Color#

Provides tools for color manipulation.

Note

All numerical color values are by default returned using the range [0,1].

color(arg, alpha=None, as_int=False, int_type=<class 'int'>)[source]#

Converts color arguent to rgb values

Arguments

argobject: Color specifiction, e.g. a rgb tuple, color name from matplotlib or vispy, hex code
alphaNone, bool or float: Include the alpha value in the rgb tuple. If None and an alpha value exists, it is kept, otherwise it is not included. If False the alpha value is not included. If True, the alpha value is included and set to 1 in case its not given in the input.
as_intbool: If True, return colors as integers in range 0 to 255.

Returns

rgblist of float or int: RBG or RGBA values for the colors.

color_map(cmap=None, alpha=True, as_int=False, int_type=<class 'int'>)#

Convert argument to a color map function.

Arguments

cmapNone, string, tuple or list of colors: Color map specification. If a tuple is given a colormap that linearly interpolates is returned.
alphaNone, bool, int or float: Include the alpha value in the color map.
as_intbool: If True return color maps as integers in range 0 to 255.
int_typedtype: The type to use for integer color maps.

Returns

cmapfunction: A color map function that maps floats in [0,1] to a RBG or RGBA tuples.

colormap(cmap=None, alpha=True, as_int=False, int_type=<class 'int'>)[source]#

Convert argument to a color map function.

Arguments

cmapNone, string, tuple or list of colors: Color map specification. If a tuple is given a colormap that linearly interpolates is returned.
alphaNone, bool, int or float: Include the alpha value in the color map.
as_intbool: If True return color maps as integers in range 0 to 255.
int_typedtype: The type to use for integer color maps.

Returns

cmapfunction: A color map function that maps floats in [0,1] to a RBG or RGBA tuples.

darker(arg, fraction=0.3)[source]#

gray_image_to_rgb(image, color_name, pseudo_z_score=False, normalize=False, range_max=None)[source]#

Convert a grayscale image to a colored RGB image.

Parameters: image (numpy.ndarray): The grayscale image to convert. color (str): The color to convert to. Must be one of ‘cyan’, ‘magenta’, ‘yellow’, ‘red’, ‘green’, ‘blue’.

Returns: numpy.ndarray: The converted RGB image.

hex_to_rgb(color, alpha=None, as_int=False)[source]#

Return rgb color from hex code

Arguments

colorstring: Hex code of the color
alphaNone, bool, int or float: Include the alpha value in the rgb tuple. If None the alpha value is included if given in the hex code, if False no alpha value is given, if True the alpha value is included and set to 1 in case its not given in the input.
as_intbool: If True return colors as integers in range 0 to 255.

Returns

rgblist of float or int: RBG or RGBA values for the colors.

lighter(arg, fraction=0.3)[source]#

orientation_to_boys(orientations, alpha=None, as_int=False, normalize=True)[source]#

Colormap mapping 3d orientation vectors into rgb colors.

Arguments

orientationsarray: List of 3d vectors as nx3 array
alphaNone, bool, int or float: Include the alpha value in the color map.
as_intbool: If True return color maps as integers in range 0 to 255.
normalizebool: Normalize vectors to unit length. set to False to avoid overhead when passing normalized vectors.

Returns

colorsarray: RGB colors for the orientation vectors according to Boys coloring.

Note

The Boys color map is a smooth way of coloring orientations.

References

[1] https://ieeexplore.ieee.org/abstract/document/5290761

orientation_to_rgb(orientation, alpha=None, as_int=False)[source]#

Color map mapping 3d orientation vectors into rgb colors using normalized coordinates.

Arguments

orientationsarray: List of 3d vectors as nx3 array.
alphaNone, bool, int or float: Include the alpha value in the color map.
as_intbool: If True return color maps as integers in range 0 to 255.

Returns

colorsarray: RGB colors for the orientation vectors according to standard coloring.

Note

This color map is not continuous.

rand_cmap(n_labels, map_type='bright', first_color_black=True, last_color_black=False, cmap_name='Paired')[source]#

Creates a random colormap to be used together with matplotlib. Useful for segmentation tasks

Arguments

n_labelsint: Number of labels (size of colormap)
map_typestr: ‘bright’ for strong colors, ‘soft’ for pastel colors
first_color_blackbool: Option to use first color as black, True or False
last_color_blackbool: Option to use last color as black, True or False

Returns

random_colormaplist of RGB colors: colormap for matplotlib

rgb_LUT()[source]#

Returns a lookup table listing all integer rgb colors

Note

Useful to color data and plot in imagej.

rgb_to_LUT(rgb)[source]#

Converts the rgb colors to the index color in the full rgb color look up table

Arguments

rgbarray: Integer rgb values as nX3 array

Returns

indexarray: The indices of the rgb values in the full rgb LUT.

rgb_to_hex(rgb, alpha=None, as_int=False)[source]#

Return hex code from rgb or rgba colors

Arguments

colortuple of int or float: Hex code of the color
alphaNone, bool or float: Include the alpha value in the rgb tuple
as_intbool: If True return colors as integers in range 0 to 255.

Returns

rgblist of float or int: RBG or RGBA values for the colors.

write_LUT(filename, colors)[source]#

Write a lut lookup table file from a list of colors for use with imagej

Arguments

filenamestr: file name of the lookup table
colorsarray: Colors as nX3 array to write to te ookup table

Returns

filenamestr: Filename of the lookup table.

write_PAL(filename, colors)[source]#

Write a pal pallette file from a list of colors for use with e.g. imaris

Arguments

filenamestr: file name of the lookup table
colorsarray: Colors as nX3 array to write to te ookup table

Returns

filenamestr: Filename of the lookup table.