Hi Sascha,
sorry for replying so late - I was on vacation and after that had some trouble
generating the stack traces you need. Since the program mostly does not crash,
but merely throws an exception, the stack trace is not very informative.
I discovered several problems with loading and saving DICOM data and will
describe them in detail. They only occur with the manually compiled
mitkWorkbench - everything is fine with the pre-compiled binary for OS X as
well as running the code on its own without MITK.
1. Loading large DICOM datasets
The datasets from http://www.osirix-viewer.com/datasets/ produce the following
errors:
1a: When loading using the "Open" button from the toolbar, and when using the
following code:
mitk::DataNodeFactory::Pointer reader = mitk::DataNodeFactory::New();
try
{
reader->SetFileName(m_imageData.getFileNames()[0].toStdString().c_str());
reader->Update();
// Add the node to the DataStorage
mitk::DataNode::Pointer node = reader->GetOutput();
node->SetProperty( "name", mitk::StringProperty::New(
QString("DICOM").toStdString().c_str() ));
//node->SetData( reader->GetOutput() );
GetDataStorage()->Add( node);
// show the newly created image
mitk::BaseData::Pointer basedata = node->GetData();
mitk::RenderingManager::GetInstance()->InitializeViews(basedata->GetTimeSlicedGeometry(),
mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
}
catch (...)
{
MITK_INFO << "Mitk: Could not open file " <<
m_imageData.getFileNames()[0];
return;
}
The following error occurs:
[19.786] DataNodeFactory: Loading DICOM series 0: Series UID
1.3.12.2.1107.5.1.4.51964.4.0.3816613618801152
[19.787] 1559 'CT' files (CT Image Storage) loaded into 1 mitk::Image
[19.787] multi-frame: No
[19.787] reader support: Supported
[19.787] pixel spacing type: In Patient
[19.787] gantry tilt corrected: No
[19.787] 3D+t: No
[19.787]
--------------------------------------------------------------------------------
#20.914# ERROR: Error encountered when loading DICOM series:std::exception
#20.914# ERROR: DataNodeFactory: Skipping series 0 due to some unspecified
error...
Das Programm ist abgestürzt.
And the following stack trace is reported:
Process: mitkWorkbench [14398]
Path: /Users/USER/*/mitkWorkbench.app/Contents/MacOS/mitkWorkbench
Identifier: ???
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: Qt Creator [7949]
User ID: 501
Date/Time: 2013-09-23 10:55:08.174 +0200
OS Version: Mac OS X 10.8.5 (12F37)
Report Version: 10
Interval Since Last Report: 63214 sec
Crashes Since Last Report: 36
Per-App Interval Since Last Report: 5731 sec
Per-App Crashes Since Last Report: 1
Anonymous UUID: 4B7B1138-FD68-8E77-97ED-802190EFDA80
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000000c8
VM Regions Near 0xc8:
-->
__TEXT 0000000102aa2000-0000000102acf000 [ 180K] r-x/rwx
SM=COW /Users/USER/*/mitkWorkbench.app/Contents/MacOS/mitkWorkbench
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libMitk.dylib 0x0000000102daba6c
itk::SmartPointer<mitk::TimeSlicedGeometry>::GetPointer() const + 12
(itkSmartPointer.h:94)
1 libMitk.dylib 0x0000000102da8b1c
mitk::BaseData::GetTimeSlicedGeometry() + 28 (mitkBaseData.h:67)
2 liborg_mitk_gui_qt_tenslices.dylib 0x0000000119fb56d2
QmitkTenSlicesView::OnLoadButton_pressed() + 1282 (QmitkTenSlicesView.cpp:178)
[…]
1b: When using ITK and GDCM to open the same datasets with the following code:
typedef itk::Image<ItkPixelType, 3> ItkInputImageType;
typedef itk::ImageSeriesReader<ItkInputImageType> ItkReaderType;
m_gdcmIO = itk::GDCMImageIO::New();
ItkReaderType::Pointer reader = ItkReaderType::New();
reader->SetImageIO(m_gdcmIO);
reader->SetFileNames(filenames);
try
{
reader->Update();
}
catch(itk::ExceptionObject &excp)
{
qDebug() << "Exception thrown while reading DICOM series\n" <<
excp.GetDescription();
return false;
}
I get the following exception:
Exception thrown while reading DICOM series
itk::ERROR: GDCMImageIO(0x7fdb7cb48880): Failed to get the buffer!
2. Saving any DICOM images
2a. Right-click on a dataset in the DataManager and click save, then save it
as DICOM in the dialog, the following error message is displayed:
error saving file:
/Users/peter/Forschung/code/MITK-2013.06.0-src/Core/Code/IO/mitkIOUtil.cpp:206:
An exception occured during writing the file /Users/peter/Desktop/test/bla_.
Exception says std::bad_cast
2b. Using ITK and GDCM, the same std::bad_cast exception is thrown. I used the
code from the ITK DICOM resampling example
>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
which runs fine when compiled on its own, and integrated it into MITK. The
important code is the following:
OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
std::string seriesFormat("/Users/peter/Desktop/test");
seriesFormat = seriesFormat + "/" + "IM%d.dcm";
outputNames->SetSeriesFormat (seriesFormat.c_str());
outputNames->SetStartIndex (1);
outputNames->SetEndIndex (outputSize[2]);
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput( shiftScale->GetOutput() );
seriesWriter->SetImageIO( gdcmIO );
seriesWriter->SetFileNames( outputNames->GetFileNames() );
seriesWriter->SetMetaDataDictionaryArray( &outputArray );
try
{
seriesWriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown while writing the series " << std::endl;
std::cerr << excp.what() << std::endl;
return;
}
catch (std::bad_cast &excp)
{
std::cerr << "Bad Cast: " << excp.what() << std::endl;
void *array[50];
size_t size;
size = backtrace(array, 50);
backtrace_symbols_fd(array, size, STDERR_FILENO);
return;
}
The following exception is thrown:
Bad Cast: std::bad_cast
And the stack trace is not very helpful since the program does not crash:
0 liborg_mitk_gui_qt_resample.dylib 0x000000012a9a21f0
_ZN17QmitkResampleView17DoImageProcessingEv + 10784
1 liborg_mitk_gui_qt_resample.dylib 0x000000012aa05c32
_ZN17QmitkResampleView18qt_static_metacallEP7QObjectN11QMetaObject4CallEiPPv +
130
2 QtCore 0x000000011301f09e
_ZN11QMetaObject8activateEP7QObjectPKS_iPPv + 1566
3 QtGui 0x00000001128e9ef1
_ZN15QAbstractButton7clickedEb + 49
[…]
I'm not sure whether this is a problem with MITK, ITK, GDCM or OS X since the
"std::bad_cast" exception is quite mysterious. Also, the loading error of the
mentioned large datasets is very strange.
Again, here is my coding environment:
>>
>> Mac OS X 10.8.4 / 10.8.5
>> MITK 2013.06 Superbuild,
>> ITK 4.3.2,
>> VTK 5.10.1,
>> Boost 1.45,
>> GDCM 2.2.1,
>> DCMTK 3.6.1
>> Qt 4.8.4
>>
>> (I built all these libraries myself and pointed the superbuild towards them)
This is the only configuration where I got MITK to run on OS X, newer versions
of ITK and GDCM deliver compiler errors that are another story.
I hope that you can reproduce the error and that you have some insight what
could be the cause. I am trying to implement a very important project for
clinical researchers in Leipzig, and right now I'm pretty much stuck because of
these errors. Also, if these errors do not occur on other platforms (Windows or
Linux), I would consider switching platforms since MITK and OS X 10.8 do not
seem to like each other very much.
Kind regards,
Peter Salz
Am 16.08.2013 um 15:37 schrieb Sascha Zelzer <[email protected]>:
> Hi Peter,
>
> how do you exactly save the image? Are using the context menu in the
> datamanger or are you calling some code yourself?
>
> Could you please also provide a full stack trace and the complete error
> message, ideally attached to a bug report at bugs.mitk.org?
>
> Thanks,
>
> Sascha
>
> On 08/13/2013 10:09 PM, Peter Salz wrote:
>> Hi,
>>
>> it's me again. I encountered another severe bug with the custom-build MITK
>> on Mac OS X 10.8. When trying to save a volume into a series of DICOM
>> images, a std::bad_cast exception is thrown. This happens when you load a
>> DICOM dataset with MITK and try to save it again (with the following error
>> message):
>>
>> Could not save image.
>> Error:
>> .../MITK-2013.06.0-src/Core/Code/IO/mitkIOUtil.cpp:206:
>> An exception occurred during writing the file …. Exception says std::bad_cast
>>
>> It also happens when I try to save a DICOM volume that I loaded myself with
>> ITK - I use an itk::ImageSeriesWriter, and I even imported the code for the
>> ITK DICOM Resampling Example into a MITK plugin because this code works when
>> compiled separately.
>> But when executed from the MITK as a plugin, the same std::bad_cast error
>> happens (note that MITK is not involved at all - I just press the "Do
>> something" button from the generic plugin and execute the code as presented
>> here:
>>
>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>
>>
>>
>> Here is my coding environment:
>>
>> Mac OS X 10.8.4
>> MITK 2013.06 Superbuild,
>> ITK 4.3.2,
>> VTK 5.10.1,
>> Boost 1.45,
>> GDCM 2.2.1,
>> DCMTK 3.6.1
>> Qt 4.8.4
>>
>> (I built all these libraries myself and pointed the superbuild towards them)
>>
>>
>> Hope anyone can help with this because this is a very severe bug and I
>> wonder whether it is OS X 10.8 specific.
>>
>>
>> Best regards,
>>
>> Peter Salz
>>
>> TU Kaiserslautern, Germany
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