[Insight-users] [Software Feedback] Bioformat cpp withitk

[Bill Lorensen]

You cannot reshuffle the builtin I/O's. You could unregister each of them
and reregister the ones you want in the order you want.


On Mon, Jul 2, 2012 at 1:25 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Matthias,
>
>
>
> I want to use the cpp wrapped bioformat reader with itk to read ome.tif
>> files. The interfacing with itk however is kind of not working properly.
>> First I have to unregister the base readers (jpg, png etc. )using the
>> command itk::ObjectFactoryBase::**ReHash(); If I don't do this, one of
>> base readers will try to load the tiff image. Namely the TiffImageIO. Since
>> the image in question is tiled, this read operation will fail. And therfore
>> the bioformat reader will never be activated. If I use the ReHash()
>> function, the bioformat reading works, but all other reader/writers are
>> unregistered in the ObjectFactoryBase. In registering them manually for
>> e.g. png saving a output region of the read ome.tiff image. The bioformat
>> reader will always tell itk that he can write the input image. But he sould
>> not, since I choose .png as the output format. I'm not quite shure what I'm
>> doing wrong concerning the reader. I thought the plugin should behave as a
>> normal itk reader/writer.
>>
>
> I am CCing the ITK-users list, since I think your question is a more
> general one about the ITK ImageIO plugin mechanism. It seems to me that all
> you really need is a simple way to reshuffle the order of the available
> ImageIO plugins—in this case, to give the Bio-Formats ITK plugin a higher
> priority than the built-in TIFF ImageIO plugin. Does anyone know a good way
> to do this?
>
> Thanks,
> Curtis
>
> P.S. The ImageIO plugin Matthias is talking about is here:
>    http://loci.wisc.edu/bio-formats/itk
>
>
> On Mon, Jul 2, 2012 at 11:09 AM, <matthias.noll at igd.fraunhofer.de> wrote:
>
>> Matthias Noll sent a message using the contact form at
>> http://loci.wisc.edu/contact.
>>
>> Hello,
>> I want to use the cpp wrapped bioformat reader with itk to read ome.tif
>> files. The interfacing with itk however is kind of not working properly.
>> First I have to unregister the base readers (jpg, png etc. )using the
>> command itk::ObjectFactoryBase::**ReHash(); If I don't do this, one of
>> base readers will try to load the tiff image. Namely the TiffImageIO. Since
>> the image in question is tiled, this read operation will fail. And therfore
>> the bioformat reader will never be activated. If I use the ReHash()
>> function, the bioformat reading works, but all other reader/writers are
>> unregistered in the ObjectFactoryBase. In registering them manually for
>> e.g. png saving a output region of the read ome.tiff image. The bioformat
>> reader will always tell itk that he can write the input image. But he sould
>> not, since I choose .png as the output format. I'm not quite shure what I'm
>> doing wrong concerning the reader. I thought the plugin should behave as a
>> normal itk reader/writer.
>> I'm greatful for any kind of help.
>> Thanks Matthias
>>
>
>
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