void addPath(std::string dir)
{
namespace bp = ::boost::python;
SLM_ERROR_IF("Python must be initialized before adding a new dir", Py_IsInitialized());
bp::object sys = bp::import("sys");
sys.attr("path").attr("insert")(0, dir);
OSLM_INFO(dir << " appended to Python Path");
}
void Video::doUpdate() throw(fwTools::Failed)
{
::fwData::Video::sptr video = this->getObject< ::fwData::Video >();
if (!video->dataAvailable())
return;
const ::boost::uint8_t * _pImageBuffer = video->getImageBuffer();
int size[3];
size[0] = video->getXSize() ;
size[1] = video->getYSize();
size[2] = 1;
m_array->SetNumberOfComponents(video->m_ui8BPP );
m_array->SetVoidArray( (unsigned char*)_pImageBuffer, video->getXSize() * video->getYSize() ,1);
m_imageData->AllocateScalars(VTK_UNSIGNED_CHAR, video->m_ui8BPP);
m_imageData->GetPointData()->SetScalars(m_array) ;
m_imageData->SetDimensions(size) ;
m_imageData->SetSpacing(1.0, 1.0, 1.0 );
m_imageData->SetOrigin(0.0, 0.0, 0.0 );
if(!bText_init)
{
m_texture->SetInputData(m_imageData ) ;
this->getActor()->SetScale(size[0], size[1], 1.0);
this->getRenderer()->InteractiveOff();
this->getRenderer()->GetActiveCamera()->ParallelProjectionOn();
this->getRenderer()->ResetCamera();
//fit the image to the render window
this->getRenderer()->GetActiveCamera()->SetParallelScale(size[1] / 2.0);
this->addToRenderer(this->getActor());
bText_init = true;
::boost::filesystem::path pathShaderVP ( "Bundles/visuVTKAdaptor_" + std::string(VISUVTKADAPTOR_VER) + "/vp.glsl" );
::boost::filesystem::path pathShaderFP ( "Bundles/visuVTKAdaptor_" + std::string(VISUVTKADAPTOR_VER) + "/fp.glsl" );
vtkSmartPointer<vtkShaderProgram2> pProgram;
pProgram = ::fwRenderVTK::vtk::buildShaderFromFile(this->getRenderer()->GetRenderWindow(),
pathShaderVP.string().c_str(),
pathShaderFP.string().c_str());
SLM_ERROR_IF("Failed to build shader program", !pProgram);
vtkProperty *property = this->getActor()->GetProperty();
vtkOpenGLProperty *pOpenGLProperty = vtkOpenGLProperty::SafeDownCast(property);
SLM_ASSERT("Shader program not supported", pOpenGLProperty);
pOpenGLProperty->SetPropProgram(pProgram);
}
m_imageData->Modified();
this->setVtkPipelineModified();
}
void setHome(std::string dir)
{
if(!Py_IsInitialized())
{
if (::fwPython::Config::home)
{
delete [] ::fwPython::Config::home;
}
::fwPython::Config::home = charFromString(dir);
Py_SetPythonHome( ::fwPython::Config::home );
OSLM_INFO("Python Home set to " << dir);
}
SLM_ERROR_IF("Python home must be set before python initialisation", Py_IsInitialized());
}
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());
}
void SeriesDBReader::addSeries( const ::fwMedData::SeriesDB::sptr& seriesDB,
const std::vector< std::string >& filenames)
{
//gdcm::Trace::SetDebug( 1 );
//gdcm::Trace::SetWarning( 1 );
//gdcm::Trace::SetError( 1 );
::gdcm::Scanner scanner;
const ::gdcm::Tag seriesUIDTag(0x0020, 0x000e);
const ::gdcm::Tag seriesDateTag(0x0008, 0x0021);
const ::gdcm::Tag seriesTimeTag(0x0008, 0x0031);
const ::gdcm::Tag seriesTypeTag(0x0008, 0x0060);
const ::gdcm::Tag seriesDescriptionTag(0x0008, 0x103e);
const ::gdcm::Tag seriesPhysicianNamesTag(0x0008, 0x1050);
const ::gdcm::Tag equipmentInstitutionNameTag(0x0008, 0x0080);
const ::gdcm::Tag patientNameTag(0x0010, 0x0010);
const ::gdcm::Tag patientIDTag(0x0010, 0x0020);
const ::gdcm::Tag patientBirthdateTag(0x0010, 0x0030);
const ::gdcm::Tag patientSexTag(0x0010, 0x0040);
const ::gdcm::Tag studyUIDTag(0x0020, 0x000d);
const ::gdcm::Tag studyDateTag(0x0008, 0x0020);
const ::gdcm::Tag studyTimeTag(0x0008, 0x0030);
const ::gdcm::Tag studyReferingPhysicianNameTag(0x0008, 0x0090);
const ::gdcm::Tag studyDescriptionTag(0x0008, 0x1030);
const ::gdcm::Tag studyPatientAgeTag(0x0010, 0x1010);
const ::gdcm::Tag imageTypeTag(0x0008, 0x0008);
const ::gdcm::Tag acquisitionDateTag(0x0008, 0x0022);
const ::gdcm::Tag acquisitionTimeTag(0x0008, 0x0032);
scanner.AddTag( seriesUIDTag );
scanner.AddTag( seriesDateTag );
scanner.AddTag( seriesTimeTag );
scanner.AddTag( seriesTypeTag );
scanner.AddTag( seriesDescriptionTag );
scanner.AddTag( seriesPhysicianNamesTag );
scanner.AddTag( equipmentInstitutionNameTag );
scanner.AddTag( studyUIDTag );
scanner.AddTag( patientNameTag );
scanner.AddTag( patientIDTag );
scanner.AddTag( patientBirthdateTag );
scanner.AddTag( patientSexTag );
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 );
try
{
const bool isScanned = scanner.Scan( filenames );
if( !isScanned )
{
SLM_ERROR("Scanner failed");
return;
}
const ::gdcm::Directory::FilenamesType keys = scanner.GetKeys();
typedef std::map< std::string, std::vector< std::string > > MapSeriesType;
MapSeriesType mapSeries;
for(const std::string& filename : keys)
{
SLM_ASSERT("'"+filename+"' is not a key in the mapping table", scanner.IsKey(filename.c_str()));
const char* seriesUID = scanner.GetValue( filename.c_str(), seriesUIDTag );
const char* acqDate = scanner.GetValue( filename.c_str(), acquisitionDateTag );
if (seriesUID)
{
std::string fileSetId = seriesUID;
if (acqDate)
{
fileSetId += "_";
fileSetId += acqDate;
}
const char* imageType = scanner.GetValue(filename.c_str(), imageTypeTag);
if(imageType)
{
// Treatment of secondary capture dicom file.
SLM_TRACE("Image Type : " + std::string(imageType));
fileSetId += "_";
fileSetId += imageType;
}
mapSeries[fileSetId].push_back(filename);
}
else
{
SLM_ERROR("No series name found in : " + filename );
}
}
for(const auto& elt : mapSeries)
{
::fwMedData::ImageSeries::sptr series = ::fwMedData::ImageSeries::New();
::fwMedData::Patient::sptr patient = series->getPatient();
::fwMedData::Study::sptr study = series->getStudy();
::fwMedData::Equipment::sptr equipment = series->getEquipment();
seriesDB->getContainer().push_back(series);
SLM_TRACE( "Processing: '" + elt.first + "' file set.");
const MapSeriesType::mapped_type& files = elt.second;
if ( !files.empty() )
{
vtkSmartPointer< vtkStringArray > fileArray = vtkSmartPointer< vtkStringArray >::New();
vtkSmartPointer< vtkGDCMImageReader > reader = vtkSmartPointer< vtkGDCMImageReader >::New();
reader->FileLowerLeftOn();
::gdcm::IPPSorter ippSorter;
ippSorter.SetComputeZSpacing( true );
ippSorter.SetZSpacingTolerance( 1e-3 );
bool isSorted = ippSorter.Sort( files );
std::vector<std::string> sorted;
double zspacing = 0.;
if(isSorted)
{
sorted = ippSorter.GetFilenames();
zspacing = ippSorter.GetZSpacing();
OSLM_TRACE("Found z-spacing:" << ippSorter.GetZSpacing());
}
else
{
// Else an error has been encountered.
// We fall back to a more trivial sorting based on the InstanceNumber DICOM tag.
SLM_WARN("IPP Sorting failed. Falling back to Instance Number sorting.");
::gdcm::Sorter sorter;
sorter.SetSortFunction(sortByInstanceNumber);
isSorted = sorter.StableSort( filenames);
if(isSorted)
{
// If the custom sorted returns true, it worked
// and the filenames are sorted by InstanceNumber (ASC).
sorted = sorter.GetFilenames();
}
else
{
// There is nothing more we can do to sort DICOM files.
SLM_ERROR("Failed to sort '"+elt.first+"'");
}
}
fileArray->Initialize();
if(isSorted)
{
SLM_TRACE("Success to sort '" + elt.first+"'");
if (!zspacing && sorted.size() > 1)
{
SLM_TRACE( "Guessing zspacing ..." );
if (!sorted.empty())
{
::gdcm::Reader localReader1;
::gdcm::Reader localReader2;
const std::string& f1 = *(sorted.begin());
const std::string& f2 = *(sorted.begin() + 1);
SLM_TRACE( "Search spacing in: '" + f1 +"'");
SLM_TRACE( "Search spacing in: '" + f2 +"'");
localReader1.SetFileName( f1.c_str() );
localReader2.SetFileName( f2.c_str() );
const bool canRead = localReader1.Read() && localReader2.Read();
if(canRead)
{
const std::vector<double> vOrigin1 =
::gdcm::ImageHelper::GetOriginValue(localReader1.GetFile());
const std::vector<double> vOrigin2 =
::gdcm::ImageHelper::GetOriginValue(localReader2.GetFile());
zspacing = vOrigin2[2] - vOrigin1[2];
OSLM_TRACE(
"Found z-spacing:" << zspacing << " from : << " << vOrigin2[2] << " | " <<
vOrigin1[2]);
}
SLM_ERROR_IF("Cannot read: '" + f1 + "' or: '" + f2 +"'", !canRead);
}
}
}
for(const std::string& file : sorted)
{
SLM_TRACE("Add '" + file + "' to vtkGdcmReader");
fileArray->InsertNextValue(file.c_str());
}
::fwData::Image::sptr pDataImage = ::fwData::Image::New();
bool res = false;
if (fileArray->GetNumberOfValues() > 0)
{
reader->SetFileNames( fileArray );
try
{
SLM_TRACE("Read Series: '" + elt.first + "'");
//add progress observation
vtkSmartPointer< ::fwVtkIO::helper::vtkLambdaCommand > progressCallback =
vtkSmartPointer< ::fwVtkIO::helper::vtkLambdaCommand >::New();
progressCallback->SetCallback([this](vtkObject* caller, long unsigned int, void* )
{
auto filter = static_cast<vtkGDCMImageReader*>(caller);
m_job->doneWork( filter->GetProgress()*100 );
});
reader->AddObserver(vtkCommand::ProgressEvent, progressCallback);
m_job->addSimpleCancelHook( [&]()
{
reader->AbortExecuteOn();
} );
reader->Update();
reader->UpdateInformation();
reader->PropagateUpdateExtent();
try
{
::fwVtkIO::fromVTKImage(reader->GetOutput(), pDataImage);
res = true;
}
catch(std::exception& e)
{
OSLM_ERROR("VTKImage to fwData::Image failed : "<<e.what());
}
}
catch (std::exception& e)
{
OSLM_ERROR( "Error during conversion : " << e.what() );
}
catch (...)
{
SLM_ERROR( "Unexpected error during conversion" );
}
m_job->finish();
}
if (res)
{
SLM_ASSERT("No file to read", !files.empty());
// Read medical info
vtkMedicalImageProperties* medprop = reader->GetMedicalImageProperties();
const std::string patientName = medprop->GetPatientName(); //"0010|0010"
const std::string patientId = medprop->GetPatientID();
const std::string patientBirthdate = medprop->GetPatientBirthDate(); //"0010|0030"
const std::string patientSex = medprop->GetPatientSex(); //"0010|0040"
const ::gdcm::Scanner::ValuesType gdcmPhysicianNames = scanner.GetValues( seriesPhysicianNamesTag );
const char* seriesUIDStr = scanner.GetValue( files[0].c_str(), seriesUIDTag );
const char* seriesTimeStr = scanner.GetValue( files[0].c_str(), seriesTimeTag );
const char* seriesDateStr = scanner.GetValue( files[0].c_str(), seriesDateTag );
const std::string seriesModality = medprop->GetModality(); //"0008|0060"
const std::string seriesDescription = medprop->GetSeriesDescription();
const std::string seriesDate = ( seriesDateStr ? seriesDateStr : "" );
const std::string seriesTime = ( seriesTimeStr ? seriesTimeStr : "" );
::fwMedData::DicomValuesType seriesPhysicianNames;
for(const std::string& name : gdcmPhysicianNames)
{
::fwMedData::DicomValuesType result;
::boost::split( result, name, ::boost::is_any_of("\\"));
seriesPhysicianNames.reserve(seriesPhysicianNames.size() + result.size());
seriesPhysicianNames.insert(seriesPhysicianNames.end(), result.begin(), result.end());
}
const char* studyUIDStr = scanner.GetValue( files[0].c_str(), studyUIDTag );
const char* studyReferingPhysicianNameStr =
scanner.GetValue( files[0].c_str(), studyReferingPhysicianNameTag );
const std::string studyDate = medprop->GetStudyDate();
const std::string studyTime = medprop->GetStudyTime();
const std::string studyDescription = medprop->GetStudyDescription(); //"0008|1030"
const std::string studyPatientAge = medprop->GetPatientAge();
const std::string equipementInstitution = medprop->GetInstitutionName(); //"0008|0080"
const std::string studyReferingPhysicianName =
( studyReferingPhysicianNameStr ? studyReferingPhysicianNameStr : "" );
const double thickness = medprop->GetSliceThicknessAsDouble();//"0018|0050"
double center = 0.0;
double width = 0.0;
if (medprop->GetNumberOfWindowLevelPresets())//FIXME : Multiple preset !!!
{
medprop->GetNthWindowLevelPreset(0, &width, ¢er); //0028|1050,1051
}
// Image must have 3 dimensions
if(pDataImage->getNumberOfDimensions() == 2)
{
::fwData::Image::SizeType imgSize = pDataImage->getSize();
imgSize.resize(3);
imgSize[2] = 1;
pDataImage->setSize(imgSize);
::fwData::Image::OriginType imgOrigin = pDataImage->getOrigin();
imgOrigin.resize(3);
imgOrigin[2] = 0.;
pDataImage->setOrigin(imgOrigin);
}
::fwData::Image::SpacingType vPixelSpacing = pDataImage->getSpacing();
vPixelSpacing.resize(3);
// assume z-spacing = 1 if not guessed
vPixelSpacing[2] = zspacing ? zspacing : (thickness ? thickness : 1.);
pDataImage->setSpacing(vPixelSpacing);
pDataImage->setWindowCenter(center);
pDataImage->setWindowWidth(width);
// Get the series instance UID.
SLM_ASSERT("No series UID", seriesUIDStr);
series->setInstanceUID(( seriesUIDStr ? seriesUIDStr : "UNKNOWN-UID" ));
series->setModality( seriesModality );
series->setDescription( seriesDescription );
series->setDate( seriesDate );
series->setTime( seriesTime );
series->setPerformingPhysiciansName( seriesPhysicianNames );
series->setImage(pDataImage);
SLM_ASSERT("No study UID", studyUIDStr);
study->setInstanceUID(( studyUIDStr ? studyUIDStr : "UNKNOWN-UID" ));
study->setDate(studyDate);
study->setTime(studyTime);
study->setDescription(studyDescription);
study->setPatientAge(studyPatientAge);
study->setReferringPhysicianName(studyReferingPhysicianName);
patient->setName(patientName);
patient->setPatientId(patientId);
patient->setBirthdate(patientBirthdate);
patient->setSex(patientSex);
equipment->setInstitutionName(equipementInstitution);
} // if res
} // if !files.empty()
}
} // try
catch (std::exception& e)
{
OSLM_ERROR( "Try with another reader or retry with this reader on a specific subfolder : " << e.what() );
for(const auto filename : filenames)
{
SLM_ERROR("file error : " + filename );
}
}
}
