roimarker 0.2.0

A ROI marker using matplotlib

Roimarker

A simple region of interest (ROI) creator using matplotlib to annotate images with rectangular ROI.

Warning: Roimarker is still quite plain and unfinished.

Installing

pip install roimarker

Usage

Both (1) and (2) (below) launch the same interface, iterating over the given images.

1) Standalone

python -m roimarker DIRECTORY

where DIRECTORY contains all the image files to annotate. This saves markings.json file when finished (see below).

2) As part of your program

import matplotlib.pyplot as plt
from roimarker import Marker

# Create matplotlib figure and ax
fig, ax = plt.subplots()

# List of images to annotate
image_fns = ['image1.tif', 'image2.tif', 'image3.tif']

marker = Marker(fig, ax, image_fns, 'markings.json')
marker.run()

This opens a window where the user can draw a number of rectangle ROIs on the images. Pressing n advances to the next image, and z, x, c and v can be used to adjust brightness/contrast. After going through all the images or when manually pressing w, a markings.json file in the current directory, containin the ROIs in the following format

{fn1: [ROI_1, ROI_2, ROI_3, ..], fn2: [ROI_1, ...], ...}

where
	ROI_i = [x,y,w,h]