Merge remote-tracking branch 'origin/master' into AutoTune

SGpp · Feb 9, 2016 · 0b504ad · 0b504ad
2 parents ff6599b + ecab811
commit 0b504ad
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Showing 66 changed files with 2,995 additions and 1,760 deletions.
diff --git a/Doxyfile_template b/Doxyfile_template
diff --git a/SConstruct b/SConstruct
@@ -95,7 +95,7 @@ env['LIBDIR'] = env.get( 'LIBDIR', os.path.join( env['EPREFIX'], "lib" ) )
 env['INCLUDEDIR'] = env.get( 'INCLUDEDIR', os.path.join( env['PREFIX'], "include" ) )
 
 # no docu if clean:
-if not env.GetOption('clean'):
+if not env['PYDOC'] and not env.GetOption('clean'):
   prepareDoxyfile(moduleFolders)
 
 if 'CXX' in ARGUMENTS:
@@ -179,12 +179,9 @@ if env['PLATFORM'] == 'win32':
 env.Append(LIBPATH=[BUILD_DIR])
 
 # # add C++ defines for all modules
-cppdefines = []
 for module in moduleNames:
     if env[module]:
         env['CPPDEFINES'][module] = '1'
-#         cppdefines.append(module)
-# env.Append(CPPDEFINES=cppdefines)
 
 # environement setup finished, export environment
 Export('env')
@@ -224,16 +221,24 @@ if env['COMPILE_BOOST_TESTS']:
     builder = Builder(action="./$SOURCE --log_level=test_suite")
     env.Append(BUILDERS={'BoostTest' : builder})
 
+
+
 libraryTargetList = []
 installTargetList = []
 testTargetList = []
 boostTestTargetList = []
 exampleTargetList = []
+pydocTargetList = []
+headerSourceList = []
+headerDestList = []
 env.Export('libraryTargetList')
 env.Export('installTargetList')
 env.Export('testTargetList')
 env.Export('boostTestTargetList')
 env.Export('exampleTargetList')
+env.Export('pydocTargetList')
+env.Export('headerSourceList')
+env.Export('headerDestList')
 
 # compile selected modules
 flattenedDependencyGraph = []
@@ -252,7 +257,7 @@ for moduleFolder in moduleFolders:
 
 Export('flattenedDependencyGraph')
 
-if env['PYDOC'] and env['SG_PYTHON']:
+if env['PYDOC'] and env['SG_PYTHON'] and not env.GetOption('clean'):
   with open('moduleDoxy', 'r') as template:
     data = template.read()
     for module in moduleFolders:
@@ -391,10 +396,19 @@ dependencies.append(env.Command('printFinished', [], printFinished))
 for i in range(len(dependencies) - 1):
   env.Depends(dependencies[i + 1], dependencies[i])
 
+# Stuff needed for system install
 env.Clean("distclean",
   [
     "config.log",
   ])
 Default(libraryTargetList, dependencies)
 
-env.Alias('install-lib-sgpp', Install(os.path.join( env.get('LIBDIR'), 'sgpp'), libraryTargetList))
+ils = env.Alias('install-lib-sgpp', Install(os.path.join( env.get('LIBDIR'), 'sgpp'), libraryTargetList))
+
+headerFinalDestList = []
+for headerDest in headerDestList:
+  headerFinalDestList.append(os.path.join( env.get('INCLUDEDIR'), headerDest))
+
+iis = env.Alias('install-inc-sgpp', InstallAs(headerFinalDestList, headerSourceList))
+
+env.Alias('install', [ils, iis])
diff --git a/base/SConscript b/base/SConscript
@@ -15,6 +15,8 @@ Import('moduleName')
 Import('libraryTargetList')
 Import('installTargetList')
 Import('exampleTargetList')
+Import('headerSourceList')
+Import('headerDestList')
 
 moduleDependencies = []
 Export('moduleDependencies')
@@ -36,7 +38,10 @@ for currentFolder, subdirNames, fileNames in os.walk("src", topdown=True):
     for fileName in fnmatch.filter(fileNames, '*.cpp'):
       sourceFile = os.path.join(currentFolder, fileName)
       objs.append(env.SharedObject(sourceFile))
-
+    if currentFolder != 'src':
+      for fileName in fnmatch.filter(fileNames, '*.hpp'):
+        headerSourceList.append(os.path.join(moduleName, currentFolder, fileName))
+        headerDestList.append(os.path.join(currentFolder, fileName).split(os.sep,1)[1])
 
 libname = "sgpp%s" % moduleName
 if env['USE_STATICLIB']:

diff --git a/base/examples/.gitignore b/base/examples/.gitignore
@@ -0,0 +1,6 @@
+/JSONTest
+/platformConfigurationTest
+/predictive_refinement
+/quadrature
+/refinement
+/tutorial
diff --git a/base/src/sgpp/base/grid/Grid.hpp b/base/src/sgpp/base/grid/Grid.hpp
@@ -63,9 +63,9 @@ struct RegularGridConfiguration {
   /// number of levels
   int level_;
   /// max. polynomial degree for poly basis
-  size_t maxDegree;
+  size_t maxDegree_;
   /// level of boundary grid
-  size_t boundaryLevel;
+  size_t boundaryLevel_;
 };
 
 /**

diff --git a/base/src/sgpp/base/grid/generation/hashmap/HashRefinementBoundaries.cpp b/base/src/sgpp/base/grid/generation/hashmap/HashRefinementBoundaries.cpp
@@ -175,6 +175,7 @@ size_t HashRefinementBoundaries::getNumberOfRefinablePoints(
         // if there no more grid points --> test if we should refine the grid
         if (child_iter == end_iter) {
           counter++;
+	  break;
         }
       } else {
         // left child
@@ -184,6 +185,7 @@ size_t HashRefinementBoundaries::getNumberOfRefinablePoints(
         // if there no more grid points --> test if we should refine the grid
         if (child_iter == end_iter) {
           counter++;
+	  break;
         }
 
         // right child
@@ -192,6 +194,7 @@ size_t HashRefinementBoundaries::getNumberOfRefinablePoints(
 
         if (child_iter == end_iter) {
           counter++;
+	  break;
         }
       }
 

diff --git a/base/tests/test_DataVectorSP.cpp b/base/tests/test_DataVectorSP.cpp
@@ -68,7 +68,7 @@ BOOST_AUTO_TEST_CASE(testMinMax) {
 }
 
 BOOST_AUTO_TEST_CASE(testOps) {
-  float tol = 1e-5f;
+  float tol = 1e-4f;
 
   DataVectorSP d = d_rand;
   DataVectorSP d2(N);

diff --git a/base/tests/test_DirichletGridConverter.cpp b/base/tests/test_DirichletGridConverter.cpp
@@ -0,0 +1,142 @@
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include <sgpp/base/grid/common/DirichletGridConverter.hpp>
+
+#include <sgpp/base/grid/Grid.hpp>
+#include <sgpp/base/grid/type/LinearGrid.hpp>
+#include <sgpp/base/grid/type/LinearStretchedGrid.hpp>
+#include <sgpp/base/operation/BaseOpFactory.hpp>
+#include <sgpp/base/datatypes/DataVector.hpp>
+
+using namespace SGPP::base;
+
+
+BOOST_AUTO_TEST_CASE(test_DirichletGridConverter){
+	/// number of the boundary grid's grid points
+	size_t numTotalGridPoints;
+	/// number of the inner grid's grid points
+	size_t numInnerGridPoints;
+	/**
+	* array to store the position of i-th inner point in
+	* the boundary grid's coefficients
+	*/
+	size_t* conCoefArray;
+	Grid* innerGridExact;
+
+	int level = 3;
+	int dimension = 2;
+	Grid* linearBoundaryGrid = Grid::createLinearBoundaryGrid(dimension);
+	GridStorage* linearBoundaryGridStorageExact = linearBoundaryGrid->getStorage();
+	GridGenerator* gridGen = linearBoundaryGrid->createGridGenerator();
+    gridGen->regular(level);
+
+	// determine the number of grid points for both grids
+	numTotalGridPoints = linearBoundaryGridStorageExact->size();
+	numInnerGridPoints = linearBoundaryGridStorageExact->getNumInnerPoints();
+
+	DataVector boundaryGridCoeffs(numTotalGridPoints);
+	GridIndex* gp;
+	for(size_t i = 0; i < numTotalGridPoints; ++i){
+		gp = linearBoundaryGridStorageExact->get(i);
+		boundaryGridCoeffs[i] =
+				gp->getCoord(0) * (gp->getCoord(0)) + gp->getCoord(1) * (gp->getCoord(1));
+	}
+
+	SGPP::op_factory::createOperationHierarchisation(*linearBoundaryGrid)->
+			doHierarchisation(boundaryGridCoeffs);
+
+	// allocate the translation array for the coefficients
+	conCoefArray = new size_t[numInnerGridPoints];
+
+	// Get the algorithmic dimensions
+	std::vector<size_t> BSalgoDims = linearBoundaryGrid->getAlgorithmicDimensions();
+
+	// create new inner Grid, with one grid point
+	innerGridExact = new LinearGrid(*(linearBoundaryGrid->getBoundingBox()));
+
+	// Set algorithmic dimensions for inner Grid
+	innerGridExact->setAlgorithmicDimensions(BSalgoDims);
+
+	// create new DataVector for storing the inner grid's coefficients
+	DataVector innerCoeffsExact(numInnerGridPoints);
+
+	// Iterate through all grid points and filter inner points
+	size_t numInner = 0;
+
+	for (size_t i = 0; i < numTotalGridPoints; ++i) {
+		GridIndex* curPoint = linearBoundaryGridStorageExact->get(i);
+		if (curPoint->isInnerPoint() == true) {
+		  // handle coefficients
+		  conCoefArray[numInner] = i;
+		  innerCoeffsExact.set(numInner, boundaryGridCoeffs.get(i));
+		  numInner++;
+		  // insert point into inner grid
+		  innerGridExact->getStorage()->insert(*curPoint);
+		}
+	}
+
+	//Test BUILD
+	DirichletGridConverter dirichGridConverter;
+	Grid* innerGridActual;
+	DataVector* innerCoeffsActual;
+	dirichGridConverter.buildInnerGridWithCoefs(
+			*linearBoundaryGrid, boundaryGridCoeffs, &innerGridActual, &innerCoeffsActual);
+
+	BOOST_CHECK_EQUAL(innerCoeffsActual->getSize(), innerCoeffsExact.getSize());
+
+	for(size_t i = 0; i < innerCoeffsActual->getSize(); ++i){
+		BOOST_CHECK_EQUAL(innerCoeffsActual->get(i), innerCoeffsExact.get(i));
+	}
+
+	GridIndex* curPointExact;
+	GridIndex* curPointActual;
+	int innerPointIndex = 0;
+	GridStorage* linearBoundaryGridStorageActual = innerGridActual->getStorage();
+	for(size_t i = 0; i < numTotalGridPoints; ++i){
+		curPointExact = linearBoundaryGridStorageExact->get(i);
+		if (curPointExact->isInnerPoint() == true) {
+			curPointActual = linearBoundaryGridStorageActual->get(innerPointIndex);
+			for (size_t curDim = 0; curDim < curPointExact->dim(); ++curDim){
+				BOOST_CHECK_EQUAL(curPointActual->getCoord(curDim), curPointExact->getCoord(curDim));
+			}
+			innerPointIndex++;
+		}
+	}
+
+	//TEST REBUILD
+	dirichGridConverter.rebuildInnerGridWithCoefs(
+			*linearBoundaryGrid, boundaryGridCoeffs, &innerGridActual, &innerCoeffsActual);
+
+	BOOST_CHECK_EQUAL(innerCoeffsActual->getSize(), innerCoeffsExact.getSize());
+
+	for(size_t i = 0; i < innerCoeffsActual->getSize(); ++i){
+		BOOST_CHECK_EQUAL(innerCoeffsActual->get(i), innerCoeffsExact.get(i));
+	}
+
+	innerPointIndex = 0;
+	linearBoundaryGridStorageActual = innerGridActual->getStorage();
+	for(size_t i = 0; i < numTotalGridPoints; ++i){
+		curPointExact = linearBoundaryGridStorageExact->get(i);
+		if (curPointExact->isInnerPoint() == true) {
+			curPointActual = linearBoundaryGridStorageActual->get(innerPointIndex);
+			for (size_t curDim = 0; curDim < curPointExact->dim(); ++curDim){
+				BOOST_CHECK_EQUAL(curPointActual->getCoord(curDim), curPointExact->getCoord(curDim));
+			}
+			innerPointIndex++;
+		}
+	}
+
+	//TEST calcInnerCoefs
+	dirichGridConverter.calcInnerCoefs(boundaryGridCoeffs, *innerCoeffsActual);
+	for(size_t i = 0; i < innerCoeffsActual->getSize(); ++i){
+		BOOST_CHECK_EQUAL(innerCoeffsActual->get(i), innerCoeffsExact.get(i));
+	}
+
+	//TEST updateBoundaryCoefs
+	DataVector boundaryGridCoeffsActual(boundaryGridCoeffs);
+	dirichGridConverter.updateBoundaryCoefs(boundaryGridCoeffsActual, *innerCoeffsActual);
+	for(size_t i = 0; i < innerCoeffsActual->getSize(); ++i){
+		BOOST_CHECK_EQUAL(boundaryGridCoeffsActual.get(i), boundaryGridCoeffs.get(i));
+	}
+}
diff --git a/combigrid/SConscript b/combigrid/SConscript
@@ -15,6 +15,8 @@ Import('moduleName')
 Import('libraryTargetList')
 Import('installTargetList')
 Import('exampleTargetList')
+Import('headerSourceList')
+Import('headerDestList')
 
 #moduleDependencies = ['sgppbase']
 moduleDependencies = []
@@ -45,6 +47,10 @@ for currentFolder, subdirNames, fileNames in os.walk("src"):
     for fileName in fnmatch.filter(fileNames, '*.cpp'):
         sourceFile = os.path.join(currentFolder, fileName)
         objs.append(env.SharedObject(sourceFile))
+    if currentFolder != 'src':
+      for fileName in fnmatch.filter(fileNames, '*.hpp'):
+        headerSourceList.append(os.path.join(moduleName, currentFolder, fileName))
+        headerDestList.append(os.path.join(currentFolder, fileName).split(os.sep,1)[1])
 
 if env['USE_STATICLIB']:
     libsuffix = env['LIBSUFFIX']

diff --git a/datadriven/SConscript b/datadriven/SConscript
@@ -16,6 +16,8 @@ Import('moduleName')
 Import('libraryTargetList')
 Import('installTargetList')
 Import('exampleTargetList')
+Import('headerSourceList')
+Import('headerDestList')
 
 avxFolders = ['src/sgpp/datadriven/operation/hash/OperationMultipleEvalSubspace/', 'src/sgpp/datadriven/operation/hash/OperationMultiEvalStreaming']
 
@@ -59,6 +61,10 @@ for currentFolder, subdirNames, fileNames in os.walk("src", topdown=True):
     for fileName in fnmatch.filter(fileNames, '*.cpp'):
       sourceFile = os.path.join(currentFolder, fileName)
       objs.append(env.SharedObject(sourceFile))
+    if currentFolder != 'src':
+      for fileName in fnmatch.filter(fileNames, '*.hpp'):
+        headerSourceList.append(os.path.join(moduleName, currentFolder, fileName))
+        headerDestList.append(os.path.join(currentFolder, fileName).split(os.sep,1)[1])
 
 
 if env['USE_STATICLIB']:

diff --git a/datadriven/examples/.gitignore b/datadriven/examples/.gitignore
@@ -0,0 +1,24 @@
+/batchLearnerExample
+/debug
+/detectPlatform
+/integrationTest
+/kernelTuner
+/kernelTunerHelper
+/learnerSGDETest
+/memoryTest
+/multiEvalPerformance
+/multiEvalPerformanceBSpline
+/multModTest
+/multTest
+/multTestAdaptive
+/multTransposeModTest
+/multTransposeTest
+/multTransposeTestAdaptive
+/piecewiseConstantSmoothedRegressionLearner
+/piecewiseSmoothingRegressor
+/regressionByInterpolation
+/regressionLearner
+/sampler
+/samplerMod
+/writeScenario
+/zeroCopyTest
diff --git a/datadriven/examples/learnerSGDETest.cpp b/datadriven/examples/learnerSGDETest.cpp
@@ -19,7 +19,7 @@ int main(int argc, char** argv) {
   cout << "# loading file: " << filename << endl;
   SGPP::datadriven::Dataset dataset = SGPP::datadriven::ARFFTools::readARFF(
                                         filename);
-  SGPP::base::DataMatrix& samples = dataset.getTrainingData();
+  SGPP::base::DataMatrix& samples = dataset.getData();
 
   // configure grid
   cout << "# create grid config" << endl;

diff --git a/datadriven/examples/multTransposeTestAdaptive.cpp b/datadriven/examples/multTransposeTestAdaptive.cpp
@@ -91,7 +91,7 @@ int main(int argc, char** argv) {
   SGPP::datadriven::ARFFTools arffTools;
   SGPP::datadriven::Dataset dataset = arffTools.readARFF(fileName);
 
-  SGPP::base::DataMatrix& trainingData = dataset.getTrainingData();
+  SGPP::base::DataMatrix& trainingData = dataset.getData();
 
   size_t dim = dataset.getDimension();
   SGPP::base::Grid* grid = SGPP::base::Grid::createLinearGrid(dim);

diff --git a/datadriven/examples/multiEvalPerformance.cpp b/datadriven/examples/multiEvalPerformance.cpp
@@ -63,7 +63,7 @@ int main(int argc, char** argv) {
   SGPP::datadriven::Dataset dataset = arffTools.readARFF(fileName);
 
   //SGPP::base::DataVector *classes = dataset.getClasses();
-  SGPP::base::DataMatrix& trainingData = dataset.getTrainingData();
+  SGPP::base::DataMatrix& trainingData = dataset.getData();
 
   // create a two-dimensional piecewise bi-linear grid
   size_t dim = dataset.getDimension();

diff --git a/datadriven/examples/multiEvalPerformanceBSpline.cpp b/datadriven/examples/multiEvalPerformanceBSpline.cpp
@@ -27,7 +27,7 @@ int main(int argc, char** argv) {
   SGPP::datadriven::ARFFTools arffTools;
   SGPP::datadriven::Dataset dataset = arffTools.readARFF(fileName);
 
-  SGPP::base::DataMatrix& trainingData = dataset.getTrainingData();
+  SGPP::base::DataMatrix& trainingData = dataset.getData();
 
   // create a two-dimensional piecewise bi-linear grid
   const size_t dim = dataset.getDimension();