[OpenWalnut-Dev] Write file reader for WDataSetScalar
Mathias Goldau
Mathias.Goldau at nf.mpg.de
Mon May 14 16:26:57 CEST 2012
Hehe ;), Alex you was right, just the wget + URL was not sufficient. However,
fslview showing me a valid but strange image (attached).
Cheers,
Mathias
On 14.05.2012 16:09, Alexander Wiebel wrote:
> Mathias,
> are you sure you downloaded the file and not the html page? I did this
> first and had the problems you describe. Now I have the file itself and
> I am able to load the data set. I will start to analyze it in a second.
>
> Alex
>
> On 05/14/2012 01:00 PM, Mathias Goldau wrote:
>> This file is possibly broken: fslview as well as nifti_tool segfault on it. OW
>> loader module crashes.
>>
>> math at voltaire# /tmp >nifti_tool -disp_hdr -in out.nii
>> header file 'out.nii', num_fields = 43
>>
>> all fields:
>> name offset nvals values
>> ------------------- ------ ----- ------
>> sizeof_hdr 0 1 1329865020
>> data_type 4 10 CTYPE html
>> db_name 14 18 ><html lang="en" x
>> extents 32 1 1815768173
>> session_error 36 1 28257
>> regular 38 1 g
>> dim_info 39 1 61
>> dim 40 8 25890 8814 25376 24940 29555 8765 8226
>> 28024
>> intent_p1 56 1 0.059431
>> *** buffer overflow detected ***: nifti_tool terminated
>> ======= Backtrace: =========
>> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fb0ef544007]
>>
>> FSL is a bit more specific on whats the issue here:
>>
>> math at voltaire# /tmp >nifti_tool -disp_hdr -in out.nii
>> [...]
>> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> ** ERROR (nifti_image_read): cannot create nifti image from header
>> '/tmp/out.nii'
>> ** ERROR: nifti_image_open(/tmp/out): bad header info
>> Error: failed to open file /tmp/out
>> Mutex destroy failure: Device or resource busy
>> Failed to open file /tmp/out
>> [...]
>> E: Child terminated by signal ‘Segmentation fault’
>>
>> Mathias
>>
>> On 14.05.2012 12:12, 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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>>>>
>>>>
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>>
>>
>
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