My email to the list from my university email account account was rejected. Re-sending from my gmail account. Please see below.
Ghassan
Date: May 23, 2011 12:11:52 AM GMT+02:00
Subject: Re: [SCIRUN-USERS] running ITK filters from Matlab: new architecture
Hello Ramón et al. The source code for MATITK is available. We have made the code available as part of our Insight Journal publication: http://www.insight-journal.org/browse/publication/66Please let me (and/or Vincent, cc-ed) know if you have any questions. Best regards, /Ghassan ---- Ghassan Hamarneh, PhD School of Computing Science, Associate Professor Medical Image Analysis Lab, Co-founder/director IEEE Senior Member and ACM Senior Member Personal homepage: http://www.cs.sfu.ca/~hamarneh Lab homepage: http://mial.cs.sfu.ca Office: Technology and Science Complex (TASC): 9417 Tel: +1.778.782.3007 SofTel: +1.778.782.2214 (internet-based) Fax: +1.778.782.3045 Postal Address: School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada v-card: http://www.cs.sfu.ca/~hamarneh/GhassanHamarneh.vcf On 2011-05-21, at 2:04 PM, Ramón Casero Cañas wrote:
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/
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