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Newest_Patch_Geometries_and_Segmentation_Tools.patch
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Authored By
graser
Nov 18 2010, 1:24 PM
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15 KB
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Newest_Patch_Geometries_and_Segmentation_Tools.patch
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Index: Core/Code/DataManagement/mitkGeometry3D.cpp
===================================================================
--- Core/Code/DataManagement/mitkGeometry3D.cpp (revision 26530)
+++ Core/Code/DataManagement/mitkGeometry3D.cpp (working copy)
@@ -623,3 +623,39 @@
mitk::Geometry3D::ResetSubTransforms()
{
}
+
+void
+mitk::Geometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry )
+{
+ // If Geometry is switched to ImageGeometry, you have to put an offset to the origin, because
+ // imageGeometries origins are pixel-center-based
+ // ... and remove the offset, if you switch an imageGeometry back to a normal geometry
+
+ if(m_ImageGeometry == isAnImageGeometry)
+ return;
+
+ const BoundingBox::BoundsArrayType& boundsarray =
+ this->GetBoundingBox()->GetBounds();
+
+ Point3D originIndex;
+ FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]);
+
+ if(isAnImageGeometry == true)
+ FillVector3D( originIndex,
+ originIndex[0] + 0.5,
+ originIndex[1] + 0.5,
+ originIndex[2] + 0.5 );
+ else
+ FillVector3D( originIndex,
+ originIndex[0] - 0.5,
+ originIndex[1] - 0.5,
+ originIndex[2] - 0.5 );
+
+ Point3D originWorld;
+ originWorld = GetIndexToWorldTransform()
+ ->TransformPoint( originIndex );
+
+ SetOrigin(originWorld);
+
+ this->SetImageGeometry(isAnImageGeometry);
+}
\ No newline at end of file
Index: Core/Code/DataManagement/mitkGeometry3D.h
===================================================================
--- Core/Code/DataManagement/mitkGeometry3D.h (revision 26530)
+++ Core/Code/DataManagement/mitkGeometry3D.h (working copy)
@@ -145,6 +145,11 @@
//## @brief Set the bounding box (in index/unit coordinates) via a double array
virtual void SetFloatBounds(const double bounds[6]);
+
+ /// Changes Geometry Origin, if switching from imageGeometry to normal Geometry (and the other way around)
+ virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry );
+
+
//##Documentation
//## @brief Get the time bounds (in ms)
itkGetConstReferenceMacro(TimeBounds, TimeBounds);
@@ -279,7 +284,7 @@
virtual void Compose( const vtkMatrix4x4 * vtkmatrix, bool pre = 0 );
//##Documentation
- //## @brief Get the origin, i.e. the upper-left corner of the plane
+ //## @brief Get the origin, e.g. the upper-left corner of the plane
const Point3D& GetOrigin() const
{
return m_Origin;
Index: Core/Code/DataManagement/mitkImage.cpp
===================================================================
--- Core/Code/DataManagement/mitkImage.cpp (revision 26530)
+++ Core/Code/DataManagement/mitkImage.cpp (working copy)
@@ -765,6 +765,7 @@
TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New();
timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]);
+ timeSliceGeometry->ImageGeometryOn();
SetGeometry(timeSliceGeometry);
@@ -997,6 +998,7 @@
TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New();
timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]);
+ timeSliceGeometry->ImageGeometryOn();
SetGeometry(timeSliceGeometry);
@@ -1168,6 +1170,21 @@
void mitk::Image::SetGeometry(Geometry3D* aGeometry3D)
{
+ // ATTENTION!!! Please be aware of the 0.5 offset/pixel-center issue!
+ // The geometry of an image should have the bool value "ImageGeometry" as true, to indicate it belongs to an image.
+ // While "normal" geometries have their origin usually on a corner (e.g. 0,0,0), image geometries are pixel-center based.
+ // That means, they have their origin in the middle of the first pixel (e.g. 0.5,0.5,0.5).
+ // When you call mitk::Image::SetGeometry(..) please be sure, that the geometry
+ // a) is center-based
+ // b) has the bool flag "ImageGeometry" on true
+ //
+ // If ImageGeometry==false, you can call "Geometry3D::ChangeImageGeometryConsideringOriginOffset(true)" to make it centerbased and turn on the flag.
+ // If ImageGeometry==true, you can call "Geometry3D::ChangeImageGeometryConsideringOriginOffset(false)" to make it cornerbased again and turn off the flag.
+
+ if(aGeometry3D->GetImageGeometry()==false)
+ {
+ MITK_INFO << "WARNING: Applied a non-image geometry onto an image. If you are SURE that this this geometry is pixel-center-based, please turn the imageGeometry flag on by calling 'ImageGeometryOn()'. If the geometry is not center-based yet, please call 'ChangeImageGeometryConsideringOriginOffset(true)' to make it center-based and flag it.\n";
+ }
Superclass::SetGeometry(aGeometry3D);
GetTimeSlicedGeometry()->ImageGeometryOn();
}
Index: Core/Code/DataManagement/mitkSlicedGeometry3D.cpp
===================================================================
--- Core/Code/DataManagement/mitkSlicedGeometry3D.cpp (revision 26530)
+++ Core/Code/DataManagement/mitkSlicedGeometry3D.cpp (working copy)
@@ -459,6 +459,25 @@
}
}
+void
+mitk::SlicedGeometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry )
+{
+ mitk::Geometry3D* geometry;
+
+ unsigned int s;
+ for ( s = 0; s < m_Slices; ++s )
+ {
+ geometry = m_Geometry2Ds[s];
+ if ( geometry!=NULL )
+ {
+ geometry->ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry );
+ }
+ }
+
+ Superclass::ChangeImageGeometryConsideringOriginOffset( isAnImageGeometry );
+}
+
+
bool
mitk::SlicedGeometry3D::IsValidSlice( int s ) const
{
Index: Core/Code/DataManagement/mitkSlicedGeometry3D.h
===================================================================
--- Core/Code/DataManagement/mitkSlicedGeometry3D.h (revision 26530)
+++ Core/Code/DataManagement/mitkSlicedGeometry3D.h (working copy)
@@ -112,6 +112,9 @@
*/
virtual bool SetGeometry2D( mitk::Geometry2D *geometry2D, int s );
+ /// Changes Geometry Origin, if switching from imageGeometry to normal Geometry (and the other way around)
+ virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry );
+
virtual void SetTimeBounds( const mitk::TimeBounds& timebounds );
Index: Core/Code/DataManagement/mitkTimeSlicedGeometry.cpp
===================================================================
--- Core/Code/DataManagement/mitkTimeSlicedGeometry.cpp (revision 26530)
+++ Core/Code/DataManagement/mitkTimeSlicedGeometry.cpp (working copy)
@@ -313,6 +313,22 @@
}
}
+
+void mitk::TimeSlicedGeometry::ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry)
+{
+ mitk::Geometry3D* geometry3d;
+ unsigned int t;
+ for(t=0; t<m_TimeSteps; ++t)
+ {
+ geometry3d = m_Geometry3Ds[t];
+ if(geometry3d!=NULL)
+ geometry3d->ChangeImageGeometryConsideringOriginOffset(isAnImageGeometry);
+ }
+
+ Superclass::ChangeImageGeometryConsideringOriginOffset(isAnImageGeometry);
+}
+
+
void mitk::TimeSlicedGeometry::SetEvenlyTimed(bool on)
{
m_EvenlyTimed = on;
Index: Core/Code/DataManagement/mitkTimeSlicedGeometry.h
===================================================================
--- Core/Code/DataManagement/mitkTimeSlicedGeometry.h (revision 26530)
+++ Core/Code/DataManagement/mitkTimeSlicedGeometry.h (working copy)
@@ -78,6 +78,9 @@
//## @brief Set the Geometry3D for time @a t
virtual bool SetGeometry3D(mitk::Geometry3D* geometry3D, int t);
+ /// Changes Geometry Origin, if switching from imageGeometry to normal Geometry (and the other way around)
+ virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry );
+
//##Documentation
//## @brief Get the Geometry3D at time @a t
virtual mitk::Geometry3D* GetGeometry3D(int t) const;
Index: Core/Code/Testing/mitkSlicedGeometry3DTest.cpp
===================================================================
--- Core/Code/Testing/mitkSlicedGeometry3DTest.cpp (revision 26530)
+++ Core/Code/Testing/mitkSlicedGeometry3DTest.cpp (working copy)
@@ -142,7 +142,34 @@
}
std::cout<<"[PASSED]"<<std::endl;
+ //xxx neu
+ //MITK_TEST_OUTPUT(<< "Testing whether slicedWorldGeometry->GetImageGeometry() is false by default");
+ //MITK_TEST_CONDITION_REQUIRED( slicedWorldGeometry->GetImageGeometry()==false, "");
+ //MITK_TEST_OUTPUT(<< "Testing whether first geometry in the SlicedGeometry3D has GetImageGeometry()==false by default");
+ //MITK_TEST_CONDITION_REQUIRED( accessedplanegeometry3->GetImageGeometry()==false, "");
+ //MITK_TEST_OUTPUT(<< "Testing whether last geometry in the SlicedGeometry3D has GetImageGeometry()==false by default");
+ //MITK_TEST_CONDITION_REQUIRED( accessedplanegeometry3last->GetImageGeometry()==false, "");
+ //slicedWorldGeometry->GetCornerPoint(0)
+ // accessedplanegeometry3->GetCornerPoint(0)
+ // accessedplanegeometry3last->GetCornerPoint(0)
+
+ //MITK_TEST_OUTPUT(<< "Calling slicedWorldGeometry->ChangeImageGeometry(true)");
+ //slicedWorldGeometry->ChangeImageGeometry(true);
+
+ //accessedplanegeometry3 = dynamic_cast<mitk::PlaneGeometry*>(slicedWorldGeometry->GetGeometry2D(0));
+ //accessedplanegeometry3last = dynamic_cast<mitk::PlaneGeometry*>(slicedWorldGeometry->GetGeometry2D(numSlices-1));
+
+ //MITK_TEST_OUTPUT(<< "Testing whether slicedWorldGeometry->GetImageGeometry() is now true");
+ //MITK_TEST_CONDITION_REQUIRED( slicedWorldGeometry->GetImageGeometry()==true, "");
+ //MITK_TEST_OUTPUT(<< "Testing whether first geometry in the SlicedGeometry3D has GetImageGeometry()==true");
+ //MITK_TEST_CONDITION_REQUIRED( accessedplanegeometry3->GetImageGeometry()==true, "");
+ //MITK_TEST_OUTPUT(<< "Testing whether last geometry in the SlicedGeometry3D has GetImageGeometry()==true");
+ //MITK_TEST_CONDITION_REQUIRED( accessedplanegeometry3last->GetImageGeometry()==true, "");
+
+ //slicedWorldGeometry->GetOrigin()
+
+
std::cout<<"[TEST DONE]"<<std::endl;
return EXIT_SUCCESS;
}
Index: Modules/MitkExt/Algorithms/mitkContourUtils.cpp
===================================================================
--- Modules/MitkExt/Algorithms/mitkContourUtils.cpp (revision 26530)
+++ Modules/MitkExt/Algorithms/mitkContourUtils.cpp (working copy)
@@ -49,7 +49,7 @@
Point3D projectedPointIn2D;
projectedPointIn2D.Fill(0.0);
sliceGeometry->WorldToIndex( currentPointIn3D, projectedPointIn2D );
- MITK_DEBUG << "world point " << currentPointIn3D << " in index is " << projectedPointIn2D;
+ MITK_INFO << "world point " << currentPointIn3D << " in index is " << projectedPointIn2D;
if ( !sliceGeometry->IsIndexInside( projectedPointIn2D ) && constrainToInside )
{
@@ -81,7 +81,7 @@
Point3D worldPointIn3D;
worldPointIn3D.Fill(0.0);
sliceGeometry->IndexToWorld( currentPointIn2D, worldPointIn3D );
- MITK_DEBUG << "index " << currentPointIn2D << " world " << worldPointIn3D << std::endl;
+ MITK_INFO << "index " << currentPointIn2D << " world " << worldPointIn3D << std::endl;
worldContour->AddVertex( worldPointIn3D );
}
@@ -104,9 +104,9 @@
iter != pointsIn2D->end();
++iter, ++index )
{
- picContour[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)[0] + 0.5);
- picContour[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)[1] + 0.5);
- MITK_DEBUG << "mitk 2d [" << (*iter)[0] << ", " << (*iter)[1] << "] pic [" << picContour[ 2*index+0] << ", " << picContour[ 2*index+1] << "]";
+ picContour[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)[0] + 1.0 ); // +0.5 wahrscheinlich richtiger
+ picContour[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)[1] + 1.0 );
+ MITK_INFO << "mitk 2d [" << (*iter)[0] << ", " << (*iter)[1] << "] pic [" << picContour[ 2*index+0] << ", " << picContour[ 2*index+1] << "]";
}
assert( sliceImage->GetSliceData() );
Index: Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.cpp
===================================================================
--- Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.cpp (revision 26530)
+++ Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.cpp (working copy)
@@ -154,8 +154,8 @@
iter != pointsIn2D->end();
++iter, ++index )
{
- _points[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)[0] + 1.0 );
- _points[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)[1] + 1.0 );
+ _points[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)[0] + 0.5 );
+ _points[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)[1] + 0.5 );
}
// store ofsets of the drawn line in array
Index: Modules/MitkExt/Algorithms/mitkExtractImageFilter.cpp
===================================================================
--- Modules/MitkExt/Algorithms/mitkExtractImageFilter.cpp (revision 26530)
+++ Modules/MitkExt/Algorithms/mitkExtractImageFilter.cpp (working copy)
@@ -96,6 +96,7 @@
PlaneGeometry::Pointer planeGeometry = PlaneGeometry::New();
planeGeometry->InitializeStandardPlane( inputImageGeometry, orientation, (ScalarType)m_SliceIndex + 0.5 , true, false );
Image::Pointer resultImage = ImageToImageFilter::GetOutput();
+ planeGeometry->ChangeImageGeometryConsideringOriginOffset(true);
resultImage->SetGeometry( planeGeometry );
}
Index: Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp
===================================================================
--- Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp (revision 26530)
+++ Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp (working copy)
@@ -237,13 +237,13 @@
// round to nearest voxel center (abort if this hasn't changed)
if ( m_Size % 2 == 0 ) // even
{
- indexCoordinates[firstDimension] = ROUND( indexCoordinates[firstDimension] + 0.5 );
+ indexCoordinates[firstDimension] = ROUND( indexCoordinates[firstDimension] + 0.5);
indexCoordinates[secondDimension] = ROUND( indexCoordinates[secondDimension] + 0.5 );
}
else // odd
{
- indexCoordinates[firstDimension] = ROUND( indexCoordinates[firstDimension] ) ;//+ 0.5;
- indexCoordinates[secondDimension] = ROUND( indexCoordinates[secondDimension] );// + 0.5;
+ indexCoordinates[firstDimension] = ROUND( indexCoordinates[firstDimension] ) ;
+ indexCoordinates[secondDimension] = ROUND( indexCoordinates[secondDimension] ) ;
}
static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me
@@ -300,11 +300,11 @@
for (unsigned int index = 0; index < contour->GetNumberOfPoints(); ++index)
{
Point3D point = contour->GetPoints()->ElementAt(index);
- if ( m_Size % 2 != 0 ) // even
+ /*if ( m_Size % 2 != 0 ) // even
{
point[0] += 0.5;
point[1] += 0.5;
- }
+ }*/
displayContour->AddVertex( point );
}
Index: Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp
===================================================================
--- Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp (revision 26530)
+++ Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp (working copy)
@@ -524,7 +524,7 @@
newPoint[1] = contourPoints[ 2 * index + 1];
newPoint[2] = 0;
- contourInImageIndexCoordinates->AddVertex( newPoint );
+ contourInImageIndexCoordinates->AddVertex( newPoint + 0.5);
}
free(contourPoints);
Index: Modules/MitkExt/Interactions/mitkSetRegionTool.cpp
===================================================================
--- Modules/MitkExt/Interactions/mitkSetRegionTool.cpp (revision 26530)
+++ Modules/MitkExt/Interactions/mitkSetRegionTool.cpp (working copy)
@@ -188,7 +188,7 @@
newPoint[1] = contourPoints[ 2 * index + 1];
newPoint[2] = 0;
- contourInImageIndexCoordinates->AddVertex( newPoint );
+ contourInImageIndexCoordinates->AddVertex( newPoint - 0.5 );
}
m_SegmentationContourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSlice, contourInImageIndexCoordinates, true ); // true, correct the result from ipMITKSegmentationGetContour8N

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Newest_Patch_Geometries_and_Segmentation_Tools.patch (15 KB)

Event Timeline

graser added a comment.Nov 18 2010, 1:24 PM

Newest Patch for Geometries and Segmentation Tools

MITK · MIC · IMSY · DKFZ