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Sim sampleplane

sim_sampleplane.py#

This module defines classes for simulating a sample plane, including fluorescent objects, spatial indexing, and time-based tracking.

Constants#

  • EMPTY_STATE_HISTORY_DICT: A placeholder dictionary indicating no transmittance at a given wavelength.

Classes#

FluorescentObject#

Represents a fluorescent object in the sample plane.

  • Attributes:
  • object_id: Unique identifier for the object.
  • position: Current position (x, y, z) in μm.
  • fluorophore: Fluorophore instance defining the object's properties.
  • position_history: Dictionary tracking position over time.

  • state_history: Dictionary tracking state history over time.

  • Methods:

  • __post_init__(): Initializes position and state history at t=0.
CellSpaceView#

Represents a 3D field of view with bounds in x, y, and z dimensions.

  • Attributes:
  • x_bounds: Tuple defining the x-axis bounds.
  • y_bounds: Tuple defining the y-axis bounds.

  • z_bounds: Tuple defining the z-axis bounds.

  • Methods:

  • __post_init__(): Validates that bounds have min < max.
  • contains(position: Tuple[float, float, float]) -> bool: Checks if a position is within the FOV.
  • bounds: Property returning the FOV bounds.
SampleSpace#

Represents the total 3D space available for simulation.

  • Attributes:
  • x_max: Maximum x-coordinate.
  • y_max: Maximum y-coordinate.
  • z_min: Minimum z-coordinate.

  • z_max: Maximum z-coordinate.

  • Methods:

  • contains_fov(fov: CellSpaceView) -> bool: Checks if a FOV fits within the sample space.
  • contains_position(position: Tuple[float, float, float]) -> bool: Checks if a position is within the sample space.
  • bounds: Property returning the space bounds.
SamplePlane#

Manages the simulation of fluorescent objects within a sample plane.

  • Attributes:
  • _space: SampleSpace instance defining the total simulation volume.
  • _fov: CellSpaceView instance defining the FOV.
  • _objects: Dictionary of FluorescentObject instances.
  • _spatial_index: Spatial index for fast lookup of objects.
  • _grid_size: Size of grid cells in μm.
  • dt: Time step in milliseconds.
  • dt_s: Time step in seconds.
  • t_end: End time in milliseconds.

  • time_points: List of time points for simulation.

  • Methods:

  • __init__(sample_space: SampleSpace, fov: Tuple[Tuple[float, float], Tuple[float, float], Tuple[float, float]], oversample_motion_time: int, t_end: int): Initializes the sample plane.
  • add_object(object_id: str, position: Tuple[float, float, float], fluorophore: Fluorophore, trajectory: Optional[Dict[int, Tuple[float, float, float]]] = None) -> bool: Adds a fluorescent object to the sample plane.
  • get_all_objects() -> List[FluorescentObject]: Retrieves all objects in the sample plane.
  • get_objects_in_range(center: Tuple[float, float, float], radius: float, t: int) -> List[FluorescentObject]: Retrieves objects within a specified radius of a point at a given time.
  • is_within_fov(position: Tuple[float, float, float]) -> bool: Checks if a position is within the FOV.
  • _update_spatial_index(object_id: str, position: Tuple[float, float, float], t: int): Updates the spatial index for an object at a specific time.
  • get_object(object_id: str) -> Optional[FluorescentObject]: Retrieves an object by its ID.
  • __iter__() -> Iterator[FluorescentObject]: Makes the sample plane iterable.
  • __len__() -> int: Returns the number of objects in the sample plane.
  • _get_grid_position(position: Tuple[float, float, float]) -> Tuple[int, int, int]: Converts a position to grid coordinates.
  • _distance(p1: Tuple[float, float, float], p2: Tuple[float, float, float]) -> float: Calculates the Euclidean distance between two points.
  • fov_bounds: Property returning the FOV bounds.
  • sample_space_bounds: Property returning the sample space bounds.