// Realign OCT
// 
//  This is a set of tools to relign an OCT image


//GLOBAL VARIABLES
var slicewidth = 1, topslice = 50, bottomslice = 49, offset = 0, pixelsperslice = 10, noslices = 100, noslicesout = 100, sequencetype = 1, skanlabel, skanlabeltype; 
var imageid = 0, stackid = 0, resliceid = 0, skanlabel = "skan", imagechoice;
var imagedir = "", newfolder = "", templatedir;
var stackwidth = 0, stackheight = 0, imagewidth = 0, imageheight = 0;
var scrheight, scrwidth;

var protocolin = newArray("7mm x 7mm", "10mm x 10mm", "5mm x 5mm", "5mm x 10mm", "8mm x 12mm");
var protocolout = newArray("7mm x 7mm", "10mm x 10mm", "5mm x 5mm", "12mm x 12mm");
var protocolinchoice = "5mm x 10mm",  protocoloutchoice = "10mm x 10mm", Ascanspacing = 1.1, Bscanspacing = 1.1;

var template = 1, recentre = 0, reverse = 1, fovea  = 1, eye = 1, eyestring = "right";
var firstname = "X", lastname = "X", gender = "1", day = "1", month = "1", year = "2000";
var testday = "1", testmonth = "1", testyear = "2010", testtime = "12:00:00";
var superlative = newArray("FINE", "FINE", "FINE", "FINE", "FINE", "FINE", "FINE", "FINE","FINE","FINE","FINE");

var edgerpe = newArray("Non-oblique","Internally oblique", "Internally oblique with Bruch's membrane overhang", "Externally oblique","Other");
var rpedeflection = newArray("Straight", "Downwards", "Upwards","Other");
var typevessel = newArray("None", "Hyaloid", "Vessel", "Other");
var locationvessel = newArray("None","Upper half of cup", "Lower half of cup", "Cup bottom", "Along whole edge","Other");

var picname = "CHANGE NAME";

var rpe=newArray(2000);
var ilm=newArray(2000);
var rnfl=newArray(2000);
var bruchs=newArray(2000);

var optionstrings = newArray ("Go to select area to analyse", "Go to adjust brightness / contrast", "Go to anisometropic filter", "Go to flatten disk", "Go to ABSnake", "CONTINUE");
var option = 0;

var optionstringsfirst = newArray ("Go to select area to analyse", "Go to adjust brightness / contrast", "Go to anisometropic filter", "CONTINUE");


call("java.lang.System.gc");



/////COPY THIS SECTION

var imageJdir = getDirectory("imagej");						//IMAGEJ FOLDER		

var mainOCTdir = imageJdir+"\\OCT_Analysis\\";					//FOLDER WITH CONFIG FILES ETC

var layerimagesdir = imageJdir+"\\images\\layers\\ONH\\";		//FOLDER WITH CONFIG FILES ETC

var onhfolder = imageJdir+"\\ONH_ANALYSIS\\";				//TEXT FILES RESULTS ARE SAVED HERE


///////////////////////////////////////////////////////////////


  var xx = setup(); // runs when macros are installed
  function setup() {
      setOption("QueueMacros", true);
      return true;
  }

macro "START Action Tool - 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"{

//SET UP VARIABLES AND IMPORT DATA

scrheight = screenHeight();
scrwidth = screenWidth();
stackid = nImages;



//IF BUTTONS ARE PRESSED BEFORE LAST SET OF FILES ARE CLOSED

if (stackid>0) {
waitForUser("Realign Tool", "THERE ARE FILES ALREADY OPEN! PLEASE CLOSE THEM FIRST!");
}
else
{


imagechoice = getBoolean("DO YOU WANT TO ANALYSE A SINGLE PREVIOUSLY SAVED IMAGE (NO FOR STACK)?");

if (imagechoice==1){
open();
picname=getInfo("image.filename");
picname=substring(picname, 0, lengthOf(picname)-4);

}
else
{

run("OCT Reader", "select=[]");
run("Flip Vertically", "stack");
run("Reverse");
}


protocolinchoice = "8mm x 12mm";
protocoloutchoice = "12mm x 12mm";

sequencetype=0;


//GET IMPORTANT PARAMETERS

stackwidth = getWidth();
stackheight = getHeight();
noslices = nSlices();

stackid = getImageID();
imagedir = getDirectory("image");

setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));


run("Point Tool...", "mark=0 label selection=yellow");


//shortenchoice = getBoolean("DO YOU WANT TO SHORTEN HEIGHT TO 1010?");
//if(shortenchoice==1){
//Fill out canvas to required size
stackheight = 1010;
//}

//eye = getBoolean("IS THIS RIGHT EYE DATA (NO FOR LEFT)?");

//if (eye==0){
eyestring="left";
//}
//else
//{
//eyestring="right";
//}

}

if (noslices>300){
waitForUser("Realign Tool", "THERE ARE TOO MANY SLICES FOR THIS PROGRAM (MAX = 300)!");
}
else
{


if (imagechoice!=1){

//CREAT DIALOG BOX

Dialog.create("PLEASE SET INPUT SETTINGS FOR THE FILE ANALYSIS");
Dialog.addMessage("FILE SETTINGS");
Dialog.addMessage("Stack width is "+stackwidth+" pixels");
Dialog.addMessage("Stack height is "+stackheight+" pixels");
Dialog.addMessage("No of slices is "+noslices);
Dialog.addMessage("");
Dialog.addMessage("PROTOCOL SETTINGS");
Dialog.addChoice("Choose original protocol used", protocolin, protocolinchoice);
Dialog.addChoice("Choose final protocol to save", protocolout, protocoloutchoice);

Dialog.show();

//GET VALUES OUT OF DIALOG BOX

protocolinchoice = Dialog.getChoice();
protocoloutchoice = Dialog.getChoice();


//SET UP PARAMETERS BASED ON CHOICES


if (protocolinchoice=="7mm x 7mm")
{
Ascanspacing = 7000/stackwidth;
Bscanspacing = 7000/noslices;
}

if (protocolinchoice=="10mm x 10mm")
{
Ascanspacing = 10000/stackwidth;
Bscanspacing = 10000/noslices;
}

if (protocolinchoice=="5mm x 5mm")
{
Ascanspacing = 5000/stackwidth;
Bscanspacing = 5000/noslices;
}

if (protocolinchoice=="5mm x 10mm")
{
Ascanspacing = 10000/stackwidth;
Bscanspacing = 5000/noslices;
}

if (protocolinchoice=="8mm x 12mm")
{
Ascanspacing = 12000/stackwidth;
Bscanspacing = 8000/noslices;
}

if (protocoloutchoice=="7mm x 7mm")
{
imagewidth = round(7000/Ascanspacing);
noslicesout = round(7000/Bscanspacing);
templatedir = mainOCTdir+"Copernicus_Templates\\7mmx7mm";
}

if (protocoloutchoice=="10mm x 10mm")
{
imagewidth = round(10000/Ascanspacing);
noslicesout = round(10000/Bscanspacing);
templatedir = mainOCTdir+"Copernicus_Templates\\10mmx10mm";
}

if (protocoloutchoice=="5mm x 5mm")
{
imagewidth = round(5000/Ascanspacing);
noslicesout = round(5000/Bscanspacing);
templatedir = mainOCTdir+"Copernicus_Templates\\10mmx10mm";
}


if (protocoloutchoice=="12mm x 12mm")
{
imagewidth = round(12000/Ascanspacing);
noslicesout = round(12000/Bscanspacing);
templatedir = mainOCTdir+"Copernicus_Templates\\12mmx12mm";
}


templatedir =templatedir+"_"+stackwidth+"Ascans";
templatedir = templatedir+"_"+noslicesout+"Bscans"; 
//templatedir = templatedir+"_200Bscans";



if (fovea==1){
templatedir = templatedir+"_fovea";
}
else
{
templatedir = templatedir+"_ONH";
}

pixelsperslice = round(Bscanspacing/Ascanspacing);
imageheight = pixelsperslice * noslicesout;


if (sequencetype==0) {

// CHANGE CANVAS WIDTH BASED ON PARAMETERS

run("Canvas Size...", "width="+imagewidth+" height="+stackheight+" position=Center zero");
run("Out");


//put default in centre slice and middle 

if(recentre==1)
{
Stack.setSlice(noslices/2);
run("Colors...", "foreground=blue background=white selection=yellow");
makePoint(imagewidth/2, stackheight/2);
setTool(7);

setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));

waitForUser("SET POINT AND SLICE AT MIDPOINT OF FOVEA TO RECENTRE");
n=getSliceNumber();
getSelectionCoordinates(a, b);

//will move
run("Translate...", "x="+((imagewidth/2)-a[0])+" y=0 interpolation=None stack");
}
else
{
n=round(noslices/2);
}



if (noslicesout>noslices)
{


i=round((noslicesout/2)-(noslices-n));
j=noslicesout-noslices-i;


Stack.setSlice(noslices); 

if (i>0){
for (l=0; l<i; l++){
run("Add Slice");
}
}

if (i<0){
for (l=0; l<(i*-1); l++){
run("Delete Slice");
}
}

//sort out first slice which will be in wrong place
if(j>0){
Stack.setSlice(0);
run("Add Slice");
Stack.swap(1, 2);
}

if(j>1){
Stack.setSlice(0);
for (l=1;l<j;l++){
run("Add Slice");
}

if(j<0){
for (l=1;l<j*-1);l++){
Stack.setSlice(0);
run("Delete Slice");
}


}

}

}

//DO RESLICE TO GET Z PROJECTION FROM ABOVE
selectImage(stackid);
makeRectangle(0, 0, imagewidth, stackheight);

run("Reslice [/]...", "slice=1.000 start=Top");
resliceid = getImageID();

run("Z Project...", "start=1 stop=1010 projection=[Sum Slices]");
imageid = getImageID();

selectImage(resliceid);
close();
selectImage(imageid);

run("Size...", "width="+imagewidth+" height="+imageheight+" interpolation=None");

if (sequencetype==1) {
run("Brightness/Contrast...");
setMinAndMax(-3000, 50000);
setLocation((scrwidth*0.35), (scrheight*0.15), (scrwidth*0.7), (scrheight*0.7));
run("Close");
}
else 
{
selectImage(stackid);
setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));
run("Select All");
run("Subtract...", "value=50 stack");

selectImage(imageid);
run("Brightness/Contrast...");
setMinAndMax(71000, 90000);
setLocation((scrwidth*0.35), (scrheight*0.15), (scrwidth*0.7), (scrheight*0.7));
run("Close");
}

bottomslice = round(noslicesout/2);
topslice =bottomslice-1;
slicewidth = bottomslice - topslice;

offset = 0;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Colors...", "foreground=blue background=white selection=yellow");
setLocation((scrwidth*0.35), (scrheight*0.15), (scrwidth*0.7), (scrheight*0.7));

selectImage(stackid);
setSlice(topslice+1);

}
}
}

}

macro "FORWARDS Action Tool - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D37D38D3fD40D47D48D4fD50D57D58D5fD60D67D68D6fD70D72D73D74D75D76D77D78D79D7aD7bD7cD7dD7fD80D82D83D84D85D86D87D88D89D8aD8bD8cD8dD8fD90D97D98D9fDa0Da7Da8DafDb0Db7Db8DbfDc0Dc7Dc8DcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC246D27C356D28C456D66Dd7C467Dd8C577D69D96C687D36D46D56D62D63D64D65D6aD6bD6cDa6Db6Dc6C798D99C898D6dC8a8D26C9a8D39D49D59D71D92D93D94D95D9aD9bD9cDa9Db9Dc9Dd6Cab9D81D9dCac9D29Dd9Ccd9D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D22D23D24D25D2aD2bD2cD2dD2eD31D32D33D34D35D3aD3bD3cD3dD3eD41D42D43D44D45D4aD4bD4cD4dD4eD51D52D53D54D55D5aD5bD5cD5dD5eD61D6eD7eD8eD91D9eDa1Da2Da3Da4Da5DaaDabDacDadDaeDb1Db2Db3Db4Db5DbaDbbDbcDbdDbeDc1Dc2Dc3Dc4Dc5DcaDcbDccDcdDceDd1Dd2Dd3Dd4Dd5DdaDdbDdcDddDdeDe1De2De3De4De5De6De7De8De9DeaDebDecDedDee"{


topslice = topslice - 1;
bottomslice = bottomslice-1;

if (topslice<0){
topslice=0;
}

if (bottomslice<1){
bottomslice=1;
}

slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}



macro "BACKWARDS Action Tool  - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D3fD40D4fD50D57D58D5fD60D67D68D6fD70D77D78D7fD80D87D88D8fD90D97D98D9fDa0Da7Da8DafDb0DbfDc0DcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC687D56D66D76D86D96Da6C9a8D47D48D59D69D79D89D99Da9Db7Db8Cbc9D46Ccd9D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D22D23D24D25D26D27D28D29D2aD2bD2cD2dD2eD31D32D33D34D35D36D37D38D39D3aD3bD3cD3dD3eD41D42D43D44D45D49D4aD4bD4cD4dD4eD51D52D53D54D55D5aD5bD5cD5dD5eD61D62D63D64D65D6aD6bD6cD6dD6eD71D72D73D74D75D7aD7bD7cD7dD7eD81D82D83D84D85D8aD8bD8cD8dD8eD91D92D93D94D95D9aD9bD9cD9dD9eDa1Da2Da3Da4Da5DaaDabDacDadDaeDb1Db2Db3Db4Db5Db6Db9DbaDbbDbcDbdDbeDc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDcbDccDcdDceDd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDe1De2De3De4De5De6De7De8De9DeaDebDecDedDee"{

topslice = topslice + 1;
bottomslice = bottomslice + 1;


if (topslice>noslicesout-1){
topslice=noslicesout-1;
}

if (bottomslice>noslicesout){
bottomslice=noslicesout;
}


slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}


macro "LEFT Action Tool - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D3fD40D48D4fD50D57D58D5fD60D67D68D69D6fD70D76D77D78D79D7fD80D85D86D87D88D89D8aD8fD90D95D96D97D98D99D9aD9fDa0Da4Da5Da6Da7Da8Da9DaaDabDafDb0Db4Db5Db6Db7Db8Db9DbaDbbDbcDbfDc0Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDcbDccDcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC246D66D7aD9bC247D47D59Db3C468D38D94DcdC579D75DacC68aD56D8bDd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddC79bDc2Dd2C89bD37D6aC9bcD49Da3CabdD84DbdCbcdD9cCbceD28D46D65D7bDdeCcdfD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D22D23D24D25D26D27D29D2aD2bD2cD2dD2eD31D32D33D34D35D36D39D3aD3bD3cD3dD3eD41D42D43D44D45D4aD4bD4cD4dD4eD51D52D53D54D55D5aD5bD5cD5dD5eD61D62D63D64D6bD6cD6dD6eD71D72D73D74D7cD7dD7eD81D82D83D8cD8dD8eD91D92D93D9dD9eDa1Da2DadDaeDb1Db2DbeDc1DceDd1De1De2De3De4De5De6De7De8De9DeaDebDecDedDee"{

offset = offset-1;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=-1 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=-1 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}


macro "RIGHT Action Tool - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D33D34D35D36D37D38D39D3aD3bD3cD3fD40D44D45D46D47D48D49D4aD4bD4cD4fD50D54D55D56D57D58D59D5aD5bD5fD60D65D66D67D68D69D6aD6bD6fD70D75D76D77D78D79D7aD7fD80D86D87D88D89D8aD8fD90D96D97D98D99D9fDa0Da7Da8DafDb0Db7Db8DbfDc0DcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC246D43Da9C247D3dD64Dc8C357D5cC468D85C468D7bDa6C579D32C679D9aC68aD53Db9Dc7C89bD4dD74C9bcD22D23D24D25D26D27D28D29D2aD2bD2cD2dD6cD95Dd8CbcdD8bDb6CbceD2eD3eD42D63DaaDd7CcdfD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D31D41D4eD51D52D5dD5eD61D62D6dD6eD71D72D73D7cD7dD7eD81D82D83D84D8cD8dD8eD91D92D93D94D9bD9cD9dD9eDa1Da2Da3Da4Da5DabDacDadDaeDb1Db2Db3Db4Db5DbaDbbDbcDbdDbeDc1Dc2Dc3Dc4Dc5Dc6Dc9DcaDcbDccDcdDceDd1Dd2Dd3Dd4Dd5Dd6Dd9DdaDdbDdcDddDdeDe1De2De3De4De5De6De7De8De9DeaDebDecDedDee"{

offset = offset+1;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=1 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=1 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}



macro "FORWARDSKey [q]"{ 

topslice = topslice - 1;
bottomslice = bottomslice-1;

if (topslice<0){
topslice=0;
}

if (bottomslice<1){
bottomslice=1;
}

slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}


macro "BACKWARDSKey [a]"{

topslice = topslice + 1;
bottomslice = bottomslice + 1;


if (topslice>noslicesout-1){
topslice=noslicesout-1;
}

if (bottomslice>noslicesout){
bottomslice=noslicesout;
}


slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}


macro "LEFTKey [n]"{

offset = offset-1;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=-1 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=-1 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}


macro "RIGHTKey [m]"{

offset = offset+1;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=1 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=1 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}




macro "LEFTFIVEKey [j]"{

offset = offset-5;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=-5 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=-5 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}


macro "RIGHTFIVEKey [k]"{

offset = offset+5;
selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);
run("Translate...", "x=5 y=0 interpolation=None");
selectImage(stackid);

for (loop=topslice+1; loop<bottomslice+1; loop++) {
setSlice(loop);
run("Translate...", "x=5 y=0 interpolation=None slice");
}
setSlice(topslice+1);
run("Reset...", "reset=[Locked Image]");
}


macro "MOVETOPUPKey [w]"{ 

topslice = topslice - 1;

if (topslice<0){
topslice=0;
}


slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}



macro "MOVETOPDOWNKey [s]"{ 

topslice = topslice + 1;

if (topslice>noslicesout-1){
topslice=noslicesout-1;
}

if (topslice==bottomslice){
topslice=topslice-1;
}

slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}


macro "MOVEBOTTOMUPKey [e]"{

bottomslice = bottomslice - 1;


if (bottomslice==topslice){
bottomslice = bottomslice + 1;
}

if (bottomslice>noslicesout){
bottomslice=noslicesout;
}

slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}


macro "MOVEBOTTOMDOWNKey [d]"{

bottomslice = bottomslice + 1;


if (bottomslice>noslicesout){
bottomslice=noslicesout;
}


slicewidth = bottomslice - topslice;

selectImage(stackid);
setSlice(topslice+1);

selectImage(imageid);
makeRectangle(0, topslice*pixelsperslice, imagewidth, slicewidth*pixelsperslice);

}








macro "UP Action Tool - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D3cD3fD40D4aD4bD4cD4fD50D58D59D5aD5bD5cD5fD60D67D68D69D6aD6bD6cD6fD70D75D76D77D78D79D7aD7bD7cD7fD80D84D85D86D87D88D89D8aD8bD8cD8fD90D96D97D98D99D9aD9bD9cD9fDa0Da8Da9DaaDabDacDafDb0DbaDbbDbcDbfDc0DcbDccDcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC246D66Da7Db9C247D3bD74D95C468D49D83DdcC579D57DcaC68aD3dD4dD5dD65D6dD7dD8dD9dDadDb8DbdDcdDddC79bD2cD2dC89bD73Da6C9bcD3aD94CabdD48DdbCbcdDc9CbceD56D64D82Db7DedCcdfD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D22D23D24D25D26D27D28D29D2aD2bD2eD31D32D33D34D35D36D37D38D39D3eD41D42D43D44D45D46D47D4eD51D52D53D54D55D5eD61D62D63D6eD71D72D7eD81D8eD91D92D93D9eDa1Da2Da3Da4Da5DaeDb1Db2Db3Db4Db5Db6DbeDc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8DceDd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdeDe1De2De3De4De5De6De7De8De9DeaDebDecDee"{

selectImage(stackid);
run("Translate...", "x=0 y=-1 interpolation=None slice");

}



macro "DOWN Action Tool - Cff0Cf0fCf00C0ffC0f0C00fC000C135D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D1fD20D2fD30D33D3fD40D43D44D45D4fD50D53D54D55D56D57D5fD60D63D64D65D66D67D68D69D6fD70D73D74D75D76D77D78D79D7aD7bD7fD80D83D84D85D86D87D88D89D8aD8bD8fD90D93D94D95D96D97D98D99D9fDa0Da3Da4Da5Da6Da7Da8DafDb0Db3Db4Db5Db6DbfDc0Dc3Dc4DcfDd0DdfDe0DefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDffC246D34D9aC247D46D8cDd3C357D58C468D6aDc5C468Db7C579D23C679D7cC68aD35Da9C79bD9bC89bD47Dd4C9bcD22D32D42D52D59D62D72D82D92Da2Db2Dc2Dc6Dd2CabdD8dCbcdD6bDb8CbceD24D36D7dDaaDe2De3CcdfD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD21D25D26D27D28D29D2aD2bD2cD2dD2eD31D37D38D39D3aD3bD3cD3dD3eD41D48D49D4aD4bD4cD4dD4eD51D5aD5bD5cD5dD5eD61D6cD6dD6eD71D7eD81D8eD91D9cD9dD9eDa1DabDacDadDaeDb1Db9DbaDbbDbcDbdDbeDc1Dc7Dc8Dc9DcaDcbDccDcdDceDd1Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDe1De4De5De6De7De8De9DeaDebDecDedDee"{

selectImage(stackid);
run("Translate...", "x=0 y=1 interpolation=None slice");

}





macro "ONH Action Tool - 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"{


thisslice=topslice+1;

selectImage(stackid);

scrheight = screenHeight();
scrwidth = screenWidth();

xindex=0;
k=1;
option=0;

stackwidth = getWidth();
stackheight = getHeight();
noslices = nSlices();
imagewidthmm=10;
pixheightmm=2.4;

//picname = "CHANGE NAME";


noascans = stackwidth;

//CREAT DIALOG BOX

Dialog.create("PLEASE SET INPUT SETTINGS FOR B SCAN FLATTENING");
Dialog.addMessage("FILE SETTINGS");
Dialog.addMessage("Stack width is "+stackwidth+" pixels");
Dialog.addMessage("Stack height is "+stackheight+" pixels");
Dialog.addMessage("No of slices is "+noslices);
Dialog.addString("Image filename ",picname, 50);
Dialog.addString("Save results to folder ",onhfolder, 50);
Dialog.addMessage("");
Dialog.addMessage("PROTOCOL SETTINGS");
Dialog.addNumber("IMAGE WIDTH (mm)", imagewidthmm);
Dialog.addNumber("NO OF A SCANS",noascans);
Dialog.addNumber("PIXEL HEIGHT (mm)",pixheightmm);
Dialog.addNumber("Rectangle Width", 40);
Dialog.addNumber("Step Size", 20);
Dialog.addNumber("Threshold", 25);
Dialog.addNumber("Line Width", 6);
Dialog.addNumber("Line Height", 60);
Dialog.addMessage("");
Dialog.addCheckbox("Use Anisometropic Filter?", true);
Dialog.addCheckbox("Use ABSnake for ILM Detection?", true);
Dialog.addCheckbox("Flatten using spline (uncheck for linear)?",false);
Dialog.show();

//GET VALUES OUT OF DIALOG BOX

pname = Dialog.getString();
onhfolder = Dialog.getString();
imagewidthmm = Dialog.getNumber();
noascans = Dialog.getNumber();
pixheightmm = Dialog.getNumber();
recwidth = Dialog.getNumber();
step = Dialog.getNumber();
threshold = Dialog.getNumber();
linewidth = Dialog.getNumber();
lineheight = Dialog.getNumber();
anisofilter = Dialog.getCheckbox();
absnakeplugin = Dialog.getCheckbox();
splineflatten = Dialog.getCheckbox();


//MAIN LOOP STARTS HERE

//GET AXIAL LENGTH ROUTINE

years = 0.0;
months = 0.0;
weeks = 0.0;
prem=false;
addgp=0;
almethod="MEASURED";
axiallength=0;
change=0;

do{

if (years==NaN)
years=0;

if (months==NaN)
months=0;

if (weeks==NaN)
weeks=0;

prevgestage=(years*52.17857143)+(months*4.348214286)+weeks+(addgp*39.14);

ageans=false;
Dialog.create("GET AXIAL LENGTH");
Dialog.addMessage("PLEASE INPUT GESTATIONAL AGE");
Dialog.addNumber("Years", years);
Dialog.addNumber("Months", months);
Dialog.addNumber("Weeks", weeks);
Dialog.addCheckbox("Premature infant", prem);
Dialog.addCheckbox("For normals add 39 weeks?", addgp);
Dialog.addMessage("");
Dialog.addMessage("");
Dialog.addMessage("ALTERNATIVELY INPUT AXIAL LENGTH");
Dialog.addNumber("AXIAL LENGTH - "+almethod, axiallength);
Dialog.show();

years = Dialog.getNumber();
months = Dialog.getNumber();
weeks = Dialog.getNumber();
prem = Dialog.getCheckbox();
addgp = Dialog.getCheckbox();
axiallength = Dialog.getNumber();


gestage=(years*52.17857143)+(months*4.348214286)+weeks+(addgp*39.14);

if(gestage>0){
axiallength=getcorrectionfactor(gestage, prem);
almethod="ESTIMATED";
}
else
{
almethod="MEASURED";
}

if(axiallength<=0)
ageans=getBoolean("AGE IS OUT OF RANGE. INPUT AGE AGAIN? (PRESS 'NO' TO CONTINUE)?");

}while ((ageans==true)||(prevgestage!=gestage));

if(axiallength<=0){
axiallength=23.98;
almethod="DEFAULT";
}


///////////////////////////////////////////////////////////////////////////




anssaveimage = 3;

do{

do{

if (option==0){

selectImage(stackid);

run("Duplicate...", "title=[SINGLESLICE] duplicate range="+thisslice+"-"+thisslice);


picid = getImageID();


setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));


tempnas=getBoolean("IS THE IMAGE FROM THE LEFT EYE ('NO' FOR RIGHT)?");

if (tempnas==0){
picname=pname+"_R";
}
else
{
picname=pname+"_L";
}


flipans=getBoolean("IS NASAL ON THE LEFT ('NO' WILL FLIP THE IMAGE)?");

if(flipans==0){
run("Select All");
run("Flip Horizontally");
}


if (anssaveimage==3){

anssaveimage = getBoolean("WOULD YOU LIKE TO SAVE A COPY OF THE IMAGE?");
if (anssaveimage==1){
saveAs("tiff", onhfolder+pname+".tif");
}

}


// SET ANALYSIS AREA AND ADD BORDER

run("Point Tool...", "mark=0 label selection=yellow");

makeRectangle(100, 100, 300, 500);

waitForUser("SET RECTANGLE FOR ANALYSIS AREA");

run("Crop");

stackwidth = getWidth();
stackheight = getHeight();
noslices = nSlices();

run("Canvas Size...", "width="+(stackwidth+100)+" height="+(stackheight+100)+" position=Center");

stackwidth = stackwidth+100;
stackheight = stackheight+100;

norecs = round(stackwidth/step);

}


if (option<2){						//ADJUST BRIGHTNESS CONTRAST

selectImage(picid);
setLocation(0, 0, (scrwidth*0.4), (scrheight*0.95));
run("Brightness/Contrast...");
waitForUser("ADJUST BRIGHTNESS  / CONTRAST");
run("Close");

}



if(option<3){						//ANISOTROPIC FILTER

//anisofilter = getBoolean("DO YOU WANT TO APPLY THE ANISOTROPIC FILTER?");


if (anisofilter==true){


selectImage(picid);

setLocation(0, 0, (scrwidth*0.4), (scrheight*0.95));

makeRectangle(0, 0, stackwidth, stackheight);

run("Anisotropic Diffusion 2D","");

anpicid = getImageID();

selectImage(picid);
setLocation((scrwidth*0.8), (scrheight*0.8) ,(scrwidth*0.2), (scrheight*0.2));

selectImage(anpicid);
setLocation(0, 0, (scrwidth*0.4), (scrheight*0.95));

}



rnd=round(random()*10);
optionstringsfirst[3]="Image looks "+superlative[rnd]+"!";

Dialog.create("MAKE SELECTION AND PRESS OK");
Dialog.addChoice("Please choose place to return to: ", optionstringsfirst, optionstringsfirst[3])
Dialog.show();

menuchoice = Dialog.getChoice();

for (v=0; v<4; v++)
{
if (menuchoice == optionstringsfirst[v])
option=v;
}


if (option==0)
{
selectImage(picid);
run("Close"); 
}


if (option<3)
{
selectImage(anpicid);
run("Close"); 
}


}


}while (option<3);


if (option==3){
option=5; 
}




if (option<4 || option==5){

//FLATTEN DISC

selectImage(anpicid);

if (splineflatten==1)
{

layerimagelocation=layerimagesdir+"rpe_choroid.tif";

meanrpe=polylinetoarray(50, stackwidth-50, stackwidth, "LOWER RPE BORDER",1, layerimagelocation, anpicid, rpe);			//FLATTEN USING RPE


for (s=50; s<stackwidth-50; s++)
{
pixoffset=(rpe[s]-meanrpe)*-1;
makeRectangle(s, 0, 1, stackheight);
run("Translate...", "x=0 y="+round(pixoffset)+" interpolation=None");

}


setTool("point");
setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));
makePoint(stackwidth/2, stackheight/2);
waitForUser("SET POINT TO LEFT (NASAL) EDGE OF RPE");
getSelectionCoordinates(leftx, lefty);
wait(200);

Dialog.create("SELECT APPEARANCE OF LEFT (NASAL) RPE");
Dialog.addChoice("Appearance", edgerpe, edgerpe[0]);
Dialog.addChoice("Deflection", rpedeflection, rpedeflection[0]);
Dialog.show();

lrpeedge = Dialog.getChoice();
lrpedeflection = Dialog.getChoice();

selectImage(anpicid);
setTool("point");
makePoint(stackwidth/2, stackheight/2);
waitForUser("SET POINT TO RIGHT (TEMPORAL) EDGE OF RPE");
getSelectionCoordinates(rightx, righty);

wait(200);

Dialog.create("SELECT APPEARANCE OF RIGHT (TEMPORAL) RPE");
Dialog.addChoice("Appearance", edgerpe, edgerpe[0]);
Dialog.addChoice("Deflection", rpedeflection, rpedeflection[0]);
Dialog.show();

rrpeedge = Dialog.getChoice();
rrpedeflection = Dialog.getChoice();

disccentre=(leftx[0]+rightx[0])/2;
discwidth=rightx[0]-leftx[0];

disclx=round(leftx[0]);
discly=lefty[0];

discrx=round(rightx[0]);
discry=righty[0];

discwidth=discrx-disclx;
discref=(discly+discry)/2;

}
else
{


setTool("point");
setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));
makePoint(stackwidth/2, stackheight/2);

waitForUser("SET POINT TO LEFT (NASAL) EDGE OF RPE");
getSelectionCoordinates(leftx, lefty);

wait(200);

selectImage(anpicid);
setTool("point");
makePoint(stackwidth/2, stackheight/2);

waitForUser("SET POINT TO RIGHT (TEMPORAL) EDGE OF RPE");
getSelectionCoordinates(rightx, righty);

wait(200);


pixshift=(lefty[0]-righty[0])/(leftx[0]-rightx[0])*-1;

disccentre=(leftx[0]+rightx[0])/2;
discwidth=rightx[0]-leftx[0];

disclx=round(leftx[0]);
discly=lefty[0];

discrx=round(rightx[0]);
discry=righty[0];

meanrpe=(discly+discry)/2;
discref=meanrpe;

setLocation(0, 0, (scrwidth*0.5), (scrheight*0.95));

pixoffset=disccentre*pixshift*-1;

for (s=0; s<stackwidth; s++)
{

makeRectangle(s, 0, 1, stackheight);
run("Translate...", "x=0 y="+round((s*pixshift)+pixoffset)+" interpolation=None");

}


Dialog.create("SELECT APPEARANCE OF LEFT (NASAL) RPE");
Dialog.addChoice("Appearance", edgerpe, edgerpe[0]);
Dialog.addChoice("Deflection", rpedeflection, rpedeflection[0]);
Dialog.show();

lrpeedge = Dialog.getChoice();
lrpedeflection = Dialog.getChoice();

wait(200);


Dialog.create("SELECT APPEARANCE OF RIGHT (TEMPORAL) RPE");
Dialog.addChoice("Appearance", edgerpe, edgerpe[0]);
Dialog.addChoice("Deflection", rpedeflection, rpedeflection[0]);
Dialog.show();

rrpeedge = Dialog.getChoice();
rrpedeflection = Dialog.getChoice();

wait(200);


}


//SET POINT AT CUP / FOVEA BOTTOM

selectImage(anpicid);
setTool("point");
makePoint(disccentre, meanrpe);

waitForUser("SET POINT TO BOTTOM OF CUP");
getSelectionCoordinates(cupx, cupy);
wait(200);

Dialog.create("SET POINT AT BOTTOM OF CUP AND SELECT APPEARANCE OF VESSELS");
Dialog.addMessage("LEFT (NASAL) ASPECT OF CUP");
Dialog.addChoice("Appearance", typevessel, typevessel[0]);
Dialog.addChoice("Location",  locationvessel,  locationvessel[0]);
Dialog.addCheckbox("Vessel cropped", false);
Dialog.addMessage("");

Dialog.addMessage("RIGHT (TEMPORAL) ASPECT OF CUP");
Dialog.addChoice("Appearance", typevessel, typevessel[0]);
Dialog.addChoice("Location",  locationvessel,  locationvessel[0]);
Dialog.addCheckbox("Vessel cropped", false);
Dialog.addMessage("");

Dialog.addMessage("FURTHER DESCRIPTION");
Dialog.addString("Enter any more details ","", 50);
Dialog.show();


ncupvessel = Dialog.getChoice();
ncuplocation = Dialog.getChoice();
ncupcutoff = Dialog.getCheckbox();

tcupvessel = Dialog.getChoice();
tcuplocation = Dialog.getChoice();
tcupcutoff = Dialog.getCheckbox();

cupdescription = Dialog.getString();

getSelectionCoordinates(cupx, cupy);

run("16-bit");



//FIND ILM

ilmfitx = newArray(norecs+1);
ilmfity = newArray(norecs+1);

ilmfitx[0] = 0;
ilmfity[0] = 0;

xindex=0;
k=0;


}



//if (curveok==0){
//absnakeplugin = getBoolean("DO YOU WANT TO USE ABSnake TO GET THE CONTOUR?");
//}


if (absnakeplugin==1){

run("Duplicate...", "title=[ImageCopy.jpg]");

piccopyid = getImageID();

run("Canvas Size...", "width="+(stackwidth+100)+" height="+(stackheight+50)+" position=Top-Center");

setLocation(0, 0, (scrwidth*0.5), scrheight);

//setTool("freehand");

//INSTEAD OF FREEHAND USE FREELINE AND WILL ADD REST TO BOTTOM

setTool("freeline");

waitForUser("SET A LINE NEAR THE SURFACE");

getSelectionCoordinates(freelinex, freeliney);

cornerx=newArray(4);
cornery=newArray(4);

cornerx[0]=stackwidth+100;
cornery[0]=freeliney[freeliney.length-1];

cornerx[1]=stackwidth+100;
cornery[1]=stackheight+50;

cornerx[2]=0;
cornery[2]=stackheight+50;

cornerx[3]=0;
cornery[3]=freeliney[0];

freelinex=Array.concat(freelinex,cornerx);
freeliney=Array.concat(freeliney,cornery);

makeSelection("freehand", freelinex, freeliney);

run("ABSnake","");
absnakeid = getImageID();

for (a=0; a<norecs; a++)
{

//profile2 = newArray(stackheight);

xindex=a*step+50;
i=0;
findred=0;

//makeLine(xindex, 0, xindex, stackheight);


while (findred==0 && i<stackheight){

v = getPixel(xindex,i);

red = (v>>16)&0xff;  // extract red byte (bits 23-17)
green = (v>>8)&0xff; // extract green byte (bits 15-8)
blue = v&0xff;       // extract blue byte (bits 7-0)

if (red>250 && green<5 && blue<5){
findred=1;
}

i=i+1;

}




//setKeyDown("alt");
//  profile = getProfile();
//i=0;
//threshold=240;

//Array.getStatistics(profile, min, max, mean, stdDev);

//while (profile[i]<threshold){
//i=i+1;
//}


ilmfitx[a] = (a*step);
ilmfity[a] = i;

}


ilmfitx = Array.trim(ilmfitx, a);
ilmfity = Array.trim(ilmfity, a);

selectImage(absnakeid);
run("Close"); 
selectImage(piccopyid);
run("Close"); 
roiManager("delete");
selectWindow("ROI Manager");
run("Close"); 
selectWindow("Log");
run("Close"); 


}


else


{


for (a=0; a<norecs; a++)
{

profile2 = newArray(stackheight);

xindex=a*step;

makeRectangle(xindex, 0, recwidth, stackheight);

//setSelectionLocation(xindex, 0);

//waitForUser("MAKE RECTANGLE");


setKeyDown("alt");
  profile = getProfile();
j=0; 

Array.getStatistics(profile, min, max, mean, stdDev);

for (i=0; i<profile.length; i++)
{	
if (profile[i]>threshold)
{
profile2[j] = i;
j=j+1;
}

}

profile2 = Array.trim(profile2, j-1);

Array.getStatistics(profile2, min, max, mean, stdDev);

ilmfitx[k] = xindex+(recwidth/2);
ilmfity[k] = min;

if (ilmfity[k]<((lineheight/2)+1))
ilmfity[k]=stackheight/2;

if (ilmfity[k]>stackheight-((lineheight/2)+1))
ilmfity[k]=stackheight/2;


///CORRECT ILMFIT TO SHARPEST CONTRAST

makeLine(ilmfitx[k], ilmfity[k]-(lineheight/2), ilmfitx[k], ilmfity[k]+(lineheight/2), linewidth);

//waitForUser("MAKE LINE");

lineprofile = getProfile();

maxdiff=0;
diff=0;
maxdiffindex=0;

for (l=0; l<(lineheight-2); l++)
{	
diff=abs(lineprofile[l]-lineprofile[l+1]);

if (diff>maxdiff)
{
maxdiff=diff;
maxdiffindex=l;
}

}

ilmfity[k]=ilmfity[k]-(lineheight/2)+maxdiffindex;


///////


k=k+1;

}


ilmfitx = Array.trim(ilmfitx, k);
ilmfity = Array.trim(ilmfity, k);

ilmfitx[k-1]=stackwidth;
ilmfity[k-1]=(2*ilmfity[k-2])-ilmfity[k-3];

ilmfity[0]=(2*ilmfity[1])-ilmfity[2];



}


//END OF LOOPS

selectImage(anpicid);

makeSelection("polyline", ilmfitx, ilmfity);

layerimagelocation=layerimagesdir+"ilm.tif";
polylinetoarray(50, stackwidth-50, stackwidth, "INTERNAL LIMITING MEMBRANE",0, layerimagelocation, anpicid, ilm);


rnd=round(random()*10);
optionstrings[5] ="Results look "+superlative[rnd]+"!";

Dialog.create("MAKE SELECTION AND PRESS OK");
Dialog.addChoice("Please choose place to return to: ", optionstrings, optionstrings[5])
Dialog.show();

menuchoice = Dialog.getChoice();

for (v=0; v<6; v++)
{
if (menuchoice == optionstrings[v])
option=v;
}


if (option==0)
{
selectImage(picid);
run("Close"); 
}


if (option<3)
{
selectImage(anpicid);
run("Close"); 
}

}while (option<5);


getSelectionCoordinates(ilmx, ilmy);



//EXTRA LAYERS GO HERE


analysernflrt=getBoolean("DO YOU WANT ANALYSE RNFL ANDBRUCH'S ON BOTH SIDES?");

if (analysernflrt==true){
addrnfl=true;
addbruchs=true;
}


//RNFL

Array.fill(rnfl, -7777);

if (analysernflrt==false)
addrnfl=getBoolean("DO YOU WANT ADD LEFT RNFL TO THE TEXT FILE?");

if(addrnfl ==true)
{
layerimagelocation=layerimagesdir+"rnfl_nasal.tif";
polylinetoarray(50, disclx, stackwidth, "LEFT RNFL",1, layerimagelocation, anpicid, rnfl);
}

if (analysernflrt==false)
addrnfl=getBoolean("DO YOU WANT ADD RIGHT RNFL TO THE TEXT FILE?");

if(addrnfl ==true)
{
layerimagelocation=layerimagesdir+"rnfl_temp.tif";
polylinetoarray(discrx, stackwidth-50, stackwidth, "RIGHT RNFL",1, layerimagelocation, anpicid, rnfl);
}


//BRUCH'S

Array.fill(bruchs, meanrpe);

if(splineflatten ==false)
{

Array.fill(bruchs, -7777);

if (analysernflrt==false)
addbruchs=getBoolean("DO YOU WANT ADD LEFT BRUCH'S TO THE TEXT FILE?");

if (addbruchs==true){
layerimagelocation=layerimagesdir+"bruchs_nasal.tif";
polylinetoarray(50, disclx, stackwidth, "NASAL BRUCH'S",1, layerimagelocation, anpicid, bruchs);
}

if (analysernflrt==false)
addbruchs=getBoolean("DO YOU WANT ADD RIGHT BRUCH'S TO THE TEXT FILE?");

if (addbruchs==true){
layerimagelocation=layerimagesdir+"bruchs_temp.tif";
polylinetoarray(discrx, stackwidth-50, stackwidth, "TEMPORAL BRUCH'S",1, layerimagelocation, anpicid, bruchs);
}

}

//PRINT OUTPUT

//OPEN FILE AND HEADER INFORMATION

f = File.open(onhfolder+picname+".txt");

print(f,  "PATIENT PARAMETERS\n");
print(f,  picname+"\n");
print(f,  "gestational age (weeks)\t" + d2s(gestage,2) + "\n");
print(f,  "axial length (mm)\t" + d2s(axiallength,2) +"\t" + almethod+"\n");
print(f,  "correction factor\t" + d2s(axiallength/23.98,2) + "\n");

print(f,  "SCAN PARAMETERS\n");
print(f,  "no Ascans\t" + d2s(noascans,0) + "\n");
print(f,  "image width\t" + d2s(imagewidthmm,4) + "\n");
print(f,  "analysed image width\t" + d2s(stackwidth-100,0) + "\n");
print(f,  "pixel height\t" + d2s(pixheightmm,4) + "\n");

pixwidthmm=(axiallength/23.98)*((imagewidthmm*1000)/noascans);
print(f,  "pixel width\t" + d2s(pixwidthmm,4) + "\n");

print(f,  "DISC PARAMETERS\n");
print(f,  "disc width\t" + d2s((discwidth),2) + "\n");
print(f,  "y disc offset\t" + d2s((meanrpe-discref),2) + "\n");
print(f,  "nasal disc edge\t" + lrpeedge + "\n");
print(f,  "nasal disc deflection\t" + lrpedeflection + "\n");
print(f,  "temporal disc edge\t" + rrpeedge + "\n");
print(f,  "temporal disc deflection\t" + rrpedeflection + "\n");

print(f,  "CUP PARAMETERS\n");
print(f,  "cup depth\t" + d2s((cupy[0]-discref),0) + "\n");

print(f,  "nasal vessel type\t" + ncupvessel + "\n");
print(f,  "nasal vessel location\t" + ncuplocation + "\n");
print(f,  "nasal vessel cutoff\t" + d2s(ncupcutoff,0) + "\n");

print(f,  "temporal vessel type\t" + tcupvessel + "\n");
print(f,  "temporal vessel location\t" + tcuplocation + "\n");
print(f,  "temporal vessel cutoff\t" + d2s(tcupcutoff,0) + "\n");

print(f,  "cup description\t" + cupdescription + "\n");

print(f,  "LAYERS\n");
print(f,  "x_pixel\tdisc centre\tindex\tcup bottom\tILM\tRNFL\tBruch's\n");


//LOOP THROUGH PIXELS FROM LEFT TO RIGHT INTERPOLATING BETWEEN POINTS IN ARRAY

phase=1;
tnsym=1;
tncup=1;
xval=(disccentre-50)*-1;


for (p=50; p<(stackwidth-50); p++)			// I.E. WHOLE SELECTION
{

phase=1;

if (p>disclx)					// SORT OUT 4 PHASES
phase=2;

if (p>=cupx[0])
phase=3;

if (p>=discrx)
phase=4;


if (rnfl[p]>0)					//SUBTRACT FROM MEAN RPE
rnfl[p]=meanrpe-rnfl[p];

ilm[p]=meanrpe-ilm[p];

if (bruchs[p]>0)					//SUBTRACT FROM MEAN RPE
bruchs[p]=meanrpe-bruchs[p];


if (p>disccentre)					//SORT OUT DISC AND CUP CENTRE
tnsym=2;

if (p>cupx[0])
tncup=2;


print(f, d2s(xval,2) + "\t"+ d2s(tnsym,0) + "\t" + d2s(phase,0) + "\t" +d2s(tncup,0) + "\t"+ d2s(ilm[p],2) + "\t" + d2s(rnfl[p],2) + "\t" + d2s(bruchs[p],2) + "\n");

xval=xval+1;

}

File.close(f); 

finalquestion = getBoolean("GO TO "+onhfolder+" FOR RESULTS. DO YOU WANT TO USE THE SAME STACK AGAIN?");

anssaveimage = 3;

selectImage(anpicid);
run("Close"); 

if (finalquestion==0)
{

if (imagechoice==0){
selectImage(imageid);
run("Close"); 
}

selectImage(stackid);
run("Close"); 
}

selectImage(picid);
run("Close"); 
}


}



function polylinetoarray(xmin, xmax, width, layername, lineoption, linesimage, analysisimageid, testarray){

polyx=newArray(0);
polyy=newArray(0);
splinex=newArray(0);
spliney=newArray(0);

//LINEOPTION: 0:LINE PRESENT - CHECKED FOR WIDTH, 1: ADD LINE - CHECKED FOR WIDTH, 2: ADD LINE - CHECKED ON LEFT, 3: ADDLINE - CHECKED ON RIGHT, 4: ADD LINE NO CHECKING

if (lineoption<=1)
addanalysistype="ALONG THE WHOLE PROFILE";

if (lineoption==2)
addanalysistype="ALONG THE NASAL SEGMENT";

if (lineoption==3)
addanalysistype="ALONG THE TEMPORAL SEGMENT";


open(linesimage);
linesimageid = getImageID();

setLocation((scrwidth*0.5), (scrheight*0.3), (scrwidth*0.4), (scrheight*0.5));


selectImage(analysisimageid);


if (lineoption==0){			//JUST SORT OUT SPLINE AS LINE IS PRESENT

polyx = Array.trim(polyx, 1);
polyy = Array.trim(polyy, 1);
getSelectionCoordinates(polyx, polyy);

do{
nopoints=0;
run("Select None");
makeSelection("polyline", polyx, polyy);
run("Fit Spline");

waitForUser("MAKE FINE ADJUSTMENTS TO SPLINE FOR LAYER '"+layername+"'");
wait(200);
if(selectionType()!=-1){
getSelectionCoordinates(splinex, spliney);
nopoints=splinex.length;
}
} while ((selectionType()==-1)||(nopoints<20));					//I.E. IF NO SELECTION OR POLYLINE RATHER THAN SPLINE
	

}



//ADD A LINE SINCE NOT ONE PRESENT 

if (lineoption>=1){

do{
run("Select None");

rightButton=4;
ctrl=2;
setTool("polyline");
getCursorLoc(x, y, z, flags);
	while ((flags&rightButton==0)&&(flags&ctrl==0)) {
                getCursorLoc(x, y, z, flags);        
                }

} while (selectionType()==-1);

polyx = Array.trim(polyx, 1);
polyy = Array.trim(polyy, 1);
getSelectionCoordinates(polyx, polyy);

do{
nopoints=0;
run("Select None");
makeSelection("polyline", polyx, polyy);
run("Fit Spline");

waitForUser("MAKE FINE ADJUSTMENTS TO SPLINE FOR LAYER '"+layername+"'");
wait(200);
if(selectionType()!=-1){
getSelectionCoordinates(splinex, spliney);
nopoints=splinex.length;
}
} while ((selectionType()==-1)||(nopoints<20));					//I.E. IF NO SELECTION OR POLYLINE RATHER THAN SPLINE

}


splinex = Array.trim(splinex, 1);
spliney = Array.trim(spliney, 1);
selectImage(analysisimageid);
getSelectionCoordinates(splinex, spliney);


if (splinex[0]>splinex[1]){							//REVERSE IF WRONG WAY AROUND
Array.reverse(splinex);
Array.reverse(spliney);
}


//LINEOPTION: 0:LINE PRESENT - CHECKED FOR WIDTH, 1: ADD LINE - CHECKED FOR WIDTH, 2: ADD LINE - CHECKED ON LEFT, 3: ADDLINE - CHECKED ON RIGHT, 4: ADD LINE NO CHECKING

if (lineoption<=1){

while ((splinex[0]>=xmin)||(splinex[splinex.length-1]<=xmax)){			//MAKE LINE LONGER IF NOT LONG ENOUGH
	do{
	nopoints=0;
	run("Select None");
	makeSelection("polyline", polyx, polyy);
	run("Fit Spline");
	waitForUser("YOU NEED TO MAKE THE LINE LONGER!!");
	wait(200);
	if(selectionType()!=-1){
	getSelectionCoordinates(splinex, spliney);
	nopoints=splinex.length;
	}
	} while ((selectionType()==-1)||(nopoints<20));					//I.E. IF NO SELECTION OR POLYLINE RATHER THAN SPLINE


	splinex = Array.trim(splinex, 1);
	spliney = Array.trim(spliney, 1);
	getSelectionCoordinates(splinex, spliney);

		if (splinex[0]>splinex[1]){							//REVERSE IF WRONG WAY AROUND
		Array.reverse(splinex);
		Array.reverse(spliney);
		}
}

}

if (lineoption==2){

while (splinex[0]>=xmin){			//MAKE LINE LONGER IF NOT LONG ENOUGH
	do{	
	nopoints=0;
	run("Select None");
	makeSelection("polyline", polyx, polyy);
	run("Fit Spline");
	waitForUser("YOU NEED TO MAKE THE LINE LONGER ON THE LEFT!!");
	wait(200);
	if(selectionType()!=-1){
	getSelectionCoordinates(splinex, spliney);
	nopoints=splinex.length;
	}
	} while ((selectionType()==-1)||(nopoints<20));					//I.E. IF NO SELECTION OR POLYLINE RATHER THAN SPLINE


	splinex = Array.trim(splinex, 1);
	spliney = Array.trim(spliney, 1);
	getSelectionCoordinates(splinex, spliney);



		if (splinex[0]>splinex[1]){							//REVERSE IF WRONG WAY AROUND
		Array.reverse(splinex);
		Array.reverse(spliney);
		}

}
									
xmax=splinex[splinex.length-1];								//MAKE MAX = SPLINE END
testarray[xmax]=spliney[spliney.length-1];

}



if (lineoption==3){

while (splinex[splinex.length-1]<=xmax){									//MAKE LINE LONGER IF NOT LONG ENOUGH
	do{	
	nopoints=0;
	run("Select None");
	makeSelection("polyline", polyx, polyy);
	run("Fit Spline");
	waitForUser("YOU NEED TO MAKE THE LINE LONGER ON THE RIGHT!!");
	wait(200);
	if(selectionType()!=-1){
	getSelectionCoordinates(splinex, spliney);
	nopoints=splinex.length;
	}
	} while ((selectionType()==-1)||(nopoints<20));					//I.E. IF NO SELECTION OR POLYLINE RATHER THAN SPLINE

	splinex = Array.trim(splinex, 1);
	spliney = Array.trim(spliney, 1);
	getSelectionCoordinates(splinex, spliney);

		if (splinex[0]>splinex[1]){							//REVERSE IF WRONG WAY AROUND
		Array.reverse(splinex);
		Array.reverse(spliney);
		}

}
									
xmin=splinex[0];										//MAKE MAX = SPLINE END
testarray[0]=spliney[0];									//SORT OUT FIRST AND LAST POINTS
}



if (lineoption==4){
xmin=splinex[0];										//MAKE MIN AND MAX = SPLINE ENDS
xmax=splinex[splinex.length-1];

testarray[0]=spliney[0];									//SORT OUT FIRST AND LAST POINTS
testarray[xmax]=spliney[spliney.length-1];
}



selectImage(linesimageid);
close();
selectImage(analysisimageid);



novals=0;
sumvals=0;

//LOOP THROUGH PIXELS FROM LEFT TO RIGHT INTERPOLATING BETWEEN POINTS IN ARRAY

for (s=xmin; s<=xmax; s++){

	for (q=0; q<(splinex.length-1);q++){

		if ((s>=splinex[q])&(s<splinex[q+1])){

			frac=(s-splinex[q])/(splinex[q+1]-splinex[q]); 
			testarray[s]=(frac*(spliney[q+1]-spliney[q]))+spliney[q];
			novals=novals+1;
			sumvals=sumvals+testarray[s];
		}
	}
}

if (novals>0){
return (sumvals/novals);
}

}






function getcorrectionfactor(age, prem){

premsweeks = newArray(27.99, 32.01, 36.01, 40.01, 44.01, 52.01, 56.01);
normsweeks = newArray(31.99, 39.14, 66.08, 114.99, 167.45, 222.03, 270.95, 325.53, 380.11, 457.38, 692.02, 951.47, 1500.14, 3169.86, 3691.64, 4213.43, 5257.00);

premsaxial = newArray(14.86, 15.44, 16.09, 16.84, 17.43, 18.58, 19.27);
normsaxial = newArray(16.61, 16.80, 17.40, 18.60, 18.87, 19.20, 20.07, 21.27, 21.75, 22.14, 22.26, 22.66, 23.98, 23.60, 23.44, 23.39, 23.20);

axiallength=-1;

if (prem==1){

	for (q=0; q<(premsweeks.length-1);q++){

		if ((age>=premsweeks[q])&(age<premsweeks[q+1])){

			frac=(age-premsweeks[q])/(premsweeks[q+1]-premsweeks[q]); 
			axiallength=(frac*(premsaxial[q+1]-premsaxial[q]))+premsaxial[q];
		}
	}

}
else
{

	for (q=0; q<(normsweeks.length-1);q++){

		if ((age>=normsweeks[q])&(age<normsweeks[q+1])){

			frac=(age-normsweeks[q])/(normsweeks[q+1]-normsweeks[q]); 
			axiallength=(frac*(normsaxial[q+1]-normsaxial[q]))+normsaxial[q];
		}
	}

}

return axiallength;

}