// itk
#include <deque>
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkLabelImageToStatisticsLabelMapFilter.h"
-#include "itkRegionOfInterestImageFilter.h"
-#include "itkBinaryThresholdImageFilter.h"
-#include "itkBinaryErodeImageFilter.h"
-#include "itkBinaryBallStructuringElement.h"
+#include <itkStatisticsLabelMapFilter.h>
+#include <itkLabelImageToStatisticsLabelMapFilter.h>
+#include <itkRegionOfInterestImageFilter.h>
+#include <itkBinaryThresholdImageFilter.h>
+#include <itkBinaryErodeImageFilter.h>
+#include <itkBinaryBallStructuringElement.h>
+#include <itkAddImageFilter.h>
+#include <itkDivideByConstantImageFilter.h>
// itk [Bloch et al]
#include "RelativePositionPropImageFilter.h"
SetFuzzyThreshold(0.6);
SetBackgroundValue(0);
SetObjectBackgroundValue(0);
- SetOrientationType(LeftTo);
+ ClearOrientationType();
ResampleBeforeRelativePositionFilterOn();
SetIntermediateSpacing(10);
- AutoCropOn();
+ AutoCropFlagOn();
+ InverseOrientationFlagOff();
+ RemoveObjectFlagOn();
+ CombineWithOrFlagOff();
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
+ClearOrientationType()
+{
+ m_OrientationTypeString.clear();
+ m_OrientationType.clear();
+ m_Angle1.clear();
+ m_Angle2.clear();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+int
+clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
+GetNumberOfAngles()
+{
+ return m_OrientationType.size();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
+AddOrientationTypeString(std::string t)
+{
+ m_OrientationTypeString.push_back(t);
+ switch (t[0]) {
+ case 'L' : AddOrientationType(LeftTo); break;
+ case 'R' : AddOrientationType(RightTo);break;
+ case 'A' : AddOrientationType(AntTo);break;
+ case 'P' : AddOrientationType(PostTo);break;
+ case 'S' : AddOrientationType(SupTo);break;
+ case 'I' : AddOrientationType(InfTo);break;
+ default: clitkExceptionMacro("Error, you must provide L,R or A,P or S,I");
+ }
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
template <class ImageType>
void
template <class ImageType>
void
clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
-SetAngle1(double a)
+AddAngles(double a, double b)
{
- SetOrientationType(Angle);
- m_Angle1 = a;
+ AddOrientationTypeString("Angle");
+ m_Angle1.push_back(a);
+ m_Angle2.push_back(b);
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
-SetAngle2(double a)
+AddOrientationType(OrientationTypeEnumeration orientation)
{
- SetOrientationType(Angle);
- m_Angle2 = a;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void
-clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
-SetOrientationType(OrientationTypeEnumeration orientation)
-{
- m_OrientationType = orientation;
- switch (m_OrientationType) {
- case LeftTo: m_Angle1 = clitk::deg2rad(0); m_Angle2 = clitk::deg2rad(0); break;
- case RightTo: m_Angle1 = clitk::deg2rad(180); m_Angle2 = clitk::deg2rad(0); break;
- case AntTo: m_Angle1 = clitk::deg2rad(90); m_Angle2 = clitk::deg2rad(0); break;
- case PostTo: m_Angle1 = clitk::deg2rad(-90); m_Angle2 = clitk::deg2rad(0); break;
- case InfTo: m_Angle1 = clitk::deg2rad(0); m_Angle2 = clitk::deg2rad(90); break;
- case SupTo: m_Angle1 = clitk::deg2rad(0); m_Angle2 = clitk::deg2rad(-90); break;
- case Angle: break;
+ m_OrientationType.push_back(orientation);
+ switch (orientation) {
+ case LeftTo:
+ m_Angle1.push_back(clitk::deg2rad(0));
+ m_Angle2.push_back(clitk::deg2rad(0));
+ break;
+ case RightTo:
+ m_Angle1.push_back(clitk::deg2rad(180));
+ m_Angle2.push_back(clitk::deg2rad(0));
+ break;
+ case AntTo:
+ m_Angle1.push_back(clitk::deg2rad(90));
+ m_Angle2.push_back(clitk::deg2rad(0));
+ break;
+ case PostTo:
+ m_Angle1.push_back(clitk::deg2rad(-90));
+ m_Angle2.push_back(clitk::deg2rad(0));
+ break;
+ case InfTo:
+ m_Angle1.push_back(clitk::deg2rad(0));
+ m_Angle2.push_back(clitk::deg2rad(90));
+ break;
+ case SupTo:
+ m_Angle1.push_back(clitk::deg2rad(0));
+ m_Angle2.push_back(clitk::deg2rad(-90));
+ break;
+ case Angle: break;
}
/* A1 A2
Left 0 0
clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
GenerateData()
{
+ if (GetNumberOfAngles() <1) {
+ clitkExceptionMacro("Add at least one orientation type");
+ }
+
// Get input pointer
input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
//--------------------------------------------------------------------
//--------------------------------------------------------------------
static const unsigned int dim = ImageType::ImageDimension;
- StartNewStep("Initial resample and pad");
+ StartNewStep("Initial resample");
// Step 1 : resample
if (m_ResampleBeforeRelativePositionFilter) {
typedef clitk::ResampleImageWithOptionsFilter<ImageType> ResampleFilterType;
resampleFilter->SetInput(object);
resampleFilter->SetOutputIsoSpacing(m_IntermediateSpacing);
resampleFilter->SetGaussianFilteringEnabled(false);
- // resampleFilter->SetVerboseOptions(true);
+ // resampleFilter->SetVerboseOptions(true);
resampleFilter->Update();
working_image = resampleFilter->GetOutput();
}
else {
working_image = object;
}
+ StopCurrentStep<ImageType>(working_image);
// Step 2: object pad to input image -> we want to compute the
// relative position for each point belonging to the input image
// domain, so we have to extend (pad) the object image to fit the
// domain size
if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, working_image)) {
+ StartNewStep("Pad object to image size");
typename ImageType::Pointer output = ImageType::New();
SizeType size;
for(unsigned int i=0; i<dim; i++) {
- size[i] = lrint((input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i])/(double)working_image->GetSpacing()[i]);
+ size[i] = lrint((input->GetLargestPossibleRegion().GetSize()[i]*
+ input->GetSpacing()[i])/(double)working_image->GetSpacing()[i]);
}
+
+ // The index of the input is not necessarily zero, so we have to
+ // take it into account (not done)
RegionType region;
+ IndexType index = input->GetLargestPossibleRegion().GetIndex();
region.SetSize(size);
+ for(unsigned int i=0; i<dim; i++) {
+ if (index[i] != 0) {
+ std::cerr << "Index diff from zero : " << index << ". not done yet !" << std::endl;
+ exit(0);
+ }
+ }
// output->SetLargestPossibleRegion(region);
output->SetRegions(region);
- output->SetSpacing(working_image->GetSpacing());
- output->SetOrigin(input->GetOrigin());
+ output->SetSpacing(working_image->GetSpacing());
+ PointType origin = input->GetOrigin();
+ for(unsigned int i=0; i<dim; i++) {
+ origin[i] = index[i]*input->GetSpacing()[i] + input->GetOrigin()[i];
+ }
+ output->SetOrigin(origin);
+ // output->SetOrigin(input->GetOrigin());
+
output->Allocate();
output->FillBuffer(m_BackgroundValue);
typename PadFilterType::Pointer padFilter = PadFilterType::New();
- typename PadFilterType::InputImageIndexType index;
+ // typename PadFilterType::InputImageIndexType index;
for(unsigned int i=0; i<dim; i++) {
- index[i] = lrint((working_image->GetOrigin()[i] - input->GetOrigin()[i])/working_image->GetSpacing()[i]);
+ index[i] = -index[i]*input->GetSpacing()[i]/(double)working_image->GetSpacing()[i]
+ + lrint((working_image->GetOrigin()[i] - input->GetOrigin()[i])/working_image->GetSpacing()[i]);
}
padFilter->SetSourceImage(working_image);
padFilter->SetDestinationImage(output);
padFilter->SetSourceRegion(working_image->GetLargestPossibleRegion());
padFilter->Update();
working_image = padFilter->GetOutput();
+ StopCurrentStep<ImageType>(working_image);
}
else {
// DD("[debug] RelPos : same size and spacing : no padding");
}
// Keep object image (with resampline and pad)
object_resampled = working_image;
- StopCurrentStep<ImageType>(working_image);
+ // StopCurrentStep<ImageType>(working_image);
// Step 3: compute rel pos in object
StartNewStep("Relative Position Map");
typedef itk::RelativePositionPropImageFilter<ImageType, FloatImageType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->SetInput(working_image);
- relPosFilter->SetAlpha1(m_Angle1); // xy plane
- relPosFilter->SetAlpha2(m_Angle2);
- relPosFilter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
- relPosFilter->SetFast(true);
- relPosFilter->SetRadius(1); // seems sufficient in this cas
- // relPosFilter->SetVerboseProgress(true);
- relPosFilter->Update();
- relPos = relPosFilter->GetOutput();
+ typename RelPosFilterType::Pointer relPosFilter;
+
+ typename FloatImageType::Pointer m_FuzzyMap;
+ for(int i=0; i<GetNumberOfAngles(); i++) {
+ // Compute fuzzy map
+ relPosFilter = RelPosFilterType::New();
+ relPosFilter->SetInput(working_image);
+ relPosFilter->SetAlpha1(m_Angle1[i]); // xy plane
+ relPosFilter->SetAlpha2(m_Angle2[i]);
+ relPosFilter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
+ relPosFilter->SetFast(true);
+ relPosFilter->SetRadius(1); // seems sufficient in this case
+ // relPosFilter->SetVerboseProgress(true);
+ relPosFilter->Update();
+ relPos = relPosFilter->GetOutput();
+
+ if (GetNumberOfAngles() != 1) {
+ // Creation of the first m_FuzzyMap
+ if (i==0) {
+ m_FuzzyMap = clitk::NewImageLike<FloatImageType>(relPos, true);
+ m_FuzzyMap->FillBuffer(0.0);
+ }
+
+ // Add to current fuzzy map
+ typedef itk::AddImageFilter<FloatImageType, FloatImageType, FloatImageType> AddImageFilter;
+ typename AddImageFilter::Pointer addFilter = AddImageFilter::New();
+ addFilter->SetInput1(m_FuzzyMap);
+ addFilter->SetInput2(relPos);
+ addFilter->Update();
+ m_FuzzyMap = addFilter->GetOutput();
+ }
+ else m_FuzzyMap = relPos;
+ }
+
+ // Divide by the number of relpos
+ if (GetNumberOfAngles() != 1) {
+ typedef itk::DivideByConstantImageFilter<FloatImageType, float, FloatImageType> DivideFilter;
+ typename DivideFilter::Pointer divideFilter = DivideFilter::New();
+ divideFilter->SetInput(m_FuzzyMap);
+ divideFilter->SetConstant(GetNumberOfAngles());
+ divideFilter->Update();
+ m_FuzzyMap = divideFilter->GetOutput();
+ }
+
+ relPos = m_FuzzyMap;
StopCurrentStep<FloatImageType>(relPos);
//--------------------------------------------------------------------
// resampleFilter->SetVerboseOptions(true);
resampleFilter->Update();
working_image = resampleFilter->GetOutput();
- StopCurrentStep<ImageType>(working_image);
+ StopCurrentStep<ImageType>(working_image);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Pre Step 6: pad if not the same size : it can occur when downsample and upsample
+ //if (!HaveSameSizeAndSpacing(working_image, input)) {
if (working_image->GetLargestPossibleRegion() != input->GetLargestPossibleRegion()) {
StartNewStep("Pad to get the same size than input");
typename ImageType::Pointer temp = ImageType::New();
temp->CopyInformation(input);
temp->SetRegions(input->GetLargestPossibleRegion()); // Do not forget !!
temp->Allocate();
- temp->FillBuffer(m_BackgroundValue);
- typename PadFilterType::Pointer padFilter2 = PadFilterType::New(); // if yes : redo relpos
+ temp->FillBuffer(m_BackgroundValue);
+ typename PadFilterType::Pointer padFilter2 = PadFilterType::New();
padFilter2->SetSourceImage(working_image);
padFilter2->SetDestinationImage(temp);
+ // DD(input->GetLargestPossibleRegion().GetIndex());
padFilter2->SetDestinationIndex(input->GetLargestPossibleRegion().GetIndex());
padFilter2->SetSourceRegion(working_image->GetLargestPossibleRegion());
padFilter2->Update();
StartNewStep("Combine with initial input (boolean And)");
typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
typename BoolFilterType::Pointer combineFilter = BoolFilterType::New();
- writeImage<ImageType>(input, "i.mhd");
- writeImage<ImageType>(working_image, "w.mhd");
combineFilter->SetBackgroundValue(m_BackgroundValue);
combineFilter->SetBackgroundValue1(m_BackgroundValue);
combineFilter->SetBackgroundValue2(m_BackgroundValue);
combineFilter->SetForegroundValue(m_BackgroundValue+1);
combineFilter->SetInput1(input);
combineFilter->SetInput2(working_image);
- combineFilter->SetOperationType(BoolFilterType::And);
- combineFilter->InPlaceOn();
+ if (GetInverseOrientationFlag())
+ combineFilter->SetOperationType(BoolFilterType::AndNot);
+ else {
+ if (GetCombineWithOrFlag())
+ combineFilter->SetOperationType(BoolFilterType::Or);
+ else
+ combineFilter->SetOperationType(BoolFilterType::And);
+ }
+ combineFilter->InPlaceOff(); // Do not modify initial input (!)
combineFilter->Update();
working_image = combineFilter->GetOutput();
- // writeImage<ImageType>(working_image, "res.mhd");
-
- combineFilter = BoolFilterType::New();
- combineFilter->SetInput1(working_image);
- combineFilter->SetInput2(object);
- combineFilter->SetOperationType(BoolFilterType::AndNot);
- combineFilter->InPlaceOn();
- combineFilter->Update();
- working_image = combineFilter->GetOutput();
+ // Remove (if needed the object from the support)
+ if (GetRemoveObjectFlag()) {
+ combineFilter = BoolFilterType::New();
+ combineFilter->SetInput1(working_image);
+ combineFilter->SetInput2(object);
+ combineFilter->SetOperationType(BoolFilterType::AndNot);
+ combineFilter->InPlaceOn();
+ combineFilter->Update();
+ working_image = combineFilter->GetOutput();
+ }
+ // In the other case, we must *add* the initial object to keep it
+ // but not more than the initial support
+ else {
+ combineFilter = BoolFilterType::New();
+ combineFilter->SetInput1(working_image);
+ combineFilter->SetInput2(object);
+ combineFilter->SetOperationType(BoolFilterType::Or);
+ combineFilter->InPlaceOn();
+ combineFilter->Update();
+ working_image = combineFilter->GetOutput(); // not needed because InPlaceOn ?
+ combineFilter = BoolFilterType::New();
+ combineFilter->SetInput1(working_image);
+ combineFilter->SetInput2(input);
+ combineFilter->SetOperationType(BoolFilterType::And);
+ combineFilter->InPlaceOn();
+ combineFilter->Update();
+ working_image = combineFilter->GetOutput();
+ }
+
StopCurrentStep<ImageType>(working_image);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Step 7: autocrop
- if (GetAutoCrop()) {
+ if (GetAutoCropFlag()) {
StartNewStep("Final AutoCrop");
typedef clitk::AutoCropFilter<ImageType> CropFilterType;
typename CropFilterType::Pointer cropFilter = CropFilterType::New();
// Final Step -> set output
this->SetNthOutput(0, working_image);
- return;
+ // this->GraftOutput(working_image);
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff