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elaScannerWin2023.py
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import os, sys
#from Tkinter import Frame, Tk, Label, Button, Scale, HORIZONTAL, Checkbutton, IntVar
from tkinter import *
#from tkFileDialog import *
from tkinter import filedialog
from tkinter.filedialog import askopenfilename, askdirectory
from PIL import Image, ImageStat, ImageDraw, ImageFont, TiffImagePlugin, ImageTk
import tkinter as tk
from scipy import ndimage
import math
import scipy
#import pylab
from scipy import polyval, polyfit, ndimage
from pylab import polyfit, polyval
import numpy as np
def Show_pic(pic):
im = pic.copy()
im.thumbnail((800,800), Image.ANTIALIAS)
imtk=ImageTk.PhotoImage(im)
label = tk.Label(image=imtk, height =600, width = 800)
# label = Label(image=imtk, height =600, width = 800)
label.image= imtk
label.grid(row =5, rowspan=50, column =2)
main.update()
def Pixel_check(curFile, dirF, file):
pic = Image.open(curFile)
pic2= Image.open(curFile)
picr= Image.open(curFile)
if (rotPic.get()):
print ("Rotating picture 180")
pic = pic.rotate(180)
if (flipPic.get()):
print ("Flipping picture")
pic = pic.transpose(Image.FLIP_LEFT_RIGHT)
imgdata = pic.load()
print (file, " loaded")
###################
totleaflength=0
###################
speedP=speedPscale.get()
xsize, ysize = pic.size
xsize=xsize/speedP
ysize=ysize/speedP
pic=pic.resize((int(xsize),int(ysize)))
pic2=pic2.resize((int(xsize),int(ysize)))
picr=picr.resize((int(xsize),int(ysize)))
xsize, ysize = pic.size
print (xsize,"x", ysize)
#minG=minGscale.get()
minR=minRscale.get()
#ratG=ratGscale.get()
#ratGb=ratGbscale.get()
threshW = threshWscale.get()
ratR=ratRscale.get()
##################################
#################################
#print minG, minR, ratG, ratR
pic = pic.convert("RGB")
pixels = pic.load() # create the pixel map
leafpix = []
scalepix = []
backpix = []
leafonly = pic2.load()
scaleonly = picr.load()
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
#print pixels[i,j]
r, g, b = pixels[i,j]
if r>minR and g*ratR<r and b*ratR<r :
scalepix.append((i,j))
#pixels[i,j] = (0,0,255)
scaleonly[i,j] = (255,0,0)
leafonly[i,j] = (0,0,0)
else:
scaleonly[i,j] = (0,0,0)
if r < threshW and b< threshW and g< threshW :
leafpix.append((i,j))
leafonly[i,j] = (0,255,0)
#scaleonly[i,j] = (0,0,0)
else:
leafonly[i,j] = (0,0,0)
backpix.append((i,j))
gCnt=len(leafpix)
#rCnt=len(scalepix)
if (delBack.get()):
for i in backpix:
pixels[i] = (255,255,255)
#pic2 = Image.open(pic2)
pic2 = pic2.convert('L')
flat = np.array(pic2)
# picr = Image.open(picr)
picr = picr.convert('L')
flatr = np.array(picr)
# flat = scipy.misc.fromimage(pic2,flatten=1)
# flatr= scipy.misc.fromimage(picr,flatten=1)
blobs, leaves = ndimage.label(flat)
blobsr, scales = ndimage.label(flatr)
scalehist=ndimage.measurements.histogram(blobsr, 1,scales,scales)
#########################################
#Blob analysis. Only the largest red blob is analyzed as scale area
try: maxscale=max(scalehist)
except: pass
cnt=1
gcnt=0
parcnt=0
rCnt=0
largescale = []
#totleaflength=0
for s in scalehist:
#print s
#if s>1000:
if s == maxscale:
cnti=0
cntj=0
gcnt=0
parcnt=parcnt+1
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
if blobsr[j,i]==cnt:
gcnt=gcnt+1
rCnt=rCnt+1
cnti=cnti+i
cntj=cntj+j
pixels[i,j]=(255,0,0)
flat[j,i] = (0)
cnti=cnti/gcnt
cntj=cntj/gcnt
largescale.append(gcnt)
if labpix.get():
draw=ImageDraw.Draw(pic)
draw.text((cnti,cntj),str(gcnt), (0,0,0))
cnt=cnt+1
####################
scalesize = SSscale.get()
if scalesize ==0:
print ("No scale. Leaf lengths not to scale")
#scalesize =1
scalesquarelength=1
scalelength=1
else:
scalesquarelength=math.sqrt(gcnt)
if scalesquarelength ==0:
scalesquarelength=1
scalelength = math.sqrt(SSscale.get())
##########
##########
############
#Leaf blob analysis
blobhist=ndimage.measurements.histogram(blobs, 1,leaves,leaves)
minPsize=minPscale.get()
########largest leaf elements only instead of minimum particle size
try: maxleaf=max(blobhist)
except: pass
if ThereCanBeOnlyOne.get():
cnt=1
gcnt=0
parcnt=0
gCnt=0
largeleaf = []
############
########
totleaflength=0
#########
#############
for s in blobhist:
if s == maxleaf:
cnti=0
cntj=0
gcnt=0
parcnt=parcnt+1
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
if blobs[j,i]==cnt:
gcnt=gcnt+1
gCnt=gCnt+1
cnti=cnti+i
cntj=cntj+j
pixels[i,j]=(0,255,0)
flat[j,i] = (0)
cnti=cnti/gcnt
cntj=cntj/gcnt
##############
########
#print gcnt
if SSscale.get()>0:
gcnt = float(gcnt)/float(rCnt)*SSscale.get()
gcnt = "%.3f" % gcnt
#gcnt=int(gcnt)
#print gcnt
########
##########################################
largeleaf.append(gcnt)
##############
##########
leaflength=0
templength=0
#########
###########
##########################
##########################
#Creates an outline array for leaf
##################
if (doleaflength.get()):
blobedgepix = []
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
if blobs[j,i]==cnt:
try:
if blobs[j-1,i]!=cnt or blobs[j,i-1]!=cnt or blobs[j,i+1]!=cnt or blobs[j+1,i]!=cnt:
blobedgepix.append((i,j))
except IndexError:
blobedgepix.append((i,j))
###########
#Checks for maximum length between any two pixels in perimeter of leaf.
##################
for i in blobedgepix:
xpix,ypix =i
for j in blobedgepix:
xtemp,ytemp = j
templength=math.sqrt((xpix-xtemp)**2+(ypix-ytemp)**2)
if leaflength< templength:
leaflength=templength
totleaflength=totleaflength+leaflength
############
#################
####################
###########
if (doleaflength.get()):
if scalesize ==0:
#print "No scale. Leaf length not to scale"
leaflength=int(leaflength)
#print leaflength
#scalesize =1
else:
leaflength=int(10*scalelength/scalesquarelength*leaflength)
#print "Maximum Length in mm (Only if your scale is square)"
#leaflength=int(leaflength)
#print leaflength
largeleaf.append(gcnt)
############
#####################
##############
if labpix.get():
draw=ImageDraw.Draw(pic)
##############
##############
if scalesize ==0:
draw.text((cnti,cntj),str(gcnt)+' pixels area', (0,0,0))
if (doleaflength.get()):
draw.text((cnti,cntj-10),str(leaflength)+' pixels long', (0,0,0))
#scalesize =1
else:
##
draw.text((cnti,cntj),str(gcnt)+' cm^2', (0,0,0))
if (doleaflength.get()):
draw.text((cnti,cntj-10),str(leaflength)+' mm', (0,0,0))
####gcnt=gcnt*scalesize/
#draw.text((cnti,cntj),str(gcnt), (0,0,0))
cnt=cnt+1
###############
###########
if (doleaflength.get()):
if scalesize ==0:
totleaflength=int(totleaflength)
else:
totleaflength=int(10*scalelength/scalesquarelength*totleaflength)
print ("Total length in mm (Only if your scale is square)")
#largeleaf.append(int(totleaflength))
leafprint= ', '.join(map(str, largeleaf))
#print int(totleaflength)
###########
####################
#leafprint= ', '.join(map(str, largeleaf))
#Leaf element minimum particle size:
elif minPsize>10:
cnt=1
gcnt=0
parcnt=0
gCnt=0
############
########
totleaflength=0
#########
#############
largeleaf = []
for s in blobhist:
if s>minPsize:
cnti=0
cntj=0
gcnt=0
##############
##########
leaflength=0
templength=0
#########
###########
parcnt=parcnt+1
##########################
#Creates an outline array for leaf
##################
if (doleaflength.get()):
blobedgepix = []
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
if blobs[j,i]==cnt:
try:
if blobs[j-1,i]!=cnt or blobs[j,i-1]!=cnt or blobs[j,i+1]!=cnt or blobs[j+1,i]!=cnt:
blobedgepix.append((i,j))
except IndexError:
blobedgepix.append((i,j))
###########
#Checks for maximum length between any two pixels in perimeter of leaf.
##################
for i in blobedgepix:
xpix,ypix =i
for j in blobedgepix:
xtemp,ytemp = j
templength=math.sqrt((xpix-xtemp)**2+(ypix-ytemp)**2)
if leaflength< templength:
leaflength=templength
totleaflength=totleaflength+leaflength
############
#################
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
if blobs[j,i]==cnt:
gcnt=gcnt+1
gCnt=gCnt+1
cnti=cnti+i
cntj=cntj+j
pixels[i,j]=(0,255,0)
flat[j,i] = (0)
cnti=cnti/gcnt
cntj=cntj/gcnt
####################
###########
if (doleaflength.get()):
if scalesize ==0:
#print "No scale. Leaf areas not to scale"
leaflength=int(leaflength)
#print leaflength
#scalesize =1
else:
leaflength=int(10*scalelength/scalesquarelength*leaflength)
#print "Maximum Length in mm (Only if your scale is square)"
#leaflength=int(leaflength)
#print leaflength
largeleaf.append(leaflength)
############
#####################
##############
########
if SSscale.get()>0:
gcnt = float(gcnt)/float(rCnt)*SSscale.get()
gcnt = "%.3f" % gcnt
#gcnt=(gcnt*100)
########
##########################################
largeleaf.append(gcnt)
if labpix.get():
draw=ImageDraw.Draw(pic)
#draw.text((cnti,cntj),str(gcnt), (0,0,0))
##############
if scalesize ==0:
draw.text((cnti,cntj),str(gcnt)+' pixels area', (0,0,0))
if (doleaflength.get()):
draw.text((cnti,cntj-10),str(leaflength)+' pixels long', (0,0,0))
#scalesize =1
else:
draw.text((cnti,cntj),str(gcnt)+' cm^2', (0,0,0))
if (doleaflength.get()):
draw.text((cnti,cntj-10),str(leaflength)+' mm', (0,0,0))
####gcnt=gcnt*scalesize/
##############
cnt=cnt+1
###############
###########
if (doleaflength.get()):
if scalesize ==0:
totleaflength=int(totleaflength)
else:
totleaflength=int(10*scalelength/scalesquarelength*totleaflength)
print ("Total length in mm (Only if your scale is square)")
print (int(totleaflength))
##########
#largeleaf.append(int(totleaflength))
leafprint= ', '.join(map(str, largeleaf))
###########
####################
#leafprint= ', '.join(map(str, largeleaf))
else:
print ("NO CONNECTED COMPONENT ANALYSIS")
for i in leafpix:
pixels[i] = (0,255,0)
leafprint = "No connected component analysis"
if rCnt < 1:
rCnt+=1
scalesize = SSscale.get()
#if scalesize ==0:
# print ("No scale. Leaf areas not to scale")
#scalesize =1
leafarea = float(gCnt)/float(rCnt)*scalesize
Show_pic(pic)
highlightfile = dirF+'/leafarea.csv'
pixdata=file+', '+str(gCnt)+', '+str(rCnt)+', '+'%.2f' % leafarea+','+str(int(totleaflength))+','+leafprint+'\n'
#pixdata=file+', '+str(gCnt)+', '+str(rCnt)+', '+'%.2f' % leafarea+','+leafprint+'\n'
return totleaflength, gCnt, rCnt, pic, pixdata
def test_LA():
print ("Measuring...")
global chosfile
global dirF
#get absolute path
dirF = os.path.dirname(chosfile)
pic = Image.open(chosfile)
xsize, ysize = pic.size
file = os.path.basename(chosfile)
(totleaflength, gCnt, rCnt, pic, pixdata) = Pixel_check(chosfile, dirF, file)
if rCnt < 1:
rCnt+=1
scalesize = SSscale.get()
if scalesize ==0:
print ("No scale. Leaf area not to scale.")
#######
####
######
#scalesize =1
leafarea = float(gCnt)/float(rCnt)*scalesize
if rCnt <2:
rCnt = 0
filelabel= Label (main, height =1, width=60)
speedP=speedPscale.get()
xsize=xsize/speedP
ysize=ysize/speedP
filelabel.configure (text = file+" "+str(xsize)+ "x"+str(ysize))
filelabel.grid (row =1, column =2)
Pixlabel = Label(main, height = 1, width = 60)
#################
scalesquarelength=math.sqrt(rCnt)
######
######
if scalesquarelength ==0:
scalesquarelength =1
scalelength = math.sqrt(SSscale.get())
if (doleaflength.get()):
if scalesize ==0:
totleaflength=int(totleaflength)
Pixlabel.configure (text = "Leaf pixels: "+ str(gCnt)+ " Scale pixels: "+ str(rCnt)+ " Leaf length pixels: "+ str(totleaflength))
else:
#print ("scale square length ", scalesquarelength, ", ")
#print ("total leaf length ", totleaflength, ", ")
#print ("scale length ", scalelength, ", ")
#totleaflength=int(10*scalelength/scalesquarelength*totleaflength)
print ("Total length in mm (Only if your scale is square)")
#####
#print ("scale square length ", scalesquarelength, ", ")
#print ("total leaf length ", totleaflength, ", ")
#print ("scale length ", scalelength, ", ")
########
Pixlabel.configure (text = "Leaf pix: "+ str(gCnt)+ " Scale pix: "+ str(rCnt)+ " Leaf area: "+ '%.2f' % leafarea+ "cm^2"+" Length mm: "+ str(totleaflength))
else:
Pixlabel.configure (text = "Leaf pixels: "+ str(gCnt)+ " Scale pixels: "+ str(rCnt)+ " Leaf area: "+ '%.2f' % leafarea+ "cm^2")
#############
##################
#########################
#Pixlabel.configure (text = "Leaf pixels: "+ str(gCnt)+ " Scale pixels: "+ str(rCnt)+ " Leaf area: "+ '%.2f' % leafarea+ "cm^2")
Pixlabel.grid(row =2, column =2)
print ("Finished processing image")
def single_LA():
print ("Measuring...")
global chosfile
global dirF
dirF = os.path.dirname(chosfile)
pic = Image.open(chosfile)
xsize, ysize = pic.size
file = os.path.basename(chosfile)
(totleaflength, gCnt, rCnt, pic, pixdata) = Pixel_check(chosfile, dirF, file)
if rCnt < 1:
rCnt+=1
leafarea = float(gCnt)/float(rCnt)*4.0
if rCnt <2:
rCnt = 0
filelabel= Label (main, height =1, width=60)
speedP=speedPscale.get()
xsize=xsize/speedP
ysize=ysize/speedP
filelabel.configure (text = file+" "+str(xsize)+ "x"+str(ysize))
filelabel.grid (row =1, column =2)
Pixlabel = Label(main, height = 1, width = 60)
Pixlabel.configure (text = "Leaf pixels: "+ str(gCnt)+ " Scale pixels: "+ str(rCnt)+ " Leaf area: "+ '%.2f' % leafarea+ "cm^2")
Pixlabel.grid(row =2, column =2)
highlightfile = dirF+'/leafarea.csv'
try:
with open(highlightfile, "a") as f:
####################
if (doleaflength.get()):
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length pixels, Component length pixels:, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length mm, Component length mm:, Component area cm^2:")
else:
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component area cm^2:")
# f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length, Component green pixels:")
f.write("\n")
except:
open (dirF+'/leafarea.csv', "w")
print ("creating new output file")
with open(highlightfile, "a") as f:
####################
####################
if (doleaflength.get()):
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length pixels, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length mm, Component area cm^2:")
else:
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component area cm^2:")
#f.write("filename,total green pixels,red pixels (4 cm^2),leaf area cm^2, Component green pixels:")
#f.write("\n")
f.write("\n")
save_Output(highlightfile, file, pixdata, pic, dirF)
print ("Finished processing image")
def run_LA():
print ("Measuring...")
global dirS
global dirF
global chosfile
dirS = os.path.abspath(dirS)
dirF = os.path.abspath(dirF)
filesInCurDir = os.listdir(dirS)
try:
with open(dirF+'/leafarea.csv', "a") as f:
####################
if (doleaflength.get()):
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length pixels, Component length pixels, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length mm, Component length mm:, Component area cm^2:")
else:
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component area cm^2:")
# f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length, Component green pixels:")
f.write("\n")
except:
open (dirF+'/leafarea.csv', "w")
#print "creating new output file"
with open(dirF+'/leafarea.csv', "a") as f:
###################
if (doleaflength.get()):
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length pixels, Component length pixels, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, leaf length mm, Component length mm:, Component area cm^2:")
else:
if SSscale.get() ==0:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component green pixels:")
else:
f.write("filename,total green pixels,red pixels (scale),leaf area cm^2, Component area cm^2:")
# f.write("filename,total green pixels,red pixels (4 cm^2),leaf area cm^2, leaf length, Component green pixels:")
f.write("\n")
# f.write("filename,total green pixels,red pixels (4 cm^2),leaf area cm^2, Component green pixels:")
# f.write("\n")
# except:
# open (dirF+'/leafarea.csv', "w")
# with open(dirF+'/leafarea.csv', "a") as f:
# f.write("filename,total green pixels,red pixels (4 cm^2),leaf area cm^2, Component green pixels:")
# f.write("\n")
for file in filesInCurDir:
curFile = os.path.join(dirS, file)
try:
pic = Image.open(curFile)
xsize, ysize = pic.size
except:
continue
Show_pic(pic)
chosfile = curFile
if (autocheck.get()):
global ConsData
ConsData = [0,0,0,0,0]
auto_Settings(ConsData)
(totleaflength, gCnt, rCnt, pic, pixdata) = Pixel_check(curFile, dirF, file)
if rCnt < 1:
rCnt+=1
leafarea = float(gCnt)/float(rCnt)*4.0
if rCnt <2:
rCnt = 0
filelabel= Label (main, height =1, width=60)
speedP=speedPscale.get()
xsize=xsize/speedP
ysize=ysize/speedP
filelabel.configure (text = file+" "+str(xsize)+ "x"+str(ysize))
filelabel.grid (row =1, column =2)
Pixlabel = Label(main, height = 1, width = 60)
Pixlabel.configure (text = "Leaf pixels: "+ str(gCnt)+ " Scale pixels: "+ str(rCnt)+ " Leaf area: "+ '%.2f' % leafarea+ "cm^2")
Pixlabel.grid(row =2, column =2)
highlightfile = dirF+'/leafarea.csv'
save_Output(highlightfile, file, pixdata, pic, dirF)
print ("Finished processing images")
def S_dir():
global dirS
dirS = askdirectory()
Slabel.configure(text = dirS)
def F_dir():
global dirF
dirF = askdirectory()
Flabel.configure(text = dirF)
def check_Sett():
print ("Batch processing")
run_LA()
def chos_file():
global chosfile
chosfile = askopenfilename()
#chosfile = askopenfilename(filetypes=[("image file", "*.jpg; *.jpe; *.jpeg; *.tiff; *.tif")])
pic = Image.open(chosfile)
xsize, ysize = pic.size
Show_pic(pic)
file = os.path.basename(chosfile)
filelabel= Label (main, height =1, width=60)
filelabel.configure (text = file+" "+str(xsize)+ "x"+str(ysize))
filelabel.grid (row =1, column =2)
Pixlabel = Label(main, height = 1, width = 60)
Pixlabel.configure (text = " ")
Pixlabel.grid(row =2, column =2)
print ("loaded "+chosfile)
def chos_calib():
global choscalib
choscalib = askopenfilename(filetypes=[("comma-delimited","*.csv")])
print ("loading calib file")
with open(choscalib) as csvfile:
#next(csvfile) # ignore header
a = [row.strip().split(',') for row in csvfile]
######linear regression for min G
x = [float(i[0]) for i in a]
y = [float(i[3]) for i in a]
(m,b) =polyfit(x,y,1)
mg=m
bg=b
######linear regression for G/R
x = [float(i[1]) for i in a]
y = [float(i[4]) for i in a]
(m,b) =polyfit(x,y,1)
mgr=m
bgr=b
######linear regression for G/B
x = [float(i[2]) for i in a]
y = [float(i[5]) for i in a]
(m,b) =polyfit(x,y,1)
mgb=m
bgb=b
############
############
x = [float(i[6]) for i in a]
y = [float(i[8]) for i in a]
(m,b) =polyfit(x,y,1)
mmr=m
bmr=b
x = [float(i[7]) for i in a]
y = [float(i[9]) for i in a]
(m,b) =polyfit(x,y,1)
mmg=m
bmg=b
print ("min G equation:",mg, "x+", bg,"\n G/R equation:", mgr,"x+",bgr,"\n G/B equation:",mgb, "x+",bgb)
print ("min R equation:",mmr, "x+", bmr,"\n R/G&R/B equation:", mmg,"x+",bmg)
print ("Loaded calib file")
return mg,bg,mgr,bgr,mgb,bgb, mmr, bmr, mmg, bmg
def load_calib():
try:
with open(os.path.join(sys.path[0], "calib.csv")) as csvfile:
#next(csvfile) # ignore header
a = [row.strip().split(',') for row in csvfile]
######linear regression for min G
x = [float(i[0]) for i in a]
y = [float(i[3]) for i in a]
(m,b) =polyfit(x,y,1)
####################
print (sum((polyval(polyfit(x,y,1),x)-y)**2)/(len(x)))
####################
mg=m
bg=b
######linear regression for G/R
x = [float(i[1]) for i in a]
y = [float(i[4]) for i in a]
(m,b) =polyfit(x,y,1)
mgr=m
bgr=b
######linear regression for G/B
x = [float(i[2]) for i in a]
y = [float(i[5]) for i in a]
(m,b) =polyfit(x,y,1)
mgb=m
bgb=b
############
############
x = [float(i[6]) for i in a]
y = [float(i[8]) for i in a]
(m,b) =polyfit(x,y,1)
mmr=m
bmr=b
x = [float(i[7]) for i in a]
y = [float(i[9]) for i in a]
(m,b) =polyfit(x,y,1)
mmg=m
bmg=b
print ("loaded calib")
except:
mg= 1.223
bg=-111
mgr=0.360
bgr=0.589
mgb=0.334
bgb=0.534
mmr=1.412
bmr=-140.6
mmg=0.134
bmg=0.782
print ("calib file not found")
print ("Set to default arabidopsis values")
return mg,bg,mgr,bgr,mgb,bgb, mmr, bmr, mmg, bmg
def sing_Meas():
print ("Measuring image")
test_LA()
def show_Output():
global dirF
print (dirF)
print ("Opening output file in default application")
#Below is the code for windows
outputfile = 'start '+dirF+'/leafarea.csv'
#Below shoul dbe the code for Mac
#outputfile = 'open "'+dirF+'/leafarea.csv"'
print (outputfile)
os.system(outputfile)
def save_Output(highlightfile, file, pixdata, pic, dirF):
print ("save output")
with open(highlightfile, "a") as f:
f.write(pixdata)
tifffile = file.replace('.jpg', '.tiff')
pic.save(dirF+'/highlight'+tifffile)
def auto_Settings(WhatData):
global chosfile
pic = Image.open(chosfile)
speedP=8
xsize, ysize = pic.size
xsize=xsize/speedP
ysize=ysize/speedP
pic=pic.resize((int(xsize),int(ysize)))
xsize, ysize = pic.size
print (xsize,"x", ysize)
#ratG=2
#ratGb=1.8
thresW = 75
cnt =0
lpcntb = 0
lpcnt =-1
pixMinGreen = xsize*ysize*0.0025
pic = pic.convert("RGB")
pixels = pic.load() # create the pixel map
ratR=2
minR = 150
cnt =0
lpcntb = 0
lpcnt =0
# Conservative pixel selection of 200+ pixels at 1/8th resolution:
while cnt <pixMinGreen:
scalepix=[]
for i in range(pic.size[0]): # for every pixel:
for j in range(pic.size[1]):
r, g, b = pixels[i,j]
if g*ratR < r and b*(ratR)< r and r> minR:
scalepix.append((r,g,b))
cnt=len(scalepix)
lpcnt=lpcnt+1
if lpcnt <8:
ratR = 0.94*ratR
if lpcnt >7:
ratR = 2
minR = 0.99*minR
if lpcnt >10:
cnt =(pixMinGreen+10)
print (minR, ratR, "to select >",pixMinGreen," scale pixels after", lpcnt, "loops")
ravg=0
rgavg=0
rbavg=0
cnt=len(scalepix)
if cnt>0:
for i in scalepix:
r, g, b = i
if g<1: g=r
if b<1: b=r
ravg=ravg+r
rgavg= rgavg+(float(r)/float(g))
rbavg= rbavg+(float(r)/float(b))
ravg=float(ravg)/float(cnt)
rgavg=float(rgavg)/float(cnt)
rbavg=float(rbavg)/float(cnt)
rgavg=(rgavg+rbavg)/2
rrat=mmrgset*rgavg+bmrgset
if rrat <1.011: rrat=1.01
minRscale.set(mmrset*ravg+bmrset)
ratRscale.set(rrat)
else:
minRscale.set(255)
ratRscale.set(2)
print ("No Scale detected")
#ConsData = [gavg, gravg, bravg, ravg, rgavg]
ConsData = [ravg, rgavg]
#print ConsData, "Values can be added to calib file"
print (ravg, mmrset, bmrset, (mmrset*ravg+bmrset))
#ratGbscale.set(0.334*bravg+0.534)
return ConsData
def auto_Sing():
global ConsData
ConsData = [0,0,0,0,0]
auto_Settings(ConsData)
sing_Meas()
#load calib file on first run
#mgset, bgset, mgrset, bgrset, mgbset, bgbset = load_calib()
#load calib file on first run
mgset, bgset, mgrset, bgrset, mgbset, bgbset, mmrset, bmrset, mmrgset, bmrgset = load_calib()
main = Tk()
main.title("Easy Leaf Area (Scanner edition with length measurements")
Frame1 = Frame(main)
Frame1.grid (row= 1, column = 1, rowspan = 17)
runsingbut = Button(Frame1, text ="Analyze with current settings", command = test_LA)
saveresults = Button(Frame1, text ="Save analysis", command = single_LA)
SObut = Button(main, text ="Open output csv file", command = show_Output)
singbut = Button(Frame1, text = "Open an image", command = chos_file)
singlabel = Label(Frame1)
###############################
#loadcalibbut= Button(Frame1, text = "Load calib File", command = calib_set)
###############################
Batchlabel = Label(Frame1)
Batchlabel.configure (text ="Batch Processing:")
dirS ="C:/"
Sbut = Button(Frame1, text = "Select batch source Folder", command = S_dir)
Slabel = Label(Frame1)
Slabel.configure (text ="C:/")
dirF ="C:/"
Fbut = Button(Frame1, text = "Select batch output Folder", command = F_dir)
Flabel = Label(Frame1)
Flabel.configure (text ="C:/")
CSbut = Button(Frame1, text ="Start Batch with current settings", command = check_Sett)
Frame3 = Frame(main)
Frame3.grid (row= 1, column = 3, rowspan = 10)
##################
#addTocalibbut = Button (Frame1,text = "Add to calib File", command =addTocalib)
###############
#minG =100
#minGscale = Scale(Frame3, from_=0, to=255, label="Leaf minimum Green RGB value:", orient=HORIZONTAL, tickinterval = 50, length = 250, variable = minG )
#minGscale.set(25)
minR =200
minRscale = Scale(Frame3, from_=0, to=255, label="Scale minimum Red RGB value:", orient=HORIZONTAL, tickinterval = 50, length = 250, variable = minR )
minRscale.set(225)
#ratG =1.2
#ratGscale = Scale(Frame3, from_=0.9, to=2, resolution = 0.02, label="Leaf Green Ratio: (G/R)", orient=HORIZONTAL, tickinterval = 0.5, length = 200, variable = ratG )
#ratGscale.set(1.05)
threshW =220
threshWscale = Scale(Frame3, from_=0, to=255, resolution = 1, label="Scanner threshold", orient=HORIZONTAL, tickinterval = 50, length = 200, variable = threshW )
threshWscale.set(190)
#ratGb =1.35
#ratGbscale = Scale(Frame3, from_=0.8, to=2, resolution = 0.02, label="Leaf Green Ratio: (G/B)", orient=HORIZONTAL, tickinterval = 0.5, length = 200, variable = ratGb )
#ratGbscale.set(1.07)
ratR =1.3
ratRscale = Scale(Frame3, from_=1, to=2, resolution = 0.02, label="Scale Red Ratio: (R/G & R/B)", orient=HORIZONTAL, tickinterval = 0.5, length = 200, variable = ratR )
ratRscale.set(1.95)
speedP =1
speedPscale = Scale(Frame3, from_=1, to=8, resolution = 1, label="Processing Speed:", orient=HORIZONTAL, tickinterval = 1, length = 200, variable = speedP )
speedPscale.set(4)
minPsize =500
minPscale = Scale(Frame3, from_=1, to=5000, resolution = 10, label="Minimum Leaf Size (pixels):", orient=HORIZONTAL, tickinterval = 1000, length = 250, variable = minPsize )
minPscale.set(0)
#################
Scalesize =4.1
SSscale = Scale(Frame3, from_=0, to=20, resolution = 0.1, label="Scale area (cm^2):", orient=HORIZONTAL, tickinterval = 4, length = 250, variable = Scalesize )
SSscale.set(4)
###################
flipPic = IntVar()
C1 = Checkbutton(Frame1, text = "Flip image horizontal", variable = flipPic)
flipPic.get()
rotPic = IntVar()
C2 = Checkbutton(Frame1, text = "Rotate image 180 deg", variable = rotPic)
rotPic.get()
delBack = IntVar()
C3 = Checkbutton(Frame1, text = "Delete background", variable = delBack)
delBack.get()
labpix = IntVar()