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

[Curtis Rueden]

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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