morphoclass.console.cmd_xai module

XAI subcommands.

morphoclass.console.cmd_xai.check_overwrite_file(file_path)

Ask user if an existing file can be overwritten.

Parameters

file_path – A file path that shall be overwritten.

Returns

Whether or not the file can be overwritten.

Return type

bool

morphoclass.console.cmd_xai.get_datasets(input_csv, fitted_scaler=None)

Load datasets from a CSV file.

morphoclass.console.cmd_xai.to_persistence_dataset(dataset, feature='radial_distances')

Create a persistence dataset from MorphologyDataset.

Parameters

  • dataset – an instance of MorphologyDataset

  • feature –

    which feature to use as a filtration function. The default

    feature ‘radial_distances’ should be used for all datasets except those containing inverted cells (IPCs). For the inverted cells the feature ‘projection’ might be more useful as it retains information about orientation. Note, however, that ‘projection’ is not rotation-invariant, so the cells have to be properly oriented. For more information on this parameter see get_persistence_diagram in the tmd package.

Returns

  • diagrams – persistence diagrams

  • images – persistence images

  • labels – labels