colonyCounter.js

const http = require('http');
const fs = require('fs');
const url = require('url');
const cv = require('opencv');

const server =  http.createServer( (req, res) => {
	var request = url.parse(req.url, true);
	var action = request.pathname;

	if (action == '/copy.png') {
		var img = fs.readFileSync('./copy.png');
		res.writeHead(200, {'Content-Type': 'image/png' });
		res.end(img, 'binary');
	} else { 
	  res.writeHead(200, {'Content-Type': 'text/html'});
	  countColonies(res);
		res.end();
	}
});

function countColonies(res) {
	cv.readImage('./private/imgs/7.jpg', function(err, im) {
	  if (err) reject(err);

	  im = im.copy();

	  // store the dimensions in variables for later processing
	  var width = im.width();
	  var height = im.height();

	  if (width < 1 || height < 1) throw new Error('Image has no size');
		
		// set the width of the image to 1000 pixels
		nw = 1000;

		// maintain pixel ratio of image 
		nh = (height / width) * nw;

		// resize image to create standard variables for sizes of 
		// colonies to detect later
		im.resize(nw,nh);

		// copy resized image and store it in a variableto later draw  
		// circles around colonies for visualization
		var copied = im.copy();
		
		// apply gaussian blur
		im.gaussianBlur([11,11]);

		// apply canny filter
		im.canny(50, 125);

		var contours = im.findContours();

		var colonyCount = 0;

		// only draw and count found contours within range of deinfed length
	  for(i = 0; i < contours.size(); i++) {
	    if(contours.arcLength(i, true) < 100) {
	    	// draw contours for each found contour and color green
	      copied.drawContour(contours, i, [0, 255, 0], 3);
	      colonyCount += 1;
	    }
	  }

  	copied.save('./copy.png');

	  res.write('<div>'
	  	+ '<h1>'+colonyCount+'</h1>'
	  	+ '<img src="./copy.png" width="500"/>'
	  	+ '</div>'
	  );

	});
}

server.listen(8080);