[OpenWalnut-Dev] Write file reader for WDataSetScalar

[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.

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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