Module iaf.color

Color functions.

Functions

def get_hilo_cmap(n: int = 256) ‑> matplotlib.colors.ListedColormap

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 : ListedColormap

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

def get_labels_cmap(n: int = 256) ‑> matplotlib.colors.ListedColormap

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 : ListedColormap

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

def to_composite(images: list[numpy.ndarray], colors: list[typing.Union[iaf.color._color.Color, list, tuple]], clip_percentile: float = 0.1) ‑> numpy.ndarray

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 : np.ndarray

RGB composite image

def to_rgb(img: numpy.ndarray, color: Union[iaf.color._color.Color, list, tuple], clip_percentile: float = 0.1) ‑> numpy.ndarray

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 : np.ndarray

RGB image

Classes

class Color (*args, **kwds)

A few predefined colors.

Expand source code

class Color(Enum):
    """A few predefined colors."""

    Red = (1.0, 0.0, 0.0)
    """Red = (1.0, 0.0, 0.0)"""
    Green = (0.0, 1.0, 0.0)
    """Green = (0.0, 1.0, 0.0)"""
    Blue = (0.0, 0.0, 1.0)
    """Blue = (0.0, 0.0, 1.0)"""
    Yellow = (1.0, 1.0, 0.0)
    """Yellow = (1.0, 1.0, 0.0)"""
    Cyan = (0.0, 1.0, 1.0)
    """Cyan = (0.0, 1.0, 1.0)"""
    Orange = (1.0, 0.5, 0.0)
    """Orange = (1.0, 0.5, 0.0)"""
    Gray = (1.0, 1.0, 1.0)
    """Gray = (1.0, 1.0, 1.0)"""

Ancestors

• enum.Enum

Class variables

var Blue

Blue = (0.0, 0.0, 1.0)

var Cyan

Cyan = (0.0, 1.0, 1.0)

var Gray

Gray = (1.0, 1.0, 1.0)

var Green

Green = (0.0, 1.0, 0.0)

var Orange

Orange = (1.0, 0.5, 0.0)

var Red

Red = (1.0, 0.0, 0.0)

var Yellow

Yellow = (1.0, 1.0, 0.0)