illumination_geometries
- class DiskIlluminationGeometry(beam_radius_mm=None, device_position_mm=None, field_of_view_extent_mm=None)[source]
Bases:
IlluminationGeometryBaseThis class represents a disk illumination geometry. The device position is defined as the middle of the disk.
- Parameters:
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- class GaussianBeamIlluminationGeometry(beam_radius_mm=None, focal_length_mm=None, device_position_mm=None, field_of_view_extent_mm=None)[source]
Bases:
IlluminationGeometryBaseThis class represents a Gaussian beam illumination geometry. The position is defined as the middle of the beam.
- Parameters:
beam_radius_mm – Initial radius of the gaussian beam at half maximum (full width at half maximum (FWHM))
in mm. :type beam_radius_mm: int, float :param focal_length_mm: Focal length of the gaussian beam in mm. Can be positive (focussed beam), negative (cone-shaped beam) or None (collimated beam). :type focal_length_mm: int, float :param device_position_mm: Each device has an internal position which serves as origin for internal representations of illuminator positions. :type device_position_mm: ndarray :param field_of_view_extent_mm: Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions. :type field_of_view_extent_mm: ndarray
- class IlluminationGeometryBase(device_position_mm=None, source_direction_vector=None, field_of_view_extent_mm=None)[source]
Bases:
DigitalDeviceTwinBaseThis class is the base class for representing all illumination geometries.
- Parameters:
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
source_direction_vector (ndarray) – Direction of the illumination source.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- check_settings_prerequisites(global_settings) bool[source]
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. To this end, a PAI device should use this method to inform the user about a mismatch of the desired device and throw a ValueError if that is the case.
- Parameters:
global_settings (Settings) – Settings for the entire simulation pipeline.
- Raises:
ValueError – raises a value error if the prerequisites are not matched.
- Returns:
True if the prerequisites are met, False if they are not met, but no exception has been raised.
- Return type:
- abstract get_mcx_illuminator_definition(global_settings) dict[source]
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.
- update_settings_for_use_of_model_based_volume_creator(global_settings) Settings[source]
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.
- Parameters:
global_settings (Settings) – Settings for the entire simulation pipeline.
- class MSOTAcuityIlluminationGeometry[source]
Bases:
IlluminationGeometryBaseThis class represents the illumination geometry of the MSOT Acuity (Echo) photoacoustic device. The position is defined as the middle of the illumination slit.
Initializes the illumination source.
- class MSOTInVisionIlluminationGeometry(invision_position=None)[source]
Bases:
IlluminationGeometryBaseThis class represents the illumination geometry of the MSOT InVision photoacoustic device.
- Parameters:
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
source_direction_vector (ndarray) – Direction of the illumination source.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- class PencilArrayIlluminationGeometry(pitch_mm=0.5, number_illuminators_x=100, number_illuminators_y=100, device_position_mm=None, field_of_view_extent_mm=None)[source]
Bases:
IlluminationGeometryBaseThis class represents a pencil array illumination geometry. The device position is defined as the middle of the array.
- Parameters:
pitch_mm (float) – Defines the x and y distance between the illumination positions
number_illuminators_x (int) – Defines the number of illuminators in the x direction
number_illuminators_y (int) – Defines the number of illuminators in the y direction
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- class PencilBeamIlluminationGeometry(device_position_mm=None, source_direction_vector=None, field_of_view_extent_mm=None)[source]
Bases:
IlluminationGeometryBaseThis class represents a pencil beam illumination geometry. The device position is defined as the exact position of the pencil beam.
- Parameters:
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
source_direction_vector (ndarray) – Direction of the illumination source.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- class RectangleIlluminationGeometry(length_mm: int = 10, width_mm: int = 10, device_position_mm: Optional[ndarray] = None, source_direction_vector: Optional[ndarray] = None, field_of_view_extent_mm: Optional[ndarray] = None)[source]
Bases:
IlluminationGeometryBaseDefines a rectangle illumination geometry. The device position is defined as the UPPER LEFT CORNER of the rectangle.
Note: To create a global light which illuminates the entire tissue evenly (= creating a planar illumination geometry), create the following geometry using the tissue length and width:
>>> global_light = RectangleIlluminationGeometry(length_mm=tissue_length_mm, width_mm=tissue_width_mm)
- Parameters:
length_mm – The length of the rectangle in mm.
width_mm – The width of the rectangle in mm.
device_position_mm – The device position in mm, the UPPER LEFT CORNER of the rectangle.
If None, the position is defined as [0, 0, 0]. :param source_direction_vector: Direction of the illumination source. If None, the direction is defined as [0, 0, 1]. :param field_of_view_extent_mm: Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- static deserialize(dictionary_to_deserialize: dict) SerializableSIMPAClass[source]
Deserializes the provided dict into an object of this type. :param dictionary_to_deserialize: The dictionary to deserialize.
- Returns:
The deserialized object from the dictionary.
- class RingIlluminationGeometry(outer_radius_in_mm: float = 1, inner_radius_in_mm: float = 0, lower_angular_bound: float = 0, upper_angular_bound: float = 0, device_position_mm: Optional[ndarray] = None, source_direction_vector: Optional[ndarray] = None, field_of_view_extent_mm: Optional[ndarray] = None)[source]
Bases:
IlluminationGeometryBaseDefines a ring illumination geometry. The device position is defined as the center of the ring.
Note: To create a ring light which illuminates a square tissue with the same center and any inner radius r, create the following geometry using the tissue width:
>>> ring_light = RingIlluminationGeometry(inner_radius_in_mm=r, outer_radius_in_mm=tissue_width / 2., device_position_mm=np.array([tissue_width / 2., tissue_width / 2., 0]))
- Parameters:
outer_radius_in_mm – The outer radius of the ring in mm.
inner_radius_in_mm – The inner radius of the ring in mm. If 0, should match the disk illumination.
lower_angular_bound – The lower angular bound in radians. If both bounds are 0, than no bound is applied.
Note that the bound of 0 starts from the x-axis on the right side and is applied clockwise. :param upper_angular_bound: The upper angular bound in radians. If both bounds are 0, than no bound is applied. Note that the bound is applied clockwise in relation to the lower bound. :param device_position_mm: The device position in mm, the center of the ring. If None, the position is defined as [0, 0, 0]. :param source_direction_vector: Direction of the illumination source. If None, the direction is defined as [0, 0, 1]. :param field_of_view_extent_mm: Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.
- static deserialize(dictionary_to_deserialize: dict) SerializableSIMPAClass[source]
Deserializes the provided dict into an object of this type. :param dictionary_to_deserialize: The dictionary to deserialize. :return: The deserialized object from the dictionary.
- class SlitIlluminationGeometry(slit_vector_mm=None, direction_vector_mm=None, device_position_mm=None, field_of_view_extent_mm=None)[source]
Bases:
IlluminationGeometryBaseThis class represents a slit illumination geometry. The device position is defined as the middle of the slit.
- Parameters:
slit_vector_mm (list) – Defines the slit in vector form. For example a slit along the x-axis with length 5mm would be defined as [5, 0, 0].
direction_vector_mm (list) – Direction vector in which the slit illuminates. Defined analogous to the slit vector.
device_position_mm (ndarray) – Each device has an internal position which serves as origin for internal representations of illuminator positions.
field_of_view_extent_mm (ndarray) – Field of view which is defined as a numpy array of the shape [xs, xe, ys, ye, zs, ze], where x, y, and z denote the coordinate axes and s and e denote the start and end positions.