#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: FreeSAS
# https://github.com/kif/freesas
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
"""
Contains helper functions for loading SAS data from differents sources.
"""
__authors__ = ["Martha Brennich"]
__contact__ = "martha.brennich@googlemail.com"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "25/07/2020"
__status__ = "development"
__docformat__ = "restructuredtext"
from typing import List, Union
from os import PathLike
from numpy import loadtxt, array, ndarray
PathType = Union[PathLike, str, bytes]
[docs]def load_scattering_data(filename: PathType) -> ndarray:
"""
Load scattering data q, I, err into a numpy array.
:param filename: ASCII file, 3 column (q,I,err)
:return: numpy array with 3 column (q,I,err)
"""
try:
data = loadtxt(filename)
except OSError:
raise OSError("File could not be read.")
except ValueError:
try:
with open(filename) as data_file:
text = data_file.readlines()
except OSError:
raise OSError("File could not be read.")
else:
try:
data = parse_ascii_data(text, number_of_columns=3)
except ValueError:
raise ValueError(
"File does not seem to be " "in the format q, I, err. "
)
return data
[docs]def parse_ascii_data(
input_file_text: List[str], number_of_columns: int
) -> ndarray:
"""
Parse data from an ascii file into an N column numpy array
:param input_file_text: List containing one line of input data per element
:param number_of_columns: Expected number of lines in the data file
:return: numpy array with 3 column (q,I,err)
"""
data = []
for line in input_file_text:
split = line.split()
if len(split) == number_of_columns:
try:
data.append([float(x) for x in split])
except ValueError as err:
if "could not convert string to float" in err.args[0]:
pass
else:
raise
if data == []:
raise ValueError
return array(data)
[docs]def convert_inverse_angstrom_to_nanometer(
data_in_inverse_angstrom: ndarray,
) -> ndarray:
"""
Convert data with q in 1/Å to 1/nm.
:param data_in_inverse_angstrom: numpy array in format
(q_in_inverse_Angstrom,I,err)
:return: numpy array with 3 column (q_in_inverse_nm,I,err)
"""
q_in_angstrom, intensity, err = data_in_inverse_angstrom.T
return array([q_in_angstrom * 10.0, intensity, err]).T