ascii_reader.py @ 5385a9e

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 5385a9e was a7a5886, checked in by Gervaise Alina <gervyh@…>, 14 years ago
working pylint
Property mode set to `100644`
File size: 15.6 KB

Rev	Line
[8bd8ea4]	1
	2
[0997158f]	3	############################################################################
	4	#This software was developed by the University of Tennessee as part of the
	5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	6	#project funded by the US National Science Foundation.
	7	#If you use DANSE applications to do scientific research that leads to
	8	#publication, we ask that you acknowledge the use of the software with the
	9	#following sentence:
	10	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	11	#copyright 2008, University of Tennessee
	12	#############################################################################
	13
[8bd8ea4]	14
	15	import numpy
	16	import os
	17	from DataLoader.data_info import Data1D
	18
[daa56d0]	19	# Check whether we have a converter available
[99d1af6]	20	has_converter = True
	21	try:
	22	from data_util.nxsunit import Converter
	23	except:
	24	has_converter = False
	25
[8bd8ea4]	26	class Reader:
	27	"""
[0997158f]	28	Class to load ascii files (2, 3 or 4 columns).
[8bd8ea4]	29	"""
[8780e9a]	30	## File type
[28caa03]	31	type_name = "ASCII"
	32
	33	## Wildcards
[8780e9a]	34	type = ["ASCII files (.txt)\|.txt",
[470bf7e]	35	"ASCII files (.dat)\|.dat",
	36	"ASCII files (.abs)\|.abs"]
[8bd8ea4]	37	## List of allowed extensions
[a7a5886]	38	ext = ['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS']
[8bd8ea4]	39
[e082e2c]	40	## Flag to bypass extension check
	41	allow_all = True
	42
[8bd8ea4]	43	def read(self, path):
	44	"""
[0997158f]	45	Load data file
	46
	47	:param path: file path
	48
	49	:return: Data1D object, or None
	50
	51	:raise RuntimeError: when the file can't be opened
	52	:raise ValueError: when the length of the data vectors are inconsistent
[8bd8ea4]	53	"""
	54	if os.path.isfile(path):
	55	basename = os.path.basename(path)
[a7a5886]	56	_, extension = os.path.splitext(basename)
[e082e2c]	57	if self.allow_all or extension.lower() in self.ext:
[8bd8ea4]	58	try:
	59	input_f = open(path,'r')
	60	except :
	61	raise RuntimeError, "ascii_reader: cannot open %s" % path
	62	buff = input_f.read()
	63	lines = buff.split('\n')
[470bf7e]	64
[a7a5886]	65	#Jae could not find python universal line spliter:
	66	#keep the below for now
	67	# some ascii data has \r line separator,
	68	# try it when the data is on only one long line
[470bf7e]	69	if len(lines) < 2 :
	70	lines = buff.split('\r')
	71
[8bd8ea4]	72	x = numpy.zeros(0)
	73	y = numpy.zeros(0)
	74	dy = numpy.zeros(0)
[de1da34]	75	dx = numpy.zeros(0)
	76
	77	#temp. space to sort data
	78	tx = numpy.zeros(0)
	79	ty = numpy.zeros(0)
	80	tdy = numpy.zeros(0)
	81	tdx = numpy.zeros(0)
	82
	83	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	84	self.filename = output.filename = basename
[99d1af6]	85
	86	data_conv_q = None
	87	data_conv_i = None
	88
[ca10d8e]	89	if has_converter == True and output.x_unit != '1/A':
	90	data_conv_q = Converter('1/A')
[99d1af6]	91	# Test it
	92	data_conv_q(1.0, output.x_unit)
	93
[ca10d8e]	94	if has_converter == True and output.y_unit != '1/cm':
	95	data_conv_i = Converter('1/cm')
[99d1af6]	96	# Test it
	97	data_conv_i(1.0, output.y_unit)
	98
[8bd8ea4]	99
	100	# The first good line of data will define whether
	101	# we have 2-column or 3-column ascii
[de1da34]	102	has_error_dx = None
	103	has_error_dy = None
[8bd8ea4]	104
[892f246]	105	#Initialize counters for data lines and header lines.
[0e5e586]	106	is_data = False #Has more than 5 lines
[a7a5886]	107	# More than "5" lines of data is considered as actual
	108	# data unless that is the only data
	109	mum_data_lines = 5
	110	# To count # of current data candidate lines
	111	i = -1
	112	# To count total # of previous data candidate lines
	113	i1 = -1
	114	# To count # of header lines
	115	j = -1
	116	# Helps to count # of header lines
	117	j1 = -1
	118	#minimum required number of columns of data; ( <= 4).
	119	lentoks = 2
[8bd8ea4]	120	for line in lines:
	121	toks = line.split()
	122	try:
[5f2d3c78]	123	#Make sure that all columns are numbers.
	124	for colnum in range(len(toks)):
	125	float(toks[colnum])
	126
[8bd8ea4]	127	_x = float(toks[0])
	128	_y = float(toks[1])
	129
[892f246]	130	#Reset the header line counters
	131	if j == j1:
	132	j = 0
	133	j1 = 0
	134
	135	if i > 1:
	136	is_data = True
[d508be9]	137
[99d1af6]	138	if data_conv_q is not None:
	139	_x = data_conv_q(_x, units=output.x_unit)
	140
	141	if data_conv_i is not None:
	142	_y = data_conv_i(_y, units=output.y_unit)
	143
[8bd8ea4]	144	# If we have an extra token, check
	145	# whether it can be interpreted as a
	146	# third column.
	147	_dy = None
[a7a5886]	148	if len(toks) > 2:
[8bd8ea4]	149	try:
	150	_dy = float(toks[2])
[99d1af6]	151
	152	if data_conv_i is not None:
	153	_dy = data_conv_i(_dy, units=output.y_unit)
	154
[8bd8ea4]	155	except:
	156	# The third column is not a float, skip it.
	157	pass
	158
	159	# If we haven't set the 3rd column
	160	# flag, set it now.
[de1da34]	161	if has_error_dy == None:
	162	has_error_dy = False if _dy == None else True
	163
	164	#Check for dx
	165	_dx = None
[a7a5886]	166	if len(toks) > 3:
[de1da34]	167	try:
	168	_dx = float(toks[3])
	169
	170	if data_conv_i is not None:
	171	_dx = data_conv_i(_dx, units=output.x_unit)
	172
	173	except:
	174	# The 4th column is not a float, skip it.
	175	pass
	176
	177	# If we haven't set the 3rd column
	178	# flag, set it now.
	179	if has_error_dx == None:
	180	has_error_dx = False if _dx == None else True
[892f246]	181
[a7a5886]	182	#After talked with PB, we decided to take care of only
	183	# 4 columns of data for now.
[d508be9]	184	#number of columns in the current line
[a7a5886]	185	#To remember the # of columns in the current
	186	#line of data
[0e5e586]	187	new_lentoks = len(toks)
[d508be9]	188
[a7a5886]	189	#If the previous columns not equal to the current,
	190	#mark the previous as non-data and reset the dependents.
[272b107]	191	if lentoks != new_lentoks :
	192	if is_data == True:
	193	break
	194	else:
[d508be9]	195	i = -1
	196	i1 = 0
	197	j = -1
	198	j1 = -1
	199
[272b107]	200
[a7a5886]	201	#Delete the previously stored lines of data candidates
	202	# if is not data.
	203	if i < 0 and -1 < i1 < mum_data_lines and \
	204	is_data == False:
[892f246]	205	try:
[a7a5886]	206	x = numpy.zeros(0)
	207	y = numpy.zeros(0)
[892f246]	208	except:
	209	pass
	210
[8bd8ea4]	211	x = numpy.append(x, _x)
	212	y = numpy.append(y, _y)
[892f246]	213
[de1da34]	214	if has_error_dy == True:
[a7a5886]	215	#Delete the previously stored lines of
	216	# data candidates if is not data.
	217	if i < 0 and -1 < i1 < mum_data_lines and \
	218	is_data == False:
[892f246]	219	try:
	220	dy = numpy.zeros(0)
	221	except:
	222	pass
[8bd8ea4]	223	dy = numpy.append(dy, _dy)
[892f246]	224
[de1da34]	225	if has_error_dx == True:
[a7a5886]	226	#Delete the previously stored lines of
	227	# data candidates if is not data.
	228	if i < 0 and -1 < i1 < mum_data_lines and \
	229	is_data == False:
[892f246]	230	try:
	231	dx = numpy.zeros(0)
	232	except:
	233	pass
[de1da34]	234	dx = numpy.append(dx, _dx)
	235
	236	#Same for temp.
[a7a5886]	237	#Delete the previously stored lines of data candidates
	238	# if is not data.
	239	if i < 0 and -1 < i1 < mum_data_lines and\
	240	is_data == False:
[892f246]	241	try:
	242	tx = numpy.zeros(0)
	243	ty = numpy.zeros(0)
	244	except:
[a7a5886]	245	pass
[892f246]	246
[de1da34]	247	tx = numpy.append(tx, _x)
	248	ty = numpy.append(ty, _y)
[892f246]	249
[de1da34]	250	if has_error_dy == True:
[a7a5886]	251	#Delete the previously stored lines of
	252	# data candidates if is not data.
	253	if i < 0 and -1 < i1 < mum_data_lines and \
	254	is_data == False:
[892f246]	255	try:
	256	tdy = numpy.zeros(0)
	257	except:
	258	pass
[de1da34]	259	tdy = numpy.append(tdy, _dy)
	260	if has_error_dx == True:
[a7a5886]	261	#Delete the previously stored lines of
	262	# data candidates if is not data.
	263	if i < 0 and -1 < i1 < mum_data_lines and \
	264	is_data == False:
[892f246]	265	try:
	266	tdx = numpy.zeros(0)
	267	except:
[a7a5886]	268	pass
[de1da34]	269	tdx = numpy.append(tdx, _dx)
[d508be9]	270
	271	#reset i1 and flag lentoks for the next
[a7a5886]	272	if lentoks < new_lentoks:
[d508be9]	273	if is_data == False:
	274	i1 = -1
[a7a5886]	275	#To remember the # of columns on the current line
	276	# for the next line of data
[0e5e586]	277	lentoks = len(toks)
[8bd8ea4]	278
[a7a5886]	279	#Reset # of header lines and counts #
	280	# of data candidate lines
	281	if j == 0 and j1 == 0:
[892f246]	282	i1 = i + 1
[a7a5886]	283	i += 1
[8bd8ea4]	284	except:
[892f246]	285
	286	# It is data and meet non - number, then stop reading
	287	if is_data == True:
	288	break
[d508be9]	289	lentoks = 2
[892f246]	290	#Counting # of header lines
[a7a5886]	291	j += 1
	292	if j == j1 + 1:
[892f246]	293	j1 = j
	294	else:
	295	j = -1
	296	#Reset # of lines of data candidates
	297	i = -1
	298
[8bd8ea4]	299	# Couldn't parse this line, skip it
	300	pass
[892f246]	301
[c7c5ef8]	302	input_f.close()
[8bd8ea4]	303	# Sanity check
[de1da34]	304	if has_error_dy == True and not len(y) == len(dy):
[a7a5886]	305	msg = "ascii_reader: y and dy have different length"
	306	raise RuntimeError, msg
[de1da34]	307	if has_error_dx == True and not len(x) == len(dx):
[a7a5886]	308	msg = "ascii_reader: y and dy have different length"
	309	raise RuntimeError, msg
[8bd8ea4]	310	# If the data length is zero, consider this as
	311	# though we were not able to read the file.
[a7a5886]	312	if len(x) == 0:
[daa56d0]	313	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	314
[a7a5886]	315	#Let's re-order the data to make cal.
	316	# curve look better some cases
	317	ind = numpy.lexsort((ty, tx))
[de1da34]	318	for i in ind:
	319	x[i] = tx[ind[i]]
	320	y[i] = ty[ind[i]]
	321	if has_error_dy == True:
	322	dy[i] = tdy[ind[i]]
	323	if has_error_dx == True:
	324	dx[i] = tdx[ind[i]]
[892f246]	325	#Data
[8bd8ea4]	326	output.x = x
	327	output.y = y
[fca90f82]	328	output.dy = dy if has_error_dy == True else numpy.zeros(len(y))
	329	output.dx = dx if has_error_dx == True else numpy.zeros(len(x))
	330
[99d1af6]	331	if data_conv_q is not None:
	332	output.xaxis("\\rm{Q}", output.x_unit)
	333	else:
	334	output.xaxis("\\rm{Q}", 'A^{-1}')
	335	if data_conv_i is not None:
[0e2aa40]	336	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	337	else:
[0e2aa40]	338	output.yaxis("\\rm{Intensity}","cm^{-1}")
[fe78c7b]	339
	340	# Store loading process information
	341	output.meta_data['loader'] = self.type_name
	342
[8bd8ea4]	343	return output
[892f246]	344
[8bd8ea4]	345	else:
	346	raise RuntimeError, "%s is not a file" % path
	347	return None
	348
	349	if __name__ == "__main__":
	350	reader = Reader()
	351	#print reader.read("../test/test_3_columns.txt")
	352	print reader.read("../test/empty.txt")
	353
	354
	355

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source: sasview/DataLoader/readers/ascii_reader.py @ 5385a9e

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