TIFF: batch LZW compression via a macro

[Guenter Giese]

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

[ctrueden]

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

[Guenter Giese]

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 [phone] (Fax: -325)
e-mail: [hidden email]

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

[ctrueden]

Hi Guenter,

> I am using Fiji. Is there any difference in using ImageJ1 instead of
> Fiji in this respect (tiff LZW compression)?

ImageJ1's built in TIFF logic cannot save LZW—only read it.

Whether you use ImageJ1 or ImageJ2 to save LZW-compressed TIFFs via
Bio-Formats should not matter.

> 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?

That would not always work -- e.g., if you have a very large TIFF file
opened as a virtual stack. You would destroy the original before you finish
reading all its pixels.

Instead, Save the file to a new name, delete the original, then rename the
new file to the original name. You can use the File.rename and File.delete
functions of the IJ1 macro language.

Regards,
Curtis

On Thu, May 21, 2015 at 1:00 PM, Guenter Giese <
[hidden email]> wrote:

> 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 [phone] (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