FITS Format Support

[Cayanan, Michael D (398G)]

Hi,

I have been using the ImageJ library to read FITS images and converting them to jpeg, gif, etc.

I have a FITS file containing 2 images within the file, but ImageJ looks like it only recognizes the first image. Is there a way to get to that second image?

Thanks in advance for your help,
Michael

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

[ctrueden]

Hi Michael,

> I have a FITS file containing 2 images within the file, but ImageJ
> looks like it only recognizes the first image. Is there a way to get
> to that second image?

Did you try using Bio-Formats [1]? It supports multi-plane FITS files
(NAXIS3 > 1).

> I have been using the ImageJ library

Bio-Formats is usable as a standalone Java library [2] and also has an
ImageJ-compatible API (e.g., [3]).

Regards,
Curtis

[1] http://fiji.sc/Bio-Formats
[2] http://openmicroscopy.org/info/bio-formats/developers/java-library.html
[3]
https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/bio-formats-plugins/utils/Simple_Read.java

On Thu, Jan 8, 2015 at 12:44 PM, Cayanan, Michael D (398G) <
[hidden email]> wrote:

> Hi,
>
> I have been using the ImageJ library to read FITS images and converting
> them to jpeg, gif, etc.
>
> I have a FITS file containing 2 images within the file, but ImageJ looks
> like it only recognizes the first image. Is there a way to get to that
> second image?
>
> Thanks in advance for your help,
> Michael
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Cayanan, Michael D (398G)]

Hi Curtis,

Thanks for the Bio-Formats library recommendation. I was able to install
it into the ImageJ library, but unfortunately, it does not appear to
support FITS files that contain multiple images within them.

I have a fits file with 2 HDUs, each describing an image (both 2-D
images). Not sure if I'm overlooking one of the Bio-Formats settings or
the menu options available through imageJ.

I see that there are javadocs for this library, so I'll go through this to
see if there is some sort of browse feature to support my use case.

Thanks,
Michael


On 1/8/15 12:44 PM, "Curtis Rueden" <[hidden email]> wrote:

>Hi Michael,
>
>> I have a FITS file containing 2 images within the file, but ImageJ
>> looks like it only recognizes the first image. Is there a way to get
>> to that second image?
>
>Did you try using Bio-Formats [1]? It supports multi-plane FITS files
>(NAXIS3 > 1).
>
>> I have been using the ImageJ library
>
>Bio-Formats is usable as a standalone Java library [2] and also has an
>ImageJ-compatible API (e.g., [3]).
>
>Regards,
>Curtis
>
>[1] http://fiji.sc/Bio-Formats
>[2]
>http://openmicroscopy.org/info/bio-formats/developers/java-library.html
>[3]
>https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/bio-fo
>rmats-plugins/utils/Simple_Read.java
>
>On Thu, Jan 8, 2015 at 12:44 PM, Cayanan, Michael D (398G) <
>[hidden email]> wrote:
>
>> Hi,
>>
>> I have been using the ImageJ library to read FITS images and converting
>> them to jpeg, gif, etc.
>>
>> I have a FITS file containing 2 images within the file, but ImageJ looks
>> like it only recognizes the first image. Is there a way to get to that
>> second image?
>>
>> Thanks in advance for your help,
>> Michael
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Michael,

> unfortunately, it does not appear to support FITS files that contain
> multiple images within them.

I checked the source code of Bio-Formats, and it definitely supports
certain types of multi-plane FITS files. Perhaps yours are a different type.

You can write to the ome-users list [1] for further assistance. The
Bio-Formats team may be able to enhance the FITS format support, if you are
willing to upload a sample image to the OME QA system [2].

Regards,
Curtis

[1] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
[2] http://qa.openmicroscopy.org.uk/qa/upload/

On Thu, Jan 8, 2015 at 3:59 PM, Cayanan, Michael D (398G) <
[hidden email]> wrote:

> Hi Curtis,
>
> Thanks for the Bio-Formats library recommendation. I was able to install
> it into the ImageJ library, but unfortunately, it does not appear to
> support FITS files that contain multiple images within them.
>
> I have a fits file with 2 HDUs, each describing an image (both 2-D
> images). Not sure if I'm overlooking one of the Bio-Formats settings or
> the menu options available through imageJ.
>
> I see that there are javadocs for this library, so I'll go through this to
> see if there is some sort of browse feature to support my use case.
>
> Thanks,
> Michael
>
>
> On 1/8/15 12:44 PM, "Curtis Rueden" <[hidden email]> wrote:
>
> >Hi Michael,
> >
> >> I have a FITS file containing 2 images within the file, but ImageJ
> >> looks like it only recognizes the first image. Is there a way to get
> >> to that second image?
> >
> >Did you try using Bio-Formats [1]? It supports multi-plane FITS files
> >(NAXIS3 > 1).
> >
> >> I have been using the ImageJ library
> >
> >Bio-Formats is usable as a standalone Java library [2] and also has an
> >ImageJ-compatible API (e.g., [3]).
> >
> >Regards,
> >Curtis
> >
> >[1] http://fiji.sc/Bio-Formats
> >[2]
> >http://openmicroscopy.org/info/bio-formats/developers/java-library.html
> >[3]
> >
> https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/bio-fo
> >rmats-plugins/utils/Simple_Read.java
> >
> >On Thu, Jan 8, 2015 at 12:44 PM, Cayanan, Michael D (398G) <
> >[hidden email]> wrote:
> >
> >> Hi,
> >>
> >> I have been using the ImageJ library to read FITS images and converting
> >> them to jpeg, gif, etc.
> >>
> >> I have a FITS file containing 2 images within the file, but ImageJ looks
> >> like it only recognizes the first image. Is there a way to get to that
> >> second image?
> >>
> >> Thanks in advance for your help,
> >> Michael
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >--
> >ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Frederic V. Hessman]

Neither the ImageJ FITS library nor the Bio-Format libraries support multiple Header-Data-Units.  You could write your own ImageJ plugin using the nom.tam.fits library but I’ve usually simply used a pyfits script to transform the multiple HDU’s to multiple images or n-dimensional images, depending upon your needs (quite often, the multiple HDU’s are actually useless).

The new version of ImageJ should definitely be given better FITS support, e.g. via nom.tam.fits;  unforunately, the question of metadata hasn’t really been settled….

Rick

On 8 Jan 2015, at 14:59, Cayanan, Michael D (398G) <[hidden email]> wrote:

> Hi Curtis,
>
> Thanks for the Bio-Formats library recommendation. I was able to install
> it into the ImageJ library, but unfortunately, it does not appear to
> support FITS files that contain multiple images within them.
>
> I have a fits file with 2 HDUs, each describing an image (both 2-D
> images). Not sure if I'm overlooking one of the Bio-Formats settings or
> the menu options available through imageJ.
>
> I see that there are javadocs for this library, so I'll go through this to
> see if there is some sort of browse feature to support my use case.
>
> Thanks,
> Michael
>
>
> On 1/8/15 12:44 PM, "Curtis Rueden" <[hidden email]> wrote:
>
>> Hi Michael,
>>
>>> I have a FITS file containing 2 images within the file, but ImageJ
>>> looks like it only recognizes the first image. Is there a way to get
>>> to that second image?
>>
>> Did you try using Bio-Formats [1]? It supports multi-plane FITS files
>> (NAXIS3 > 1).
>>
>>> I have been using the ImageJ library
>>
>> Bio-Formats is usable as a standalone Java library [2] and also has an
>> ImageJ-compatible API (e.g., [3]).
>>
>> Regards,
>> Curtis
>>
>> [1] http://fiji.sc/Bio-Formats
>> [2]
>> http://openmicroscopy.org/info/bio-formats/developers/java-library.html
>> [3]
>> https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/bio-fo
>> rmats-plugins/utils/Simple_Read.java
>>
>> On Thu, Jan 8, 2015 at 12:44 PM, Cayanan, Michael D (398G) <
>> [hidden email]> wrote:
>>
>>> Hi,
>>>
>>> I have been using the ImageJ library to read FITS images and converting
>>> them to jpeg, gif, etc.
>>>
>>> I have a FITS file containing 2 images within the file, but ImageJ looks
>>> like it only recognizes the first image. Is there a way to get to that
>>> second image?
>>>
>>> Thanks in advance for your help,
>>> Michael
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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