foreach ( mitk::DataNode::Pointer node, selectedNodes )
{
if (node)
{
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>( node->GetData() );
if (image.IsNull()) return;
mitk::ProgressBar::GetInstance()->AddStepsToDo(10);
mitk::ProgressBar::GetInstance()->Progress(2);
qApp->processEvents();
mitk::AutoCropImageFilter::Pointer cropFilter = mitk::AutoCropImageFilter::New();
cropFilter->SetInput( image );
cropFilter->SetBackgroundValue( 0 );
try
{
cropFilter->Update();
image = cropFilter->GetOutput();
if (image.IsNotNull())
{
if (image->GetDimension() == 4)
{
MITK_INFO << "4D AUTOCROP DOES NOT WORK AT THE MOMENT";
throw "4D AUTOCROP DOES NOT WORK AT THE MOMENT";
unsigned int timesteps = image->GetDimension(3);
for (unsigned int i = 0; i < timesteps; i++)
{
mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New();
imageTimeSelector->SetInput(image);
imageTimeSelector->SetTimeNr(i);
imageTimeSelector->UpdateLargestPossibleRegion();
// We split a long nested code line into separate calls for debugging:
mitk::ImageSource::OutputImageType *_3dSlice = imageTimeSelector->GetOutput();
mitk::Image::Pointer _cropped3dSlice = this->IncreaseCroppedImageSize(_3dSlice);
// +++ BUG +++ BUG +++ BUG +++ BUG +++ BUG +++ BUG +++ BUG +++
mitk::ImageWriteAccessor imAccess(_cropped3dSlice);
void *_data = imAccess.GetData();
// <ToBeRemoved>
// We write some stripes into the image
if ((i & 1) == 0)
{
int depth = _cropped3dSlice->GetDimension(2);
int height = _cropped3dSlice->GetDimension(1);
int width = _cropped3dSlice->GetDimension(0);
for (int z = 0; z < depth; ++z)
for (int y = 0; y < height; ++y)
for (int x = 0; x < width; ++x)
reinterpret_cast<unsigned char *>(_data)[(width * height * z) + (width * y) + x] = x & 1;
// </ToBeRemoved>
}
image->SetVolume(_data, i);
}
node->SetData( image ); // bug fix 3145
}
else
{
node->SetData( this->IncreaseCroppedImageSize(image) ); // bug fix 3145
}
// Reinit node
mitk::RenderingManager::GetInstance()->InitializeViews(
node->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
catch(...)
{
MITK_ERROR << "Cropping image failed...";
}
mitk::ProgressBar::GetInstance()->Progress(8);
}
else
{
MITK_INFO << " a NULL node selected";
}
}
void QmitkTbssRoiAnalysisWidget::PlotFiberBundles(const mitk::PixelType ptype, TractContainerType tracts, mitk::Image *img, bool avg)
{
m_PlottingFiberBundle = true;
this->Clear();
std::vector<TractType>::iterator it = tracts.begin();
std::vector< std::vector <mitk::ScalarType > > profiles;
mitk::ImagePixelReadAccessor<T,3> imAccess(img,img->GetVolumeData(0));
it = tracts.begin();
while(it != tracts.end())
{
TractType tract = *it;
TractType::iterator tractIt = tract.begin();
std::vector<mitk::ScalarType> profile;
while(tractIt != tract.end())
{
PointType p = *tractIt;
// Get value from image
profile.push_back( (mitk::ScalarType) imAccess.GetPixelByWorldCoordinates(p) );
++tractIt;
}
profiles.push_back(profile);
std::cout << std::endl;
++it;
}
if(profiles.size() == 0)
return;
m_IndividualProfiles = profiles;
std::string title = "Fiber bundle plot";
this->SetPlotTitle( title.c_str() );
// initialize average profile
std::vector<mitk::ScalarType> averageProfile;
std::vector<mitk::ScalarType> profile = profiles.at(0); // can do this because we checked the size of profiles before
for(unsigned int i=0; i<profile.size(); ++i)
{
averageProfile.push_back(0.0);
}
std::vector< std::vector<mitk::ScalarType> >::iterator profit = profiles.begin();
int id=0;
while(profit != profiles.end())
{
std::vector<mitk::ScalarType> profile = *profit;
std::vector<mitk::ScalarType> xAxis;
for(unsigned int i=0; i<profile.size(); ++i)
{
xAxis.push_back((mitk::ScalarType)i);
averageProfile.at(i) += profile.at(i) / profiles.size();
}
int curveId = this->InsertCurve( "" );
this->SetCurveData( curveId, xAxis, profile );
++profit;
id++;
}
m_Average = averageProfile;
if(avg)
{
// Draw the average profile
std::vector<mitk::ScalarType> xAxis;
for(unsigned int i=0; i<averageProfile.size(); ++i)
{
xAxis.push_back((mitk::ScalarType)i);
}
int curveId = this->InsertCurve( "" );
this->SetCurveData( curveId, xAxis, averageProfile );
QPen pen( Qt::SolidLine );
pen.setWidth(3);
pen.setColor(Qt::red);
this->SetCurvePen( curveId, pen );
id++;
}
this->Replot();
}
