Re: TIFF: batch LZW compression via a macro

Posted by ctrueden on May 20, 2015; 9:02pm
URL: http://imagej.273.s1.nabble.com/TIFF-batch-LZW-compression-via-a-macro-tp5012892p5012893.html

Hi Guenter,

> The image is loaded via the script, and it is subsequently saved, but
> with an increased file size (1.0 MB expanded to 1.7 MB)

If the file already exists, then Bio-Formats tries to append additional
data. Make sure you are saving to a file which does not already exist.

> I receive the error message: "OME-XML java library not found"

Hmm, not sure why that would be the case! Are you using Fiji? Or plain
ImageJ1?

Regards,
Curtis

On Wed, May 20, 2015 at 3:35 PM, Guenter Giese <
[hidden email]> wrote:

> Dear ImageJ users,
>
> I try to set up a macro for batch LZW compression of multiple TIFF 16bit
> grayscale image files.
>
> I started with macro recording. When I opened a TIFF file from the ImageJ
> GUI and exported it with the BioFormats exporter as a LZW compressed TIFF,
> I ended up with a TIFF image with a reduced file size (1.0 MB reduced to
> 0.7 MB):
>  open("D:\\temp2\\test3\\d1_cropxyz_z0000.tif");
>  run("Bio-Formats Exporter",
> "save=D:\\temp2\\test3\\macro_recorder.ome.tif compression=LZW");
>
>
> Now I tried to include the recorded sequence for TIFF export and LZW
> compression in an ImageJ macro:
>
>  run("Bio-Formats Exporter", "save="+path+" compression=LZW"); //(path is
> defined during loading, can also be specified like above)
>
> The image is loaded via the script, and it is subsequently saved, but with
> an increased file size (1.0 MB expanded to 1.7 MB), and I receive the error
> message: "OME-XML java library not found"
>
> What is the cause for the difference between manual conversion via the
> GUI, and the loading and saving via a macro? It seems that the path to the
> OME-XML java library is found when using the GI, but not from inside the
> macro.
>
> Is there any path variable to be set before running the LZW compression
> macro, or to be included in the macro code?
>
>
> Thanks for any suggestion,
>
> Guenter
>
>
> --
> Dr. Guenter Giese
> Light Microscopy Facility Manager
> Dept. of Biomedical Optics
> MPI fuer Medizinische Forschung
> D-69120 Heidelberg, Germany
> phone xx49 or 0 -6221-486-360 fax -325
> e-mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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