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Bmz IO

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Function to export to the BioImage Model Zoo format.

export_to_bmz(model, config, path_to_archive, model_name, general_description, data_description, authors, input_array, output_array, covers=None, channel_names=None, model_version='0.1.0')

Export the model to BioImage Model Zoo format.

Arrays are expected to be SC(Z)YX with singleton dimensions allowed for S and C.

model_name should consist of letters, numbers, dashes, underscores and parentheses only.

Parameters:

  • model (CAREamicsModule) –

    CAREamics model to export.

  • config (Configuration) –

    Model configuration.

  • path_to_archive (Union[Path, str]) –

    Path to the output file.

  • model_name (str) –

    Model name.

  • general_description (str) –

    General description of the model.

  • data_description (str) –

    Description of the data the model was trained on.

  • authors (list[dict]) –

    Authors of the model.

  • input_array (ndarray) –

    Input array, should not have been normalized.

  • output_array (ndarray) –

    Output array, should have been denormalized.

  • covers (list of pathlib.Path or str, default: None ) –

    Paths to the cover images.

  • channel_names (Optional[list[str]], default: None ) –

    Channel names, by default None.

  • model_version (str, default: "0.1.0" ) –

    Model version.

load_from_bmz(path)

Load a model from a BioImage Model Zoo archive.

Parameters:

  • path ((Path, str or HttpUrl)) –

    Path to the BioImage Model Zoo archive. A Http URL must point to a downloadable location.

Returns:

  • FCNModel or VAEModel –

    The loaded CAREamics model.

  • Configuration –

    The loaded CAREamics configuration.

Raises: