ascii_reader.py @ d508be9

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 d508be9 was d508be9, checked in by Jae Cho <jhjcho@…>, 15 years ago
line with fewer/larger columns now considered as a header
Property mode set to `100644`
File size: 14.4 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
[d508be9]	96	mum_data_lines = 3 # More than "3" lines of data is considered as actual data unless that is the only data
[892f246]	97
[d508be9]	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	lentoks = 2 # minimum required number of columns of data; ( <= 4).
[892f246]	103
[8bd8ea4]	104	for line in lines:
	105	toks = line.split()
[892f246]	106
[8bd8ea4]	107	try:
[892f246]	108
[8bd8ea4]	109	_x = float(toks[0])
	110	_y = float(toks[1])
	111
[d508be9]	112	#To reject the line when reader meets less columns of data
	113	if lentoks == 3:
	114	_dy = float(toks[2])
	115	elif lentoks == 4:
	116	_dx = float(toks[3])
	117
[892f246]	118	#Reset the header line counters
	119	if j == j1:
	120	j = 0
	121	j1 = 0
	122
	123	if i > 1:
	124	is_data = True
[d508be9]	125
[99d1af6]	126	if data_conv_q is not None:
	127	_x = data_conv_q(_x, units=output.x_unit)
	128
	129	if data_conv_i is not None:
	130	_y = data_conv_i(_y, units=output.y_unit)
	131
[8bd8ea4]	132	# If we have an extra token, check
	133	# whether it can be interpreted as a
	134	# third column.
	135	_dy = None
	136	if len(toks)>2:
	137	try:
	138	_dy = float(toks[2])
[99d1af6]	139
	140	if data_conv_i is not None:
	141	_dy = data_conv_i(_dy, units=output.y_unit)
	142
[8bd8ea4]	143	except:
	144	# The third column is not a float, skip it.
	145	pass
	146
	147	# If we haven't set the 3rd column
	148	# flag, set it now.
[de1da34]	149	if has_error_dy == None:
	150	has_error_dy = False if _dy == None else True
	151
	152	#Check for dx
	153	_dx = None
	154	if len(toks)>3:
	155	try:
	156	_dx = float(toks[3])
	157
	158	if data_conv_i is not None:
	159	_dx = data_conv_i(_dx, units=output.x_unit)
	160
	161	except:
	162	# The 4th column is not a float, skip it.
	163	pass
	164
	165	# If we haven't set the 3rd column
	166	# flag, set it now.
	167	if has_error_dx == None:
	168	has_error_dx = False if _dx == None else True
[892f246]	169
[d508be9]	170	#After talked with PB, we decided to take care of only 4 columns of data for now.
	171	#number of columns in the current line
	172	if len(toks)>= 4:
	173	new_lentoks = 4
	174	else:
	175	new_lentoks = len(toks)
	176
	177	#If the previous columns are less than the current, mark the previous as non-data and reset the dependents.
	178	if lentoks < new_lentoks :
	179	if is_data == False:
	180	i = -1
	181	i1 = 0
	182	j = -1
	183	j1 = -1
	184
[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	x= numpy.zeros(0)
	189	y= numpy.zeros(0)
	190
	191	except:
	192	pass
	193
[8bd8ea4]	194	x = numpy.append(x, _x)
	195	y = numpy.append(y, _y)
[892f246]	196
[de1da34]	197	if has_error_dy == True:
[892f246]	198	#Delete the previously stored lines of data candidates if is not data.
	199	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	200	try:
	201	dy = numpy.zeros(0)
	202	except:
	203	pass
[8bd8ea4]	204	dy = numpy.append(dy, _dy)
[892f246]	205
[de1da34]	206	if has_error_dx == True:
[892f246]	207	#Delete the previously stored lines of data candidates if is not data.
	208	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	209	try:
	210	dx = numpy.zeros(0)
	211	except:
	212	pass
[de1da34]	213	dx = numpy.append(dx, _dx)
	214
	215	#Same for temp.
[892f246]	216	#Delete the previously stored lines of data candidates if is not data.
	217	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	218	try:
	219	tx = numpy.zeros(0)
	220	ty = numpy.zeros(0)
	221	except:
	222	pass
	223
[de1da34]	224	tx = numpy.append(tx, _x)
	225	ty = numpy.append(ty, _y)
[892f246]	226
[de1da34]	227	if has_error_dy == True:
[892f246]	228	#Delete the previously stored lines of data candidates if is not data.
	229	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	230	try:
	231	tdy = numpy.zeros(0)
	232	except:
	233	pass
[de1da34]	234	tdy = numpy.append(tdy, _dy)
	235	if has_error_dx == True:
[892f246]	236	#Delete the previously stored lines of data candidates if is not data.
	237	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	238	try:
	239	tdx = numpy.zeros(0)
	240	except:
	241	pass
[de1da34]	242	tdx = numpy.append(tdx, _dx)
[d508be9]	243
	244	#reset i1 and flag lentoks for the next
	245	if lentoks < new_lentoks :
	246	if is_data == False:
	247	i1 = -1
	248	if len(toks)>= 4:
	249	lentoks = 4
	250	else:
	251	lentoks = len(toks)
[8bd8ea4]	252
[892f246]	253	#Reset # of header lines and counts # of data candidate lines
	254	if j == 0 and j1 ==0:
	255	i1 = i + 1
	256	i+=1
	257
[8bd8ea4]	258	except:
[892f246]	259
	260	# It is data and meet non - number, then stop reading
	261	if is_data == True:
	262	break
[d508be9]	263	lentoks = 2
[892f246]	264	#Counting # of header lines
	265	j+=1
	266	if j == j1+1:
	267	j1 = j
	268	else:
	269	j = -1
	270	#Reset # of lines of data candidates
	271	i = -1
	272
[8bd8ea4]	273	# Couldn't parse this line, skip it
	274	pass
[892f246]	275
	276
[8bd8ea4]	277
	278	# Sanity check
[de1da34]	279	if has_error_dy == True and not len(y) == len(dy):
	280	raise RuntimeError, "ascii_reader: y and dy have different length"
	281	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	282	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	283
	284	# If the data length is zero, consider this as
	285	# though we were not able to read the file.
	286	if len(x)==0:
[daa56d0]	287	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	288
[470bf7e]	289	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	290	ind = numpy.lexsort((ty,tx))
	291	for i in ind:
	292	x[i] = tx[ind[i]]
	293	y[i] = ty[ind[i]]
	294	if has_error_dy == True:
	295	dy[i] = tdy[ind[i]]
	296	if has_error_dx == True:
	297	dx[i] = tdx[ind[i]]
[892f246]	298
[d508be9]	299
[892f246]	300	#Data
[8bd8ea4]	301	output.x = x
	302	output.y = y
[de1da34]	303	output.dy = dy if has_error_dy == True else None
	304	output.dx = dx if has_error_dx == True else None
	305
[99d1af6]	306	if data_conv_q is not None:
	307	output.xaxis("\\rm{Q}", output.x_unit)
	308	else:
	309	output.xaxis("\\rm{Q}", 'A^{-1}')
	310	if data_conv_i is not None:
[0e2aa40]	311	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	312	else:
[0e2aa40]	313	output.yaxis("\\rm{Intensity}","cm^{-1}")
[d508be9]	314	print "output",output
[8bd8ea4]	315	return output
[892f246]	316
[8bd8ea4]	317	else:
	318	raise RuntimeError, "%s is not a file" % path
	319	return None
	320
	321	if __name__ == "__main__":
	322	reader = Reader()
	323	#print reader.read("../test/test_3_columns.txt")
	324	print reader.read("../test/empty.txt")
	325
	326
	327

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source: sasview/DataLoader/readers/ascii_reader.py @ d508be9

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