ascii_reader.py @ 9ec4406

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 9ec4406 was fca90f82, checked in by Jae Cho <jhjcho@…>, 14 years ago
put zeros for dx,dy when no errs are given: asked by Mathieu
Property mode set to `100644`
File size: 15.0 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
[470bf7e]	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)
	56	root, 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
[892f246]	65	#Jae could not find python universal line spliter: keep the below for now
[730c9eb]	66	# some ascii data has \r line separator, try it when the data is on only one long line
[470bf7e]	67	if len(lines) < 2 :
	68	lines = buff.split('\r')
	69
[8bd8ea4]	70	x = numpy.zeros(0)
	71	y = numpy.zeros(0)
	72	dy = numpy.zeros(0)
[de1da34]	73	dx = numpy.zeros(0)
	74
	75	#temp. space to sort data
	76	tx = numpy.zeros(0)
	77	ty = numpy.zeros(0)
	78	tdy = numpy.zeros(0)
	79	tdx = numpy.zeros(0)
	80
	81	output = Data1D(x, y, dy=dy, dx=dx)
[8bd8ea4]	82	self.filename = output.filename = basename
[99d1af6]	83
	84	data_conv_q = None
	85	data_conv_i = None
	86
[ca10d8e]	87	if has_converter == True and output.x_unit != '1/A':
	88	data_conv_q = Converter('1/A')
[99d1af6]	89	# Test it
	90	data_conv_q(1.0, output.x_unit)
	91
[ca10d8e]	92	if has_converter == True and output.y_unit != '1/cm':
	93	data_conv_i = Converter('1/cm')
[99d1af6]	94	# Test it
	95	data_conv_i(1.0, output.y_unit)
	96
[8bd8ea4]	97
	98	# The first good line of data will define whether
	99	# we have 2-column or 3-column ascii
[de1da34]	100	has_error_dx = None
	101	has_error_dy = None
[8bd8ea4]	102
[892f246]	103	#Initialize counters for data lines and header lines.
[0e5e586]	104	is_data = False #Has more than 5 lines
	105	mum_data_lines = 5 # More than "5" lines of data is considered as actual data unless that is the only data
[892f246]	106
[d508be9]	107	i=-1 # To count # of current data candidate lines
	108	i1=-1 # To count total # of previous data candidate lines
	109	j=-1 # To count # of header lines
	110	j1=-1 # Helps to count # of header lines
	111	lentoks = 2 # minimum required number of columns of data; ( <= 4).
[892f246]	112
[8bd8ea4]	113	for line in lines:
	114	toks = line.split()
[892f246]	115
[8bd8ea4]	116	try:
[5f2d3c78]	117	#Make sure that all columns are numbers.
	118	for colnum in range(len(toks)):
	119	float(toks[colnum])
	120
[8bd8ea4]	121	_x = float(toks[0])
	122	_y = float(toks[1])
	123
[892f246]	124	#Reset the header line counters
	125	if j == j1:
	126	j = 0
	127	j1 = 0
	128
	129	if i > 1:
	130	is_data = True
[d508be9]	131
[99d1af6]	132	if data_conv_q is not None:
	133	_x = data_conv_q(_x, units=output.x_unit)
	134
	135	if data_conv_i is not None:
	136	_y = data_conv_i(_y, units=output.y_unit)
	137
[8bd8ea4]	138	# If we have an extra token, check
	139	# whether it can be interpreted as a
	140	# third column.
	141	_dy = None
	142	if len(toks)>2:
	143	try:
	144	_dy = float(toks[2])
[99d1af6]	145
	146	if data_conv_i is not None:
	147	_dy = data_conv_i(_dy, units=output.y_unit)
	148
[8bd8ea4]	149	except:
	150	# The third column is not a float, skip it.
	151	pass
	152
	153	# If we haven't set the 3rd column
	154	# flag, set it now.
[de1da34]	155	if has_error_dy == None:
	156	has_error_dy = False if _dy == None else True
	157
	158	#Check for dx
	159	_dx = None
	160	if len(toks)>3:
	161	try:
	162	_dx = float(toks[3])
	163
	164	if data_conv_i is not None:
	165	_dx = data_conv_i(_dx, units=output.x_unit)
	166
	167	except:
	168	# The 4th column is not a float, skip it.
	169	pass
	170
	171	# If we haven't set the 3rd column
	172	# flag, set it now.
	173	if has_error_dx == None:
	174	has_error_dx = False if _dx == None else True
[892f246]	175
[d508be9]	176	#After talked with PB, we decided to take care of only 4 columns of data for now.
	177	#number of columns in the current line
[0e5e586]	178	#To remember the # of columns in the current line of data
	179	new_lentoks = len(toks)
[d508be9]	180
[3aed0eb]	181	#If the previous columns not equal to the current, mark the previous as non-data and reset the dependents.
[272b107]	182	if lentoks != new_lentoks :
	183	if is_data == True:
	184	break
	185	else:
[d508be9]	186	i = -1
	187	i1 = 0
	188	j = -1
	189	j1 = -1
	190
[272b107]	191
[892f246]	192	#Delete the previously stored lines of data candidates if is not data.
	193	if i < 0 and -1< i1 < mum_data_lines and is_data == False:
	194	try:
	195	x= numpy.zeros(0)
	196	y= numpy.zeros(0)
	197
	198	except:
	199	pass
	200
[8bd8ea4]	201	x = numpy.append(x, _x)
	202	y = numpy.append(y, _y)
[892f246]	203
[de1da34]	204	if has_error_dy == True:
[892f246]	205	#Delete the previously stored lines of data candidates if is not data.
	206	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	207	try:
	208	dy = numpy.zeros(0)
	209	except:
	210	pass
[8bd8ea4]	211	dy = numpy.append(dy, _dy)
[892f246]	212
[de1da34]	213	if has_error_dx == True:
[892f246]	214	#Delete the previously stored lines of data candidates if is not data.
	215	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	216	try:
	217	dx = numpy.zeros(0)
	218	except:
	219	pass
[de1da34]	220	dx = numpy.append(dx, _dx)
	221
	222	#Same for temp.
[892f246]	223	#Delete the previously stored lines of data candidates if is not data.
	224	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	225	try:
	226	tx = numpy.zeros(0)
	227	ty = numpy.zeros(0)
	228	except:
	229	pass
	230
[de1da34]	231	tx = numpy.append(tx, _x)
	232	ty = numpy.append(ty, _y)
[892f246]	233
[de1da34]	234	if has_error_dy == True:
[892f246]	235	#Delete the previously stored lines of data candidates if is not data.
	236	if i < 0 and -1<i1 < mum_data_lines and is_data== False:
	237	try:
	238	tdy = numpy.zeros(0)
	239	except:
	240	pass
[de1da34]	241	tdy = numpy.append(tdy, _dy)
	242	if has_error_dx == True:
[892f246]	243	#Delete the previously stored lines of data candidates if is not data.
	244	if i < 0 and -1< i1 < mum_data_lines and is_data== False:
	245	try:
	246	tdx = numpy.zeros(0)
	247	except:
	248	pass
[de1da34]	249	tdx = numpy.append(tdx, _dx)
[d508be9]	250
	251	#reset i1 and flag lentoks for the next
	252	if lentoks < new_lentoks :
	253	if is_data == False:
	254	i1 = -1
[0e5e586]	255	#To remember the # of columns on the current line for the next line of data
	256	lentoks = len(toks)
[8bd8ea4]	257
[892f246]	258	#Reset # of header lines and counts # of data candidate lines
	259	if j == 0 and j1 ==0:
	260	i1 = i + 1
	261	i+=1
	262
[8bd8ea4]	263	except:
[892f246]	264
	265	# It is data and meet non - number, then stop reading
	266	if is_data == True:
	267	break
[d508be9]	268	lentoks = 2
[892f246]	269	#Counting # of header lines
	270	j+=1
	271	if j == j1+1:
	272	j1 = j
	273	else:
	274	j = -1
	275	#Reset # of lines of data candidates
	276	i = -1
	277
[8bd8ea4]	278	# Couldn't parse this line, skip it
	279	pass
[892f246]	280
	281
[c7c5ef8]	282	input_f.close()
[8bd8ea4]	283	# Sanity check
[de1da34]	284	if has_error_dy == True and not len(y) == len(dy):
	285	raise RuntimeError, "ascii_reader: y and dy have different length"
	286	if has_error_dx == True and not len(x) == len(dx):
[daa56d0]	287	raise RuntimeError, "ascii_reader: y and dy have different length"
[8bd8ea4]	288
	289	# If the data length is zero, consider this as
	290	# though we were not able to read the file.
	291	if len(x)==0:
[daa56d0]	292	raise RuntimeError, "ascii_reader: could not load file"
[de1da34]	293
[470bf7e]	294	#Let's re-order the data to make cal. curve look better some cases
[de1da34]	295	ind = numpy.lexsort((ty,tx))
	296	for i in ind:
	297	x[i] = tx[ind[i]]
	298	y[i] = ty[ind[i]]
	299	if has_error_dy == True:
	300	dy[i] = tdy[ind[i]]
	301	if has_error_dx == True:
	302	dx[i] = tdx[ind[i]]
[892f246]	303
[d508be9]	304
[892f246]	305	#Data
[8bd8ea4]	306	output.x = x
	307	output.y = y
[fca90f82]	308	output.dy = dy if has_error_dy == True else numpy.zeros(len(y))
	309	output.dx = dx if has_error_dx == True else numpy.zeros(len(x))
	310
[99d1af6]	311	if data_conv_q is not None:
	312	output.xaxis("\\rm{Q}", output.x_unit)
	313	else:
	314	output.xaxis("\\rm{Q}", 'A^{-1}')
	315	if data_conv_i is not None:
[0e2aa40]	316	output.yaxis("\\rm{Intensity}", output.y_unit)
[99d1af6]	317	else:
[0e2aa40]	318	output.yaxis("\\rm{Intensity}","cm^{-1}")
[fe78c7b]	319
	320	# Store loading process information
	321	output.meta_data['loader'] = self.type_name
	322
[8bd8ea4]	323	return output
[892f246]	324
[8bd8ea4]	325	else:
	326	raise RuntimeError, "%s is not a file" % path
	327	return None
	328
	329	if __name__ == "__main__":
	330	reader = Reader()
	331	#print reader.read("../test/test_3_columns.txt")
	332	print reader.read("../test/empty.txt")
	333
	334
	335

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source: sasview/DataLoader/readers/ascii_reader.py @ 9ec4406

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