abs_reader.py @ d3966c2

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 d3966c2 was 148ad64, checked in by Jae Cho <jhjcho@…>, 15 years ago
Added a flexibility to read whole different formats of abs files (w/wo header).
Property mode set to `100644`
File size: 12.1 KB

Rev	Line
[d8a5f12]	1	"""
	2	This software was developed by the University of Tennessee as part of the
	3	Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	4	project funded by the US National Science Foundation.
	5
	6	See the license text in license.txt
	7
	8	copyright 2008, University of Tennessee
	9	"""
	10
	11	import numpy
	12	import os
[99d1af6]	13	from DataLoader.data_info import Data1D, Detector
[d8a5f12]	14
[99d1af6]	15	has_converter = True
	16	try:
	17	from data_util.nxsunit import Converter
	18	except:
	19	has_converter = False
	20
[d8a5f12]	21	class Reader:
	22	"""
	23	Class to load IGOR reduced .ABS files
	24	"""
[8780e9a]	25	## File type
	26	type = ["IGOR 1D files (.abs)\|.abs"]
[d8a5f12]	27	## List of allowed extensions
[8bd8ea4]	28	ext=['.abs', '.ABS']
[d8a5f12]	29
	30	def read(self, path):
	31	"""
	32	Load data file
	33
	34	@param path: file path
	35	@return: Data1D object, or None
	36	@raise RuntimeError: when the file can't be opened
	37	@raise ValueError: when the length of the data vectors are inconsistent
	38	"""
	39	if os.path.isfile(path):
	40	basename = os.path.basename(path)
	41	root, extension = os.path.splitext(basename)
	42	if extension.lower() in self.ext:
	43	try:
	44	input_f = open(path,'r')
	45	except :
	46	raise RuntimeError, "abs_reader: cannot open %s" % path
	47	buff = input_f.read()
	48	lines = buff.split('\n')
	49	x = numpy.zeros(0)
	50	y = numpy.zeros(0)
	51	dy = numpy.zeros(0)
[148ad64]	52	dx = numpy.zeros(0)
	53	output = Data1D(x, y, dy=dy, dx=dx)
[99d1af6]	54	detector = Detector()
	55	output.detector.append(detector)
[b99ac227]	56	output.filename = basename
[d8a5f12]	57
	58	is_info = False
	59	is_center = False
	60	is_data_started = False
[148ad64]	61	right_line_is = -2
	62	line_n = 0
	63	col = 0
[d8a5f12]	64
[99d1af6]	65	data_conv_q = None
	66	data_conv_i = None
	67
[ca10d8e]	68	if has_converter == True and output.x_unit != '1/A':
	69	data_conv_q = Converter('1/A')
[99d1af6]	70	# Test it
	71	data_conv_q(1.0, output.x_unit)
	72
[ca10d8e]	73	if has_converter == True and output.y_unit != '1/cm':
	74	data_conv_i = Converter('1/cm')
[99d1af6]	75	# Test it
	76	data_conv_i(1.0, output.y_unit)
	77
[d8a5f12]	78	for line in lines:
[148ad64]	79	#print "line",line
[d8a5f12]	80	# Information line 1
	81	if is_info==True:
	82	is_info = False
	83	line_toks = line.split()
	84
	85	# Wavelength in Angstrom
	86	try:
[99d1af6]	87	value = float(line_toks[1])
	88	if has_converter==True and output.source.wavelength_unit != 'A':
	89	conv = Converter('A')
	90	output.source.wavelength = conv(value, units=output.source.wavelength_unit)
	91	else:
	92	output.source.wavelength = value
[d8a5f12]	93	except:
[148ad64]	94	pass
	95	#raise ValueError,"IgorReader: can't read this file, missing wavelength"
[d8a5f12]	96
	97	# Distance in meters
	98	try:
[99d1af6]	99	value = float(line_toks[3])
	100	if has_converter==True and detector.distance_unit != 'm':
	101	conv = Converter('m')
	102	detector.distance = conv(value, units=detector.distance_unit)
	103	else:
	104	detector.distance = value
[d8a5f12]	105	except:
[148ad64]	106	pass
	107	#raise ValueError,"IgorReader: can't read this file, missing distance"
[d8a5f12]	108
[99d1af6]	109	# Transmission
[d8a5f12]	110	try:
	111	output.sample.transmission = float(line_toks[4])
	112	except:
	113	# Transmission is not a mandatory entry
	114	pass
	115
[99d1af6]	116	# Thickness in mm
[d8a5f12]	117	try:
[99d1af6]	118	value = float(line_toks[5])
[b99ac227]	119	if has_converter==True and output.sample.thickness_unit != 'cm':
	120	conv = Converter('cm')
[99d1af6]	121	output.sample.thickness = conv(value, units=output.sample.thickness_unit)
	122	else:
	123	output.sample.thickness = value
[d8a5f12]	124	except:
	125	# Thickness is not a mandatory entry
	126	pass
	127
[148ad64]	128	#MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP
	129	if line.count("LAMBDA")>0:
	130	is_info = True
	131
	132	# Find center info line
	133	if is_center==True:
	134	is_center = False
	135	line_toks = line.split()
	136	# Center in bin number
	137	center_x = float(line_toks[0])
	138	center_y = float(line_toks[1])
	139
	140	# Bin size
	141	if has_converter==True and detector.pixel_size_unit != 'mm':
	142	conv = Converter('mm')
	143	detector.pixel_size.x = conv(5.0, units=detector.pixel_size_unit)
	144	detector.pixel_size.y = conv(5.0, units=detector.pixel_size_unit)
	145	else:
	146	detector.pixel_size.x = 5.0
	147	detector.pixel_size.y = 5.0
	148
	149	# Store beam center in distance units
	150	# Det 640 x 640 mm
	151	if has_converter==True and detector.beam_center_unit != 'mm':
	152	conv = Converter('mm')
	153	detector.beam_center.x = conv(center_x*5.0, units=detector.beam_center_unit)
	154	detector.beam_center.y = conv(center_y*5.0, units=detector.beam_center_unit)
	155	else:
	156	detector.beam_center.x = center_x*5.0
	157	detector.beam_center.y = center_y*5.0
	158
	159	# Detector type
	160	try:
	161	detector.name = line_toks[7]
	162	except:
	163	# Detector name is not a mandatory entry
	164	pass
[99d1af6]	165
[148ad64]	166	#BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP
	167	if line.count("BCENT")>0:
	168	is_center = True
[99d1af6]	169
[148ad64]	170	# Parse the data
	171	# Specify one line of data
	172	if len(lines)<2:
	173	colnum = 6
	174	else:
	175	colnum = len(line.split())
[d8a5f12]	176
[148ad64]	177	#If # of row = # of data points
	178	if colnum == 0:
	179	rangeiter = 0
	180	#If # of row = 1
	181	else:
	182	rangeiter=numpy.ceil(len(line.split())/colnum)
[d8a5f12]	183
[148ad64]	184	#If all data is in one line, chop the line by every 6 columns and read x, y, dy, dx data
	185	for col in range(0,rangeiter):
	186	#The 6 columns are \| Q (1/A) \| I(Q) (1/cm) \| std. dev. I(Q) (1/cm) \| sigmaQ \| meanQ \| ShadowFactor\|
	187	#Check the file format whether or not it read all header lines and if it has a header
	188	if line.count("The 6 columns")>0 or (output.source.wavelength==None):
	189	#if it has a full header
	190	if line.count("The 6 columns")>0:
	191	right_line_is = line_n
	192	#If no header in the file
	193	else:
	194	right_line_is = 0
	195	is_data_started = True
[99d1af6]	196
[d8a5f12]	197
[148ad64]	198	# If on the of data, not header, read data
	199	if is_data_started==True and right_line_is >= 0: #and line_n > right_line_is
	200	#print "col",col
	201	toks = line.split()
	202	try:
	203
	204	if float(toks[col*6+0]) > 1:
	205	continue
	206	else:
	207	not_data_line = False
	208
	209	_x = float(toks[col*6+0])
	210	_y = float(toks[col*6+1])
	211	_dy = float(toks[col*6+2])
	212	_dx = float(toks[col*6+3])
	213
	214
	215	if data_conv_q is not None:
	216	_x = data_conv_q(_x, units=output.x_unit)
	217	_dx = data_conv_i(_dx, units=output.x_unit)
	218
	219	if data_conv_i is not None:
	220	_y = data_conv_i(_y, units=output.y_unit)
	221	_dy = data_conv_i(_dy, units=output.y_unit)
	222
	223	x =numpy.append(x, _x)
	224	y = numpy.append(y, _y)
	225	dy = numpy.append(dy, _dy)
	226	dx = numpy.append(dx, _dx)
	227
	228	except:
	229	# Could not read this data line. If we are here
	230	# it is because we are in the data section. Just
	231	# skip it.
	232	pass
	233
	234	line_n = line_n +1
[d8a5f12]	235	# Sanity check
	236	if not len(y) == len(dy):
	237	raise ValueError, "abs_reader: y and dy have different length"
[148ad64]	238	if not len(x) == len(dx):
	239	raise ValueError, "abs_reader: x and dx have different length"
[8bd8ea4]	240
	241	# If the data length is zero, consider this as
	242	# though we were not able to read the file.
	243	if len(x)==0:
	244	raise ValueError, "ascii_reader: could not load file"
[d8a5f12]	245
	246	output.x = x
	247	output.y = y
	248	output.dy = dy
[148ad64]	249	output.dx = dx
[99d1af6]	250	if data_conv_q is not None:
	251	output.xaxis("\\rm{Q}", output.x_unit)
	252	else:
	253	output.xaxis("\\rm{Q}", 'A^{-1}')
	254	if data_conv_i is not None:
	255	output.yaxis("\\{I(Q)}", output.y_unit)
	256	else:
	257	output.yaxis("\\rm{I(Q)}","cm^{-1}")
[148ad64]	258	#print " x,y,dx,dy", output.x,output.y,output.dy,output.dx
[d8a5f12]	259	return output
	260	else:
	261	raise RuntimeError, "%s is not a file" % path
	262	return None
	263
	264	if __name__ == "__main__":
	265	reader = Reader()
[148ad64]	266	#print reader.read("../test/jan08002.ABS")
[d8a5f12]	267
	268
	269

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source: sasview/DataLoader/readers/abs_reader.py @ d3966c2

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