[ome-devel] Discrepancies between IFormatReader and IFormatWriter

[Roger Leigh]

On 06/09/2014 15:14, Curtis Rueden wrote:
> Hi Roger,
>
>  > While converting IFormatWriter for the C++ implementation
>
>  From this mail, I infer that a full C++ version of Bio-Formats is in
> the works? And that other possible solutions such as Avian [1] have been
> discarded as unsuitable? If so, I would find it very helpful if more
> information about the project directions for native Bio-Formats could be
> shared on ome-devel. Unless I missed a mail (and apologies if so), this
> is the first I have seen talking about a language translated version of
> IFormatHandler/Reader/Writer to C++.

Hi Curtis,

This is certainly nothing new.  I have been working on this as my
primary responsibility for over 18 months now.  I spent a good part of
last year getting the xsd-fu code and templates ported to generate C++
OME-XML model and metadatastore code, and following that have been
working through all the basic Bio-Formats interfaces.

Code in git:
https://github.com/openmicroscopy/bioformats/tree/develop/cpp

Build instructions:
http://ci.openmicroscopy.org/view/Docs/job/BIOFORMATS-5.1-release-docs/ws/src/docs/sphinx/_build/html/developers/cpp.html

Doxygen API reference showing which classes have currently been ported:
http://ci.openmicroscopy.org/job/BIOFORMATS-5.1-latest-cpp/label=snipe/ws/install/bioformats-cpp-apidoc-5.1.0-m0.2-727-gc6fa36a/html/annotated.html

Development plan (internal OME doc):
https://trello.com/c/JCc9hiWo/10-bio-formats-c

We aim to have a native C++ implementation of all the base Bio-Formats
interfaces and classes, an OME-TIFF reader/writer, plus tools such as
showinf and bfconvert for the 5.1 release.  Note that it does not yet
contain any additional readers/writers from Bio-Formats at this time,
though there is already interest in doing so for several formats,
particularly those which already have native C or C++ bindings.  The
primary focus for now is on native C++ OME-TIFF reading and writing.
There is absolutely no reason why Avian/VIGRA could not be used to
provide the additional Java readers, and I think that doing so would be
well worth investigating once we have the initial OME-TIFF support in
place.  I said as much last year (18th Oct) in reply to Johannes' email
about Avian.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096