FITS data cube: Save as?

[David Nicholls]

I'm exploring ImageJ as a way of editing the images contained in a FITS data cube.  It's very handy for editing out cosmic ray noise manually.  However, while imageJ knows how to open FITS data cubes, it looks like it can't save them - 'Save as FITS' merely saves the currently viewed frame as a single image FITS file.

Is there any way ( plugin etc) to save the data cube back as an edited data cube?

DN
__________
Research School of Astronomy & Astrophysics
Mt Stromlo Observatory
Australian National University

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[Peter Haub]

Dear all,
following the instructions on
http://imagej.nih.gov/ij/plugins/download/misc/Command_Listener.java
I implemented a CommandListener to force a function to be executed when
ImageJ is closed.

The code look like this and works fine in IJ version 1.45:
     ..
     public String commandExecuting(String command) {
         IJ.showMessage(command);
         if (command.equals("Quit")) {
                 IJ.showMessage(command);
         }
         return command;
     }
     ..

With newer versions of IJ there is a problem when ImageJ is closed with
the window icon.
IJ don't 'fire' a "Quit" command in this case and the CommandListener
will not execute the code.
If IJ is closed with the menu entry "Quit" everything works as expected.

Is this a bug or a feature?

Thanks for help
Peter

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[ctrueden]

Hi David,

> Is there any way ( plugin etc) to save the data cube back as an edited
> data cube?

Not that I know of. We would love to have this feature in the SCIFIO [1]
library though (which is what ImageJ2 uses for its core image I/O). Right
now we only support reading FITS data cubes. So I expect that ImageJ2 will
eventually support saving FITS data cubes. If you have any programmers in
your group interested in doing this work, we would be happy to give some
pointers on how to get started.

In the meantime, ImageJ does support saving multiple image planes to many
other file formats including multi-page TIFF. Perhaps the other software
you are using (that expects to receive a FITS data cube) supports reading
one of these other formats?

Regards,
Curtis

[1] http://scif.io/


On Sun, Oct 6, 2013 at 5:06 AM, David Nicholls <[hidden email]>wrote:

> I'm exploring ImageJ as a way of editing the images contained in a FITS
> data cube.  It's very handy for editing out cosmic ray noise manually.
>  However, while imageJ knows how to open FITS data cubes, it looks like it
> can't save them - 'Save as FITS' merely saves the currently viewed frame as
> a single image FITS file.
>
> Is there any way ( plugin etc) to save the data cube back as an edited
> data cube?
>
> DN
> __________
> Research School of Astronomy & Astrophysics
> Mt Stromlo Observatory
> Australian National University
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Stephan Preibisch]

Hi David,

I have a hacked version of a FITS exporter for ImgLib lying around ... let me know, I can send it to you ...

Cheers,
Stephan
---

Dr. Stephan Preibisch
Robert H. Singer / Eugene Myers lab

Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG

email: [hidden email] / [hidden email] / [hidden email]
web: http://fly.mpi-cbg.de/preibisch



On Oct 23, 2013, at 15:24 , Curtis Rueden wrote:

> Hi David,
>
>> Is there any way ( plugin etc) to save the data cube back as an edited
>> data cube?
>
> Not that I know of. We would love to have this feature in the SCIFIO [1]
> library though (which is what ImageJ2 uses for its core image I/O). Right
> now we only support reading FITS data cubes. So I expect that ImageJ2 will
> eventually support saving FITS data cubes. If you have any programmers in
> your group interested in doing this work, we would be happy to give some
> pointers on how to get started.
>
> In the meantime, ImageJ does support saving multiple image planes to many
> other file formats including multi-page TIFF. Perhaps the other software
> you are using (that expects to receive a FITS data cube) supports reading
> one of these other formats?
>
> Regards,
> Curtis
>
> [1] http://scif.io/
>
>
> On Sun, Oct 6, 2013 at 5:06 AM, David Nicholls <[hidden email]>wrote:
>
>> I'm exploring ImageJ as a way of editing the images contained in a FITS
>> data cube.  It's very handy for editing out cosmic ray noise manually.
>> However, while imageJ knows how to open FITS data cubes, it looks like it
>> can't save them - 'Save as FITS' merely saves the currently viewed frame as
>> a single image FITS file.
>>
>> Is there any way ( plugin etc) to save the data cube back as an edited
>> data cube?
>>
>> DN
>> __________
>> Research School of Astronomy & Astrophysics
>> Mt Stromlo Observatory
>> Australian National University
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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