cellmil.graph¶

class cellmil.graph.GraphCreator(config: GraphCreatorConfig)[source]¶

Bases: object

Main class for graph creation from segmented cells.

__init__(config: GraphCreatorConfig) → None[source]¶

_load_morphological_features(feature_extractors: list[cellmil.interfaces.FeatureExtractorConfig.ExtractorType]) → None[source]¶: Load morphological features for similarity-based graph creation.

_load_cells()[source]¶: Load cell data from the specified path.

create_graph() → None[source]¶: Create a graph from the segmented cells.

_launch_debug_visualizer() → None[source]¶: Launch the interactive debug visualizer.

_save_graph(node_features: Tensor, edge_indices: Tensor, edge_features: Tensor)[source]¶: Save the graph to a PyTorch file.

_plot_graph(node_features: Tensor, edge_indices: Tensor) → None[source]¶: Create and save a Plotly visualization of the graph.

_get_cells_position(node_features: Tensor) → Tensor[source]¶: Get the positions of the cell centroid for visualization.

Modules

`cellmil.graph.creator`
`cellmil.graph.debug_visualizer`	Interactive debug visualizer for graph creation hyperparameter tuning.
`cellmil.graph.graph_creator`