ADD_IMAGE_TYPE(Dim, float);
ADD_IMAGE_TYPE(Dim, double);
ADD_IMAGE_TYPE(Dim, unsigned short);
-
-
}
//--------------------------------------------------------------------
template<class args_info_type>
void MedianImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
mArgsInfo=a;
- SetIOVerbose(mArgsInfo.verbose_flag);
-
+ SetIOVerbose(mArgsInfo.verbose_flag);
if (mArgsInfo.input_given) {
SetInputFilename(mArgsInfo.input_arg);
SetOutputFilename(mArgsInfo.output_arg);
}
-
}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//--------------------------------------------------------------------
void
MedianImageGenericFilter<args_info_type>::UpdateWithInputImageType()
{
- // Reading input
+ // Reading input
typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
-// Typedef
- typedef typename InputImageType::PixelType PixelType;
+ // Typedef
+ typedef typename InputImageType::PixelType PixelType;
-
-
-
- // typedef itk::Image<PixelType,InputImageType::ImageDimension> OutputImageType;
+ // typedef itk::Image<PixelType,InputImageType::ImageDimension> OutputImageType;
- // Main filter
-
- typedef itk::Image<uchar, InputImageType::ImageDimension> OutputImageType;
- typename InputImageType::SizeType indexRadius;
+ // Main filter
+ typedef itk::Image<PixelType, InputImageType::ImageDimension> OutputImageType;
+ class InputImageType::SizeType indexRadius;
// Filter
- typedef itk::MedianImageFilter<InputImageType, OutputImageType> MedianImageFilterType;
-
-
+ typedef itk::MedianImageFilter<InputImageType, OutputImageType> MedianImageFilterType;
typename MedianImageFilterType::Pointer thresholdFilter=MedianImageFilterType::New();
thresholdFilter->SetInput(input);
-
-indexRadius[0]=mArgsInfo.radius_arg[0];
-indexRadius[1]=mArgsInfo.radius_arg[1];
-indexRadius[2]=mArgsInfo.radius_arg[2];
-
-
-
+ indexRadius[0]=mArgsInfo.radius_arg[0];
+ indexRadius[1]=mArgsInfo.radius_arg[1];
+ indexRadius[2]=mArgsInfo.radius_arg[2];
-// indexRadius[0] = 1;
- // indexRadius[1] = 1;
+ // indexRadius[0] = 1;
+ // indexRadius[1] = 1;
-thresholdFilter->SetRadius( indexRadius );
-
+ thresholdFilter->SetRadius( indexRadius );
typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
- thresholdFilter->Update();
+ thresholdFilter->Update();
- // Write/Save results
- this->template SetNextOutput<OutputImageType>(outputImage);
-
-
- }
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
//--------------------------------------------------------------------
}//end clitk
-
#endif //#define clitkMedianImageGenericFilter_txx
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
-#ifndef vvImageReader_CXX
-#define vvImageReader_CXX
+ ======================================================================-====*/
+#ifndef VVIMAGEREADER_CXX
+#define VVIMAGEREADER_CXX
+
#include <QApplication>
#include <itkImageFileReader.h>
#include "vvImageReader.h"
#include "vvImageReader.txx"
-
-//====================================================================
+//------------------------------------------------------------------------------
vvImageReader::vvImageReader()
{
- mImage = NULL;
- mInputFilenames.resize(0);
- mLastError = "";
- mType = UNDEFINEDIMAGETYPE;
+ mImage = NULL;
+ mInputFilenames.resize(0);
+ mLastError = "";
+ mType = UNDEFINEDIMAGETYPE;
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
vvImageReader::~vvImageReader() { }
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::Update()
{
- Update(mType);
+ Update(mType);
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::Update(LoadedImageType type)
{
- itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
- if (!reader) {
- mLastError="Unable to read file.";
- }
- else {
- reader->SetFileName(mInputFilenames[0]);
- reader->ReadImageInformation();
- if (mInputFilenames.size() > 1)
- Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
- else
- Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
- }
+ itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
+ if (!reader) {
+ mLastError="Unable to read file.";
+ }
+ else {
+ reader->SetFileName(mInputFilenames[0]);
+ reader->ReadImageInformation();
+ if (mInputFilenames.size() > 1)
+ Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+ else
+ Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+ }
}
+//------------------------------------------------------------------------------
-//====================================================================
+
+//------------------------------------------------------------------------------
void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType type) {
- //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
- mType = type;
- mDim = dim;
- mInputPixelType=inputPixelType;
- this->start(); //Start heavy read operation in a separate thread
- while (this->isRunning())
+ //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
+ mType = type;
+ mDim = dim;
+ mInputPixelType=inputPixelType;
+ this->start(); //Start heavy read operation in a separate thread
+ while (this->isRunning())
{
- qApp->processEvents();
- this->wait(50);
+ qApp->processEvents();
+ this->wait(50);
}
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::run()
{
- switch(mDim)
- {
- case 2:
- UpdateWithDim<2>(mInputPixelType);
- break;;
- case 3:
- UpdateWithDim<3>(mInputPixelType);
- break;;
- case 4:
- UpdateWithDim<4>(mInputPixelType);
- break;;
- default:
- std::cerr << "dimension unknown in Update ! " << std::endl;
- }
+ switch(mDim) {
+ case 2:
+ UpdateWithDim<2>(mInputPixelType);
+ break;;
+ case 3:
+ UpdateWithDim<3>(mInputPixelType);
+ break;;
+ case 4:
+ UpdateWithDim<4>(mInputPixelType);
+ break;;
+ default:
+ std::cerr << "dimension unknown in Update ! " << std::endl;
+ }
}
-//====================================================================
+//------------------------------------------------------------------------------
+
-//====================================================================
-/*void vvImageReader::Extract(int dim, std::string inputPixelType, int slice) {
- CALL_FOR_ALL_DIMS(dim, ExtractWithDim, inputPixelType, slice);
-}*/
-//====================================================================
+//------------------------------------------------------------------------------
void vvImageReader::SetInputFilename(const std::string & filename)
{
- mInputFilenames.resize(0);
- mInputFilenames.push_back(filename);
+ mInputFilenames.resize(0);
+ mInputFilenames.push_back(filename);
}
+//------------------------------------------------------------------------------
+
-//====================================================================
+//------------------------------------------------------------------------------
void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames) {
- mInputFilenames = filenames;
+ mInputFilenames = filenames;
}
-//====================================================================
+//------------------------------------------------------------------------------
#endif
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
-#ifndef vvImageReader_TXX
-#define vvImageReader_TXX
-#include<string>
+ ======================================================================-====*/
+#ifndef VVIMAGEREADER_TXX
+#define VVIMAGEREADER_TXX
+
+#include <string>
#include <itkImageFileReader.h>
#include <itkImageSeriesReader.h>
-
#include "clitkCommon.h"
#include "itkImageToVTKImageFilter.h"
#include "vvFromITK.h"
#include "vvConstants.h"
+//----------------------------------------------------------------------------
template<unsigned int VImageDimension>
-void vvImageReader::UpdateWithDim(std::string InputPixelType)
-{
- if (mType == VECTORFIELD)
- UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
- else if (InputPixelType == "short")
- UpdateWithDimAndInputPixelType<short,VImageDimension>();
- else if (InputPixelType == "unsigned_short")
- UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
- else if (InputPixelType == "char")
- UpdateWithDimAndInputPixelType<char,VImageDimension>();
- else if (InputPixelType == "unsigned_char")
- UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
- else if (InputPixelType == "int")
- UpdateWithDimAndInputPixelType<int,VImageDimension>();
- else if (InputPixelType == "double")
- UpdateWithDimAndInputPixelType<double,VImageDimension>();
- else if (InputPixelType == "float")
- UpdateWithDimAndInputPixelType<float,VImageDimension>();
- else
- std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
+void vvImageReader::UpdateWithDim(std::string InputPixelType) {
+ if (mType == VECTORFIELD)
+ UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
+ else if (InputPixelType == "short")
+ UpdateWithDimAndInputPixelType<short,VImageDimension>();
+ else if (InputPixelType == "unsigned_short")
+ UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
+ else if (InputPixelType == "char")
+ UpdateWithDimAndInputPixelType<char,VImageDimension>();
+ else if (InputPixelType == "unsigned_char")
+ UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
+ else if (InputPixelType == "int")
+ UpdateWithDimAndInputPixelType<int,VImageDimension>();
+ else if (InputPixelType == "double")
+ UpdateWithDimAndInputPixelType<double,VImageDimension>();
+ else if (InputPixelType == "float")
+ UpdateWithDimAndInputPixelType<float,VImageDimension>();
+ else
+ std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
}
-//====================================================================
+//----------------------------------------------------------------------------
+
+//----------------------------------------------------------------------------
template<class InputPixelType, unsigned int VImageDimension>
-void vvImageReader::UpdateWithDimAndInputPixelType()
-{
- if (mType == MERGEDWITHTIME) // In this case we can load the images
- // one at the time to avoid excessive
- // memory use
+void vvImageReader::UpdateWithDimAndInputPixelType() {
+
+ // DD(mType);
+
+ if (mType == MERGEDWITHTIME) // In this case we can load the images
+ // one at the time to avoid excessive
+ // memory use
{
- typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
- typedef itk::ImageFileReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
- typename ConnectorType::Pointer connector = ConnectorType::New();
- connector->SetInput(reader->GetOutput());
- mImage=vvImage::New();
- for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
+ typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
+ typename ConnectorType::Pointer connector = ConnectorType::New();
+ connector->SetInput(reader->GetOutput());
+ mImage=vvImage::New();
+ for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
{
- std::cout << (*i) << std::endl;
- reader->SetFileName(*i);
- try {
- reader->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while reading " << mInputFilenames[0].c_str()
- << " " << err << std::endl;
- std::stringstream error;
- error << err;
- mLastError = error.str();
- return;
- }
- try {
- connector->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
- << " " << err << std::endl;
- }
- vtkImageData *image = vtkImageData::New();
- image->DeepCopy(connector->GetOutput());
- mImage->AddImage(image);
+ std::cout << (*i) << std::endl;
+ reader->SetFileName(*i);
+ try {
+ reader->Update();
+ }
+ catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while reading " << mInputFilenames[0].c_str()
+ << " " << err << std::endl;
+ std::stringstream error;
+ error << err;
+ mLastError = error.str();
+ return;
+ }
+ try {
+ connector->Update();
+ }
+ catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
+ << " " << err << std::endl;
+ }
+ vtkImageData *image = vtkImageData::New();
+ image->DeepCopy(connector->GetOutput());
+ mImage->AddImage(image);
}
}
- else
+ else
{
- if (mInputFilenames.size() > 1)
+ if (mInputFilenames.size() > 1)
{
- typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
- typedef itk::ImageSeriesReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
- std::cout << (*i) << std::endl;
- reader->SetFileNames(mInputFilenames);
- //if (mUseAnObserver) {
- //reader->AddObserver(itk::ProgressEvent(), mObserver);
- //}
- try {
- reader->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while reading image series:" << err << std::endl;
- std::stringstream error;
- error << err;
- mLastError = error.str();
- return;
- }
- if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
- else
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
+ typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+ typedef itk::ImageSeriesReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
+ std::cout << (*i) << std::endl;
+ reader->SetFileNames(mInputFilenames);
+ //if (mUseAnObserver) {
+ //reader->AddObserver(itk::ProgressEvent(), mObserver);
+ //}
+ try {
+ reader->Update();
+ }
+ catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while reading image series:" << err << std::endl;
+ std::stringstream error;
+ error << err;
+ mLastError = error.str();
+ return;
+ }
+
+ // DD(reader->GetOutput()->GetImageDimension());
+ // DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
+ // for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
+ // DD(reader->GetOutput()->GetSpacing()[i]);
+ // }
+
+ if (mType == IMAGEWITHTIME)
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+ else
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
}
- else
+ else
{
- typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
- typedef itk::ImageFileReader<InputImageType> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- reader->SetFileName(mInputFilenames[0]);
- //if (mUseAnObserver) {
- //reader->AddObserver(itk::ProgressEvent(), mObserver);
- //}
- try {
- reader->Update();
- }
- catch ( itk::ExceptionObject & err ) {
- std::cerr << "Error while reading " << mInputFilenames[0].c_str()
- << " " << err << std::endl;
- std::stringstream error;
- error << err;
- mLastError = error.str();
- return;
- }
- if (mType == IMAGEWITHTIME)
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
- else
- mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
+ typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+ typedef itk::ImageFileReader<InputImageType> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName(mInputFilenames[0]);
+ //if (mUseAnObserver) {
+ //reader->AddObserver(itk::ProgressEvent(), mObserver);
+ //}
+ try {
+ reader->Update();
+ }
+ catch ( itk::ExceptionObject & err ) {
+ std::cerr << "Error while reading " << mInputFilenames[0].c_str()
+ << " " << err << std::endl;
+ std::stringstream error;
+ error << err;
+ mLastError = error.str();
+ return;
+ }
+
+ // DD(reader->GetOutput()->GetImageDimension());
+ // DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
+ // for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
+ // DD(reader->GetOutput()->GetSpacing()[i]);
+ // DD(reader->GetOutput()->GetOrigin()[i]);
+ // }
+
+
+ if (mType == IMAGEWITHTIME)
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+ else
+ mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
}
}
}
-//====================================================================
+//----------------------------------------------------------------------------
#endif /* end #define vvImageReader_TXX */
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff