[Insight-users] Reading Dicom series
charfeddine amir
charfeddine_amir at yahoo.fr
Fri Jan 27 10:38:37 EST 2006
wa alaykom assalam
plz read the itk software guide.pdf section 7.12.3 Reading a 2D DICOM Series and Writing a Volume
and this is a part of code of file Examples/IO/DicomSeriesReadImageWrite2.cxx :
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
reader->SetImageIO( dicomIO );
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( argv[1] );
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
//here we browse all the series in the directory
while( seriesItr != seriesEnd )
{
std::cout << seriesItr->c_str() << std::endl;
seriesItr++;
}
// and here we choose one serie from the list by its ID given in the command line
//and if no ID specifies by user, we take the first serie in the list
std::string seriesIdentifier;
if( argc > 3 ) // If no optional series identifier
{
seriesIdentifier = argv[3];
}
else
{
seriesIdentifier = seriesUID.begin()->c_str();
}
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
//here we read list of files belonging to the serie we choose
fileNames = nameGenerator->GetFileNames( seriesIdentifier );
reader->SetFileNames( fileNames );
try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
***********************************************************************************
//so if u want to deal with every slice alone, u might write something like this
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
std::string seriesIdentifier;
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
//here we browse all the series in the directory
while( seriesItr != seriesEnd )
{
seriesIdentifier = seriesItr->c_str();
fileNames = nameGenerator->GetFileNames( seriesIdentifier );
reader->SetFileNames( fileNames );
reader->Update();
{
// here you write code to process each serie alone
}
seriesItr++;
}
For more comments plz read the ITK SOFTWARE GUIDE.PDF from page 298.
let me know if u resolve your problem, or didn't i understand what u need.
Amir.
Technology & Medical Imaging Lab
Biophysics Departement
Faculty of Medecine Monastir-Tunisia
mahmoud ismail <mahmoudtheleader2003 at yahoo.com> a écrit : salamo alikom
My problem is that i use vtkDicomReader class and it has a restriction which is
(the folder that contains the images must have images that belong to the same series and are ordered) . but in most cases the folder contain images that belongs to more than one series
so i want to deal with every series alone
is it clear
Note my name is mahmoud mohamed Ahmed
and I am in fourth year systems & and biomedical enginnering department Cairo university Egypt
what about u
charfeddine amir <charfeddine_amir at yahoo.fr> wrote:
salam
sorry i didn't understand your problem
i hope you finded a solution, if not, rewrite me and explain me your problem
because i think i can help u
i make an application that read dicom series but don't show me all image...
regards,
mahmoud ismail <mahmoudtheleader2003 at yahoo.com> a écrit : hi Amir
first i have no answer to your question and hope that the message yuo have recieved
is enough but
I try to open Dicom Images using VTKDicomReader class
but it cann't distinguish between images that belong to different series
so i used GDCM but i have some problems with it
Do u have any suggestions
Thanks
charfeddine amir <charfeddine_amir at yahoo.fr> wrote:
hi All
I'm developping an application that
reads the first serie of
Dicom images from a directory, show each image and save it
in bmp format.
the problem is that image series is well readed, and image
are well saved in bmp format, but image are not well showed
in the vtkrenderwindow used ( i get a black window with
two
white line on it and not the image readed).
this code in the main file :
this function is for reading first series from a given
directory and showing it's first dicom image(invoked by
pushing the Read Directory button in the GUI)
void
migAppBase
::ReadImage()
{
// Can only read an image once
if(m_InputImage.IsNotNull())
return;
char* chooserName = fl_dir_chooser("select a dicom directory", 0, 0);
// Store the filename
strcpy( m_InputImageDirectoryname, chooserName );
reader = ReaderType::New();
dicomIO = ImageIOType::New();
nameGenerator = NamesGeneratorType::New();
reader->SetImageIO( dicomIO );
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( m_InputImageDirectoryname );
seriesUID = nameGenerator->GetSeriesUIDs();
seriesIdentifier = seriesUID.begin()->c_str();
fileNames =
nameGenerator->GetFileNames( seriesIdentifier );
FileNamesItr = fileNames.begin ();
FileNamesEnd = fileNames.end();
rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );
reader->SetFileName( FileNamesItr->c_str() );
try
{
rescaler->SetInput( reader->GetOutput() );
reader->Update();
m_InputImage = reader->GetOutput();
m_InputImage->SetRequestedRegionToLargestPossibleRegion();
// Create the input image VTK pipeline
this->CreateInputImageWindow();
}
catch
(itk::ExceptionObject &ex)
{
}
FileNamesItr++;
}
this function is for reading the next image in the serie
(invoked by pushing the Read Next button in the GUI)
void
migAppBase
::ReadNext()
{
if ( FileNamesItr != FileNamesEnd
)
{
reader->SetFileName( FileNamesItr->c_str() );
try
{
rescaler->SetInput( reader->GetOutput() );
m_InputImage = reader->GetOutput();
m_InputImage->SetRequestedRegionToLargestPossibleRegion();
reader->Update();
// Create the input image VTK pipeline
this->CreateInputImageWindow();
}
catch (itk::ExceptionObject &ex)
{
}
FileNamesItr++;
}
}
this function is for saving the actual image (that should
be showed in the vtk window) in bmp format (invoked by
pushing the save Image in the GUI)
void
migAppBase
::SaveImage()
{
Writer2Type::Pointer writer2 = Writer2Type::New();
std::string OutputFilename1 = FileNamesItr->c_str() + std::string(".bmp");
writer2->SetFileName( OutputFilename1.c_str() );
writer2->SetInput( rescaler->GetOutput() );
try
{
writer2->Update();
}
catch (itk::ExceptionObject & e)
{
}
}
this is the fuction for showing the actual image
void
migAppBase
::CreateInputImageWindow()
{
// If this is the first time we've hit Image Suivante there's other stuff
// that needs to happen
if(m_IsFirstUpdate)
{
// Display the output image
CreateWindowWithRWI(m_InputInteractor, m_InputWindow, "Input Image");
// these two steps are VERY IMPORTANT, you have to show() the fltk window
// containing the vtkFlRenderWindowInteractor, and then the
// vtkFlRenderWindowInteractor
itself
m_InputWindow->show();
m_InputInteractor->show();
// now we get to setup our VTK rendering pipeline
CreateInputImageVTKPipeline(m_InputInteractor);
// No longer the first update
m_IsFirstUpdate = false;
}
else
{
// Refresh the output window if not the
first update
// NB: doing this on the first update on Windows causes a new
// renderwindow to spawn (not sure why)
m_InputRenderWindow->Render();
}
}
function(s) for fltk and vtk interaction( creation of the
vtkrenderwindow and integrating it to the fltk window)
void
migAppBase
::CreateWindowWithRWI(vtkFlRenderWindowInteractor *&flrwi, Fl_Window *&flw, char *title)
{
// set up main FLTK window
flw = new Fl_Window(300,330,title);
// and instantiate vtkFlRenderWindowInteractor (here it acts like a
// FLTK window, i.e. you could also
instantiate it as child of a
// Fl_Group in a window)
flrwi = new vtkFlRenderWindowInteractor(5,5,290,260,NULL);
// this will result in a little message under the rendering
Fl_Box* box = new Fl_Box(5,261,290,34,
"3 = stereo, j = joystick, t = trackball, "
"w = wireframe, s = surface, p = pick; "
"you can also resize the window");
box->labelsize(10);
box->align(FL_ALIGN_WRAP);
// we're done populating the flw
flw->end();
// if the main window gets resized, the vtk window should resize with it
flw->resizable(flrwi);
}
void
migAppBase
::CreateInputImageVTKPipeline(vtkFlRenderWindowInteractor *flrwi)
{
// Abort if the user is being stupid
if(m_InputImage.IsNull())
return;
// create a rendering window and renderer
m_InputRenderer =
vtkRenderer::New();
m_InputRenderer->SetBackground(0.0, 0.0, 0.0);
m_InputRenderWindow = vtkRenderWindow::New();
m_InputRenderWindow->AddRenderer(m_InputRenderer);
// NB: here we treat the vtkFlRenderWindowInteractor just like any other
// old vtkRenderWindowInteractor
flrwi->SetRenderWindow(m_InputRenderWindow);
// Hook the VTK pipeline up to the ITK pipeline
m_InputImageITKtoVTKexporter = itk::VTKImageExport<InputImageType>::New();
m_InputImageVTKimporter = vtkImageImport::New();
m_InputImageITKtoVTKexporter->SetInput( m_InputImage );
ConnectPipelines(m_InputImageITKtoVTKexporter, m_InputImageVTKimporter);
// Need to update prior to creating the cutting planes
m_InputImageITKtoVTKexporter->Update();
m_InputImageVTKimporter->Update();
// Create the image cutting planes
m_InputImagePlaneX = vtkImagePlaneWidget::New();
m_InputImagePlaneX->RestrictPlaneToVolumeOn();
m_InputImagePlaneX->SetResliceInterpolateToCubic();
m_InputImagePlaneX->SetInput( (vtkDataSet*) m_InputImageVTKimporter->GetOutput() );
m_InputImagePlaneX->SetPlaneOrientationToXAxes();
m_InputImagePlaneX->SetSliceIndex( 0 );
m_InputImagePlaneY =
vtkImagePlaneWidget::New();
m_InputImagePlaneY->RestrictPlaneToVolumeOn();
m_InputImagePlaneY->SetResliceInterpolateToCubic();
m_InputImagePlaneY->SetInput( (vtkDataSet*) m_InputImageVTKimporter->GetOutput() );
m_InputImagePlaneY->SetPlaneOrientationToYAxes();
m_InputImagePlaneY->SetSliceIndex( 0 );
// Set the position of the image planes to the center of the volume
this->ResetInputImagePlaneWidgets();
// Link the image planes to the interactor
m_InputImagePlaneX->SetInteractor( flrwi );
m_InputImagePlaneY->SetInteractor( flrwi );
// Turn on the
image plane so they display
m_InputImagePlaneX->On();
m_InputImagePlaneY->On();
// just like with any other vtkRenderWindowInteractor(), you HAVE to call
// Initialize() before the interactor will function. See the docs in
// vtkRenderWindowInteractor.h
// This must occur AFTER the image planes have
been added to the interactor
flrwi->Initialize();
// Clean up memory allocation (NB: not actually deleted until program returns)
m_InputRenderer->Delete();
m_InputRenderWindow->Delete();
}
thx for help
any comment is welcome
Amir
---------------------------------
Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta._______________________________________________
This is the private VTK discussion list.
Please keep messages on-topic. Check the FAQ at: http://www.vtk.org/Wiki/VTK_FAQ
Follow this link to subscribe/unsubscribe:
http://www.vtk.org/mailman/listinfo/vtkusers
---------------------------------
Yahoo! Photos
Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever.
---------------------------------
Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta.
---------------------------------
Do you Yahoo!?
With a free 1 GB, there's more in store with Yahoo! Mail.
---------------------------------
Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://public.kitware.com/pipermail/insight-users/attachments/20060127/4a99c653/attachment.htm
More information about the Insight-users
mailing list