included blood volume fraction in output file:

- new Tags.DATA_FIELD_BLOOD_VOLUME_FRACTION
- this tag is added to TissueProperties
- new function calculate_bvf
- calculate_bvf used in MolecularComposition

simpa/utils/calculate.py

@@ -34,6 +34,30 @@ def calculate_oxygenation(molecule_list):
     return hbO2 / (hb + hbO2)
 
 
+def calculate_bvf(molecule_list):
+    """
+    :return: the blood volume fraction value between 0 and 1, or 0, if oxy and deoxy not present.
+    """
+    hb = None
+    hbO2 = None
+
+    for molecule in molecule_list:
+        if molecule.spectrum.spectrum_name == "Deoxyhemoglobin":
+            hb = molecule.volume_fraction
+        if molecule.spectrum.spectrum_name == "Oxyhemoglobin":
+            hbO2 = molecule.volume_fraction
+
+    if hb is None and hbO2 is None:
+        return 0
+
+    if hb is None:
+        return hbO2
+    elif hbO2 is None:
+        return hb
+
+    return (hb + hbO2)
+
+
 def create_spline_for_range(xmin_mm=0, xmax_mm=10, maximum_y_elevation_mm=1, spacing=0.1):
     """
     Creates a functional that simulates distortion along the y position

simpa/utils/libraries/molecule_library.py

@@ -9,7 +9,7 @@
 from simpa.utils.libraries.literature_values import OpticalTissueProperties, StandardProperties
 from simpa.utils.libraries.spectrum_library import AnisotropySpectrumLibrary, ScatteringSpectrumLibrary
 from simpa.utils import Spectrum
-from simpa.utils.calculate import calculate_oxygenation, calculate_gruneisen_parameter_from_temperature
+from simpa.utils.calculate import calculate_oxygenation, calculate_gruneisen_parameter_from_temperature, calculate_bvf
 from simpa.utils.serializer import SerializableSIMPAClass
 from simpa.utils.libraries.spectrum_library import AbsorptionSpectrumLibrary
 
@@ -35,6 +35,7 @@ def update_internal_properties(self):
         self.internal_properties = TissueProperties()
         self.internal_properties[Tags.DATA_FIELD_SEGMENTATION] = self.segmentation_type
         self.internal_properties[Tags.DATA_FIELD_OXYGENATION] = calculate_oxygenation(self)
+        self.internal_properties[Tags.DATA_FIELD_BLOOD_VOLUME_FRACTION] = calculate_bvf(self)
         for molecule in self:
             self.internal_properties.volume_fraction += molecule.volume_fraction
             self.internal_properties[Tags.DATA_FIELD_GRUNEISEN_PARAMETER] += \

simpa/utils/tags.py

@@ -864,6 +864,13 @@ class Tags:
     Usage: SIMPA package, naming convention
     """
 
+
+    DATA_FIELD_BLOOD_VOLUME_FRACTION = "bvf"
+    """
+    Blood volume fraction of the generated volume/structure.\n
+    Usage: SIMPA package, naming convention
+    """
+
     DATA_FIELD_SEGMENTATION = "seg"
     """
     Segmentation of the generated volume/structure.\n

simpa/utils/tissue_properties.py

@@ -13,6 +13,7 @@ class TissueProperties(dict):
                      Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
                      Tags.DATA_FIELD_SEGMENTATION,
                      Tags.DATA_FIELD_OXYGENATION,
+                     Tags.DATA_FIELD_BLOOD_VOLUME_FRACTION,
                      Tags.DATA_FIELD_DENSITY,
                      Tags.DATA_FIELD_SPEED_OF_SOUND,
                      Tags.DATA_FIELD_ALPHA_COEFF]