Merge pull request #3 from jcfr/improve-and-fix-buildsystem

Improve and fix buildsystem
giogadi · Aug 26, 2017 · 1a0fc89 · 1a0fc89
2 parents 8e9a570 + 818dbc8
commit 1a0fc89
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Showing 19 changed files with 188 additions and 155 deletions.
diff --git a/AutoPortPlacement/CMakeLists.txt b/AutoPortPlacement/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.5)
 
 if(NOT DEFINED CMAKE_MACOSX_RPATH)
   set(CMAKE_MACOSX_RPATH OFF)

diff --git a/AutoPortPlacement/Logic/CMake/FindEigen3.cmake b/AutoPortPlacement/Logic/CMake/FindEigen3.cmake
diff --git a/AutoPortPlacement/Logic/CMake/FindNLopt.cmake b/AutoPortPlacement/Logic/CMake/FindNLopt.cmake
diff --git a/AutoPortPlacement/Logic/CMakeLists.txt b/AutoPortPlacement/Logic/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.5)
 
 if(NOT DEFINED CMAKE_MACOSX_RPATH)
   set(CMAKE_MACOSX_RPATH OFF)
@@ -7,22 +7,14 @@ endif()
 #-----------------------------------------------------------------------------
 project(vtkSlicer${MODULE_NAME}ModuleLogic)
 
-set(CMAKE_MODULE_PATH
-  ${CMAKE_CURRENT_SOURCE_DIR}/CMake
-  ${CMAKE_MODULE_PATH})
-
-find_package(Eigen3 REQUIRED)
-find_package(NLopt REQUIRED)
+find_package(Eigen3 REQUIRED CONFIG)
 
 set(KIT ${PROJECT_NAME})
 
 set(${KIT}_EXPORT_DIRECTIVE "VTK_SLICER_${MODULE_NAME_UPPER}_MODULE_LOGIC_EXPORT")
 
 set(${KIT}_INCLUDE_DIRECTORIES
-  ${EIGEN3_INCLUDE_DIR}
-  ${NLopt_INCLUDE_DIRS}
   )
-include_directories(${${KIT}_INCLUDE_DIRECTORIES})
 
 set(${KIT}_SRCS
   vtkSlicer${MODULE_NAME}Logic.cxx
@@ -33,7 +25,7 @@ set(${KIT}_TARGET_LIBRARIES
   collisions
   davinci
   ${ITK_LIBRARIES}
-  ${NLopt_LIBRARIES}
+  Eigen3::Eigen
   optim
   vtkSlicerAnnotationsModuleMRML
   vtkSlicerMarkupsModuleMRML

diff --git a/AutoPortPlacement/Logic/collisions/CMakeLists.txt b/AutoPortPlacement/Logic/collisions/CMakeLists.txt
@@ -2,4 +2,8 @@ add_library(collisions STATIC
   collisions.cxx
   collisions.h
   )
+target_link_libraries(collisions PUBLIC Eigen3::Eigen)
+
 set_property(TARGET collisions PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+set_property(GLOBAL APPEND PROPERTY Slicer_TARGETS collisions)
diff --git a/AutoPortPlacement/Logic/davinci-kinematics/CMakeLists.txt b/AutoPortPlacement/Logic/davinci-kinematics/CMakeLists.txt
@@ -11,3 +11,5 @@ target_link_libraries(davinci
   ${ITK_LIBRARIES}
   ${VTK_LIBRARIES}
   )
+
+set_property(GLOBAL APPEND PROPERTY Slicer_TARGETS davinci)
diff --git a/AutoPortPlacement/Logic/davinci-kinematics/davinci.cxx b/AutoPortPlacement/Logic/davinci-kinematics/davinci.cxx
@@ -721,26 +721,6 @@ void DavinciKinematics::unscentedIK(const Eigen::Matrix4d& portFrame,
   covariance_qOut->swap(covariance_q);
 }
 
-namespace
-{
-  double fromPoseToExtraClearance(const DavinciKinematics& kin,
-                                  const Eigen::Matrix4d& portFrameL,
-                                  const Eigen::Matrix4d& portFrameR,
-                                  const Eigen::Matrix4d& targetPose)
-  {
-    std::vector<double> qL(6);
-    std::vector<double> qR(6);
-    std::vector<Collisions::Cylisphere> cylL, cylR;
-    std::vector<Collisions::Sphere> sL, sR;
-
-    kin.intraIK(portFrameL, targetPose, &qL);
-    kin.intraIK(portFrameR, targetPose, &qR);
-    kin.getExtraCylispheres(portFrameL, qL, &cylL);
-    kin.getExtraCylispheres(portFrameR, qR, &cylR);
-    return Collisions::distance(cylL, sL, cylR, sR);
-  }
-}
-
 double DavinciKinematics::fullClearances(const Eigen::Matrix4d& baseFrameL,
                                          const Eigen::Matrix4d& baseFrameR,
                                          const std::vector<double>& qL,

diff --git a/AutoPortPlacement/Logic/optim/CMakeLists.txt b/AutoPortPlacement/Logic/optim/CMakeLists.txt
@@ -1,10 +1,19 @@
+
+find_package(NLopt REQUIRED CONFIG)
+
 add_library(optim STATIC
   optim.cxx
   optim.h
   )
 set_property(TARGET optim PROPERTY POSITION_INDEPENDENT_CODE ON)
 target_link_libraries(optim
   davinci
-  ${NLopt_LIBRARIES}
+  ${NLOPT_LIBRARIES}
   ${VTK_LIBRARIES}
   )
+
+target_include_directories(optim PUBLIC
+  ${NLOPT_INCLUDE_DIRS}
+  )
+
+set_property(GLOBAL APPEND PROPERTY Slicer_TARGETS optim)
diff --git a/AutoPortPlacement/Logic/tests/da-vinci-params-load-test.cxx b/AutoPortPlacement/Logic/tests/da-vinci-params-load-test.cxx
@@ -1,7 +1,7 @@
 #include <davinci-kinematics/davinci.h>
 #include <cmath>
 
-int main(int argc, char** argv)
+int main(int, char* [])
 {
   DavinciKinematics kinematics;
 

diff --git a/AutoPortPlacement/Logic/tests/da-vinci-passive-ik-test.cxx b/AutoPortPlacement/Logic/tests/da-vinci-passive-ik-test.cxx
@@ -3,7 +3,7 @@
 
 #include <iostream>
 
-int main(int argc, char* argv[])
+int main(int, char* [])
 {
   DavinciKinematics kinematics;
 

diff --git a/AutoPortPlacement/Logic/tests/jacobian-test.cxx b/AutoPortPlacement/Logic/tests/jacobian-test.cxx
@@ -1,7 +1,7 @@
 #include <davinci-kinematics/davinci.h>
 #include <iostream>
 
-int main(int argc, char** argv)
+int main(int, char* [])
 {
   std::vector<double> q(6, 0.0);
   q[0] = 0.5;

diff --git a/AutoPortPlacement/Logic/tests/min-distance-test.cxx b/AutoPortPlacement/Logic/tests/min-distance-test.cxx
@@ -2,7 +2,7 @@
 
 #include <iostream>
 
-int main(int argc, char* argv[])
+int main(int, char* [])
 {
   std::vector<Collisions::Cylisphere> c1, c2;
   std::vector<Collisions::Sphere> s1, s2;

diff --git a/AutoPortPlacement/Logic/vtkSlicerAutoPortPlacementLogic.cxx b/AutoPortPlacement/Logic/vtkSlicerAutoPortPlacementLogic.cxx
@@ -158,6 +158,11 @@ void vtkSlicerAutoPortPlacementLogic::RenderRobot()
 // Initializes the models and transforms for visualizing the Davinci robot.
 void vtkSlicerAutoPortPlacementLogic::InitRobot()
 {
+  if (!this->GetMRMLScene())
+    {
+    return;
+    }
+
   std::vector<Collisions::Cylisphere> cylispheres;
   std::vector<Collisions::Sphere> spheres(2);
 

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModule.cxx b/AutoPortPlacement/qSlicerAutoPortPlacementModule.cxx
@@ -26,7 +26,10 @@
 #include "qSlicerAutoPortPlacementModuleWidget.h"
 
 //-----------------------------------------------------------------------------
+#if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
+#include <QtPlugin>
 Q_EXPORT_PLUGIN2(qSlicerAutoPortPlacementModule, qSlicerAutoPortPlacementModule);
+#endif
 
 //-----------------------------------------------------------------------------
 /// \ingroup Slicer_QtModules_ExtensionTemplate

diff --git a/AutoPortPlacement/qSlicerAutoPortPlacementModule.h b/AutoPortPlacement/qSlicerAutoPortPlacementModule.h
@@ -31,6 +31,9 @@ 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/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.5)
 
 project(PortPlacement)
 
@@ -9,19 +9,41 @@ set(EXTENSION_CONTRIBUTORS "Luis G. Torres (UNC)")
 set(EXTENSION_DESCRIPTION "Assists in the planning of surgical port placement in a laparoscopic procedure.")
 set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/PortPlacement/PortPlacement.png?revision=21747&view=co")
 set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/e/e2/Slicer-r19441-PortPlacement-screenshot.png")
+set(EXTENSION_DEPENDS "Eigen3")
+set(EXTENSION_BUILD_SUBDIRECTORY inner-build)
+
+set(SUPERBUILD_TOPLEVEL_PROJECT inner)
 
 #
 # Implementation agnostic fPIC
 #
 set( CMAKE_POSITION_INDEPENDENT_CODE ON )
 
 #-----------------------------------------------------------------------------
+# Extension dependencies
 find_package(Slicer REQUIRED)
 include(${Slicer_USE_FILE})
+mark_as_superbuild(Slicer_DIR)
+
+find_package(Git REQUIRED)
+mark_as_superbuild(GIT_EXECUTABLE)
+
+find_package(Eigen3 REQUIRED CONFIG)
+mark_as_superbuild(Eigen3_DIR)
+
+#-----------------------------------------------------------------------------
+# SuperBuild setup
+option(${EXTENSION_NAME}_SUPERBUILD "Build ${EXTENSION_NAME} and the projects it depends on." ON)
+mark_as_advanced(${EXTENSION_NAME}_SUPERBUILD)
+if(${EXTENSION_NAME}_SUPERBUILD)
+  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
+  return()
+endif()
 
 #-----------------------------------------------------------------------------
 add_subdirectory(PortPlacement)
 add_subdirectory(AutoPortPlacement)
 
 #-----------------------------------------------------------------------------
+include(${Slicer_EXTENSION_GENERATE_CONFIG})
 include(${Slicer_EXTENSION_CPACK})
diff --git a/PortPlacement/PortPlacement.py b/PortPlacement/PortPlacement.py
@@ -235,7 +235,7 @@ def onRemovePortButton(self):
     # Problem: currentIndex() can be valid even when there is no
     # visible selection. This will have to do for now while I figure
     # out how to making Python bindings to QList<QModelIndex> (ugh)
-    index = self.portsTable.selectionModel().currentIndex()
+    index = self.portsTable.selectionModel().currentIndex
     self.logic.markupsNode.RemoveMarkup(index.row())
     self.updateTable()
 
@@ -718,7 +718,7 @@ def test_PortPlacement1(self):
 
     target_p = [0,0,0]
     targetNode.GetNthFiducialPosition(0, target_p)
-    targetWorld = target_p + [1]
+    targetWorld = target_p
 
     # check retargeting by verifying that tools' positions are
     # unchanged and that their y-axes are oriented toward point
@@ -731,7 +731,7 @@ def test_PortPlacement1(self):
       diff = numpy.array(p) - numpy.array(tool_pos)
       self.assertTrue(numpy.dot(diff,diff) < 1e-10)
 
-      targetLocal = [0,0,0,1]
+      targetLocal = [0,0,0]
       logic.toolList[i].modelNode.TransformPointFromWorld(targetWorld, targetLocal)
 
       targetLocal = numpy.array(targetLocal)[0:3]