Source code for sas.sascalc.dataloader.readers.abs_reader

"""
    IGOR 1D data reader
"""
#####################################################################
# This software was developed by the University of Tennessee as part of the
# Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
# project funded by the US National Science Foundation.
# See the license text in license.txt
# copyright 2008, University of Tennessee
######################################################################

import logging

import numpy as np

from sas.sascalc.data_util.nxsunit import Converter
from ..file_reader_base_class import FileReader
from ..data_info import DataInfo, plottable_1D, Data1D, Detector
from ..loader_exceptions import FileContentsException, DefaultReaderException

logger = logging.getLogger(__name__)


[docs]class Reader(FileReader): """ Class to load IGOR reduced .ABS files """ # File type type_name = "IGOR 1D" # Wildcards type = ["IGOR 1D files (*.abs)|*.abs", "IGOR 1D USANS files (*.cor)|*.cor"] # List of allowed extensions ext = ['.abs', '.cor']
[docs] def get_file_contents(self): """ Get the contents of the file :raise RuntimeError: when the file can't be opened :raise ValueError: when the length of the data vectors are inconsistent """ buff = self.readall() filepath = self.f_open.name lines = buff.splitlines() self.output = [] self.current_datainfo = DataInfo() self.current_datainfo.filename = filepath detector = Detector() data_line = 0 x_index = 4 self.reset_data_list(len(lines)) self.current_datainfo.detector.append(detector) self.current_datainfo.filename = filepath is_info = False is_center = False is_data_started = False base_q_unit = '1/A' base_i_unit = '1/cm' data_conv_q = Converter(base_q_unit) data_conv_i = Converter(base_i_unit) for line in lines: # Information line 1 if line.find(".bt5") > 0: x_index = 0 if is_info: is_info = False line_toks = line.split() # Wavelength in Angstrom try: value = float(line_toks[1]) if self.current_datainfo.source.wavelength_unit != 'A': conv = Converter('A') self.current_datainfo.source.wavelength = conv(value, units=self.current_datainfo.source.wavelength_unit) else: self.current_datainfo.source.wavelength = value except KeyError: msg = "ABSReader cannot read wavelength from %s" % filepath self.current_datainfo.errors.append(msg) # Detector distance in meters try: value = float(line_toks[3]) if detector.distance_unit != 'm': conv = Converter('m') detector.distance = conv(value, units=detector.distance_unit) else: detector.distance = value except Exception: msg = "ABSReader cannot read SDD from %s" % filepath self.current_datainfo.errors.append(msg) # Transmission try: self.current_datainfo.sample.transmission = \ float(line_toks[4]) except ValueError: # Transmission isn't always in the header pass # Sample thickness in mm try: # ABS writer adds 'C' with no space to the end of the # thickness column. Remove it if it is there before # converting the thickness. if line_toks[5][-1] not in '012345679.': value = float(line_toks[5][:-1]) else: value = float(line_toks[5]) if self.current_datainfo.sample.thickness_unit != 'cm': conv = Converter('cm') self.current_datainfo.sample.thickness = conv(value, units=self.current_datainfo.sample.thickness_unit) else: self.current_datainfo.sample.thickness = value except ValueError: # Thickness is not a mandatory entry pass # MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP if line.count("LAMBDA") > 0: is_info = True # Find center info line if is_center: is_center = False line_toks = line.split() # Center in bin number center_x = float(line_toks[0]) center_y = float(line_toks[1]) # Bin size if detector.pixel_size_unit != 'mm': conv = Converter('mm') detector.pixel_size.x = conv(5.08, units=detector.pixel_size_unit) detector.pixel_size.y = conv(5.08, units=detector.pixel_size_unit) else: detector.pixel_size.x = 5.08 detector.pixel_size.y = 5.08 # Store beam center in distance units # Det 640 x 640 mm if detector.beam_center_unit != 'mm': conv = Converter('mm') detector.beam_center.x = conv(center_x * 5.08, units=detector.beam_center_unit) detector.beam_center.y = conv(center_y * 5.08, units=detector.beam_center_unit) else: detector.beam_center.x = center_x * 5.08 detector.beam_center.y = center_y * 5.08 # Detector type try: detector.name = line_toks[7] except: # Detector name is not a mandatory entry pass # BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP if line.count("BCENT") > 0: is_center = True # Parse the data if is_data_started: toks = line.split() try: _x = float(toks[x_index]) _y = float(toks[1]) _dy = float(toks[2]) _dx = float(toks[3]) if data_conv_q is not None: _x = data_conv_q(_x, units=base_q_unit) _dx = data_conv_q(_dx, units=base_q_unit) if data_conv_i is not None: _y = data_conv_i(_y, units=base_i_unit) _dy = data_conv_i(_dy, units=base_i_unit) self.current_dataset.x[data_line] = _x self.current_dataset.y[data_line] = _y self.current_dataset.dy[data_line] = _dy if _dx > 0: self.current_dataset.dx[data_line] = _dx else: if data_line == 0: self.current_dataset.dx = None self.current_dataset.dxl = np.zeros(len(lines)) self.current_dataset.dxw = np.zeros(len(lines)) self.current_dataset.dxl[data_line] = abs(_dx) self.current_dataset.dxw[data_line] = 0 data_line += 1 except ValueError: # Could not read this data line. If we are here # it is because we are in the data section. Just # skip it. pass # SANS Data: # The 6 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. # I(Q) (1/cm) | sigmaQ | meanQ | ShadowFactor| # USANS Data: # EMP LEVEL: <value> ; BKG LEVEL: <value> if line.startswith("The 6 columns") or line.startswith("EMP LEVEL"): is_data_started = True self.remove_empty_q_values() # Sanity check if not len(self.current_dataset.y) == len(self.current_dataset.dy): self.set_all_to_none() msg = "abs_reader: y and dy have different length" raise ValueError(msg) # If the data length is zero, consider this as # though we were not able to read the file. if len(self.current_dataset.x) == 0: self.set_all_to_none() raise ValueError("ascii_reader: could not load file") self.current_dataset = self.set_default_1d_units(self.current_dataset) if data_conv_q is not None: self.current_dataset.xaxis("\\rm{Q}", base_q_unit) if data_conv_i is not None: self.current_dataset.yaxis("\\rm{Intensity}", base_i_unit) # Store loading process information self.current_datainfo.meta_data['loader'] = self.type_name self.send_to_output()