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BATCH_Personalize_FociFeatureAnalyzer
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BATCH_Personalize_FociFeatureAnalyzer
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var channelarray, chnamearray, fociarray, ROIcharray, selectedarray, roiarray, SettingsTableName, NumbersTableName,distkick,objname, focitype, seed, image,gaussian, tophat, minsizevar, maxsizevar, objectname, kickarray, maxdistance, kickedsmall, kickedbig,roimain,once,kickedarray,nbtotal, nb_total, arraycheck, ;
setOption("ExpandableArrays", true);
run("Set Measurements...", "area mean min integrated redirect=None decimal=6");
once = 0;
close("Results");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
#@ File (label = "Input directory", style = "directory") input
#@ File (label = "Output directory", style = "directory") output
#@ String (label = "File suffix", value = ".tif") suffix
channelarray = newArray;
chnamearray = newArray;
fociarray = newArray;
roiarray = newArray;
kickedarray = newArray;
kickarray = newArray;
distkick = newArray;
selectedarray = newArray;
ROIcharray = newArray;
//Closes all images
close("*");
//User Changeable Variables
SettingsTableName = "Settings";
NumbersTableName = "Foci_Count";
//Settings Table designated rows
focityperow = 0;
seedrow = 1;
imagerow = 2;
gaussianrow = 3;
tophatrow = 4;
minsizerow = 5;
maxsizerow = 6;
maxdistancerow = 7;
nbrow = 8;
kickedsmallrow = 9;
kickedbigrow = 10;
kickedDistrow = 11;
finalfocirow = 12;
//Creates Initial Dialog
Dialog.create("Channels to Process"); //checks which channels to apply segmentation
Dialog.addCheckbox("Channel 1", true);
Dialog.addCheckbox("Channel 2", true);
Dialog.addCheckbox("Channel 3", false);
Dialog.addCheckbox("Channel 4", false);
Dialog.addCheckbox("Channel 5", false);
Dialog.addCheckbox("Find Nearest Neighbor", false);
Dialog.addCheckbox("Find Channel Volume", true);
Dialog.addMessage("Intrachannel Options");
Dialog.addCheckbox("Associated Foci Threshold", false);
Dialog.addCheckbox("Find All Nearest Neighbor", false);
Dialog.addCheckbox("All Distances (painfully slow)", false);
Dialog.addCheckbox("Find 2nd Neirest Neighbors:", false);
Dialog.show();
doch1 = Dialog.getCheckbox();
doch2 = Dialog.getCheckbox();
doch3 = Dialog.getCheckbox();
doch4 = Dialog.getCheckbox();
doch5 = Dialog.getCheckbox();
doNN = Dialog.getCheckbox();
doChVol = Dialog.getCheckbox();
doAFT = Dialog.getCheckbox();
doallNN = Dialog.getCheckbox();
doAD = Dialog.getCheckbox();
do2NN = Dialog.getCheckbox();
//Creates settings table
Table.create(NumbersTableName);
Table.create(SettingsTableName);
selectWindow(SettingsTableName);
Table.showRowNumbers(false);
Table.set("Name", focityperow, "Foci Type");
Table.set("Name", seedrow, "Seed Threshold");
Table.set("Name", imagerow, "Image Threshold");
Table.set("Name", gaussianrow, "3D Gaussian Blur");
Table.set("Name", tophatrow, "Seed Top Hat");
Table.set("Name", minsizerow, "Minimum Allowed Particle Size");
Table.set("Name", maxsizerow, "Maximum Allowed Particle Size");
Table.set("Name", maxdistancerow, "Maximum Allowed Distance");
Table.set("Name", nbrow, "Number of Signals before Filtering");
Table.set("Name", kickedsmallrow, "Number of Kicked Signals by Size (small)");
Table.set("Name", kickedbigrow, "Number of Kicked Signals by Size (big)");
Table.set("Name", kickedDistrow, "Number of Kicked Signals by Distance");
Table.set("Name", finalfocirow, "Final Number of Signals");
Table.update(SettingsTableName);
vararray = 0;
if(doch1 == true){
channelarray[vararray]="channel1";
chnamearray[vararray]= "C1-";
kickedarray[vararray] = 0;
vararray++;
}
if(doch2 == true){
channelarray[vararray]="channel2";
chnamearray[vararray]= "C2-";
kickedarray[vararray] = 0;
vararray++;
}
if(doch3 == true){
channelarray[vararray]="channel3";
chnamearray[vararray]= "C3-";
kickedarray[vararray] = 0;
vararray++;
}
if(doch4 == true){
channelarray[vararray]="channel4";
chnamearray[vararray]= "C4-";
kickedarray[vararray] = 0;
vararray++;
}
if(doch5 == true){
channelarray[vararray]="channel5";
chnamearray[vararray]= "C5-";
kickedarray[vararray] = 0;
vararray++;
}
if(doNN == true || doAFT==true){
if(vararray<2){
exit("Nearest Neighbor and Associated Foci thresholding Requires 2 channels");
}
Dialog.create("Channel Hierarchy");
Dialog.addChoice("Main Channel", channelarray,channelarray[1]);
Dialog.addNumber("Max Distance (microns)", 0.250);
Dialog.show();
mainch = Dialog.getChoice();
maxdistance = Dialog.getNumber();
List.set("maxdistance", maxdistance);
}
for (f = 0; f < vararray; f++) {
TableSetup();
fociarray[f] = focitype;
addList();
}
if(doNN == true || doAFT==true){
for(q = 0; q<channelarray.length; q++){
if (channelarray[q]==mainch) {
mainch = chnamearray[q];
break;
}
}
}
processFolder(input);
// function to scan folders/subfolders/files to find files with correct suffix
function processFolder(input) {
list = getFileList(input);
list = Array.sort(list);
for (b = 0; b < list.length; b++) {
if(File.isDirectory(input + File.separator + list[b]))
processFolder(input + File.separator + list[b]);
if(endsWith(list[b], suffix))
processFile(input, output, list[b]);
}
}
function processFile(input, output, file) {
if (doAD == true && once==0) {
ADdir = output + File.separator + "Distance_Files"; //directory to save the files
File.makeDirectory(ADdir);
}
//Open image from folder
open(input+File.separator+list[b]);
//gets properties from image
noExt = File.nameWithoutExtension;
filename = getTitle();
//find channel file names
ch1 = "C1-" + filename; //channel1
ch2 = "C2-" + filename; //channel2
ch3 = "C3-" + filename; //channel3
ch4 = "C4-" + filename; //channel4
ch5 = "C5-" + filename; //channel5
ch1ne = "C1-" + noExt; //channel1 no extension
ch2ne = "C2-" + noExt; //channel2 no extension
ch3ne = "C3-" + noExt; //channel3 no extension
ch4ne = "C4-" + noExt; //channel4 no extension
ch5ne = "C5-" + noExt; //channel5 no extension
//gets original image properties
getVoxelSize(width, height, depth, unit);
voxw = width;
voxh = height;
voxd = depth;
voxu = unit;
//makes folder for image
dir = output + File.separator + noExt; //directory to save the files
File.makeDirectory(dir);
selectImage(filename);
saveAs("tiff", dir+File.separator+filename);
//Image Prep
run("Split Channels");
run("3D Manager");
Ext.Manager3D_MultiSelect();
resultsrow = nResults; //numbers of entries in results table
for(i=0; i<vararray; i++){
distkick[i]=0;
activech = channelarray[i];
active = chnamearray[i]+filename;
activene = chnamearray[i]+noExt;
ProgramOrder();
}
filelist = getFileList(dir);
filelistsort = Array.sort(filelist);
if(doAFT==true) {
doNNthr();
}
if(doAFT==false){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Delete();
ptq=0;
for (d = 0; d < filelistsort.length; d++) {
if(endsWith(filelistsort[d], ".zip")){
print("poop2");
Ext.Manager3D_Load(dir + File.separator + filelistsort[d]);
print("poop2");
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb_obj);
roiarray[ptq] = nb_obj;
ptq++;
}
}
}
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb_total);
ROIcharray = newArray;
amount=0;
for(qt = 0; qt<vararray; qt++){
for(h = 0; h<nb_total; h++){
Ext.Manager3D_GetName(h, name);
if(indexOf(name, channelarray[qt])>=0){
amount++;
}
}
ROIcharray[qt] = amount;
}
if (doNN==true) {
findNN();
}
else {
print("nalyzing");
analyze();
}
if(doallNN==true){
findallNN();
}
if(doAD==true) {
allDist();
}
print("steppy");
selectWindow(NumbersTableName);
size=Table.size;
if(size>0){
cellcheck=Table.getString("Cell", size-1);
if(cellcheck==noExt){
for(l = 0; l<vararray; l++){
selectWindow(SettingsTableName);
nbtotal = Table.get(channelarray[l], nbrow);
Table.set(channelarray[l], kickedDistrow, distkick[l]);
Table.set(channelarray[l], finalfocirow, nbtotal-kickedarray[l]-distkick[l]);
Table.update(SettingsTableName);
selectWindow(NumbersTableName);
Table.set("Cell", size-1, noExt);
Table.set(channelarray[l], size-1, nbtotal-kickedarray[l]-distkick[l]);
Table.update(NumbersTableName);
}
}
}
else {
for(l = 0; l<vararray; l++){
print("steppy2");
selectWindow(SettingsTableName);
nbtotal = Table.get(channelarray[l], nbrow);
Table.set(channelarray[l], kickedDistrow, distkick[l]);
Table.set(channelarray[l], finalfocirow, nbtotal-kickedarray[l]-distkick[l]);
Table.update(SettingsTableName);
selectWindow(NumbersTableName);
Table.set("Cell", size, noExt);
Table.set(channelarray[l], size, nbtotal-kickedarray[l]-distkick[l]);
Table.update(NumbersTableName);
}
}
Ext.Manager3D_SelectAll();
Ext.Manager3D_Delete();
Ext.Manager3D_Close();
close("*");
selectWindow(SettingsTableName);
saveAs("results", dir + File.separator + "Settings_of_"+noExt+".csv");
Table.rename("Settings_of_"+noExt+".csv", SettingsTableName);
selectWindow("Results");
saveAs("results", output + File.separator + "Results.csv");
selectWindow(NumbersTableName);
saveAs("results", output + File.separator + "Foci_Count.csv");
Table.rename("Foci_Count.csv", NumbersTableName);
Array.fill(kickedarray, 0);
Array.fill(kickarray, 0);
Array.fill(distkick, 0);
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
}
function ProgramOrder() {
Ext.Manager3D_DeselectAll();
Ext.Manager3D_SelectAll();
Ext.Manager3D_Delete();
//get seed and segment
GetSeed();
//Gets segmented ROIs and do size filter
useROImanager();
if(doChVol == true) {
maskvolume();
}
selectImage("imgext");
rename(active);
}
function addList(){
List.set("focitype"+f, focitype);
List.set("seed"+f, seed);
List.set("image"+f, image);
List.set("gaussian"+f, gaussian);
List.set("tophat"+f, tophat);
List.set("minsizevar"+f, minsizevar);
List.set("maxsizevar"+f, maxsizevar);
}
function TableSetup() {
Dialog.create("Settings for " + channelarray[f]);
Dialog.addString("Foci Type (no spaces):", channelarray[f]);
Dialog.addMessage("Seed Settings");
Dialog.addNumber("Seed Threshold:", 8.1);
Dialog.addNumber("Image Threshold:", 2);
Dialog.addNumber("3D Gaussian Blur Filter:", 1);
Dialog.addNumber("Top Hat:", 2);
Dialog.addMessage("Segmented Foci Settings");
Dialog.addNumber("Minimum Particle Size (voxel):", 10);
Dialog.addNumber("Maximum Particle Size (voxel):", 150);
Dialog.show();
focitype = Dialog.getString();
seed = Dialog.getNumber();
image = Dialog.getNumber();
gaussian = Dialog.getNumber();
tophat = Dialog.getNumber();
minsizevar = Dialog.getNumber();
maxsizevar = Dialog.getNumber();
//Prepare Table for Data
selectWindow(SettingsTableName);
Table.set(channelarray[f], focityperow, focitype);
Table.set(channelarray[f], seedrow, seed);
Table.set(channelarray[f], imagerow, image);
Table.set(channelarray[f], gaussianrow, gaussian);
Table.set(channelarray[f], tophatrow, tophat);
Table.set(channelarray[f], minsizerow, minsizevar);
Table.set(channelarray[f], maxsizerow, maxsizevar);
Table.set(channelarray[f], maxdistancerow, maxdistance);
Table.update(SettingsTableName);
}
function GetSeed() {
//get image histogram properties
selectImage(active);
Stack.getStatistics(voxelCount, mean, min, max, stdDev);
//calculates image thr
imgmult = List.getValue("image"+i);
seedmult = List.getValue("seed"+i);
seedthr = mean + ((2 * stdDev) * seedmult);
imagethr = seedthr/imgmult;
simagethr = seedthr/1.2;
//prepares image for seed by creating duplicate
selectImage(active);
rename("imgext");
run("Duplicate...", "title=seedroll duplicate");
//applies filters to seed
selectImage("seedroll");
gb = List.getValue("gaussian"+i);
run("Gaussian Blur 3D...", "x="+gb+" y="+gb+" z="+gb);
th = List.getValue("tophat"+i);
run("3D Fast Filters","filter=TopHat radius_x_pix="+th+" radius_y_pix="+th+" radius_z_pix=1.0 Nb_cpus=4");
selectImage("3D_TopHat");
rename("seedroll2");
//calculate seed thr
Stack.getStatistics(voxelCount, mean, min, max, stdDev);
seedthr2 = mean + ((2 * stdDev) * seedmult);
imagethr2 = seedthr2/imgmult;
simagethr2 = seedthr2/1.2;
//creates seed
run("3D Watershed", "seeds_threshold="+seedthr2 + " image_threshold="+simagethr2+ " image=seedroll2 seeds=Automatic radius=1");
selectImage("watershed");
rename("seed");
//Segments image with seed
run("3D Watershed", "seeds_threshold=1 image_threshold="+imagethr+ " image=imgext seeds=seed radius=1");
}
function useROImanager(){
//applies original iamge properties to segmented watershed image
selectWindow("watershed");
setVoxelSize(voxw, voxh, voxd, voxu);
//Creates ROIs
Ext.Manager3D_AddImage();
Ext.Manager3D_SelectAll();
ROItidy();
//saves rois
Ext.Manager3D_Save(dir+File.separator+"ROIs_of_"+activene+".zip");
//Saves mask
selectWindow("watershed");
saveAs("tiff", dir+File.separator+"Masks_of_"+activene);
close();
close("seedroll");
close("seedroll2");
close("seed");
}
function ROItidy() {
//counts numbers of objects
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb_total);
//adds objects before filtering
selectWindow(SettingsTableName);
Table.set(activech, nbrow, nb_total);
Table.update(SettingsTableName);
//Get Size Values
minsizevar = List.getValue("minsizevar"+i);
maxsizevar = List.getValue("maxsizevar"+i);
kicked = 0;
kickedsmall=0;
kickedbig=0;
for(a=0; a<nb_total; a++){
Ext.Manager3D_Measure3D(a,"NbVox",mnbvox);
if (mnbvox<minsizevar) {
Ext.Manager3D_DeselectAll();
Ext.Manager3D_Select(a);
Ext.Manager3D_Delete();
kickedsmall++;
kickedarray[i]++;
a=a-1;
}
if (mnbvox>maxsizevar){
Ext.Manager3D_DeselectAll();
Ext.Manager3D_Select(a);
Ext.Manager3D_Delete();
kickedbig++;
kickedarray[i]++;
a=a-1;
}
}
selectWindow(SettingsTableName);
Table.set(activech, kickedbigrow, kickedbig);
Table.set(activech, kickedsmallrow, kickedsmall);
Table.update(SettingsTableName);
fltnb = nb_total - kickedbig - kickedsmall;
Ext.Manager3D_SelectAll();
selectWindow(SettingsTableName);
Ext.Manager3D_Rename(activech+"-");
}
function analyze(){
qt=0;
pt=0;
qtt=0;
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb);
for(qt = 0; qt<vararray; qt++){
selectImage(chnamearray[qt]+filename);
//Select Object
for(h = 0; h<nb; h++){
Ext.Manager3D_GetName(h, name);
if(indexOf(name, channelarray[qt])>=0){
Ext.Manager3D_Measure3D(h,"Vol",mvol);
Ext.Manager3D_Measure3D(h,"Feret",mferet);
Ext.Manager3D_Measure3D(h,"NbVox",mvox);
Ext.Manager3D_Measure3D(h,"Elon1",melon);
Ext.Manager3D_Measure3D(h,"Comp",mcomp);
Ext.Manager3D_Centroid3D(h,cx,cy,cz);
Ext.Manager3D_Quantif3D(h,"IntDen",qintden);
Ext.Manager3D_Quantif3D(h,"Mean",qmean);
Ext.Manager3D_Quantif3D(h,"Max",qmax);
Ext.Manager3D_Quantif3D(h,"Min",qmin);
Ext.Manager3D_GetName(h, first);
setResult("Cell", resultsrow + pt, noExt);
setResult("ROI", resultsrow + pt, first);
setResult("cX", resultsrow + pt, cx);
setResult("cY", resultsrow + pt, cy);
setResult("cZ", resultsrow + pt, cz);
setResult("Volume_unit", resultsrow + pt, mvol);
setResult("Volume_voxel", resultsrow + pt, mvox);
setResult("Feret", resultsrow + pt, mferet);
setResult("Compactness", resultsrow + pt, mcomp);
setResult("Elongation", resultsrow + pt, melon);
setResult("IntDen", resultsrow + pt, qintden);
setResult("Mean", resultsrow + pt, qmean);
setResult("Min", resultsrow + pt, qmin);
setResult("Max", resultsrow + pt, qmax);
pt++;
}
}
updateResults();
Ext.Manager3D_SelectAll();
Ext.Manager3D_Save(dir+File.separator+"ROIs_of_"+noExt+".zip");
}
}
function doNNthr(){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Delete();
ptq=0;
for (d = 0; d < filelistsort.length; d++) {
if(endsWith(filelistsort[d], ".zip")){
Ext.Manager3D_Load(dir + File.separator + filelistsort[d]);
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb_obj);
roiarray[ptq] = nb_obj;
if(indexOf(filelistsort[d], mainch)>1){
roimain=ptq;
}
ptq++;
}
}
maxdistance = List.getValue("maxdistance");
if(roimain==0){
range1 = 0;
range2 = roiarray[roimain];
}
else{
range1 = roiarray[roimain-1];
range2 = roiarray[roimain];
}
ptq=0;
Ext.Manager3D_DeselectAll();
for (e = 0; e < roiarray[vararray-1]; e++) {
Ext.Manager3D_SelectFor(range1,range2,1);
if (e<range2 && e>=range1) {
}
else{
Ext.Manager3D_Select(e);
Ext.Manager3D_GetName(e,objname);
Ext.Manager3D_Closest(e,"cc",closestcc);
Ext.Manager3D_GetName(closestcc,namecc);
Ext.Manager3D_Dist2(e,closestcc,"cc",distcc);
Ext.Manager3D_Closest(e,"cc",closestbb);
Ext.Manager3D_GetName(closestbb,namebb);
Ext.Manager3D_Dist2(e,closestbb,"bb",distbb);
if (distcc > maxdistance) {
kickarray[ptq] = e;
ptq++;
for(t=0;t<vararray;t++){
if(indexOf(objname, channelarray[t])>=0){
distkick[t]++;
}
}
}
Ext.Manager3D_DeselectAll();
}
}
Ext.Manager3D_DeselectAll();
for(g = 0; g<ptq; g++){
Ext.Manager3D_Select(kickarray[g]);
}
if (ptq!=0) {
Ext.Manager3D_Delete();
}
Ext.Manager3D_SelectAll();
Ext.Manager3D_Save(dir+File.separator+"ROIs_of_"+noExt+".zip");
}
function findNN(){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb);
Ext.Manager3D_DeselectAll();
qt=0;
pt=0;
for(qt = 0; qt<vararray; qt++){
lower=0;
upper=0;
selectImage(chnamearray[qt]+filename);
Ext.Manager3D_DeselectAll();
for(h = 0; h<nb; h++){
Ext.Manager3D_GetName(h, name);
if(indexOf(name, channelarray[qt])>=0){
Ext.Manager3D_Select(h);
lower++;
upper=h;
}
}
for(m = (upper-lower)+1 ; m<=upper; m++){
Ext.Manager3D_Closest(m,"cc",closestcc);
Ext.Manager3D_GetName(closestcc,namecc);
Ext.Manager3D_Dist2(m,closestcc,"cc",distcc);
Ext.Manager3D_Closest(m,"cc",closestbb);
Ext.Manager3D_GetName(closestbb,namebb);
Ext.Manager3D_Dist2(m,closestbb,"bb",distbb);
Ext.Manager3D_Measure3D(m,"Vol",mvol);
Ext.Manager3D_Measure3D(m,"Feret",mferet);
Ext.Manager3D_Measure3D(m,"NbVox",mvox);
Ext.Manager3D_Measure3D(m,"Elon1",melon);
Ext.Manager3D_Measure3D(m,"Comp",mcomp);
Ext.Manager3D_Centroid3D(m,cx,cy,cz);
Ext.Manager3D_Quantif3D(m,"IntDen",qintden);
Ext.Manager3D_Quantif3D(m,"Mean",qmean);
Ext.Manager3D_Quantif3D(m,"Max",qmax);
Ext.Manager3D_Quantif3D(m,"Min",qmin);
Ext.Manager3D_GetName(m, first);
setResult("Cell", resultsrow + pt, noExt);
setResult("ROI", resultsrow + pt, first);
setResult("cX", resultsrow + pt, cx);
setResult("cY", resultsrow + pt, cy);
setResult("cZ", resultsrow + pt, cz);
setResult("Volume_unit", resultsrow + pt, mvol);
setResult("Volume_voxel", resultsrow + pt, mvox);
setResult("Feret", resultsrow + pt, mferet);
setResult("Compactness", resultsrow + pt, mcomp);
setResult("Elongation", resultsrow + pt, melon);
setResult("IntDen", resultsrow + pt, qintden);
setResult("Mean", resultsrow + pt, qmean);
setResult("Min", resultsrow + pt, qmin);
setResult("Max", resultsrow + pt, qmax);
setResult("NN_SameCh_CC", resultsrow + pt, namecc);
setResult("NN_SameCh_BB", resultsrow + pt, namebb);
setResult("NNDistance_SameCh_CC", resultsrow + pt, distcc);
setResult("NNDistance_SameCh_BB", resultsrow + pt, distbb);
pt++;
updateResults();
}
}
updateResults();
if(doAFT==false){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Save("ROIs_of_"+noExt+".zip");
}
}
function findallNN(){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb);
Ext.Manager3D_DeselectAll();
qt=0;
pt=0;
qtt=0;
for(qt = 0; qt<vararray; qt++){
//Select Object
for(h = 0; h<nb; h++){
Ext.Manager3D_GetName(h, name);
if(indexOf(name, channelarray[qt])>=0){
//Select objects to compare to
for(qtt = 0; qtt<vararray; qtt++){
if(qtt!=qt){
if(qtt==0){
Ext.Manager3D_SelectFor(0,ROIcharray[0],1);
}
else {
Ext.Manager3D_SelectFor(ROIcharray[qtt-1],ROIcharray[qtt],1);
}
Ext.Manager3D_Select(h);
//checks there more than 1 object
errorarray = newArray;
Ext.Manager3D_GetSelected(list);
errorarray=split(list,":");
Array.getStatistics(errorarray, emin, emax, emean, estdDev);
//find NN
if(emin!=emax){
Ext.Manager3D_Closest(h,"cc",closestcc);
Ext.Manager3D_GetName(closestcc,namecc);
Ext.Manager3D_Dist2(h,closestcc,"cc",distcc);
Ext.Manager3D_Closest(h,"cc",closestbb);
Ext.Manager3D_GetName(closestbb,namebb);
Ext.Manager3D_Dist2(h,closestbb,"bb",distbb);
setResult("NN_CC_to_"+channelarray[qtt] , resultsrow + pt, namecc);
setResult("NN_BB_to_"+channelarray[qtt], resultsrow + pt, namebb);
setResult("NNDistance_CC_to_"+channelarray[qtt], resultsrow + pt, distcc);
setResult("NNDistance_BB_to_"+channelarray[qtt], resultsrow + pt, distbb);
//finds second NN
if (do2NN==true) {
selectedarray = newArray;
Ext.Manager3D_GetSelected(list);
selectedarray=split(list,":");
Array.getStatistics(selectedarray, amin, amax, amean, astdDev);
Ext.Manager3D_DeselectAll();
if(amin!=amax){
for (t = 0; t < selectedarray.length; t++) {
arraycheck = selectedarray[t];
if (arraycheck!=closestcc) {
Ext.Manager3D_Select(selectedarray[t]);
}
}
Ext.Manager3D_Closest(h,"cc",closestcc);
Ext.Manager3D_GetName(closestcc,namecc);
Ext.Manager3D_Dist2(h,closestcc,"cc",distcc);
Ext.Manager3D_Closest(h,"cc",closestbb);
Ext.Manager3D_GetName(closestbb,namebb);
Ext.Manager3D_Dist2(h,closestbb,"bb",distbb);
setResult("SecondNN_CC_to_"+channelarray[qtt] , resultsrow + pt, namecc);
setResult("SecondNN_CCNN_BB_to_"+channelarray[qtt], resultsrow + pt, namebb);
setResult("SecondNN_CCNNDistance_CC_to_"+channelarray[qtt], resultsrow + pt, distcc);
setResult("SecondNN_CCNNDistance_BB_to_"+channelarray[qtt], resultsrow + pt, distbb);
}
}
Ext.Manager3D_DeselectAll();
}
}
}
pt++;
}
}
}
updateResults();
}
/*function findallNN(){
Ext.Manager3D_SelectAll();
Ext.Manager3D_Count(nb);
Ext.Manager3D_DeselectAll();
qt=0;
pt=0;
qtt=0;
for(qt = 0; qt<vararray; qt++){
for(h = 0; h<nb; h++){
Ext.Manager3D_GetName(h, name);
if(indexOf(name, channelarray[qt])>=0){
Ext.Manager3D_Select(h);
for(qtt = 0; qtt<vararray; qtt++){
if(qtt!=qt){
for(m=0;m<nb;m++){
Ext.Manager3D_GetName(m, name2);
if(indexOf(name2, channelarray[qtt])>=0){
Ext.Manager3D_Select(m);
}
}
errorarray = newArray;
Ext.Manager3D_GetSelected(list);
errorarray=split(list,":");
Array.getStatistics(errorarray, emin, emax, emean, estdDev);
if(emin!=emax){
Ext.Manager3D_Closest(h,"cc",closestcc);
Ext.Manager3D_GetName(closestcc,namecc);
Ext.Manager3D_Dist2(h,closestcc,"cc",distcc);
Ext.Manager3D_Closest(h,"bb",closestbb);
Ext.Manager3D_GetName(closestbb,namebb);
Ext.Manager3D_Dist2(h,closestbb,"bb",distbb);
setResult("NN_CC"+channelarray[qt]+"_to_"+channelarray[qtt] , resultsrow + pt, namecc);
setResult("NN_BB"+channelarray[qt]+"_to_"+channelarray[qtt], resultsrow + pt, namebb);
setResult("NNDistance_CC"+channelarray[qt]+"_to_"+channelarray[qtt], resultsrow + pt, distcc);
setResult("NNDistance_BB"+channelarray[qt]+"_to_"+channelarray[qtt], resultsrow + pt, distbb);