[Insight-users] running ITK filters from Matlab: new architecture

[Luis Ibanez]

Hi Ramon,

Many thanks for making your code available.

--

Just to clarify,

    The source code for MATITK is available
     as part the Insight Journal publication:

"MATITK: EXTENDING MATLAB WITH ITK"
by Chu V., Hamarneh G.
Simon Fraser University, BC, Canada.

http://www.insight-journal.org/browse/publication/66
http://hdl.handle.net/1926/155


The Insight Journal, being the *only* Reproducible Journal
in the domain of image analysis, requires all papers to include
source code, data and parameters, according to the principles
of "Reproducible Research Standards":

http://www.stanford.edu/~vcs/talks/VictoriaStoddenCommuniaJune2009-2.pdf

"Enabling Reproducible Research: Open Licensing For Scientific Innovation"
http://www.stanford.edu/~vcs/papers/ERROLSI03092009.pdf


---

The daily practice of reproducibility verification, also makes
of the Insight Journal the *only* scientific journal in the
domain of image analysis.


---

Many thanks for making your code available as well.

Openness and resource sharing is our best shot at taking
the image analysis field out of its current state of stagnation.


     Best,


          Luis


-------------------------------------------------------------------------------
2011/5/21 Ramón Casero Cañas <ramon.casero at comlab.ox.ac.uk>:
>
> Dear Utah group,
>
> This is a bit off-topic, but because the function can read your NRRD format,
> I thought you may be interested.
>
> Our group (lead by Vicente Grau, Blanca Rodríguez, Peter Kohl and David
> Gavaghan) is developing a function to run ITK filters from Matlab. Like
> MATITK, but as far as I know, they don't provide the source code, while ours
> is open source.
>
> More details below, in the original release email.
>
> Best regards,
>
> Ramón.
>
> ---
>
> Hi all,
>
> Exciting news, after a substantial change in the architecture of
> itk_imfilter(), the Matlab function that allows to run ITK filters from
> Matlab has a new release
>
> http://code.google.com/p/gerardus/source/browse/#svn%2Ftags%2Frelease-0.4.0%2Fmatlab%2FItkToolbox
>
> Now it looks more like a software project rather than a quick-and-dirty
> hack. (Despite the lack of testing units or documentation! ;) )
>
> First of all, many thanks to Miguel Bernabeu, Joe Pitt-Francis, Raf Bordas
> and Pras Pathmanathan, for the useful discussions, pointing in the right
> direction, solving compilation problems, etc. Without their vast programming
> knowledge and willingness to help, I doubt this could have been finished.
>
>
> Features in the new release:
> ============================
>
> - Any type of Matlab data is accepted at the input (boolean, double, single,
> uint8, int8, etc). Also empty matrices.
>
> - Output type is automatically computed depending on the filter and the
> image.
>
> - 2D/3D Images can be loaded as a Matlab array, or an NRRD struct (e.g.
> images produced by Seg3D), so it's possible to work in voxel units or real
> world units.
>
> - Currently, 3 filters are available: 3D skeletonization, Signed Maurer
> distance map, and Danielsson distance map.
>
> - Multiple output arguments are allowed, if the corresponding ITK filter
> produces more than 1 output.
>
> - The new architecture makes it quite easy to add new filters to the
> program.
>
> - Project built with CMake, so in theory it should be multi-platform and
> work with Linux, Windows and MacOS X. (But I have tested it only with
> Linux.)
>
> - Polymorphism and dynamic casting are used to have a BaseFilter class with
> the default code for typical filters, while at the same time it's possible
> to override the defaults for filters with special requirements.
>
> - Parser functions allow to map the run time input/output voxel type and
> filter type variables to compilation time templates as required by ITK
> without having to code a nesting nightmare.
>
> - General code has been written for all input/output type combination.
> Thanks to a macro FILTEREXCLUDE, forbidden combinations can be cleanly
> prevented from compilation.
>
> - Code distributed in several files makes compilation a lot faster and the
> code easier to expand and maintain.
>
> - A macro FILTERINST is used for clean explicit template instantiation of
> the allowed input/output type combinations.
>
> - The filtering process is clearly split up into:
>
>   + filter->CopyMatlabInputsToItkImages();
>   + filter->FilterSetup();
>   + filter->RunFilter();
>   + filter->CopyAllFilterOutputsToMatlab();
>
>
> Best regards,
>
> Ramon.
>
> --
> Dr. Ramón Casero Cañas
>
> Computational Biology
> Computing Laboratory
> University of Oxford
> Wolfson Building, Parks Rd
> Oxford OX1 3QD
>
> tlf     +44 (0) 1865 610737
> web     http://web.comlab.ox.ac.uk/people/Ramon.CaseroCanas
> photos  http://www.flickr.com/photos/rcasero/
>