#!/usr/bin/env python3 ''' PySpectrometer2 Les Wright 2022 https://www.youtube.com/leslaboratory https://github.com/leswright1977 This project is a follow on from: https://github.com/leswright1977/PySpectrometer This is a more advanced, but more flexible version of the original program. Tk Has been dropped as the GUI to allow fullscreen mode on Raspberry Pi systems and the iterface is designed to fit 800*480 screens, which seem to be a common resolutin for RPi LCD's, paving the way for the creation of a stand alone benchtop instrument. Whats new: Higher resolution (800px wide graph) 3 row pixel averaging of sensor data Fullscreen option for the Spectrometer graph 3rd order polymonial fit of calibration data for accurate measurement. Improved graph labelling Labelled measurement cursors Optional waterfall display for recording spectra changes over time. Key Bindings for all operations All old features have been kept, including peak hold, peak detect, Savitsky Golay filter, and the ability to save graphs as png and data as CSV. For instructions please consult the readme! ''' import cv2 import time import numpy as np from specFunctions import wavelength_to_rgb,savitzky_golay,peakIndexes,readcal,writecal,background,generateGraticule import base64 import argparse from picamera2 import Picamera2 parser = argparse.ArgumentParser() group = parser.add_mutually_exclusive_group() group.add_argument("--fullscreen", help="Fullscreen (Native 800*480)",action="store_true") group.add_argument("--waterfall", help="Enable Waterfall (Windowed only)",action="store_true") args = parser.parse_args() dispFullscreen = False dispWaterfall = False if args.fullscreen: print("Fullscreen Spectrometer enabled") dispFullscreen = True if args.waterfall: print("Waterfall display enabled") dispWaterfall = True frameWidth = 800 frameHeight = 600 picam2 = Picamera2() #need to spend more time at: https://datasheets.raspberrypi.com/camera/picamera2-manual.pdf #but this will do for now! #min and max microseconds per frame gives framerate. #30fps (33333, 33333) #25fps (40000, 40000) picamGain = 10.0 video_config = picam2.create_video_configuration(main={"format": 'RGB888', "size": (frameWidth, frameHeight)}, controls={"FrameDurationLimits": (33333, 33333)}) picam2.configure(video_config) picam2.start() #Change analog gain #picam2.set_controls({"AnalogueGain": 10.0}) #Default 1 #picam2.set_controls({"Brightness": 0.2}) #Default 0 range -1.0 to +1.0 #picam2.set_controls({"Contrast": 1.8}) #Default 1 range 0.0-32.0 title1 = 'PySpectrometer 2 - Spectrograph' title2 = 'PySpectrometer 2 - Waterfall' stackHeight = 320+80+80 #height of the displayed CV window (graph+preview+messages) if dispWaterfall == True: #watefall first so spectrum is on top cv2.namedWindow(title2,cv2.WINDOW_GUI_NORMAL) cv2.resizeWindow(title2,frameWidth,stackHeight) cv2.moveWindow(title2,200,200); if dispFullscreen == True: cv2.namedWindow(title1,cv2.WND_PROP_FULLSCREEN) cv2.setWindowProperty(title1,cv2.WND_PROP_FULLSCREEN,cv2.WINDOW_FULLSCREEN) else: cv2.namedWindow(title1,cv2.WINDOW_GUI_NORMAL) cv2.resizeWindow(title1,frameWidth,stackHeight) cv2.moveWindow(title1,0,0); #settings for peak detect savpoly = 7 #savgol filter polynomial max val 15 mindist = 50 #minumum distance between peaks max val 100 thresh = 20 #Threshold max val 100 calibrate = False clickArray = [] cursorX = 0 cursorY = 0 def handle_mouse(event,x,y,flags,param): global clickArray global cursorX global cursorY mouseYOffset = 160 if event == cv2.EVENT_MOUSEMOVE: cursorX = x cursorY = y if event == cv2.EVENT_LBUTTONDOWN: mouseX = x mouseY = y-mouseYOffset clickArray.append([mouseX,mouseY]) #listen for click on plot window cv2.setMouseCallback(title1,handle_mouse) font=cv2.FONT_HERSHEY_SIMPLEX intensity = [0] * frameWidth #array for intensity data...full of zeroes holdpeaks = False #are we holding peaks? measure = False #are we measuring? recPixels = False #are we measuring pixels and recording clicks? #messages msg1 = "" saveMsg = "No data saved" #blank image for Waterfall waterfall = np.zeros([320,frameWidth,3],dtype=np.uint8) waterfall.fill(0) #fill black #Go grab the computed calibration data caldata = readcal(frameWidth) wavelengthData = caldata[0] calmsg1 = caldata[1] calmsg2 = caldata[2] calmsg3 = caldata[3] #generate the craticule data graticuleData = generateGraticule(wavelengthData) tens = (graticuleData[0]) fifties = (graticuleData[1]) def snapshot(savedata): now = time.strftime("%Y%m%d--%H%M%S") timenow = time.strftime("%H:%M:%S") imdata1 = savedata[0] graphdata = savedata[1] if dispWaterfall == True: imdata2 = savedata[2] cv2.imwrite("waterfall-" + now + ".png",imdata2) cv2.imwrite("spectrum-" + now + ".png",imdata1) #print(graphdata[0]) #wavelengths #print(graphdata[1]) #intensities f = open("Spectrum-"+now+'.csv','w') f.write('Wavelength,Intensity\r\n') for x in zip(graphdata[0],graphdata[1]): f.write(str(x[0])+','+str(x[1])+'\r\n') f.close() message = "Last Save: "+timenow return(message) while True: # Capture frame-by-frame frame = picam2.capture_array() y=int((frameHeight/2)-40) #origin of the vertical crop #y=200 #origin of the vert crop x=0 #origin of the horiz crop h=80 #height of the crop w=frameWidth #width of the crop cropped = frame[y:y+h, x:x+w] bwimage = cv2.cvtColor(cropped,cv2.COLOR_BGR2GRAY) rows,cols = bwimage.shape halfway =int(rows/2) #show our line on the original image #now a 3px wide region cv2.line(cropped,(0,halfway-2),(frameWidth,halfway-2),(255,255,255),1) cv2.line(cropped,(0,halfway+2),(frameWidth,halfway+2),(255,255,255),1) #banner image decoded_data = base64.b64decode(background) np_data = np.frombuffer(decoded_data,np.uint8) img = cv2.imdecode(np_data,3) messages = img #blank image for Graph graph = np.zeros([320,frameWidth,3],dtype=np.uint8) graph.fill(255) #fill white #Display a graticule calibrated with cal data textoffset = 12 #vertial lines every whole 10nm for position in tens: cv2.line(graph,(position,15),(position,320),(200,200,200),1) #vertical lines every whole 50nm for positiondata in fifties: cv2.line(graph,(positiondata[0],15),(positiondata[0],320),(0,0,0),1) cv2.putText(graph,str(positiondata[1])+'nm',(positiondata[0]-textoffset,12),font,0.4,(0,0,0),1, cv2.LINE_AA) #horizontal lines for i in range (320): if i>=64: if i%64==0: #suppress the first line then draw the rest... cv2.line(graph,(0,i),(frameWidth,i),(100,100,100),1) #Now process the intensity data and display it #intensity = [] for i in range(cols): #data = bwimage[halfway,i] #pull the pixel data from the halfway mark #print(type(data)) #numpy.uint8 #average the data of 3 rows of pixels: dataminus1 = bwimage[halfway-1,i] datazero = bwimage[halfway,i] #pull the pixel data from the halfway mark dataplus1 = bwimage[halfway+1,i] data = (int(dataminus1)+int(datazero)+int(dataplus1))/3 data = np.uint8(data) if holdpeaks == True: if data > intensity[i]: intensity[i] = data else: intensity[i] = data if dispWaterfall == True: #waterfall.... #data is smoothed at this point!!!!!! #create an empty array for the data wdata = np.zeros([1,frameWidth,3],dtype=np.uint8) index=0 for i in intensity: rgb = wavelength_to_rgb(round(wavelengthData[index]))#derive the color from the wavelenthData array luminosity = intensity[index]/255 b = int(round(rgb[0]*luminosity)) g = int(round(rgb[1]*luminosity)) r = int(round(rgb[2]*luminosity)) #print(b,g,r) #wdata[0,index]=(r,g,b) #fix me!!! how do we deal with this data?? wdata[0,index]=(r,g,b) index+=1 #bright and contrast of final image contrast = 2.5 brightness =10 wdata = cv2.addWeighted( wdata, contrast, wdata, 0, brightness) waterfall = np.insert(waterfall, 0, wdata, axis=0) #insert line to beginning of array waterfall = waterfall[:-1].copy() #remove last element from array hsv = cv2.cvtColor(waterfall, cv2.COLOR_BGR2HSV) #Draw the intensity data :-) #first filter if not holding peaks! if holdpeaks == False: intensity = savitzky_golay(intensity,17,savpoly) intensity = np.array(intensity) intensity = intensity.astype(int) holdmsg = "Holdpeaks OFF" else: holdmsg = "Holdpeaks ON" #now draw the intensity data.... index=0 for i in intensity: rgb = wavelength_to_rgb(round(wavelengthData[index]))#derive the color from the wvalenthData array r = rgb[0] g = rgb[1] b = rgb[2] #or some reason origin is top left. cv2.line(graph, (index,320), (index,320-i), (b,g,r), 1) cv2.line(graph, (index,319-i), (index,320-i), (0,0,0), 1,cv2.LINE_AA) index+=1 #find peaks and label them textoffset = 12 thresh = int(thresh) #make sure the data is int. indexes = peakIndexes(intensity, thres=thresh/max(intensity), min_dist=mindist) #print(indexes) for i in indexes: height = intensity[i] height = 310-height wavelength = round(wavelengthData[i],1) cv2.rectangle(graph,((i-textoffset)-2,height),((i-textoffset)+60,height-15),(0,255,255),-1) cv2.rectangle(graph,((i-textoffset)-2,height),((i-textoffset)+60,height-15),(0,0,0),1) cv2.putText(graph,str(wavelength)+'nm',(i-textoffset,height-3),font,0.4,(0,0,0),1, cv2.LINE_AA) #flagpoles cv2.line(graph,(i,height),(i,height+10),(0,0,0),1) if measure == True: #show the cursor! cv2.line(graph,(cursorX,cursorY-140),(cursorX,cursorY-180),(0,0,0),1) cv2.line(graph,(cursorX-20,cursorY-160),(cursorX+20,cursorY-160),(0,0,0),1) cv2.putText(graph,str(round(wavelengthData[cursorX],2))+'nm',(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA) if recPixels == True: #display the points cv2.line(graph,(cursorX,cursorY-140),(cursorX,cursorY-180),(0,0,0),1) cv2.line(graph,(cursorX-20,cursorY-160),(cursorX+20,cursorY-160),(0,0,0),1) cv2.putText(graph,str(cursorX)+'px',(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA) else: #also make sure the click array stays empty clickArray = [] if clickArray: for data in clickArray: mouseX=data[0] mouseY=data[1] cv2.circle(graph,(mouseX,mouseY),5,(0,0,0),-1) #we can display text :-) so we can work out wavelength from x-pos and display it ultimately cv2.putText(graph,str(mouseX),(mouseX+5,mouseY),cv2.FONT_HERSHEY_SIMPLEX,0.4,(0,0,0)) #stack the images and display the spectrum spectrum_vertical = np.vstack((messages,cropped, graph)) #dividing lines... cv2.line(spectrum_vertical,(0,80),(frameWidth,80),(255,255,255),1) cv2.line(spectrum_vertical,(0,160),(frameWidth,160),(255,255,255),1) #print the messages cv2.putText(spectrum_vertical,calmsg1,(490,15),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,calmsg3,(490,33),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,saveMsg,(490,51),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,"Gain: "+str(picamGain),(490,69),font,0.4,(0,255,255),1, cv2.LINE_AA) #Second column cv2.putText(spectrum_vertical,holdmsg,(640,15),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,"Savgol Filter: "+str(savpoly),(640,33),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,"Label Peak Width: "+str(mindist),(640,51),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(spectrum_vertical,"Label Threshold: "+str(thresh),(640,69),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.imshow(title1,spectrum_vertical) if dispWaterfall == True: #stack the images and display the waterfall waterfall_vertical = np.vstack((messages,cropped, waterfall)) #dividing lines... cv2.line(waterfall_vertical,(0,80),(frameWidth,80),(255,255,255),1) cv2.line(waterfall_vertical,(0,160),(frameWidth,160),(255,255,255),1) #Draw this stuff over the top of the image! #Display a graticule calibrated with cal data textoffset = 12 #vertical lines every whole 50nm for positiondata in fifties: for i in range(162,480): if i%20 == 0: cv2.line(waterfall_vertical,(positiondata[0],i),(positiondata[0],i+1),(0,0,0),2) cv2.line(waterfall_vertical,(positiondata[0],i),(positiondata[0],i+1),(255,255,255),1) cv2.putText(waterfall_vertical,str(positiondata[1])+'nm',(positiondata[0]-textoffset,475),font,0.4,(0,0,0),2, cv2.LINE_AA) cv2.putText(waterfall_vertical,str(positiondata[1])+'nm',(positiondata[0]-textoffset,475),font,0.4,(255,255,255),1, cv2.LINE_AA) cv2.putText(waterfall_vertical,calmsg1,(490,15),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(waterfall_vertical,calmsg3,(490,33),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(waterfall_vertical,saveMsg,(490,51),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(waterfall_vertical,"Gain: "+str(picamGain),(490,69),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.putText(waterfall_vertical,holdmsg,(640,15),font,0.4,(0,255,255),1, cv2.LINE_AA) cv2.imshow(title2,waterfall_vertical) keyPress = cv2.waitKey(1) if keyPress == ord('q'): break elif keyPress == ord('h'): if holdpeaks == False: holdpeaks = True elif holdpeaks == True: holdpeaks = False elif keyPress == ord("s"): #package up the data! graphdata = [] graphdata.append(wavelengthData) graphdata.append(intensity) if dispWaterfall == True: savedata = [] savedata.append(spectrum_vertical) savedata.append(graphdata) savedata.append(waterfall_vertical) else: savedata = [] savedata.append(spectrum_vertical) savedata.append(graphdata) saveMsg = snapshot(savedata) elif keyPress == ord("c"): calcomplete = writecal(clickArray) if calcomplete: #overwrite wavelength data #Go grab the computed calibration data caldata = readcal(frameWidth) wavelengthData = caldata[0] calmsg1 = caldata[1] calmsg2 = caldata[2] calmsg3 = caldata[3] #overwrite graticule data graticuleData = generateGraticule(wavelengthData) tens = (graticuleData[0]) fifties = (graticuleData[1]) elif keyPress == ord("x"): clickArray = [] elif keyPress == ord("m"): recPixels = False #turn off recpixels! if measure == False: measure = True elif measure == True: measure = False elif keyPress == ord("p"): measure = False #turn off measure! if recPixels == False: recPixels = True elif recPixels == True: recPixels = False elif keyPress == ord("o"):#sav up savpoly+=1 if savpoly >=15: savpoly=15 elif keyPress == ord("l"):#sav down savpoly-=1 if savpoly <=0: savpoly=0 elif keyPress == ord("i"):#Peak width up mindist+=1 if mindist >=100: mindist=100 elif keyPress == ord("k"):#Peak Width down mindist-=1 if mindist <=0: mindist=0 elif keyPress == ord("u"):#label thresh up thresh+=1 if thresh >=100: thresh=100 elif keyPress == ord("j"):#label thresh down thresh-=1 if thresh <=0: thresh=0 elif keyPress == ord("t"):#Gain up! picamGain += 1 if picamGain >=50: picamGain = 50.0 picam2.set_controls({"AnalogueGain": picamGain}) print("Camera Gain: "+str(picamGain)) elif keyPress == ord("g"):#Gain down picamGain -= 1 if picamGain <=0: picamGain = 0.0 picam2.set_controls({"AnalogueGain": picamGain}) print("Camera Gain: "+str(picamGain)) #Everything done cv2.destroyAllWindows()