ascii_reader.py @ ecc58e72

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 ecc58e72 was e082e2c, checked in by Mathieu Doucet <doucetm@…>, 15 years ago
dataloader: allow all file extensions to be read by the ascii reader.
Property mode set to `100644`
File size: 14.3 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	"""
[730c9eb]	24	Class to load ascii files (2, 3 or 4 columns)
[8bd8ea4]	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
[e082e2c]	36	## Flag to bypass extension check
	37	allow_all = True
	38
[8bd8ea4]	39	def read(self, path):
	40	"""
	41	Load data file
	42
	43	@param path: file path
	44	@return: Data1D object, or None
	45	@raise RuntimeError: when the file can't be opened
	46	@raise ValueError: when the length of the data vectors are inconsistent
	47	"""
	48	if os.path.isfile(path):
	49	basename = os.path.basename(path)
	50	root, extension = os.path.splitext(basename)
[e082e2c]	51	if self.allow_all or extension.lower() in self.ext:
[8bd8ea4]	52	try:
	53	input_f = open(path,'r')
	54	except :
	55	raise RuntimeError, "ascii_reader: cannot open %s" % path
	56	buff = input_f.read()
	57	lines = buff.split('\n')
[470bf7e]	58
[892f246]	59	#Jae could not find python universal line spliter: keep the below for now
[730c9eb]	60	# some ascii data has \r line separator, try it when the data is on only one long line
[470bf7e]	61	if len(lines) < 2 :
	62	lines = buff.split('\r')
	63
[8bd8ea4]	64	x = numpy.zeros(0)
	65	y = numpy.zeros(0)
	66	dy = numpy.zeros(0)
[de1da34]	67	dx = numpy.zeros(0)
	68
	69	#temp. space to sort data
	70	tx = numpy.zeros(0)
	71	ty = numpy.zeros(0)
	72	tdy = numpy.zeros(0)
	73	tdx = numpy.zeros(0)
	74
	75	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	76	self.filename = output.filename = basename
[99d1af6]	77
	78	data_conv_q = None
	79	data_conv_i = None
	80
[ca10d8e]	81	if has_converter == True and output.x_unit != '1/A':
	82	data_conv_q = Converter('1/A')
[99d1af6]	83	# Test it
	84	data_conv_q(1.0, output.x_unit)
	85
[ca10d8e]	86	if has_converter == True and output.y_unit != '1/cm':
	87	data_conv_i = Converter('1/cm')
[99d1af6]	88	# Test it
	89	data_conv_i(1.0, output.y_unit)
	90
[8bd8ea4]	91
	92	# The first good line of data will define whether
	93	# we have 2-column or 3-column ascii
[de1da34]	94	has_error_dx = None
	95	has_error_dy = None
[8bd8ea4]	96
[892f246]	97	#Initialize counters for data lines and header lines.
[0e5e586]	98	is_data = False #Has more than 5 lines
	99	mum_data_lines = 5 # More than "5" lines of data is considered as actual data unless that is the only data
[892f246]	100
[d508be9]	101	i=-1 # To count # of current data candidate lines
	102	i1=-1 # To count total # of previous data candidate lines
	103	j=-1 # To count # of header lines
	104	j1=-1 # Helps to count # of header lines
	105	lentoks = 2 # minimum required number of columns of data; ( <= 4).
[892f246]	106
[8bd8ea4]	107	for line in lines:
	108	toks = line.split()
[892f246]	109
[8bd8ea4]	110	try:
[892f246]	111
[8bd8ea4]	112	_x = float(toks[0])
	113	_y = float(toks[1])
	114
[892f246]	115	#Reset the header line counters
	116	if j == j1:
	117	j = 0
	118	j1 = 0
	119
	120	if i > 1:
	121	is_data = True
[d508be9]	122
[99d1af6]	123	if data_conv_q is not None:
	124	_x = data_conv_q(_x, units=output.x_unit)
	125
	126	if data_conv_i is not None:
	127	_y = data_conv_i(_y, units=output.y_unit)
	128
[8bd8ea4]	129	# If we have an extra token, check
	130	# whether it can be interpreted as a
	131	# third column.
	132	_dy = None
	133	if len(toks)>2:
	134	try:
	135	_dy = float(toks[2])
[99d1af6]	136
	137	if data_conv_i is not None:
	138	_dy = data_conv_i(_dy, units=output.y_unit)
	139
[8bd8ea4]	140	except:
	141	# The third column is not a float, skip it.
	142	pass
	143
	144	# If we haven't set the 3rd column
	145	# flag, set it now.
[de1da34]	146	if has_error_dy == None:
	147	has_error_dy = False if _dy == None else True
	148
	149	#Check for dx
	150	_dx = None
	151	if len(toks)>3:
	152	try:
	153	_dx = float(toks[3])
	154
	155	if data_conv_i is not None:
	156	_dx = data_conv_i(_dx, units=output.x_unit)
	157
	158	except:
	159	# The 4th column is not a float, skip it.
	160	pass
	161
	162	# If we haven't set the 3rd column
	163	# flag, set it now.
	164	if has_error_dx == None:
	165	has_error_dx = False if _dx == None else True
[892f246]	166
[d508be9]	167	#After talked with PB, we decided to take care of only 4 columns of data for now.
	168	#number of columns in the current line
[0e5e586]	169	#To remember the # of columns in the current line of data
	170	new_lentoks = len(toks)
[d508be9]	171
[3aed0eb]	172	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
[272b107]	173	if lentoks != new_lentoks :
	174	if is_data == True:
	175	break
	176	else:
[d508be9]	177	i = -1
	178	i1 = 0
	179	j = -1
	180	j1 = -1
	181
[272b107]	182
[892f246]	183	#Delete the previously stored lines of data candidates if is not data.
	184	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	185	try:
	186	x= numpy.zeros(0)
	187	y= numpy.zeros(0)
	188
	189	except:
	190	pass
	191
[8bd8ea4]	192	x = numpy.append(x, _x)
	193	y = numpy.append(y, _y)
[892f246]	194
[de1da34]	195	if has_error_dy == True:
[892f246]	196	#Delete the previously stored lines of data candidates if is not data.
	197	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	198	try:
	199	dy = numpy.zeros(0)
	200	except:
	201	pass
[8bd8ea4]	202	dy = numpy.append(dy, _dy)
[892f246]	203
[de1da34]	204	if has_error_dx == True:
[892f246]	205	#Delete the previously stored lines of data candidates if is not data.
	206	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	207	try:
	208	dx = numpy.zeros(0)
	209	except:
	210	pass
[de1da34]	211	dx = numpy.append(dx, _dx)
	212
	213	#Same for temp.
[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	tx = numpy.zeros(0)
	218	ty = numpy.zeros(0)
	219	except:
	220	pass
	221
[de1da34]	222	tx = numpy.append(tx, _x)
	223	ty = numpy.append(ty, _y)
[892f246]	224
[de1da34]	225	if has_error_dy == True:
[892f246]	226	#Delete the previously stored lines of data candidates if is not data.
	227	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	228	try:
	229	tdy = numpy.zeros(0)
	230	except:
	231	pass
[de1da34]	232	tdy = numpy.append(tdy, _dy)
	233	if has_error_dx == True:
[892f246]	234	#Delete the previously stored lines of data candidates if is not data.
	235	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	236	try:
	237	tdx = numpy.zeros(0)
	238	except:
	239	pass
[de1da34]	240	tdx = numpy.append(tdx, _dx)
[d508be9]	241
	242	#reset i1 and flag lentoks for the next
	243	if lentoks < new_lentoks :
	244	if is_data == False:
	245	i1 = -1
[0e5e586]	246	#To remember the # of columns on the current line for the next line of data
	247	lentoks = len(toks)
[8bd8ea4]	248
[892f246]	249	#Reset # of header lines and counts # of data candidate lines
	250	if j == 0 and j1 ==0:
	251	i1 = i + 1
	252	i+=1
	253
[8bd8ea4]	254	except:
[892f246]	255
	256	# It is data and meet non - number, then stop reading
	257	if is_data == True:
	258	break
[d508be9]	259	lentoks = 2
[892f246]	260	#Counting # of header lines
	261	j+=1
	262	if j == j1+1:
	263	j1 = j
	264	else:
	265	j = -1
	266	#Reset # of lines of data candidates
	267	i = -1
	268
[8bd8ea4]	269	# Couldn't parse this line, skip it
	270	pass
[892f246]	271
	272
[8bd8ea4]	273
	274	# Sanity check
[de1da34]	275	if has_error_dy == True and not len(y) == len(dy):
	276	raise RuntimeError, "ascii_reader: y and dy have different length"
	277	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	278	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	279
	280	# If the data length is zero, consider this as
	281	# though we were not able to read the file.
	282	if len(x)==0:
[daa56d0]	283	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	284
[470bf7e]	285	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	286	ind = numpy.lexsort((ty,tx))
	287	for i in ind:
	288	x[i] = tx[ind[i]]
	289	y[i] = ty[ind[i]]
	290	if has_error_dy == True:
	291	dy[i] = tdy[ind[i]]
	292	if has_error_dx == True:
	293	dx[i] = tdx[ind[i]]
[892f246]	294
[d508be9]	295
[892f246]	296	#Data
[8bd8ea4]	297	output.x = x
	298	output.y = y
[de1da34]	299	output.dy = dy if has_error_dy == True else None
	300	output.dx = dx if has_error_dx == True else None
	301
[99d1af6]	302	if data_conv_q is not None:
	303	output.xaxis("\\rm{Q}", output.x_unit)
	304	else:
	305	output.xaxis("\\rm{Q}", 'A^{-1}')
	306	if data_conv_i is not None:
[0e2aa40]	307	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	308	else:
[0e2aa40]	309	output.yaxis("\\rm{Intensity}","cm^{-1}")
[8bd8ea4]	310	return output
[892f246]	311
[8bd8ea4]	312	else:
	313	raise RuntimeError, "%s is not a file" % path
	314	return None
	315
	316	if __name__ == "__main__":
	317	reader = Reader()
	318	#print reader.read("../test/test_3_columns.txt")
	319	print reader.read("../test/empty.txt")
	320
	321
	322

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source: sasview/DataLoader/readers/ascii_reader.py @ ecc58e72

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