Configurable temporary directory when running macros

[k-dominik]

Use-case

When running ilastik via the Fiji plugin in BARD, it is desirable to run ilastik from a different container (to avoid duplication). The plugin writes temporary files per default into /tmp on linux, which is inside the container - so that plugin in and ilastik cannot exchange data.

A solution would be to write to a path in the home folder that is mounted on both the Fiji and the ilastik container

ilastik4ij/src/main/java/org/ilastik/ilastik4ij/util/TempDir.java

Line 58 in a49f4ab

path = Files.createTempDirectory(Objects.requireNonNull(prefix));

I tried

• setting env variables TMP, TEMP, TMP_DIR but it doesn't have an effect
• stating fiji passing the option to the jvm: ImageJ-macosx -- -Djava.io.tempdir=/Users/kutra/scratch but also no effect

cc: @sunyi000

[emilmelnikov]

Setting java.io.tmpdir should definitely work. I tried to run the following test program:

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;

public class TempDirExample {

    public static void main(String[] args) {
        // Get the value of the "java.io.tmpdir" system property
        String tmpdir = System.getProperty("java.io.tmpdir");
        System.out.println("Temporary directory path (java.io.tmpdir): " + tmpdir);
        
        // Create a temporary directory and handle potential IOExceptions
        try {
            // Create a temporary directory
            Path tempDirectory = Files.createTempDirectory("myTempDirPrefix");
            
            // Print the path of the created temporary directory
            System.out.println("Temporary directory created at: " + tempDirectory.toString());
            
        } catch (IOException e) {
            // Handle any I/O error that might occur
            System.err.println("Error while creating a temporary directory: " + e.getMessage());
        }
    }
}

$ java TempDirExample.java
Temporary directory path (java.io.tmpdir): /var/folders/9p/b9r84sb110l14gcn7_3qd4p00000gn/T/
Temporary directory created at: /var/folders/9p/b9r84sb110l14gcn7_3qd4p00000gn/T/myTempDirPrefix12787915166943295779

$ mkdir mytmpdir
$ java -Djava.io.tmpdir=$(realpath mytmpdir) TempDirExample.java
Temporary directory path (java.io.tmpdir): /Users/em/projects/mytmpdir
Temporary directory created at: /Users/em/projects/mytmpdir/myTempDirPrefix11257023116559662220

I suspect that either ImageJ-macosx wrapper script doesn't pass arguments to java, or ImageJ messes with this property itself.

[k-dominik]

Hi @emilmelnikov,

thank you so much for looking into this. I guess then I'll try zulip with the Fiji team...

[k-dominik]

./ImageJ-macosx -Djava.io.tmpdir=/Users/kutra/scratch -- (I had the order wrong (option before the -- and also an extra e in tmpdir...) will set the temporary directory correctly (thank you @ctrueden). @sunyi000, would this work for your use-case?

[sunyi000]

./ImageJ-macosx -Djava.io.tmpdir=/Users/kutra/scratch -- (I had the order wrong (option before the -- and also an extra e in tmpdir...) will set the temporary directory correctly (thank you @ctrueden). @sunyi000, would this work for your use-case?

I will test it out. I think this could fix it. Thanks