Added function for general tissue definition from optical parameters …

simpa/utils/libraries/tissue_library.py

@@ -1,10 +1,13 @@
 # SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
+import typing
 
 from simpa.utils import OpticalTissueProperties, SegmentationClasses, StandardProperties, MolecularCompositionGenerator
 from simpa.utils import Molecule
 from simpa.utils import MOLECULE_LIBRARY
+from simpa.utils import Spectrum
+from simpa.utils.libraries.molecule_library import MolecularComposition
 from simpa.utils.libraries.spectrum_library import AnisotropySpectrumLibrary, ScatteringSpectrumLibrary
 from simpa.utils.calculate import randomize_uniform
 from simpa.utils.libraries.spectrum_library import AbsorptionSpectrumLibrary
@@ -21,17 +24,46 @@ def get_blood_volume_fractions(self, total_blood_volume_fraction=1e-10, oxygenat
         """
         return [total_blood_volume_fraction*oxygenation, total_blood_volume_fraction*(1-oxygenation)]
 
-    def constant(self, mua=1e-10, mus=1e-10, g=1e-10):
+    def constant(self, mua: float = 1e-10, mus: float = 1e-10, g: float = 1e-10) -> MolecularComposition:
         """
-        TODO
+        Returns a generic issue defined by the provided constant optical parameters.
+
+        :param mua: The absorption coefficient in cm^{-1}.
+        :param mus: The scattering coefficient in cm^{-1}.
+        :param g: The anisotropy.
+
+        :returns: The molecular composition of the tissue.
+        """
+        mua_as_spectrum = AbsorptionSpectrumLibrary().CONSTANT_ABSORBER_ARBITRARY(mua)
+        mus_as_spectrum = ScatteringSpectrumLibrary.CONSTANT_SCATTERING_ARBITRARY(mus)
+        g_as_spectrum = AnisotropySpectrumLibrary.CONSTANT_ANISOTROPY_ARBITRARY(g)
+        return self.generic_tissue(mua_as_spectrum, mus_as_spectrum, g_as_spectrum, "constant_mua_mus_g")
+
+    def generic_tissue(self,
+                       mua: Spectrum = AbsorptionSpectrumLibrary().CONSTANT_ABSORBER_ARBITRARY(1e-10),
+                       mus: Spectrum = AbsorptionSpectrumLibrary().CONSTANT_ABSORBER_ARBITRARY(1e-10),
+                       g: Spectrum = AbsorptionSpectrumLibrary().CONSTANT_ABSORBER_ARBITRARY(1e-10),
+                       molecule_name: typing.Optional[str] = "generic_tissue") -> MolecularComposition:
         """
-        return (MolecularCompositionGenerator().append(Molecule(name="constant_mua_mus_g",
-                                                                absorption_spectrum=AbsorptionSpectrumLibrary().CONSTANT_ABSORBER_ARBITRARY(mua),
+        Returns a generic issue defined by the provided optical parameters.
+
+        :param mua: The absorption coefficient spectrum in cm^{-1}.
+        :param mus: The scattering coefficient spectrum in cm^{-1}.
+        :param g: The anisotropy spectrum.
+        :param molecule_name: The molecule name.
+
+        :returns: The molecular composition of the tissue.
+        """
+        assert isinstance(mua, Spectrum), type(mua)
+        assert isinstance(mus, Spectrum), type(mus)
+        assert isinstance(g, Spectrum), type(g)
+        assert isinstance(molecule_name, str) or molecule_name is None, type(molecule_name)
+
+        return (MolecularCompositionGenerator().append(Molecule(name=molecule_name,
+                                                                absorption_spectrum=mua,
                                                                 volume_fraction=1.0,
-                                                                scattering_spectrum=ScatteringSpectrumLibrary.
-                                                                CONSTANT_SCATTERING_ARBITRARY(mus),
-                                                                anisotropy_spectrum=AnisotropySpectrumLibrary.
-                                                                CONSTANT_ANISOTROPY_ARBITRARY(g)))
+                                                                scattering_spectrum=mus,
+                                                                anisotropy_spectrum=g))
                 .get_molecular_composition(SegmentationClasses.GENERIC))
 
     def muscle(self, background_oxy=None, blood_volume_fraction=None):

simpa_tests/automatic_tests/tissue_library/test_tissue_library.py

@@ -0,0 +1,80 @@
+# SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
+# SPDX-FileCopyrightText: 2021 Janek Groehl
+# SPDX-License-Identifier: MIT
+
+import numpy as np
+import pytest
+
+from simpa import Spectrum, SegmentationClasses, TISSUE_LIBRARY, Molecule
+
+
+def test_if_optical_parameter_spectra_are_provided_correct_tissue_definition_is_returned_from_generic_tissue():
+    wavelengths_sample = np.arange(400, 800, 25)
+    mua_sample = np.linspace(1e-6, 1e-5, wavelengths_sample.shape[0])
+    mus_sample = np.linspace(1e-5, 5e-6, wavelengths_sample.shape[0])
+    g_sample = np.linspace(0.8, 0.9, wavelengths_sample.shape[0])
+
+    mua_spectrum = Spectrum("Mua", wavelengths_sample, mua_sample)
+    mus_spectrum = Spectrum("Mus", wavelengths_sample, mus_sample)
+    g_spectrum = Spectrum("g", wavelengths_sample, g_sample)
+
+    actual_tissue = TISSUE_LIBRARY.generic_tissue(mua_spectrum, mus_spectrum, g_spectrum)
+    assert actual_tissue.segmentation_type == SegmentationClasses.GENERIC
+
+    assert len(actual_tissue) == 1
+    molecule: Molecule = actual_tissue[0]
+    assert molecule.volume_fraction == 1.0
+    assert molecule.spectrum == mua_spectrum
+    assert molecule.scattering_spectrum == mus_spectrum
+    assert molecule.anisotropy_spectrum == g_spectrum
+
+
+def test_if_generic_tissue_is_called_with_invalid_arguments_error_is_raised():
+    wavelengths_sample = np.arange(400, 800, 25)
+    mua_sample = np.linspace(1e-6, 1e-5, wavelengths_sample.shape[0])
+    mus_sample = np.linspace(1e-5, 5e-6, wavelengths_sample.shape[0])
+    g_sample = np.linspace(0.8, 0.9, wavelengths_sample.shape[0])
+
+    mua_spectrum = Spectrum("Mua", wavelengths_sample, mua_sample)
+    mus_spectrum = Spectrum("Mus", wavelengths_sample, mus_sample)
+    g_spectrum = Spectrum("g", wavelengths_sample, g_sample)
+
+    with pytest.raises(AssertionError):
+        TISSUE_LIBRARY.generic_tissue(None, mus_spectrum, g_spectrum)
+
+    with pytest.raises(AssertionError):
+        TISSUE_LIBRARY.generic_tissue(mua_spectrum, None, g_spectrum)
+
+    with pytest.raises(AssertionError):
+        TISSUE_LIBRARY.generic_tissue(mua_spectrum, mus_spectrum, None)
+
+
+def test_if_optical_parameter_spectra_are_provided_correct_tissue_definition_is_returned_from_constant():
+    mua_sample = 1e-5
+    mus_sample = 3e-6
+    g_sample = 0.85
+
+    actual_tissue = TISSUE_LIBRARY.constant(mua_sample, mus_sample, g_sample)
+    assert actual_tissue.segmentation_type == SegmentationClasses.GENERIC
+
+    assert len(actual_tissue) == 1
+    molecule: Molecule = actual_tissue[0]
+    assert molecule.volume_fraction == 1.0
+    assert (molecule.spectrum.values == mua_sample).all()
+    assert (molecule.scattering_spectrum.values == mus_sample).all()
+    assert (molecule.anisotropy_spectrum.values == g_sample).all()
+
+
+def test_if_constant_is_called_with_invalid_arguments_error_is_raised():
+    mua_sample = 1e-5
+    mus_sample = 3e-6
+    g_sample = 0.85
+
+    with pytest.raises(TypeError):
+        TISSUE_LIBRARY.constant(None, mus_sample, g_sample)
+
+    with pytest.raises(TypeError):
+        TISSUE_LIBRARY.constant(mua_sample, None, g_sample)
+
+    with pytest.raises(TypeError):
+        TISSUE_LIBRARY.constant(mua_sample, mus_sample, None)