[Insight-developers] Proposal for writing ITK transforms as MATLAB Level 4 Binary MAT files

[kent williams]

This is a good proposal.  It is probably preferable to the quick and dirty
thing I did yesterday.

Dpes VTK have a file format for a vtk transform?  I'm not seeing any classes
in the VTK documentation for reading and writing transforms.


On 8/3/07 7:42 AM, "Luis Ibanez" <luis.ibanez at kitware.com> wrote:

> 
> Hi Kent,
> 
> A couple of questions:
> 
> 
> 1) Why is that the TransformFileWriterBase class is necessary ?
>     Is it because the Update() method in the current
>     TransformFileWriter is not "virtual" ?
> 
> 2) Should we consider setting up a Factory mechanism similar
>     to the ImageIO ?
> 
>     In your proposal, we would be following rather the VTK model
>     where the user has to explicitly specify the writer, as opposed
>     to the ITK model where the ImageFileWriter (and presumably the
>     TransformFileWriter) used the filename as a way of picking up
>     the actual class that will do the writing.
> 
>     We could have a "neutral" TransformFileWriter, and add classes
> 
> 
>      TranformIOBase        the basic helper class
> 
>      with derived classes:
> 
>      MatlabTransformIO
>      VTKTransformIO        (a common request from users )
>      OpenGLTransformIO
>      MetaTransformIO       (the current implementation in ITK)
> 
> 
>      The extension of the filename will be used for picking up
>      the correct TransformIO class from a factory.
> 
> 
> 3) We would like to stay away from code covered by the GPL
>     license, but if you find code out there the is the perfect
>     fit for what you want, we always have the option of supporting
>     it the way we support FFTW: CMake will allow developers to
>     use the software if it is available in their machine, and it
>     they turn ON a CMake variable.
> 
>     However, in the case of writing a Matlab transform, the tasks
>     doesn't seem to be as daunting as to require a helper library.
> 
> 
> 
> 4) You bring up a very important point regarding the precision
>     of the numerical values written in the Transform files.
> 
>     This was discussed a while ago in the list, but looking at the
>     code, it seems that we are still writing the transforms in
>     ASCII.
> 
>     It is definitely worth to consider the "binary" option.
>     Note that it brings with it all the local machine
>     architecture issues of endianness and byte swapping....
> 
>     We may reuse a lot of the code from ImageIO that already handles
>     that...., but we will need to add a couple of fields to the
>     Transform file format to indicate "binary", and "endianness".
> 
> 
> 
> We probably should discuss this further at the ITK Tcon...
> 
> 
> 
> 
>     Luis
> 
> 
> 
> ---------------------
> kent williams wrote:
>> I need some feedback on how I should go about this.  For our lab's purposes,
>> we need a binary format for writing out transformations, primarily as a way
>> to ensure that no rounding errors happen due to writing floating point
>> numbers as text.   It would also be useful to be able to load transforms
>> saved out of Matlab.
>> 
>> What I propose to do:
>> 
>> 1. Create a new class itk::TransformFileWriterBase. Almost all the code from
>> TransformFileReader/Writer would be pushed up to this class, except for the
>> Update method, in which the actual File/IO and Formatting would take place.
>> 
>> 2. Modify itk::TransformFileReader/Writer such that it derives from
>> itk::TransformFileReader/WriterBase, and has the code particular to
>> text-format ITK transforms in its version of Update().
>> 
>> 3. Add new classes itk::MatlabTransformFileReader/Writer, derived from
>> itk::TransformFileReader/WriterBase.  Write new versions of Update, to
>> read/write Matlab Level 4 files.
>> 
>> Using the Matlab Level 4 Format:
>> 
>> Matlab Level 4 file format is simple and straightforward. Furthermore, VNL
>> has classes for reading and writing Matlab level 4 files.  Matlab has a
>> newer format that supports serializing nearly any Matlab variable, and
>> supports data compression.  Unfortunately Matlab Level 5 files are much more
>> complex than Level 4, and the libraries I've found that read and write Level
>> 5 files are GPL, which are incompatible with ITK licensing.
>> 
>> For the purposes of writing ITK transforms, the following sequence would be
>> used, one per transform added to the file before writing.
>> 
>> <Parameters>
>> <Fixed Parameters>
>> 
>> The parameters are written out using
>> vnl_matlab_filewrite(vnl_vector<double>,varname);  The 'varname' field of
>> the parameters gives the class name for the transform to create when
>> reading. The 'varname' of the FixedParameters is simply 'FIXED'.
>> 
>> I don't use Matlab, so I don't know how difficult this will make writing out
>> transforms from Matlab -- perhaps some Matlab users would have an opinion?
>> 
>> Since there's no standard for transform file naming, I don't think that that
>> it makes sense to try and parallel the way that ImageIO works -- a user
>> would choose either writing out binary Matlab files or ITK text files for
>> transforms.
>> 
>> An alternative way of handling this would be to add Set/GetBinaryFile
>> boolean functions to the existing TransformFileReader/Writer classes, and
>> incorporate the matlab I/O code in those classes.
>> 
>> Opinions?
>> 
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