//open("/home/jeff/Bureau/3d/cell_02_majSat_P_split-3Dseg.tif");
//Dialog
gwid=getWidth();
ghei=getHeight();
nS=nSlices();
Dialog.create("Distances objects 3D");
Dialog.addMessage("Distance Centre-Centre       ");
Dialog.addCheckbox("2D Plot", false);
Dialog.addCheckbox("Cluster analysis", false);
Dialog.addCheckbox("Histogram", false);
Dialog.addMessage("Distance Border-Border");
Dialog.addCheckbox("2D Plot", false);
Dialog.addCheckbox("Cluster analysis", false);
Dialog.addCheckbox("Histogram", false);
Dialog.show();
tablecc = Dialog.getCheckbox();
fillcc = Dialog.getCheckbox();
histocc = Dialog.getCheckbox();
tablebb = Dialog.getCheckbox();
fillbb = Dialog.getCheckbox();
histobb = Dialog.getCheckbox();
setBatchMode(true);
run("3D Manager");
Ext.install("RoiManager3D_");
Ext.Manager3D_AddImage();
Ext.Manager3D_Count(nb);
proxcc = newArray(nb);		// closest object (centre-centre)
dccmin = newArray(nb);		// distance to closest object (centre-centre)
cluscocc= newArray(nb);		// cluster (centre-centre)
proxbb = newArray(nb);		// closest object (border-border)
dbbmin = newArray(nb);		// distance to closest object (border-border)
cluscobb= newArray(nb);		// cluster (border-border)
//Tableau cc
minccAll=10000; maxccAll=0;
minbbAll=10000; maxbbAll=0;
for(i=0; i<nb; i++){				// C-C et B-B
	dccmin[i]=10000; dbbmin[i]=10000;
	for(j=1; j<nb; j++){
		Ext.Manager3D_Dist2(i,j,"cc",cc);
		if ((cc<dccmin[i])&&(i!=j)){
			dccmin[i]=cc; proxcc[i]=j;
		}
		Ext.Manager3D_Dist2(i,j,"bb",bb);
		if ((bb<dbbmin[i])&&(i!=j)){
			dbbmin[i]=bb; proxbb[i]=j;
		}
	}
	if(minccAll>=dccmin[i]){
		minccAll=dccmin[i];
	}
	if(maxccAll<=dccmin[i]){
		maxccAll=dccmin[i];
	}
	if(minbbAll>=dbbmin[i]){
		minbbAll=dbbmin[i];
	}
	if(maxbbAll<=dbbmin[i]){
		maxbbAll=dbbmin[i];
	}
	cluscocc[i]=-1;
	cluscobb[i]=-1;
}
print("min cc", minccAll);
print("max cc", maxccAll);
print("min bb", minbbAll);
print("max bb", maxbbAll);
setBatchMode(false);
//Table c-c
if(tablecc==true){
	newImage("Closest_C-C", "RGB White", nb*10+10, nb*10+10, 1);
	for(i=0; i<nb; i++){
		setColor(0, 0, 0);
		fillRect(0, 0, 10, 10);
		fillRect((i+1)*10, (i+1)*10, 10, 10);
		x=12; y=9;
		setFont("SansSerif", 5);
		drawString(i, i*10+x, y);
		x=1; y=19;
		setFont("SansSerif", 6);
		drawString(i, x, i*10+y);
		setColor(255*(dccmin[i]-minccAll)/(maxccAll-minccAll), 255, 0);
		fillRect(proxcc[i]*10+10, i*10+10, 10, 10);
		fillRect(i*10+10, proxcc[i]*10+10, 10, 10);
		print("closest object of "+i+" is object "+proxcc[i]+" with  a distance centre-centre of "+ dccmin[i]);
	}
}
//Cluster c-c
if(fillcc==true){
	newImage("cluster_C-C", "16-bit black", gwid, ghei, nS);
	n=0;//valeur d'incrémentation pour clustco
	change=true;
	while(change==true){
	change=false;
		for(i=0; i<nb; i++){	
			if (cluscocc[i]<0){
				cluscocc[i]=n++;
				change=true;
			}
			else if(cluscocc[i]!=cluscocc[proxcc[i]]){
				if(cluscocc[proxcc[i]]>cluscocc[i]){
				cluscocc[proxcc[i]]=cluscocc[i];}
				else {cluscocc[i]=cluscocc[proxcc[i]];}
				change=true;
			}
		}
	}	
	coloMaxC=0;
	for(i=0; i<nb; i++){			
		if(coloMaxC<cluscocc[i]){
			coloMaxC=cluscocc[i];
		}
		//print("cluster", cluscocc[i]);
	}
	nclucc= newArray(coloMaxC+1);		
	for(j=0; j<=coloMaxC; j++){
		n=1;
		for(i=0; i<nb; i++){
			if(cluscocc[i]==j){
				nclucc[j]=n++;
				Ext.Manager3D_Select(i);
				Ext.Manager3D_Fill(j, j, j);
				// lines
				Ext.Manager3D_Centroid3D(i,c0x,c0y,c0z);
				Ext.Manager3D_Centroid3D(proxcc[i],c1x,c1y,c1z);
				run("3D Line", "size_x=&gwid size_y=&ghei size_z=&nS x0=&c0x y0=&c0y z0=&c0z x1=&c1x y1=&c1y z1=&c1z thickness=1 value=&j overwrite");
			}
		}
	}
	for(j=0; j<=coloMaxC; j++){
		if(nclucc[j]>0) 
			print("nb objects in cluster "+j+" = "+nclucc[j]);
	}
}
//histogram C-C
if(histocc==true){
	newImage("HistoImageC", "32-bit White", nb, 1, 1);
	for(i=0; i<nb; i++){
		setPixel(i, 0, dccmin[i]);
	}
	setKeyDown("alt");
	run("Histogram", "bins="+nb/5+" x_min="+minccAll+" x_max="+maxccAll+" y_max="+nb);
	selectImage("HistoImageC"); close();
}
//Table B-B
if(tablebb==true){
	newImage("closest_B-B", "RGB White", nb*10+10, nb*10+10, 1);
	for(i=0; i<nb; i++){
		setColor(0, 0, 0);
		fillRect(0, 0, 10, 10);
		fillRect((i+1)*10, (i+1)*10, 10, 10);
		x=12; y=9;
		setFont("SansSerif", 5);
		drawString(i, i*10+x, y);
		x=1; y=19;
		setFont("SansSerif", 6);
		drawString(i, x, i*10+y);
		setColor(255*(dbbmin[i]-minbbAll)/(maxbbAll-minbbAll), 255, 0);
		fillRect(proxbb[i]*10+10, i*10+10, 10, 10);
		fillRect(i*10+10, proxbb[i]*10+10, 10, 10);
		print("closest object of "+i+" is  object "+proxbb[i]+" with a distance border-border of "+ dbbmin[i]);
	}
}
//cluster B-B
if(fillbb==true){
	newImage("AmasProche_B-B", "16-bit black", gwid, ghei, nS);
	n=0;					
	change=true;
	while(change==true){
	change=false;
		for(i=0; i<nb; i++){	
			if (cluscobb[i]<0){
				cluscobb[i]=n++;
				change=true;
			}
			else if(cluscobb[i]!=cluscobb[proxbb[i]]){
				if(cluscobb[proxbb[i]]>cluscobb[i]){
				cluscobb[proxbb[i]]=cluscobb[i];}
				else {cluscobb[i]=cluscobb[proxbb[i]];}
				change=true;
			}
		}
	}	
	coloMaxB=0;
	for(i=0; i<nb; i++){			
		if(coloMaxB<cluscobb[i]){
			coloMaxB=cluscobb[i];
		}
	}
	nclubb= newArray(coloMaxB+1);		
	for(j=0; j<=coloMaxB; j++){
		n=1;
		for(i=0; i<nb; i++){
			if(cluscobb[i]==j){
				nclubb[j]=n++;
				Ext.Manager3D_Select(i);
				Ext.Manager3D_Fill(j, j, j);
				// lines
				Ext.Manager3D_Centroid3D(i,c0x,c0y,c0z);
				Ext.Manager3D_Centroid3D(proxcc[i],c1x,c1y,c1z);
				run("3D Line", "size_x=&gwid size_y=&ghei size_z=&nS x0=&c0x y0=&c0y z0=&c0z x1=&c1x y1=&c1y z1=&c1z thickness=1 value=&j overwrite");
			}
		}
	}
	for(j=0; j<=coloMaxB; j++){
		if(nclubb[j]>0)
			print("nb objects in cluster "+j+" = "+nclubb[j]);
	}
}
//histogram B-B
if(histobb==true){
	newImage("HistoImageB", "32-bit White", nb, 1, 1);
	for(i=0; i<nb; i++){
		setPixel(i, 0, dbbmin[i]);
	}
	setKeyDown("alt");
	run("Histogram", "bins="+nb/5+" x_min="+minbbAll+" x_max="+maxbbAll+" y_max="+nb);
	selectImage("HistoImageB"); close();
}