visualizations

visualizations#

Source code: armscan_env/util/visualizations.py

show_clusters(tissue_clusters: TissueClusters, slice: ndarray, ax: Axes | None = None, extent: tuple[int, int, int, int] | None = None, **imshow_kwargs: Any) → AxesImage | Axes[source]#

Plot the clusters of all tissues in a slice.

Parameters:

  • tissue_clusters -- dictionary of tissues and their clusters

  • slice -- image slice to cluster

  • ax -- axis to plot on

  • extent -- extent of the image, can be set to change the reference frame

Returns:

None.

show_slices(data: ndarray, start: int, end: int, lap: int, col: int = 5, extent: tuple[int, int, int, int] | None = None, cmap: str | None = None, axis: bool = False, **imshow_kwargs: Any) → ndarray[Any, Any][source]#

Function to display row of image slices.

Parameters:

  • data -- 3D image data

  • start -- starting slice number

  • end -- ending slice number

  • lap -- number of slices to skip

  • col -- number of columns to display

  • extent -- extent of the image, can be set to change the reference frame

  • cmap -- color map to use

  • axis -- whether to display axis

  • imshow_kwargs -- additional keyword arguments to pass to imshow

Returns:

None.

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