[OpenWalnut-Dev] Write file reader for WDataSetScalar

[Frank Zisko]

Hi Alex,

here is a file exported from OW. 

https://www.dropbox.com/s/xnrgvnsqxryayco/out.nii

Greetings

Frank


Am Donnerstag, den 10.05.2012, 23:46 +0200 schrieb 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
> > 
> > 
> > _______________________________________________
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> > 
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