Configmodels

Configuration Models Documentation

Overview

The configuration models module defines Pydantic BaseModel classes for validating and managing microscopy simulation parameters. Each model class represents a specific set of configuration parameters with built-in validation and type conversion.

Models

CellParameters

Defines the physical parameters of the cell being simulated.

class CellParameters(BaseModel)

Fields

• cell_type: Union[str, CellType]
• Type of cell.

• Supported: RectangularCell, SphericalCell, OvoidCell, RodCell, BuddingCell

• params: Dict[str, Any]

• Key value pairs of the parameters of the specified cell.

# SphericalCell
params = {
    "center": [0, 0, 0],   # 3D center coordinates
    "radius": 10.0         # Radius of sphere
}

# RodCell
params = {
    "center": [0, 0, 0],       # 3D center coordinates
    "direction": [0, 0, 1],    # Direction vector (will be normalized)
    "height": 20.0,            # Length of the rod
    "radius": 5.0              # Radius of the rod
}

# RectangularCell
params = {
    "bounds": [-10, 10, -10, 10, -10, 10]  # [xmin, xmax, ymin, ymax, zmin, zmax]
}

# OvoidCell
params = {
    "center": [0, 0, 0],       # 3D center coordinates
    "direction": [0, 0, 1],    # Direction vector (will be normalized)
    "xradius": 10.0,           # Radius in x-direction
    "yradius": 15.0,           # Radius in y-direction
    "zradius": 20.0            # Radius in z-direction
}

MoleculeParameters

Defines parameters for molecular motion and behavior simulation.

class MoleculeParameters(BaseModel)

Fields

• num_molecules: List[int]

• Description: Number of molecules for each type

• track_type: List[Literal["fbm", "constant"]]

• Description: Type of molecular motion

• Valid values: "fbm" (fractional Brownian motion) or "constant"

• diffusion_coefficient: List[List[float]]

• Description: Diffusion coefficients in μm²/s

• 2D array automatically converted to numpy array

• hurst_exponent: List[List[float]]

• Description: Hurst exponents for fractional Brownian motion

• 2D array automatically converted to numpy array

• allow_transition_probability: List[bool]

• Description: Whether to allow state transitions

• transition_matrix_time_step: List[int]

• Description: Time step in milliseconds for transition matrices

• diffusion_transition_matrix: List[List[List[float]]]

• Description: State transition probabilities for diffusion

• 3D array automatically converted to numpy array

• hurst_transition_matrix: List[List[List[float]]]

• Description: State transition probabilities for Hurst exponent

• 3D array automatically converted to numpy array

• state_probability_diffusion: List[List[float]]

• Description: Initial state probabilities for diffusion

• 2D array automatically converted to numpy array

• state_probability_hurst: List[List[float]]

• Description: Initial state probabilities for Hurst exponent
• 2D array automatically converted to numpy array

GlobalParameters

Defines global simulation parameters.

class GlobalParameters(BaseModel)

Fields

• sample_plane_dim: List[float]
• Description: Sample plane dimensions in micrometers

• Automatically converted to numpy array

• cycle_count: int

• Description: Number of simulation cycles

• exposure_time: int

• Description: Exposure time in milliseconds

• interval_time: int

• Description: Interval time in milliseconds

• oversample_motion_time: int

• Description: Oversample motion time in milliseconds

CondensateParameters

Defines parameters for molecular condensate simulation.

class CondensateParameters(BaseModel)

Fields

First dimension represents the types of molecules. (similar to the MoleculeParameters) - initial_centers: List[List[List[float]]] - Description: Initial centers in micrometers - 2D array automatically converted to numpy array

• initial_scale: List[List[float]]
• Description: Initial scale in micrometers

• Automatically converted to numpy array

• diffusion_coefficient: List[List[float]]

• Description: Diffusion coefficients in μm²/s

• Automatically converted to numpy array

• hurst_exponent: List[List[float]]

• Description: Hurst exponents for motion

• Automatically converted to numpy array

• density_dif: List[int]

• Description: Density difference parameter

OutputParameters

Defines parameters for simulation output.

class OutputParameters(BaseModel)

Fields

• output_path: str

• Description: Path for output files

• output_name: str

• Description: Base name for output files

• subsegment_type: str

• Description: Type of subsegmentation

• subsegment_number: int

• Description: Number of subsegments

ConfigList

Container model that combines all parameter models.

class ConfigList(BaseModel)

Fields

• CellParameters: CellParameters
• MoleculeParameters: MoleculeParameters
• GlobalParameters: GlobalParameters
• CondensateParameters: CondensateParameters
• OutputParameters: OutputParameters

Validation Features

All models include automatic validation and conversion: - Numeric arrays are automatically converted to numpy arrays - Field types are strictly enforced - Required fields must be present - Literal fields must match specified values

Usage Example

# Create configuration instance
config = ConfigList(
    CellParameter=CellParameters(
        cell_space=[[0, 10], [0, 10]],
        cell_axial_radius=5.0
    ),
    MoleculeParameter=MoleculeParameters(
        num_molecules=[100],
        track_type=["fbm"],
        # ... other required fields ...
    ),
    GlobalParameter=GlobalParameters(
        sample_plane_dim=[20.0, 20.0],
        cycle_count=100,
        exposure_time=100,
        interval_time=100,
        oversample_motion_time=10
    ),
    CondensateParameter=CondensateParameters(
        initial_centers=[[[5.0, 5.0]]],
        initial_scale=[[2.0]],
        diffusion_coefficient=[[0.1]],
        hurst_exponent=[[0.7]],
        density_dif=[2]
    ),
    OutputParameter=OutputParameters(
        output_path="./output",
        output_name="simulation",
        subsegment_type="uniform",
        subsegment_number=10
    )
)

Dependencies

• pydantic: For data validation and settings management
• numpy: For array operations
• typing: For type hints