jicbioimage.illustrate

Module for creating illustrations.

To create an annotated image we need an instance of the jicbioimage.illustrate.AnnotatedImage class.

>>> from jicbioimage.illustrate import AnnotatedImage

Suppose that we have an existing image.

>>> from jicbioimage.core.image import Image
>>> im = Image((50,50))

We can use this image to create an canvas instance populated with the data as a RGB gray scale image.

>>> canvas = AnnotatedImage.from_grayscale(im)

The jicbioimage.illustrate.Canvas instance has built in annotation functionality.

One can use it to draw crosses.

>>> canvas.draw_cross(10, 20)

One can use it to mask out bitmaps (in the example below with the color cyan).

>>> bitmap = np.zeros((50, 50), dtype=bool)
>>> bitmap[30:40, 30:40] = True
>>> canvas.mask_region(bitmap, color=(0, 255, 255))

One can use it to add text at particular locations on the canvas.

>>> canvas.text_at("Hello", 30, 60)

class jicbioimage.illustrate.AnnotatedImage

Class for building up annotated images.

static from_grayscale(im, channels_on=(True, True, True))

Return a canvas from a grayscale image.

Parameters:im – single channel image Channels_on:channels to populate with input image Returns:jicbioimage.illustrate.Canvas

class jicbioimage.illustrate.Canvas

Class for building up annotated images.

static blank_canvas(width, height)

Return a blank canvas to annotate.

Parameters:

• width – xdim (int)
• height – ydim (int)

Returns:

jicbioimage.illustrate.Canvas

draw_cross(position, color=(255, 0, 0), radius=4)

Draw a cross on the canvas.

Parameters:

• position – (row, col) tuple
• color – RGB tuple
• radius – radius of the cross (int)

draw_line(pos1, pos2, color=(255, 0, 0))

Draw a line between pos1 and pos2 on the canvas.

Parameters:

• pos1 – position 1 (row, col) tuple
• pos2 – position 2 (row, col) tuple
• color – RGB tuple

mask_region(region, color=(0, 255, 0))

Mask a region with a color.

Parameters:

• region – jicbioimage.core.region.Region
• color – RGB tuple

text_at(text, position, color=(255, 255, 255), size=12, antialias=False, center=False)

Write text at x, y top left corner position.

By default the x and y coordinates represent the top left hand corner of the text. The text can be centered vertically and horizontally by using setting the center option to True.

Parameters:

• text – text to write
• position – (row, col) tuple
• color – RGB tuple
• size – font size
• antialias – whether or not the text should be antialiased
• center – whether or not the text should be centered on the input coordinate