ascii_reader.py @ f338d3b

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 f338d3b was 5f2d3c78, checked in by Jae Cho <jhjcho@…>, 15 years ago
data line should be composed only with numbers in any of the columns. Added unittest and testdata
Property mode set to `100644`
File size: 14.6 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:
[5f2d3c78]	111	#Make sure that all columns are numbers.
	112	for colnum in range(len(toks)):
	113	float(toks[colnum])
	114
[8bd8ea4]	115	_x = float(toks[0])
	116	_y = float(toks[1])
	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
[0e5e586]	172	#To remember the # of columns in the current line of data
	173	new_lentoks = len(toks)
[d508be9]	174
[3aed0eb]	175	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
[272b107]	176	if lentoks != new_lentoks :
	177	if is_data == True:
	178	break
	179	else:
[d508be9]	180	i = -1
	181	i1 = 0
	182	j = -1
	183	j1 = -1
	184
[272b107]	185
[892f246]	186	#Delete the previously stored lines of data candidates if is not data.
	187	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	188	try:
	189	x= numpy.zeros(0)
	190	y= numpy.zeros(0)
	191
	192	except:
	193	pass
	194
[8bd8ea4]	195	x = numpy.append(x, _x)
	196	y = numpy.append(y, _y)
[892f246]	197
[de1da34]	198	if has_error_dy == True:
[892f246]	199	#Delete the previously stored lines of data candidates if is not data.
	200	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	201	try:
	202	dy = numpy.zeros(0)
	203	except:
	204	pass
[8bd8ea4]	205	dy = numpy.append(dy, _dy)
[892f246]	206
[de1da34]	207	if has_error_dx == True:
[892f246]	208	#Delete the previously stored lines of data candidates if is not data.
	209	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	210	try:
	211	dx = numpy.zeros(0)
	212	except:
	213	pass
[de1da34]	214	dx = numpy.append(dx, _dx)
	215
	216	#Same for temp.
[892f246]	217	#Delete the previously stored lines of data candidates if is not data.
	218	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	219	try:
	220	tx = numpy.zeros(0)
	221	ty = numpy.zeros(0)
	222	except:
	223	pass
	224
[de1da34]	225	tx = numpy.append(tx, _x)
	226	ty = numpy.append(ty, _y)
[892f246]	227
[de1da34]	228	if has_error_dy == True:
[892f246]	229	#Delete the previously stored lines of data candidates if is not data.
	230	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	231	try:
	232	tdy = numpy.zeros(0)
	233	except:
	234	pass
[de1da34]	235	tdy = numpy.append(tdy, _dy)
	236	if has_error_dx == True:
[892f246]	237	#Delete the previously stored lines of data candidates if is not data.
	238	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	239	try:
	240	tdx = numpy.zeros(0)
	241	except:
	242	pass
[de1da34]	243	tdx = numpy.append(tdx, _dx)
[d508be9]	244
	245	#reset i1 and flag lentoks for the next
	246	if lentoks < new_lentoks :
	247	if is_data == False:
	248	i1 = -1
[0e5e586]	249	#To remember the # of columns on the current line for the next line of data
	250	lentoks = len(toks)
[8bd8ea4]	251
[892f246]	252	#Reset # of header lines and counts # of data candidate lines
	253	if j == 0 and j1 ==0:
	254	i1 = i + 1
	255	i+=1
	256
[8bd8ea4]	257	except:
[892f246]	258
	259	# It is data and meet non - number, then stop reading
	260	if is_data == True:
	261	break
[d508be9]	262	lentoks = 2
[892f246]	263	#Counting # of header lines
	264	j+=1
	265	if j == j1+1:
	266	j1 = j
	267	else:
	268	j = -1
	269	#Reset # of lines of data candidates
	270	i = -1
	271
[8bd8ea4]	272	# Couldn't parse this line, skip it
	273	pass
[892f246]	274
	275
[8bd8ea4]	276
	277	# Sanity check
[de1da34]	278	if has_error_dy == True and not len(y) == len(dy):
	279	raise RuntimeError, "ascii_reader: y and dy have different length"
	280	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	281	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	282
	283	# If the data length is zero, consider this as
	284	# though we were not able to read the file.
	285	if len(x)==0:
[daa56d0]	286	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	287
[470bf7e]	288	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	289	ind = numpy.lexsort((ty,tx))
	290	for i in ind:
	291	x[i] = tx[ind[i]]
	292	y[i] = ty[ind[i]]
	293	if has_error_dy == True:
	294	dy[i] = tdy[ind[i]]
	295	if has_error_dx == True:
	296	dx[i] = tdx[ind[i]]
[892f246]	297
[d508be9]	298
[892f246]	299	#Data
[8bd8ea4]	300	output.x = x
	301	output.y = y
[de1da34]	302	output.dy = dy if has_error_dy == True else None
	303	output.dx = dx if has_error_dx == True else None
	304
[99d1af6]	305	if data_conv_q is not None:
	306	output.xaxis("\\rm{Q}", output.x_unit)
	307	else:
	308	output.xaxis("\\rm{Q}", 'A^{-1}')
	309	if data_conv_i is not None:
[0e2aa40]	310	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	311	else:
[0e2aa40]	312	output.yaxis("\\rm{Intensity}","cm^{-1}")
[fe78c7b]	313
	314	# Store loading process information
	315	output.meta_data['loader'] = self.type_name
	316
[8bd8ea4]	317	return output
[892f246]	318
[8bd8ea4]	319	else:
	320	raise RuntimeError, "%s is not a file" % path
	321	return None
	322
	323	if __name__ == "__main__":
	324	reader = Reader()
	325	#print reader.read("../test/test_3_columns.txt")
	326	print reader.read("../test/empty.txt")
	327
	328
	329

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source: sasview/DataLoader/readers/ascii_reader.py @ f338d3b

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