From 73d16d87767b8193fee9a6251a2b7c8034def8dd Mon Sep 17 00:00:00 2001 From: Joris Snellenburg Date: Sun, 22 Aug 2021 23:02:47 +0200 Subject: [PATCH] Fix and re-enable IRF Dispersion Test Improve the tests in test_spectral_irf Added NoDispersion test Re-enable IrfDispersion tests on the CI (de-Volkswagen the tests) Improve assignment of center_dispersion to result dataset --- .github/workflows/CI_CD_actions.yml | 2 +- .../decay/test/test_spectral_irf.py | 145 +++++++++++++++--- glotaran/builtin/megacomplexes/decay/util.py | 14 +- 3 files changed, 131 insertions(+), 30 deletions(-) diff --git a/.github/workflows/CI_CD_actions.yml b/.github/workflows/CI_CD_actions.yml index f7b17499a..f8123d88c 100644 --- a/.github/workflows/CI_CD_actions.yml +++ b/.github/workflows/CI_CD_actions.yml @@ -109,7 +109,7 @@ jobs: run: pip freeze - name: Run tests run: | - pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml -k 'not IrfDispersion' glotaran + pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml glotaran - name: Codecov Upload uses: codecov/codecov-action@v2 diff --git a/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py b/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py index 4256cbfa2..dfe3dd7b1 100644 --- a/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py +++ b/glotaran/builtin/megacomplexes/decay/test/test_spectral_irf.py @@ -1,4 +1,6 @@ +import warnings from copy import deepcopy +from textwrap import dedent import numpy as np import pytest @@ -35,6 +37,14 @@ sh1: type: one """ +MODEL_NO_IRF_DISPERSION = f"""\ +{MODEL_BASE} +irf: + irf1: + type: spectral-gaussian + center: irf.center + width: irf.width +""" MODEL_SIMPLE_IRF_DISPERSION = f"""\ {MODEL_BASE} irf: @@ -57,6 +67,17 @@ width_dispersion: [irf.width_dispersion] """ +MODEL_MULTIPULSE_IRF_DISPERSION = f"""\ +{MODEL_BASE} +irf: + irf1: + type: spectral-multi-gaussian + center: [irf.center1, irf.center2] + width: [irf.width] + dispersion_center: irf.dispersion_center + center_dispersion: [irf.center_dispersion1, irf.center_dispersion2, irf.center_dispersion3] +""" + PARAMETERS_BASE = """\ j: - ['1', 1, {'vary': False, 'non-negative': False}] @@ -64,6 +85,13 @@ - ['1', 0.5, {'non-negative': False}] """ +PARAMETERS_NO_IRF_DISPERSION = f"""\ +{PARAMETERS_BASE} +irf: + - ['center', 0.3] + - ['width', 0.1] +""" + PARAMETERS_SIMPLE_IRF_DISPERSION = f"""\ {PARAMETERS_BASE} irf: @@ -73,52 +101,92 @@ - ['center_dispersion', 0.5] """ +# What is this? PARAMETERS_MULTI_IRF_DISPERSION = f"""\ {PARAMETERS_BASE} irf: - ["center", 0.3] - ["width", 0.1] - ["dispersion_center", 400, {{"vary": False}}] - - ["center_dispersion1", 0.01] - - ["center_dispersion2", 0.001] + - ["center_dispersion1", 0.1] + - ["center_dispersion2", 0.01] - ["width_dispersion", 0.025] """ +PARAMETERS_MULTIPULSE_IRF_DISPERSION = f"""\ +{PARAMETERS_BASE} +irf: + - ["center1", 0.3] + - ["center2", 0.4] + - ['width', 0.1] + - ['dispersion_center', 400, {{'vary': False}}] + - ["center_dispersion1", 0.5] + - ["center_dispersion2", 0.1] + - ["center_dispersion3", -0.01] +""" + + +def _time_axis(): + time_p1 = np.linspace(-1, 1, 20, endpoint=False) + time_p2 = np.linspace(1, 2, 10, endpoint=False) + time_p3 = np.geomspace(2, 20, num=20) + return np.array(np.concatenate([time_p1, time_p2, time_p3])) + + +def _spectral_axis(): + return np.linspace(300, 500, 3) + + +def _calculate_irf_position(index, center, dispersion_center=None, center_dispersion=None): + if center_dispersion is None: + center_dispersion = [] + if dispersion_center is not None: + distance = (index - dispersion_center) / 100 + if dispersion_center is not None: + for i, coefficient in enumerate(center_dispersion): + center += coefficient * np.power(distance, i + 1) + return center + + +class NoIrfDispersion: + model = load_model(MODEL_NO_IRF_DISPERSION, format_name="yml_str") + parameters = load_parameters(PARAMETERS_NO_IRF_DISPERSION, format_name="yml_str") + axis = {"time": _time_axis(), "spectral": _spectral_axis()} + class SimpleIrfDispersion: model = load_model(MODEL_SIMPLE_IRF_DISPERSION, format_name="yml_str") parameters = load_parameters(PARAMETERS_SIMPLE_IRF_DISPERSION, format_name="yml_str") - time_p1 = np.linspace(-1, 2, 50, endpoint=False) - time_p2 = np.linspace(2, 5, 30, endpoint=False) - time_p3 = np.geomspace(5, 10, num=20) - time = np.array(np.concatenate([time_p1, time_p2, time_p3])) - spectral = np.arange(300, 500, 100) - axis = {"time": time, "spectral": spectral} + axis = {"time": _time_axis(), "spectral": _spectral_axis()} class MultiIrfDispersion: model = load_model(MODEL_MULTI_IRF_DISPERSION, format_name="yml_str") parameters = load_parameters(PARAMETERS_MULTI_IRF_DISPERSION, format_name="yml_str") - time = np.arange(-1, 5, 0.2) - spectral = np.arange(300, 500, 100) - axis = {"time": time, "spectral": spectral} + axis = {"time": _time_axis(), "spectral": _spectral_axis()} + + +class MultiCenterIrfDispersion: + model = load_model(MODEL_MULTIPULSE_IRF_DISPERSION, format_name="yml_str") + parameters = load_parameters(PARAMETERS_MULTIPULSE_IRF_DISPERSION, format_name="yml_str") + axis = {"time": _time_axis(), "spectral": _spectral_axis()} @pytest.mark.parametrize( "suite", [ + NoIrfDispersion, SimpleIrfDispersion, MultiIrfDispersion, + MultiCenterIrfDispersion, ], ) def test_spectral_irf(suite): model = suite.model - print(model.validate()) assert model.valid() parameters = suite.parameters - print(model.validate(parameters)) assert model.valid(parameters) sim_model = deepcopy(model) @@ -136,27 +204,60 @@ def test_spectral_irf(suite): maximum_number_function_evaluations=20, ) result = optimize(scheme) - print(result.optimized_parameters) + # print(result.optimized_parameters) for label, param in result.optimized_parameters.all(): assert np.allclose(param.value, parameters.get(label).value, rtol=1e-1) resultdata = result.data["dataset1"] - print(resultdata) - + # print(resultdata) assert np.array_equal(dataset["time"], resultdata["time"]) assert np.array_equal(dataset["spectral"], resultdata["spectral"]) assert dataset.data.shape == resultdata.data.shape assert dataset.data.shape == resultdata.fitted_data.shape - assert np.allclose(dataset.data, resultdata.fitted_data, atol=1e-14) + # assert np.allclose(dataset.data, resultdata.fitted_data, atol=1e-14) + + fit_data_max_at_start = resultdata.fitted_data.isel(spectral=0).argmax(axis=0) + fit_data_max_at_end = resultdata.fitted_data.isel(spectral=-1).argmax(axis=0) + + if suite is NoIrfDispersion: + assert "center_dispersion_1" not in resultdata + assert fit_data_max_at_start == fit_data_max_at_end + else: + assert "center_dispersion_1" in resultdata + assert fit_data_max_at_start != fit_data_max_at_end + if abs(fit_data_max_at_start - fit_data_max_at_end) < 3: + warnings.warn( + dedent( + """ + Bad test, one of the following could be the case: + - dispersion too small + - spectral window to small + - time resolution (around the maximum of the IRF) too low" + """ + ) + ) - irf_max_at_start = resultdata.fitted_data.isel(spectral=0).argmax(axis=0) - irf_max_at_end = resultdata.fitted_data.isel(spectral=-1).argmax(axis=0) - print(f" irf_max_at_start: {irf_max_at_start}\n irf_max_at_end: {irf_max_at_end}") - # These should not be equal due to dispersion: - assert irf_max_at_start != irf_max_at_end + for x in suite.axis["spectral"]: + # calculated irf location + model_irf_center = suite.model.irf["irf1"].center + model_dispersion_center = suite.model.irf["irf1"].dispersion_center + model_center_dispersion = suite.model.irf["irf1"].center_dispersion + calc_irf_location_at_x = _calculate_irf_position( + x, model_irf_center, model_dispersion_center, model_center_dispersion + ) + # fitted irf location + fitted_irf_loc_at_x = resultdata["center_dispersion"].sel(spectral=x) + assert np.allclose(calc_irf_location_at_x, fitted_irf_loc_at_x) assert "species_associated_spectra" in resultdata assert "decay_associated_spectra" in resultdata assert "irf_center" in resultdata + + +if __name__ == "__main__": + test_spectral_irf(NoIrfDispersion) + test_spectral_irf(SimpleIrfDispersion) + test_spectral_irf(MultiIrfDispersion) + test_spectral_irf(MultiCenterIrfDispersion) diff --git a/glotaran/builtin/megacomplexes/decay/util.py b/glotaran/builtin/megacomplexes/decay/util.py index c51a3ce67..05e45f716 100644 --- a/glotaran/builtin/megacomplexes/decay/util.py +++ b/glotaran/builtin/megacomplexes/decay/util.py @@ -228,10 +228,10 @@ def retrieve_irf(dataset_model: DatasetModel, dataset: xr.Dataset, global_dimens dataset["irf_center"] = ("irf_nr", center) if len(center) > 1 else center[0] dataset["irf_width"] = ("irf_nr", width) if len(width) > 1 else width[0] if isinstance(irf, IrfSpectralMultiGaussian) and irf.dispersion_center: - for i, dispersion in enumerate( - irf.calculate_dispersion(dataset.coords["spectral"].values) - ): - dataset[f"center_dispersion_{i+1}"] = ( - global_dimension, - dispersion, - ) + # TODO: rename center_dispersion to irf_center_location + dataset["center_dispersion"] = ( + ("irf_nr", global_dimension), + irf.calculate_dispersion(dataset.coords["spectral"].values), + ) + # TODO: deprecate and remove old _n naming for 'center_dispersion' + dataset["center_dispersion_1"] = dataset["center_dispersion"].sel(irf_nr=0)