ascii_reader.py @ 3ba03a4c

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 3ba03a4c was 3aed0eb, checked in by Jae Cho <jhjcho@…>, 16 years ago
cleaned up mess
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	"""
	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
[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
	166	if len(toks)>= 4:
	167	new_lentoks = 4
	168	else:
	169	new_lentoks = len(toks)
	170
[3aed0eb]	171	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
[272b107]	172	if lentoks != new_lentoks :
	173	if is_data == True:
	174	break
	175	else:
[d508be9]	176	i = -1
	177	i1 = 0
	178	j = -1
	179	j1 = -1
	180
[272b107]	181
[892f246]	182	#Delete the previously stored lines of data candidates if is not data.
	183	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	184	try:
	185	x= numpy.zeros(0)
	186	y= numpy.zeros(0)
	187
	188	except:
	189	pass
	190
[8bd8ea4]	191	x = numpy.append(x, _x)
	192	y = numpy.append(y, _y)
[892f246]	193
[de1da34]	194	if has_error_dy == True:
[892f246]	195	#Delete the previously stored lines of data candidates if is not data.
	196	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	197	try:
	198	dy = numpy.zeros(0)
	199	except:
	200	pass
[8bd8ea4]	201	dy = numpy.append(dy, _dy)
[892f246]	202
[de1da34]	203	if has_error_dx == True:
[892f246]	204	#Delete the previously stored lines of data candidates if is not data.
	205	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	206	try:
	207	dx = numpy.zeros(0)
	208	except:
	209	pass
[de1da34]	210	dx = numpy.append(dx, _dx)
	211
	212	#Same for temp.
[892f246]	213	#Delete the previously stored lines of data candidates if is not data.
	214	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	215	try:
	216	tx = numpy.zeros(0)
	217	ty = numpy.zeros(0)
	218	except:
	219	pass
	220
[de1da34]	221	tx = numpy.append(tx, _x)
	222	ty = numpy.append(ty, _y)
[892f246]	223
[de1da34]	224	if has_error_dy == True:
[892f246]	225	#Delete the previously stored lines of data candidates if is not data.
	226	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	227	try:
	228	tdy = numpy.zeros(0)
	229	except:
	230	pass
[de1da34]	231	tdy = numpy.append(tdy, _dy)
	232	if has_error_dx == True:
[892f246]	233	#Delete the previously stored lines of data candidates if is not data.
	234	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	235	try:
	236	tdx = numpy.zeros(0)
	237	except:
	238	pass
[de1da34]	239	tdx = numpy.append(tdx, _dx)
[d508be9]	240
	241	#reset i1 and flag lentoks for the next
	242	if lentoks < new_lentoks :
	243	if is_data == False:
	244	i1 = -1
	245	if len(toks)>= 4:
	246	lentoks = 4
	247	else:
	248	lentoks = len(toks)
[8bd8ea4]	249
[892f246]	250	#Reset # of header lines and counts # of data candidate lines
	251	if j == 0 and j1 ==0:
	252	i1 = i + 1
	253	i+=1
	254
[8bd8ea4]	255	except:
[892f246]	256
	257	# It is data and meet non - number, then stop reading
	258	if is_data == True:
	259	break
[d508be9]	260	lentoks = 2
[892f246]	261	#Counting # of header lines
	262	j+=1
	263	if j == j1+1:
	264	j1 = j
	265	else:
	266	j = -1
	267	#Reset # of lines of data candidates
	268	i = -1
	269
[8bd8ea4]	270	# Couldn't parse this line, skip it
	271	pass
[892f246]	272
	273
[8bd8ea4]	274
	275	# Sanity check
[de1da34]	276	if has_error_dy == True and not len(y) == len(dy):
	277	raise RuntimeError, "ascii_reader: y and dy have different length"
	278	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	279	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	280
	281	# If the data length is zero, consider this as
	282	# though we were not able to read the file.
	283	if len(x)==0:
[daa56d0]	284	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	285
[470bf7e]	286	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	287	ind = numpy.lexsort((ty,tx))
	288	for i in ind:
	289	x[i] = tx[ind[i]]
	290	y[i] = ty[ind[i]]
	291	if has_error_dy == True:
	292	dy[i] = tdy[ind[i]]
	293	if has_error_dx == True:
	294	dx[i] = tdx[ind[i]]
[892f246]	295
[d508be9]	296
[892f246]	297	#Data
[8bd8ea4]	298	output.x = x
	299	output.y = y
[de1da34]	300	output.dy = dy if has_error_dy == True else None
	301	output.dx = dx if has_error_dx == True else None
	302
[99d1af6]	303	if data_conv_q is not None:
	304	output.xaxis("\\rm{Q}", output.x_unit)
	305	else:
	306	output.xaxis("\\rm{Q}", 'A^{-1}')
	307	if data_conv_i is not None:
[0e2aa40]	308	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	309	else:
[0e2aa40]	310	output.yaxis("\\rm{Intensity}","cm^{-1}")
[8bd8ea4]	311	return output
[892f246]	312
[8bd8ea4]	313	else:
	314	raise RuntimeError, "%s is not a file" % path
	315	return None
	316
	317	if __name__ == "__main__":
	318	reader = Reader()
	319	#print reader.read("../test/test_3_columns.txt")
	320	print reader.read("../test/empty.txt")
	321
	322
	323

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source: sasview/DataLoader/readers/ascii_reader.py @ 3ba03a4c

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