« Profile

ImageJ Macro Fragments

Some notes on ImageJ macro

Getting the number of Cores

        
              th = eval("script","Runtime.getRuntime().availableProcessors();");
print(th);

Loading ROIs from a file in Internet

shell command “curl” should be available in your local machine. See here for installation.

1

2

3

4

5

6

7

run("Blobs (25K)");
path = getDirectory('imagej')+"RoiSet.zip";
print(path)
exec("curl", "-LJO", "https://github.com/mutterer/weird/raw/master/RoiSet.zip", "--output", path);
roiManager("Open",path);
roiManager("Show All");
File.delete(path);

Getting Pixel Coordinates within a Polygon ROI

        
              Roi.getContainedPoints(xps, yps); 
for(i=0; i<xps.length; i++) {
    xpos = xps[i];
    ypos = yps[i];
    pixval = getPixel(xpos, ypos);
    print("("+ xpos + ", " + ypos + ") ", pixval);
}

Ways of getting the file basename

        
              filepath = "/my/path/to/great_image.tif";
 
//Method 1, string indexing
basename = substring(filepath, lastIndexOf(filepath, "/")+1, lastIndexOf(filepath, "."));
print("Method 1: ", basename);
 
//Method 2, regular expression
basename = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$2");
print("Method 2: ", basename);
//... in this case, it's also possible to get the parent directry just with a small modification
parent = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$1");
print(".... parent: ", parent);
 
//Method 3, use a specific command
//from ver. 1.52r
basename = File.getNameWithoutExtension(filepath);
print("Method 3: ", basename);
//... it's also possible to get the parent directory with a command. 
parent = File.getDirectory(filepath);
print(".... parent: ", parent);

Convert black pixels to white in RGB image

        
          
          
              
              for (j =0; j<getHeight();j++){
    for (i=0; i<getWidth();i++){
        pix =  getPixel(i, j);
        sum = sumRGB(pix);
        if (sum == 0){
            setPixel(i, j, 0xffffff);
        }
    }
}
 
 
function sumRGB(RGBpixval){
    sum = getR(pix) + getG(pix) + getB(pix);
    return sum;
}
 
function getR(RGBpixval){
    rf = (RGBpixval & 0xff0000)>>16;
    return rf;       
}
function getG(RGBpixval){
    gf = (RGBpixval & 0x00ff00)>>8;
    return gf; 
}
function getB(RGBpixval){
    bf = (RGBpixval & 0x0000ff); 
    return bf;        
}   

            

        
      

Creation Date: 2020/10/21 14:06, Last modified:: 2021/12/07 09:09, Author: Kota Miura, Tags:

Document