medical image analysis Blog

As of version 2.0.9, MIA is now an official Debian package availabe in unstable.
The command line tools are named mia-tools and the development files package is called libmia-2.0-dev. This means there is a good chance that MIA will it make into the next Ubuntu release. For now, Ubuntu 12.04 packages for version are provided via the MIA-PPA. ... read more

Version 2.0.8 has been released but unfortunately it was not really tested on i386, so if you run MIA on a 32 bit installation, some tests will fail because of lack of floating point accuracy. I guess this is because on Intel 32 bit the processor has less floating point registers and has to store, and hence, truncate intermediate results. Interestingly, this problem doesn't appear on 33 bit PowerPC (i.e. the G4). In addition, if you want to develop with MIA, the miacore.pc file has a bug so that pkg-config will not provide the proper C-flags.
Both issues have been fixed in git head, and a hotfix patch to the source code is provided. ... read more

The Debian package was rejected in the first round because of some licencing documentation issues. For that reason I will take the chance to apply some ABI changes that would otherwise be postponed for more time. Among these are removing some unused parameters [tickets:#70], and preparing the new interface for the transformation penalty terms.

The MIA Debian packages are still stuck in the NEW pipeline of ftpmaster, which means apart from the odd minor fixes and enhancements to the code, I'm currently focusing on improving the documentation of the web site:

The ticket system is now split into trackers for the different sub-projects and a tracker for the web site itself has been add, and some [wiki:Tutorials] are now available.... read more

Finally, MIA has seen a new release (2.0.6) that might be considered "stable". The code has seen a lot of cleanups and added functionality since the 2.0.3 release, and therefore, it is binary incompatible. Nevertheless, from now on the 2.0 releases will no longer see updates that may break binary compatibility.

The next milestone is to get the software accepted into Debian-med. There exists already an Ubuntu PPA. ... read more

In order to get rid of the useless duplication of dimension specifiers a big cleanup of the file names has now been pushed to origin/master.

To change the file names dependent projects the following script should be helpful (assuming your header files are named ".hh" and cour implementation files ".cc", if you should adjust the script accordingly.):

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#!/bin/bash 
files=$(grep -l "<mia/2d/2[dD].*>" $(find . -name "*.hh" -o -name "*.cc"))

for f in $files; do 
    sed -ie "s/\(<mia\/2d\/\)2[dD]/\1/g" $f ; echo $f; 
done... [read more](/p/mia/blog/2012/11/big-file-name-cleanup/)

Latest changes to the auto-documentation is the linking of String command line tools with plug-in handlers. With this addition, now all programs should print the supported file types in their help output, and the man pages and on-line help is also updated accordingly.

What is still missing is that help also informs the user what pixel types a file type supports and whether multiple images can be stored in one file. ... read more

Finally, I got the issues with the viewer resolved and the lightning is correct now. Next thing is to get all the test data running that is planned for a paper in Source Code in Biology and Medicine. When the paper gets submitted, the new version will be released and the visualization tool will also see a revival as proper release.

With C++11 a lot of constructs have become obsolete and can now be replaced by cleaner implementations. One example is the THROW macro that used a construct of strings and values added together by the "<<" operator to form the actual message to be passed to the exception.
With variadic templates, this construct has become obsolete and one can now use the template function create_execption to construct an exception of any type with a constructor that expects a std::string as argument. ... read more

As you can see, MIA switched to the new sourceforge backend Allure. In the context of this transitition the organisation of the SCM repositories of MIA will be reviewed and old code will be droppend from the repositories.

If you where using code from the repositories, you might want to reconfigure the origin of your code base. For git repositories this can be done by using

git remote set-url origin <newurl> <oldurl>... [read more](/p/mia/blog/2012/08/starting-with-allura/)