ascii_reader.py @ 25dd9c9

Last change on this file since 25dd9c9 was 235f514, checked in by andyfaff, 8 years ago
MAINT: replace '== None' by 'is None'
Property mode set to `100644`
File size: 9.6 KB

Rev	Line
[959eb01]	1	"""
	2	ASCII reader
	3	"""
	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.
	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
	10	#following sentence:
	11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	12	#copyright 2008, University of Tennessee
	13	#############################################################################
	14
	15
	16	import numpy as np
	17	import os
	18	from sas.sascalc.dataloader.data_info import Data1D
	19
	20	# Check whether we have a converter available
	21	has_converter = True
	22	try:
	23	from sas.sascalc.data_util.nxsunit import Converter
	24	except:
	25	has_converter = False
	26	_ZERO = 1e-16
	27
	28
	29	class Reader:
	30	"""
	31	Class to load ascii files (2, 3 or 4 columns).
	32	"""
	33	## File type
	34	type_name = "ASCII"
	35
	36	## Wildcards
	37	type = ["ASCII files (.txt)\|.txt",
	38	"ASCII files (.dat)\|.dat",
	39	"ASCII files (.abs)\|.abs",
	40	"CSV files (.csv)\|.csv"]
	41	## List of allowed extensions
	42	ext = ['.txt', '.TXT', '.dat', '.DAT', '.abs', '.ABS', 'csv', 'CSV']
	43
	44	## Flag to bypass extension check
	45	allow_all = True
	46
	47	def read(self, path):
	48	"""
	49	Load data file
	50
	51	:param path: file path
	52	:return: Data1D object, or None
	53
	54	:raise RuntimeError: when the file can't be opened
	55	:raise ValueError: when the length of the data vectors are inconsistent
	56	"""
	57	if os.path.isfile(path):
	58	basename = os.path.basename(path)
	59	_, extension = os.path.splitext(basename)
	60	if self.allow_all or extension.lower() in self.ext:
	61	try:
	62	# Read in binary mode since GRASP frequently has no-ascii
	63	# characters that breaks the open operation
	64	input_f = open(path,'rb')
	65	except:
	66	raise RuntimeError, "ascii_reader: cannot open %s" % path
	67	buff = input_f.read()
	68	lines = buff.splitlines()
	69
	70	# Arrays for data storage
	71	tx = np.zeros(0)
	72	ty = np.zeros(0)
	73	tdy = np.zeros(0)
	74	tdx = np.zeros(0)
	75
	76	# The first good line of data will define whether
	77	# we have 2-column or 3-column ascii
	78	has_error_dx = None
	79	has_error_dy = None
	80
	81	#Initialize counters for data lines and header lines.
	82	is_data = False
	83	# More than "5" lines of data is considered as actual
	84	# data unless that is the only data
	85	min_data_pts = 5
	86	# To count # of current data candidate lines
	87	candidate_lines = 0
	88	# To count total # of previous data candidate lines
	89	candidate_lines_previous = 0
	90	#minimum required number of columns of data
	91	lentoks = 2
	92	for line in lines:
	93	toks = self.splitline(line)
	94	# To remember the # of columns in the current line of data
	95	new_lentoks = len(toks)
	96	try:
	97	if new_lentoks == 1 and not is_data:
	98	## If only one item in list, no longer data
	99	raise ValueError
	100	elif new_lentoks == 0:
	101	## If the line is blank, skip and continue on
	102	## In case of breaks within data sets.
	103	continue
	104	elif new_lentoks != lentoks and is_data:
	105	## If a footer is found, break the loop and save the data
	106	break
	107	elif new_lentoks != lentoks and not is_data:
	108	## If header lines are numerical
	109	candidate_lines = 0
	110	candidate_lines_previous = 0
	111
	112	#Make sure that all columns are numbers.
	113	for colnum in range(len(toks)):
	114	# Any non-floating point values throw ValueError
	115	float(toks[colnum])
	116
	117	candidate_lines += 1
	118	_x = float(toks[0])
	119	_y = float(toks[1])
	120	_dx = None
	121	_dy = None
	122
	123	#If 5 or more lines, this is considering the set data
	124	if candidate_lines >= min_data_pts:
	125	is_data = True
	126
	127	# If a 3rd row is present, consider it dy
	128	if new_lentoks > 2:
	129	_dy = float(toks[2])
[235f514]	130	has_error_dy = False if _dy is None else True
[959eb01]	131
	132	# If a 4th row is present, consider it dx
	133	if new_lentoks > 3:
	134	_dx = float(toks[3])
[235f514]	135	has_error_dx = False if _dx is None else True
[959eb01]	136
	137	# Delete the previously stored lines of data candidates if
	138	# the list is not data
	139	if candidate_lines == 1 and -1 < candidate_lines_previous < min_data_pts and \
	140	is_data == False:
	141	try:
	142	tx = np.zeros(0)
	143	ty = np.zeros(0)
	144	tdy = np.zeros(0)
	145	tdx = np.zeros(0)
	146	except:
	147	pass
	148
	149	if has_error_dy == True:
	150	tdy = np.append(tdy, _dy)
	151	if has_error_dx == True:
	152	tdx = np.append(tdx, _dx)
	153	tx = np.append(tx, _x)
	154	ty = np.append(ty, _y)
	155
	156	#To remember the # of columns on the current line
	157	# for the next line of data
	158	lentoks = new_lentoks
	159	candidate_lines_previous = candidate_lines
	160	except ValueError:
	161	# It is data and meet non - number, then stop reading
	162	if is_data == True:
	163	break
	164	lentoks = 2
	165	has_error_dx = None
	166	has_error_dy = None
	167	#Reset # of lines of data candidates
	168	candidate_lines = 0
	169	except:
	170	pass
	171
	172	input_f.close()
	173	if not is_data:
	174	msg = "ascii_reader: x has no data"
	175	raise RuntimeError, msg
	176	# Sanity check
	177	if has_error_dy == True and not len(ty) == len(tdy):
	178	msg = "ascii_reader: y and dy have different length"
	179	raise RuntimeError, msg
	180	if has_error_dx == True and not len(tx) == len(tdx):
	181	msg = "ascii_reader: y and dy have different length"
	182	raise RuntimeError, msg
	183	# If the data length is zero, consider this as
	184	# though we were not able to read the file.
	185	if len(tx) == 0:
	186	raise RuntimeError, "ascii_reader: could not load file"
	187
	188	#Let's re-order the data to make cal.
	189	# curve look better some cases
	190	ind = np.lexsort((ty, tx))
	191	x = np.zeros(len(tx))
	192	y = np.zeros(len(ty))
	193	dy = np.zeros(len(tdy))
	194	dx = np.zeros(len(tdx))
	195	output = Data1D(x, y, dy=dy, dx=dx)
	196	self.filename = output.filename = basename
	197
	198	for i in ind:
	199	x[i] = tx[ind[i]]
	200	y[i] = ty[ind[i]]
	201	if has_error_dy == True:
	202	dy[i] = tdy[ind[i]]
	203	if has_error_dx == True:
	204	dx[i] = tdx[ind[i]]
	205	# Zeros in dx, dy
	206	if has_error_dx:
	207	dx[dx == 0] = _ZERO
	208	if has_error_dy:
	209	dy[dy == 0] = _ZERO
	210	#Data
	211	output.x = x[x != 0]
	212	output.y = y[x != 0]
	213	output.dy = dy[x != 0] if has_error_dy == True\
	214	else np.zeros(len(output.y))
	215	output.dx = dx[x != 0] if has_error_dx == True\
	216	else np.zeros(len(output.x))
	217
	218	output.xaxis("\\rm{Q}", 'A^{-1}')
	219	output.yaxis("\\rm{Intensity}", "cm^{-1}")
	220
	221	# Store loading process information
	222	output.meta_data['loader'] = self.type_name
	223	if len(output.x) < 1:
	224	raise RuntimeError, "%s is empty" % path
	225	return output
	226
	227	else:
	228	raise RuntimeError, "%s is not a file" % path
	229	return None
	230
	231	def splitline(self, line):
	232	"""
	233	Splits a line into pieces based on common delimeters
	234	:param line: A single line of text
	235	:return: list of values
	236	"""
	237	# Initial try for CSV (split on ,)
	238	toks = line.split(',')
	239	# Now try SCSV (split on ;)
	240	if len(toks) < 2:
	241	toks = line.split(';')
	242	# Now go for whitespace
	243	if len(toks) < 2:
	244	toks = line.split()
[67cc2f7]	245	return toks

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source: sasview/src/sas/sascalc/dataloader/readers/ascii_reader.py @ 25dd9c9

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