[Insight-users] CovarianceCalculator
Lucas Lorenzo
lucas at cvrti.utah.edu
Wed Jun 16 16:32:21 EDT 2004
Hi Luis,
thanks again.
1) the processing that I plan to do on it is:
a) to pass individual pixels (vectors) as arguments for the
MahalanobisDistanceMembershipFunction class;
b) to pass a sample list of pixels (vectors) as an argument for
theMean Calculator class;
c) to pass a sample list of pixels (vectors) as an argument for the
CovarianceCalculator class.
2) Let's say that I'm going to write my own ImageIO object. Is there
any documentation and/or example I could use ?
Thanks,
Lucas
On Jun 16, 2004, at 1:43 PM, Luis Ibanez wrote:
>
> Hi Lucas,
>
> If the vector size is not known at compliation time,
> you are probably having to defined the images as:
>
> itk::Image< std::vector< float >, Dimension >
>
> and.. in that case you will have to write your own
> ImageIO object in order to read the fileformat.
>
>
> Another option for you could be to store individual
> components per file. That is, instead of a file with
> and image with 60 components per pixel, you could
> store 60 files each one with an image of 1 component
> per pixel.
>
> You could read these images sequencially using any
> of the existing fileformats, an then copy the content
> fron the incoming image into the i-th component of
> the
>
> itk::Image< std::vector< float >, Dimension >
>
> You may want to sit in a peaceful place with some
> coffee and do the math for the memory footprint of
> such an image, because it can easily get out of control.
>
> Note also that you must consider upfront the type
> of processing that you expect to apply to such an
> image.
>
> Are you planning to do segmentation on it ?
> maybe statistical classification ?
>
>
> Note that the above image type may not satisfy the
> API expected by some ITK filters.
>
>
>
> Regards,
>
>
> Luis
>
>
>
> --------------------
> Lucas Lorenzo wrote:
>
>> Hi Luis,
>> thanks a lot for your answer.
>> mmm ... my problem is that I'll have to deal with 2D images of
>> vectors (right now I've defined them as itk::Vector type) but the
>> length of these vectors might change from one file to another.
>> Is there any way to load such an image from a file without knowing
>> the vector size at compilation time ?
>> Thanks,
>> Lucas
>> On Jun 15, 2004, at 11:31 PM, Luis Ibanez wrote:
>>>
>>> Hi Lucas,
>>>
>>> The source of the problem is that VXL uses explicit
>>> instantiation of Templates as opposed to ITK that
>>> uses implicit instatiation.
>>>
>>> This means that in vnl you can only use types that
>>> have already been explicity instantiated in the
>>> library. If you need to use a new combination, then
>>> you have to add the corresponding explicit instantiation.
>>>
>>> The vnl_fixed_matrix is only instantiated for a
>>> certain number of template parameters.
>>>
>>> You will find them under:
>>>
>>> Insight/Utilities/vxl/core/vnl/Templates
>>>
>>> They are
>>>
>>> vnl_matrix_fixed+double.1.1-.cxx
>>> vnl_matrix_fixed+double.1.2-.cxx
>>> vnl_matrix_fixed+double.1.3-.cxx
>>> vnl_matrix_fixed+double.2.1-.cxx
>>> vnl_matrix_fixed+double.2.2-.cxx
>>> vnl_matrix_fixed+double.2.3-.cxx
>>> vnl_matrix_fixed+double.2.4-.cxx
>>> vnl_matrix_fixed+double.2.6-.cxx
>>> vnl_matrix_fixed+double.3.1-.cxx
>>> vnl_matrix_fixed+double.3.2-.cxx
>>> vnl_matrix_fixed+double.3.3-.cxx
>>> vnl_matrix_fixed+double.3.4-.cxx
>>> vnl_matrix_fixed+double.3.5-.cxx
>>> vnl_matrix_fixed+double.4.1-.cxx
>>> vnl_matrix_fixed+double.4.2-.cxx
>>> vnl_matrix_fixed+double.4.3-.cxx
>>> vnl_matrix_fixed+double.4.4-.cxx
>>> vnl_matrix_fixed+double.6.6-.cxx
>>> vnl_matrix_fixed+float.1.2-.cxx
>>> vnl_matrix_fixed+float.1.3-.cxx
>>> vnl_matrix_fixed+float.2.1-.cxx
>>> vnl_matrix_fixed+float.2.2-.cxx
>>> vnl_matrix_fixed+float.3.1-.cxx
>>> vnl_matrix_fixed+float.3.3-.cxx
>>> vnl_matrix_fixed+float.3.4-.cxx
>>> vnl_matrix_fixed+float.3.5-.cxx
>>> vnl_matrix_fixed+float.4.3-.cxx
>>> vnl_matrix_fixed+float.4.4-.cxx
>>> vnl_matrix_fixed+int.2.2-.cxx
>>> vnl_matrix_fixed+int.3.4-.cxx
>>> vnl_matrix_fixed+vnl_bignum.3.3-.cxx
>>> vnl_matrix_fixed+vnl_rational.3.3-.cxx
>>> vnl_matrix_fixed_pairwise_ops.cxx
>>> vnl_matrix_fixed_ref+double.3.3-.cxx
>>> vnl_matrix_fixed_ref+double.3.4-.cxx
>>> vnl_matrix_fixed_ref+float.3.3-.cxx
>>> vnl_matrix_fixed_ref+float.3.4-.cxx
>>>
>>>
>>> As you can see, there is no instantiation for a matrix
>>> of size 60 x 60 which is what you seems to be trying
>>> to instantiate.
>>>
>>> BTW, Do you realy have a problem where your
>>> feature vector has 60 components ?
>>>
>>>
>>> If you really want to have 60 x 60 for
>>> the matrix dimension, then you could add
>>> a new file for explicit instantiation of
>>> your matrix type. Note that you must add
>>> this new file to the CMakeLists.txt file
>>> in that directory.
>>>
>>> You may want to take a file such as:
>>>
>>> vnl_matrix_fixed+double.6.6-.cxx
>>>
>>> and copy/rename it as
>>>
>>> vnl_matrix_fixed+double.60.60-.cxx
>>>
>>> and change its internals in order to
>>> use 60 x 60 as template arguments for
>>> the matrix dimensions.
>>>
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Luis
>>>
>>>
>>>
>>> ---------------------
>>> Lucas Lorenzo wrote:
>>>
>>>> Hi all,
>>>> I'm having a linking problem when compiling the following code (I'm
>>>> including only the important parts):
>>>> /
>>>> #include "itkVector.h"
>>>> #include "itkListSample.h"
>>>> #include "itkCovarianceCalculator.h"
>>>> int main( int argc, char * argv[] )
>>>> {
>>>> const unsigned int vsize = 60;
>>>> typedef itk::Vector< float, vsize > InputPixelType;
>>>> typedef itk::Statistics::ListSample< InputPixelType > SampleType ;
>>>> SampleType::Pointer sample = SampleType::New() ;
>>>> // here I create the samplelist
>>>> typedef itk::Statistics::CovarianceCalculator< SampleType >
>>>> CovarianceAlgorithmType;
>>>> CovarianceAlgorithmType::Pointer covarianceAlgorithm =
>>>> CovarianceAlgorithmType::New();
>>>> covarianceAlgorithm->SetInputSample( sample );
>>>> // I've already calculated the mean:
>>>> covarianceAlgorithm->SetMean( meanAlgorithm->GetOutput() );
>>>> covarianceAlgorithm->Update();
>>>> return 0;
>>>> }
>>>> /
>>>> The error message looks as follows:
>>>> /lucas:Seg_Code> make
>>>> Building dependencies cmake.check_depends...
>>>> Building object file ThresholdSegPrSh.o...
>>>> Building executable
>>>> /private/var/automount/Seg_Code/ThresholdSegPrSh...
>>>> ld: Undefined symbols:
>>>> vnl_matrix_fixed<double, (unsigned)60, (unsigned)60>::div(double
>>>> const*, double, double*)
>>>> vnl_matrix_fixed<double, (unsigned)60, (unsigned)60>::fill(double)
>>>> vnl_matrix_fixed<double, (unsigned)60,
>>>> (unsigned)60>::print(std::basic_ostream<char,
>>>> std::char_traits<char> >&) const
>>>> make[1]: *** [/private/var/automount/Seg_Code/ThresholdSegPrSh]
>>>> Error 1
>>>> make: *** [default_target] Error 2
>>>> /
>>>> Could anyone please help me with this problem ?
>>>> Thanks,
>>>> Lucas Lorenzo
>>>> University of Utah
>>>> Nora Eccles Harrison CardioVascular Research and Training Institute
>>>> Fellows Room
>>>> 95 South 2000 East
>>>> Salt Lake City, UT 84112-5000
>>>> e-mail: lucas at cvrti.utah.edu
>>>> telephone: 801-587-9536
>>>> --------------------------------------------------------------------
>>>> -- --
>>>> _______________________________________________
>>>> Insight-users mailing list
>>>> Insight-users at itk.org
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>> Lucas Lorenzo
>> University of Utah
>> Nora Eccles Harrison CardioVascular Research and Training Institute
>> Fellows Room
>> 95 South 2000 East
>> Salt Lake City, UT 84112-5000
>> e-mail: lucas at cvrti.utah.edu
>> telephone: 801-587-9536
>
>
>
>
Lucas Lorenzo
University of Utah
Nora Eccles Harrison CardioVascular Research and Training Institute
Fellows Room
95 South 2000 East
Salt Lake City, UT 84112-5000
e-mail: lucas at cvrti.utah.edu
telephone: 801-587-9536
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