Out of memory (sooner or later...)

Posted by Marco Bravi on Mar 21, 2007; 3:36pm
URL: http://imagej.273.s1.nabble.com/Out-of-memory-sooner-or-later-tp3699999.html

Dear All,

I am using ImageJ to monitor the hydrolysis of lignocellulosic biomass. As
such, I take timed snapshots of the process, store it and
subsequently analyze them. As the individual treatment takes time, I am
preparing a macro (below) that recursively applies the same processing
sequence
to each image found inside one directory and saves the results of each
analysis in one subdirectory.

Unfortunately, sooner or later (depending on the amount of memory I
dedicate to ImageJ upon startup) the heap memory is exhausted and the
analysis process stops.

I went over and over my (simple) code looking for missing "Close"
commands that would progressively exhaust memory, but did not find any.
However, this is my first experience as a macro coder, neither do I know
much of ImageJ internals.

I would appreciate any hint that could help me chase the bug away.

Best regards to all those working at such a nice, open piece of
software!

Marco Bravi

==== macro ==============
image_dir = getDirectory("Scegli la cartella di base:");
result_dir = image_dir + "risultati/"
start = getTime();
setBatchMode(true); // runs up to 6 times faster
list = getFileList(image_dir);
for (i = 0; i < list.length; i++) {
  if (endsWith(list[i], ".jpg")) {
    open(image_dir + list[i]);
    nome_immagine = getTitle();
    fine_nome = lastIndexOf(nome_immagine, ".jpg");
    nome_immagine_base = substring(nome_immagine, 0, fine_nome);
    rename("mia_immagine");
    run("8-bit");
    run("Enhance Contrast", "saturated=0.5");
    run("Pseudo Flat Field", "mean=150 keep 32-bit");
    imageCalculator("Divide create 32-bit", "mia_immagine","Flat"); //
Abbiamo ottenuto "Result of mia_immagine"
    selectWindow("Flat");
    //close();
    run("Close");
    //wait(2000);
    selectWindow("mia_immagine");
    close();
    selectWindow("Result of mia_immagine");
    run("Threshold");
    run("Fill Holes");
    // Analizziamo immagine binaria: "Result of mia_immagine"
    run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Nothing exclude exclude clear include summarize record");
    // Salviamo il file dei risultati
    nome_out = result_dir + nome_immagine_base + ".txt";
    save_cmd = nome_out;
    selectWindow("Summary of Result of mia_immagine");
    saveAs("Text", save_cmd);
    // Chiudiamo la finestra dei risultati
    selectWindow("Summary of Result of mia_immagine");
    run("Close");
    // Salviamo l'immagine binaria "Result of mia_immagine"
    // con il nome originario
    selectWindow("Result of mia_immagine");
    nome_out = result_dir + nome_immagine;
    saveAs("Jpeg", nome_out);
    wait(2000);
    close();
    wait(2000);
  }
}
//print((getTime()-start)/1000);
//setBatchMode(false);