[ome-users] [Software Feedback] accessiblity compressed Dicoms

[Curtis Rueden]

Hi Maarten,

> A problem that we need to catch is opening compressed Dicoms. They
> refer to your Loci plugin. I installed it, and that seems to work... I
> can open the compressed images.

Glad to hear it.

> Is there a possibilty to share a part of your code that allows to open
> these compressed images, please?

Bio-Formats is open source:
https://github.com/openmicroscopy/bioformats

Code relevant to compressed DICOM files:
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/scifio/src/loci/formats/in/DicomReader.java
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/scifio/src/loci/formats/codec/JPEG2000Codec.java
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/scifio/src/loci/formats/codec/JPEGCodec.java
https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/scifio/src/loci/formats/codec/PackbitsCodec.java

But rather than extracting any code, why not simply call Bio-Formats
directly? Here is a simple example:

https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/Simple_Read.java

Regards,
Curtis


On Tue, Mar 19, 2013 at 4:32 PM, <maarten.depuydt at mobelife.be> wrote:

> Maarten Depuydt sent a message using the contact form at
> http://loci.wisc.edu/contact.
>
> Dear,
>
> I'm developing little ImageJ plugin to sort Medical Dicoms and extraction
> of relevant data from the headers, fully automated to our needs.
> A problem that we need to catch is opening compressed Dicoms. They refer
> to your Loci plugin. I installed it, and that seems to work... I can open
> the compressed images.
> Is there a possibilty to share a part of your code that allows to open
> these compressed images, please?
>
> Thank you a lot in advance.
> Kind regards,
>
> Maarten Depuydt
> Mobelife, Belgium
>
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