///////////////////////////////////////////////////////////////////////
// Dot Blot Analyzer
//
// avaible in the IJ macros toolsets repertory at
// http://rsb.info.nih.gov/ij/macros/toolsets/Dot Blot Analyzer.txt
///////////////////////////////////////////////////////////////////////
// Author: Gilles Carpentier, Faculte des Sciences et
// Technologies, Universite Paris 12 Val de Marne, France
// More information is available at
// http://image.bio.methods.free.fr/dotblot.html
// First version 4/09/2008
// Requires the ImageJ 1.40a
// graphic interface variable
var defaultradius=25,subTitleofImage="no",radius="",theVolume="",rmBack ="Linear";
var blotscale=1;
var blotName="",blotinitName="",Linter=600,Hinter=120,xSizeBlot=0,ySizeBlot=0;
var resultFolderName="Result Documents";
var Topmarge=10,Botommarge=10,Leftmarge=10,Rightmarge=10;
var paletteName="Dot Blot Analyzer Palette",winName2= "Analysed Dot Blot",folderpath="",endPalette="",nomSavedPalette="",gridModelName="";
var workingI="working blot",workingID,tempclip;
var largeline=1,Lpalette=0,Hpalette=0,largbuton=60, hautbuton=25,distBord=15,disthaut=5;
var Hdisplay=40,xDisplay,yDisplay,larDisplay,livedisplay=1;
var palette=0,reponse=0,cancel=0,analyseIt=0;
var dyn=0,cursorok=0,KindofArea="";
var blotx1,blotx2,bloty1,bloty2;
var interx1,interx2,intery1,intery2;
var cancelx1,cancelx2,cancely1,cancely2;
var colboxOriY,kindofColoBox="",SelectedColor="";
var analysex1,analysex2,analysey1,analysey2;
var enhX1, enhY1, enhX2, enhY2, enhenceChoice=0,sat=0,incresat=0.2;
var lutX1,lutX2,lutY1,lutY2,lutChoice=0,lutDisplay="LUT: Grey";
var resX1,resX2,resY1,resY2;
var sizex1,sizex2,sizey1,sizey2;
var box1x,box1y;
var box2x,box2y;
var box3x,box3y;
var box4x,box4y;
// cursor variables and settings
var addMx1,addMy1,addMx2,addMy2;
var rmMx1,rmMy1,rmMx2,rmMy2;
var erMx1,erMy1,erMx2,erMy2;
var mesurx1,mesury1,mesurx2,mesury2;
var x, y, w=-1, h=-1, xx, yy, px = newArray(6), py = newArray(6);
var selectionRayon=17,increment=1,xmes,ymes;
var selectionColor="magenta",initselectionColor="",initiate=0;
var r, g, b;
var ForGColor="cyan", initForGColor="";
var BackGColor="", initBackGColor="";
// single measurement variables and graphic interface elements
var addMx1,addMy1,addMx2,addMy2;
var rmMx1,rmMy1,rmMx2,rmMy2;
var erMx1,erMy1,erMx2,erMy2;
var mesurx1,mesury1,mesurx2,mesury2;
var measurementTab="Measurements - Tab";
var measurementTabEXL;
var resultListSize=0;
var mes=newArray(200);
var mesX=newArray(200);
var mesY=newArray(200);
var mesRadius=newArray(200);
// grid variables
var alteuu=0,lastmesnumber=0;
var nbcol=7,nbline=4;
var nbcolX1,nbcolX2,nbcolY1,nbcolY2;
var nblineX1,nblineX2,nblineY1,nblineY2;
var HLboxX1, HLboxY1,HLboxX2, HLboxY2,HLX=0,HLY=0,statutHL=0;
var HRboxX1, HRboxY1,HRboxX2, HRboxY2,HRX=0,HRY=0,statutHR=0;
var LLboxX1, LLboxY1,LLboxX2, LLboxY2,LLX=0,LLY=0,statutLL=0;
var LRX=0,LRY=0;
var ansvers1,ansvers2;
var showmes=0,showrep=0,showgrid=0;
var DotStatus = "Single";
var GridStatus=1;
var singX1=0,singX2=0,singY1=0;
var gridCx1=0,gridCx2=0,gridCy1=0,gridCy2;
var endx1=0, endx2=0, endy1=0, endy2=0;
var ImaDemo="";
var Ax=0,XhorizontalOrd=0,Ay=0,YhorizontalOrd=0,spaceX=0,spaceY=0,deltaspaceY=0,deltaspaceY=0;
var windowTabName="Grid Measurements Table",nameOfGridTab="["+windowTabName+"]";
var gridcol=0,gridline=0;
var Red="", Green="", Blue="", color ="", previousColor="";
var gridModelName="Grid Modelled";
var gridModelStatus=0;
var errorNetMessage ="Error: ";
var onlinedoclink = "http://image.bio.methods.free.fr/dotblot.html";
var urllist = "http://image.bio.methods.free.fr/ij/ijupdatetest/ListOfMacros.txt";// to check the internet access
var demoimagelink1 ="/ij/images/Dot_Blot.jpg",demoimagename1="Dot_Blot.jpg";
var demoimagelink2 ="http://image.bio.methods.free.fr/ij/ijmacro/dotblot/Dot_Blot-ScionNIH_Image.tif.zip",demoimagename2="Dot_Blot-scion_NIH.tif";
var xx = requires140a (); // check version at install time
function requires140a() {requires("1.40a"); return 0;}
// Tool to allow user interaction
macro "User Interaction Tool - " {
if (palette==1 && getTitle == paletteName && dyn ==1 && cancel==0 && reponse ==0) {
if (isOpen(paletteName)) {
if (isKeyDown("alt")) {alteuu=1; } else {alteuu=0;}
goGraphInt ();
}
}
if (palette==0 && getTitle ==paletteName && dyn ==1 && cancel==1 && reponse ==1) {
palette=0;cursorok=1;
if (isOpen(paletteName)) {
selectImage (paletteName);
close ();
if (isOpen(blotName)) {selectImage(blotName);close ();}
if (isOpen(gridModelName)) {selectImage(gridModelName);close ();}
if (isOpen(measurementTab)) {selectWindow(measurementTab);print(measurementTabEXL, "\\Close");}
if (isOpen(windowTabName)) {selectWindow(windowTabName);print(nameOfGridTab, "\\Close");}
}
if (initselectionColor != "") {setColorComponent (initForGColor,initBackGColor,initselectionColor);}
}
if (palette==1 && (getTitle !=paletteName || ! isOpen(paletteName)) && dyn ==1 && cancel==0 && reponse ==0) {
palette=0;cursorok=0;
if (isOpen(paletteName)) {
selectImage (paletteName);
close ();
showMessage("No user ansvers from the \""+paletteName+"\". \nThe tool has been unselected.");
}
if (isOpen(blotName)) {selectImage(blotName);close ();}
if (initselectionColor != "") {setColorComponent (initForGColor,initBackGColor,initselectionColor);}
}
if (palette==0 && getTitle ==paletteName && dyn ==1 && cancel==0 && reponse ==1 && analyseIt==0 && cursorok==1) {
locationCursor (1);
analyseIt=0;reponse=0;cursorok=0;palette=1;
}
}
var mCmds = newMenu("Dot Blot Analysis Menu Tool",newArray("Analyse a Dot Blot","-","Download\/Open The ImageJ Demo Dot Blot Image \(28 wells\)","Download\/Open Demo Dot Blot Image \(96 wells\)"));
macro "Dot Blot Analysis Menu Tool - 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"{
cmd = getArgument();
if (cmd !="-" && cmd == "Download\/Open The ImageJ Demo Dot Blot Image \(28 wells\)") {OpenImageLink(0,demoimagelink1,demoimagename1);}
if (cmd !="-" && cmd == "Download\/Open Demo Dot Blot Image \(96 wells\)") {OpenImageLink(0,demoimagelink2,demoimagename2);}
if (cmd !="-" && cmd =="Analyse a Dot Blot") {doBlotAnalyse();}
}
var ftabCmds = newMenu("Measurement Documents Menu Tool",newArray("Save Results Documents","Save Results Documents at the Dot Blot Image Location","-","Close Results Documents","-" ,"Save Grid Results Table as Excel Type File","Save Single Measurements Table as Excel Type File", "-","Save Grid Results Table as Excel Type File at the Dot Blot Image Location","Save Single Measurements Table as Excel Type File at the Dot Blot Image Location"));
macro "Measurement Documents Menu Tool - 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" {
cmd = getArgument();
if (cmd !="-" && cmd == "Save Results Documents at the Dot Blot Image Location") {SaveDocRes(folderpath);}
if (cmd !="-" && cmd == "Save Results Documents") {SaveDocRes("--");}
if (cmd !="-" && cmd == "Close Results Documents") {CloseDocRes();}
if (cmd !="-" && cmd == "Save Grid Results Table as Excel Type File") {saveTab ("",windowTabName);}
if (cmd !="-" && cmd == "Save Single Measurements Table as Excel Type File") {saveTab ("",measurementTab);}
if (cmd !="-" && cmd == "Save Grid Results Table as Excel Type File at the Dot Blot Image Location") {saveTab (folderpath,windowTabName);}
if (cmd !="-" && cmd == "Save Single Measurements Table as Excel Type File at the Dot Blot Image Location") {saveTab (folderpath,measurementTab);}
}
macro "Abort \(Download\/Erase Cursor\) Action Tool - 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" {
ereaseCursor ();
abortProcess ();
}
macro "On Line Documentation Action Tool - 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"{
doc ();
}
macro "Version and Update Infos Action Tool - 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" {
VersionInfos ();
}
macro "About \"Dot Blot Analyzer\" Action Tool - 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" {
about1 ();
}
///////////////// Functions ////////////////////
function locationCursor (curs) {
// set the location of the cursor and kind of cursor (single analyse or grid repair setting)
display ("");
if (curs == 1) {
if (x ==0) {ereaseCursor ();initiate=1;}
checkInitColor ();
getCursorLoc(x, y, z, flags);
if (initiate ==1) {makeCursor(x,y,w,h,1);initiate=0;}
xstart=x; ystart=y;
w = getWidth(); h = getHeight();
x2=x; y2=y;
while (flags&16!=0) {
getCursorLoc(x, y, z, flags);
if (x!=x2 || y!=y2) {
makeCursor(x,y,w,h,1);
}
x2=x; y2=y;
wait(10);
};
if (initselectionColor != "") {setColorComponent (initForGColor,initBackGColor,initselectionColor);}
}
// when the cursor is set
if (x!=xstart || y!=ystart) {
measureCircle ();
display ("Blot Cursor coordinates: x="+ floor (xx-blotx1) + " \("+ floor (xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+floor (yy-bloty1)*blotscale +"\)"+ "\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)"+ " " + kindofColoBox + " "+ SelectedColor);
if (statutHL ==1 || statutHR ==1 || statutLL ==1) {
ansvers2=1;
HautDroite (0,0,1);
BasGauche (0,0,1);
HautGauche (0,0,1);
}
palette=1;dyn=1;reponse=0;cancel=0;cursorok=0;
setTool(10);
}
}
function makeCursor(x,y,w,h,undo) {
if (undo == 1) run("Undo");
showStatus("Target: x image="+ x + " \(x blot="+(x-blotx1) +"\) " +", y image="+y + " \(y blot="+ (y-bloty1)+"\)");
xori=blotx1;yori=bloty1;w=blotx2;h=bloty2;
if ((x-selectionRayon) < blotx1) {x=blotx1+selectionRayon;}
if ((y-selectionRayon) < bloty1) {y=bloty1+selectionRayon;}
if ((x+selectionRayon) >= blotx2) {x=blotx2-1-selectionRayon;}
if ((y+selectionRayon) >= bloty2) {y=bloty2-1-selectionRayon;}
if (livedisplay ==1) display ("Blot Cursor coordinates: x="+ floor(x-blotx1) + " \("+ floor(x-blotx1)*blotscale +"\) " +", y="+floor(y-bloty1) + " \("+ floor(y-bloty1)*blotscale +"\)"+"\n" + "\("+KindofArea + "\)" + " " + radius +kindofColoBox + " "+ SelectedColor);
px[0]=xori; py[0]=y;
px[1]=w; py[1]=y;
px[2]=x; py[2]=y;
px[3]=x; py[3]=yori;
px[4]=x; py[4]=h;
px[5]=x; py[5]=y;
setupUndo();
makeSelection("polgon", px, py);
setLineWidth(1);
// set the grid repair selection color
if (statutHL ==1 || statutHR ==1 || statutLL ==1) {
setColor (220,220,0);
setColorComponent (ForGColor,BackGColor,selectionColor);
}
else {
setColorComponent (ForGColor,BackGColor,selectionColor);
getColorValues(ForGColor); setColor (r,g,b);
}
drawOval((x-selectionRayon),(y-selectionRayon),2*selectionRayon,2*selectionRayon);
xx=x; yy=y;
}
function makeCircle(x,y,w,h,undo,radius) {
setLineWidth(1);
drawOval((x-radius),(y-radius),2*radius,2*radius);
}
function makeLine(x1,y1,x2,y2) {
if (x1>blotx1 && x1 < blotx2 && y1 >bloty1 && y1 <bloty2 && x2 < blotx2 && x2 > blotx1 && y2 <bloty2 && y2 >bloty1) {
setLineWidth(1);
drawLine(floor(x1),floor(y1),floor(x2),floor(y2));
}
}
function ChangeSize (CSize) {
if ((selectionRayon+CSize)>4) selectionRayon=selectionRayon+CSize;
measureCircle ();
KindofArea="Interface";radius="radius="+toString(selectionRayon)+ " \("+toString(selectionRayon*2)+"\)";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius+ kindofColoBox + " "+ SelectedColor);
}
function measureCircle () {
makeWork (); // create-select the batch working image
xmes=xx-blotx1;
ymes=yy-bloty1;
makeOval((xmes*blotscale-selectionRayon*blotscale),(ymes*blotscale-selectionRayon*blotscale),2*selectionRayon*blotscale,2*selectionRayon*blotscale);
getStatistics(area, mean);
volume = floor (area*mean);
theVolume=toString(volume);
selectImage (paletteName);
setBatchMode(false);
}
function addvalue (clickx, clicky) {
if (clickx > addMx1 && clickx < addMx2 && clicky > addMy1 && clicky <addMy2) {
DotStatus = "Single";
if (theVolume != "") {
resultListSize=resultListSize+1;
lastmesnumber=resultListSize;
if (! isOpen(measurementTab)) {
measurementTabEXL="["+measurementTab + "]";
run("New... ", "name="+measurementTabEXL+" type=Table");
print(measurementTabEXL, "\\Headings:Number\t X coordinate\tY coordinate\tIntegrated Area\tRadius\t");
selectWindow (measurementTab);
setLocation(0,Hpalette+138);
selectImage (paletteName);
}
if (resultListSize > 0) {
mes[resultListSize-1]=theVolume;
mesX[resultListSize-1]=xmes*blotscale; mesY[resultListSize-1]=ymes*blotscale;
mesRadius[resultListSize-1]=selectionRayon;
printrayon=toString (mesRadius[resultListSize-1]+ " \("+ (blotscale*mesRadius[resultListSize-1])+"\)");
print(measurementTabEXL, (resultListSize) + "\t" + mesX[resultListSize-1] + "\t" + mesY[resultListSize-1] + "\t" + mes[resultListSize-1] + "\t" + printrayon + "\t");
}
test3cursor ();
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)"+ "\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)"+ ": One added value " + kindofColoBox + " "+ SelectedColor);
}
updateSingleStatusInfo ();
}
}
function rmvalue (clickx, clicky) {
if (clickx > rmMx1 && clickx < rmMx2 && clicky > rmMy1 && clicky <rmMy2) {
DotStatus = "Single";
if (isOpen (measurementTab) ) {
if (alteuu == 1 && lastmesnumber != 0 ) {resultListSize=lastmesnumber;}
if (resultListSize > 0) {
print(measurementTabEXL, "\\Clear");
if (alteuu == 0 && resultListSize >0) {lastmesnumber=resultListSize;resultListSize=resultListSize-1;}
for (i=0; i<resultListSize; i++) {
printrayon=toString (mesRadius[i]+ " \("+ (blotscale*mesRadius[i])+"\)");
print(measurementTabEXL, (i+1) + "\t" +mesX[i] + "\t" + mesY[i] + "\t" + mes[i] + "\t" + printrayon+ "\t");
}
test3cursor ();
}
}
updateSingleStatusInfo ();
if (alteuu == 1 && lastmesnumber != 0) {
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Restored measurement " + kindofColoBox + " "+ SelectedColor);
}
if (alteuu == 0 && lastmesnumber != 0) {
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Erased measurement " + kindofColoBox + " "+ SelectedColor);
}
}
}
function erMeasurement (clickx, clicky) {
if (clickx > erMx1 && clickx < erMx2 && clicky > erMy1 && clicky < erMy2) {
DotStatus = "Single";
if ( isOpen(measurementTab)) {
if (alteuu == 0 && resultListSize >0) {
lastmesnumber=resultListSize;
Dialog.create("User Choice");
Dialog.addChoice("Delete the measurements ?", newArray("No","Yes") ,"no");
Dialog.show();
choix=Dialog.getChoice();
if (choix == "Yes") {print(measurementTabEXL, "\\Clear");resultListSize=0;resetblot (1,1,1,1);}
}
if (alteuu == 1) {
resultListSize=lastmesnumber;
}
test3cursor ();
}
updateSingleStatusInfo ();
if (alteuu == 0) {
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Erased Measurement(s) " + kindofColoBox + " "+ SelectedColor);
}
if (alteuu == 1) {
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Restored Measurement(s) " + kindofColoBox + " "+ SelectedColor);
}
}
}
function restaureMes () {
DotStatus = "Single";
if ( isOpen(measurementTab)) {
if (lastmesnumber != 0 ) {
print(measurementTabEXL, "\\Clear");
for (i=0; i<resultListSize; i++) {
printrayon=toString (mesRadius[i]+ " \("+ (blotscale*mesRadius[i])+"\)");
print(measurementTabEXL, (i+1) + "\t" +mesX[i] + "\t" + mesY[i] + "\t" + mes[i] + "\t"+ printrayon +"\t");
}
}
}
updateSingleStatusInfo ();
}
function showMesure (clickx,clicky) {
if (clickx > mesurx1 && clickx < (mesurx1+mesurx2) && clicky > mesury1 && clicky < (mesury1+mesury2/2)) {
DotStatus = "Single";
test3cursor ();
updateSingleStatusInfo ();
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Single measure mode " + kindofColoBox + " "+ SelectedColor);
}
}
function circleAutoSize (clickx,clicky) {
if (clickx > sizex1 && clickx < (sizex1+sizex2-24) && clicky > sizey1 && clicky < (sizey1+sizey2)) {
run("Undo");
run("Select None");
makeTemps (0);
makeWork ();
run("Make Binary");
run("Set Measurements...", "area center fit redirect=None decimal=0");
run("Clear Results");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing");
close ();
nmes=nResults;
if (nmes >0) {
elipselist=newArray(nmes);
elipselistx=newArray(nmes);
elipselisty=newArray(nmes);
for (a=0 ; a< nmes ; a++) {
elipselist[a]=getResult("Major", a);
elipselistx[a]=getResult("XM", a);
elipselisty[a]=getResult("YM", a);
}
sort (elipselist,elipselistx,elipselisty);
pertinantnumber=(elipselist.length-1);
pertinantvalue=xSizeBlot/10;
perttest=elipselist[elipselist.length-1];
while (elipselist[pertinantnumber] >= (xSizeBlot/10) && pertinantnumber>=0) {
pertinantnumber = pertinantnumber-1;
if (pertinantnumber <0) exit ("Pertinant circle radius can't be found. Tool desactivated."); }
if (pertinantnumber>-1) {
xauto=floor (elipselistx[pertinantnumber]);
yauto=floor (elipselisty[pertinantnumber]);
selectionRayon=floor (elipselist[pertinantnumber]/blotscale/2+1);
setBatchMode(false);
test3cursor ();
makeCursor((xauto/blotscale+blotx1),(yauto/blotscale+bloty1),w,h,1);
measureCircle ();
KindofArea="Interface";radius="Auto Radius="+toString(selectionRayon)+ " \("+toString(selectionRayon*2)+"\)";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius+ kindofColoBox + " "+ SelectedColor);
x=xauto/blotscale+blotx1;y=yauto/blotscale+bloty1;
} else showMessage ("Pertinant circle radius can't be found.");
}
}
}
function updateSingleStatusInfo () {
// update the single statut interface
setBatchMode(true);
setColor (90,90,130);
fillRect ((singX1+1), (singY1+1), (singX2-2), 15);
fillRect (gridCx1+1, gridCy1+1, gridCx2-2, gridCy2/2);
fillRect (gridCx1+1, gridCy1+gridCy2/2+2, gridCx2-2, gridCy2/2-2);
if (DotStatus == "Single") {setColor(0,220,0);} else {setColor(220,0,0);}
setJustification("center");
setFont("SansSerif", 12,"antialiased");
drawString("Measurements:", singX1+1+(singX2)/2,singY1+15) ;
if (DotStatus == "Grid") {setColor(0,220,0);} else {setColor(220,0,0);}
setJustification("center");
drawString("Grid:", gridCx1+1+(gridCx2)/2,gridCy1+15);
if (gridModelStatus == 1) {setColor(0,220,0);} else {setColor(220,0,0);}
setJustification("center");
drawString("Model", gridCx1+1+(gridCx2)/2,gridCy1+32);
}
function showGrid (clickx,clicky) {
if (clickx > gridCx1 && clickx < (gridCx1+gridCx2) && clicky > gridCy1 && clicky < (gridCy1+gridCy2/2)) {
DotStatus = "Grid";
test3cursor ();
updateSingleStatusInfo ();
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + ": Grid measure mode " + kindofColoBox + " "+ SelectedColor);
}
}
function showModel (clickx,clicky) {
if (clickx > gridCx1 && clickx < (gridCx1+gridCx2) && clicky > (gridCy1 +gridCy2/2+2) && clicky < (gridCy1+gridCy2)) {
if (gridModelStatus==0) { gridModelStatus =1;}
else {if (gridModelStatus==1) gridModelStatus =0;}
if (gridModelStatus==0) { if (isOpen(gridModelName)) {selectImage(gridModelName);close ();}}
DotStatus = "Grid";
test3cursor ();
updateSingleStatusInfo ();
KindofArea="Interface";
if (gridModelStatus==1) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Model selected "+ kindofColoBox + " "+ SelectedColor);
if (gridModelStatus==0) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Model unselected "+ kindofColoBox + " "+ SelectedColor);
}
}
// Derived from http://rsb.info.nih.gov/ij/macros/SortDemo.txt
// author Wayne Rasband
function sort(a,b,c) {quickSort(a,b,c, 0, lengthOf(a)-1);}
function quickSort(a,b,c, from, to) {
i = from; j = to;
center = a[(from+to)/2];
do {
while (i<to && center>a[i]) i++;
while (j>from && center<a[j]) j--;
if (i<j) {
temp=a[i]; a[i]=a[j]; a[j]=temp;
temp=b[i];b[i]=b[j]; b[j]=temp;
temp=c[i];c[i]=c[j]; c[j]=temp;
}
if (i<=j) {i++; j--;}
} while(i<=j);
if (from<j) quickSort(a,b,c, from, j);
if (i<to) quickSort(a,b,c, i, to);
}
function ereaseCursor () {
run("Undo");
run("Select None");
if (initselectionColor != "") {setColorComponent (initForGColor,initBackGColor,initselectionColor);}
}
function makeTemps (option) {
setBatchMode(true);
if (option == 1 && isOpen(tempclip)) {
selectImage (tempclip);
run("Select All");
run("Copy");
} else {
if (! isOpen(tempclip)) {
newImage(workingI,"8-bit Black",xSizeBlot,ySizeBlot,1);
run("Paste");
run("Select None");
tempclip =getImageID();
}
}
}
function makeWork () {
setBatchMode(true);
if (! isOpen(workingID)) {
newImage(workingI,"8-bit Black",xSizeBlot,ySizeBlot,1);
run("Paste");
run("Select None");
workingID =getImageID();
}
}
function OpenImageLink(question,demoimagelink,demoim) {
// download demo images
// Check if already downloaded.
if (isOpen(demoim)) exit ("The \"" + demoim + "\" is already opened");
demoimalocation = getDirectory("startup");
fildestination = demoimalocation+ "Downloaded Demo Images/" + demoim;
if (File.exists(fildestination)) {
if (question ==1 ) showMessageWithCancel ("The \"" + demoim + "\" has already been downloaded. Open it?");
open(fildestination);
}
else {
netTest ();
showMessageWithCancel ("ImageJ will download a demo image. Continue?");
run("URL...", "url=["+demoimagelink+"]");
imageid = getImageID();
nomdimage = getTitle;
// Create a <Downloaded Demo Images> repertory in ImageJ folder.
ImaDemo = demoimalocation+"Downloaded Demo Images"+File.separator;
File.makeDirectory(ImaDemo);
if (!File.exists(ImaDemo)) exit("Unable to create directory, something wrong in the ImageJ folder");
selectWindow(nomdimage);
save(""+ImaDemo+""+ nomdimage +"");
}
}
function UndoLast () {run("Undo");}
//////////////////
// graphic interface
//////////////////
function goGraphInt () {
kindofColoBox="";SelectedColor="";radius="";
clickx=0;clicky=0;
reponse=0;cancel=0;dyn =0;
if (! isOpen(paletteName)) {reponse=1;cancel=1;}
getCursorLoc(clickx, clicky, z, flags);
// test color boxes for cross hair
testcolor= coloBoxes(0,1,clickx,clicky,"crosshair",0);
if (testcolor != "") {
kindofColoBox="crosshair";SelectedColor=testcolor;selectionColor=SelectedColor;
KindofArea="Interface";
ereaseCursor ();
test3cursor ();
makeCursor(x,y,w,h,1);
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + kindofColoBox + " "+ SelectedColor);
}
// test color boxes for circle
testcolor= coloBoxes(0,1,clickx,clicky,"circle",0);
if (testcolor != "") {
kindofColoBox="circle";SelectedColor=testcolor;ForGColor=SelectedColor;
KindofArea="Interface";
ereaseCursor ();
test3cursor ();
makeCursor(x,y,w,h,1);
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\)" + " " + radius + kindofColoBox + " "+ SelectedColor);
}
// test the circle size
boxstatut=adjustBoxes(box1x,box1y,0,1,clickx,clicky);
if (boxstatut == 2) {
if (statutHL !=1 && statutHR !=1 && statutLL !=1) {ChangeSize (-1);test3cursor ();gridAnalyse ();}
}
if (boxstatut == 3) {
if (statutHL !=1 && statutHR !=1 && statutLL !=1) {ChangeSize (1);test3cursor ();gridAnalyse ();}
}
// test the histogram normalisation
enhenceHisto (clickx,clicky);
// test the lut choice for blot preview
lutanvers=checkLUT (clickx,clicky);
if (lutanvers ==1) {
applyLut ();
test3cursor ();
measureCircle ();
KindofArea ="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + lutDisplay + radius+ kindofColoBox + " "+ SelectedColor);
}
// test the saturation level for histogram normalisation
boxstatut=adjustBoxes(box2x,box2y,0,1,clickx,clicky);
if (boxstatut == 2) {satHisto (-incresat);}
if (boxstatut == 3) {satHisto (incresat);}
// test the reset blot preview
if (checkClean (clickx,clicky)==1) {
resetblot (0,0,0,1);
test3cursor ();
KindofArea ="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + " Initial Blot Preview "+ kindofColoBox + " "+ SelectedColor);
}
// test the autosize cursor
if (statutHL !=1 && statutHR !=1 && statutLL !=1) {circleAutoSize (clickx,clicky);}
// test the result table management
addvalue (clickx,clicky);
rmvalue (clickx, clicky);
erMeasurement (clickx, clicky);
showMesure (clickx,clicky);
// adjust the number of columns of the grid
boxstatut=adjustBoxes(box3x,box3y,0,1,clickx,clicky);
if (boxstatut == 2) {DotStatus = "Grid";setColNumber (-1);} if (boxstatut == 3) {DotStatus = "Grid";setColNumber (1);}
// adjust the number of lines of the grid
boxstatut=adjustBoxes(box4x,box4y,0,1,clickx,clicky);
if (boxstatut == 2) {DotStatus = "Grid";setLineNumber (-1);}
if (boxstatut == 3) {DotStatus = "Grid";setLineNumber (1);}
// check for the 3 angle limiting the grid
HautDroite (clickx,clicky,0);
BasGauche (clickx,clicky,0);
HautGauche (clickx,clicky,0);
// test the grid box
showGrid (clickx,clicky);
// test the model box
showModel (clickx,clicky);
// cancel !!rajouter la reinitialisation du foreground color?
if (Cancel (clickx,clicky) == 1) {cancel=1;reponse=1;palette=0;}
// end, finish analysis
endQuit (clickx,clicky);
// location of the click into the blot area
if (Blot (clickx,clicky) == 1) {KindofArea="Dot blot";reponse =1; palette=0;analyseIt=0;cursorok=1;} else {KindofArea="Interface";}
// check for the erease drawing
if (eraseDraw (clickx,clicky) ==1) {
resetblot (1,1,1,1);
}
dyn =1;
}
function getBlotSample () {
run("Select None");
selectImage (blotName);
run("Duplicate...", "title=temp");
run("Invert");
makeRectangle(0,0,xSizeBlot,ySizeBlot);
run("Copy");run("Select None");close ();
}
function resetblot (saturation,enh,lut,curs) {
// reset the visualisations settings: if saturation, enh, lut != 0 user settings are kept
if (saturation==0) sat=0;
if (enh==0) enhenceChoice=0;
if (lut ==0) lutChoice=0;
applyLut ();
if (curs ==1) makeCursor(x,y,w,h,1);
}
function blotForPalette () {
makeTemps (0);
makeWork ();
if ( isOpen(workingID)) {
selectImage (workingID);
run("Size...", "width=["+xSizeBlot/blotscale+"] height=["+ySizeBlot/blotscale+"] interpolate");
run("Select All");run("Copy");close ();
selectImage(paletteName);
run("Paste");run("Select None");
}
makeTemps (1);
selectImage(paletteName);
}
function coloBoxes(draw,detect,clickx,clicky,kind,update) {
if (kind == "crosshair") ori=40+interx1;
if (kind == "circle") ori=Linter/2+20+interx1;
colboxOriY=yDisplay-25;
xcolorbox=20;ycolorbox=10;spcol=(Linter-8*xcolorbox)/48;
setLineWidth(largeline);detectcol=-1;democolor="";
for (a=0;a<8;a++) {
setColor(255,0,93);
if (detect==1) {
if (clicky >colboxOriY && clicky < (colboxOriY+ycolorbox)) {
if (clickx > (a*xcolorbox+a*spcol+spcol)+ori && clickx < ((a*xcolorbox+a*spcol+spcol)+xcolorbox)+ ori) {detectcol=a;kindofColoBox=kind;}
}
}
if (draw==1) {setLineWidth(largeline);drawRect ((a*xcolorbox+a*spcol+spcol)+ori, colboxOriY, xcolorbox, ycolorbox);}
if (a==0) {getColorValues ("red");if (detect==1 && detectcol==0) {democolor ="red";}}
if (a==1) {getColorValues ("green");if (detect==1 && detectcol==1) {democolor ="green";}}
if (a==2) {getColorValues ("blue");if (detect==1 && detectcol==2) {democolor ="blue";}}
if (a==3) {getColorValues ("cyan");if (detect==1 && detectcol==3) {democolor ="cyan";}}
if (a==4) {getColorValues ("yellow");if (detect==1 && detectcol==4) {democolor ="yellow";}}
if (a==5) {getColorValues ("magenta");if (detect==1 && detectcol==5) {democolor ="magenta";}}
if (a==6) {getColorValues ("black");if (detect==1 && detectcol==6) {democolor ="black";}}
if (a==7) {getColorValues ("white");if (detect==1 && detectcol==7) {democolor ="white";}}
if (draw==1) {setColor(r, g, b);fillRect ((a*xcolorbox+a*spcol+spcol+1) +ori, colboxOriY+1 , (xcolorbox-2), (ycolorbox-2));}
}
// draw graphique legend
if (update==1) {
getColorValues(ForGColor); setColor (r,g,b);
setLineWidth(largeline);
drawOval((Linter-16+interx1-22),(colboxOriY-3),16,16);
drawOval((interx1+Linter/2-8),(colboxOriY-3),16,16);
getColorValues(selectionColor); setColor (r,g,b);
drawLine((Linter/2+interx1),(colboxOriY-8),(Linter/2+interx1),(colboxOriY+18));
drawLine((Linter/2-14+interx1),(colboxOriY+5),(Linter/2+14+interx1),(colboxOriY+5));
drawLine((30+interx1),(colboxOriY-8),(30+interx1),(colboxOriY+18));
drawLine((30+interx1-11),(colboxOriY+5),(30+interx1+11),(colboxOriY+5));
}
return democolor;
}
function adjustBoxes(xbx,ybx,draw,detect,clickx,clicky) {
xadjustbox=14;yadjustbox=25;
setLineWidth(1);status=0;
if (detect==1) {
if (clicky >(ybx) && clicky < (ybx+yadjustbox/2-1) && clickx > (xbx) && clickx < (xbx+xadjustbox)) {status=3;}
if (clicky >(ybx+yadjustbox/2) && clicky < (ybx+yadjustbox) && clickx > xbx && clickx < (xbx+xadjustbox)) {status=2;}
}
if (draw==1) {
setColor(100,50,50);fillRect ((xbx+1), (ybx+1), (xadjustbox-1), (yadjustbox-1));run("Select None");
setColor(255,0,93);drawRect (xbx, ybx, xadjustbox, yadjustbox); run("Select None");
drawLine ((xbx), (ybx+yadjustbox/2-1), (xbx+xadjustbox-1), (ybx+yadjustbox/2-1));
setFont("SansSerif", 15,"antialiased");setColor(0,255,0);
setJustification("left");
drawString("-",(xbx+3),(ybx+27));
drawString("+",(xbx+1),(ybx+15));
}
return status;
}
function enhenceHisto (clickx,clicky) {
// normalize the histogram, taking account the saturation level, and lut choices
if (clickx > enhX1 && clickx < enhX1+enhX2-20 && clicky > enhY1 && clicky < enhY1+enhY2) {
run("Undo");
makeTemps (0);
makeWork ();
if (enhenceChoice ==0) {
run("Enhance Contrast", "saturated=["+sat+"] normalize");
enhenceChoice =1;
} else {enhenceChoice =0;}
if (lutChoice==0) run("Grays");
if (lutChoice==1) {run("Grays");run("Invert");}
if (lutChoice==2) {run("Fire");}
if (lutChoice==3) {if (File.exists(getDirectory("imagej")+"luts/royal.lut")) {run("royal");} else {run("Spectrum");}}
run("Size...", "width=["+xSizeBlot/blotscale+"] height=["+ySizeBlot/blotscale+"] interpolate");
run("Select All");run("Copy");
selectImage (paletteName);
makeRectangle (blotx1, bloty1, xSizeBlot/blotscale, ySizeBlot/blotscale);
run("Paste");
run("Select None");
makeTemps (1);
selectImage (paletteName);
setBatchMode(false);
test3cursor ();
KindofArea= "Interface";
measureCircle ();
if (enhenceChoice == 1) {histo="Normalized Contrast Sat="+d2s(sat,2)+"%";} else {histo="Initial Contrast";}
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + histo + radius+ kindofColoBox + " "+ SelectedColor);
}
}
function checkClean (clickx,clicky) {
// locate click for supress visuals improvements
statut=0;
if (clickx > resX1 && clickx < (resX1+ resX2) && clicky > resY1 && clicky < (resY1+resY2)) {statut=1;}
return statut;
}
function Cancel (clickx,clicky) {
// locate click for cancel the analysis
testcancel=0;
if (clickx > cancelx1 && clickx < cancelx2 && clicky > cancely1 && clicky < cancely2) {testcancel=1;}
return testcancel;
}
function Blot (clickx,clicky) {
// locate the actions into the blot area
if (clickx >= blotx1 && clickx < blotx2 && clicky >= bloty1 && clicky < bloty2) {testpal=1;} else {testpal=0;} return testpal;
}
function eraseDraw (clickx,clicky) {
// locate click for erease the drawings onto blot area
testErase=0;
if (clickx > analysex1 && clickx < analysex2 && clicky > analysey1-4 && clicky < analysey2+4) {testErase=1;}
return testErase;
}
function endQuit (clickx,clicky) {
if (clickx > endx1 && clickx < (endx2+endx1) && clicky > endy1 && clicky < endy1+endy2) {
palette=0;cursorok=0;dyn=0;
if (isOpen(paletteName)) {
selectImage (paletteName);
makeRectangle (blotx1, bloty1, xSizeBlot/blotscale, ySizeBlot/blotscale);
run("Crop");
rename(blotinitName+ "-Grph");
endPalette=getTitle;
showMessage("End of analyse");
}
if (initselectionColor != "") {setColorComponent (initForGColor,initBackGColor,initselectionColor);}
}
}
function updateThePalette () {
setBatchMode(true);
run("Select None");
coloBoxes(1,0,0,0,"crosshair",1);
coloBoxes(1,0,0,0,"circle",1);
// update-refresh the single measures
if (showmes ==1) {
run("Undo");
run("Select None");
if ( isOpen(measurementTab)) {
if (lastmesnumber != 0 ) {
resetblot (1,1,1,0);
setBatchMode(true);
restaureMes ();
setColorComponent (ForGColor,BackGColor,selectionColor);
getColorValues(ForGColor); setColor (r,g,b);
for (i=0; i<resultListSize; i++) {
makeCircle((mesX[i]/blotscale+blotx1),(mesY[i]/blotscale+bloty1),w,h,0, mesRadius[i]);
}
makeCursor(x,y,w,h,1);
}
}
makeCursor(x,y,w,h,1);
}
// update-refresh the grid limits
if (showrep ==1) {
resetblot (1,1,1,0);
if (LLX !=0 && LLY !=0) {
setColor(0,255,0);
if (updateRefCircle(LLX,LLY) == 1) {
makeCircle((LLX+blotx1),(LLY+bloty1),w,h,0,(selectionRayon));
} else {
LLX=0; LLY=0; LRX=0; LRY=0;
updateThePalette ();
waitForUser("Setting mistake 1","Out of blot area, \"Low Left\" grid cursor has been reinitialized. \nIt is incompatible with the circle RADIUS and\/or LINES and \nCOLUMNS numbers set");
}
}
if (HRX !=0 && HRY !=0) {
setColor(0,255,0);
if (updateRefCircle(HRX,HRY) == 1) {
makeCircle((HRX+blotx1),(HRY+bloty1),w,h,0,(selectionRayon));
} else {
HRX=0; HRY=0; LRX=0; LRY=0;
updateThePalette ();
waitForUser("Setting mistake 2","Out of blot area, \"High Right\" grid cursor has been reinitialized. \nIt is incompatible with the circle RADIUS and\/or LINES and \nCOLUMNS numbers set");
}
}
if (HLX !=0 && HLY !=0) {
setColor(0,255,0);
if (updateRefCircle(HLX,HLY) == 1) {
makeCircle((HLX+blotx1),(HLY+bloty1),w,h,0,(selectionRayon));
} else {
HLX=0; HLY=0; LRX=0; LRY=0;
updateThePalette ();
waitForUser("Setting mistake 3","Out of blot area, \"High Left\" grid cursor has been reinitialized. \nIt is incompatible with the circle RADIUS and\/or LINES and \nCOLUMNS numbers set");
}
}
// check for the grid ref cursors positions (limits) regarding the circle radius changing
if (LRX >0 && LRY >0 && HLX >0 && HRX >0 && LLX>0 ) {
if (updateRefCircle(LRX,LRY) == 1) {
dxc= ((HRX-HLX)/(nbcol-1));
dyc= ((LLY-HLY)/(nbline-1));
// grid lines calculations. make grid measure tab
if (GridStatus ==1) makeGridTab (); // for grid tab
for (i=0; i< nbline; i++) {
setColor(128,128,128);
makeLine ((((HLY+bloty1+i*dyc)-YhorizontalOrd)/Ay) ,((HLX+blotx1)*Ax+XhorizontalOrd+i*dyc),(((HLY+bloty1+i*dyc)-YhorizontalOrd)/Ay+(HRX-HLX)),((HRX+blotx1)*Ax+XhorizontalOrd+i*dyc));
setColorComponent (ForGColor,BackGColor,selectionColor);
getColorValues(ForGColor); setColor (r,g,b);
lineTitles=" L"+ (i+1); // for grid tab
for (k=0; k < nbcol; k++) {
xx=(((HLY+bloty1+i*dyc)-YhorizontalOrd)/Ay +dxc*k);
yy=((HLX+ dxc*k+blotx1)*Ax+XhorizontalOrd +dyc*i);
if ((i !=0 || k != 0) && ( i != (nbline-1) || k != (nbcol-1)) && ( i != 0 || k != (nbcol-1)) && ( i != (nbline-1) || k != 0)) {
makeCircle(xx,yy,w,h,0,selectionRayon);
}
if (GridStatus ==1) {
measureCircle (); // for grid tab
lineTitles=lineTitles+ "\t" + theVolume; // for grid tab
}
}
if (GridStatus ==1) {if (lineTitles != "") print(nameOfGridTab, lineTitles); }// for grid tab
}
for (i=0; i< nbcol; i++) {
setColor(128,128,128);
makeLine((HLX+blotx1+i*dxc),((HLX+ dxc*i+blotx1)*Ax+XhorizontalOrd),(LLX+blotx1+i*dxc),((HLX+ dxc*i+blotx1)*Ax+XhorizontalOrd +(LLY-HLY)));
}
// yellow guide lines
setColor(255,255,0);
makeLine ((((HLY+bloty1)-YhorizontalOrd)/Ay) ,((HLX+blotx1)*Ax+XhorizontalOrd),(((HLY+bloty1)-YhorizontalOrd)/Ay+(HRX-HLX)),((HRX+blotx1)*Ax+XhorizontalOrd));
makeLine((HLX+blotx1),((HLX+blotx1)*Ax+XhorizontalOrd),(LLX+blotx1),((HLX+blotx1)*Ax+XhorizontalOrd +(LLY-HLY)));
setColor(0,255,0);
makeCircle((LRX+blotx1),(LRY+bloty1),w,h,0,(selectionRayon));
} else {
LRX=0; LRY=0;
if (HLX >0 && HRX >0 && LLX>0) {
HRX=0;HRY=0;LLX=0;LLY=0; //LRX=0;LRY=0;
//pb with the 4th grid repair
updateThePalette ();
waitForUser("Setting mistake","These grid cursors settings give the \"low\-right\" dot partially out of the blot area.\nhight\-right and low\-left cursors have been reinitialized.");
}
}
}
statutHL =0; statutHR =0; statutLL =0;
testCursButtonColor (0,0,0,1,"none");
run("Select None");
// draw the model
if (gridModelStatus ==1) makeModel ();
}
setBatchMode("exit and display");
setLocation (0,95);
run("View 100%");
}
function makeGridTab () {
if (gridcol==0) gridcol=nbcol;
if (gridline==0) gridline= nbline;
colTitles=""; lineTitles="";
for (i=1; i<= nbcol; i++) {
colTitles=colTitles+ " C"+i +"\t";
}
if (isOpen(windowTabName) && ((gridcol != nbcol) || (gridline !=nbline))) {
selectWindow (windowTabName); run("Close");
gridcol=nbcol;gridline= nbline;
}
// built the table
if (!isOpen(windowTabName)) {
run("New... ", "name="+nameOfGridTab+" type=Table");
print(nameOfGridTab, "\\Headings:Lin.\/Col.\t" + colTitles);
selectWindow (windowTabName);
setLocation(Lpalette+11,96);
}
print(nameOfGridTab, "\\Clear");
selectImage (paletteName);
}
function makeModel () {
setBatchMode(true);
wellValue=0;maxValue=0;
if (nbcol > 0 && nbline >0 && HLX >0 && HRX >0 && LLX > 0 && LRX >0 && isOpen(windowTabName )) {
selectWindow(windowTabName);
gridResults = getInfo();
// get the highest value
for (i=1; i<= nbcol; i++) {
for (j=1; j<= nbline; j++) {
colval=" C" +i; lineval =" L"+j;
wellValue=getWellValue (colval,lineval);
maxValue=maxOf(maxValue,wellValue);
}
}
// create the model window
spacerModel=10; wellModel=20;
if (! isOpen(gridModelName)) {
makeModelWindow(spacerModel,wellModel);
}
selectImage (gridModelName);
xmodel=((nbcol+1)*wellModel+(nbcol+1)*spacerModel);
ymodel=((nbline+2)*wellModel+(nbline+2)*spacerModel);
curentModelx=getWidth();
curentModely=getHeight();
if (curentModely != ymodel || curentModelx != xmodel) {
close ();
makeModelWindow(spacerModel,wellModel);
}
selectImage (gridModelName);
if (lutChoice==1) {run("Grays");}
if (lutChoice==2) {run("Fire");}
if (lutChoice==3) {if (File.exists(getDirectory("imagej")+"luts/royal.lut")) {run("royal");} else {run("Spectrum");}}
setColor (0);
fillRect(0, (wellModel+spacerModel), xmodel, ymodel-(wellModel+spacerModel));
for (i=1; i<= nbcol; i++) {
setColor(255,255,255);setJustification("center");setFont("SansSerif", 10,"bold");
ecriture = "C"+toString(i);
drawString(ecriture,((i)*wellModel+i*spacerModel+(wellModel/2+2)), (2*wellModel+spacerModel));run("Select None");
}
for (i=1; i<= nbline; i++) {
setColor(255,255,255);setJustification("center");setFont("SansSerif", 10,"bold");
ecriture = "L"+toString(i);
drawString(ecriture,(wellModel/2+spacerModel/2), ((i+2)*wellModel+(i+1)*spacerModel)-2);run("Select None");
}
for (i=1; i<= nbcol; i++) {
for (j=1; j<= nbline; j++) {
colval=" C" +i; lineval =" L"+j;
wellValue=getWellValue (colval,lineval);
wellValueRescaled=round(parseFloat(wellValue)*255/maxValue);
if (wellValueRescaled <= 255) setColor(wellValueRescaled);
fillOval(((i)*wellModel+i*spacerModel), ((j+1)*wellModel+(j+1)*spacerModel), wellModel, wellModel);
}
}
setBatchMode(false);
selectImage (paletteName);
}
}
function makeModelWindow (spacerModel,wellModel) {
setBatchMode(false);
newImage(gridModelName, "8-bit ramp", ((nbcol+1)*wellModel+(nbcol+1)*spacerModel), ((nbline+2)*wellModel+(nbline+2)*spacerModel), 1);
setLocation(Lpalette+11,348);
setBatchMode(true);
}
function getMaxValue(gridValues) {
max=gridValues[0];
for (i=0;i<gridValues.length;i++) {max=maxOf(max,gridValues[i]);}
return max;
}
function getWellValue (Coltab,Linetab) {
val=-1;
ansversGridCol=columnLabelList (Coltab);
ansversGridLine=lineLabelList (Linetab);
if (ansversGridCol >0 && ansversGridLine >0) {
lines = split(gridResults, "\n");
colums =split(lines[ansversGridLine], ",\t");
val= colums[ansversGridCol];
} else {waitForUser("model can\'t be made from the \"Grid Measurements Table\"");}
return val;
}
// return the number of the column who's title is in kind
function columnLabelList (kind) {
columnNumber=-1;
lines = split(gridResults, "\n");
headings = lines[0];
titlesofcolumns = split(headings, ",\t");
for (a=0; a<titlesofcolumns.length; a++) {if (titlesofcolumns[a] == kind) columnNumber=a;}
return columnNumber;
}
//return the number of the line who's title is in kind
function lineLabelList (kind) {
lineNumber=-1;
if (nbline > 0 && isOpen(windowTabName)) {
lines = split(gridResults, "\n");
for (a=0; a<lines.length; a++) {
linea=split(lines[a], ",\t");
if (linea[0] == kind) lineNumber=a;
}
}
return lineNumber;
}
function drawPalette () {
// draw a palette containing the blot preview and analysis graphical interface
setBatchMode(true);
if (isOpen(paletteName)) exit ("A \"" +paletteName+ "\" window is already opened.\nFirst, close it before run a new analysis.") ;
setBatchMode(true);
getBlotSample ();
setLineWidth(largeline);
Hpalette=ySizeBlot/blotscale+Topmarge+Botommarge+Hinter;Lpalette=Linter;
if ((xSizeBlot /blotscale+Leftmarge+Rightmarge) > Linter) Lpalette=(xSizeBlot /blotscale +Leftmarge+Rightmarge);
blotx1=floor ((Lpalette-xSizeBlot/blotscale)/2); blotx2= floor (blotx1+xSizeBlot/blotscale);
bloty1=floor (Topmarge);bloty2=floor (bloty1+ySizeBlot/blotscale);
run("Line Width...", "line="+largeline+"");
interx1=(Lpalette-Linter)/2;interx2=(interx1+Linter);
intery2=(Hpalette-Botommarge); intery1=(intery2-Hinter);
// cancel and analyse buttons coodinates
cancelx1=(interx1+distBord); cancelx2=(cancelx1+largbuton);
cancely1=(intery2 - disthaut-hautbuton); cancely2=(cancely1+hautbuton);
analysex1= (interx2-distBord-largbuton); analysex2=(analysex1+largbuton);
analysey1= intery2-(disthaut)-(hautbuton); analysey2=(analysey1+hautbuton);
newImage(paletteName,"RGB Black",Lpalette,Hpalette,1);
setForegroundColor(32,0,93);
run("Select All");run("Fill");run("Select None");
setColor(255,0,93);
setLineWidth(largeline);
drawRect (blotx1-1, bloty1-1, xSizeBlot/blotscale+2, ySizeBlot/blotscale+2); run("Select None");
makeRectangle (blotx1, bloty1, xSizeBlot/blotscale, ySizeBlot/blotscale);
blotForPalette ();
setLocation(5, 105);
setColor(255,0,0);// button cancel
setLineWidth(largeline);
drawRect ( cancelx1, cancely1-5, largbuton, hautbuton+9);run("Select None");
setColor(255,255,20);// button analyse
setLineWidth(largeline);
drawRect (analysex1, analysey1-5, largbuton, hautbuton+9);run("Select None");
setColor(80,90,120);
fillRect (cancelx1+1, cancely1-4, largbuton-2, hautbuton+7);
fillRect (analysex1+1, analysey1-4, largbuton-2, hautbuton+7);
setFont("SansSerif", 12,"bold");setColor(255,20,20);
drawString("Cancel",(cancelx1+9),(cancely1+19));run("Select None");
setColor(255,255,20);setJustification("center");setFont("SansSerif", 12,"antialiased");
drawString("Erase\nDrawings",(analysex1+31),(analysey1+11));run("Select None");
xDisplay= cancelx2+4;yDisplay=cancely1-8;
larDisplay= analysex1-cancelx2-8;
setColor(140,140,180);
setLineWidth(largeline);
drawRect ( xDisplay, yDisplay, larDisplay, Hdisplay);run("Select None");
display (" ");
setColor(140,140,180);
setLineWidth(largeline);
drawRect (cancelx1, yDisplay-35, (analysex1+largbuton-cancelx1), 32);run("Select None");
setColor(90,90,130);
fillRect (cancelx1+1, yDisplay-34, (analysex1+largbuton-cancelx1-2), 30);
coloBoxes(1,0,0,0,"crosshair",1);
coloBoxes(1,0,0,0,"circle",1);
ax=interx1+20;ay=colboxOriY-37;ar=16;
sizex1=cancelx1;sizex2=3*ar-1;sizey1=ay-7;sizey2=ar+15;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (sizex1, sizey1, sizex2, ar+15);
setColor (90,90,130);
fillRect (sizex1+1, sizey1+1, sizex2-2, sizey2-2);
box1x=interx1+(3*ar-4);box1y=ay-4;
getColorValues("magenta"); setColor (r,g,b);
drawOval(ax,ay,ar,ar);
getColorValues("yellow"); setColor (r,g,b);
drawLine(ax+ar/2+1,ay+(ar/2),ax+ar+1,ay+(ar/2));
drawLine((ax+ar/2+1),(ay+ar/2-3),(ax+ar/2+1),(ay+ar/2+3));
drawLine((ax+ar+1),(ay+ar/2-3),(ax+ar+1),(ay+ar/2+3));
adjustBoxes(box1x,box1y,1,0,0,0);
enhX1=ax+45; enhX2=45;
enhY1=ay-7;enhY2=ar+15;
box2x=enhX1+27;
box2y=box1y;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (enhX1, enhY1, enhX2, enhY2);
setColor (90,90,130);
fillRect (enhX1+1, enhY1+1, enhX2-2, enhY2-2);
setColor (0,250,200);
drawLine(enhX1+1,enhY1+28,enhX1+3,enhY1+17);
drawLine(enhX1+3,enhY1+17,enhX1+6,enhY1+28);
drawLine(enhX1+6,enhY1+28,enhX1+9,enhY1+20);
drawLine(enhX1+9,enhY1+20,enhX1+12,enhY1+28);
drawLine(enhX1+12,enhY1+28,enhX1+23,enhY1+28);
setColor (0,250,0);
drawLine(enhX1+1,enhY1+15,enhX1+6,enhY1+3);
drawLine(enhX1+6,enhY1+3,enhX1+12,enhY1+15);
drawLine(enhX1+12,enhY1+15,enhX1+18,enhY1+7);
drawLine(enhX1+18,enhY1+7,enhX1+23,enhY1+15);
adjustBoxes(box2x,box2y,1,0,0,0);
lutX1=enhX1+enhX2+3; lutX2=50;
lutY1=enhY1; lutY2=enhY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (lutX1, lutY1, lutX2, lutY2);
setColor (90,90,130);
fillRect (lutX1+1, lutY1+1, lutX2-2, lutY2-2);
makeSampleLut (0,lutX1+2,lutY1+2);
makeSampleLut (1,lutX1+14,lutY1+2);
makeSampleLut (2,lutX1+26,lutY1+2);
makeSampleLut (3,lutX1+38,lutY1+2);
resX1=lutX1+lutX2+3; resX2=30;
resY1=lutY1; resY2=lutY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (resX1, resY1, resX2, resY2);
setColor (90,90,130);
fillRect (resX1+1, resY1+1, resX2-2, resY2-2);
getColorValues("yellow"); setColor (r,g,b);
ax=resX1+resX2/2-9;ay=(resY1+resY2/2-8);
drawOval(ax,ay,ar,ar);
getColorValues("green"); setColor (r,g,b);
setLineWidth(largeline+1);
drawLine(ax+1,ay+ar/2+3,ax-3,ay+(ar/2-4));
drawLine(ax+1,ay+ar/2+3,ax+4,ay+(ar/2-4));
drawLine(ax+ar,ay+ar/2-5,ax+ar-4,ay+(ar/2+3));
drawLine(ax+ar,ay+ar/2-5,ax+ar+3,ay+(ar/2+3));
setLineWidth(largeline);
singX1=resX1+resX2+3; singX2=100;
singY1=lutY1; singY2=resY2;
mesurx1=singX1; mesury1=singY1; mesurx2=singX2; mesury2=singY2;
addMx1= singX1+2;
addMy1= singY1+16;
addMx2= singX1+30;
addMy2= singY1+singY2-1;
rmMx1= addMx2;
rmMy1= addMy1;
rmMx2= singX1+singX2-15;
rmMy2= addMy2;
erMx1= rmMx2;
erMy1= rmMy1;
erMx2= singX1+singX2-2;
erMy2= rmMy2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (singX1, singY1, singX2, singY2);
setColor (90,90,130);
fillRect (singX1+1, singY1+1, singX2-2, singY2-2);
setColor(140,140,180);
drawLine (singX1, addMy1, erMx2+1, addMy1);
drawLine (singX1+singX2-15, addMy1, rmMx2, addMy2);
drawLine (addMx2, addMy1, addMx2, addMy2);
setFont("SansSerif", 12,"antialiased");
setColor(220,220,0);
setJustification("center");
drawString("Measurements:", singX1+1+(singX2)/2,singY1+15);
setColor(220,220,0);
setJustification("left");
drawString("Add Remove", singX1+2,singY1+31) ;
setColor(220,0,0);
setLineWidth(2);
drawLine (singX1+singX2-2, singY1+18, singX1+singX2-13, singY1+singY2-2);
drawLine (singX1+singX2-2, singY1+singY2-2, singX1+singX2-13, singY1+18);
setLineWidth(largeline);
nbcolX1=singX1+singX2+3;
nbcolX2=50;
nbcolY1=singY1;
nbcolY2=singY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (nbcolX1, nbcolY1, nbcolX2, nbcolY2);
setColor (90,90,130);
fillRect (nbcolX1+1, nbcolY1+1, nbcolX2-2, nbcolY2-2);
setColor(140,140,180);
box3x=nbcolX1+nbcolX2-17;box3y=nbcolY1+3;
adjustBoxes(box3x,box3y,1,0,0,0);
setColor(80,80,120);
fillRect (nbcolX1+1, (nbcolY1+15), nbcolX2-19, 15);
setFont("SansSerif", 12,"antialiased");setColor(220,220,0);setJustification("center");
drawString("nCol.", nbcolX1+1+(nbcolX2-17)/2,nbcolY1+15) ;
setColor(255,200,50);setFont("SansSerif", 12,"bold");
drawString(toString(nbcol), nbcolX1+1+(nbcolX2-17)/2,nbcolY1+31) ;
nblineX1=nbcolX1+nbcolX2+3;
nblineX2=50;
nblineY1=nbcolY1;
nblineY2=nbcolY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (nblineX1, nblineY1, nblineX2, nblineY2);
setColor (90,90,130);
fillRect (nblineX1+1, nblineY1+1, nblineX2-2, nblineY2-2);
setColor(140,140,180);
box4x=nblineX1+nblineX2-17;box4y=nblineY1+3;
adjustBoxes(box4x,box4y,1,0,0,0);
setColor(80,80,120);
fillRect (nblineX1+1, (nblineY1+15), nblineX2-19, 15);
setFont("SansSerif", 12,"antialiased");setColor(220,220,0);setJustification("center");
drawString("nLin.", nblineX1+1+(nblineX2-17)/2,nblineY1+15) ;
setColor(255,200,50);setFont("SansSerif", 12,"bold");
drawString(toString(nbline), nblineX1+1+(nblineX2-17)/2,nblineY1+31) ;
HLboxX1=nblineX1+nblineX2+3;
HLboxX2=30;
HLboxY1=nblineY1;
HLboxY2= nblineY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (HLboxX1, HLboxY1, HLboxX2, HLboxY2);
setColor (90,90,130);
fillRect (HLboxX1+1, HLboxY1+1, HLboxX2-2, HLboxY2-2);
setColor (255,20,20);
HLcurs ();
HRboxX1=HLboxX1+HLboxX2+3;
HRboxX2=30;
HRboxY1=HLboxY1;
HRboxY2= HLboxY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (HRboxX1, HLboxY1, HRboxX2, HLboxY2);
setColor (90,90,130);
fillRect (HRboxX1+1, HRboxY1+1, HRboxX2-2, HRboxY2-2);
setColor (255,20,20);
HRcurs ();
LLboxX1=HRboxX1+HRboxX2+3;
LLboxX2=30;
LLboxY1=HRboxY1;
LLboxY2= HRboxY2;
setColor(140,140,180);
setLineWidth(largeline);
drawRect (LLboxX1, LLboxY1, LLboxX2, LLboxY2);
setColor (90,90,130);
fillRect (LLboxX1+1, LLboxY1+1, LLboxX2-2, LLboxY2-2);
setColor (255,20,20);
LLcurs ();
gridCx1=LLboxX1+LLboxX2+3;
gridCx2=40;
gridCy1=LLboxY1;
gridCy2=LLboxY2;
setColor (90,90,130);
fillRect (gridCx1+1, gridCy1+1, gridCx2-2, gridCy2-2);
setColor(140,140,180);
setLineWidth(largeline);
drawRect (gridCx1, gridCy1, gridCx2, gridCy2);
drawLine(gridCx1, (gridCy1+gridCy2/2), gridCx1+gridCx2-1, (gridCy1+gridCy2/2));
setFont("SansSerif", 12,"antialiased");
setColor(220,220,0);
setJustification("center");
drawString("Grid:", gridCx1+1+(gridCx2)/2,gridCy1+15);
drawString("Model", gridCx1+1+(gridCx2)/2,gridCy1+32);
setColor(140,140,180);
endx1=gridCx1+gridCx2+3; endx2=(Lpalette-distBord-endx1); endy1=gridCy1; endy2=gridCy2;
drawRect (endx1,endy1,endx2, endy2);
setColor (90,90,130);
fillRect (endx1+1, endy1+1, endx2-2, endy2-2);
setFont("SansSerif", 12,"bold");
setColor(255,150,0);
setJustification("center");
drawString("END:\nQuit", endx1+(endx2)/2,endy1+15);
setColor (255,20,20);
setBatchMode("exit and display");
setLocation (0,95);
run("View 100%");
}
function makeSampleLut (kindlut,xl,yl) {
makeTemps (0);
newImage("lut", "8-bit Ramp", 27, 10, 1);
run("Rotate 90 Degrees Left");
if (kindlut==0) {run("Grays");}
if (kindlut==1) {run("Grays");run("Invert");}
if (kindlut==2) {run("Fire");}
if (kindlut==3) {if (File.exists(getDirectory("imagej")+"luts/royal.lut")) {run("royal");}
else {showMessage ("The \"royal\" LUT isn't available in this ImageJ configuration.\nUpdate LUTs to install it. \"spectrum\" LUT will be used.");run("Spectrum");}
}
run("Select All");
run("Copy");
close();
selectImage (paletteName);
makeRectangle(xl,yl,10,27);
run("Paste");
run("Select None");
makeTemps (1);
selectImage (tempclip); close ();
selectImage (paletteName);
}
function applyLut () {
run("Undo");
setBatchMode(true);
makeTemps (0);
makeWork ();
run("Grays");
if (enhenceChoice ==1) {run("Enhance Contrast", "saturated=["+sat+"] normalize");}
if (lutChoice==1) {run("Grays");run("Invert");}
if (lutChoice==2) {run("Fire");}
if (lutChoice==3) {if (File.exists(getDirectory("imagej")+"luts/royal.lut")) {run("royal");} else {run("Spectrum");}}
run("Size...", "width=["+xSizeBlot/blotscale+"] height=["+ySizeBlot/blotscale+"] interpolate");
run("Select All");run("Copy");
run("Grays");
selectImage (paletteName);
makeRectangle (blotx1, bloty1, xSizeBlot/blotscale, ySizeBlot/blotscale);
run("Paste");
run("Select None");
makeTemps (1);
selectImage (paletteName);
setBatchMode(false);
}
function checkLUT (clickx,clicky) {
test=0;
if (clicky >= (lutY1+2) && clicky < (lutY1 + lutY2-1)) {
if (clickx >= (lutX1+2) && clickx < (lutX1+2 +10)) {
lutChoice=0; lutDisplay="LUT: Grey";test=1; }
if (clickx >= (lutX1+14) && clickx < (lutX1+14 +10)) {
lutChoice=1; lutDisplay="LUT: Invert Grey";test=1;
}
if (clickx >= (lutX1+26) && clickx < (lutX1+26 +10)) {
lutChoice=2; lutDisplay="LUT: Fire";applyLut ();test=1;
}
if (clickx >= (lutX1+38) && clickx < (lutX1+38 +10)) {
lutChoice=3;applyLut ();test=1;
if (File.exists(getDirectory("imagej")+"luts/royal.lut")) {lutDisplay="LUT: Royal";} else {lutDisplay="LUT: Spectrum";}
}
}
return test;
}
function satHisto (variation) {
if ((sat+variation) >= 0) {
sat = sat+variation;
enhenceChoice=1;
if (sat<0.001) sat=0;
}
applyLut ();
test3cursor ();
measureCircle ();
KindofArea ="Interface";
if (enhenceChoice == 1) {histo="Normalized Contrast Sat="+ d2s(sat,2)+"%";} else {histo="Initial Contrast";}
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + histo + radius+ kindofColoBox + " "+ SelectedColor);
}
function setColNumber (incrValue) {
if ((nbcol + incrValue) > 1) {
nbcol=nbcol+incrValue;
setBatchMode(true);
updatGridRef (0,1,0);
setColor(80,80,120);
fillRect (nbcolX1+1, (nbcolY1+15), nbcolX2-19, 15);
setColor(255,200,50);setFont("SansSerif", 12,"bold");setJustification("center");
drawString(toString(nbcol), nbcolX1+1+(nbcolX2-17)/2,nbcolY1+31) ;
KindofArea="Interface";
if (incrValue > 0) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": One added column "+ kindofColoBox + " "+ SelectedColor);
if (incrValue < 0) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": One suppressed column "+ kindofColoBox + " "+ SelectedColor);
}
updateSingleStatusInfo ();
}
function setLineNumber (incrValue) {
if ((nbline + incrValue) > 1) {
nbline=nbline+incrValue;
setBatchMode(true);
updatGridRef (0,1,0);
setColor(80,80,120);
fillRect (nblineX1+1, (nblineY1+15), nblineX2-19, 15);
setColor(255,200,50);setFont("SansSerif", 12,"bold");setJustification("center");
drawString(toString(nbline), nblineX1+1+(nblineX2-17)/2,nblineY1+31) ;
KindofArea="Interface";
if (incrValue > 0) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": One added line "+ kindofColoBox + " "+ SelectedColor);
if (incrValue < 0) display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": One suppressed line "+ kindofColoBox + " "+ SelectedColor);
}
updateSingleStatusInfo ();
}
function display (ecriture) {
setBatchMode(true);
setColor(80,80,120);
fillRect (xDisplay+1, yDisplay+1, larDisplay-2, Hdisplay-2);
setColor(220,220,0);
setFont("SansSerif", 12,"antialiased");
setJustification("center");
drawString(ecriture, xDisplay+1+(larDisplay-2)/2,yDisplay+18) ;
setJustification("left");
}
function checkInitColor () {
// get and store initial foreground, background and selection colors
if (initselectionColor == "") {
initselectionColor=getSelectionColors(call("ij.gui.Roi.getColor"));
if (selectionColor == "") selectionColor=initselectionColor;
}
if (initForGColor == "") {
initForGColor = getColorSetting("foreground");
if (ForGColor == "") ForGColor= initForGColor;
}
if (initBackGColor == "") {
initBackGColor =getColorSetting("background");
if (BackGColor == "") BackGColor = initBackGColor;
}
}
function setColorComponent (forg,bacg,sel) {
// set the foreground, background and selection colors
run("Colors...", "foreground=["+forg+"] background=["+bacg+"] selection=["+sel+"]");
}
function getColorValues(ColorName) {
// specific to foreground color
if (ColorName == "yellow") {r =255 ; g =255 ; b =0;}
if (ColorName == "red") {r =255 ; g =0 ; b =0;}
if (ColorName == "green") {r =0 ; g =255 ; b =0;}
if (ColorName == "blue") {r =0 ; g =0 ; b =255;}
if (ColorName == "magenta") {r =255 ; g =0 ; b =255;}
if (ColorName == "cyan") {r =0 ; g =255 ; b =255;}
if (ColorName == "orange") {r =255 ; g =200 ; b =0;}
if (ColorName == "black") {r =0 ; g =0 ; b =0;}
if (ColorName == "white") {r =255 ; g =255 ; b =255;}
}
function getColorSetting(KindColor) {
// specific to background and foreground colors
// get the current red, green and blue values
setBatchMode(true);
newImage("Test Image color", "RGB White", 1, 1, 1);
testimage=getImageID();
// derived from Wayne Rasband code
value = getPixel(0,0);
if (KindColor == "background") {makeRectangle(0,0,1,1);run("Clear");run("Select None");}
if (KindColor == "foreground") {fillRect(0,0,1,1);}
color = getPixel(0,0);
setPixel(0,0, value);
red = (color>>16)&0xff; // extract red byte (bits 23-17)
green = (color>>8)&0xff; // extract green byte (bits 15-8)
blue = color&0xff ; // extract blue byte (bits 7-0)
colorName=getColorName(toString(red),toString(green),toString(blue));
getColorValues(ForGColor); setColor (r,g,b);
if (isActive(testimage) ==1) {close ();setBatchMode(false);}
return colorName;
}
function getSelectionColors (color) {
// specific to color selection
// decodes a color in the form "java.awt.Color[r=255,g=255,b=0]"
red = substring(color, (indexOf(color, "r=")+2), (indexOf(color, "g=")-1));
green= substring(color, (indexOf(color, "g=")+2), (indexOf(color, "b=")-1));
blue= substring(color, (indexOf(color, "b=")+2), indexOf(color, "]"));
colorName=getColorName(red,green,blue);
return colorName;
}
function getColorName(r,g,b) {
ColorName="";
if (r=="255" && g=="255" && b=="0") ColorName ="yellow";
if (r=="255" && g=="0" && b=="0") ColorName ="red";
if (r=="0" && g=="255" && b=="0") ColorName ="green";
if (r=="0" && g=="0" && b=="255") ColorName ="blue";
if (r=="255" && g=="0" && b=="255") ColorName ="magenta";
if (r=="0" && g=="255" && b=="255") ColorName ="cyan";
if (r=="255" && g=="200" && b=="0") ColorName ="orange";
if (r=="0" && g=="0" && b=="0") ColorName ="black";
if (r=="255" && g=="255" && b=="255") ColorName ="white";
return ColorName;
}
function HautGauche (clickx,clicky,ansvers) {
if (ansvers == 0) {
if (clickx > HLboxX1 && clickx < (HLboxX1+HLboxX2) && clicky > HLboxY1 && clicky < (HLboxY1+HLboxY2)) {
if (DotStatus == "Single") resetblot (1,1,1,0);
DotStatus = "Grid";
setBatchMode(true);
updateSingleStatusInfo ();
updatGridRef (0,1,0);
ansvers1=0;ansvers2=0;
statutHL=1;statutHR=0;statutLL=0;
ereaseCursor ();
makeCursor((HLX+blotx1),(HLY+bloty1),w,h,1);
testCursButtonColor (0,0,0,1,"HL");
testCursButtonColor (1,0,0,0,"HL");
if (HLX !=0 && HLY !=0) {ansvers1=1;} else {ansvers1 = 0;}
KindofArea ="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": High left dot setting "+ kindofColoBox + " "+ SelectedColor);
}
}
if (ansvers == 1) {
if (statutHL == 1) {
ereaseCursor ();
statutHL = 0;
tempHLX=HLX;tempHLY=HLY;
HLX= xx-blotx1; HLY=yy-bloty1;
testCursButtonColor (0,0,1,0,"HL");
KindofArea ="Interface";
updatGridRef (0,1,0);
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Grid measure mode "+ kindofColoBox + " "+ SelectedColor);
if (gridTest (1) == 0) {HLX=tempHLX;HLY=tempHLY;updatGridRef (0,1,0);HautGauche ((HLboxX1+2),(HLboxY1+2),0);}
}
}
}
function HautDroite (clickx,clicky,ansvers) {
if (ansvers == 0) {
if (clickx > HRboxX1 && clickx < (HRboxX1+HRboxX2) && clicky > HRboxY1 && clicky < (HRboxY1+HRboxY2)) {
if (DotStatus == "Single") resetblot (1,1,1,0);
DotStatus = "Grid";
setBatchMode(true);
updateSingleStatusInfo ();
updatGridRef (0,1,0);
ansvers1=0;ansvers2=0;
statutHR=1;statutHL=0;statutLL=0;
ereaseCursor ();
makeCursor((HRX+blotx1),(HRY+bloty1),w,h,1);
testCursButtonColor (0,0,0,1,"HR");
testCursButtonColor (1,0,0,0,"HR");
if (HRX !=0 && HRY !=0) {ansvers1=1;} else {ansvers1 = 0;}
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": High right dot setting "+ kindofColoBox + " "+ SelectedColor);
}
}
if (ansvers == 1) {
if (statutHR == 1) {
ereaseCursor ();
statutHR = 0;
tempHRX=HRX; tempHRY=HRY;
HRX= xx-blotx1; HRY=yy-bloty1;
testCursButtonColor (0,0,1,0,"HR");
KindofArea ="Interface";
updatGridRef (0,1,0);
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Grid measure mode "+ kindofColoBox + " "+ SelectedColor);
if (gridTest (1) == 0) {HRX=tempHRX;HRY=tempHRY;updatGridRef (0,1,0);HautDroite ((HRboxX1+2),(HRboxY1+2),0);}
}
}
}
function BasGauche (clickx,clicky,ansvers) {
if (ansvers == 0) {
if (clickx > LLboxX1 && clickx < (LLboxX1+LLboxX2) && clicky > LLboxY1 && clicky < (LLboxY1+LLboxY2)) {
if (DotStatus == "Single") resetblot (1,1,1,0);
DotStatus = "Grid";
setBatchMode(true);
updatGridRef (0,1,0);
updateSingleStatusInfo ();
ansvers1=0;ansvers2=0;
statutLL=1;statutHR=0;statutHL=0;
ereaseCursor ();
makeCursor((LLX+blotx1),(LLY+bloty1),w,h,1);
testCursButtonColor (0,0,0,1,"LL");
testCursButtonColor (1,0,0,0,"LL");
if (LLX !=0 && LLY !=0) {ansvers1=1;} else {ansvers1 = 0;}
KindofArea="Interface";
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Low left dot setting "+ kindofColoBox + " "+ SelectedColor);
}
}
if (ansvers == 1) {
if (statutLL == 1) {
ereaseCursor ();
statutLL=0;
tempLLX=LLX; tempLLY=LLY;
LLX= xx-blotx1; LLY=yy-bloty1;
testCursButtonColor (0,0,1,0,"LL");
KindofArea ="Interface";
updatGridRef (0,1,0);
display ("Blot Cursor coordinates: x="+ floor(xx-blotx1) + " \("+ floor(xx-blotx1)*blotscale +"\) " +", y="+floor(yy-bloty1) + " \("+ floor(yy-bloty1)*blotscale +"\)" +"\n" +"Integrated Area=" + theVolume+" "+ "\("+KindofArea + "\) " + ": Grid measure mode "+ kindofColoBox + " "+ SelectedColor);
if (gridTest (1) == 0) {LLX=tempLLX;LLY=tempLLY;updatGridRef (0,1,0);BasGauche ((LLboxX1+2),(LLboxY1+2),0);}
}
}
}
function updatGridRef (showM,showR,showG) {
showmes=showM;showrep=showR;showgrid=showG;
gridAnalyse ();
updateThePalette ();
showmes=0;showrep=0;showgrid=0;
}
function updateRefCircle (testxcercle,testycercle) {
possible=1;
if (testxcercle > 0 && testycercle >0) {
if ((testxcercle-selectionRayon) < 0) {possible=0;}
if ((testycercle-selectionRayon) < 0) {possible=0;}
if ((testxcercle+selectionRayon) >= (xSizeBlot/blotscale)) {possible=0;}
if ((testycercle+selectionRayon) >= (ySizeBlot/blotscale)) {possible=0;}
}
return possible;
}
function testCursButtonColor (oneclick,move,unclick,update,kind) {
if (statutHR == 1 && kind !="none") {setColor (255,255,20);HRcurs ();}
if (statutHR == 0 && ansvers1==0 && ansvers2==1 && kind == "HR") {setColor (20,255,20);HRcurs ();}
if (statutHL == 1 && kind !="none") {setColor (255,255,20);HLcurs ();}
if (statutHL == 0 && ansvers1==0 && ansvers2==1 && kind == "HL") {setColor (20,255,20);HLcurs ();}
if (statutLL == 1 && kind !="none") {setColor (255,255,20);LLcurs ();}
if (statutLL == 0 && ansvers1==0 && ansvers2==1 && kind == "LL") {setColor (20,255,20); LLcurs ();}
if (update ==1 && kind !="none") {
if (kind =="LL") {
if (HRX !=0 && HRY !=0) {setColor (20,255,20);HRcurs ();} else {setColor (255,20,20);HRcurs ();}
if (HLX !=0 && HLX !=0) {setColor (20,255,20);HLcurs ();} else {setColor (255,20,20);HLcurs ();}
}
if (kind =="HL") {
if (HRX !=0 && HRY !=0) {setColor (20,255,20);HRcurs ();} else {setColor (255,20,20);HRcurs ();}
if (LLX !=0 && LLX !=0) {setColor (20,255,20);LLcurs ();} else {setColor (255,20,20);LLcurs ();}
}
if (kind =="HR") {
if (HLX !=0 && HLX !=0) {setColor (20,255,20);HLcurs ();} else {setColor (255,20,20);HLcurs ();}
if (LLX !=0 && LLX !=0) {setColor (20,255,20);LLcurs ();} else {setColor (255,20,20);LLcurs ();}
}
}
if (kind =="none") {
if (HRX !=0 && HRY !=0) {setColor (20,255,20);HRcurs ();} else {setColor (255,20,20);HRcurs ();}
if (HLX !=0 && HLX !=0) {setColor (20,255,20);HLcurs ();} else {setColor (255,20,20);HLcurs ();}
if (LLX !=0 && LLX !=0) {setColor (20,255,20);LLcurs ();} else {setColor (255,20,20);LLcurs ();}
}
}
function LLcurs () {
drawLine (LLboxX1+1, LLboxY1+LLboxY2-8, LLboxX1+LLboxX2-2, LLboxY1+LLboxY2-8);
drawLine (LLboxX1+6, LLboxY1+1, LLboxX1+6, LLboxY1+LLboxY2-2);
}
function HLcurs () {
drawLine (HLboxX1+1, HLboxY1+5, HLboxX1+HLboxX2-2, HLboxY1+5);
drawLine (HLboxX1+6, HLboxY1+1, HLboxX1+6, HLboxY1+HLboxY2-2);
}
function HRcurs () {
drawLine (HRboxX1+1, HRboxY1+5, HRboxX1+HRboxX2-2, HRboxY1+5);
drawLine (HRboxX1+HRboxX2-6, HRboxY1+1, HRboxX1+HRboxX2-6, HRboxY1+HRboxY2-2);
}
function test3cursor () {
// check for the single measure or grid analysis graphic update
if (DotStatus == "Grid") {
updatGridRef (0,1,0);
}
if (DotStatus == "Single") {
statutHL =0; statutHR =0; statutLL =0;
updatGridRef (1,0,0);
}
}
function gridTest (message) {
testgrid=1;
if (HLX >= HRX && HLX != 0 && HRX != 0 && testgrid != 0) {if (message ==1) {showMessage ("High Left dot must be at the left of the High Right dot");} testgrid=0;}
if (HLY >= LLY && HLY != 0 && LLY != 0 && testgrid != 0) {if (message ==1) {showMessage ("High Left dot must above the Low Left dot");} testgrid=0;}
if (HRY >= LLY && HRY != 0 && LLY != 0 && testgrid != 0) {if (message ==1) {showMessage ("High Right dot must above the Low Left dot");} testgrid=0;}
if (LLX >= HRX && LLX != 0 && HRX != 0 && testgrid != 0) {if (message ==1) {showMessage ("Low Left dot must be at the left of the High Right dot");} testgrid=0;}
return testgrid;
}
function gridAnalyse () {
Ax=0;XhorizontalOrd=0;Ay=0;YhorizontalOrd=0;spaceX=0;spaceY=0;deltaspaceY=0;deltaspaceY=0;
testgrid = 1;
if (gridTest (0) != 0) {
alphaX = atan2 ((HRY - HLY),(HRX - HLX));
spaceX = ((HRX - HLX)/cos(alphaX));
deltaspaceX = floor (spaceX / (nbcol-1));
deltaspaceX2 = deltaspaceX -2*selectionRayon;
alphaY = atan2 ((LLY - HLY),(LLX - HLX));
spaceY = ((LLX - HLX)/cos(alphaY));
if (floor(alphaY*(180/PI)) ==90) {spaceY=LLY - HLY;}
deltaspaceY = floor (spaceY / (nbline-1));
deltaspaceY2 = deltaspaceY -2*selectionRayon;
delX=sin (PI/2 -alphaY) * spaceY;
LRX=floor (HRX+delX);
delY=sin (alphaX) * spaceX;
LRY=floor (LLY+delY);
if (deltaspaceX2 <1) {
if (HRX>0 && HLX>0 ) {
waitForUser("Setting mistake","Horizontal number of dots \(\"nCol.\"\) incompatible with this circle radius \n\(\"High Left\" and \"High Right\" grid cursor have been reinitialized\)");
HRX=0; HRY=0;
HLX=0; HLY=0;
LRX=0; LRY=0;
testgrid=0;
}
}
if (deltaspaceY2 <1) {
if (LLX>0 && HLX>0 ) {
waitForUser("Setting mistake","Vertical number of dots \(\"nLin.\"\) incompatible with this circle radius \n\(\"High Left\" and \"Low Left\" grid cursor have been reinitialized\)");
HLX=0; HLY=0;
LLX=0; LLY=0;
LRX=0; LRY=0;
testgrid=0;
}
}
if (testgrid==1) {
Ax=tan (alphaX);
XhorizontalOrd=(HLY+bloty1)-((HLX+blotx1) * tan (alphaX));
Ay=tan (alphaY);
YhorizontalOrd=(HLY+bloty1)-((HLX+blotx1) * tan (alphaY));
}
}
}
function doBlotAnalyse() {
// prepare the dot blot initial image to the analysis
DotStatus = "Single";
enhenceChoice=0;sat=0;
checkInitColor ();
if (isOpen(measurementTab)) {
selectWindow(measurementTab);
print(measurementTabEXL, "\\Clear");
xmes=0;ymes=0;theVolume="";resultListSize=0;lastmesnumber=0;
}
if (isOpen(windowTabName)) {
selectWindow(windowTabName);
print(nameOfGridTab, "\\Clear");
}
Ax=0;XhorizontalOrd=0;Ay=0;YhorizontalOrd=0;spaceX=0;spaceY=0;deltaspaceY=0;deltaspaceY=0;
xmes=0;ymes=0;theVolume="";resultListSize=0;lastmesnumber=0;
blotscale=0;
blotName=getTitle; blotinitName=blotName;
folderpath =getDirectory("image");
HRX=0;HLX=0;LLX=0;HRY=0;HLY=0;LLY=0;
LRX=0;LRY=0;
if (blotName == winName2 || blotName == paletteName) {
if (blotName == winName2) exit ("Analyse doesn't work onto \""+ winName2 + "\" windows.");
if (blotName == paletteName) exit ("Analyse doesn't work onto \""+ paletteName + "\" windows.");
}
if (bitDepth() !=8) {showMessageWithCancel ("Conversion into 8 bit will be performed."); run("8-bit");}
xSizeBlot=getWidth(); ySizeBlot=getHeight();
subTitleofImage= getInfo("image.subtitle");
if (lastIndexOf (blotName, "-DA") > 0) {exit ("Start from the original image (without the \"-DA\" suffix).");}
if (lastIndexOf(blotName, ".") > 0) {
blotinitName=substring(blotName, 0, lastIndexOf(blotName, "."));
blotName= substring(blotName, 0, lastIndexOf(blotName, "."));
}
blotName= blotName + "-DA";
run("Duplicate...", "title=["+blotName+"]");
if (indexOf(subTitleofImage, "(inverting LUT)") > 0) {;run("Grays");run("Invert");}
Dialog.create("Pre-treatment Choices \(2D Rolling Ball\)");
Dialog.addChoice("Subtract Background ?", newArray ("None","Linear","Paraboloid"), rmBack);
Dialog.addNumber("Radius for 2D Rolling Ball subtract background ?", defaultradius, 0, 3, "");
Dialog.show();
rmBack=Dialog.getChoice();
defaultradius=Dialog.getNumber();
if (rmBack != "None") {
if (rmBack =="Linear") {run("Subtract Background...", "rolling=["+defaultradius+"] light");}
if (rmBack =="Paraboloid") {run("Subtract Background...", "rolling=["+defaultradius+"] light sliding");}
}
if (xSizeBlot+Leftmarge+Rightmarge > screenWidth || ySizeBlot > (screenHeight - Hinter-Topmarge-Botommarge-70-100)) {
test=(screenHeight - Hinter-Topmarge-Botommarge-70-100);
a=ySizeBlot;
while (a > test) {
blotscale=(blotscale+2);
a=floor(a/blotscale);
}
showMessageWithCancel ("The size of the image \""+ blotName + "\" is too high for the screen resolution.\nIt will be rescaled for visualisation \(divided by a factor "+blotscale+"\).");
}
if (blotscale == 0) blotscale=1;
test=xSizeBlot;
while ( (test/blotscale/2 - floor (test/blotscale/2)) !=0 ) {test=test-1;} // x impair showMessage ("x impair:" + test);
xSizeBlot=test;
test=ySizeBlot;
while ((test/blotscale/2 - floor (test/blotscale/2)) !=0 ) {test=test-1;} // y impair showMessage ("y impair:" + test);
ySizeBlot=test;
drawPalette ();
palette=1;dyn=1;reponse=0;cancel=0;cursok=0;
applyLut ();
setTool(10);
}
// saving a tab as excel type file
function saveTab (path,WinTab) {
if (isOpen(WinTab)) {
if (path == "") {
selectWindow (WinTab);
run("Input/Output...", "jpeg=75 gif=-1 file=.xls");
saveAs("Text");
}
if (path != "") {
a=0;
selectWindow(WinTab);
thepath = path+blotinitName+"-"+WinTab+".xls";
while ( File.exists(thepath) ) {
if (a != 0) thepath = path+blotinitName+"-"+WinTab+ "-" + toString (a) +".xls"; a ++;
}
saveAs("Text", thepath);
}
}
}
function SaveDocRes(path) {
if (path != "") {
if (dyn ==1) dyn=0;
if (isOpen(windowTabName) || isOpen(measurementTab) || isOpen(endPalette) || isOpen(gridModelName) ) {
a=0;
if (path == "--") path=getDirectory("Choose Master Destination Directory ");
thepath = path+blotinitName+"_"+resultFolderName + File.separator;
while ( File.exists(thepath) ) {
if (a != 0) thepath = path+blotinitName+"_"+resultFolderName+ "-"+ toString (a)+ File.separator;
a ++;
}
File.makeDirectory(thepath);
if (!File.exists(thepath)) exit("Unable to create directory, something wrong in the ImageJ folder");
saveTab (thepath,windowTabName);
saveTab (thepath,measurementTab);
if (isOpen(blotName)) {
setBatchMode(true);
selectImage(blotName);
nom=blotName+".tif";
run("Duplicate...", "title=["+nom+"]");
save(""+thepath+""+ nom +"");close();
}
if (isOpen(gridModelName)) {
setBatchMode(true);
selectImage(gridModelName);
nomSavedModel=blotinitName+"-"+gridModelName+".tif";
run("Duplicate...", "title=["+nomSavedModel+"]");
save(""+thepath+""+ nomSavedModel +"");close();
}
if (isOpen(endPalette)) {
setBatchMode(true);
selectImage(endPalette);
nomSavedPalette=endPalette+".tif";
run("Duplicate...", "title=["+nomSavedPalette+"]");
save(""+thepath+""+ nomSavedPalette +"");close();
}
} else {showMessage ("No document found");}
if (isOpen(paletteName)) {selectImage (paletteName);dyn=1;}
}
}
function CloseDocRes () {
if (isOpen(endPalette)) {selectImage(endPalette);close ();}
if (isOpen(blotName)) {selectImage(blotName);close ();}
if (isOpen(gridModelName)) {selectImage(gridModelName);close ();}
if (isOpen(measurementTab)) {selectWindow(measurementTab);print(measurementTabEXL, "\\Close");}
if (isOpen(windowTabName)) {selectWindow(windowTabName);print(nameOfGridTab, "\\Close");}
}
function netTest () {
if (indexOf (File.openUrlAsString(urllist), errorNetMessage) >0) exit("You need an internet access to run this function.");
}
function abortProcess () {setKeyDown("Esc");}
function about1() {
about="";
about=about+"\n -- Dot Blot Analyzer --";
about=about +"\n\nAuthor: Gilles Carpentier"+"\nFaculte des Sciences et Technologies, Universite Paris 12 Val de Marne, France.";
about=about+"\n----------------------------------------------------------------------------------------------------";
about=about+"\n* Description:";
about=about+"\n";
about=about+"\n This toolset allows easy analyse of dot blot images, using a graphical interface helper.";
about=about+"\n----------------------------------------------------------------------------------------------------";
about=about+"\n\n* Notice - ImageJ Menu Tool Bar:
about=about+"\n";
about=about+"\n - The \"Dot Blot Analysis Menu\" regroups analyse and training functions:";
about=about+"\n - \"Analyse a Dot Blot\" displays the graphical interface required to analyse an opened dot blot image.";
about=about+"\n - \"Download\/Open The ImageJ Demo Dot Blot Image \(28 wells\)\" opens the ImageJ Dot Blot image sample";
about=about+"\n \(28 dots\).
about=about+"\n - \"Download\/Open Demo Dot Blot Image \(96 wells\)\") opens a demo image \(96 wells\) useful to test the";
about=about+"\n program with other settings than the defaults ones.";
about=about+"\n - The \"Measurement Documents Menu\" regroups tabs and analysed images management functions:";
about=about+"\n - \"Save Results Documents\" saves every document concerning one analysis \(model, tabs, images\) into";
about=about+"\n a folder at the user choiced master repertory."
about=about+"\n - \"Save Results Documents at the Dot Blot Image Location\" saves every documents concerning one analysis";
about=about+"\n \(model, tabs, images\) into a folder placed at the dot blot image repertory."
about=about+"\n - \"Close Results Documents\" closes every document concerning one analysis \(models, tabs, images\)";
about=about+"\n - \"Save Grid Results Table as Excel Type File\" saves the current grid analysis table at the user's choice";
about=about+"\n location.";
about=about+"\n - \"Save Single Measurements Table as Excel Type File\" saves the current manual analysis table at the ";
about=about+"\n user's choice location."
about=about+"\n - \"Save Grid Results Table as Excel Type File at the Dot Blot Image Location\" saves the current grid analysis ";
about=about+"\n table in the dot blot image repertory.";
about=about+"\n - \"Save Single Measurements Table as Excel Type File at the Dot Blot Image Location\" saves the current";
about=about+"\n manual analysis table.";
about=about+"\n - Click on the \"Abort Process\" ImageJ tool bar icon to cancel demo downloading or erease the palette's cursor.";
about=about+"\n - Click on the \"On Line Documentation\" ImageJ tool bar icon for on line documentation and tutorial."; about=about+"\n - Click on the \"Version and Update Infos\" ImageJ tool bar icon to look for new beta versions.";
about=about+"\n";
about=about+"\n* Notice - Graphical Interface:";
about=about+"\n";
about=about+"\n Once activated, the \"Dot Blot Analysis Menu\" builds a graphical interface \"Palette\"containing a dot blot ";
about=about+"\n preview. Here are the \"clickable\" available actions:";
about=about+"\n - Volume measurement using the composite cursor:";
about=about+"\n - Activate the measurement cursor by staying clicked and moving into the dot blot preview area. Cursor";
about=about+"\n ploted and real coordinates are dynamically showed into the display area, the measured volume, is available";
about=about+"\n when unclicked.";
about=about+"\n - Customize the composite cursor aspect:";
about=about+"\n - Optimize the visual aspect by choosing appropriate colors for the circle and the the cross hair of the cursor
about=about+"\n componants, using the colored rectangles.
about=about+"\n - Find a pertinant circle radius by clicking onto the circle containing radius icone. Adjust the cursor circle
about=about+"\n size using the \"+\" and \"-\� subbuttons.
about=about+"\n - Optimize the dot blot preview visualization:";
about=about+"\n - Normalize the histogram from the \"stretch curve\" icon. Adjust the saturation level using the \"+\" and \"-\�
about=about+"\n subbuttons.
about=about+"\n - Choose the appropriate Look Up Table \(LUT\) by clicking into the LUT ramps icone. Restore the initial preview
about=about+"\n properties with the Counterclockwise symbol.";
about=about+"\n - Single measurement recoding in a tab:";
about=about+"\n - Click \"Add\" to generate a tab with the current value given by the cursor, \"Remove\" to delete it. \(CTRL click";
about=about+"\n undo the delete action\)";
about=about+"\n - Erase all the measurements of the tab by the red \"X\". This action in undo by \"CTRL click\".";
about=about+"\n - Grid measurements mode:";
about=about+"\n - Adjust the column \(\"nCol.\"\) and the line \(\"nLin.\"\) numbers, corresponding to the total or sub-area dot ";
about=about+"\n blot to analyse.";
about=about+"\n - Set the three required dots forming angle \(hight-left, hight-right and low-left\) using the three green cross";
about=about+"\n hair icones. Marks can be adjusted, by re-selecting the appropriate cross hair ";
about=about+"\n - Get a modelled image of the grid analysis by clicking on \"Model\".";
about=about+"\n";
about=about+"\n - Shift between the grid measurements mode and the single measurements mode can be performed by clicking";
about=about+"\n onto \"Measurements:\" and \"Grid:\"."
about=about+"\n - \"Cancel\" box closes every thing concerning one analysis, including the Palette.";
about=about+"\n - \"Erase\" box removes every drawed dot contours. They can be redrawed by clicking onto \"Measurements:\" or \"Grid:\"." ;
about=about+"\n";
about=about+"\n - Activate \"End: Quit\" to finish an analyse \(deactivate the Palette, keeping an image or the current drawings\). " ;
about=about+"\n";
about=about+"\n";
about=about+"\n----------------------------------------------------------------------------------------------------";
// from PrintToTextWindow macro available at the http://rsbweb.nih.gov/ij/macros/PrintToTextWindow.txt
// author: Wayne Rasband
title1 = "Info for the Dot Blot Analyzer";
title2 = "["+title1+"]";
f = title2;
if (isOpen(title1)) {
print(f, "\\Update:"); // clears the window
print(f, about);
selectWindow (title1);
} else {
run("New... ", "name="+title2+" type=[Text File] width=80 height=16");
print(f, about);
}
}
function doc () {
netTest ();
showMessageWithCancel ("A notice is avaible on line. Open it with your default web browser?");
run("URL...", "url=["+onlinedoclink +"]");
}
// --- End of code of the macro project ---//
// ----------------------------------//
//
//
//
//
//
//
//
//
//
//
//
//
//
//
// -------------------*** Additionnal code for on line update resources ***-----------------------------
//Developer info
//Kind:Toolset
//Title:"Dot Blot Analyzer"
//Version:1.0
//Date: 24/07/2008
//Origin:NIH
//End info
function VersionInfos () {
// variables for on line update resources
beginsign="//Developer info";endsign="//End info";
kind="toolsets/";
urlrep="http://image.bio.methods.free.fr/ij/ijmacro/dotblot/";
name="Dot Blot Analyzer.txt";
namedev="Dot Blot Analyzer-dev.txt";
favoritefoldername= "Image.Bio.Methods";
version=versionMessage();
if (indexOf(version, "install it?" ) > 0 ) {
macrotext=getdistantmacro (namedev,urlrep);macrolocal="";
macropath=getDirectory("macros")+kind+namedev;
if (File.exists(macropath)) {macrolocal=File.openAsString(macropath);}
if (macrotext != macrolocal) {
//perfom the installation
Dialog.create("New version installation option");
Dialog.addMessage(version);
Dialog.addCheckbox("Install a Plugin Shortcut?", 0);
Dialog.addMessage("(This option provides a shortcut in the plugins menu of ImageJ, making easier\nthe next use of the new installed version).");
Dialog.show();
plugin= Dialog.getCheckbox();
f= File.open(macropath);
print (f,macrotext);
File.close(f);
if (plugin ==1) {InstallPluginsStarter(namedev);}
message="The installation of the "+giveDevInfo (macrotext,1)+ " "+ giveDevInfo (macrotext,2)+ "is completed.";
message=message+ " Do you want to run it?";
showMessageWithCancel(message);
run("Install...", "install=["+macropath+"]");
}
} else {showMessage (version); // comment without installation available}
}
function versionMessage() {
version="";
if (getDirectory("startup") == 0) exit ("Unable to find the startup directory, something wrong in the ImageJ folder");
if (getDirectory("macros") == 0) exit ("Unable to find the macros directory, something wrong in the ImageJ folder");
MacroPath=getDirectory("macros");thismacropath=MacroPath+kind+name;
if (! File.exists(thismacropath)) exit ("This macro has to be recorded under the name of \"" +name+"\"\ninto the \"macros/"+kind+"\" folder of ImageJ.");
macrotext=File.openAsString(thismacropath);
macrotextdistant=getdistantmacro (namedev,urlrep);
version="";macrolocal="";
version=version + "\n \nThis version of the " + giveDevInfo (macrotext,1) + " " + giveDevInfo (macrotext,2);
version=version + "is provided by the " + giveDevInfo (macrotext,5)+ " web site.";
version=version + "\nVersion number: " + giveDevInfo (macrotext,3)+ " - " + giveDevInfo (macrotext,4) +".";
if (macrotextdistant !="" ) {
new=giveDevInfo (macrotextdistant,3);old=giveDevInfo (macrotext,3);
if (new > old) {
macropath=getDirectory("macros")+kind+namedev;
if (File.exists(macropath)) {macrolocal=File.openAsString(macropath);}
if (macrotextdistant != macrolocal) {
update="\n \nA new beta version "+new+ " is available on the " +giveDevInfo (macrotextdistant,5)+ " web site: ";
update=update+ "\n \nDo you want to install it?";
} else {
update ="\n \nThe new "+new+" beta version called \"" +namedev+ "\" provided by \nthe "+giveDevInfo (macrotextdistant,5) +" web site has already be installed";
update = update+ " in the \"" +kind+ "\" repertory \nof ImageJ.";
}
} else {
update="No new Beta version available.";
}
version=version +"\n" + update ;
}
return version;
}
function giveDevInfo (text,n) {
lines=split(text,"\n");
if ( (indexOf(text, beginsign)<0) || (indexOf(text, endsign)<0) ) exit ("Not upgradable macro code.");
for (i=0; lines[i] != endsign; i ++) {}
for (j=i; lines[j] != beginsign; j --) {}
infotext=newArray(i-j-1);
for (i=0; i < infotext.length; i ++) {infotext[i]=lines[i+j+1];}
info=infotext[n-1]; signature=":";
cut = indexOf(info, signature);
info = substring(info,(cut+lengthOf(signature)),lengthOf(info));
return info;
}
// Function giving the content of a distant macro (name) located at the distant repertory (urlrep).
function getdistantmacro (name,urlrep) {
macrotextnih="";
erNetMessage ="Error: ";
testlink = "/ij/macros/Arrays.txt";
if (indexOf (File.openUrlAsString(testlink), erNetMessage) < 0) {
distantmacrolink = urlrep + name;
if (indexOf(distantmacrolink, " ") > -1) {
while (indexOf(distantmacrolink, " ") > -1) {
distantmacrolink=substring(distantmacrolink, 0, (indexOf(distantmacrolink, " ")))+"%20"+substring(distantmacrolink, (indexOf(distantmacrolink, " ")+1),lengthOf(distantmacrolink) );
}
}
showStatus("Internet link...");
macrotextnih =File.openUrlAsString(distantmacrolink);
showStatus("");
} else { showMessage ("No internet connection to looks for beta version.");}
return macrotextnih;
}
function InstallPluginsStarter(macroname) {
// from MacroPluginShortcutsTool.txt
codestarter = "run\(\"Install...\", \"install=[\"+getDirectory(\"macros\")+\""+kind+ macroname + "\]\"\);";
if (getDirectory("plugins") == "") exit ("Unable to find the Plugins directory; something wrong in the ImageJ folder.");
if (endsWith(macroname, ".txt") || endsWith(macroname, ".ijm")) pluginname = substring(macroname, 0, (lengthOf(macroname)-4));
StarterDir = getDirectory("plugins")+favoritefoldername+File.separator;
File.makeDirectory(StarterDir);
if (!File.exists(StarterDir)) exit ("Unable to create "+favoritefoldername+" Macros directory, something wrong in the ImageJ folder.");
starterplugin = StarterDir + pluginname +"_ .ijm";
f= File.open(StarterDir + pluginname +"_ .ijm");
print (f,codestarter);
File.close(f);
showMessage ("The plugin shortcut \"" +pluginname+ "\" will be available after\nImageJ restarting, in the \"Plugins->" + favoritefoldername + "\" menu.");
}
// *** End of additionnal code for on line update ressources ***