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Patching

Source

A module to contain type definitions relating to patching strategies.

PatchSpecs

Bases: TypedDict

A dictionary that specifies a single patch in a series of ImageStacks.

Attributes:

  • data_idx (int) –

    Determines which ImageStack a patch belongs to, within a series of ImageStacks.

  • sample_idx (int) –

    Determines which sample a patch belongs to, within an ImageStack.

  • coords (sequence of int) –

    The top-left (and first z-slice for 3D data) of a patch. The sequence will have length 2 or 3, for 2D and 3D data respectively.

  • patch_size (sequence of int) –

    The size of the patch. The sequence will have length 2 or 3, for 2D and 3D data respectively.

Patching

Bases: Protocol

An interface for patching strategies.

Patching strategies are a component of the CAREamicsDataset; they determine how patches are extracted from the underlying data.

Attributes:

  • n_patches (int) –

    The number of patches that the patching strategy will return.

Methods:

  • get_patch_spec –

    Get a patch specification for a given patch index.

n_patches property

The number of patches that the patching strategy will return.

It also determines the maximum index that can be given to get_patch_spec, and the length of the CAREamicsDataset.

Returns:

  • int –

    Number of patches.

get_patch_indices(data_idx)

Get the patch indices will return patches for a specific image_stack.

The image_stack corresponds to the given data_idx.

Parameters:

  • data_idx (int) –

    An index that corresponds to a given image_stack.

Returns:

  • sequence of int –

    A sequence of patch indices, that when used to index the CAREamicsDataset will return a patch that comes from theimage_stackcorresponding to the givendata_idx`.

get_patch_spec(index)

Get a patch specification for a given patch index.

This method is intended to be called from within the CAREamicsDataset.__getitem__. The index will be passed through from this method.

Parameters:

  • index (int) –

    A patch index.

Returns:

  • PatchSpecs –

    A dictionary that specifies a single patch in a series of ImageStacks.

TileSpecs

Bases: PatchSpecs

A dictionary that specifies a single patch in a series of ImageStacks.

Attributes:

  • data_idx (int) –

    Determines which ImageStack a patch belongs to, within a series of ImageStacks.

  • sample_idx (int) –

    Determines which sample a patch belongs to, within an ImageStack.

  • coords (sequence of int) –

    The top-left (and first z-slice for 3D data) of a patch. The sequence will have length 2 or 3, for 2D and 3D data respectively.

  • patch_size (sequence of int) –

    The size of the patch. The sequence will have length 2 or 3, for 2D and 3D data respectively.

  • crop_coords (sequence of int) –

    The top-left side of where the tile will be cropped, in coordinates relative to the tile.

  • crop_size (sequence of int) –

    The size of the cropped tile.

  • stitch_coords (sequence of int) –

    Where the tile will be stitched back into an image, taking into account that the tile will be cropped, in coords relative to the image.

  • total_tiles (int) –

    Number of tiles belonging to the same data.

is_tile_specs(specs)

Determine whether a given PatchSpecs is a TileSpecs.

Used for type checking.

Parameters:

Returns:

  • bool –

    Whether the given specs is a TileSpecs.