Re: pixels coordinates

Posted by Tiago Ferreira-2 on Aug 04, 2009; 2:10pm
URL: http://imagej.273.s1.nabble.com/AltGr-key-tp3691584p3691587.html

matthews <matthews@...> writes:

>
> Dear ImageJ users,
>
> I want to obtain the coordinates of all the pixels of an object.
> When I use getselectioncoordinates I obtain only the pixel coordinates of the
object edge.

> Do you have an easy solution
>
> Thank you for your help
>
> Cédric Matthews
> CNRS - IBDML -  UMR 6216
> coresponsable technique
> Service Imagerie -  Case 907
> Route de luminy
> 13288 Marseille cedex 9
> tél: [phone] / fax: [phone]
>
> matthews@...
> pacaimagerie@...
> http://rtmfm.ibl.fr/
> http://www.gdr2588.cnrs.fr/
>

Dear Cédric

This macro would do that.

---------------------------------------------------
// List All Pixels Inside a ROI
//
// Select 'Image>Adjust>Threshold' before running this macro to list only
// thresholded pixels. For large ROIs it may be rather slow.
// Works with stacks and RGB images;
//
// Tiago Ferreira - 2009.01
//
// Credits: http://rsb.info.nih.gov/ij/macros/js/ListPixelsInROI.js
//          http://rsb.info.nih.gov/ij/macros/tools/ColorPickerTool.txt


   if(selectionType==-1 || selectionType>4 && selectionType!=9)
         exit("Area selection required");
   w=getWidth; h=getHeight; nC=getSliceNumber; nF=nSlices; b=bitDepth;
  getThreshold(minInt, maxInt);
  if(minInt==-1 || maxInt==-1) {minInt=0; maxInt=255;}
   if(nF>1 && b!=24 ) {
         Dialog.create("List ROI Pixels");
         Dialog.addNumber("Start at Slice",nC);
         Dialog.addNumber("End at Slice", nF);
         Dialog.addMessage(" ");
         Dialog.addNumber("Min Intensity", minInt);
         Dialog.addNumber("Max Intensity", maxInt);
         Dialog.show;
         nC=Dialog.getNumber; nF=Dialog.getNumber;
         minInt=Dialog.getNumber; maxInt=Dialog.getNumber;
         if(nC<1 || nC>nF || nF>nSlices || nF<nC)
               exit("Invalid Parameters...");
   } else if(nF>1 && b==24 ) {
         Dialog.create("List ROI Pixels");
         Dialog.addNumber("Start at Slice",nC);
         Dialog.addNumber("End at Slice", nF);
         Dialog.show;
         nC=Dialog.getNumber; nF=Dialog.getNumber;
         if(nC<1 || nC>nF || nF>nSlices || nF<nC)
               exit("Invalid Parameters...");
   } else if(nF==1 && b!=24 ) {
         Dialog.create("List ROI Pixels");
         Dialog.addNumber("Min Intensity", minInt);
         Dialog.addNumber("Max Intensity", maxInt);
         Dialog.show;
         minInt=Dialog.getNumber; maxInt=Dialog.getNumber;
   }

setBatchMode(true);
   count=1; start = getTime;
   f=prepareTable("ROI Pixels List", "#\tX\tY\tZ\tIntensity");
   getSelectionBounds(xTL, yTL, selWidth, selHeight);
   if(selWidth==w) selWidth=selWidth-1;
   if(selHeight==h) selHeight= selHeight-1;
   run("Create Mask"); //make mask img
   m=newArray(w*h);
   for(x=0;x<w;x++)
      for(y=0;y<h;y++)
         m[y*w+x]=getPixel(x,y);
   close; //close mask img
   for (i=nC; i<=nF; i++) {
      call("java.lang.System.gc");
      setSlice(i);
      for(x=xTL;(x<=xTL+selWidth);x++) {
         for(y=yTL;(y<=yTL+selHeight);y++) {
            showStatus("Listing "+i+"/"+nF+"...");
            showProgress(i-1,nF);
            v= getPixel(x, y);
            if (bitDepth==24) {
               r= (v>>16)&0xff;  // extract red byte (bits 23-17)
               g= (v>>8)&0xff;   // extract green byte (bits 15-8)
               b= v&0xff;        // extract blue byte (bits 7-0)
               v1=""+r+","+g+","+b+"";
               maxInt=-1; minInt=-16777216;  //white; black
            } else
               v1=v;  
            if (m[y*w+x]!=0 && v>=minInt && v<=maxInt)
               print (f, count++ +"\t"+x+"\t"+y+"\t"+i+"\t"+v1);
            }
         }
      }
   stop= getTime;  
   showStatus("Finished... ("+count-1+" out of "+(selWidth*selHeight)*(nF-
nC+1)+
   " pixels listed in "+((stop-start)/1000)+" seconds)");
setBatchMode(false);


function prepareTable(title,csvHeadings) {
   title2= "["+title+"]"; f= title2;
   if(isOpen(title))
      print(f, "\\Clear");
   else
      run("New... ", "name="+title2+" type=Table width=250 height=600");
   print(f, "\\Headings:"+csvHeadings);
   return f;
}