Out of memory (sooner or later...)

[Marco Bravi]

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);

[Wayne Rasband]

I ran this macro with

     print(i, nImages);

at the end of the for loop and got

    0 1
    1 2
    2 3
    3 4

in the Log window so it appears that one window was not getting closed.
Adding

     // close all image windows
     while (nImages>0) {
         selectImage(nImages);
         close();
     }

to the end of the loop seems to fix the problem.

-wayne

On Mar 21, 2007, at 9:36 AM, Marco Bravi wrote:

> 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);
>

[Marco Bravi]

Il giorno mer, 21/03/2007 alle 13.07 -0500, Wayne Rasband ha scritto:

> it appears that one window was not getting closed.
> Adding
>
>      // close all image windows
>      while (nImages>0) {
>          selectImage(nImages);
>          close();
>      }
>
> to the end of the loop seems to fix the problem.

Thanks a lot for your help, Wayne (as well as Volker and Michael) for
your helpful hand. The problem is now solved. Hope to be able for
somebody else myself soon!

Bye,

Marco