void DebugTool::Draw(void){
if(display){
Engine &ObjEngine = Engine::GetEngine();
CL_Draw::fill(ObjEngine.graphicContext, 10.0f, (float)consoleBottom, 260.0f, ObjEngine.windowHeight - 175.0f, CL_Colorf(1.0f, 1.0f, 1.0f, 0.07f));
PrintLogStack();
PrintFps();
#ifdef WIN32
PrintMemoryUsage();
#endif
}
}
void QmitkDiffusionDicomImport::DicomLoadStartLoad()
{
itk::TimeProbesCollectorBase clock;
bool imageSuccessfullySaved = true;
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, NULL) << " to '" << locale << "'";
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
int nrFolders = m_Controls->listWidget->count();
if(!nrFolders)
{
Error(QString("No input folders were selected. ABORTING."));
return;
}
Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion()));
PrintMemoryUsage();
QString status;
mitk::DataNode::Pointer node;
mitk::ProgressBar::GetInstance()->AddStepsToDo(2*nrFolders);
std::string folder = m_Controls->m_OutputLabel->text().toStdString();
if(berry::Platform::IsWindows())
{
folder.append("\\import.log");
}
else
{
folder.append("/import.log");
}
ofstream logfile;
if(m_OutputFolderNameSet) logfile.open(folder.c_str());
while(m_Controls->listWidget->count())
{
// RETREIVE FOLDERNAME
QListWidgetItem * item = m_Controls->listWidget->takeItem(0);
QString folderName = item->text();
if(m_OutputFolderNameSet) logfile << "Reading " << folderName.toStdString() << '\n';
// PARSING DIRECTORY
PrintMemoryUsage();
clock.Start(folderName.toAscii());
std::vector<std::string> seriesUIDs(0);
std::vector<std::vector<std::string> > seriesFilenames(0);
Status("== Initial Directory Scan ==");
if(m_OutputFolderNameSet) logfile << "== Initial Directory Scan ==\n";
gdcm::Directory d;
d.Load( folderName.toStdString().c_str(), true ); // recursive !
const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
const unsigned int ntotalfiles = l1.size();
Status(QString(" ... found %1 different files").arg(ntotalfiles));
if(m_OutputFolderNameSet)logfile << "...found " << ntotalfiles << " different files\n";
Status("Scanning Headers");
if(m_OutputFolderNameSet) logfile << "Scanning Headers\n";
gdcm::Scanner s;
const gdcm::Tag t1(0x0020,0x000d); // Study Instance UID
const gdcm::Tag t2(0x0020,0x000e); // Series Instance UID
const gdcm::Tag t5(0x0028, 0x0010); // number rows
const gdcm::Tag t6(0x0028, 0x0011); // number cols
s.AddTag( t1 );
s.AddTag( t2 );
s.AddTag( t5 );
s.AddTag( t6 );
bool b = s.Scan( d.GetFilenames() );
if( !b )
{
Error("Scanner failed");
if(m_OutputFolderNameSet )logfile << "ERROR: scanner failed\n";
continue;
}
// Only get the DICOM files:
gdcm::Directory::FilenamesType l2 = s.GetKeys();
gdcm::Directory::FilenamesType::iterator it;
for (it = l2.begin() ; it != l2.end(); ++it) {
MITK_INFO << "-------FN " << *it;
}
const int nfiles = l2.size();
if(nfiles < 1)
{
Error("No DICOM files found");
if(m_OutputFolderNameSet)logfile << "ERROR: No DICOM files found\n";
continue;
}
Status(QString(" ... successfully scanned %1 headers.").arg(nfiles));
if(m_OutputFolderNameSet) logfile << "...succesfully scanned " << nfiles << " headers\n";
Status("Sorting");
if(m_OutputFolderNameSet) logfile << "Sorting\n";
const gdcm::Scanner::ValuesType &values1 = s.GetValues(t1);
int nvalues;
if(m_Controls->m_DuplicateID->isChecked())
{
nvalues = 1;
}
else
{
nvalues = values1.size();
}
if(nvalues>1)
{
Error("Multiple sSeries tudies found. Please limit to 1 study per folder");
if(m_OutputFolderNameSet) logfile << "Multiple series found. Limit to one. If you are convinced this is an error use the merge duplicate study IDs option \n";
continue;
}
const gdcm::Scanner::ValuesType &values5 = s.GetValues(t5);
const gdcm::Scanner::ValuesType &values6 = s.GetValues(t6);
if(values5.size()>1 || values6.size()>1)
{
Error("Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING.");
if(m_OutputFolderNameSet) logfile << "Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING\n.";
continue;
}
const gdcm::Scanner::ValuesType &values2 = s.GetValues(t2);
int nSeries;
if(m_Controls->m_DuplicateID->isChecked())
{
nSeries = 1;
}
else
{
nSeries = values2.size();
}
gdcm::Directory::FilenamesType files;
if(nSeries > 1)
{
gdcm::Sorter sorter;
sorter.SetSortFunction( SortBySeriesUID );
if (sorter.StableSort( l2 ))
{
files = sorter.GetFilenames();
}
else
{
Error("Loading of at least one DICOM file not successfull!");
return;
}
}
else
{
files = l2;
}
unsigned int nTotalAcquis = 0;
if(nfiles % nSeries != 0)
{
Error("Number of files in series not equal, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files in series not equal, Some volumes are probably incomplete. ABORTING \n";
continue;
}
int filesPerSeries = nfiles / nSeries;
gdcm::Scanner::ValuesType::const_iterator it2 = values2.begin();
for(int i=0; i<nSeries; i++)
{
gdcm::Directory::FilenamesType sub( files.begin() + i*filesPerSeries, files.begin() + (i+1)*filesPerSeries);
gdcm::Scanner s;
const gdcm::Tag t3(0x0020,0x0012); // Acquisition ID
const gdcm::Tag t4(0x0018,0x0024); // Sequence Name (in case acquisitions are equal for all)
// const gdcm::Tag t5(0x20,0x32) ); // Image Position (Patient)
s.AddTag(t3);
s.AddTag(t4);
// s.AddTag(t5);
bool b = s.Scan( sub );
if( !b )
{
Error("Scanner failed");
if(m_OutputFolderNameSet) logfile << "Scanner failed\n";
continue;
}
gdcm::Sorter subsorter;
gdcm::Scanner::ValuesType::const_iterator it;
const gdcm::Scanner::ValuesType &values3 = s.GetValues(t3);
const gdcm::Scanner::ValuesType &values4 = s.GetValues(t4);;
unsigned int nAcquis = values3.size();
if(nAcquis > 1) // More than one element must have this tag (Not != )
{
subsorter.SetSortFunction( SortByAcquisitionNumber );
it = values3.begin();
}
else if (values4.size() > 1)
{
nAcquis = values4.size();
subsorter.SetSortFunction( SortBySeqName );
it = values4.begin();
}
// Hotfix for Bug 14758, better fix by selecting always availible tags.
else
{
Error("Sorting tags (0x0020,0x0012) and (0x0018,0x0024) missing, ABORTING");
if(m_OutputFolderNameSet) logfile << "Sorting tags (0x0020,0x0012) and (0x0018,0x0024) missing, ABORTING\n";
continue;
}
nTotalAcquis += nAcquis;
subsorter.Sort( sub );
if(filesPerSeries % nAcquis != 0)
{
Error("Number of files per acquisition not equal, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files per acquisition not equal, ABORTING \n";
continue;
}
int filesPerAcqu = filesPerSeries / nAcquis;
gdcm::Directory::FilenamesType subfiles = subsorter.GetFilenames();
for ( unsigned int j = 0 ; j < nAcquis ; ++j )
{
std::string identifier = "serie_" + *it2 + "_acquis_" + *it++;
gdcm::IPPSorter ippsorter;
gdcm::Directory::FilenamesType ipplist((j)*filesPerAcqu+subfiles.begin(),(j+1)*filesPerAcqu+subfiles.begin());
ippsorter.SetComputeZSpacing( true );
if( !ippsorter.Sort( ipplist ) )
{
Error(QString("Failed to sort acquisition %1, ABORTING").arg(identifier.c_str()));
if(m_OutputFolderNameSet) logfile << "Failed to sort acquisition " << identifier.c_str() << " , Aborting\n";
continue;
}
const std::vector<std::string> & list = ippsorter.GetFilenames();
seriesFilenames.push_back(list);
seriesUIDs.push_back(identifier.c_str());
}
++it2;
}
// Hot Fix for Bug 14758, checking if no file is acuired.
if (nTotalAcquis < 1) // Test if zero, if true than error because no file was selected
{
Error("Nno files in acquisitions, ABORTING");
if(m_OutputFolderNameSet) logfile << "Nno files in acquisitions, ABORTING \n";
continue;
}
if(nfiles % nTotalAcquis != 0)
{
Error("Number of files per acquisition differs between series, ABORTING");
if(m_OutputFolderNameSet) logfile << "Number of files per acquisition differs between series, ABORTING \n";
continue;
}
int slices = nfiles/nTotalAcquis;
Status(QString("Series is composed of %1 different 3D volumes with %2 slices.").arg(nTotalAcquis).arg(slices));
if(m_OutputFolderNameSet) logfile << "Series is composed of " << nTotalAcquis << " different 3D volumes with " << slices << " slices\n";
// READING HEADER-INFOS
PrintMemoryUsage();
Status(QString("Reading Headers %1").arg(folderName));
if(m_OutputFolderNameSet) logfile << "Reading Headers "<< folderName.toStdString() << "\n";
mitk::DicomDiffusionImageHeaderReader::Pointer headerReader;
typedef short PixelValueType;
typedef mitk::DicomDiffusionImageReader< PixelValueType, 3 > VolumesReader;
VolumesReader::HeaderContainer inHeaders;
unsigned int size2 = seriesUIDs.size();
for ( unsigned int i = 0 ; i < size2 ; ++i )
{
// Hot Fix for Bug 14459, catching if no valid data in datafile.
try
{
Status(QString("Reading header image #%1/%2").arg(i+1).arg(size2));
headerReader = mitk::DicomDiffusionImageHeaderReader::New();
headerReader->SetSeriesDicomFilenames(seriesFilenames[i]);
headerReader->Update();
inHeaders.push_back(headerReader->GetOutput());
}
catch (mitk::Exception e)
{
Error("Could not read file header, ABORTING");
if(m_OutputFolderNameSet) logfile << e;
continue;
}
//Status(std::endl;
}
mitk::ProgressBar::GetInstance()->Progress();
// // GROUP HEADERS
// mitk::GroupDiffusionHeadersFilter::Pointer grouper
// = mitk::GroupDiffusionHeadersFilter::New();
// mitk::GroupDiffusionHeadersFilter::OutputType outHeaders;
// grouper->SetInput(inHeaders);
// grouper->Update();
// outHeaders = grouper->GetOutput();
// READ VOLUMES
PrintMemoryUsage();
if(m_OutputFolderNameSet) logfile << "Loading volumes\n";
Status(QString("Loading Volumes %1").arg(folderName));
VolumesReader::Pointer vReader = VolumesReader::New();
VolumesReader::HeaderContainer hc = inHeaders;
// hc.insert(hc.end(), outHeaders[1].begin(), outHeaders[1].end() );
// hc.insert(hc.end(), outHeaders[2].begin(), outHeaders[2].end() );
if(hc.size()>1)
{
vReader->SetHeaders(hc);
vReader->Update();
VolumesReader::OutputImageType::Pointer vecImage;
vecImage = vReader->GetOutput();
Status(QString("Volumes Loaded (%1)").arg(folderName));
// CONSTRUCT CONTAINER WITH DIRECTIONS
typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
typedef itk::VectorContainer< unsigned int,
GradientDirectionType > GradientDirectionContainerType;
GradientDirectionContainerType::Pointer directions =
GradientDirectionContainerType::New();
std::vector<double> b_vals;
double maxb = 0;
for(unsigned int i=0; i<hc.size(); i++)
{
double bv = hc[i]->bValue;
if(maxb<bv)
{
maxb = bv;
}
b_vals.push_back(bv);
}
for(unsigned int i=0; i<hc.size(); i++)
{
vnl_vector_fixed<double, 3> vect = hc[i]->DiffusionVector;
// since some protocols provide a gradient direction of (0,0,0) in their dicom files when isotropic diffusion is assumed,
// the nrrd compatible way of storing b-values is not possible, so in this case we overwrite
// the gradient direction to (1,1,1)
if (b_vals[i] > 0 && vect[0] == 0.0 && vect[1] == 0.0 && vect[2] ==0.0)
{
vect.fill(1.0);
}
vect.normalize();
vect *= sqrt(b_vals[i]/maxb);
directions->push_back(vect);
}
// DWI TO DATATREE
PrintMemoryUsage();
Status(QString("Initializing Diffusion Image"));
if(m_OutputFolderNameSet) logfile << "Initializing Diffusion Image\n";
typedef mitk::DiffusionImage<PixelValueType> DiffVolumesType;
DiffVolumesType::Pointer diffImage = DiffVolumesType::New();
diffImage->SetDirections(directions);
diffImage->SetVectorImage(vecImage);
diffImage->SetB_Value(maxb);
diffImage->InitializeFromVectorImage();
diffImage->UpdateBValueMap();
Status(QString("Diffusion Image initialized"));
if(m_OutputFolderNameSet) logfile << "Diffusion Image initialized\n";
if(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked())
{
PrintMemoryUsage();
Status(QString("Averaging gradient directions"));
logfile << "Averaging gradient directions\n";
diffImage->AverageRedundantGradients(m_Controls->m_Blur->value());
}
QString descr = QString("%1_%2_%3")
.arg(((inHeaders)[0])->seriesDescription.c_str())
.arg(((inHeaders)[0])->seriesNumber)
.arg(((inHeaders)[0])->patientName.c_str());
descr = descr.trimmed();
descr = descr.replace(" ", "_");
if(!m_OutputFolderNameSet)
{
node=mitk::DataNode::New();
node->SetData( diffImage );
GetDefaultDataStorage()->Add(node);
SetDwiNodeProperties(node, descr.toStdString().c_str());
Status(QString("Image %1 added to datastorage").arg(descr));
}
else
{
typedef mitk::NrrdDiffusionImageWriter<PixelValueType> WriterType;
WriterType::Pointer writer = WriterType::New();
QString fullpath = QString("%1/%2.dwi")
.arg(m_OutputFolderName)
.arg(descr);
// if the override option is not checked, we need to make sure that the current filepath
// does not point to an existing file
if( !(m_Controls->m_OverrideOptionCheckbox->isChecked()) )
{
QFile outputFile( fullpath );
// generate new filename if file exists
int file_counter = 0;
while( outputFile.exists() )
{
// copy base name
QString newdescr = descr;
file_counter++;
MITK_WARN << "The file "<< fullpath.toStdString() << " exists already.";
QString appendix = QString("_%1").arg( QString::number(file_counter) );
newdescr.append(appendix);
fullpath = QString("%1/%2.dwi")
.arg(m_OutputFolderName)
.arg(newdescr);
// set the new generated filename for next check
outputFile.setFileName( fullpath );
}
}
writer->SetFileName(fullpath.toStdString());
writer->SetInput(diffImage);
try
{
writer->Update();
}
catch (itk::ExceptionObject &ex)
{
imageSuccessfullySaved = false;
Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
logfile << QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()).toStdString() << "\n";
node=mitk::DataNode::New();
node->SetData( diffImage );
GetDefaultDataStorage()->Add(node);
SetDwiNodeProperties(node, descr.toStdString().c_str());
Status(QString("Image %1 added to datastorage").arg(descr));
logfile << "Image " << descr.toStdString() << " added to datastorage\n";
continue ;
}
Status(QString("Image %1 written to disc (%1)").arg(fullpath.toStdString().c_str()));
logfile << "Image " << fullpath.toStdString() << "\n";
}
}
else
{
Status(QString("No diffusion information found (%1)").arg(folderName));
if(m_OutputFolderNameSet) logfile << "No diffusion information found "<< folderName.toStdString();
}
Status(QString("Finished processing %1 with memory:").arg(folderName));
if(m_OutputFolderNameSet) logfile << "Finished processing " << folderName.toStdString() << "\n";
PrintMemoryUsage();
clock.Stop(folderName.toAscii());
mitk::ProgressBar::GetInstance()->Progress();
int lwidget = m_Controls->listWidget->count();
std::cout << lwidget <<std::endl;
logfile << "\n";
}
logfile.close();
Status("Timing information");
clock.Report();
if(!m_OutputFolderNameSet && node.IsNotNull())
{
mitk::BaseData::Pointer basedata = node->GetData();
if (basedata.IsNotNull())
{
mitk::RenderingManager::GetInstance()->InitializeViews(
basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
}
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
try
{
MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, NULL) << " to '" << currLocale << "'";
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch (itk::ExceptionObject &ex)
{
Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
return ;
}
if (!imageSuccessfullySaved)
QMessageBox::warning(NULL,"WARNING","One or more files could not be saved! The according files where moved to the datastorage.");
Status(QString("Finished import with memory:"));
PrintMemoryUsage();
}
int main(int argc, char *argv[])
{
int ierr = 0, i;
#ifdef HAVE_MPI
MPI_Init(&argc,&argv);
Epetra_MpiComm Comm( MPI_COMM_WORLD );
#else
Epetra_SerialComm Comm;
#endif
bool success = false;
bool verbose = true;
try {
//int myRank = Comm.MyPID();
//int numGlobalElements = 10000000;
int numGlobalElements = 100;
Teuchos::CommandLineProcessor cmdp(false,true);
cmdp.setOption("numGlobalElements",&numGlobalElements,"Global problem size.");
if (cmdp.parse(argc,argv) != Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL) {
throw -1;
}
Epetra_Map Map(numGlobalElements, 0, Comm);
int NumMyElements = Map.NumMyElements();
std::vector<int> MyGlobalElements(NumMyElements);
Map.MyGlobalElements(&MyGlobalElements[0]);
int NumNz = 3;
// std::vector<int> NumNz(NumMyElements);
// for (i=0; i<NumMyElements; i++)
// if (MyGlobalElements[i]==0 || MyGlobalElements[i] == numGlobalElements-1)
// NumNz[i] = 2;
// else
// NumNz[i] = 3;
// Epetra_CrsMatrix A(Copy, Map, &NumNz[0]);
MemoryUsageStart("Epetra");
PrintMemoryUsage("Initial memory usage", "epetra-init.heap");
Epetra_CrsMatrix A(Copy, Map, NumNz);
PrintMemoryUsage("Memory after CrsMatrix constructor", "epetra-after-ctor.heap");
std::vector<double> Values(2);
Values[0] = -1.0; Values[1] = -1.0;
std::vector<int> Indices(2);
double two = 2.0;
int NumEntries;
for (i=0; i<NumMyElements; i++) {
if (MyGlobalElements[i]==0) {
Indices[0] = 1;
NumEntries = 1;
} else if (MyGlobalElements[i] == numGlobalElements-1) {
Indices[0] = numGlobalElements-2;
NumEntries = 1;
} else {
Indices[0] = MyGlobalElements[i]-1;
Indices[1] = MyGlobalElements[i]+1;
NumEntries = 2;
}
ierr = A.InsertGlobalValues(MyGlobalElements[i], NumEntries, &Values[0], &Indices[0]);
assert(ierr==0);
// Put in the diagonal entry
ierr = A.InsertGlobalValues(MyGlobalElements[i], 1, &two, &MyGlobalElements[i]);
assert(ierr==0);
}
PrintMemoryUsage("Memory after InsertGlobalValues()", "epetra-after-insert.heap");
ierr = A.FillComplete();
assert(ierr == 0);
PrintMemoryUsage("Memory after FillComplete()", "epetra-after-fillcomplete.heap");
MemoryUsageStop();
success = true;
}
TEUCHOS_STANDARD_CATCH_STATEMENTS(verbose, std::cerr, success);
#ifdef HAVE_MPI
MPI_Finalize();
#endif
return ( success ? EXIT_SUCCESS : EXIT_FAILURE );
}
