abs_reader.py @ c3eb858

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since c3eb858 was 1efbc190, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
fix merge errors
Property mode set to `100644`
File size: 8.6 KB

Rev	Line
[959eb01]	1	"""
[ad92c5a]	2	IGOR 1D data reader
[959eb01]	3	"""
	4	#####################################################################
[ad92c5a]	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	# See the license text in license.txt
	9	# copyright 2008, University of Tennessee
[959eb01]	10	######################################################################
	11
[ad92c5a]	12	import logging
[46cf4c9]	13
[959eb01]	14	import numpy as np
[46cf4c9]	15
	16	from sas.sascalc.data_util.nxsunit import Converter
	17	from ..file_reader_base_class import FileReader
	18	from ..data_info import DataInfo, plottable_1D, Data1D, Detector
	19	from ..loader_exceptions import FileContentsException, DefaultReaderException
[ad92c5a]	20
	21	logger = logging.getLogger(__name__)
	22
	23
	24	class Reader(FileReader):
[959eb01]	25	"""
	26	Class to load IGOR reduced .ABS files
	27	"""
[ad92c5a]	28	# File type
[959eb01]	29	type_name = "IGOR 1D"
[ad92c5a]	30	# Wildcards
[959eb01]	31	type = ["IGOR 1D files (.abs)\|.abs"]
[ad92c5a]	32	# List of allowed extensions
	33	ext = ['.abs']
[574adc7]	34
[ad92c5a]	35	def get_file_contents(self):
[574adc7]	36	"""
[ad92c5a]	37	Get the contents of the file
[574adc7]	38
[959eb01]	39	:raise RuntimeError: when the file can't be opened
	40	:raise ValueError: when the length of the data vectors are inconsistent
	41	"""
[46cf4c9]	42	buff = self.readall()
[ad92c5a]	43	filepath = self.f_open.name
	44	lines = buff.splitlines()
	45	self.output = []
	46	self.current_datainfo = DataInfo()
	47	self.current_datainfo.filename = filepath
	48	self.reset_data_list(len(lines))
	49	detector = Detector()
	50	data_line = 0
	51	self.reset_data_list(len(lines))
	52	self.current_datainfo.detector.append(detector)
	53	self.current_datainfo.filename = filepath
	54
	55	is_info = False
	56	is_center = False
	57	is_data_started = False
	58
	59	base_q_unit = '1/A'
	60	base_i_unit = '1/cm'
	61	data_conv_q = Converter(base_q_unit)
	62	data_conv_i = Converter(base_i_unit)
	63
	64	for line in lines:
	65	# Information line 1
	66	if is_info:
	67	is_info = False
	68	line_toks = line.split()
	69
	70	# Wavelength in Angstrom
[959eb01]	71	try:
[ad92c5a]	72	value = float(line_toks[1])
[46cf4c9]	73	if self.current_datainfo.source.wavelength_unit != 'A':
[ad92c5a]	74	conv = Converter('A')
	75	self.current_datainfo.source.wavelength = conv(value,
	76	units=self.current_datainfo.source.wavelength_unit)
	77	else:
	78	self.current_datainfo.source.wavelength = value
	79	except KeyError:
	80	msg = "ABSReader cannot read wavelength from %s" % filepath
	81	self.current_datainfo.errors.append(msg)
	82
	83	# Detector distance in meters
	84	try:
	85	value = float(line_toks[3])
[46cf4c9]	86	if detector.distance_unit != 'm':
[ad92c5a]	87	conv = Converter('m')
	88	detector.distance = conv(value,
	89	units=detector.distance_unit)
	90	else:
	91	detector.distance = value
[46cf4c9]	92	except Exception:
[ad92c5a]	93	msg = "ABSReader cannot read SDD from %s" % filepath
	94	self.current_datainfo.errors.append(msg)
	95
	96	# Transmission
	97	try:
	98	self.current_datainfo.sample.transmission = \
	99	float(line_toks[4])
	100	except ValueError:
	101	# Transmission isn't always in the header
	102	pass
	103
	104	# Sample thickness in mm
	105	try:
[9e6aeaf]	106	# ABS writer adds 'C' with no space to the end of the
	107	# thickness column. Remove it if it is there before
	108	# converting the thickness.
[1efbc190]	109	if line_toks[5][-1] not in '012345679.':
[9e6aeaf]	110	value = float(line_toks[5][:-1])
	111	else:
	112	value = float(line_toks[5])
[46cf4c9]	113	if self.current_datainfo.sample.thickness_unit != 'cm':
[ad92c5a]	114	conv = Converter('cm')
	115	self.current_datainfo.sample.thickness = conv(value,
	116	units=self.current_datainfo.sample.thickness_unit)
	117	else:
	118	self.current_datainfo.sample.thickness = value
	119	except ValueError:
	120	# Thickness is not a mandatory entry
	121	pass
	122
	123	# MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP
	124	if line.count("LAMBDA") > 0:
	125	is_info = True
	126
	127	# Find center info line
	128	if is_center:
[959eb01]	129	is_center = False
[ad92c5a]	130	line_toks = line.split()
	131	# Center in bin number
	132	center_x = float(line_toks[0])
	133	center_y = float(line_toks[1])
	134
	135	# Bin size
[46cf4c9]	136	if detector.pixel_size_unit != 'mm':
[ad92c5a]	137	conv = Converter('mm')
	138	detector.pixel_size.x = conv(5.08,
	139	units=detector.pixel_size_unit)
	140	detector.pixel_size.y = conv(5.08,
	141	units=detector.pixel_size_unit)
[959eb01]	142	else:
[ad92c5a]	143	detector.pixel_size.x = 5.08
	144	detector.pixel_size.y = 5.08
	145
	146	# Store beam center in distance units
	147	# Det 640 x 640 mm
[46cf4c9]	148	if detector.beam_center_unit != 'mm':
[ad92c5a]	149	conv = Converter('mm')
	150	detector.beam_center.x = conv(center_x * 5.08,
	151	units=detector.beam_center_unit)
	152	detector.beam_center.y = conv(center_y * 5.08,
[46cf4c9]	153	units=detector.beam_center_unit)
[959eb01]	154	else:
[ad92c5a]	155	detector.beam_center.x = center_x * 5.08
	156	detector.beam_center.y = center_y * 5.08
	157
	158	# Detector type
	159	try:
	160	detector.name = line_toks[7]
	161	except:
	162	# Detector name is not a mandatory entry
	163	pass
	164
	165	# BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP
	166	if line.count("BCENT") > 0:
	167	is_center = True
	168
	169	# Parse the data
	170	if is_data_started:
	171	toks = line.split()
	172
	173	try:
	174	_x = float(toks[0])
	175	_y = float(toks[1])
	176	_dy = float(toks[2])
	177	_dx = float(toks[3])
	178
	179	if data_conv_q is not None:
	180	_x = data_conv_q(_x, units=base_q_unit)
	181	_dx = data_conv_q(_dx, units=base_q_unit)
	182
	183	if data_conv_i is not None:
	184	_y = data_conv_i(_y, units=base_i_unit)
	185	_dy = data_conv_i(_dy, units=base_i_unit)
	186
	187	self.current_dataset.x[data_line] = _x
	188	self.current_dataset.y[data_line] = _y
	189	self.current_dataset.dy[data_line] = _dy
	190	self.current_dataset.dx[data_line] = _dx
	191	data_line += 1
	192
	193	except ValueError:
	194	# Could not read this data line. If we are here
	195	# it is because we are in the data section. Just
	196	# skip it.
	197	pass
	198
	199	# The 6 columns are \| Q (1/A) \| I(Q) (1/cm) \| std. dev.
	200	# I(Q) (1/cm) \| sigmaQ \| meanQ \| ShadowFactor\|
	201	if line.count("The 6 columns") > 0:
	202	is_data_started = True
	203
[7b07fbe]	204	self.remove_empty_q_values()
[ad92c5a]	205
	206	# Sanity check
	207	if not len(self.current_dataset.y) == len(self.current_dataset.dy):
	208	self.set_all_to_none()
	209	msg = "abs_reader: y and dy have different length"
	210	raise ValueError(msg)
	211	# If the data length is zero, consider this as
	212	# though we were not able to read the file.
	213	if len(self.current_dataset.x) == 0:
	214	self.set_all_to_none()
	215	raise ValueError("ascii_reader: could not load file")
	216
	217	if data_conv_q is not None:
	218	self.current_dataset.xaxis("\\rm{Q}", base_q_unit)
[959eb01]	219	else:
[ad92c5a]	220	self.current_dataset.xaxis("\\rm{Q}", 'A^{-1}')
	221	if data_conv_i is not None:
	222	self.current_dataset.yaxis("\\rm{Intensity}", base_i_unit)
	223	else:
	224	self.current_dataset.yaxis("\\rm{Intensity}", "cm^{-1}")
	225
	226	# Store loading process information
	227	self.current_datainfo.meta_data['loader'] = self.type_name
	228	self.send_to_output()

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source: sasview/src/sas/sascalc/dataloader/readers/abs_reader.py @ c3eb858

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