ascii_reader.py @ 1d64748

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 1d64748 was 892f246, checked in by Jae Cho <jhjcho@…>, 15 years ago
enabled to read data only with more than 3 continuous lines unless that is the only data.
Property mode set to `100644`
File size: 12.8 KB

Rev	Line
[8bd8ea4]	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
	13	from DataLoader.data_info import Data1D
	14
[daa56d0]	15	# Check whether we have a converter available
[99d1af6]	16	has_converter = True
	17	try:
	18	from data_util.nxsunit import Converter
	19	except:
	20	has_converter = False
	21
[8bd8ea4]	22	class Reader:
	23	"""
	24	Class to load ascii files (2 or 3 columns)
	25	"""
[8780e9a]	26	## File type
[28caa03]	27	type_name = "ASCII"
	28
	29	## Wildcards
[8780e9a]	30	type = ["ASCII files (.txt)\|.txt",
[470bf7e]	31	"ASCII files (.dat)\|.dat",
	32	"ASCII files (.abs)\|.abs"]
[8bd8ea4]	33	## List of allowed extensions
[470bf7e]	34	ext=['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS']
[8bd8ea4]	35
	36	def read(self, path):
	37	"""
	38	Load data file
	39
	40	@param path: file path
	41	@return: Data1D object, or None
	42	@raise RuntimeError: when the file can't be opened
	43	@raise ValueError: when the length of the data vectors are inconsistent
	44	"""
	45	if os.path.isfile(path):
	46	basename = os.path.basename(path)
	47	root, extension = os.path.splitext(basename)
	48	if extension.lower() in self.ext:
	49	try:
	50	input_f = open(path,'r')
	51	except :
	52	raise RuntimeError, "ascii_reader: cannot open %s" % path
	53	buff = input_f.read()
	54	lines = buff.split('\n')
[470bf7e]	55
[892f246]	56	#Jae could not find python universal line spliter: keep the below for now
[470bf7e]	57	# some ascii data has \r line separator, try it when it has only one line
	58	if len(lines) < 2 :
	59	lines = buff.split('\r')
	60
[8bd8ea4]	61	x = numpy.zeros(0)
	62	y = numpy.zeros(0)
	63	dy = numpy.zeros(0)
[de1da34]	64	dx = numpy.zeros(0)
	65
	66	#temp. space to sort data
	67	tx = numpy.zeros(0)
	68	ty = numpy.zeros(0)
	69	tdy = numpy.zeros(0)
	70	tdx = numpy.zeros(0)
	71
	72	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	73	self.filename = output.filename = basename
[99d1af6]	74
	75	data_conv_q = None
	76	data_conv_i = None
	77
[ca10d8e]	78	if has_converter == True and output.x_unit != '1/A':
	79	data_conv_q = Converter('1/A')
[99d1af6]	80	# Test it
	81	data_conv_q(1.0, output.x_unit)
	82
[ca10d8e]	83	if has_converter == True and output.y_unit != '1/cm':
	84	data_conv_i = Converter('1/cm')
[99d1af6]	85	# Test it
	86	data_conv_i(1.0, output.y_unit)
	87
[8bd8ea4]	88
	89	# The first good line of data will define whether
	90	# we have 2-column or 3-column ascii
[de1da34]	91	has_error_dx = None
	92	has_error_dy = None
[8bd8ea4]	93
[892f246]	94	#Initialize counters for data lines and header lines.
	95	is_data = False #Has more than 3 lines
	96	mum_data_lines = 3 # More than "3" lines of data is considered as actual data unless there is only less lines of data
	97
	98	i=-1 # To count # of current data candidate lines
	99	i1=-1 # To count total # of previous data candidate lines
	100	j=-1 # To count # of header lines
	101	j1=-1 # Helps to count # of header lines
	102
[8bd8ea4]	103	for line in lines:
	104	toks = line.split()
[892f246]	105
[8bd8ea4]	106	try:
[892f246]	107
[8bd8ea4]	108	_x = float(toks[0])
	109	_y = float(toks[1])
	110
[892f246]	111	#Reset the header line counters
	112	if j == j1:
	113	j = 0
	114	j1 = 0
	115
	116	if i > 1:
	117	is_data = True
	118
[99d1af6]	119	if data_conv_q is not None:
	120	_x = data_conv_q(_x, units=output.x_unit)
	121
	122	if data_conv_i is not None:
	123	_y = data_conv_i(_y, units=output.y_unit)
	124
[8bd8ea4]	125	# If we have an extra token, check
	126	# whether it can be interpreted as a
	127	# third column.
	128	_dy = None
	129	if len(toks)>2:
	130	try:
	131	_dy = float(toks[2])
[99d1af6]	132
	133	if data_conv_i is not None:
	134	_dy = data_conv_i(_dy, units=output.y_unit)
	135
[8bd8ea4]	136	except:
	137	# The third column is not a float, skip it.
	138	pass
	139
	140	# If we haven't set the 3rd column
	141	# flag, set it now.
[de1da34]	142	if has_error_dy == None:
	143	has_error_dy = False if _dy == None else True
	144
	145	#Check for dx
	146	_dx = None
	147	if len(toks)>3:
	148	try:
	149	_dx = float(toks[3])
	150
	151	if data_conv_i is not None:
	152	_dx = data_conv_i(_dx, units=output.x_unit)
	153
	154	except:
	155	# The 4th column is not a float, skip it.
	156	pass
	157
	158	# If we haven't set the 3rd column
	159	# flag, set it now.
	160	if has_error_dx == None:
	161	has_error_dx = False if _dx == None else True
[892f246]	162
	163	#Delete the previously stored lines of data candidates if is not data.
	164	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	165	try:
	166	x= numpy.zeros(0)
	167	y= numpy.zeros(0)
	168
	169	except:
	170	pass
	171
[8bd8ea4]	172	x = numpy.append(x, _x)
	173	y = numpy.append(y, _y)
[892f246]	174
[de1da34]	175	if has_error_dy == True:
[892f246]	176	#Delete the previously stored lines of data candidates if is not data.
	177	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	178	try:
	179	dy = numpy.zeros(0)
	180	except:
	181	pass
[8bd8ea4]	182	dy = numpy.append(dy, _dy)
[892f246]	183
[de1da34]	184	if has_error_dx == True:
[892f246]	185	#Delete the previously stored lines of data candidates if is not data.
	186	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	187	try:
	188	dx = numpy.zeros(0)
	189	except:
	190	pass
[de1da34]	191	dx = numpy.append(dx, _dx)
	192
	193	#Same for temp.
[892f246]	194	#Delete the previously stored lines of data candidates if is not data.
	195	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	196	try:
	197	tx = numpy.zeros(0)
	198	ty = numpy.zeros(0)
	199	except:
	200	pass
	201
[de1da34]	202	tx = numpy.append(tx, _x)
	203	ty = numpy.append(ty, _y)
[892f246]	204
[de1da34]	205	if has_error_dy == True:
[892f246]	206	#Delete the previously stored lines of data candidates if is not data.
	207	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	208	try:
	209	tdy = numpy.zeros(0)
	210	except:
	211	pass
[de1da34]	212	tdy = numpy.append(tdy, _dy)
	213	if has_error_dx == True:
[892f246]	214	#Delete the previously stored lines of data candidates if is not data.
	215	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	216	try:
	217	tdx = numpy.zeros(0)
	218	except:
	219	pass
[de1da34]	220	tdx = numpy.append(tdx, _dx)
[8bd8ea4]	221
[892f246]	222	#Reset # of header lines and counts # of data candidate lines
	223	if j == 0 and j1 ==0:
	224	i1 = i + 1
	225	i+=1
	226
[8bd8ea4]	227	except:
[892f246]	228
	229	# It is data and meet non - number, then stop reading
	230	if is_data == True:
	231	break
	232	#Counting # of header lines
	233	j+=1
	234	if j == j1+1:
	235	j1 = j
	236	else:
	237	j = -1
	238	#Reset # of lines of data candidates
	239	i = -1
	240
[8bd8ea4]	241	# Couldn't parse this line, skip it
	242	pass
[892f246]	243
	244
[8bd8ea4]	245
	246	# Sanity check
[de1da34]	247	if has_error_dy == True and not len(y) == len(dy):
	248	raise RuntimeError, "ascii_reader: y and dy have different length"
	249	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	250	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	251
	252	# If the data length is zero, consider this as
	253	# though we were not able to read the file.
	254	if len(x)==0:
[daa56d0]	255	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	256
[470bf7e]	257	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	258	ind = numpy.lexsort((ty,tx))
	259	for i in ind:
	260	x[i] = tx[ind[i]]
	261	y[i] = ty[ind[i]]
	262	if has_error_dy == True:
	263	dy[i] = tdy[ind[i]]
	264	if has_error_dx == True:
	265	dx[i] = tdx[ind[i]]
[892f246]	266
	267	#Data
[8bd8ea4]	268	output.x = x
	269	output.y = y
[de1da34]	270	output.dy = dy if has_error_dy == True else None
	271	output.dx = dx if has_error_dx == True else None
	272
[99d1af6]	273	if data_conv_q is not None:
	274	output.xaxis("\\rm{Q}", output.x_unit)
	275	else:
	276	output.xaxis("\\rm{Q}", 'A^{-1}')
	277	if data_conv_i is not None:
[0e2aa40]	278	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	279	else:
[0e2aa40]	280	output.yaxis("\\rm{Intensity}","cm^{-1}")
[470bf7e]	281
[8bd8ea4]	282	return output
[892f246]	283
[8bd8ea4]	284	else:
	285	raise RuntimeError, "%s is not a file" % path
	286	return None
	287
	288	if __name__ == "__main__":
	289	reader = Reader()
	290	#print reader.read("../test/test_3_columns.txt")
	291	print reader.read("../test/empty.txt")
	292
	293
	294

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source: sasview/DataLoader/readers/ascii_reader.py @ 1d64748

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