ascii_reader.py @ 79492222

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 79492222 was 79492222, checked in by krzywon, 9 years ago
Changed the file and folder names to remove all SANS references.
Property mode set to `100644`
File size: 15.6 KB

Rev	Line
[7d6351e]	1	"""
	2	ASCII reader
	3	"""
[0997158f]	4	############################################################################
	5	#This software was developed by the University of Tennessee as part of the
	6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	7	#project funded by the US National Science Foundation.
[7d6351e]	8	#If you use DANSE applications to do scientific research that leads to
	9	#publication, we ask that you acknowledge the use of the software with the
[0997158f]	10	#following sentence:
[7d6351e]	11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
[0997158f]	12	#copyright 2008, University of Tennessee
	13	#############################################################################
	14
[8bd8ea4]	15
	16	import numpy
	17	import os
[79492222]	18	from sas.dataloader.data_info import Data1D
[8bd8ea4]	19
[daa56d0]	20	# Check whether we have a converter available
[99d1af6]	21	has_converter = True
	22	try:
[79492222]	23	from sas.data_util.nxsunit import Converter
[99d1af6]	24	except:
	25	has_converter = False
[da96629]	26	_ZERO = 1e-16
[99d1af6]	27
[7d6351e]	28
[8bd8ea4]	29	class Reader:
	30	"""
[0997158f]	31	Class to load ascii files (2, 3 or 4 columns).
[8bd8ea4]	32	"""
[8780e9a]	33	## File type
[28caa03]	34	type_name = "ASCII"
	35
	36	## Wildcards
[8780e9a]	37	type = ["ASCII files (.txt)\|.txt",
[470bf7e]	38	"ASCII files (.dat)\|.dat",
[ef9d209]	39	"ASCII files (.abs)\|.abs",
	40	"CSV files (.csv)\|.csv"]
[8bd8ea4]	41	## List of allowed extensions
[7d6351e]	42	ext = ['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS', 'csv', 'CSV']
[8bd8ea4]	43
[e082e2c]	44	## Flag to bypass extension check
	45	allow_all = True
	46
[8bd8ea4]	47	def read(self, path):
[7d6351e]	48	"""
[0997158f]	49	Load data file
	50
	51	:param path: file path
	52
	53	:return: Data1D object, or None
	54
	55	:raise RuntimeError: when the file can't be opened
	56	:raise ValueError: when the length of the data vectors are inconsistent
[8bd8ea4]	57	"""
	58	if os.path.isfile(path):
[7d6351e]	59	basename = os.path.basename(path)
[a7a5886]	60	_, extension = os.path.splitext(basename)
[e082e2c]	61	if self.allow_all or extension.lower() in self.ext:
[8bd8ea4]	62	try:
[9cd0baa]	63	# Read in binary mode since GRASP frequently has no-ascii
	64	# characters that brakes the open operation
[7d6351e]	65	input_f = open(path,'rb')
	66	except:
[8bd8ea4]	67	raise RuntimeError, "ascii_reader: cannot open %s" % path
	68	buff = input_f.read()
	69	lines = buff.split('\n')
[470bf7e]	70
[7d6351e]	71	#Jae could not find python universal line spliter:
[a7a5886]	72	#keep the below for now
	73	# some ascii data has \r line separator,
	74	# try it when the data is on only one long line
[7d6351e]	75	if len(lines) < 2 :
[470bf7e]	76	lines = buff.split('\r')
	77
[8bd8ea4]	78	x = numpy.zeros(0)
	79	y = numpy.zeros(0)
	80	dy = numpy.zeros(0)
[de1da34]	81	dx = numpy.zeros(0)
	82
	83	#temp. space to sort data
	84	tx = numpy.zeros(0)
	85	ty = numpy.zeros(0)
	86	tdy = numpy.zeros(0)
	87	tdx = numpy.zeros(0)
	88
	89	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	90	self.filename = output.filename = basename
[99d1af6]	91
	92	data_conv_q = None
	93	data_conv_i = None
	94
[ca10d8e]	95	if has_converter == True and output.x_unit != '1/A':
	96	data_conv_q = Converter('1/A')
[99d1af6]	97	# Test it
	98	data_conv_q(1.0, output.x_unit)
	99
[ca10d8e]	100	if has_converter == True and output.y_unit != '1/cm':
	101	data_conv_i = Converter('1/cm')
[99d1af6]	102	# Test it
	103	data_conv_i(1.0, output.y_unit)
	104
[8bd8ea4]	105	# The first good line of data will define whether
	106	# we have 2-column or 3-column ascii
[de1da34]	107	has_error_dx = None
	108	has_error_dy = None
[8bd8ea4]	109
[892f246]	110	#Initialize counters for data lines and header lines.
[7d6351e]	111	is_data = False # Has more than 5 lines
[a7a5886]	112	# More than "5" lines of data is considered as actual
	113	# data unless that is the only data
[7d6351e]	114	mum_data_lines = 5
[a7a5886]	115	# To count # of current data candidate lines
[7d6351e]	116	i = -1
	117	# To count total # of previous data candidate lines
	118	i1 = -1
	119	# To count # of header lines
[a7a5886]	120	j = -1
[7d6351e]	121	# Helps to count # of header lines
[a7a5886]	122	j1 = -1
[7d6351e]	123	#minimum required number of columns of data; ( <= 4).
	124	lentoks = 2
[8bd8ea4]	125	for line in lines:
[86d13b5]	126	# Initial try for CSV (split on ,)
[ef9d209]	127	toks = line.split(',')
[86d13b5]	128	# Now try SCSV (split on ;)
	129	if len(toks) < 2:
	130	toks = line.split(';')
	131	# Now go for whitespace
[ef9d209]	132	if len(toks) < 2:
	133	toks = line.split()
[8bd8ea4]	134	try:
[5f2d3c78]	135	#Make sure that all columns are numbers.
	136	for colnum in range(len(toks)):
	137	float(toks[colnum])
	138
[8bd8ea4]	139	_x = float(toks[0])
	140	_y = float(toks[1])
	141
[892f246]	142	#Reset the header line counters
	143	if j == j1:
	144	j = 0
	145	j1 = 0
	146
	147	if i > 1:
	148	is_data = True
[d508be9]	149
[99d1af6]	150	if data_conv_q is not None:
	151	_x = data_conv_q(_x, units=output.x_unit)
	152
	153	if data_conv_i is not None:
[7d6351e]	154	_y = data_conv_i(_y, units=output.y_unit)
[99d1af6]	155
[8bd8ea4]	156	# If we have an extra token, check
	157	# whether it can be interpreted as a
	158	# third column.
	159	_dy = None
[a7a5886]	160	if len(toks) > 2:
[8bd8ea4]	161	try:
	162	_dy = float(toks[2])
[99d1af6]	163
	164	if data_conv_i is not None:
	165	_dy = data_conv_i(_dy, units=output.y_unit)
	166
[8bd8ea4]	167	except:
	168	# The third column is not a float, skip it.
	169	pass
	170
	171	# If we haven't set the 3rd column
	172	# flag, set it now.
[de1da34]	173	if has_error_dy == None:
	174	has_error_dy = False if _dy == None else True
	175
	176	#Check for dx
	177	_dx = None
[a7a5886]	178	if len(toks) > 3:
[de1da34]	179	try:
	180	_dx = float(toks[3])
	181
	182	if data_conv_i is not None:
	183	_dx = data_conv_i(_dx, units=output.x_unit)
	184
	185	except:
	186	# The 4th column is not a float, skip it.
	187	pass
	188
	189	# If we haven't set the 3rd column
	190	# flag, set it now.
	191	if has_error_dx == None:
	192	has_error_dx = False if _dx == None else True
[892f246]	193
[7d6351e]	194	#After talked with PB, we decided to take care of only
[a7a5886]	195	# 4 columns of data for now.
[d508be9]	196	#number of columns in the current line
[7d6351e]	197	#To remember the # of columns in the current
[a7a5886]	198	#line of data
[0e5e586]	199	new_lentoks = len(toks)
[d508be9]	200
[7d6351e]	201	#If the previous columns not equal to the current,
	202	#mark the previous as non-data and reset the dependents.
	203	if lentoks != new_lentoks:
[272b107]	204	if is_data == True:
	205	break
	206	else:
[d508be9]	207	i = -1
	208	i1 = 0
	209	j = -1
	210	j1 = -1
	211
[a7a5886]	212	#Delete the previously stored lines of data candidates
	213	# if is not data.
	214	if i < 0 and -1 < i1 < mum_data_lines and \
	215	is_data == False:
[892f246]	216	try:
[a7a5886]	217	x = numpy.zeros(0)
	218	y = numpy.zeros(0)
[892f246]	219	except:
	220	pass
	221
[7d6351e]	222	x = numpy.append(x, _x)
	223	y = numpy.append(y, _y)
[892f246]	224
[de1da34]	225	if has_error_dy == 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:
[7d6351e]	231	dy = numpy.zeros(0)
[892f246]	232	except:
[7d6351e]	233	pass
[8bd8ea4]	234	dy = numpy.append(dy, _dy)
[892f246]	235
[de1da34]	236	if has_error_dx == True:
[a7a5886]	237	#Delete the previously stored lines of
	238	# data candidates if is not data.
	239	if i < 0 and -1 < i1 < mum_data_lines and \
	240	is_data == False:
[892f246]	241	try:
[7d6351e]	242	dx = numpy.zeros(0)
[892f246]	243	except:
[7d6351e]	244	pass
[de1da34]	245	dx = numpy.append(dx, _dx)
	246
	247	#Same for temp.
[a7a5886]	248	#Delete the previously stored lines of data candidates
	249	# if is not data.
	250	if i < 0 and -1 < i1 < mum_data_lines and\
	251	is_data == False:
[892f246]	252	try:
	253	tx = numpy.zeros(0)
	254	ty = numpy.zeros(0)
	255	except:
[7d6351e]	256	pass
[892f246]	257
[7d6351e]	258	tx = numpy.append(tx, _x)
	259	ty = numpy.append(ty, _y)
[892f246]	260
[de1da34]	261	if has_error_dy == 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	tdy = numpy.zeros(0)
	268	except:
[7d6351e]	269	pass
[de1da34]	270	tdy = numpy.append(tdy, _dy)
	271	if has_error_dx == True:
[a7a5886]	272	#Delete the previously stored lines of
	273	# data candidates if is not data.
	274	if i < 0 and -1 < i1 < mum_data_lines and \
	275	is_data == False:
[892f246]	276	try:
	277	tdx = numpy.zeros(0)
	278	except:
[7d6351e]	279	pass
[de1da34]	280	tdx = numpy.append(tdx, _dx)
[d508be9]	281
	282	#reset i1 and flag lentoks for the next
[a7a5886]	283	if lentoks < new_lentoks:
[d508be9]	284	if is_data == False:
[7d6351e]	285	i1 = -1
[a7a5886]	286	#To remember the # of columns on the current line
	287	# for the next line of data
[0e5e586]	288	lentoks = len(toks)
[8bd8ea4]	289
[7d6351e]	290	#Reset # of header lines and counts #
	291	# of data candidate lines
[a7a5886]	292	if j == 0 and j1 == 0:
[7d6351e]	293	i1 = i + 1
[a7a5886]	294	i += 1
[8bd8ea4]	295	except:
[892f246]	296
	297	# It is data and meet non - number, then stop reading
	298	if is_data == True:
[7d6351e]	299	break
[d508be9]	300	lentoks = 2
[7d6351e]	301	#Counting # of header lines
[a7a5886]	302	j += 1
	303	if j == j1 + 1:
[7d6351e]	304	j1 = j
	305	else:
[892f246]	306	j = -1
	307	#Reset # of lines of data candidates
	308	i = -1
	309
[7d6351e]	310	# Couldn't parse this line, skip it
[8bd8ea4]	311	pass
[892f246]	312
[7d6351e]	313	input_f.close()
[8bd8ea4]	314	# Sanity check
[de1da34]	315	if has_error_dy == True and not len(y) == len(dy):
[a7a5886]	316	msg = "ascii_reader: y and dy have different length"
	317	raise RuntimeError, msg
[de1da34]	318	if has_error_dx == True and not len(x) == len(dx):
[a7a5886]	319	msg = "ascii_reader: y and dy have different length"
	320	raise RuntimeError, msg
[8bd8ea4]	321	# If the data length is zero, consider this as
	322	# though we were not able to read the file.
[a7a5886]	323	if len(x) == 0:
[daa56d0]	324	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	325
[a7a5886]	326	#Let's re-order the data to make cal.
	327	# curve look better some cases
	328	ind = numpy.lexsort((ty, tx))
[de1da34]	329	for i in ind:
	330	x[i] = tx[ind[i]]
	331	y[i] = ty[ind[i]]
	332	if has_error_dy == True:
	333	dy[i] = tdy[ind[i]]
	334	if has_error_dx == True:
	335	dx[i] = tdx[ind[i]]
[7d6351e]	336	# Zeros in dx, dy
[da96629]	337	if has_error_dx:
[7d6351e]	338	dx[dx == 0] = _ZERO
[da96629]	339	if has_error_dy:
[7d6351e]	340	dy[dy == 0] = _ZERO
	341	#Data
	342	output.x = x[x != 0]
	343	output.y = y[x != 0]
	344	output.dy = dy[x != 0] if has_error_dy == True\
	345	else numpy.zeros(len(output.y))
	346	output.dx = dx[x != 0] if has_error_dx == True\
	347	else numpy.zeros(len(output.x))
[fca90f82]	348
[99d1af6]	349	if data_conv_q is not None:
	350	output.xaxis("\\rm{Q}", output.x_unit)
	351	else:
	352	output.xaxis("\\rm{Q}", 'A^{-1}')
	353	if data_conv_i is not None:
[0e2aa40]	354	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	355	else:
[7d6351e]	356	output.yaxis("\\rm{Intensity}", "cm^{-1}")
[fe78c7b]	357
	358	# Store loading process information
[7d6351e]	359	output.meta_data['loader'] = self.type_name
[83b81b8]	360	if len(output.x) < 1:
	361	raise RuntimeError, "%s is empty" % path
[8bd8ea4]	362	return output
[892f246]	363
[8bd8ea4]	364	else:
	365	raise RuntimeError, "%s is not a file" % path
	366	return None

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source: sasview/src/sas/dataloader/readers/ascii_reader.py @ 79492222

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