iaf.color

Color functions.

class iaf.color.Color(value)[source]

Bases: Enum

A few predefined colors.

Blue = (0.0, 0.0, 1.0)

Blue = (0.0, 0.0, 1.0)

Cyan = (0.0, 1.0, 1.0)

Cyan = (0.0, 1.0, 1.0)

Gray = (1.0, 1.0, 1.0)

Gray = (1.0, 1.0, 1.0)

Green = (0.0, 1.0, 0.0)

Green = (0.0, 1.0, 0.0)

Orange = (1.0, 0.5, 0.0)

Orange = (1.0, 0.5, 0.0)

Red = (1.0, 0.0, 0.0)

Red = (1.0, 0.0, 0.0)

Yellow = (1.0, 1.0, 0.0)

Yellow = (1.0, 1.0, 0.0)

iaf.color.get_hilo_cmap(n: int = 256) → ListedColormap[source]

Return the HiLo colormap that shows pixels at 0 intensity as blue and saturated pixels as red.

Parameters:

n (int) – Number of different colors (optional, default 256). Use 256 for 8-bit images and 65535 for 16-bit images.

Returns:

colormap – Colormap to be passed to imshow() and other matplotlib functions that take colormaps.

Return type:

ListedColormap

iaf.color.get_labels_cmap(n: int = 256) → ListedColormap[source]

Return a color map that is particularly suited to color-code labels.

Parameters:

n (int) – Number of different colors (optional, default 256). Use 256 for 8-bit images and 65535 for 16-bit images.

Returns:

colormap – Colormap to be passed to imshow() and other matplotlib functions that take colormaps.

Return type:

ListedColormap

iaf.color.to_composite(images: list[ndarray], colors: list[Color | list | tuple], clip_percentile: float = 0.1) → ndarray[source]

Create a composite image from a series of gray values images and the corresponding colors.

Parameters:

  • images (list[np.ndarray]) – List of gray-value images.

  • colors (list[Union[Color, list, tuple]]) – List of colors to be used to create a composite. One for each image. Each color is a Color, list or tuple with values for (R, G, B) between 0.0 and 1.0

  • clip_percentile (float) – Percentile to clip intensity in the low and high parts of the dynamic range.

Returns:

composite – RGB composite image

Return type:

np.ndarray

iaf.color.to_rgb(img: ndarray, color: Color | list | tuple, clip_percentile: float = 0.1) → ndarray[source]

Create an RGB image from a single-channel image using a specific color.

Adapted from: https://bioimagebook.github.io/chapters/1-concepts/4-colors/python.html

Parameters:

  • img (np.ndarray) – 2D image to be displayed.

  • color (Color, list or tuple) – Values for (R, G, B) between 0.0 and 1.0

  • clip_percentile (float) – Percentile to clip intensity in the low and high parts of the dynamic range.

Returns:

rgb – RGB image

Return type:

np.ndarray