void ModelSeries::addReconstruction( ::fwMedData::ModelSeries::sptr& _modelSeries, ::fwData::Reconstruction::sptr& _rec)
{
::fwMedData::ModelSeries::ReconstructionVectorType recDB = _modelSeries->getReconstructionDB();
FW_RAISE_IF("Reconstruction is invalid.", _rec == nullptr);
FW_RAISE_IF("Reconstruction already exists in ModelSeries.",
std::find(recDB.begin(), recDB.end(), _rec) != recDB.end());
recDB.push_back(_rec);
_modelSeries->setReconstructionDB(recDB);
}
void MetaImageReader::read()
{
assert( !m_object.expired() );
assert( m_object.lock() );
::fwData::Image::sptr pImage = this->getConcreteObject();
vtkSmartPointer< vtkMetaImageReader > reader = vtkSmartPointer< vtkMetaImageReader >::New();
reader->SetFileName(this->getFile().string().c_str());
Progressor progress(reader, this->getSptr(), this->getFile().string());
reader->Update();
reader->UpdateInformation();
reader->PropagateUpdateExtent();
vtkDataObject *obj = reader->GetOutput();
vtkImageData* img = vtkImageData::SafeDownCast(obj);
FW_RAISE_IF("MetaImageReader cannot read mhd image file :"<<this->getFile().string(), !img);
try
{
::fwVtkIO::fromVTKImage( img, pImage);
}
catch( std::exception &e)
{
FW_RAISE("MetaImage to fwData::Image failed : "<<e.what());
}
}
void ImageReader::read()
{
assert( !m_object.expired() );
assert( m_object.lock() );
::fwData::Image::sptr pImage = getConcreteObject();
vtkSmartPointer< vtkGenericDataObjectReader > reader = vtkSmartPointer< vtkGenericDataObjectReader >::New();
reader->SetFileName(this->getFile().string().c_str());
//add progress observation
Progressor progress(reader, this->getSptr(), this->getFile().string());
reader->Update();
vtkDataObject *obj = reader->GetOutput();
vtkImageData* img = vtkImageData::SafeDownCast(obj);
FW_RAISE_IF("ImageReader cannot read VTK image file :"<<this->getFile().string(), !img);
try
{
::vtkIO::fromVTKImage( img, pImage);
}
catch( std::exception &e)
{
FW_RAISE("VTKImage to fwData::Image failed "<<e.what());
}
}
void MeshReader::read()
{
assert( !m_object.expired() );
assert( m_object.lock() );
::fwData::Mesh::sptr pMesh = getConcreteObject();
vtkSmartPointer< vtkGenericDataObjectReader > reader = vtkSmartPointer< vtkGenericDataObjectReader >::New();
reader->SetFileName(this->getFile().string().c_str());
//add progress observation
Progressor progress(reader, this->getSptr(), this->getFile().string());
reader->Update();
vtkDataObject *obj = reader->GetOutput();
vtkPolyData* mesh = vtkPolyData::SafeDownCast(obj);
FW_RAISE_IF("MeshReader cannot read VTK Mesh file : "<< this->getFile().string(), !mesh);
::vtkIO::helper::Mesh::fromVTKMesh(mesh, pMesh);
}
void SeriesDBLazyReader::scanFiles( ::gdcm::Scanner & scanner, const std::vector< std::string > & filenames )
{
scanner.AddTag( seriesUIDTag );
scanner.AddTag( seriesDateTag );
scanner.AddTag( seriesTimeTag );
scanner.AddTag( seriesTypeTag );
scanner.AddTag( seriesDescriptionTag );
scanner.AddTag( seriesPhysicianNamesTag );
scanner.AddTag( equipmentInstitutionNameTag );
scanner.AddTag( patientNameTag );
scanner.AddTag( patientIDTag );
scanner.AddTag( patientBirthdateTag );
scanner.AddTag( patientSexTag );
scanner.AddTag( studyUIDTag );
scanner.AddTag( studyUIDTag );
scanner.AddTag( studyDateTag );
scanner.AddTag( studyTimeTag );
scanner.AddTag( studyReferingPhysicianNameTag );
scanner.AddTag( studyDescriptionTag );
scanner.AddTag( studyPatientAgeTag );
scanner.AddTag( imageTypeTag );
scanner.AddTag( acquisitionDateTag );
scanner.AddTag( acquisitionTimeTag );
scanner.AddTag( sliceThicknessTag );
scanner.AddTag( windowCenterTag );
scanner.AddTag( windowWidthTag );
bool scanIsOk = scanner.Scan( filenames );
FW_RAISE_IF( "Sorry, dicom scanner failed", !scanIsOk );
}
void SSliceIndexDicomPullerEditor::readImage(std::size_t selectedSliceIndex)
{
// DicomSeries
::fwMedData::DicomSeries::csptr dicomSeries = this->getInOut< ::fwMedData::DicomSeries >("series");
SLM_ASSERT("DicomSeries should not be null !", dicomSeries);
if( dicomSeries->getModality() != "CT" && dicomSeries->getModality() != "MR" && dicomSeries->getModality() != "XA")
{
return;
}
// Clear temporary seriesDB
::fwMedDataTools::helper::SeriesDB sDBTempohelper(m_tempSeriesDB);
sDBTempohelper.clear();
// Creates unique temporary folder, no need to check if exists before (see ::fwTools::System::getTemporaryFolder)
::boost::filesystem::path path = ::fwTools::System::getTemporaryFolder("dicom");
::boost::filesystem::path tmpPath = path / "tmp";
SLM_INFO("Create " + tmpPath.string());
::boost::filesystem::create_directories(tmpPath);
const auto& binaries = dicomSeries->getDicomContainer();
auto iter = binaries.find(selectedSliceIndex);
OSLM_ASSERT("Index '"<<selectedSliceIndex<<"' is not found in DicomSeries", iter != binaries.end());
const ::fwMemory::BufferObject::sptr bufferObj = iter->second;
const ::fwMemory::BufferObject::Lock lockerDest(bufferObj);
const char* buffer = static_cast<char*>(lockerDest.getBuffer());
const size_t size = bufferObj->getSize();
::boost::filesystem::path dest = tmpPath / std::to_string(selectedSliceIndex);
::boost::filesystem::ofstream fs(dest, std::ios::binary|std::ios::trunc);
FW_RAISE_IF("Can't open '" << tmpPath << "' for write.", !fs.good());
fs.write(buffer, size);
fs.close();
// Read image
m_dicomReader.lock()->setFolder(tmpPath);
if(!m_dicomReader.expired())
{
m_dicomReader.lock()->update();
if(m_dicomReader.expired() || m_dicomReader.lock()->isStopped())
{
return;
}
}
else
{
return;
}
//Copy image
::fwMedData::ImageSeries::sptr imageSeries;
if(m_tempSeriesDB->getContainer().size() > 0)
{
imageSeries = ::fwMedData::ImageSeries::dynamicCast(*(m_tempSeriesDB->getContainer().begin()));
}
if(imageSeries)
{
::fwData::Image::sptr newImage = imageSeries->getImage();
::fwData::Image::SizeType newSize = newImage->getSize();
newImage->setField(::fwDataTools::fieldHelper::Image::m_axialSliceIndexId, m_axialIndex);
m_frontalIndex->setValue(static_cast<int>(newSize[0]/2));
newImage->setField(::fwDataTools::fieldHelper::Image::m_frontalSliceIndexId, m_frontalIndex);
m_sagittalIndex->setValue(static_cast<int>(newSize[1]/2));
newImage->setField(::fwDataTools::fieldHelper::Image::m_sagittalSliceIndexId, m_sagittalIndex);
this->setOutput("image", newImage);
}
::boost::system::error_code ec;
::boost::filesystem::remove_all(path, ec);
SLM_ERROR_IF("remove_all error for path " + path.string() + ": " + ec.message(), ec.value());
}
