[ome-devel] Support for different ECAT7 version, patch and sample data

[Sebastien Besson (Staff)]

Dear Torsten,

thank you very much for your contribution. The proposed changes look reasonable.

At this point, feel free to turn your patch directly into a Pull Request against the Bio-Formats
source code [1]. We are happy to do it on your behalf if you prefer.

We will also add the sample file you uploaded to our data repository for non-regression testing.
Ideally we would like to make this sample file public under the CC-BY 4.0 license [2] so that the
community can re-use it for future development of the library (see [3] for an example). Would that
be acceptable?

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/develop/CONTRIBUTING.md
[2] http://creativecommons.org/licenses/by/4.0
[3] http://downloads.openmicroscopy.org/images/ND2/aryeh/

On 31 Jan 2017, at 13:04, Torsten Stöter <torsten.stoeter at lin-magdeburg.de<mailto:torsten.stoeter at lin-magdeburg.de>> wrote:

Dear OME developers,

I'd like to submit a tiny patch to allow reading different versions of ECAT7 files.

It appears, that ECAT7 comes in three versions with differing magic strings "MATRIX7[012]v", while the rest of the file may just be handled in the same way for all versions. Manually modifying the magic string from "MATRIX70v" to "MATRIX72v" in our data allowed us to load it correctly. Hence, I changed the ECAT7Reader to accept all three magic strings as valid ECAT7 files.

For referecence, see how ECAT7 is read in SPM: https://github.com/neurodebian/spm12/blob/master/spm_ecat2nifti.m

Please find both patch and sample data attached.

Best regards

Torsten Stöter

--
Torsten Stöter
Leibniz Institute for Neurobiology
Brenneckestr. 6
39118 Magdeburg
Germany

Tel: ++49 (0)391 62639-2171
Fax: ++49 (0)391 62639-2589
http://www.lin-magdeburg.de/cni

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