overlay

Counting connected components with the overlay library

This README provides demonstration code, documenting how to use this library to count connected components within an annotation PNG file.

package main

import (
	"fmt"
	"log"

	"github.com/carbocation/genomisc/overlay"
)

func main() {

	// Config.json file that comports with the type definition within
	// json-config.go
	configPath := "./demo.config.json"

	// Your annotation PNG. Based on the config file, pixels contributing to
	// background should be colored #000000, pixels contributing to ascending
	// aorta #010101, and pixels contributing to descending aorta #020202. No
	// other colors should exist in this image.
	filePath := "./annotation.png"

	// The connected components tool performs a secondary count that ignores
	// connected components that are built from of a small number of pixels
	// below this cutoff. This allows it to ignore small errors, such as an
	// errant, noisy pixel. The units for this value are "pixels". Here,
	// clusters with fewer than 5 pixels are ignored.
	threshold := 5

	// Those are the configurable parameters. Subsequent lines open the image
	// and your config file and apply the connected components algorithm.

	config, err := overlay.ParseJSONConfigFromPath(configPath)
	if err != nil {
		log.Fatalln(err)
	}

	rawOverlayImg, err := overlay.OpenImageFromLocalFile(filePath)
	if err != nil {
		log.Fatalln(err)
	}

	// Generate the function to count connected components within your
	// annotation file
	connected, err := overlay.NewConnected(rawOverlayImg)
	if err != nil {
		log.Fatalln(err)
	}

	// Perform the connected component count
	_, connectedCounts, _, thresholdedConnectedCounts, err := connected.Count(config.Labels, threshold)
	if err != nil {
		log.Fatalln(err)
	}

	// Report the results
	for label := range connectedCounts {
		fmt.Printf("Connected components for %s: %d\n", label.Label, connectedCounts[label])
		fmt.Printf("Connected components for %s, thresholded at %d pixels: %d\n", label.Label, threshold, thresholdedConnectedCounts[label])
	}
}