[OpenWalnut-Dev] Write file reader for WDataSetScalar
Frank Zisko
frank.zisko at gmx.net
Mon May 14 16:59:14 CEST 2012
Hi Alex, hi Mario,
thanks for looking on my problem.
Am Montag, den 14.05.2012, 16:21 +0200 schrieb Alexander Wiebel:
> On 05/14/2012 04:19 PM, Mario Hlawitschka wrote:
> > Hi Frank, Alex,
> >
> > This looks more like flipped axes when creating the file. Can you verify that the X-Y-Z dimensions are correct and you are not reading the data as, e.g., Z-Y-X?
> This is what I meant with order of values. Thank you for clarifying it.
I also think that it looks like that.
In file description is written:
"Each data element (intensity value) is represented in 1 byte. The data
is organized in three loops:
DimZ
DimY
DimX"
I ordered X-Y-Z. So I'll change X and Z. But I wonder, FSL see an image
and OW not.
Greetings
Frank
>
> Alex
>
> > Mario
> >
> > On May 14, 2012, at 4:13 PM, Alexander Wiebel wrote:
> >
> >> Hi Frank,
> >> Mario might be right about endianness related problems. It looks like
> >> something is wrong with the order of the bits or the values themselves.
> >> So you might want to look at endianness or at the order in which you
> >> have the values in the value set.
> >>
> >> See my attached snapshots that I created using Amira.
> >>
> >> Cheers,
> >> Alex
> >>
> >> On 05/14/2012 12:12 PM, Frank Zisko wrote:
> >>> 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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