ImageJ Batch Macro

[Paul Dennis]

Hello, I am new to ImageJ.

I am wondering if anyone can help?

I am trying to use a batch option to process a macro to overlay a grid on an image. In this case a folder with 70 images.

I can create a macro and I can see the batch option but is it possible to add a new macro to the batch option?

Many thanks,

Paul -

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[ERIC]

Hi Paul,
Process/Batch/Macro... allows you to write your macro (or open it if
already written).
To add an image in the overlay of all the image of a folder  :
run("Add Image...", "image=Untitled x=0 y=0 opacity=100 zero");

see enclosed exemple.

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 01/09/2014 11:00, Paul Dennis a écrit :

> Hello, I am new to ImageJ.
>
> I am wondering if anyone can help?
>
> I am trying to use a batch option to process a macro to overlay a grid on an image. In this case a folder with 70 images.
>
> I can create a macro and I can see the batch option but is it possible to add a new macro to the batch option?
>
> Many thanks,
>
> Paul -
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Paul Dennis]

Hello Eric.

thank you for the quick reply!

I have code for a macro to overlay a grid.

// This macro demonstrates how to use the Image>Overlay>Add Selection
// command to draw a

line grid on an image in a non-destructive overlay.

   requires("1.43j");
   color = "cyan";
   

nLines = 50;
   if (nImages==0) run("Boats (356K)");
   run("Remove Overlay");
   width =

getWidth;
   height = getHeight;
   tileWidth = width/(nLines+1);
   tileHeight = tileWidth;
   

xoff=tileWidth;
   while (true &&amp; xoff<width) { // draw vertical lines
      makeLine(xoff, 0,

xoff, height);
      run("Add Selection...", "stroke="+color);
      xoff += tileWidth;
   }
   

yoff=tileHeight;
   while (true &&amp; yoff<height) { // draw horizonal lines
      makeLine(0,

yoff, width, yoff);
      run("Add Selection...", "stroke="+color);
      yoff += tileHeight;
   

}
   run("Select None");

This works fine if I open an image and run the macro.

If I open batch and then open the macro or paste the macro code in and process nothing happens.  If I save the macro it doesn't show in the drop down list.  

I thought the macro would overlay/ save the grid on top of the image but maybe it's just intended to be used on an open file?

Many thanks,

Paul -

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[ERIC]

I got the following code to work on a folder.
(I removed from the while loop : true &&amp.)
Hope it helps.

  color = "cyan";

nLines = 50;
    if (nImages==0) run("Boats (356K)");
    run("Remove Overlay");
    width = getWidth;
    height = getHeight;
    tileWidth = width/(nLines+1);
    tileHeight = tileWidth;


  xoff=tileWidth;
    while ( xoff<width) { // draw vertical lines
       makeLine(xoff, 0, xoff, height);
       run("Add Selection...", "stroke="+color);
       xoff += tileWidth;
    }


yoff=tileHeight;
    while ( yoff<height) { // draw horizonal lines
       makeLine(0, yoff, width, yoff);
       run("Add Selection...", "stroke="+color);
       yoff += tileHeight;

}
    run("Select None");

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 01/09/2014 14:51, Paul Dennis a écrit :

> // This macro demonstrates how to use the Image>Overlay>Add Selection
> // command to draw a
>
> line grid on an image in a non-destructive overlay.
>
>     requires("1.43j");
>     color = "cyan";
>    
>
> nLines = 50;
>     if (nImages==0) run("Boats (356K)");
>     run("Remove Overlay");
>     width =
>
> getWidth;
>     height = getHeight;
>     tileWidth = width/(nLines+1);
>     tileHeight = tileWidth;
>    
>
> xoff=tileWidth;
>     while (true &&amp; xoff<width) { // draw vertical lines
>        makeLine(xoff, 0,
>
> xoff, height);
>        run("Add Selection...", "stroke="+color);
>        xoff += tileWidth;
>     }
>    
>
> yoff=tileHeight;
>     while (true &&amp; yoff<height) { // draw horizonal lines
>        makeLine(0,
>
> yoff, width, yoff);
>        run("Add Selection...", "stroke="+color);
>        yoff += tileHeight;
>    
>
> }
>     run("Select None");

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[Paul Dennis]

Hello Eric.

Thank you for the code.

I am able to run that fine as a record / run macro.

If I paste the code to the batch window and process (selected input and output folders) it closed the dialogue box and the images are not having the grid overlayed.

If I use the drop down and select say Borders it processes just fine.

I am sorry for the many questions!

Thanks,

Paul -

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ERIC]

I can't understand the problem. I used either imageJ 1.49b3 or Fiji  
1.48v. It works with both.
Sorry but I can't find anything else !!!!

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 01/09/2014 16:08, Paul Dennis a écrit :

> Hello Eric.
>
> Thank you for the code.
>
> I am able to run that fine as a record / run macro.
>
> If I paste the code to the batch window and process (selected input and output folders) it closed the dialogue box and the images are not having the grid overlayed.
>
> If I use the drop down and select say Borders it processes just fine.
>
> I am sorry for the many questions!
>
> Thanks,
>
> Paul -
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Paul Dennis]

Hello Eric.

Thank you for the update.

I realsie I am on version 148.

I will download and test on 149.

Thank you for your help!

Paul -

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Paul Dennis]

Hello Eric.

I just updated ImageJ to version 1.49 from the update menue item but have the same issue.  When I click porcess nothing happens and the folders contents are unchanged :( Are your original images in a TIFF format?  I wonder if that is the issue for me.

Many thanks,

Paul -

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ERIC]

I have jpeg tiff and png images in the folder and even a stack!!!!
Are you sure your output format is .tif ????
Other format will not work !!!

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 01/09/2014 17:27, Paul Dennis a écrit :

> Hello Eric.
>
> I just updated ImageJ to version 1.49 from the update menue item but have the same issue.  When I click porcess nothing happens and the folders contents are unchanged :( Are your original images in a TIFF format?  I wonder if that is the issue for me.
>
> Many thanks,
>
> Paul -
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Paul Dennis]

Hello Eric.

I have been able to get batch to work but very odd.

If I choose anything other than .TIFF as the output e.g. PNG JPG and so on it works fine no issues.  If I select TIFF as the output nothing happens.

I can use one of the other output formats so that is fine.

Thank you for your help!

Paul -

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stoyan Pavlov]

Hi Paul,
Although Fiji has a batch processing option in its Process menu, I use
the Batch process folders macro template from the ImageJ  Macros
collection. Its very nice and i think you should give it a try. It's
located here
http://imagej.nih.gov/ij/macros/BatchProcessFolders.txt
Best wishes
Stoyan
---
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]


2014-09-02 10:09 GMT+03:00 Paul Dennis <[hidden email]>:

> Hello Eric.
>
> I have been able to get batch to work but very odd.
>
> If I choose anything other than .TIFF as the output e.g. PNG JPG and so on it works fine no issues.  If I select TIFF as the output nothing happens.
>
> I can use one of the other output formats so that is fine.
>
> Thank you for your help!
>
> Paul -
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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