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Visualizing CT scans

torchmil.visualize.slices_to_canvas(slices_list, slice_size)

Given a list of images of CT scan slices, return a canvas with all the slices.

Parameters:

  • slices_list (list[ndarray]) –

    List of images of CT scan slices. Each image is a numpy array with shape (slice_size, slice_size, 3).

  • slice_size (int) –

    Size of the slices.

Returns:

  • canvas ( ndarray ) –

    Canvas with all the slices. It has shape (slice_size, bag_len*slice_size, 3).

torchmil.visualize.draw_slices_contour(canvas, slice_size, contour_prop=0.05)

Given a canvas with CT scan slices already drawn, draw a contour around each slice.

Parameters:

  • canvas (ndarray) –

    Canvas with all the slices. It has shape (slice_size, bag_len*slice_size, 3).

  • slice_size (int) –

    Size of the slices.

  • contour_prop (float, default: 0.05 ) –

    Proportion of the slice size that the contour will cover.

Returns:

  • canvas ( ndarray ) –

    Canvas with the contours drawn. It has shape (slice_size, bag_len*slice_size, 3).

torchmil.visualize.draw_heatmap_ctscan(canvas, values, slice_size, alpha=0.5, max_color=np.array([0.8392156862745098, 0.15294117647058825, 0.1568627450980392]), min_color=np.array([0.17254901960784313, 0.6274509803921569, 0.17254901960784313]))

Given a canvas with CT scan slices already drawn, draw a heatmap on top of the slices. This heatmap is defined by values, which should be normalized between 0 and 1.

Parameters:

  • canvas (ndarray) –

    Canvas with all the slices. It has shape (slice_size, bag_len*slice_size, 3).

  • values (ndarray) –

    List of values to draw the heatmap. Each value should be normalized between 0 and 1.

  • slice_size (int) –

    Size of the slices.

  • alpha (float, default: 0.5 ) –

    Alpha value for blending the heatmap with the canvas.

  • max_color (ndarray, default: array([0.8392156862745098, 0.15294117647058825, 0.1568627450980392]) ) –

    Color for the maximum value in the heatmap.

  • min_color (ndarray, default: array([0.17254901960784313, 0.6274509803921569, 0.17254901960784313]) ) –

    Color for the minimum value in the heatmap.

Returns:

  • canvas ( ndarray ) –

    Canvas with the heatmap drawn. It has shape (slice_size, bag_len*slice_size, 3).