[OpenWalnut-Dev] Write file reader for WDataSetScalar

[Alexander Wiebel]

Hi Frank,
I can not see the problem immediately. So let us approach it iteratively:
- Can you save the loaded dataset in NIfTI (.nii) format and send it to
me so I can check the data you actually loaded?

Cheers Alex

On 05/10/2012 05:58 PM, Frank Zisko wrote:
> 
> 
> Hey guys,
> 
> I've a problem in writing a file reader.
> (ROOT/src/modules/data/io/WReaderMy.cpp  .h)
> It is a anatomic file. Including a header, voxels (intensity values) and
> postheader.
> 
> I try to use a WDataSetScalar. Constructor want: WDataSetScalar aDataSet
> = new (WValueSetBase,WGrid). But something is wrong in my code. I write
> all values in WValueSet and create a WGrid. The 3D viewer shows a black
> dataset, the histogram viewer give me errors (see below). The tmp
> variable in the loop has right values. But I don't know why it doesn't
> works.
> 
> Has anybody an idea what can i do?
> 
> 
> HEADER
> 
> [...]
> protected:
> 
>     boost::shared_ptr< std::ifstream > m_ifs;
> [...]
> 
> 
> SOURCE
> 
> #include ...
> [...]
> boost::shared_ptr< WDataSet > WReaderMy::read()
> {
>     m_ifs = boost::shared_ptr< std::ifstream >( new std::ifstream() );
>     m_ifs->open( m_fname.c_str(), std::ifstream::in |
> std::ifstream::binary );
> [...]
>     wlog::info( "WReaderMy" ) << "Read array ...";
>     // My Data Array.
>     int voxelCount = dimX * dimY * dimZ;
>     int tensorDim = 1; // Scalar values.
>     int order = 0; // ?
>     boost::shared_ptr< std::vector< int > > myData =  boost::shared_ptr<
> std::vector< int > >( new std::vector< int >( voxelCount ) );
> 
>     int tmp = 0;
>     for (int i = 0; i < voxelCount; i++)
>     {
>         //m_ifs->read( reinterpret_cast<char*>(&myData->at(i) ),  1);
>         m_ifs->read( reinterpret_cast<char*>(&tmp),  1); // Read 1 byte.
>         (*myData)[i] = tmp;
>     }
>     wlog::info( "WReaderMy" ) << "Read array ... Done.";
> 
>     boost::shared_ptr< WValueSetBase > myValueSet; // For creatiung
> DataSetScalar ( WValueSetBase, WGrid).
>     myValueSet = boost::shared_ptr< WValueSetBase >( new WValueSet< int
>>( order, tensorDim, myData) );
> 
> 
> [...]
>     boost::shared_ptr< WGrid > myGrid;
>     myGrid = boost::shared_ptr< WGridRegular3D >( new WGridRegular3D(
> dimX, dimY, dimZ, WGridTransformOrtho( getStandardTransform() ) ) );
>     boost::shared_ptr< WDataSet > myDataSet;
>     wlog::debug( "WReaderMy" ) << "Load as WDataSetScalar";
>     myDataSet = boost::shared_ptr< WDataSet >( new WDataSetScalar(
> myValueSet, myGrid ) );
>     myDataSet->setFilename( m_fname );
>     m_ifs->close();
>     return myDataSet;
> }
> 
> 
> Histogram output in bash:
> 
> [...]
> *INFO    [ModuleContainer (KernelRootContainer)] Connecting Data
> Module:out with HistogramView:Input dataset #0
> *INFO    [HistogramView] Recalculating histogram.
> Exception thrown! Callstack's backtrace:
> trace: WException::WException(std::exception const&)    ->   
> lib/libopenwalnut.so.1(_ZN10WExceptionC1ERKSt9exception+0x135)
> [0x7ff3457e6715]
> trace: WThreadedRunner::threadMainSave()    ->   
> lib/libopenwalnut.so.1(_ZN15WThreadedRunner14threadMainSaveEv+0xba)
> [0x7ff34581b00a]
> trace: boost::detail::thread_data<boost::function<void ()> >::run()   
> ->   
> lib/libopenwalnut.so.1(_ZN5boost6detail11thread_dataINS_8functionIFvvEEEE3runEv+0x1e)
> [0x7ff34581d98e]
> trace: thread_proxy()    ->   
> /usr/lib/libboost_thread.so.1.46.1(thread_proxy+0x69) [0x7ff341f19ba9]
> trace: ()    ->    /usr/lib/nvidia-current-updates/libGL.so.1(+0xa7354)
> [0x7ff33f197354]
> 
> *ERROR   [KernelRootContainer] Error in module "HistogramView".
> Forwarding to nesting container.
> *INFO    [ModuleContainer (KernelRootContainer)] Disconnecting Data
> Module:out from HistogramView:Input dataset #0
> *ERROR   [Module (HistogramView)] WException. Notifying. Message:
> vector::_M_range_check
> 
> 
> _______________________________________________
> OpenWalnut-Dev mailing list
> OpenWalnut-Dev at lists.informatik.uni-leipzig.de
> http://lists.informatik.uni-leipzig.de/mailman/listinfo/openwalnut-dev
> 
> Archive: http://lists.informatik.uni-leipzig.de/pipermail/openwalnut-dev/


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 900 bytes
Desc: OpenPGP digital signature
URL: <http://lists.informatik.uni-leipzig.de/pipermail/openwalnut-dev/attachments/20120510/53939c6a/attachment.asc>