COMP: Fix build errors with Slicer-4.13

giogadi · Apr 10, 2021 · ab5d9b1 · ab5d9b1
1 parent 9830c73
commit ab5d9b1
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Showing 19 changed files with 838 additions and 856 deletions.
diff --git a/AutoPortPlacement/CMakeLists.txt b/AutoPortPlacement/CMakeLists.txt
@@ -1,11 +1,3 @@
-cmake_minimum_required(VERSION 3.5)
-
-if(NOT DEFINED CMAKE_MACOSX_RPATH)
-  set(CMAKE_MACOSX_RPATH OFF)
-endif()
-
-#-----------------------------------------------------------------------------
-project(AutoPortPlacementModuleProject)
 
 #-----------------------------------------------------------------------------
 set(MODULE_NAME AutoPortPlacement)
@@ -14,9 +6,6 @@ set(MODULE_TITLE ${MODULE_NAME})
 string(TOUPPER ${MODULE_NAME} MODULE_NAME_UPPER)
 
 #-----------------------------------------------------------------------------
-find_package(Slicer REQUIRED)
-include(${Slicer_USE_FILE})
-
 add_subdirectory(Logic)
 
 #-----------------------------------------------------------------------------
@@ -53,7 +42,7 @@ set(MODULE_RESOURCES
   )
 
 #-----------------------------------------------------------------------------
-slicerMacroBuildQtModule(
+slicerMacroBuildLoadableModule(
   NAME ${MODULE_NAME}
   TITLE ${MODULE_TITLE}
   EXPORT_DIRECTIVE ${MODULE_EXPORT_DIRECTIVE}

diff --git a/AutoPortPlacement/Logic/CMakeLists.txt b/AutoPortPlacement/Logic/CMakeLists.txt
@@ -1,14 +1,5 @@
-cmake_minimum_required(VERSION 3.5)
-
-if(NOT DEFINED CMAKE_MACOSX_RPATH)
-  set(CMAKE_MACOSX_RPATH OFF)
-endif()
-
-#-----------------------------------------------------------------------------
 project(vtkSlicer${MODULE_NAME}ModuleLogic)
 
-find_package(Eigen3 REQUIRED CONFIG)
-
 set(KIT ${PROJECT_NAME})
 
 set(${KIT}_EXPORT_DIRECTIVE "VTK_SLICER_${MODULE_NAME_UPPER}_MODULE_LOGIC_EXPORT")
@@ -25,7 +16,6 @@ set(${KIT}_TARGET_LIBRARIES
   collisions
   davinci
   ${ITK_LIBRARIES}
-  Eigen3::Eigen
   optim
   vtkSlicerAnnotationsModuleMRML
   vtkSlicerMarkupsModuleMRML

diff --git a/AutoPortPlacement/Logic/collisions/CMakeLists.txt b/AutoPortPlacement/Logic/collisions/CMakeLists.txt
@@ -2,7 +2,7 @@ add_library(collisions STATIC
   collisions.cxx
   collisions.h
   )
-target_link_libraries(collisions PUBLIC Eigen3::Eigen)
+target_link_libraries(collisions)
 
 set_property(TARGET collisions PROPERTY POSITION_INDEPENDENT_CODE ON)
 

diff --git a/AutoPortPlacement/Logic/collisions/collisions.h b/AutoPortPlacement/Logic/collisions/collisions.h
@@ -1,7 +1,7 @@
 #ifndef COLLISIONS_H
 #define COLLISIONS_H
 
-#include <Eigen/Dense>
+#include <itkeigen/Eigen/Dense>
 #include <vector>
 
 namespace Collisions

diff --git a/AutoPortPlacement/Logic/davinci-kinematics/davinci.cxx b/AutoPortPlacement/Logic/davinci-kinematics/davinci.cxx
@@ -129,7 +129,7 @@ DavinciKinematics::DavinciKinematics(const std::string& inputFilename)
     }
 
 
-  itk::DOMNode::Pointer dom = reader->GetModifiableOutput();
+  itk::DOMNode::Pointer dom = reader->GetOutput();
 
   itk::DOMNode::Pointer davinciParametersIntracorporeal = dom->Find("intracorporeal");
 

diff --git a/AutoPortPlacement/Logic/davinci-kinematics/davinci.h.in b/AutoPortPlacement/Logic/davinci-kinematics/davinci.h.in
@@ -1,8 +1,8 @@
 #ifndef DAVINCI_KINEMATICS_H
 #define DAVINCI_KINEMATICS_H
 
-#include <Eigen/Dense>
-#include <Eigen/StdVector>
+#include <itkeigen/Eigen/Dense>
+#include <itkeigen/Eigen/StdVector>
 
 #include <vector>
 

diff --git a/AutoPortPlacement/Logic/optim/optim.h b/AutoPortPlacement/Logic/optim/optim.h
@@ -2,8 +2,8 @@
 #define PORT_PLACEMENT_AUTO_PORT_PLACEMENT_LOGIC_OPTIM_OPTIM_H
 
 #include <davinci-kinematics/davinci.h>
-#include <Eigen/Dense>
-#include <Eigen/StdVector>
+#include <itkeigen/Eigen/Dense>
+#include <itkeigen/Eigen/StdVector>
 
 namespace Optim
 {

diff --git a/AutoPortPlacement/Logic/vtkSlicerAutoPortPlacementLogic.cxx b/AutoPortPlacement/Logic/vtkSlicerAutoPortPlacementLogic.cxx
@@ -46,6 +46,7 @@ vtkStandardNewMacro(vtkSlicerAutoPortPlacementLogic);
 
 namespace
 {
+
   // Given a cylisphere returned by the DavinciKinematics object,
   // returns a vtkMRMLLinearTransformNode that will transform the
   // vtkCylinderSource's output to correspond to the input cylisphere.
@@ -340,7 +341,7 @@ FindFeasiblePlan(vtkMRMLNode* taskFramesNode,
 
     // Get orientation part
     double quat[4];
-    taskFramesFiducial->GetNthMarkupOrientation(tIdx, quat);
+    taskFramesFiducial->GetNthControlPointOrientation(tIdx, quat);
     double rotMat[3][3];
     vtkMath::QuaternionToMatrix3x3(quat, rotMat);
     for (unsigned i = 0; i < 3; ++i)

diff --git a/AutoPortPlacement/Testing/Cxx/CMakeLists.txt b/AutoPortPlacement/Testing/Cxx/CMakeLists.txt
@@ -10,6 +10,7 @@ slicerMacroConfigureModuleCxxTestDriver(
   NAME ${KIT}
   SOURCES ${KIT_TEST_SRCS}
   WITH_VTK_DEBUG_LEAKS_CHECK
+  WITH_VTK_ERROR_OUTPUT_CHECK
   )
 
 #-----------------------------------------------------------------------------

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModule.cxx b/AutoPortPlacement/qSlicerAutoPortPlacementModule.cxx
@@ -15,22 +15,13 @@
 
 ==============================================================================*/
 
-// Qt includes
-#include <QtPlugin>
-
 // AutoPortPlacement Logic includes
 #include <vtkSlicerAutoPortPlacementLogic.h>
 
 // AutoPortPlacement includes
 #include "qSlicerAutoPortPlacementModule.h"
 #include "qSlicerAutoPortPlacementModuleWidget.h"
 
-//-----------------------------------------------------------------------------
-#if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
-#include <QtPlugin>
-Q_EXPORT_PLUGIN2(qSlicerAutoPortPlacementModule, qSlicerAutoPortPlacementModule);
-#endif
-
 //-----------------------------------------------------------------------------
 /// \ingroup Slicer_QtModules_ExtensionTemplate
 class qSlicerAutoPortPlacementModulePrivate
@@ -43,17 +34,15 @@ class qSlicerAutoPortPlacementModulePrivate
 // qSlicerAutoPortPlacementModulePrivate methods
 
 //-----------------------------------------------------------------------------
-qSlicerAutoPortPlacementModulePrivate
-::qSlicerAutoPortPlacementModulePrivate()
+qSlicerAutoPortPlacementModulePrivate::qSlicerAutoPortPlacementModulePrivate()
 {
 }
 
 //-----------------------------------------------------------------------------
 // qSlicerAutoPortPlacementModule methods
 
 //-----------------------------------------------------------------------------
-qSlicerAutoPortPlacementModule
-::qSlicerAutoPortPlacementModule(QObject* _parent)
+qSlicerAutoPortPlacementModule::qSlicerAutoPortPlacementModule(QObject* _parent)
   : Superclass(_parent)
   , d_ptr(new qSlicerAutoPortPlacementModulePrivate)
 {
@@ -65,19 +54,19 @@ qSlicerAutoPortPlacementModule::~qSlicerAutoPortPlacementModule()
 }
 
 //-----------------------------------------------------------------------------
-QString qSlicerAutoPortPlacementModule::helpText()const
+QString qSlicerAutoPortPlacementModule::helpText() const
 {
-  return "This is a loadable module bundled in an extension";
+  return "This is a loadable module that can be bundled in an extension";
 }
 
 //-----------------------------------------------------------------------------
-QString qSlicerAutoPortPlacementModule::acknowledgementText()const
+QString qSlicerAutoPortPlacementModule::acknowledgementText() const
 {
   return "This work was was partially funded by NIH grant 3P41RR013218-12S1";
 }
 
 //-----------------------------------------------------------------------------
-QStringList qSlicerAutoPortPlacementModule::contributors()const
+QStringList qSlicerAutoPortPlacementModule::contributors() const
 {
   QStringList moduleContributors;
   moduleContributors
@@ -88,7 +77,7 @@ QStringList qSlicerAutoPortPlacementModule::contributors()const
 }
 
 //-----------------------------------------------------------------------------
-QIcon qSlicerAutoPortPlacementModule::icon()const
+QIcon qSlicerAutoPortPlacementModule::icon() const
 {
   return QIcon(":/Icons/AutoPortPlacement.png");
 }
@@ -112,7 +101,7 @@ void qSlicerAutoPortPlacementModule::setup()
 }
 
 //-----------------------------------------------------------------------------
-qSlicerAbstractModuleRepresentation * qSlicerAutoPortPlacementModule
+qSlicerAbstractModuleRepresentation* qSlicerAutoPortPlacementModule
 ::createWidgetRepresentation()
 {
   return new qSlicerAutoPortPlacementModuleWidget;

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModule.h b/AutoPortPlacement/qSlicerAutoPortPlacementModule.h
@@ -18,7 +18,7 @@
 #ifndef __qSlicerAutoPortPlacementModule_h
 #define __qSlicerAutoPortPlacementModule_h
 
-// SlicerQt includes
+// Slicer includes
 #include "qSlicerLoadableModule.h"
 
 #include "qSlicerAutoPortPlacementModuleExport.h"
@@ -31,9 +31,7 @@ qSlicerAutoPortPlacementModule
   : public qSlicerLoadableModule
 {
   Q_OBJECT
-#ifdef Slicer_HAVE_QT5
   Q_PLUGIN_METADATA(IID "org.slicer.modules.loadable.qSlicerLoadableModule/1.0");
-#endif
   Q_INTERFACES(qSlicerLoadableModule);
 
 public:

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModuleWidget.cxx b/AutoPortPlacement/qSlicerAutoPortPlacementModuleWidget.cxx
@@ -18,7 +18,7 @@
 // Qt includes
 #include <QDebug>
 
-// SlicerQt includes
+// Slicer includes
 #include "qSlicerAutoPortPlacementModuleWidget.h"
 #include "ui_qSlicerAutoPortPlacementModuleWidget.h"
 

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModuleWidget.h b/AutoPortPlacement/qSlicerAutoPortPlacementModuleWidget.h
@@ -18,7 +18,7 @@
 #ifndef __qSlicerAutoPortPlacementModuleWidget_h
 #define __qSlicerAutoPortPlacementModuleWidget_h
 
-// SlicerQt includes
+// Slicer includes
 #include "qSlicerAbstractModuleWidget.h"
 
 #include "qSlicerAutoPortPlacementModuleExport.h"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,15 +1,16 @@
-cmake_minimum_required(VERSION 3.5)
+cmake_minimum_required(VERSION 3.13.4)
 
 project(PortPlacement)
 
 #-----------------------------------------------------------------------------
+# Extension meta-information
 set(EXTENSION_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PortPlacement")
 set(EXTENSION_CATEGORY "IGT")
 set(EXTENSION_CONTRIBUTORS "Andinet Enquobahrie (Kitware), Luis G. Torres (UNC), Jean-Christophe Fillion-Robin (Kitware)")
 set(EXTENSION_DESCRIPTION "Assists in the planning of surgical port placement in a laparoscopic procedure.")
 set(EXTENSION_ICONURL "http://www.slicer.org/slicerWiki/images/a/a7/Portplacement_icon.png")
 set(EXTENSION_SCREENSHOTURLS "http://www.slicer.org/slicerWiki/images/3/32/Portplacement.png")
-set(EXTENSION_DEPENDS "Eigen3")
+set(EXTENSION_DEPENDS "NA")
 set(EXTENSION_BUILD_SUBDIRECTORY inner-build)
 set(EXTENSION_STATUS "This extension is intended for public use and we expect to fully maintain it.")
 
@@ -29,9 +30,6 @@ mark_as_superbuild(Slicer_DIR)
 find_package(Git REQUIRED)
 mark_as_superbuild(GIT_EXECUTABLE)
 
-find_package(Eigen3 REQUIRED CONFIG)
-mark_as_superbuild(Eigen3_DIR)
-
 #-----------------------------------------------------------------------------
 # SuperBuild setup
 option(${EXTENSION_NAME}_SUPERBUILD "Build ${EXTENSION_NAME} and the projects it depends on." ON)
@@ -42,9 +40,18 @@ if(${EXTENSION_NAME}_SUPERBUILD)
 endif()
 
 #-----------------------------------------------------------------------------
-add_subdirectory(PortPlacement)
+# Extension modules
 add_subdirectory(AutoPortPlacement)
+add_subdirectory(PortPlacement)
+## NEXT_MODULE
+
+#-----------------------------------------------------------------------------
+set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS)
+list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${NLopt_DIR};NLopt;RuntimeLibraries;/")
+set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE)
 
 #-----------------------------------------------------------------------------
+list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
+list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}")
 include(${Slicer_EXTENSION_GENERATE_CONFIG})
 include(${Slicer_EXTENSION_CPACK})
diff --git a/PortPlacement/CMakeLists.txt b/PortPlacement/CMakeLists.txt
@@ -7,6 +7,7 @@ set(MODULE_PYTHON_SCRIPTS
   )
 
 set(MODULE_PYTHON_RESOURCES
+  Resources/Icons/${MODULE_NAME}.png
   )
 
 #-----------------------------------------------------------------------------
@@ -22,10 +23,8 @@ if(BUILD_TESTING)
 
   # Register the unittest subclass in the main script as a ctest.
   # Note that the test will also be available at runtime.
-  slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py
-    SLICER_ARGS "--additional-module-path" "${CMAKE_CURRENT_LIST_DIR}")
+  slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
 
   # Additional build-time testing
   add_subdirectory(Testing)
 endif()
-
-Original file line number
+Diff line change
@@ Expand Up @@
         }
-      itk::DOMNode::Pointer dom = reader->GetModifiableOutput();
+      itk::DOMNode::Pointer dom = reader->GetOutput();
       itk::DOMNode::Pointer davinciParametersIntracorporeal = dom->Find("intracorporeal");
@@ Expand Down @@