diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 1f811a3..0000000 --- a/.gitignore +++ /dev/null @@ -1,10 +0,0 @@ -__pycache__ -.backups -optifik.egg-info -*.bak -*.pyc -.ipynb_checkpoints -.venv -build/ -_build/ -dist/ diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index 65b2eeb..0000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,4 +0,0 @@ - -# x.x.x - -First version diff --git a/README.md b/README.md index b07face..be6680a 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ # Optifik -TODO: write a paragraph here... - This library replaces oospectro. @@ -50,7 +48,3 @@ cd docs make html ``` -## Licence - -The source code is released under the GNU General Public License v3.0. -See LICENSE for details. diff --git a/pyproject.toml b/pyproject.toml index e53c231..d05cb02 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = [ { name = "François Boulogne", email = "francois.boulogne@cnrs.fr" }, { name = "Victor Ziapkoff", email = "victor.ziapkoff@universite-paris-saclay.fr" }, ] -license = "GPL-3.0" +license = "GPL-3.0-or-later" readme = "README.md" requires-python = ">=3.13" dependencies = [ diff --git a/tests/test_thickness.py b/tests/test_thickness.py deleted file mode 100644 index 068b7ed..0000000 --- a/tests/test_thickness.py +++ /dev/null @@ -1,67 +0,0 @@ -import pytest -import yaml -from pathlib import Path -import os.path - -import numpy as np -from numpy.testing import assert_allclose -from numpy.testing import assert_almost_equal - -from optifik.minmax import thickness_from_minmax -from optifik.analysis import smooth_intensities -from optifik.io import load_spectrum - - -def load(): - test_data_dir = Path(__file__).parent.parent / 'data' - FOLDER = test_data_dir / 'spectraLorene' / 'sample1' - - yaml_file = os.path.join(FOLDER, 'sample1.yaml') - with open(yaml_file, "r") as yaml_file: - thickness_dict = yaml.safe_load(yaml_file) - #print(thickness_dict) - data = [(os.path.join(FOLDER, fn), val) for fn, val in thickness_dict['known_thicknesses'].items()] - return data - - -def test_minmax_sample1(): - min_peak_prominence = 0.02 - min_peak_distance = 10 - skipped = ('011137.xy', - '012426.xy', - '012795.xy', - '012979.xy', - '011321.xy', #Insufficient number of data points - ) - - for path, expected in load(): - file = os.path.split(path)[-1] - if file not in skipped: - lambdas, raw_intensities = load_spectrum(path, wavelength_min=450) - smoothed_intensities = smooth_intensities(raw_intensities) - r_index = 1.33 #TODO - - prominence = 0.02 - distance = 10 - - result = thickness_from_minmax(lambdas, - smoothed_intensities, - refractive_index=r_index, - min_peak_prominence=prominence, - min_peak_distance=distance, - method='ransac', - plot=False) - - assert_allclose(result.thickness, expected, rtol=2.3e-1) - -#def test_fft_sample1(): -# for name, value in known_values.sample1['known_thicknesses'].items(): -# index = known_values.sample1['refractive_index'] -# # this method works only for large thicknesses -# if value < 3000: -# continue -# path = os.path.join('spectra', name) -# lambdas, intensities = io.load_spectrum(path, lambda_min=450) -# result = thickness_from_fft(lambdas, intensities, refractive_index=index,) -# error = 100 * np.abs(result.thickness - value) / value -# assert(error < 5)