Update volume settings for segmentation and MSOT Acuity Echo

simpa/core/device_digital_twins/detection_geometries/curved_array.py

@@ -2,9 +2,10 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 import numpy as np
+from typing import Union
 
 from simpa.core.device_digital_twins import DetectionGeometryBase
-from simpa.utils import Tags
+from simpa import Settings, Tags
 
 
 class CurvedArrayDetectionGeometry(DetectionGeometryBase):
@@ -13,17 +14,17 @@ class CurvedArrayDetectionGeometry(DetectionGeometryBase):
     with a curved detection geometry. The origin for this device is the center (focus) of the curved array.
     """
 
-    def __init__(self, pitch_mm=0.5,
-                 radius_mm=40,
-                 number_detector_elements=256,
+    def __init__(self, pitch_mm: Union[float, int] = 0.5,
+                 radius_mm: Union[float, int] = 40,
+                 number_detector_elements: int = 256,
                  detector_element_width_mm=0.24,
                  detector_element_length_mm=13,
                  center_frequency_hz=3.96e6,
                  bandwidth_percent=55,
                  sampling_frequency_mhz=40,
-                 angular_origin_offset=np.pi,
-                 device_position_mm=None,
-                 field_of_view_extent_mm=None):
+                 angular_origin_offset: Union[float, int] = np.pi,
+                 device_position_mm: np.ndarray = None,
+                 field_of_view_extent_mm: np.ndarray = None):
         """
 
         :param pitch_mm: In-plane distance between the beginning of one detector element to the next detector element.
@@ -85,6 +86,9 @@ def check_settings_prerequisites(self, global_settings) -> bool:
     def update_settings_for_use_of_model_based_volume_creator(self, global_settings):
         pass
 
+    def update_settings_for_use_of_segmentation_based_volume_creator(self, global_settings: Settings):
+        pass
+
     def get_detector_element_positions_base_mm(self) -> np.ndarray:
 
         pitch_angle = self.pitch_mm / self.radius_mm

simpa/core/device_digital_twins/detection_geometries/detection_geometry_base.py

@@ -5,17 +5,18 @@
 from abc import abstractmethod
 from simpa.core.device_digital_twins import DigitalDeviceTwinBase
 import numpy as np
+from typing import Union
 
 
 class DetectionGeometryBase(DigitalDeviceTwinBase):
     """
     This class is the base class for representing all detector geometries.
     """
 
-    def __init__(self, number_detector_elements, detector_element_width_mm,
-                 detector_element_length_mm, center_frequency_hz, bandwidth_percent,
-                 sampling_frequency_mhz, device_position_mm: np.ndarray = None,
-                 field_of_view_extent_mm: np.ndarray = None):
+    def __init__(self, number_detector_elements: int, detector_element_width_mm: Union[float, int],
+                 detector_element_length_mm: Union[float, int], center_frequency_hz: Union[float, int],
+                 bandwidth_percent: Union[float, int], sampling_frequency_mhz: Union[float, int],
+                 device_position_mm: np.ndarray = None, field_of_view_extent_mm: np.ndarray = None):
         """
 
         :param number_detector_elements: Total number of detector elements.

simpa/core/device_digital_twins/detection_geometries/linear_array.py

@@ -2,6 +2,7 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 import numpy as np
+from typing import Union
 
 from simpa.core.device_digital_twins import DetectionGeometryBase
 from simpa.utils import Settings, Tags
@@ -15,7 +16,7 @@ class LinearArrayDetectionGeometry(DetectionGeometryBase):
 
     """
 
-    def __init__(self, pitch_mm=0.5,
+    def __init__(self, pitch_mm: Union[float, int] = 0.5,
                  number_detector_elements=100,
                  detector_element_width_mm=0.24,
                  detector_element_length_mm=0.5,
@@ -51,7 +52,7 @@ def __init__(self, pitch_mm=0.5,
         self.pitch_mm = pitch_mm
         self.probe_width_mm = (number_detector_elements - 1) * self.pitch_mm
 
-    def check_settings_prerequisites(self, global_settings: Settings) -> bool:
+    def check_settings_prerequisites(self, global_settings) -> bool:
         if global_settings[Tags.DIM_VOLUME_X_MM] < self.probe_width_mm + global_settings[Tags.SPACING_MM]:
             self.logger.error("Volume x dimension is too small to encompass MSOT device in simulation!"
                               "Must be at least {} mm but was {} mm"
@@ -63,6 +64,9 @@ def check_settings_prerequisites(self, global_settings: Settings) -> bool:
     def update_settings_for_use_of_model_based_volume_creator(self, global_settings):
         pass
 
+    def update_settings_for_use_of_segmentation_based_volume_creator(self, global_settings: Settings):
+        pass
+
     def get_detector_element_positions_base_mm(self) -> np.ndarray:
 
         detector_positions = np.zeros((self.number_detector_elements, 3))

simpa/core/device_digital_twins/detection_geometries/planar_array.py

@@ -5,6 +5,7 @@
 
 from simpa.core.device_digital_twins import DetectionGeometryBase
 from simpa.utils import Settings, Tags
+from typing import Union
 
 
 class PlanarArrayDetectionGeometry(DetectionGeometryBase):
@@ -14,7 +15,7 @@ class PlanarArrayDetectionGeometry(DetectionGeometryBase):
 
     """
 
-    def __init__(self, pitch_mm=0.5,
+    def __init__(self, pitch_mm: Union[float, int] = 0.5,
                  number_detector_elements_x=100,
                  number_detector_elements_y=100,
                  detector_element_width_mm=0.24,
@@ -81,6 +82,9 @@ def check_settings_prerequisites(self, global_settings: Settings) -> bool:
     def update_settings_for_use_of_model_based_volume_creator(self, global_settings):
         pass
 
+    def update_settings_for_use_of_segmentation_based_volume_creator(self, global_settings: Settings):
+        pass
+
     def get_detector_element_positions_base_mm(self) -> np.ndarray:
         detector_element_positions_mm = np.zeros((self.number_detector_elements, 3))
         for x in range(self.number_detector_elements_x):

simpa/core/device_digital_twins/digital_device_twin_base.py

@@ -9,6 +9,7 @@
 import uuid
 from simpa.utils.serializer import SerializableSIMPAClass
 from simpa.utils.calculate import are_equal
+from simpa.utils import Settings
 
 
 class DigitalDeviceTwinBase(SerializableSIMPAClass):
@@ -17,7 +18,7 @@ class DigitalDeviceTwinBase(SerializableSIMPAClass):
     which has representations of both.
     """
 
-    def __init__(self, device_position_mm=None, field_of_view_extent_mm=None):
+    def __init__(self, device_position_mm: np.ndarray = None, field_of_view_extent_mm: np.ndarray = None):
         """
         :param device_position_mm: Each device has an internal position which serves as origin for internal \
         representations of e.g. detector element positions or illuminator positions.
@@ -54,7 +55,7 @@ def __eq__(self, other):
         return False
 
     @abstractmethod
-    def check_settings_prerequisites(self, global_settings) -> bool:
+    def check_settings_prerequisites(self, global_settings: Settings) -> bool:
         """
         It might be that certain device geometries need a certain dimensionality of the simulated PAI volume, or that
         it requires the existence of certain Tags in the global global_settings.
@@ -72,7 +73,7 @@ def check_settings_prerequisites(self, global_settings) -> bool:
         pass
 
     @abstractmethod
-    def update_settings_for_use_of_model_based_volume_creator(self, global_settings):
+    def update_settings_for_use_of_model_based_volume_creator(self, global_settings: Settings):
         """
         This method can be overwritten by a PA device if the device poses special constraints to the
         volume that should be considered by the model-based volume creator.
@@ -82,6 +83,16 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings)
         """
         pass
 
+    @abstractmethod
+    def update_settings_for_use_of_segmentation_based_volume_creator(self, global_settings: Settings):
+        """
+        This method can be overwritten by a PA device if the device poses special constraints to the
+        volume that should be considered by the segmentation-based volume creator.
+        :param global_settings: Settings for the entire simulation pipeline.
+        :type global_settings: Settings
+        """
+        pass
+
     def get_field_of_view_mm(self) -> np.ndarray:
         """
         Returns the absolute field of view in mm where the probe position is already

simpa/core/device_digital_twins/illumination_geometries/disk_illumination.py

@@ -4,6 +4,7 @@
 
 from simpa.core.device_digital_twins import IlluminationGeometryBase
 from simpa.utils import Tags
+from typing import Union
 
 
 class DiskIlluminationGeometry(IlluminationGeometryBase):
@@ -12,7 +13,7 @@ class DiskIlluminationGeometry(IlluminationGeometryBase):
     The device position is defined as the middle of the disk.
     """
 
-    def __init__(self, beam_radius_mm=None, device_position_mm=None, field_of_view_extent_mm=None):
+    def __init__(self, beam_radius_mm: Union[int, float] = None, device_position_mm=None, field_of_view_extent_mm=None):
         """
         :param beam_radius_mm: Radius of the disk in mm.
         :type beam_radius_mm: int, float

simpa/core/device_digital_twins/illumination_geometries/gaussian_beam_illumination.py

@@ -6,6 +6,7 @@
 from collections.abc import Sized
 from simpa.core.device_digital_twins import IlluminationGeometryBase
 from simpa.utils import Tags
+from typing import Union
 
 
 class GaussianBeamIlluminationGeometry(IlluminationGeometryBase):
@@ -14,8 +15,8 @@ class GaussianBeamIlluminationGeometry(IlluminationGeometryBase):
     The position is defined as the middle of the beam.
     """
 
-    def __init__(self, beam_radius_mm=None, focal_length_mm=None, device_position_mm=None,
-                 field_of_view_extent_mm=None):
+    def __init__(self, beam_radius_mm: Union[int, float] = None, focal_length_mm: Union[int, float] = None,
+                 device_position_mm=None, field_of_view_extent_mm=None):
         """
         :param beam_radius_mm: Initial radius of the gaussian beam at half maximum (full width at half maximum (FWHM))
         in mm.

simpa/core/device_digital_twins/illumination_geometries/illumination_geometry_base.py

@@ -13,7 +13,8 @@ class IlluminationGeometryBase(DigitalDeviceTwinBase):
     This class is the base class for representing all illumination geometries.
     """
 
-    def __init__(self, device_position_mm=None, source_direction_vector=None, field_of_view_extent_mm=None):
+    def __init__(self, device_position_mm=None, source_direction_vector: np.ndarray = None,
+                 field_of_view_extent_mm=None):
         """
         :param device_position_mm: Each device has an internal position which serves as origin for internal \
         representations of illuminator positions.
@@ -38,7 +39,7 @@ def __init__(self, device_position_mm=None, source_direction_vector=None, field_
             self.source_direction_vector)
 
     @abstractmethod
-    def get_mcx_illuminator_definition(self, global_settings) -> dict:
+    def get_mcx_illuminator_definition(self, global_settings: Settings) -> dict:
         """
         IMPORTANT: This method creates a dictionary that contains tags as they are expected for the
         mcx simulation tool to represent the illumination geometry of this device.
@@ -57,6 +58,9 @@ def check_settings_prerequisites(self, global_settings) -> bool:
     def update_settings_for_use_of_model_based_volume_creator(self, global_settings) -> Settings:
         return global_settings
 
+    def update_settings_for_use_of_segmentation_based_volume_creator(self, global_settings: Settings):
+        pass
+
     def serialize(self) -> dict:
         serialized_device = self.__dict__
         device_dict = {"IlluminationGeometryBase": serialized_device}

simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py

@@ -13,13 +13,10 @@ class MSOTInVisionIlluminationGeometry(IlluminationGeometryBase):
     This class represents the illumination geometry of the MSOT InVision photoacoustic device.
     """
 
-    def __init__(self, invision_position=None):
+    def __init__(self, invision_position: list = [0, 0, 0]):
         super().__init__()
 
-        if invision_position is None:
-            self.invision_position = [0, 0, 0]
-        else:
-            self.invision_position = invision_position
+        self.invision_position = invision_position
 
         det_sep_half = 24.74 / 2
         detector_iso_distance = 74.05 / 2

simpa/core/device_digital_twins/illumination_geometries/pencil_array_illumination.py

@@ -14,8 +14,8 @@ class PencilArrayIlluminationGeometry(IlluminationGeometryBase):
     The device position is defined as the middle of the array.
     """
 
-    def __init__(self, pitch_mm=0.5, number_illuminators_x=100, number_illuminators_y=100, device_position_mm=None,
-                 field_of_view_extent_mm=None):
+    def __init__(self, pitch_mm: float = 0.5, number_illuminators_x: int = 100, number_illuminators_y: int = 100,
+                 device_position_mm=None, field_of_view_extent_mm=None):
         """
         :param pitch_mm: Defines the x and y distance between the illumination positions
         :type pitch_mm: float

simpa/core/device_digital_twins/illumination_geometries/slit_illumination.py

@@ -14,7 +14,7 @@ class SlitIlluminationGeometry(IlluminationGeometryBase):
     The device position is defined as the middle of the slit.
     """
 
-    def __init__(self, slit_vector_mm=None, direction_vector_mm=None, device_position_mm=None,
+    def __init__(self, slit_vector_mm: list = None, direction_vector_mm: list = None, device_position_mm=None,
                  field_of_view_extent_mm=None):
         """
         :param slit_vector_mm: Defines the slit in vector form. For example a slit along the x-axis with length 5mm