Fix dashboards (#83)

* BUG: Fixed typename, overload, protected variable reference, incorrect capitalization, and matrix.as_ref() usage.
* Use itkv5.3rc01

.github/workflows/build-test-package.yml

@@ -5,7 +5,7 @@ on: [push,pull_request]
 env:
   ITKMinimalPathExtraction-git-tag: v1.2.0
   vtk-git-tag: "1681cee3489800373c2e183af2d3ca8552e05940"
-  itk-git-tag: v5.2.1
+  itk-git-tag: v5.3rc01
 
 jobs:
   build-test-cxx:

.github/workflows/clang-format-linter.yml

@@ -0,0 +1,12 @@
+name: clang-format linter
+
+on: [push,pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master

setup.py

@@ -45,6 +45,7 @@
     keywords='ITK InsightToolkit',
     url=r'https://itk.org/',
     install_requires=[
+        r'numpy',
         r'itk>=5.2.1.post1',
         r'itk-minimalpathextraction>=1.2.0'
     ]

src/Filtering/itktubeSubSampleTubeSpatialObjectFilter.hxx

@@ -50,7 +50,7 @@ void
 SubSampleTubeSpatialObjectFilter< ObjectDimension >
 ::GenerateData( void )
 {
-  typename const TubeSpatialObjectType * input =
+  const TubeSpatialObjectType * input =
     dynamic_cast<const TubeSpatialObjectType *>( this->GetInput() );
   if (input == nullptr)
   {

src/Registration/itktubeInitialSpatialObjectToImageRegistrationMethod.h

@@ -56,7 +56,7 @@ class InitialSpatialObjectToImageRegistrationMethod
   //
   // Typedefs from Superclass
   //
-  typedef Superclass::SpatialObjectType           SpatialObjectType;
+  typedef typename Superclass::SpatialObjectType SpatialObjectType;
 
   itkStaticConstMacro( ImageDimension, unsigned int,
                        TImage::ImageDimension );

src/Registration/itktubeInitialSpatialObjectToImageRegistrationMethod.hxx

@@ -171,7 +171,7 @@ InitialSpatialObjectToImageRegistrationMethod<ObjectDimension, TImage>
     this->m_NumberOfMoments == 0 )
     {
     //  Moving image info
-    typedef SpatialObjectType::BoundingBoxType              BoundingBoxType;
+    typedef typename SpatialObjectType::BoundingBoxType     BoundingBoxType;
     typename BoundingBoxType::ConstPointer                  bbox;
     typename BoundingBoxType::PointType                     minPnt;
     typename BoundingBoxType::PointType                     maxPnt;
@@ -203,7 +203,7 @@ InitialSpatialObjectToImageRegistrationMethod<ObjectDimension, TImage>
       Point<double, ImageDimension>     fixedCenterPoint;
       if( this->GetFixedImageMaskObject() != nullptr )
         {
-        typedef SpatialObjectType::BoundingBoxType              BoundingBoxType;
+        typedef typename SpatialObjectType::BoundingBoxType     BoundingBoxType;
         typename BoundingBoxType::ConstPointer                  bbox;
         typename BoundingBoxType::PointType                     minPnt;
         typename BoundingBoxType::PointType                     maxPnt;

src/Registration/itktubePointBasedSpatialObjectToImageMetric.hxx

@@ -87,7 +87,7 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
   m_MaximumNumberOfSurfacePoints = 0;
 
   typename PointBasedSpatialObjectType::ChildrenConstListType * pbsoList =
-    this->GetPointBasedChildren( m_MovingSpatialObject );
+    this->GetPointBasedChildren( this->m_MovingSpatialObject );
   typename PointBasedSpatialObjectType::ChildrenConstListType::const_iterator
     pbsoIter;
   for( pbsoIter = pbsoList->begin(); pbsoIter != pbsoList->end();
@@ -158,7 +158,7 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
   unsigned int pointCount = 0;
 
   typename PointBasedSpatialObjectType::ChildrenConstListType * pbsoList =
-    this->GetPointBasedChildren( m_MovingSpatialObject );
+    this->GetPointBasedChildren( this->m_MovingSpatialObject );
   auto pbsoIter = pbsoList->begin();
   while( pbsoIter != pbsoList->end() )
   {
@@ -254,14 +254,14 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
 
   unsigned int pointCount = 0;
   typename PointBasedSpatialObjectType::ChildrenConstListType * pbsoList =
-    this->GetPointBasedChildren( m_MovingSpatialObject );
-  std::string oName = m_MovingSpatialObject->GetTypeName();
+    this->GetPointBasedChildren( this->m_MovingSpatialObject );
+  std::string oName = this->m_MovingSpatialObject->GetTypeName();
   if (oName.find("Tube") != std::string::npos ||
       oName.find("Surface") != std::string::npos ||
       oName.find("Blob") != std::string::npos ||
       oName.find("Point") != std::string::npos)
   {
-    pbsoList->push_front( m_MovingSpatialObject.GetPointer() );
+    pbsoList->push_front( this->m_MovingSpatialObject.GetPointer() );
   }
   auto pbsoIter = pbsoList->begin();
   while( pbsoIter != pbsoList->end() )
@@ -450,7 +450,7 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
   }
   if( childrenSO == nullptr )
   {
-    childrenSO = new MovingSpatialObjectType::ChildrenConstListType;
+    childrenSO = new typename MovingSpatialObjectType::ChildrenConstListType;
   }
 
   auto tmpChildren = parentSO->GetConstChildren();
@@ -503,9 +503,9 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
   transformCopy->SetFixedParameters( this->m_Transform->GetFixedParameters() );
   transformCopy->SetParameters( parameters );
 
-  NJetImageFunction< FixedImageType >::Pointer imFunc =
+  typename NJetImageFunction< FixedImageType >::Pointer imFunc =
     NJetImageFunction< FixedImageType >::New();
-  imFunc->SetInputImage( m_FixedImage );
+  imFunc->SetInputImage( this->m_FixedImage );
 
   VnlVectorType n1T, n2T;
 
@@ -599,9 +599,9 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
   transformCopy->SetFixedParameters( this->m_Transform->GetFixedParameters() );
   transformCopy->SetParameters( parameters );
 
-  NJetImageFunction< FixedImageType >::Pointer imFunc =
+  typename NJetImageFunction< FixedImageType >::Pointer imFunc =
     NJetImageFunction< FixedImageType >::New();
-  imFunc->SetInputImage( m_FixedImage );
+  imFunc->SetInputImage( this->m_FixedImage );
 
   VnlMatrixType biasV;
   VnlVectorType n1T, n2T;
@@ -687,7 +687,7 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
     {
     value = - value / weightSum;
 
-    VnlMatrixType biasVI = vnl_matrix_inverse< double >( biasV ).inverse();
+    VnlMatrixType biasVI = vnl_matrix_inverse< double >( biasV.as_ref() ).inverse();
 
     derivative.fill(0);
 
@@ -702,10 +702,10 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
       dXT = dXT * biasVI;
 
       typename TransformType::JacobianType jacobian;
-      m_Transform->ComputeJacobianWithRespectToParameters( fixedPoint,
+      this->m_Transform->ComputeJacobianWithRespectToParameters( fixedPoint,
         jacobian );
 
-      for( unsigned int p = 0; p<m_Transform->GetNumberOfParameters(); ++p)
+      for( unsigned int p = 0; p<this->m_Transform->GetNumberOfParameters(); ++p)
       {
         for( unsigned int d=0; d<ImageDimension; ++d)
         {
@@ -732,10 +732,10 @@ PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
       return false;
       }
     }
-  if( m_MovingSpatialObjectMaskObject.IsNotNull() &&
-    m_UseMovingSpatialObjectMaskObject )
+  if( this->m_MovingSpatialObjectMaskObject.IsNotNull() &&
+    this->m_UseMovingSpatialObjectMaskObject )
     {
-    if( !m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
+    if( !this->m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
       pnt.GetPositionInWorldSpace() ) )
       {
       return false;
@@ -749,10 +749,10 @@ bool
 PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
 ::IsValidMovingPoint( const SurfacePointType & pnt ) const
 {
-  if( m_MovingSpatialObjectMaskObject.IsNotNull() &&
-    m_UseMovingSpatialObjectMaskObject )
+  if( this->m_MovingSpatialObjectMaskObject.IsNotNull() &&
+    this->m_UseMovingSpatialObjectMaskObject )
     {
-    if( !m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
+    if( !this->m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
       pnt.GetPositionInWorldSpace() ) )
       {
       return false;
@@ -766,10 +766,10 @@ bool
 PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
 ::IsValidMovingPoint( const BlobPointType & pnt ) const
 {
-  if( m_MovingSpatialObjectMaskObject.IsNotNull() &&
-    m_UseMovingSpatialObjectMaskObject )
+  if( this->m_MovingSpatialObjectMaskObject.IsNotNull() &&
+    this->m_UseMovingSpatialObjectMaskObject )
     {
-    if( !m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
+    if( !this->m_MovingSpatialObjectMaskObject->IsInsideInWorldSpace(
       pnt.GetPositionInWorldSpace() ) )
       {
       return false;
@@ -783,9 +783,10 @@ bool
 PointBasedSpatialObjectToImageMetric< ObjectDimension, TFixedImage >
 ::IsValidFixedPoint( const FixedPointType & pnt ) const
 {
-  if( m_FixedImageMaskObject.IsNotNull() && m_UseFixedImageMaskObject )
+  if( this->m_FixedImageMaskObject.IsNotNull() &&
+    this->m_UseFixedImageMaskObject )
     {
-    if( !m_FixedImageMaskObject->IsInsideInWorldSpace( pnt ) )
+    if( !this->m_FixedImageMaskObject->IsInsideInWorldSpace( pnt ) )
       {
       return false;
       }

src/Registration/itktubePointBasedSpatialObjectTransformFilter.hxx

@@ -25,6 +25,7 @@ limitations under the License.
 
 #include "itktubePointBasedSpatialObjectTransformFilter.h"
 
+#include <itkSpatialObject.h>
 #include <itkSpatialObjectFactory.h>
 
 namespace itk
@@ -58,8 +59,8 @@ void
 PointBasedSpatialObjectTransformFilter< TTransformType, TDimension >
 ::GenerateData( void )
 {
-  SpatialObject<TDimension>::ConstPointer inputSO = this->GetInput();
-  SpatialObject<TDimension>::Pointer outputSO = this->GetOutput();
+  typename SpatialObject<TDimension>::ConstPointer inputSO = this->GetInput();
+  typename SpatialObject<TDimension>::Pointer outputSO = this->GetOutput();
 
   Transform(inputSO, outputSO);
 
@@ -69,7 +70,7 @@ PointBasedSpatialObjectTransformFilter< TTransformType, TDimension >
   typename ChildrenConstListType::iterator it = children->begin();
   while( it != children->end() )
     {
-    SpatialObject<TDimension>::Pointer tmpSO = (*it)->Clone();
+    typename SpatialObject<TDimension>::Pointer tmpSO = (*it)->Clone();
     this->UpdateLevel( *it, outputSO );
     ++it;
     }
@@ -87,7 +88,7 @@ PointBasedSpatialObjectTransformFilter< TTransformType, TDimension >
 ::UpdateLevel( const SpatialObject< TDimension > * inputSO,
   SpatialObject< TDimension > * parentSO )
 {
-  SpatialObject<TDimension>::Pointer outputSO = inputSO->Clone();
+  typename SpatialObject<TDimension>::Pointer outputSO = inputSO->Clone();
 
   Transform(inputSO, outputSO);
 

src/Registration/itktubeSpatialObjectToImageMetric.h

@@ -96,15 +96,15 @@ class ITK_TEMPLATE_EXPORT SpatialObjectToImageMetric : public SingleValuedCostFu
 
   /**  Type of the Transform Base class */
   using TransformType = Transform<CoordinateRepresentationType,
-    Self::ObjectDimension, Self::ImageDimension>;
+    ObjectDimension, ImageDimension>;
 
   using TransformPointer = typename TransformType::Pointer;
   using MovingPointType = typename TransformType::InputPointType;
   using FixedPointType = typename TransformType::OutputPointType;
   using TransformParametersType = typename TransformType::ParametersType;
   using TransformJacobianType = typename TransformType::JacobianType;
 
-  using MovingVectorType = vnl_vector_fixed<double, Self::ObjectDimension>;
+  using MovingVectorType = vnl_vector_fixed<double, ObjectDimension>;
   using FixedVectorType = vnl_vector_fixed<double, Self::ImageDimension>;
 
   /**  Type of the match measure */

src/Registration/itktubeSpatialObjectToImageRegistrationMethod.h

@@ -25,7 +25,7 @@ limitations under the License.
 
 #include "itkCommand.h"
 #include "itkSpatialObject.h"
-#include "itkDataobjectDecorator.h"
+#include "itkDataObjectDecorator.h"
 
 namespace itk
 {

src/Registration/itktubeSpatialObjectToImageRegistrationMethod.hxx

@@ -45,7 +45,7 @@ SpatialObjectToImageRegistrationMethod<ObjectDimension, TImage>
   this->ProcessObject::SetNthOutput( 0, transformDecorator.GetPointer() );
 
   this->m_RegistrationNumberOfWorkUnits = this->GetNumberOfWorkUnits();
-  this->GetMultiThreader()->SetNumberOfWorkUnits( this->m_RegistrationNumberOfWorkUnits );
+  this->SetNumberOfWorkUnits( this->m_RegistrationNumberOfWorkUnits );
 
   this->m_FixedImage = 0;
   this->m_MovingSpatialObject = 0;

src/Segmentation/itktubeRadiusExtractor3.hxx

@@ -103,7 +103,7 @@ public:
     d[3] /= m_Data->size();
     }
 
-  unsigned int GetNumberOfParameters(void) const
+  unsigned int GetNumberOfParameters(void) const override
     {
       return 4;
     }

src/Segmentation/itktubeRidgeExtractor.hxx

@@ -156,7 +156,7 @@ RidgeExtractor<TInputImage>
   m_FailureCodeCount.fill( 0 );
 
   m_Tube = nullptr;
-  m_TubeMaskImage == nullptr;
+  m_TubeMaskImage = nullptr;
 }
 
 /**