Real-time Microbiome Monitoring

#!/usr/bin/env python

import mraa
import time
import numpy as np 
import cv2
import os


button = mraa.Gpio(6)
button.dir(mraa.DIR_IN)

pump = mraa.Gpio(11)
pump.dir(mraa.DIR_OUT)
pump.write(0)

led = mraa.Gpio(12)
led.dir(mraa.DIR_OUT)
led.write(0)

buzzer = mraa.Gpio(4)
buzzer.dir(mraa.DIR_OUT)
buzzer.write(0)

cap = cv2.VideoCapture(0)
ret, frame = cap.read()

# delays
pumpDelay = 45
soakDelay = 15

# iteration = 0


# define range of pink color in HSV
lower_pink = np.array([110,50,50])
upper_pink = np.array([130,255,255])


def captureImage():
        # Take each frame
        ret, frame = cap.read()
        print "read ret: " + str(ret)

        # Convert BGR to HSV
        hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV)
        return hsv

def readImage(imgname):
        print "read image" + imgname
        img = cv2.imread(imgname,0)
        # Convert BGR to HSV
        hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)
        return hsv


def calculatePinkPixels(image):
        mask = cv2.inRange(image, lower_pink, upper_pink)
        return cv2.countNonZero(mask)



def getButtonPress():
        while True:
                if (button.read() == 1):
			print "Button Pressed %f" % (time.time())
                        return
                else:
                        time.sleep(0.05)

def sendCurl(message):
        command = "curl -X POST -H \"Content-Type: application/json\" -d '{\"value1\":\"%s\"}' https://maker.ifttt.com/trigger/dnaDetected/with/key/cTs_Jqc-oa-NLl-jo6dKL1" % (message)
        os.system(command)

def chirpBuzz():
	buzzer.write(1)
	time.sleep(0.05)
        buzzer.write(0)

def takeMeasurement(iteration):
        print "...cap img 1"
        img1 = captureImage()
        # img1 = readImage("test_img#1.jpg")
        cv2.imwrite('/home/root/programs/it%d-img1.jpg' % (iteration), img1, [cv2.IMWRITE_JPEG_QUALITY, 90])
        
        print "...pump 1"
        pump.write(1)
        time.sleep(pumpDelay)

        print "...pump 0"
        pump.write(0)

        time.sleep(soakDelay)
        
        print "...cap img 2"
        img2 = captureImage()
        # img1 = readImage("test_img#2.jpg")
        cv2.imwrite('/home/root/programs/it%d-img2.jpg' % (iteration), img2, [cv2.IMWRITE_JPEG_QUALITY, 90])

        print "...calc pixels"
        diffPinkPixels = calculatePinkPixels(img2) - calculatePinkPixels(img1)
        print "...diff pink pixels %d" % (diffPinkPixels)

        if diffPinkPixels > 100:
                message = "DETECTED"
        else:
                message = "UNDETECTED"

        print "...send curl"
        sendCurl(message)

def run():
        iteration = 0
        while True:
                getButtonPress()

                print "buttonPressed"
                led.write(1)
                print "led on"
                print "start measurement"
                takeMeasurement(iteration)
                print "end measurement"
                led.write(0)
                iteration = iteration + 1



def end():
        print "releasing camera"
        cap.release()        
        

try:
        run()
finally:
        end()