Added Roi and user defined plots

lut-creation.py

@@ -101,37 +101,54 @@ def find_root( f, x0s, v, *args ):
 		if( abs(f0-f1)<1e-6 ):
 			break
 	return 0.5*(x0+x1)
+	
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+def request_parameters():
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+	from fiji.util.gui import GenericDialogPlus
+	
+	Imax, Pm, a, b = 7500, 135, 0.86, 0.05
+	gdp = GenericDialogPlus("Photo Inhibition Curve")
+	gdp.addNumericField("Imax", Imax,0)
+	gdp.addNumericField("Pm",   Pm,0)
+	gdp.addNumericField("alpha",a,2)
+	gdp.addNumericField("beta", b,2)
+##	gdp.addCheckbox("Walk sub directories",False)
+	gdp.setSize(750,150)
+	gdp.showDialog()
+	Imax = gdp.getNextNumber()
+	Pm   = gdp.getNextNumber() 
+	a    = gdp.getNextNumber()
+	b    = gdp.getNextNumber()	
+	return [Imax,Pm,a,b]
 
 if( True):
-	rs,gs,bs = create_LUT()
-	lut = LUT( int2byte(rs),int2byte(gs),int2byte(bs) )
+#	rs,gs,bs = create_LUT()
+#	lut = LUT( int2byte(rs),int2byte(gs),int2byte(bs) )
 
+	[Imax,Pm,a,b]=request_parameters()
 
-	Imax = 7500.
-	Pm = 135.2
-	a = 0.87
-	b = 0.05
 	
 	# create the ETR plot
-	I = [ Imax*i/200 for i in range(201)]
+	I = [ Imax*i/200 for i in range(201)]  # max intensity values
 	
-	pmax = plat_max(Pm,a,b)
+	pmax = plat_max(Pm,a,b)                # find the max of the PI curve
 
-	print(pmax)
+	# assemble the critical points
 	I2 = pmax[0]
-	I1= find_root(plat, [0.,I2   ],0.5*pmax[1], Pm,a,b)
+	I1= find_root(plat, [0.,I2   ],0.50*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) 
+	I4= find_root(plat, [I3,I3*2 ],0.50*pmax[1], Pm,a,b) 
+	Iarr = [0.,I1,I2,I3,I4,Imax]
 
-<<<<<<< HEAD
-	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.]
-=======
-	print(I1,I2,I3,I4)
+	# the transition points in the LUT
 	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.]
->>>>>>> 345428bc9fabd5f3d21977483345cd0aa9128604
-	print(fs)
+
+	# create the LUT
 	rs,gs,bs = create_LUT(fi=fs)
 	lut = LUT( int2byte(rs),int2byte(gs),int2byte(bs) )
+
+	# Make the plot of the ETR
 	xs = [I1,I2,I3,I4]
 	Vs = plat(I,Pm,a,b)
 	plot = Plot("Plat","Light","ETR",I,Vs)
@@ -139,24 +156,48 @@ if( True):
 		i =I[j]
 		n = int((i-0)/I4*256)
 		n = min(max(0,n),255)
-		#print(n)
 		
 		plot.setColor(Color( rs[n],gs[n],bs[n],255))
-		#plot.add("line",[i,i],[0,Vs[j]])
 		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,Pm,a,b) )
 	plot.show()
 
-	ip = imp.getProcessor().duplicate()
-	ip.setMinAndMax(0.,I1)
+
+	# Measure the areas of the regions
+	from ij.process import ImageStatistics
+	from ij.plugin.frame import RoiManager
 	from ij.plugin.filter import ThresholdToSelection as TS
-	mask = ip.createMask()
-	print(type(mask))
-	dfjk
-	roi = TS().convert(mask)
-	#imp.setRoi(roi)
+	from ij.measure import Measurements, ResultsTable
+	# set up the roi
+	ip = imp.getProcessor().duplicate()
+	
+
+	
+	roim = RoiManager.getInstance()
+	if(roim is None ): roim = RoiManager()
+	roim.reset()
+
+	measure_int = Measurements.CENTROID  +Measurements.ELLIPSE + Measurements.AREA+Measurements.SHAPE_DESCRIPTORS
+	rt = ResultsTable()
+	photoclass=['unsufficent','sub-optimal','optimal','inhibited','critical']
+	Iarr = [0.,I1,I2,I3,I4,Imax]
+	for i in range(len(photoclass)):
+		rt.setValue("class",i,photoclass[i])
+		
+		ip.setThreshold(Iarr[i],Iarr[i+1],ip.NO_LUT_UPDATE)
+		roi = TS().convert(ip)	
+		if( roi is not None ):
+			roi.setName(photoclass[i])
+			roim.addRoi(roi)
+			ip.setRoi(roi)
+			stats = ImageStatistics.getStatistics(ip,measure_int,imp.getCalibration())
+			rt.setValue("Area",  i,stats.area)
+			rt.setValue("Mean I",i,stats.mean)
+		
+		
+	rt.show("Areas")