Update lut-creation.py

lut-creation.py

@@ -34,6 +34,13 @@ def create_LUT(fi=None):
 	rs = [0,  0,  0,  0,  0,  0,175,255,255]
 	gs = [0, 78,150,240,255,240,175,125,  0]
 	bs = [0,  0,  0,  0,  0,  0,  0,  0,  0]
+
+	  #black           green      orange
+	  #    |              |         |   red
+	  #    |              |         |    |
+	rs = [0,  0,  0,  0,  0, 0,255,255, 255]
+	gs = [0, 78,150,240,255, 255,255,125,  0]
+	bs = [0,  0,  0,  0,  0,  0, 64,  0,  0]	
 	ip = [ int(f*256) for f in fs]
 	r = []
 	g = []
@@ -49,9 +56,9 @@ def create_LUT(fi=None):
 		b = b + [ b0+db*j/di   for j in range(di) ]
 	return r,g,b
 
-imp = IJ.getImage()
 
 
+imp = IJ.getImage()
 lut = imp.getLuts()[0]
 bytes = lut.getBytes()
 
@@ -71,14 +78,14 @@ def plat( x, Pm, a, b ):
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 	if( isinstance(x,list) ):
 		#print("here")
-		return [ Pm*(1.-math.exp(-I*a))*math.exp(-I*b) for I in x ]
+		return [ Pm*(1.-math.exp(-I*a/Pm))*math.exp(-I*b/Pm) for I in x ]
 	else:
-		return Pm*(1.-math.exp(-x*a))*math.exp(-x*b)
+		return Pm*(1.-math.exp(-x*a/Pm))*math.exp(-x*b/Pm)
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -	
 def plat_max(Pm, a, b ):
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-	Iop = -math.log( b/(a+b))/a
-	return [Iop,plat(Iop,Pm,a,b),]
+	Iop = -math.log( b/(a+b))*Pm/a
+	return [Iop,plat(Iop,Pm,a,b)]
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 def find_root( f, x0s, v, *args ):
@@ -99,26 +106,30 @@ if( True):
 	rs,gs,bs = create_LUT()
 	lut = LUT( int2byte(rs),int2byte(gs),int2byte(bs) )
 
-	# create the ETR plot
-	I = [ 10000*i/200 for i in range(201)]
+
+	Imax = 7500.
+	Pm = 135.2
+	a = 0.87
+	b = 0.05
 	
-	a = 1./1000.
-	b = 1./2000.
-	Imax = 10000.
+	# create the ETR plot
+	I = [ Imax*i/200 for i in range(201)]
 	
-	pmax = plat_max(1,a,b)
+	pmax = plat_max(Pm,a,b)
+
+	print(pmax)
 	I2 = pmax[0]
-	I1= find_root(plat, [0.,I2   ],0.5*pmax[1], 1.,a,b)
-	I3= find_root(plat, [I2,I2*2 ],0.8*pmax[1], 1.,a,b) 
-	I4= find_root(plat, [I3,I3*2 ],0.5*pmax[1], 1.,a,b) 
+	I1= find_root(plat, [0.,I2   ],0.5*pmax[1], Pm,a,b)
+	I3= find_root(plat, [I2,I2*2 ],0.95*pmax[1], Pm,a,b) 
+	I4= find_root(plat, [I3,I3*2 ],0.5*pmax[1], Pm,a,b) 
 
 	print(I1,I2,I3,I4)
-	fs = [0., 0.5*I1/I4, I1/I4,0.5*(I1+I2)/I4, I2/I4, 0.5*(I2+I3)/I4, I3/I4, 0.5*(I3+I4)/I4, 1.]
+	fs = [0., 0.5*I1/I4, I1/I4,0.5*(I1+I2)/I4, I2/I4, I3/I4, I3/I4, 0.5*(I3+I4)/I4, 1.]
 	print(fs)
 	rs,gs,bs = create_LUT(fi=fs)
 	lut = LUT( int2byte(rs),int2byte(gs),int2byte(bs) )
 	xs = [I1,I2,I3,I4]
-	Vs = plat(I,1.,a,b)
+	Vs = plat(I,Pm,a,b)
 	plot = Plot("Plat","Light","ETR",I,Vs)
 	for j in range(1,len(I)):
 		i =I[j]
@@ -131,9 +142,19 @@ if( True):
 		plot.add("filled",[I[j-1],I[j]],[Vs[j-1],Vs[j]])
 	print(xs)
 	plot.setColor(Color(0,0,0))
-	plot.add('circles', xs, plat( xs,1,a,b) )
+	plot.add('circles', xs, plat( xs,Pm,a,b) )
 	plot.show()
+
+	ip = imp.getProcessor().duplicate()
+	ip.setMinAndMax(0.,I1)
+	from ij.plugin.filter import ThresholdToSelection as TS
+	mask = ip.createMask()
+	print(type(mask))
+	dfjk
+	roi = TS().convert(mask)
+	#imp.setRoi(roi)
 	
 
 	
-	imp.setLut(lut)
\ No newline at end of file
+	imp.setLut(lut)
+	imp.setDisplayRange(0,I4)
\ No newline at end of file