cellsium package
CellSium - _Cell_ _Si_mulator for _micro_fluidic _m_icrocolonies
- cellsium.cli package
CellSizerCellTimerCelladd_output_prefix()initialize_cells()initialize_simulator()- cellsium.cli.render package
- cellsium.cli.simulate package
BoundariesFileBoundariesScaleFactorSimulationDurationSimulationOutputFirstStateSimulationOutputIntervalSimulationTimestepadd_boundaries_from_dxf()add_boundaries_from_tunables()compose()initialize_output_times_from_tunables()measure_duration()perform_outputs()perform_simulation()prepare_output_name()subcommand_main()
- cellsium.cli.training package
- cellsium.cli.cli module
- cellsium.geometry package
- cellsium.model package
AutoMesh3DBentRodCellGeometryCoccoidCopyableEllipsoidIdCounterInitializeWithParametersPlacedCellRectangleRepresentableRodShapedShapeShape3DSimulatedCellSizerCellSquareTimerCellTimestepWithAngleWithFluorescenceWithLineageWithLineageHistoryWithPositionWithProperDivisionBehaviorWithRandomSequencesWithTemporalLineageassemble_cell()generate_cell()h_to_s()s_to_h()- cellsium.model.initialization module
- cellsium.model.agent module
- cellsium.model.geometry module
- cellsium.output package
OutputOutputIndividualFilesOutputIndividualFilesWildcardOutputIndividualFilesZerosOutputReproducibleFilescheck_overwrite()ensure_extension()ensure_number()ensure_path()ensure_path_and_extension()ensure_path_and_extension_and_number()- cellsium.output.xml module
- cellsium.output.plot module
- cellsium.output.mesh module
- cellsium.output.svg module
- cellsium.output.render module
- cellsium.output.serialization module
- cellsium.output.gt module
- cellsium.simulation package
cellsium.random module
Random number generation infrastructure.
- class cellsium.random.RRF(mode: str = 'callable')
Bases:
objectReproducible random function.
- classmethod chain(func: KwargFunction, **kwargs) Iterator
Calls func with kwargs and yields from it.
- Parameters:
func – Function to call
kwargs – Kwargs to pass
- Returns:
Iterator of values
- classmethod compose(func: KwargFunction, **kwargs) Iterator
Calls a function func with an element of the sequences from the kwargs as kwargs.
- Parameters:
func – Function to be called
kwargs – Kwargs of sequences, of which an element each will be used for each function call
- Returns:
Iterator of values
- generator = <cellsium.random.RRF object>
- classmethod seed(seed: Optional[int] = None) int
Set the seed for the RRF.
- Parameters:
seed – Seed
- Returns:
Seed
- seed_sequence = SeedSequence( entropy=1, n_children_spawned=26, )
- seed_value: int = 1
- sequence = <cellsium.random.RRF object>
- classmethod spawn_generator() Generator
Generates a new np.random.Generator from the seed and the configured bitgenerator.
- Returns:
The Generator instance
- classmethod wrap(sequence: Iterable, func: AnyFunction) Iterator
Wraps the sequence with the function func so that each returned element x becomes func(x).
- Parameters:
sequence – Input sequence
func – Function to be called
- Returns:
Iterator of values
- class cellsium.random.RandomNumberGenerator(*args, **kwargs)
Bases:
TunableRandom number generator to be used
- classmethod available_rngs() Dict[str, Type[BitGenerator]]
- default: str = 'PCG64'
- classmethod get() Type[BitGenerator]
- classmethod test(value: str) bool
- type_
alias of
str
- value = 'PCG64'
- class cellsium.random.Seed(*args, **kwargs)
Bases:
TunableSeed for the random number generator
- default: int = 1
- type_
alias of
int
- value = 1
- cellsium.random.enforce_bounds(iterator: Iterator, minimum: float = -inf, maximum: float = inf) Iterator[Union[float, ndarray]]
Will iter thru an iterator til a value is within bounds. For arrays, all values will be considered.
- Parameters:
iterator – Iterator
minimum – Minimum value
maximum – Maximum value
- Returns:
An iterator of values within bounds
cellsium.parameters module
Main set of parameters for the simulation.
- class cellsium.parameters.Calibration(*args, **kwargs)
Bases:
TunableCalibration for outputs, micrometer per pixel
- default: float = 0.065
- value = 0.065
- class cellsium.parameters.Height(*args, **kwargs)
Bases:
TunableHeight of the (outputted) simulation
- default: float = 60.0
- value = 60.0
- class cellsium.parameters.NewCellBendLowerLower(*args, **kwargs)
Bases:
RandomlyDistributedBend factor minimum for the lower part of new new cells
- default: float = -0.1
- value = -0.1
- class cellsium.parameters.NewCellBendLowerUpper(*args, **kwargs)
Bases:
RandomlyDistributedBend factor maximum for the lower part of new new cells
- default: float = 0.1
- value = 0.1
- class cellsium.parameters.NewCellBendOverallLower(*args, **kwargs)
Bases:
RandomlyDistributedBend factor minimum for new new cells
- default: float = -0.1
- value = -0.1
- class cellsium.parameters.NewCellBendOverallUpper(*args, **kwargs)
Bases:
RandomlyDistributedBend factor maximum for new new cells
- default: float = 0.1
- value = 0.1
- class cellsium.parameters.NewCellBendUpperLower(*args, **kwargs)
Bases:
RandomlyDistributedBend factor minimum for the upper part of new new cells
- default: float = -0.1
- value = -0.1
- class cellsium.parameters.NewCellBendUpperUpper(*args, **kwargs)
Bases:
RandomlyDistributedBend factor maximum for the upper part of new new cells
- default: float = 0.1
- value = 0.1
- class cellsium.parameters.NewCellCount(*args, **kwargs)
Bases:
TunableNew cells to add to the simulation
- default: int = 1
- value = 1
- class cellsium.parameters.NewCellLength1Mean(*args, **kwargs)
Bases:
RandomlyDistributedMean cell length, subtype one
- default: float = 2.5
- value = 2.5
- class cellsium.parameters.NewCellLength1Std(*args, **kwargs)
Bases:
RandomlyDistributedStandard deviation of the cell length, subtype one
- default: float = 0.15
- value = 0.15
- class cellsium.parameters.NewCellLength2Mean(*args, **kwargs)
Bases:
RandomlyDistributedMean cell length, subtype two
- default: float = 1.25
- value = 1.25
- class cellsium.parameters.NewCellLength2Std(*args, **kwargs)
Bases:
RandomlyDistributedStandard deviation of the cell length, subtype one
- default: float = 0.15
- value = 0.15
- class cellsium.parameters.NewCellLengthAbsoluteMax(*args, **kwargs)
Bases:
TunableAbsolute maximum length of new cells
- default: float = 3.5
- value = 3.5
- class cellsium.parameters.NewCellLengthAbsoluteMin(*args, **kwargs)
Bases:
TunableAbsolute minimum length of new cells
- default: float = 0.8
- value = 0.8
- class cellsium.parameters.NewCellRadiusFromCenter(*args, **kwargs)
Bases:
RandomlyDistributedMaximum radius for new cells to be spawned from the origin
- default: float = 5.0
- value = 5.0
- class cellsium.parameters.NewCellWidthAbsoluteMax(*args, **kwargs)
Bases:
TunableAbsolute maximum width of new cells
- default: float = 1.5
- value = 1.5
- class cellsium.parameters.NewCellWidthAbsoluteMin(*args, **kwargs)
Bases:
TunableAbsolute minimum width of new cells
- default: float = 0.75
- value = 0.75
- class cellsium.parameters.NewCellWidthMean(*args, **kwargs)
Bases:
RandomlyDistributedMean cell width for new cells
- default: float = 1.0
- value = 1.0
- class cellsium.parameters.NewCellWidthStd(*args, **kwargs)
Bases:
RandomlyDistributedStandard deviation of the width of new cells
- default: float = 0.1
- value = 0.1
- class cellsium.parameters.RandomlyDistributed(*args, **kwargs)
Bases:
TunableParent class for randomly distributed tunables
- class cellsium.parameters.Width(*args, **kwargs)
Bases:
TunableWidth of the (outputted) simulation
- default: float = 40.0
- value = 40.0
- cellsium.parameters.h_to_s(hours: Union[float, ndarray]) Union[float, ndarray]
Convert hours to seconds.
- Parameters:
hours – Hours
- Returns:
Seconds
- cellsium.parameters.pixel_to_um(pix: Union[float, ndarray]) Union[float, ndarray]
Convert pixel to micrometer.
- Parameters:
pix – Pixel value
- Returns:
Micrometer value
- cellsium.parameters.s_to_h(seconds: Union[float, ndarray]) Union[float, ndarray]
Convert seconds to hours.
- Parameters:
seconds – Seconds
- Returns:
Hours
- cellsium.parameters.um_to_pixel(um: Union[float, ndarray]) Union[float, ndarray]
Convert micrometer to pixel.
- Parameters:
um – Micrometer value
- Returns:
Pixel value
cellsium.typing module
Type hints definitions.
- class cellsium.typing.AnyFunction
Bases:
Protocol
- class cellsium.typing.KwargFunction
Bases:
Protocol