Seg3d Integration test and Travis fix

.gitignore

@@ -26,3 +26,5 @@
 *.exe
 *.out
 *.app
+
+bin/*

.travis.yml

@@ -1,11 +1,12 @@
-sudo: false
 language: cpp
+
 notifications:
-  email: false
+  slack: sciinstitute:lZnpQQXNd4Io5iGDPQDpJmI1
+
 compiler:
   - gcc
   - clang
-#before_cache:
+
 cache:
   directories:
     - $HOME/deps
@@ -14,13 +15,10 @@ before_install:
   - if [ ! -d $HOME/deps ]; then mkdir $HOME/deps; fi
   - if [ ! -f $HOME/deps/tetgen1.4.3.tar.gz ]; then wget --quiet --directory-prefix=$HOME/deps http://tetgen.org/files/tetgen1.4.3.tar.gz; fi
   - if [ ! -f $HOME/deps/tetgen_cmake.tgz ]; then wget --quiet --directory-prefix=$HOME/deps http://www.sci.utah.edu/devbuilds/seg3d/tetgen_cmake.tgz; fi
-  - if [ ! -f $HOME/deps/release-1.7.0.tar.gz ]; then wget --quiet --directory-prefix=$HOME/deps https://github.com/google/googletest/archive/release-1.7.0.tar.gz; fi
+  - if [ ! -f $HOME/deps/release-1.10.0.tar.gz ]; then wget --quiet --directory-prefix=$HOME/deps https://github.com/google/googletest/archive/release-1.10.0.tar.gz; fi
   - if [ ! -f $HOME/deps/3.2.10.tar.gz ]; then wget --quiet --directory-prefix=$HOME/deps http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz; fi
   - pip install --user cpp-coveralls
   - ls $HOME/deps
-install:
-  # C++11 support required
-  - if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
 addons:
   apt:
     sources:
@@ -29,10 +27,6 @@ addons:
     packages:
     - cmake
     - cmake-data
-    - gcc-4.8
-    - g++-4.8
-    - clang
-#before_script:
 script:
   # build Tetgen dependency
   - mkdir build
@@ -43,26 +37,25 @@ script:
   - tar xzf $HOME/deps/tetgen_cmake.tgz
   - popd
   # build Googletest dependency
-  - tar xzf $HOME/deps/release-1.7.0.tar.gz
-  - pushd googletest-release-1.7.0
+  - tar xzf $HOME/deps/release-1.10.0.tar.gz
+  - pushd googletest-release-1.10.0
   - mkdir build
   - cd build
   - cmake ..
-  - make -j4
+  - make -j4 CXXFLAGS:=$(CXXFLAGS) -lpthread -lm
   - popd
   # untar Eigen dependency (no build needed)
   - tar xzf $HOME/deps/3.2.10.tar.gz
   # build ImplicitFunction library
   - cmake -DBUILD_TESTING:BOOL=ON -DENABLE_COVERAGE:BOOL=ON -DTravisCI_BUILD:BOOL=ON
-          -DGTEST_INCLUDE_DIR:PATH=`pwd`/googletest-release-1.7.0/include
-          -DGTEST_LIBRARY:FILEPATH=`pwd`/googletest-release-1.7.0/build/libgtest.a
-          -DGTEST_MAIN_LIBRARY:FILEPATH=`pwd`/googletest-release-1.7.0/build/libgtest_main.a
+          -DGTEST_INCLUDE_DIR:PATH=`pwd`/googletest-release-1.10.0/googletest/include
+          -DGTEST_LIBRARY:FILEPATH=`pwd`/googletest-release-1.10.0/build/lib/libgtest.a
+          -DGTEST_MAIN_LIBRARY:FILEPATH=`pwd`/googletest-release-1.10.0/build/lib/libgtest_main.a
           -DTetgen_DIR:PATH=`pwd`/tetgen1.4.3
           -DEIGEN3_INSTALL_DIR:PATH=`pwd`/eigen-eigen-b9cd8366d4e8 ..
-  - make -j4
+  - make -j4 CXXFLAGS:=$(CXXFLAGS) -lpthread -lm
   - ./ImplicitFunction_Tests
-#after_failure:
+
 after_success:
   - cd $TRAVIS_BUILD_DIR
   - coveralls --exclude build --exclude Tests --gcov-options '\-lp'
-#after_script:

CMakeLists.txt

@@ -20,7 +20,7 @@
 # ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 # USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.5)
 
 project(ImplicitFunction)
 

ETSP.cpp

@@ -102,7 +102,7 @@ void ETSP::MST()
 
     graph[toAdd].push_back(i+j-toAdd);
     graph[i+j-toAdd].push_back(toAdd);
-	
+
   }
 
 }
@@ -119,14 +119,14 @@ vector<int> ETSP::match()
       bestMatch.push_back(i);
     }
   }
-  
+
   //for(int i=0; i<oddNodes.size(); i++)
   //  printf("%d ",oddNodes[i]);
   //printf("\n");
   if(oddNodes.size()>0)
   {
     double best=1e10;
-    do 
+    do
     {
        double curr = 0;
        for(int i=0; i<oddNodes.size(); i+=2)
@@ -154,7 +154,6 @@ void ETSP::orderFromMST()
 {
   vector<bool> visited;
   visited.resize(data.size(),false);
-  int curr=0;
   inverse_mapped_order.resize(data.size());
   traverse(0, visited);
   /*for(int i=0; i<order.size(); i++)
@@ -205,4 +204,3 @@ void ETSP::orderFromMatch()
   //  printf("%d ",order[i]);
   //printf("\n");
 }
-

RBF.cpp

@@ -167,7 +167,6 @@ void RBF::computeFunctionForData()
     case None:
     default:
       // TODO: move to function
-      const double SMALL_EPSILON = 1.0e-6, ERROR_EPSILON = 1.0e-3;
       const int N = static_cast<int>( this->data_->fnc_.size() );
 
 #ifndef NDEBUG
@@ -329,27 +328,27 @@ void RBF::fmmBuildTree(vector<int> &myPoints, BHNode *myNode)
   //printf("[%lf %lf %lf] [%lf %lf %lf] %d\n", myNode->box_.min_[0], myNode->box_.min_[1], myNode->box_.min_[2], myNode->box_.max_[0], myNode->box_.max_[1], myNode->box_.max_[2], myPoints.size());
   vector<int> children[8];
   const int N = myPoints.size();
-  
+
   myNode->index_ = fmm_->numOfNodes;
   fmm_->numOfNodes += 1;
   fmm_->nodePointer.push_back(myNode);
-  
+
   myNode->mass_ = N;
   myNode->leaf_ = (N <= 1) ? true : false;
   myNode->center_ = vec3::zero;
-  
+
   myNode->coeff_ = 1; //REPLACE
   //add all the coefficients
-  
+
   for (int i = 0; i < N; i++)
     myNode->pts_.push_back( myPoints[i] );
-  
+
   for (int i = 0; i < N; i++)
   {
     vec3 location(this->data_->surfacePoints_[0][myPoints[i]], this->data_->surfacePoints_[1][myPoints[i]], this->data_->surfacePoints_[2][myPoints[i]]);
     myNode->center_ = myNode->center_ + (location/N);
   }
-  
+
   if (N == 1)
   {
     for (int i = 0; i < 8; i++)
@@ -377,9 +376,9 @@ void RBF::fmmBuildTree(vector<int> &myPoints, BHNode *myNode)
       octant += 2;
     if (this->data_->surfacePoints_[2][myPoints[i]] > mid[2])
       octant += 4;
-    
+
     //printf("%d %d %d %lf %lf %lf\n", i,octant, myPoints[i], this->data_->surfacePoints_[0][myPoints[i]],this->data_->surfacePoints_[1][myPoints[i]], this->data_->surfacePoints_[2][myPoints[i]]);
-    
+
     children[octant].push_back(myPoints[i]);
   }
 
@@ -453,6 +452,6 @@ double RBF::fmmComputeValueRecurse(const vec3& x, BHNode *myNode)
 double RBF::fmmComputeKernel(const vec3& b, BHNode *myNode)
 {
   double r = length(myNode->center_ - b);
-  
+
   return computeRadialFunction(r);
-}
+}

Tests/CMakeLists.txt

@@ -23,10 +23,11 @@
 set(ImplicitFunction_Tests_SRCS
   ConvexHull2DTests.cpp
   ConvexHull3DTests.cpp
-#  RBFTests.cpp
+  RBFTests.cpp
   RBFInterfaceTests.cpp
   ScatteredDataTests.cpp
   Vec3Tests.cpp
+  Seg3DIntegrationTest.cpp
 )
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${ImplicitFunction_BINARY_DIR})
@@ -47,3 +48,9 @@ target_link_libraries(ImplicitFunction_Tests
   ${GTEST_LIBRARY}
   ${GTEST_MAIN_LIBRARY}
 )
+
+IF(UNIX)
+  TARGET_LINK_LIBRARIES(ImplicitFunction_Tests -lpthread -lm)
+ENDIF()
+
+ADD_TEST("ImplicitFunction_Tests" ${ImplicitFunction_BINARY_DIR}/ImplicitFunction_Tests)

Tests/RBFInterfaceTests.cpp

@@ -91,7 +91,7 @@ TEST_F(RBFInterfaceTest, BasicInterfaceTestThinPlate)
         std::string line;
         std::getline(in, line);
         //std::cerr << line << " vs " << rasterData[i][j][k] << std::endl;
-        double d = std::stod(line);
+        //double d = std::stod(line);
       }
     }
   }
@@ -124,7 +124,7 @@ TEST_F(RBFInterfaceTest, BasicInterfaceTestGaussian)
         std::string line;
         std::getline(in, line);
         //std::cerr << line << " vs " << rasterData[i][j][k] << std::endl;
-        double d = std::stod(line);
+        //double d = std::stod(line);
       }
     }
   }
@@ -157,9 +157,9 @@ TEST_F(RBFInterfaceTest, BasicInterfaceTestMultiQuad)
         std::string line;
         std::getline(in, line);
         //std::cerr << line << " vs " << rasterData[i][j][k] << std::endl;
-        double d = std::stod(line);
+        //double d = std::stod(line);
       }
     }
   }
   in.close();
-}
+}

Tests/RBFTests.cpp

@@ -44,19 +44,14 @@ class RBFTest : public ::testing::Test
 
     func10.insert(func10.begin(), 10, 0);
     axisInfo10.insert(axisInfo10.begin(), 10, axis_t::Z);
-    data = new ScatteredData( xCoords10, yCoords10, zCoords10, func10, axisInfo10 );
+    data.reset(new ScatteredData( xCoords10, yCoords10, zCoords10, func10, axisInfo10 ));
   }
 
-  virtual void TearDown()
-  {
-    delete data;
-  }
-
-  ScatteredData *data;
+  std::unique_ptr<ScatteredData> data;
 };
 
 TEST_F(RBFTest, BasicSetup)
 {
   // TODO: need to expose getters to test RBF state
-  RBF rbf(data, ThinPlate);
-}
+  RBF rbf(data.get(), ThinPlate);
+}