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Prediction Utils

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Deprecated module.

convert_outputs(predictions, tiled)

Convert the Lightning trainer outputs to the desired form.

This method allows stitching back together tiled predictions.

Parameters:

  • predictions (list) –

    Predictions that are output from Trainer.predict.

  • tiled (bool) –

    Whether the predictions are tiled.

Returns:

  • list of numpy.ndarray or numpy.ndarray –

    list of arrays with the axes SC(Z)YX. If there is only 1 output it will not be in a list.

convert_outputs_pn2v(predictions, tiled)

Convert the Lightning trainer outputs to the desired form.

This method allows stitching back together tiled predictions.

Parameters:

  • predictions (list) –

    Predictions that are output from Trainer.predict. Length of list the total number of tiles divided by the batch size. Each element consists of a tuple of ((prediction, mse), tile_info_list). 1st dimension of each tensor is the bs. Length of tile info list is the batch size.

  • tiled (bool) –

    Whether the predictions are tiled.

Returns:

  • tuple[list[NDArray], list[NDArray]] –

    Tuple of (predictions, mmse) where each is a list of arrays with axes SC(Z)YX.

stitch_prediction_single(tiles, tile_infos)

Stitch tiles back together to form a full image.

Tiles are of dimensions SC(Z)YX, where C is the number of channels and can be a singleton dimension.

Parameters:

  • tiles (list of numpy.ndarray) –

    Cropped tiles and their respective stitching coordinates.

  • tile_infos (list of TileInformation) –

    List of information and coordinates obtained from dataset.tiled_patching.extract_tiles.

Returns:

  • ndarray –

    Full image, with dimensions SC(Z)YX.