ascii_reader.py @ f50330b7

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 f50330b7 was 0e5e586, checked in by Jae Cho <jhjcho@…>, 15 years ago
changed min. required # of lines (5 lines now) and enable to distinguish # of columns (even more than 4 col.)
Property mode set to `100644`
File size: 14.2 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
	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
[730c9eb]	57	# some ascii data has \r line separator, try it when the data is on only one long line
[470bf7e]	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.
[0e5e586]	95	is_data = False #Has more than 5 lines
	96	mum_data_lines = 5 # More than "5" 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
[892f246]	112	#Reset the header line counters
	113	if j == j1:
	114	j = 0
	115	j1 = 0
	116
	117	if i > 1:
	118	is_data = True
[d508be9]	119
[99d1af6]	120	if data_conv_q is not None:
	121	_x = data_conv_q(_x, units=output.x_unit)
	122
	123	if data_conv_i is not None:
	124	_y = data_conv_i(_y, units=output.y_unit)
	125
[8bd8ea4]	126	# If we have an extra token, check
	127	# whether it can be interpreted as a
	128	# third column.
	129	_dy = None
	130	if len(toks)>2:
	131	try:
	132	_dy = float(toks[2])
[99d1af6]	133
	134	if data_conv_i is not None:
	135	_dy = data_conv_i(_dy, units=output.y_unit)
	136
[8bd8ea4]	137	except:
	138	# The third column is not a float, skip it.
	139	pass
	140
	141	# If we haven't set the 3rd column
	142	# flag, set it now.
[de1da34]	143	if has_error_dy == None:
	144	has_error_dy = False if _dy == None else True
	145
	146	#Check for dx
	147	_dx = None
	148	if len(toks)>3:
	149	try:
	150	_dx = float(toks[3])
	151
	152	if data_conv_i is not None:
	153	_dx = data_conv_i(_dx, units=output.x_unit)
	154
	155	except:
	156	# The 4th column is not a float, skip it.
	157	pass
	158
	159	# If we haven't set the 3rd column
	160	# flag, set it now.
	161	if has_error_dx == None:
	162	has_error_dx = False if _dx == None else True
[892f246]	163
[d508be9]	164	#After talked with PB, we decided to take care of only 4 columns of data for now.
	165	#number of columns in the current line
[0e5e586]	166	#To remember the # of columns in the current line of data
	167	new_lentoks = len(toks)
[d508be9]	168
[3aed0eb]	169	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
[272b107]	170	if lentoks != new_lentoks :
	171	if is_data == True:
	172	break
	173	else:
[d508be9]	174	i = -1
	175	i1 = 0
	176	j = -1
	177	j1 = -1
	178
[272b107]	179
[892f246]	180	#Delete the previously stored lines of data candidates if is not data.
	181	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	182	try:
	183	x= numpy.zeros(0)
	184	y= numpy.zeros(0)
	185
	186	except:
	187	pass
	188
[8bd8ea4]	189	x = numpy.append(x, _x)
	190	y = numpy.append(y, _y)
[892f246]	191
[de1da34]	192	if has_error_dy == True:
[892f246]	193	#Delete the previously stored lines of data candidates if is not data.
	194	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	195	try:
	196	dy = numpy.zeros(0)
	197	except:
	198	pass
[8bd8ea4]	199	dy = numpy.append(dy, _dy)
[892f246]	200
[de1da34]	201	if has_error_dx == True:
[892f246]	202	#Delete the previously stored lines of data candidates if is not data.
	203	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	204	try:
	205	dx = numpy.zeros(0)
	206	except:
	207	pass
[de1da34]	208	dx = numpy.append(dx, _dx)
	209
	210	#Same for temp.
[892f246]	211	#Delete the previously stored lines of data candidates if is not data.
	212	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	213	try:
	214	tx = numpy.zeros(0)
	215	ty = numpy.zeros(0)
	216	except:
	217	pass
	218
[de1da34]	219	tx = numpy.append(tx, _x)
	220	ty = numpy.append(ty, _y)
[892f246]	221
[de1da34]	222	if has_error_dy == True:
[892f246]	223	#Delete the previously stored lines of data candidates if is not data.
	224	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	225	try:
	226	tdy = numpy.zeros(0)
	227	except:
	228	pass
[de1da34]	229	tdy = numpy.append(tdy, _dy)
	230	if has_error_dx == True:
[892f246]	231	#Delete the previously stored lines of data candidates if is not data.
	232	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	233	try:
	234	tdx = numpy.zeros(0)
	235	except:
	236	pass
[de1da34]	237	tdx = numpy.append(tdx, _dx)
[d508be9]	238
	239	#reset i1 and flag lentoks for the next
	240	if lentoks < new_lentoks :
	241	if is_data == False:
	242	i1 = -1
[0e5e586]	243	#To remember the # of columns on the current line for the next line of data
	244	lentoks = len(toks)
[8bd8ea4]	245
[892f246]	246	#Reset # of header lines and counts # of data candidate lines
	247	if j == 0 and j1 ==0:
	248	i1 = i + 1
	249	i+=1
	250
[8bd8ea4]	251	except:
[892f246]	252
	253	# It is data and meet non - number, then stop reading
	254	if is_data == True:
	255	break
[d508be9]	256	lentoks = 2
[892f246]	257	#Counting # of header lines
	258	j+=1
	259	if j == j1+1:
	260	j1 = j
	261	else:
	262	j = -1
	263	#Reset # of lines of data candidates
	264	i = -1
	265
[8bd8ea4]	266	# Couldn't parse this line, skip it
	267	pass
[892f246]	268
	269
[8bd8ea4]	270
	271	# Sanity check
[de1da34]	272	if has_error_dy == True and not len(y) == len(dy):
	273	raise RuntimeError, "ascii_reader: y and dy have different length"
	274	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	275	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	276
	277	# If the data length is zero, consider this as
	278	# though we were not able to read the file.
	279	if len(x)==0:
[daa56d0]	280	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	281
[470bf7e]	282	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	283	ind = numpy.lexsort((ty,tx))
	284	for i in ind:
	285	x[i] = tx[ind[i]]
	286	y[i] = ty[ind[i]]
	287	if has_error_dy == True:
	288	dy[i] = tdy[ind[i]]
	289	if has_error_dx == True:
	290	dx[i] = tdx[ind[i]]
[892f246]	291
[d508be9]	292
[892f246]	293	#Data
[8bd8ea4]	294	output.x = x
	295	output.y = y
[de1da34]	296	output.dy = dy if has_error_dy == True else None
	297	output.dx = dx if has_error_dx == True else None
	298
[99d1af6]	299	if data_conv_q is not None:
	300	output.xaxis("\\rm{Q}", output.x_unit)
	301	else:
	302	output.xaxis("\\rm{Q}", 'A^{-1}')
	303	if data_conv_i is not None:
[0e2aa40]	304	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	305	else:
[0e2aa40]	306	output.yaxis("\\rm{Intensity}","cm^{-1}")
[8bd8ea4]	307	return output
[892f246]	308
[8bd8ea4]	309	else:
	310	raise RuntimeError, "%s is not a file" % path
	311	return None
	312
	313	if __name__ == "__main__":
	314	reader = Reader()
	315	#print reader.read("../test/test_3_columns.txt")
	316	print reader.read("../test/empty.txt")
	317
	318
	319

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source: sasview/DataLoader/readers/ascii_reader.py @ f50330b7

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