http://imagej.273.s1.nabble.com/TIFF-batch-LZW-compression-via-a-macro-tp5012892p5012906.html
> I am using Fiji. Is there any difference in using ImageJ1 instead of
opened as a virtual stack. You would destroy the original before you finish
new file to the original name. You can use the File.rename and File.delete
> Hi Curtis,
>
> You're right. When the target file name does not exist yet, the result
> tiff file is compressed.
>
> I am using Fiji. Is there any difference in using ImageJ1 instead of Fiji
> in this respect (tiff LZW compression)?
>
> Is there any way to simply replace the uncompressed TIFF source file with
> the compressed one (same name), leading to the same result as saving under
> a different name?
> Any option to be set in the BioFormats exporter?
>
>
> Thank you very much!
>
> Guenter
>
>
>
> Am 20.05.2015 um 23:02 schrieb Curtis Rueden:
>
>> 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>>>
>>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
>
> ------------------------------------------
> Dr. Guenter Giese
> Light Microscopy Facility Manager
> Dept. of Biomedical Optics
> MPI fuer Medizinische Forschung Jahnstr. 29
> D-69120 Heidelberg, Germany
> Phone (+49) 6221-486-360 (Fax: -325)
>
> e-mail:
[hidden email]
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>