Merge branch 'develop' into SELX-138-stop-ATen-build-if-python-is-not-found

Applications/CommandLineInterface/Demo/Scripts_Windows/2B_SuperElastix_itkv4_MSD_missingController.bat

-..\SuperElastix.exe --conf ..\Configuration\itkv4_SVF_MSD_missingController.json --graphout 2B_graph_itkv4_MSD_missingController.dot --in FixedImage=..\Data\coneA2d64.mhd MovingImage=..\Data\coneB2d64.mhd --out ResultImage=2B_image_itkv4_MSD_missingController.mhd ResultDisplacementField=2B_deformation_itkv4_MSD_missingController.mhd
-
-CALL graphviz_to_png 2B_graph_itkv4_MSD.dot
\ No newline at end of file

Modules/Blueprints/src/selxBlueprintImpl.cxx

@@ -381,6 +381,23 @@ BlueprintImpl
   return container;
 }
 
+BlueprintImpl::ComponentNamesType
+BlueprintImpl
+::GetUpdateOrder() const
+{
+  ComponentNamesType     container;
+ 
+  std::vector< ComponentIndexType > indexContainer;
+  
+  boost::topological_sort(this->m_Graph, std::back_inserter(indexContainer));
+
+  for (std::vector< ComponentIndexType >::reverse_iterator ii = indexContainer.rbegin(); ii != indexContainer.rend(); ++ii)
+  {
+    container.push_back(boost::get(boost::vertex_all, this->m_Graph, *ii).name);
+  }
+  return container;
+}
+
 
 BlueprintImpl::ConnectionIndexType
 BlueprintImpl

Modules/Blueprints/src/selxBlueprintImpl.h

@@ -25,6 +25,9 @@
 #include "boost/graph/directed_graph.hpp"
 #include "boost/graph/labeled_graph.hpp"
 
+// for UpdateOrder
+#include <boost/graph/topological_sort.hpp>
+
 // for ComposeWith
 #include "boost/graph/copy.hpp"
 
@@ -129,6 +132,8 @@ public:
   // Returns a vector of the Component names at the outgoing direction
   ComponentNamesType GetOutputNames( const ComponentNameType name ) const;
 
+  ComponentNamesType GetUpdateOrder() const;
+
   void Write( const std::string filename );
 
   void MergeFromFile(const std::string & filename);

Modules/Common/include/selxKeys.h

@@ -41,6 +41,7 @@ const char * const CoordRepType                = "CoordRepType";
 const char * const SourceInterface                      = "SourceInterface";                      // Special interface that connects to the outside of the SuperElastixFilter
 const char * const SinkInterface                        = "SinkInterface";                        // Special interface that connects to the outside of the SuperElastixFilter
 const char * const RegistrationControllerStartInterface = "RegistrationControllerStartInterface"; //Special interface by which all algorithms are started
+const char * const UpdateInterface = "UpdateInterface"; //Special interface by which any component can be executed in the correct pipeline order.
 }
 }
 #endif //selxKeys_h

Modules/Components/Controller/ModuleController.cmake

-#=========================================================================
-#
-#  Copyright Leiden University Medical Center, Erasmus University Medical 
-#  Center and contributors
-#
-#  Licensed under the Apache License, Version 2.0 (the "License");
-#  you may not use this file except in compliance with the License.
-#  You may obtain a copy of the License at
-#
-#        http://www.apache.org/licenses/LICENSE-2.0.txt
-#
-#  Unless required by applicable law or agreed to in writing, software
-#  distributed under the License is distributed on an "AS IS" BASIS,
-#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#  See the License for the specific language governing permissions and
-#  limitations under the License.
-#
-#=========================================================================
-
-set( ${MODULE}_INCLUDE_DIRS
-  ${${MODULE}_SOURCE_DIR}/include
-)
-
-# This module is header-only and does not contain any source files
-set( ${MODULE}_SOURCE_FILES
-)
-
-# This module is header-only and does not export any libraries
-set( ${MODULE}_LIBRARIES
-)
-
-set( ${MODULE}_TEST_SOURCE_FILES
-)

Modules/Components/Controller/include/selxModuleController.h

-/*=========================================================================
-*
-*  Copyright Leiden University Medical Center, Erasmus University Medical
-*  Center and contributors
-*
-*  Licensed under the Apache License, Version 2.0 (the "License");
-*  you may not use this file except in compliance with the License.
-*  You may obtain a copy of the License at
-*
-*        http://www.apache.org/licenses/LICENSE-2.0.txt
-*
-*  Unless required by applicable law or agreed to in writing, software
-*  distributed under the License is distributed on an "AS IS" BASIS,
-*  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-*  See the License for the specific language governing permissions and
-*  limitations under the License.
-*
-*=========================================================================*/
-
-#include "selxTypeList.h"
-
-//Component group Controller
-#include "selxRegistrationControllerComponent.h"
-
-namespace selx
-{
-using ModuleControllerComponents = selx::TypeList<
-  RegistrationControllerComponent< >
-  >;
-}

Modules/Components/Controller/include/selxRegistrationControllerComponent.h

-/*=========================================================================
- *
- *  Copyright Leiden University Medical Center, Erasmus University Medical
- *  Center and contributors
- *
- *  Licensed under the Apache License, Version 2.0 (the "License");
- *  you may not use this file except in compliance with the License.
- *  You may obtain a copy of the License at
- *
- *        http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- *  Unless required by applicable law or agreed to in writing, software
- *  distributed under the License is distributed on an "AS IS" BASIS,
- *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  See the License for the specific language governing permissions and
- *  limitations under the License.
- *
- *=========================================================================*/
-
-#ifndef selxRegistrationControllerComponent_h
-#define selxRegistrationControllerComponent_h
-
-#include "selxSuperElastixComponent.h"
-//#include "selxInterfaces.h"
-
-#include <string.h>
-#include <set>
-
-namespace selx
-{
-template< bool dummy = true >
-class RegistrationControllerComponent :
-  public SuperElastixComponent<
-  Accepting< RunRegistrationInterface, ReconnectTransformInterface, AfterRegistrationInterface >,
-  Providing< RegistrationControllerStartInterface >
-  >
-{
-  // RegistrationControllerComponent is a work-around for broken itk-pipelines.
-  // Both the elastix and itkv4 require to connect their transforms *after* execution of the registration.
-  // This controller explicitly performs these steps
-  // TODO: see if signals-and-slots paradigm is appropriate here.
-
-public:
-
-  /** Standard ITK typedefs. */
-  typedef RegistrationControllerComponent Self;
-  typedef SuperElastixComponent<
-    Accepting< RunRegistrationInterface, ReconnectTransformInterface, AfterRegistrationInterface >,
-    Providing< RegistrationControllerStartInterface >
-    >                   Superclass;
-  typedef std::shared_ptr< Self >       Pointer;
-  typedef std::shared_ptr< const Self > ConstPointer;
-
-  RegistrationControllerComponent(const std::string &name, LoggerImpl &logger);
-  virtual ~RegistrationControllerComponent();
-
-  // Accepting Interfaces:
-  virtual int Accept( RunRegistrationInterface::Pointer ) override;
-
-  virtual int Accept( ReconnectTransformInterface::Pointer ) override;
-
-  virtual int Accept( AfterRegistrationInterface::Pointer ) override;
-
-  // Providing Interfaces:
-  virtual void RegistrationControllerStart( void ) override;
-
-  virtual bool MeetsCriterion( const ComponentBase::CriterionType & criterion ) override;
-
-  // override default by not checking accepting connections and always return true.
-  // TODO: the controller is a bit odd since it accepts connections, but the providing components require the connections. See if we can reverse the direction of the connection.
-  virtual bool ConnectionsSatisfied() override { return true; }
-
-  static const char * GetDescription() { return "RegistrationController Component"; }
-
-private:
-
-  std::set< RunRegistrationInterface::Pointer >    m_RunRegistrationInterfaces;
-  std::set< ReconnectTransformInterface::Pointer > m_ReconnectTransformInterfaces;
-  std::set< AfterRegistrationInterface::Pointer >  m_AfterRegistrationInterfaces;
-
-protected:
-
-  // return the class name and the template arguments to uniquely identify this component.
-  static inline const std::map< std::string, std::string > TemplateProperties()
-  {
-    return { { keys::NameOfClass, "RegistrationControllerComponent" } };
-  }
-};
-} //end namespace selx
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "selxRegistrationControllerComponent.hxx"
-#endif
-#endif // #define selxRegistrationControllerComponent_h

Modules/Components/Elastix/include/selxElastixComponent.h

@@ -42,7 +42,7 @@ class ElastixComponent :
   >,
   Providing<
   itkImageInterface< Dimensionality, TPixel >,
-  RunRegistrationInterface
+  UpdateInterface
   >
   >
 {
@@ -59,7 +59,7 @@ public:
     >,
     Providing<
     itkImageInterface< Dimensionality, TPixel >,
-    RunRegistrationInterface
+    UpdateInterface
     >
     >                                   Superclass;
   typedef std::shared_ptr< Self >       Pointer;
@@ -92,7 +92,7 @@ public:
 
   virtual ItkImagePointer GetItkImage() override;
 
-  virtual void RunRegistration() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const CriterionType & criterion ) override;
 

Modules/Components/Elastix/include/selxElastixComponent.hxx

@@ -101,7 +101,7 @@ ElastixComponent< Dimensionality, TPixel >::GetItkImage()
 
 template< int Dimensionality, class TPixel >
 void
-ElastixComponent< Dimensionality, TPixel >::RunRegistration( void )
+ElastixComponent< Dimensionality, TPixel >::Update( void )
 {
   // TODO currently, the pipeline with elastix and tranformix can only be created after the update of elastix
   this->m_elastixFilter->Update();

Modules/Components/Elastix/include/selxMonolithicElastixComponent.h

@@ -43,7 +43,7 @@ class MonolithicElastixComponent :
   Providing<
   elastixTransformParameterObjectInterface< itk::Image< TPixel, Dimensionality >, itk::Image< TPixel, Dimensionality >>,
   itkImageInterface< Dimensionality, TPixel >,
-  RunRegistrationInterface
+  UpdateInterface
   >
   >
 {
@@ -61,7 +61,7 @@ public:
     Providing<
     elastixTransformParameterObjectInterface< itk::Image< TPixel, Dimensionality >, itk::Image< TPixel, Dimensionality >>,
     itkImageInterface< Dimensionality, TPixel >,
-    RunRegistrationInterface
+    UpdateInterface
     >
     >                                     Superclass;
   typedef std::shared_ptr< Self >       Pointer;
@@ -99,7 +99,7 @@ public:
 
   virtual ItkImagePointer GetItkImage() override;
 
-  virtual void RunRegistration() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const CriterionType & criterion ) override;
 

Modules/Components/Elastix/include/selxMonolithicElastixComponent.hxx

@@ -85,7 +85,7 @@ TPixel >::elastixTransformParameterObject * MonolithicElastixComponent< Dimensio
 
 template< int Dimensionality, class TPixel >
 void
-MonolithicElastixComponent< Dimensionality, TPixel >::RunRegistration( void )
+MonolithicElastixComponent< Dimensionality, TPixel >::Update( void )
 {
   this->m_elastixFilter->Update();
 }

Modules/Components/Elastix/include/selxMonolithicTransformixComponent.h

@@ -45,7 +45,7 @@ class MonolithicTransformixComponent :
   Providing<
   itkImageInterface< Dimensionality, TPixel >,
   DisplacementFieldItkImageSourceInterface< Dimensionality, TPixel >,
-  ReconnectTransformInterface
+  UpdateInterface
   >
   >
 {
@@ -64,7 +64,7 @@ public:
     Providing<
     itkImageInterface< Dimensionality, TPixel >,
     DisplacementFieldItkImageSourceInterface< Dimensionality, TPixel >,
-    ReconnectTransformInterface
+    UpdateInterface
     >
     >                                      Superclass;
   typedef std::shared_ptr< Self >       Pointer;
@@ -100,7 +100,7 @@ public:
 
   virtual typename DisplacementFieldImageType::Pointer GetDisplacementFieldItkImage() override;
 
-  virtual void ReconnectTransform() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const CriterionType & criterion ) override;
 

Modules/Components/Elastix/include/selxMonolithicTransformixComponent.hxx

@@ -145,7 +145,7 @@ MonolithicTransformixComponent< Dimensionality, TPixel >::GetDisplacementFieldIt
 
 template< int Dimensionality, class TPixel >
 void
-MonolithicTransformixComponent< Dimensionality, TPixel >::ReconnectTransform( void )
+MonolithicTransformixComponent< Dimensionality, TPixel >::Update( void )
 {
   // TODO currently, the pipeline with elastix and tranformix can only be created after the update of elastix
   this->m_transformixFilter->SetTransformParameterObject( this->m_TransformParameterObjectInterface->GetTransformParameterObject() );

Modules/Components/Elastix/test/selxElastixComponentTest.cxx

@@ -27,8 +27,6 @@
 #include "selxItkImageSourceComponent.h"
 #include "selxDisplacementFieldItkImageFilterSinkComponent.h"
 
-#include "selxRegistrationControllerComponent.h"
-
 #include "itkImageFileReader.h"
 #include "itkImageFileWriter.h"
 
@@ -54,8 +52,7 @@ public:
     ItkImageSinkComponent< 2, float >,
     DisplacementFieldItkImageFilterSinkComponent< 2, float >,
     ItkImageSourceComponent< 2, float >,
-    ItkImageSourceComponent< 3, double >,
-    RegistrationControllerComponent< >> RegisterComponents;
+    ItkImageSourceComponent< 3, double >> RegisterComponents;
 
   typedef itk::Image< float, 2 >              Image2DType;
   typedef itk::ImageFileReader< Image2DType > ImageReader2DType;
@@ -119,8 +116,6 @@ TEST_F( ElastixComponentTest, ImagesOnly )
   component3Parameters[ "Dimensionality" ] = { "2" }; // should be derived from the inputs
   blueprint->SetComponent( "ResultImageSink", component3Parameters );
 
-  blueprint->SetComponent( "Controller", { { "NameOfClass", { "RegistrationControllerComponent" } } } );
-
   ParameterMapType connection1Parameters;
   //connection1Parameters["NameOfInterface"] = { "itkImageFixedInterface" };
   blueprint->SetConnection( "FixedImageSource", "RegistrationMethod", connection1Parameters );
@@ -133,9 +128,6 @@ TEST_F( ElastixComponentTest, ImagesOnly )
   //connection3Parameters["NameOfInterface"] = { "GetItkImageInterface" };
   blueprint->SetConnection( "RegistrationMethod", "ResultImageSink", connection3Parameters );
 
-  blueprint->SetConnection( "RegistrationMethod", "Controller", { {} } ); //
-  blueprint->SetConnection( "ResultImageSink", "Controller", { {} } );    //
-
   // Set up the readers and writers
   ImageReader2DType::Pointer fixedImageReader = ImageReader2DType::New();
   fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
@@ -177,8 +169,6 @@ TEST_F( ElastixComponentTest, MonolithicElastixTransformix )
 
   blueprint->SetComponent( "ResultDisplacementFieldSink", { { "NameOfClass", { "DisplacementFieldItkImageFilterSinkComponent" } }, { "Dimensionality", { "2" } } });
 
-  blueprint->SetComponent( "Controller", { { "NameOfClass", { "RegistrationControllerComponent" } } } );
-
   blueprint->SetConnection( "FixedImageSource", "RegistrationMethod", { { "NameOfInterface", { "itkImageFixedInterface" } } } ); // ;
 
   blueprint->SetConnection( "MovingImageSource", "RegistrationMethod", { { "NameOfInterface", { "itkImageMovingInterface" } } } ); // ;
@@ -193,10 +183,6 @@ TEST_F( ElastixComponentTest, MonolithicElastixTransformix )
 
   blueprint->SetConnection( "TransformDisplacementField", "ResultDisplacementFieldSink", { { "NameOfInterface", { "DisplacementFieldItkImageSourceInterface" } } }); // ;
 
-  blueprint->SetConnection( "RegistrationMethod", "Controller", { {} } );         //
-  blueprint->SetConnection( "TransformDisplacementField", "Controller", { {} } ); //
-  blueprint->SetConnection( "ResultImageSink", "Controller", { {} } );            //
-  blueprint->SetConnection( "ResultDisplacementFieldSink", "Controller", { {} });            //
 
   // Set up the readers and writers
   ImageReader2DType::Pointer fixedImageReader = ImageReader2DType::New();

Modules/Components/Examples/include/selxIdentityTransformRegistrationComponent.h

@@ -37,7 +37,7 @@ class IdentityTransformRegistrationComponent :
   itkImageFixedInterface< Dimensionality, TPixel >,
   itkImageMovingInterface< Dimensionality, TPixel >
   >,
-  Providing< RunRegistrationInterface,
+  Providing< UpdateInterface,
   DisplacementFieldItkImageSourceInterface< Dimensionality, TPixel >
   >
   >
@@ -53,7 +53,7 @@ public:
     itkImageFixedInterface< Dimensionality, TPixel >,
     itkImageMovingInterface< Dimensionality, TPixel >
     >,
-    Providing< RunRegistrationInterface,
+    Providing< UpdateInterface,
     DisplacementFieldItkImageSourceInterface< Dimensionality, TPixel >
     >
     > Superclass;
@@ -79,7 +79,7 @@ public:
   // Providing Interfaces:
   virtual typename DisplacementFieldImageType::Pointer GetDisplacementFieldItkImage() override;
 
-  virtual void RunRegistration() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const CriterionType & criterion ) override;
 

Modules/Components/Examples/include/selxIdentityTransformRegistrationComponent.hxx

@@ -81,7 +81,7 @@ IdentityTransformRegistrationComponent< Dimensionality, TPixel >::GetDisplacemen
 
 template< int Dimensionality, class TPixel >
 void
-IdentityTransformRegistrationComponent< Dimensionality, TPixel >::RunRegistration( void )
+IdentityTransformRegistrationComponent< Dimensionality, TPixel >::Update( void )
 {
   auto fixed = this->m_ImageFixedInterface->GetItkImageFixed();
   auto moving = this->m_ImageMovingInterface->GetItkImageMoving();

Modules/Components/Niftyreg/include/selxDisplacementFieldNiftiToItkImageSinkComponent.h

@@ -39,7 +39,7 @@ template< int Dimensionality, class TPixel >
 class DisplacementFieldNiftiToItkImageSinkComponent :
   public SuperElastixComponent<
   Accepting< NiftyregDisplacementFieldImageInterface< TPixel >, itkImageDomainFixedInterface< Dimensionality >>,
-  Providing< SinkInterface, AfterRegistrationInterface >
+  Providing< SinkInterface, UpdateInterface >
   >
 {
 public:
@@ -48,7 +48,7 @@ public:
   typedef DisplacementFieldNiftiToItkImageSinkComponent< Dimensionality, TPixel > Self;
   typedef SuperElastixComponent<
     Accepting< NiftyregDisplacementFieldImageInterface< TPixel >, itkImageDomainFixedInterface< Dimensionality >>,
-    Providing< SinkInterface, AfterRegistrationInterface >
+    Providing< SinkInterface, UpdateInterface >
     >                                            Superclass;
   typedef std::shared_ptr< Self >       Pointer;
   typedef std::shared_ptr< const Self > ConstPointer;
@@ -82,7 +82,7 @@ public:
 
   virtual itk::DataObject::Pointer GetInitializedOutput( void ) override;
 
-  virtual void AfterRegistration() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const ComponentBase::CriterionType & criterion ) override;
 

Modules/Components/Niftyreg/include/selxDisplacementFieldNiftiToItkImageSinkComponent.hxx

@@ -106,7 +106,7 @@ DisplacementFieldNiftiToItkImageSinkComponent< Dimensionality, TPixel >::GetInit
 
 template< int Dimensionality, class TPixel >
 void
-DisplacementFieldNiftiToItkImageSinkComponent< Dimensionality, TPixel >::AfterRegistration()
+DisplacementFieldNiftiToItkImageSinkComponent< Dimensionality, TPixel >::Update()
 {
   auto displacementFieldNiftiImage = this->m_DisplacementFieldInterface->GetDisplacementFieldNiftiImage();
   auto displacementFieldItkImage   = NiftiToItkImage< ItkDisplacementFieldType, TPixel >::Convert( displacementFieldNiftiImage );

Modules/Components/Niftyreg/include/selxNiftiToItkImageSinkComponent.h

@@ -39,7 +39,7 @@ template< int Dimensionality, class TPixel >
 class NiftiToItkImageSinkComponent :
   public SuperElastixComponent<
   Accepting< NiftyregWarpedImageInterface< TPixel >, itkImageDomainFixedInterface< Dimensionality >>,
-  Providing< SinkInterface, AfterRegistrationInterface >
+  Providing< SinkInterface, UpdateInterface >
   >
 {
 public:
@@ -48,7 +48,7 @@ public:
   typedef NiftiToItkImageSinkComponent< Dimensionality, TPixel > Self;
   typedef SuperElastixComponent<
     Accepting< NiftyregWarpedImageInterface< TPixel >, itkImageDomainFixedInterface< Dimensionality >>,
-    Providing< SinkInterface, AfterRegistrationInterface >
+    Providing< SinkInterface, UpdateInterface >
     >                                            Superclass;
   typedef std::shared_ptr< Self >       Pointer;
   typedef std::shared_ptr< const Self > ConstPointer;
@@ -79,7 +79,7 @@ public:
 
   virtual itk::DataObject::Pointer GetInitializedOutput( void ) override;
 
-  virtual void AfterRegistration() override;
+  virtual void Update() override;
 
   virtual bool MeetsCriterion( const ComponentBase::CriterionType & criterion ) override;
 

Modules/Components/Niftyreg/include/selxNiftiToItkImageSinkComponent.hxx

@@ -106,7 +106,7 @@ NiftiToItkImageSinkComponent< Dimensionality, TPixel >::GetInitializedOutput()
 
 template< int Dimensionality, class TPixel >
 void
-NiftiToItkImageSinkComponent< Dimensionality, TPixel >::AfterRegistration()
+NiftiToItkImageSinkComponent< Dimensionality, TPixel >::Update()
 {
   auto warpedNiftiImage = this->m_WarpedImageInterface->GetWarpedNiftiImage();
   auto warpedItkImage   = NiftiToItkImage< ItkImageType, TPixel >::Convert( warpedNiftiImage );