ascii_reader.py @ 8f19b69

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 8f19b69 was 5f03524, checked in by Jae Cho <jhjcho@…>, 13 years ago
minor bug fix about dx length
Property mode set to `100644`
File size: 15.9 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
[da96629]	25	_ZERO = 1e-16
[99d1af6]	26
[8bd8ea4]	27	class Reader:
	28	"""
[0997158f]	29	Class to load ascii files (2, 3 or 4 columns).
[8bd8ea4]	30	"""
[8780e9a]	31	## File type
[28caa03]	32	type_name = "ASCII"
	33
	34	## Wildcards
[8780e9a]	35	type = ["ASCII files (.txt)\|.txt",
[470bf7e]	36	"ASCII files (.dat)\|.dat",
	37	"ASCII files (.abs)\|.abs"]
[8bd8ea4]	38	## List of allowed extensions
[a7a5886]	39	ext = ['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS']
[8bd8ea4]	40
[e082e2c]	41	## Flag to bypass extension check
	42	allow_all = True
	43
[8bd8ea4]	44	def read(self, path):
	45	"""
[0997158f]	46	Load data file
	47
	48	:param path: file path
	49
	50	:return: Data1D object, or None
	51
	52	:raise RuntimeError: when the file can't be opened
	53	:raise ValueError: when the length of the data vectors are inconsistent
[8bd8ea4]	54	"""
	55	if os.path.isfile(path):
	56	basename = os.path.basename(path)
[a7a5886]	57	_, extension = os.path.splitext(basename)
[e082e2c]	58	if self.allow_all or extension.lower() in self.ext:
[8bd8ea4]	59	try:
	60	input_f = open(path,'r')
	61	except :
	62	raise RuntimeError, "ascii_reader: cannot open %s" % path
	63	buff = input_f.read()
	64	lines = buff.split('\n')
[470bf7e]	65
[a7a5886]	66	#Jae could not find python universal line spliter:
	67	#keep the below for now
	68	# some ascii data has \r line separator,
	69	# try it when the data is on only one long line
[470bf7e]	70	if len(lines) < 2 :
	71	lines = buff.split('\r')
	72
[8bd8ea4]	73	x = numpy.zeros(0)
	74	y = numpy.zeros(0)
	75	dy = numpy.zeros(0)
[de1da34]	76	dx = numpy.zeros(0)
	77
	78	#temp. space to sort data
	79	tx = numpy.zeros(0)
	80	ty = numpy.zeros(0)
	81	tdy = numpy.zeros(0)
	82	tdx = numpy.zeros(0)
	83
	84	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	85	self.filename = output.filename = basename
[99d1af6]	86
	87	data_conv_q = None
	88	data_conv_i = None
	89
[ca10d8e]	90	if has_converter == True and output.x_unit != '1/A':
	91	data_conv_q = Converter('1/A')
[99d1af6]	92	# Test it
	93	data_conv_q(1.0, output.x_unit)
	94
[ca10d8e]	95	if has_converter == True and output.y_unit != '1/cm':
	96	data_conv_i = Converter('1/cm')
[99d1af6]	97	# Test it
	98	data_conv_i(1.0, output.y_unit)
	99
[8bd8ea4]	100
	101	# The first good line of data will define whether
	102	# we have 2-column or 3-column ascii
[de1da34]	103	has_error_dx = None
	104	has_error_dy = None
[8bd8ea4]	105
[892f246]	106	#Initialize counters for data lines and header lines.
[0e5e586]	107	is_data = False #Has more than 5 lines
[a7a5886]	108	# More than "5" lines of data is considered as actual
	109	# data unless that is the only data
	110	mum_data_lines = 5
	111	# To count # of current data candidate lines
	112	i = -1
	113	# To count total # of previous data candidate lines
	114	i1 = -1
	115	# To count # of header lines
	116	j = -1
	117	# Helps to count # of header lines
	118	j1 = -1
	119	#minimum required number of columns of data; ( <= 4).
	120	lentoks = 2
[8bd8ea4]	121	for line in lines:
	122	toks = line.split()
	123	try:
[5f2d3c78]	124	#Make sure that all columns are numbers.
	125	for colnum in range(len(toks)):
	126	float(toks[colnum])
	127
[8bd8ea4]	128	_x = float(toks[0])
	129	_y = float(toks[1])
	130
[892f246]	131	#Reset the header line counters
	132	if j == j1:
	133	j = 0
	134	j1 = 0
	135
	136	if i > 1:
	137	is_data = True
[d508be9]	138
[99d1af6]	139	if data_conv_q is not None:
	140	_x = data_conv_q(_x, units=output.x_unit)
	141
	142	if data_conv_i is not None:
	143	_y = data_conv_i(_y, units=output.y_unit)
	144
[8bd8ea4]	145	# If we have an extra token, check
	146	# whether it can be interpreted as a
	147	# third column.
	148	_dy = None
[a7a5886]	149	if len(toks) > 2:
[8bd8ea4]	150	try:
	151	_dy = float(toks[2])
[99d1af6]	152
	153	if data_conv_i is not None:
	154	_dy = data_conv_i(_dy, units=output.y_unit)
	155
[8bd8ea4]	156	except:
	157	# The third column is not a float, skip it.
	158	pass
	159
	160	# If we haven't set the 3rd column
	161	# flag, set it now.
[de1da34]	162	if has_error_dy == None:
	163	has_error_dy = False if _dy == None else True
	164
	165	#Check for dx
	166	_dx = None
[a7a5886]	167	if len(toks) > 3:
[de1da34]	168	try:
	169	_dx = float(toks[3])
	170
	171	if data_conv_i is not None:
	172	_dx = data_conv_i(_dx, units=output.x_unit)
	173
	174	except:
	175	# The 4th column is not a float, skip it.
	176	pass
	177
	178	# If we haven't set the 3rd column
	179	# flag, set it now.
	180	if has_error_dx == None:
	181	has_error_dx = False if _dx == None else True
[892f246]	182
[a7a5886]	183	#After talked with PB, we decided to take care of only
	184	# 4 columns of data for now.
[d508be9]	185	#number of columns in the current line
[a7a5886]	186	#To remember the # of columns in the current
	187	#line of data
[0e5e586]	188	new_lentoks = len(toks)
[d508be9]	189
[a7a5886]	190	#If the previous columns not equal to the current,
	191	#mark the previous as non-data and reset the dependents.
[272b107]	192	if lentoks != new_lentoks :
	193	if is_data == True:
	194	break
	195	else:
[d508be9]	196	i = -1
	197	i1 = 0
	198	j = -1
	199	j1 = -1
	200
[272b107]	201
[a7a5886]	202	#Delete the previously stored lines of data candidates
	203	# if is not data.
	204	if i < 0 and -1 < i1 < mum_data_lines and \
	205	is_data == False:
[892f246]	206	try:
[a7a5886]	207	x = numpy.zeros(0)
	208	y = numpy.zeros(0)
[892f246]	209	except:
	210	pass
	211
[8bd8ea4]	212	x = numpy.append(x, _x)
	213	y = numpy.append(y, _y)
[892f246]	214
[de1da34]	215	if has_error_dy == True:
[a7a5886]	216	#Delete the previously stored lines of
	217	# data candidates if is not data.
	218	if i < 0 and -1 < i1 < mum_data_lines and \
	219	is_data == False:
[892f246]	220	try:
	221	dy = numpy.zeros(0)
	222	except:
	223	pass
[8bd8ea4]	224	dy = numpy.append(dy, _dy)
[892f246]	225
[de1da34]	226	if has_error_dx == True:
[a7a5886]	227	#Delete the previously stored lines of
	228	# data candidates if is not data.
	229	if i < 0 and -1 < i1 < mum_data_lines and \
	230	is_data == False:
[892f246]	231	try:
	232	dx = numpy.zeros(0)
	233	except:
	234	pass
[de1da34]	235	dx = numpy.append(dx, _dx)
	236
	237	#Same for temp.
[a7a5886]	238	#Delete the previously stored lines of data candidates
	239	# if is not data.
	240	if i < 0 and -1 < i1 < mum_data_lines and\
	241	is_data == False:
[892f246]	242	try:
	243	tx = numpy.zeros(0)
	244	ty = numpy.zeros(0)
	245	except:
[a7a5886]	246	pass
[892f246]	247
[de1da34]	248	tx = numpy.append(tx, _x)
	249	ty = numpy.append(ty, _y)
[892f246]	250
[de1da34]	251	if has_error_dy == True:
[a7a5886]	252	#Delete the previously stored lines of
	253	# data candidates if is not data.
	254	if i < 0 and -1 < i1 < mum_data_lines and \
	255	is_data == False:
[892f246]	256	try:
	257	tdy = numpy.zeros(0)
	258	except:
	259	pass
[de1da34]	260	tdy = numpy.append(tdy, _dy)
	261	if has_error_dx == True:
[a7a5886]	262	#Delete the previously stored lines of
	263	# data candidates if is not data.
	264	if i < 0 and -1 < i1 < mum_data_lines and \
	265	is_data == False:
[892f246]	266	try:
	267	tdx = numpy.zeros(0)
	268	except:
[a7a5886]	269	pass
[de1da34]	270	tdx = numpy.append(tdx, _dx)
[d508be9]	271
	272	#reset i1 and flag lentoks for the next
[a7a5886]	273	if lentoks < new_lentoks:
[d508be9]	274	if is_data == False:
	275	i1 = -1
[a7a5886]	276	#To remember the # of columns on the current line
	277	# for the next line of data
[0e5e586]	278	lentoks = len(toks)
[8bd8ea4]	279
[a7a5886]	280	#Reset # of header lines and counts #
	281	# of data candidate lines
	282	if j == 0 and j1 == 0:
[892f246]	283	i1 = i + 1
[a7a5886]	284	i += 1
[8bd8ea4]	285	except:
[892f246]	286
	287	# It is data and meet non - number, then stop reading
	288	if is_data == True:
	289	break
[d508be9]	290	lentoks = 2
[892f246]	291	#Counting # of header lines
[a7a5886]	292	j += 1
	293	if j == j1 + 1:
[892f246]	294	j1 = j
	295	else:
	296	j = -1
	297	#Reset # of lines of data candidates
	298	i = -1
	299
[8bd8ea4]	300	# Couldn't parse this line, skip it
	301	pass
[892f246]	302
[c7c5ef8]	303	input_f.close()
[8bd8ea4]	304	# Sanity check
[de1da34]	305	if has_error_dy == True and not len(y) == len(dy):
[a7a5886]	306	msg = "ascii_reader: y and dy have different length"
	307	raise RuntimeError, msg
[de1da34]	308	if has_error_dx == True and not len(x) == len(dx):
[a7a5886]	309	msg = "ascii_reader: y and dy have different length"
	310	raise RuntimeError, msg
[8bd8ea4]	311	# If the data length is zero, consider this as
	312	# though we were not able to read the file.
[a7a5886]	313	if len(x) == 0:
[daa56d0]	314	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	315
[a7a5886]	316	#Let's re-order the data to make cal.
	317	# curve look better some cases
	318	ind = numpy.lexsort((ty, tx))
[de1da34]	319	for i in ind:
	320	x[i] = tx[ind[i]]
	321	y[i] = ty[ind[i]]
	322	if has_error_dy == True:
	323	dy[i] = tdy[ind[i]]
	324	if has_error_dx == True:
	325	dx[i] = tdx[ind[i]]
[da96629]	326	# Zeros in dx, dy
	327	if has_error_dx:
	328	dx[dx==0] = _ZERO
	329	if has_error_dy:
	330	dy[dy==0] = _ZERO
[892f246]	331	#Data
[121c224]	332	output.x = x[x!=0]
	333	output.y = y[x!=0]
[5f03524]	334	output.dy = dy[x!=0] if has_error_dy == True else numpy.zeros(len(output.y))
	335	output.dx = dx[x!=0] if has_error_dx == True else numpy.zeros(len(output.x))
[fca90f82]	336
[99d1af6]	337	if data_conv_q is not None:
	338	output.xaxis("\\rm{Q}", output.x_unit)
	339	else:
	340	output.xaxis("\\rm{Q}", 'A^{-1}')
	341	if data_conv_i is not None:
[0e2aa40]	342	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	343	else:
[0e2aa40]	344	output.yaxis("\\rm{Intensity}","cm^{-1}")
[fe78c7b]	345
	346	# Store loading process information
	347	output.meta_data['loader'] = self.type_name
	348
[8bd8ea4]	349	return output
[892f246]	350
[8bd8ea4]	351	else:
	352	raise RuntimeError, "%s is not a file" % path
	353	return None
	354
	355	if __name__ == "__main__":
	356	reader = Reader()
	357	#print reader.read("../test/test_3_columns.txt")
	358	print reader.read("../test/empty.txt")
	359
	360
	361

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source: sasview/DataLoader/readers/ascii_reader.py @ 8f19b69

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