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T172 tissue and molecular library inconsistency #398

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T172 tissue and molecular library inconsistency #398

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c3d35af
make use of static functions in MoleculeLibrary class instead of glob…
LeonieBoland Nov 15, 2024
b650d76
change class TissueLibrary functions to static function and removed g…
LeonieBoland Nov 15, 2024
9083f78
removed comment
LeonieBoland Nov 15, 2024
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8 changes: 4 additions & 4 deletions simpa/core/device_digital_twins/pa_devices/ithera_msot_acuity.py
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Expand Up @@ -11,7 +11,7 @@
from simpa.core.device_digital_twins.detection_geometries.curved_array import CurvedArrayDetectionGeometry
from simpa.utils.settings import Settings
from simpa.utils import Tags
from simpa.utils.libraries.tissue_library import TISSUE_LIBRARY
from simpa.utils.libraries.tissue_library import TissueLibrary
import numpy as np


Expand Down Expand Up @@ -174,7 +174,7 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings:
Tags.STRUCTURE_END_MM: [0, 0,
heavy_water_layer_height_mm + mediprene_layer_height_mm + us_gel_thickness],
Tags.CONSIDER_PARTIAL_VOLUME: consider_partial_volume,
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.ultrasound_gel(),
Tags.MOLECULE_COMPOSITION: TissueLibrary.ultrasound_gel(),
Tags.STRUCTURE_TYPE: Tags.HORIZONTAL_LAYER_STRUCTURE
})

Expand All @@ -185,7 +185,7 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings:
Tags.STRUCTURE_START_MM: [0, 0, heavy_water_layer_height_mm],
Tags.STRUCTURE_END_MM: [0, 0, heavy_water_layer_height_mm + mediprene_layer_height_mm],
Tags.CONSIDER_PARTIAL_VOLUME: consider_partial_volume,
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.mediprene(),
Tags.MOLECULE_COMPOSITION: TissueLibrary.mediprene(),
Tags.STRUCTURE_TYPE: Tags.HORIZONTAL_LAYER_STRUCTURE
})

Expand Down Expand Up @@ -214,7 +214,7 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings:
np.array([width_shift_for_structures_mm, 0, probe_size_mm]))

background_settings = Settings({
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.heavy_water(),
Tags.MOLECULE_COMPOSITION: TissueLibrary.heavy_water(),
Tags.STRUCTURE_TYPE: Tags.BACKGROUND
})
volume_creator_settings[Tags.STRUCTURES][Tags.BACKGROUND] = background_settings
Expand Down
4 changes: 2 additions & 2 deletions simpa/core/processing_components/monospectral/iterative_qPAI_algorithm.py
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Expand Up @@ -15,7 +15,7 @@
MCXAdapter
from simpa.utils import Settings
from simpa.io_handling import save_data_field, load_data_field
from simpa.utils import TISSUE_LIBRARY
from simpa.utils.libraries.tissue_library import TissueLibrary
from simpa.core.processing_components import ProcessingComponentBase
import os

Expand Down Expand Up @@ -368,7 +368,7 @@ def standard_optical_properties(self, image_data: np.ndarray) -> dict:
if Tags.DATA_FIELD_SCATTERING_PER_CM in self.global_settings:
scattering = float(self.global_settings[Tags.DATA_FIELD_SCATTERING_PER_CM]) * np.ones(shape)
else:
background_dict = TISSUE_LIBRARY.muscle()
background_dict = TissueLibrary.muscle()
scattering = float(MolecularComposition.get_properties_for_wavelength(background_dict, self.global_settings,
wavelength=800)["mus"])
scattering = scattering * np.ones(shape)
Expand Down
2 changes: 0 additions & 2 deletions simpa/utils/__init__.py
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Expand Up @@ -23,10 +23,8 @@

from .libraries.molecule_library import Molecule, MolecularCompositionGenerator
from .libraries.molecule_library import MoleculeLibrary
from .libraries.molecule_library import MOLECULE_LIBRARY

from .libraries.tissue_library import TissueLibrary
from .libraries.tissue_library import TISSUE_LIBRARY

from .calculate import calculate_oxygenation
from .calculate import calculate_gruneisen_parameter_from_temperature
Expand Down
1 change: 0 additions & 1 deletion simpa/utils/libraries/molecule_library.py
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Expand Up @@ -584,7 +584,6 @@ def air(volume_fraction: (float, torch.Tensor) = 1.0) -> Molecule:
)


MOLECULE_LIBRARY = MoleculeLibrary()


class MolecularCompositionGenerator(object):
Expand Down
118 changes: 64 additions & 54 deletions simpa/utils/libraries/tissue_library.py
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6 changes: 3 additions & 3 deletions simpa_examples/create_custom_tissues.py
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Expand Up @@ -39,11 +39,11 @@ def create_custom_tissue_type():

# Then append chromophores that you want
tissue_settings_generator.append(key="oxyhemoglobin",
value=sp.MOLECULE_LIBRARY.oxyhemoglobin(oxygenation * blood_volume_fraction))
value=sp.MoleculeLibrary.oxyhemoglobin(oxygenation * blood_volume_fraction))
tissue_settings_generator.append(key="deoxyhemoglobin",
value=sp.MOLECULE_LIBRARY.deoxyhemoglobin((1 - oxygenation) * blood_volume_fraction))
value=sp.MoleculeLibrary.deoxyhemoglobin((1 - oxygenation) * blood_volume_fraction))
tissue_settings_generator.append(key="water",
value=sp.MOLECULE_LIBRARY.water(water_volume_fraction))
value=sp.MoleculeLibrary.water(water_volume_fraction))
tissue_settings_generator.append(key="custom",
value=create_custom_chromophore(custom_chromophore_volume_fraction))

Expand Down
10 changes: 5 additions & 5 deletions simpa_examples/linear_unmixing.py
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Expand Up @@ -43,14 +43,14 @@ def create_example_tissue():
and two blood vessels.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

muscle_dictionary = sp.Settings()
muscle_dictionary[Tags.PRIORITY] = 1
muscle_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 0]
muscle_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 100]
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.muscle()
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.muscle()
muscle_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
muscle_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
muscle_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
Expand All @@ -64,7 +64,7 @@ def create_example_tissue():
12,
5]
vessel_1_dictionary[Tags.STRUCTURE_RADIUS_MM] = 3
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.blood(oxygenation=0.99)
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.blood(oxygenation=0.99)
vessel_1_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_1_dictionary[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE

Expand All @@ -77,15 +77,15 @@ def create_example_tissue():
12,
5]
vessel_2_dictionary[Tags.STRUCTURE_RADIUS_MM] = 2
vessel_2_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.blood(oxygenation=0.75)
vessel_2_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.blood(oxygenation=0.75)
vessel_2_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_2_dictionary[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE

epidermis_dictionary = sp.Settings()
epidermis_dictionary[Tags.PRIORITY] = 8
epidermis_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 0]
epidermis_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 0.1]
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.epidermis()
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.epidermis()
epidermis_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
epidermis_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
epidermis_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
Expand Down
8 changes: 4 additions & 4 deletions simpa_examples/minimal_optical_simulation.py
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Expand Up @@ -44,14 +44,14 @@ def create_example_tissue():
and a blood vessel.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

muscle_dictionary = sp.Settings()
muscle_dictionary[Tags.PRIORITY] = 1
muscle_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 10]
muscle_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 100]
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.muscle()
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.muscle()
muscle_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
muscle_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
muscle_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
Expand All @@ -65,15 +65,15 @@ def create_example_tissue():
12,
VOLUME_HEIGHT_IN_MM/2]
vessel_1_dictionary[Tags.STRUCTURE_RADIUS_MM] = 3
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.blood()
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.blood()
vessel_1_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_1_dictionary[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE

epidermis_dictionary = sp.Settings()
epidermis_dictionary[Tags.PRIORITY] = 8
epidermis_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 9]
epidermis_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 10]
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.epidermis()
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.epidermis()
epidermis_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
epidermis_dictionary[Tags.ADHERE_TO_DEFORMATION] = True
epidermis_dictionary[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
Expand Down
9 changes: 4 additions & 5 deletions simpa_examples/minimal_optical_simulation_heterogeneous_tissue.py
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Expand Up @@ -40,16 +40,15 @@ def create_example_tissue(settings):
and a blood vessel.
"""
dim_x, dim_y, dim_z = settings.get_volume_dimensions_voxels()
tissue_library = sp.TISSUE_LIBRARY
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = tissue_library.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

muscle_dictionary = sp.Settings()
muscle_dictionary[Tags.PRIORITY] = 1
muscle_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 10]
muscle_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 100]
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = tissue_library.muscle(
muscle_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.muscle(
oxygenation=sp.BlobHeterogeneity(dim_x, dim_y, dim_z, SPACING,
target_min=0.5, target_max=0.8).get_map(),
blood_volume_fraction=sp.BlobHeterogeneity(dim_x, dim_y, dim_z, SPACING,
Expand All @@ -67,7 +66,7 @@ def create_example_tissue(settings):
12,
VOLUME_HEIGHT_IN_MM/2]
vessel_1_dictionary[Tags.STRUCTURE_RADIUS_MM] = 3
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = tissue_library.blood(
vessel_1_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.blood(
oxygenation=sp.RandomHeterogeneity(dim_x, dim_y, dim_z, SPACING,
target_min=0.9, target_max=1.0).get_map())
vessel_1_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
Expand All @@ -77,7 +76,7 @@ def create_example_tissue(settings):
epidermis_dictionary[Tags.PRIORITY] = 8
epidermis_dictionary[Tags.STRUCTURE_START_MM] = [0, 0, 9]
epidermis_dictionary[Tags.STRUCTURE_END_MM] = [0, 0, 10]
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = tissue_library.epidermis(
epidermis_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.epidermis(
melanin_volume_fraction=sp.RandomHeterogeneity(dim_x, dim_y, dim_z, SPACING,
target_min=0.1, target_max=0.2).get_map())
epidermis_dictionary[Tags.CONSIDER_PARTIAL_VOLUME] = True
Expand Down
2 changes: 1 addition & 1 deletion simpa_examples/minimal_optical_simulation_uniform_cube.py
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Expand Up @@ -49,7 +49,7 @@ def create_example_tissue():
It contains only a generic background tissue material.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(1e-4, 1e-4, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

tissue_dict = sp.Settings()
Expand Down
10 changes: 5 additions & 5 deletions simpa_examples/optical_and_acoustic_simulation.py
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Expand Up @@ -43,33 +43,33 @@ def create_example_tissue():
and a blood vessel.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(1e-10, 1e-10, 1.0)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(1e-10, 1e-10, 1.0)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

tissue_dict = sp.Settings()
tissue_dict[Tags.BACKGROUND] = background_dictionary
tissue_dict["muscle"] = sp.define_horizontal_layer_structure_settings(z_start_mm=0, thickness_mm=100,
molecular_composition=sp.TISSUE_LIBRARY.constant(
molecular_composition=sp.TissueLibrary.constant(
0.05, 100, 0.9),
priority=1,
consider_partial_volume=True,
adhere_to_deformation=True)
tissue_dict["epidermis"] = sp.define_horizontal_layer_structure_settings(z_start_mm=1, thickness_mm=0.1,
molecular_composition=sp.TISSUE_LIBRARY.epidermis(),
molecular_composition=sp.TissueLibrary.epidermis(),
priority=8,
consider_partial_volume=True,
adhere_to_deformation=True)
tissue_dict["vessel_1"] = sp.define_circular_tubular_structure_settings(
tube_start_mm=[VOLUME_TRANSDUCER_DIM_IN_MM/2 - 10, 0, 5],
tube_end_mm=[VOLUME_TRANSDUCER_DIM_IN_MM/2 - 10, VOLUME_PLANAR_DIM_IN_MM, 5],
molecular_composition=sp.TISSUE_LIBRARY.blood(),
molecular_composition=sp.TissueLibrary.blood(),
radius_mm=2, priority=3, consider_partial_volume=True,
adhere_to_deformation=False
)
tissue_dict["vessel_2"] = sp.define_circular_tubular_structure_settings(
tube_start_mm=[VOLUME_TRANSDUCER_DIM_IN_MM/2, 0, 10],
tube_end_mm=[VOLUME_TRANSDUCER_DIM_IN_MM/2, VOLUME_PLANAR_DIM_IN_MM, 10],
molecular_composition=sp.TISSUE_LIBRARY.blood(),
molecular_composition=sp.TissueLibrary.blood(),
radius_mm=3, priority=3, consider_partial_volume=True,
adhere_to_deformation=False
)
Expand Down
8 changes: 4 additions & 4 deletions simpa_examples/perform_iterative_qPAI_reconstruction.py
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Expand Up @@ -48,14 +48,14 @@ def create_example_tissue():
and a blood vessel.
"""
background_dictionary = sp.Settings()
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(0.05, 30, 0.9)
background_dictionary[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(0.05, 30, 0.9)
background_dictionary[Tags.STRUCTURE_TYPE] = Tags.BACKGROUND

epidermis_structure = sp.Settings()
epidermis_structure[Tags.PRIORITY] = 1
epidermis_structure[Tags.STRUCTURE_START_MM] = [0, 0, 2]
epidermis_structure[Tags.STRUCTURE_END_MM] = [0, 0, 2.5]
epidermis_structure[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(2.2, 100.0, 0.9)
epidermis_structure[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(2.2, 100.0, 0.9)
epidermis_structure[Tags.CONSIDER_PARTIAL_VOLUME] = True
epidermis_structure[Tags.ADHERE_TO_DEFORMATION] = True
epidermis_structure[Tags.STRUCTURE_TYPE] = Tags.HORIZONTAL_LAYER_STRUCTURE
Expand All @@ -68,7 +68,7 @@ def create_example_tissue():
VOLUME_PLANAR_DIM_IN_MM, VOLUME_HEIGHT_IN_MM / 2]
vessel_structure_1[Tags.STRUCTURE_RADIUS_MM] = 1.75
vessel_structure_1[Tags.STRUCTURE_ECCENTRICITY] = 0.85
vessel_structure_1[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(5.2, 100.0, 0.9)
vessel_structure_1[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(5.2, 100.0, 0.9)
vessel_structure_1[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_structure_1[Tags.ADHERE_TO_DEFORMATION] = True
vessel_structure_1[Tags.STRUCTURE_TYPE] = Tags.ELLIPTICAL_TUBULAR_STRUCTURE
Expand All @@ -80,7 +80,7 @@ def create_example_tissue():
vessel_structure_2[Tags.STRUCTURE_END_MM] = [VOLUME_TRANSDUCER_DIM_IN_MM / 2,
VOLUME_PLANAR_DIM_IN_MM, VOLUME_HEIGHT_IN_MM / 3]
vessel_structure_2[Tags.STRUCTURE_RADIUS_MM] = 0.75
vessel_structure_2[Tags.MOLECULE_COMPOSITION] = sp.TISSUE_LIBRARY.constant(3.0, 100.0, 0.9)
vessel_structure_2[Tags.MOLECULE_COMPOSITION] = sp.TissueLibrary.constant(3.0, 100.0, 0.9)
vessel_structure_2[Tags.CONSIDER_PARTIAL_VOLUME] = True
vessel_structure_2[Tags.STRUCTURE_TYPE] = Tags.CIRCULAR_TUBULAR_STRUCTURE

Expand Down
26 changes: 13 additions & 13 deletions simpa_examples/segmentation_loader.py
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Expand Up @@ -45,21 +45,21 @@ def run_segmentation_loader(spacing: float | int = 1.0, input_spacing: float | i

def segmentation_class_mapping():
ret_dict = dict()
ret_dict[0] = sp.TISSUE_LIBRARY.heavy_water()
ret_dict[1] = sp.TISSUE_LIBRARY.blood()
ret_dict[2] = sp.TISSUE_LIBRARY.epidermis()
ret_dict[3] = sp.TISSUE_LIBRARY.muscle()
ret_dict[4] = sp.TISSUE_LIBRARY.mediprene()
ret_dict[5] = sp.TISSUE_LIBRARY.ultrasound_gel()
ret_dict[6] = sp.TISSUE_LIBRARY.heavy_water()
ret_dict[0] = sp.TissueLibrary.heavy_water()
ret_dict[1] = sp.TissueLibrary.blood()
ret_dict[2] = sp.TissueLibrary.epidermis()
ret_dict[3] = sp.TissueLibrary.muscle()
ret_dict[4] = sp.TissueLibrary.mediprene()
ret_dict[5] = sp.TissueLibrary.ultrasound_gel()
ret_dict[6] = sp.TissueLibrary.heavy_water()
ret_dict[7] = (sp.MolecularCompositionGenerator()
.append(sp.MOLECULE_LIBRARY.oxyhemoglobin(0.01))
.append(sp.MOLECULE_LIBRARY.deoxyhemoglobin(0.01))
.append(sp.MOLECULE_LIBRARY.water(0.98))
.append(sp.MoleculeLibrary.oxyhemoglobin(0.01))
.append(sp.MoleculeLibrary.deoxyhemoglobin(0.01))
.append(sp.MoleculeLibrary.water(0.98))
.get_molecular_composition(sp.SegmentationClasses.COUPLING_ARTIFACT))
ret_dict[8] = sp.TISSUE_LIBRARY.heavy_water()
ret_dict[9] = sp.TISSUE_LIBRARY.heavy_water()
ret_dict[10] = sp.TISSUE_LIBRARY.heavy_water()
ret_dict[8] = sp.TissueLibrary.heavy_water()
ret_dict[9] = sp.TissueLibrary.heavy_water()
ret_dict[10] = sp.TissueLibrary.heavy_water()
return ret_dict

settings = sp.Settings()
Expand Down
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