275
	276	output.xmin = xmin
	277	output.xmax = xmax
	278	output.ymin = ymin
	279	output.ymax = ymax
	280
	281	output.source.wavelength = wavelength
	282
	283	# Store pixel size in mm
	284	detector.pixel_size.x = pixel_x
	285	detector.pixel_size.y = pixel_y
	286
	287	# Store the sample to detector distance
	288	detector.distance = distance
	289
	290	# optional data: if any of dq data == 0, do not pass to output
	291	if len(dqx_data) == len(qx_data):
	292	output.dqx_data = dqx_data
	293	if len(dqy_data) == len(qy_data):
	294	output.dqy_data = dqy_data
	295
	296	# Units of axes
	297	if data_conv_q is not None:
	298	output.xaxis("\\rm{Q_{x}}", output.Q_unit)
	299	output.yaxis("\\rm{Q_{y}}", output.Q_unit)
	300	else:
	301	output.xaxis("\\rm{Q_{x}}", 'A^{-1}')
	302	output.yaxis("\\rm{Q_{y}}", 'A^{-1}')
	303	if data_conv_i is not None:
	304	output.zaxis("\\rm{Intensity}", output.I_unit)
	305	else:
	306	output.zaxis("\\rm{Intensity}","cm^{-1}")
	307
	308	# Store loading process information
	309	output.meta_data['loader'] = self.type_name
	310
	311	return output
	312
	313	if __name__ == "__main__":
	314	reader = Reader()
	315	print reader.read("../test/exp18_14_igor_2dqxqy.dat")
	316

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source: sasview/DataLoader/readers/red2d_reader.py @ e56869f

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