SpatialDataSimulator.py

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High-level description

The SpatialDataSimulator class in SpatialDataSimulator.py defines an abstract base class for simulating spatial data on a CassiopeiaTree. It provides a blueprint for overlaying spatial coordinates onto the tree, mimicking the spatial organization of cells in a tissue. This abstract class is intended to be subclassed for specific spatial simulation models.

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Code Structure

This code defines a single abstract class SpatialDataSimulator which inherits from the DataSimulator class. The SpatialDataSimulator class doesn’t directly interact with other symbols in the code, but it defines an abstract method overlay_data that needs to be implemented by its subclasses.

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References

This code references the following code symbols:

• cassiopeia.data.CassiopeiaTree
• cassiopeia.simulator.DataSimulator.DataSimulator

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Symbols

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SpatialDataSimulator

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Description

This abstract class serves as a template for simulating spatial data on a CassiopeiaTree. It defines the structure for overlaying spatial coordinates onto the tree nodes, representing the spatial arrangement of cells. Subclasses of SpatialDataSimulator implement the overlay_data method to apply specific spatial models.

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Inputs

This class doesn’t have an __init__ method and therefore doesn’t take any direct inputs.

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Outputs

This class doesn’t directly return any outputs.

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Internal Logic

This class doesn’t have any internal logic as it’s an abstract class.

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Side Effects

This class doesn’t have any side effects as it’s an abstract class.

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Dependencies

This code depends on the following external libraries:

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overlay_data

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Description

This abstract method defines the interface for overlaying spatial data onto a CassiopeiaTree. Subclasses must implement this method to apply specific spatial simulation models.

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Inputs

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Outputs

This method doesn’t return any value, it modifies the CassiopeiaTree object in-place.

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Internal Logic

This method is abstract and doesn’t have an implementation in this class. Subclasses are responsible for providing the implementation based on the specific spatial model.