calling imagej from excel

[Tony Collins-4]

Hi,

I'm trying to open and view files with ImageJ from within a VB excel
macro via the command line. I've modified the 'analyze' demo plugin with
some success (below).

It works unless there is a space in the file path or name. Is there a
trick to this? I've played with square brackets with no luck.

Also, I'd like the use the existing ImageJ if it's open. Is this
possible? It would be nice if the command dialog closed, but not the
ImageJ window.

Here is a snippet from excel where I'm putting the command line string
together:

pluginTxt = "jre\bin\java -Dplugins.dir=plugins -cp ij.jar;.
openfromexcel "

CmdLine = pluginTxt & Range("a1").Value & "\" & Range("A" +
Trim(currentrow)).Value

Where cell A1 in excel is the folder and A'n' the filename.
 
Any advice welcome.

Thanks,
Toby


import ij.plugin.*;
import java.awt.*;
import java.io.*;
import ij.*;
import ij.io.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.*;

/**
This is an example that shows how to write a command line utility that
uses ImageJ
as a library. Use the "Compile and Run" command to compile and test,
then run
from the command line. It requires ImageJ 1.29v or later.
*/
public class openfromexcel implements PlugIn {

    public void run(String arg) {
        OpenDialog od = new OpenDialog("Open...", "");
        if (od.getFileName()==null) return;
        String dir = od.getDirectory();
        if (dir==null)
            return;
        String name = od.getFileName();
        process(dir+name);
    }

    void process(String path) {
    if (IJ.versionLessThan("1.33b")) return;
        IJ.log("opening "+path);
        IJ.run("Bio-Formats Importer (windowless)", "open=[" + path +
"]");
   }

    public static void main(String args[]) {
        if (args.length<1)
            IJ.log("usage: openfromexcel image");
        else {
           new ImageJ(); // open the ImageJ window to see images and
results
            new openfromexcel().process(args[0]);
         //   System.exit(0);
        }
    }

}




Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

[jchanson]

Tony -
        When I've dealt with filenames from VB, I've needed to add quotes
to the filename.  You can either use 4 quotes to insert the quote marks or
the Chr command (but I forget which ascii code goes with quote):
        CmdLine = pluginTxt & """" & Range("a1").Value & "\" & Range("A" +
Trim(currentrow)).Value & """"

Good luck!
Jeff Hanson
Senior Imaging Analyst
Eli Lilly and Company
[hidden email]




Tony Collins <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
12/13/2007 01:20 PM
Please respond to
ImageJ Interest Group <[hidden email]>


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Subject
calling imagej from excel






Hi,

I'm trying to open and view files with ImageJ from within a VB excel
macro via the command line. I've modified the 'analyze' demo plugin with
some success (below).

It works unless there is a space in the file path or name. Is there a
trick to this? I've played with square brackets with no luck.

Also, I'd like the use the existing ImageJ if it's open. Is this
possible? It would be nice if the command dialog closed, but not the
ImageJ window.

Here is a snippet from excel where I'm putting the command line string
together:

pluginTxt = "jre\bin\java -Dplugins.dir=plugins -cp ij.jar;.
openfromexcel "

CmdLine = pluginTxt & Range("a1").Value & "\" & Range("A" +
Trim(currentrow)).Value

Where cell A1 in excel is the folder and A'n' the filename.
 
Any advice welcome.

Thanks,
Toby


import ij.plugin.*;
import java.awt.*;
import java.io.*;
import ij.*;
import ij.io.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.*;

/**
This is an example that shows how to write a command line utility that
uses ImageJ
as a library. Use the "Compile and Run" command to compile and test,
then run
from the command line. It requires ImageJ 1.29v or later.
*/
public class openfromexcel implements PlugIn {

    public void run(String arg) {
        OpenDialog od = new OpenDialog("Open...", "");
        if (od.getFileName()==null) return;
        String dir = od.getDirectory();
        if (dir==null)
            return;
        String name = od.getFileName();
        process(dir+name);
    }

    void process(String path) {
                 if (IJ.versionLessThan("1.33b")) return;
                         IJ.log("opening "+path);
                 IJ.run("Bio-Formats Importer (windowless)", "open=[" +
path +
"]");
   }

    public static void main(String args[]) {
        if (args.length<1)
            IJ.log("usage: openfromexcel image");
        else {
           new ImageJ(); // open the ImageJ window to see images and
results
            new openfromexcel().process(args[0]);
         //   System.exit(0);
        }
    }

}




Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca