Merge pull request #151 from royshil/roy.pygrt

PyGRT: Python bindings for GRT via SWIG

.travis.yml

@@ -10,12 +10,16 @@ env:
  - CONFIG=Release
  - CONFIG=Debug
 before_install:
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update          ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update         ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew upgrade python ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install swig   ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then pip3 install numpy  ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu $(lsb_release -cs)-backports main restricted universe multiverse" ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get -qq update ; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get -qq install g++-4.8 ; fi
- - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install cmake ; fi
+ - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y cmake swig3.0 python3-dev python3-numpy; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CXX" = "g++" ]]; then sudo apt-get install -qq libstdc++-4.8-dev; fi
  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$CXX" = "g++" ]]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
 before_script:

GRT/ClassificationModules/ANBC/ANBC_Model.cpp

@@ -118,11 +118,11 @@ Float ANBC_Model::predictUnnormed( const VectorFloat &x ){
 	return prediction;
 }
 
-inline Float ANBC_Model::gauss(const Float x,const Float mu,const Float sigma){
+Float ANBC_Model::gauss(const Float x,const Float mu,const Float sigma){
 	return ( 1.0/(sigma*sqrt(TWO_PI)) ) * exp( - ( ((x-mu)*(x-mu))/(2*(sigma*sigma)) ) );
 }
 
-inline Float ANBC_Model::unnormedGauss(const Float x,const Float mu,const Float sigma){
+Float ANBC_Model::unnormedGauss(const Float x,const Float mu,const Float sigma){
 	return exp( - ( ((x-mu)*(x-mu))/(2*(sigma*sigma)) ) );
 }
 

GRT/ClassificationModules/ANBC/ANBC_Model.h

@@ -44,8 +44,8 @@ class GRT_API ANBC_Model{
 	bool train( const UINT classLabel, const MatrixDouble &trainingData, const VectorFloat &weightsVector );
 	Float predict( const VectorFloat &x );
 	Float predictUnnormed( const VectorFloat &x );
-	inline Float gauss(const Float x,const Float mu,const Float sigma);
-	inline Float unnormedGauss(const Float x,const Float mu,const Float sigma);
+	Float gauss(const Float x,const Float mu,const Float sigma);
+	Float unnormedGauss(const Float x,const Float mu,const Float sigma);
 	void recomputeThresholdValue(const Float gamma);
 
 public:

GRT/ClassificationModules/MinDist/MinDistModel.h

@@ -68,7 +68,7 @@ class GRT_API MinDistModel
 	UINT getClassLabel() const;
 	UINT getNumFeatures() const;
 	UINT getNumClusters() const;
-	UINT getDistanceMode() const;
+//	UINT getDistanceMode() const;
     Float getRejectionThreshold() const;
     Float getGamma() const;
     Float getTrainingMu() const;

GRT/CoreModules/FeatureExtraction.h

@@ -214,7 +214,7 @@ class GRT_API FeatureExtraction : public MLBase
 template< typename T >  FeatureExtraction *createNewFeatureExtractionModule() { return new T; } ///< Returns a pointer to a new instance of the template class, the caller is responsible for deleting the pointer
 
 template< typename T > 
-class RegisterFeatureExtractionModule : FeatureExtraction { 
+class RegisterFeatureExtractionModule : public FeatureExtraction {
 public:
     RegisterFeatureExtractionModule(const std::string &newModuleId) { 
         getMap()->insert( std::pair< std::string, FeatureExtraction*(*)()>(newModuleId, &createNewFeatureExtractionModule< T > ) );

GRT/CoreModules/MLBase.h

@@ -462,7 +462,7 @@ class GRT_API MLBase : public GRTBase, public Observer< TrainingResult >, public
     
     @return returns the minimum change value
     */
-    Float getMinChange() const;
+//    Float getMinChange() const;
 
     /**
     Gets the current learningRate value, this is value used to update the weights at each step of a learning algorithm such as stochastic gradient descent.
@@ -538,7 +538,7 @@ class GRT_API MLBase : public GRTBase, public Observer< TrainingResult >, public
     
     @return returns true if the order of the training dataset should be randomized, false otherwise
     */
-    bool getRandomiseTrainingOrder() const;
+//    bool getRandomiseTrainingOrder() const;
 
     /**
     Gets if the model for the derived class has been succesfully trained.

GRT/DataStructures/VectorFloat.h

@@ -42,15 +42,15 @@ class VectorFloat : public Vector< Float >{
      
      @param size: sets the size of the vector
      */
-    GRT_API VectorFloat( const size_type size );
+    GRT_API VectorFloat( const std::vector<Float>::size_type size );
 
     /**
      Constructor, sets the size of the vector and sets all elements to value
      
      @param size: sets the size of the vector
      @param value: the value that will be written to all elements in the vector
      */
-    GRT_API VectorFloat( const size_type size, const Float &value );
+    GRT_API VectorFloat( const std::vector<Float>::size_type size, const Float &value );
 
     /**
      Copy Constructor, copies the values from the rhs VectorFloat to this VectorFloat instance

GRT/FeatureExtractionModules/FFT/FastFourierTransform.h

@@ -83,7 +83,7 @@ class GRT_API FastFourierTransform : public GRTBase{
     VectorFloat phase;
     VectorFloat power;
     Float averagePower;
-    const static int MAX_FAST_BITS = 16;
+    const int MAX_FAST_BITS = 16;
     Vector< Vector< int > > bitTable;
 };
 

GRT/PreProcessingModules/Derivative.h

@@ -176,12 +176,15 @@ class GRT_API Derivative : public PreProcessing{
     @param delta: the estimated sampling time between sensor samples, must be greater than zero
     @return returns true if delta was set, false otherwise
     */
-    bool setDelta(const Float delta);
+    inline bool setDelta(const Float delta) {
+        this->delta = delta;
+        return true;
+    }
 
     /**
     Sets if the input data will be filtered using a moving average filter before the derivative is computed.
     Updating this parameter will re-initialize this instance.
-    
+
     @param filterData: sets if the data should be filtered before computing the derivative
     @return returns true if the filterData parameter was set, false otherwise
     */

GRT/Util/Util.cpp

@@ -282,7 +282,7 @@ Float Util::getMin(const VectorFloat &x){
     return min;
 }
 
-unsigned int getMinIndex(const VectorFloat &x){
+unsigned int Util::getMinIndex(const VectorFloat &x){
     unsigned int minIndex = 0;
     Float min = std::numeric_limits< Float >::max();
     unsigned int N = (unsigned int)x.size();

build/CMakeLists.txt

@@ -2,6 +2,8 @@ cmake_minimum_required(VERSION 2.8.7)
 
 project(GRT C CXX)
 
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake-modules")
+
 # GRT library
 set(GRT_LIB_NAME grt)
 
@@ -12,6 +14,7 @@ option(BUILD_EXAMPLES “build-examples” ON)
 option(BUILD_TOOLS “build-tools” ON)
 option(BUILD_SHARED_LIB "build-shared-lib" ON)
 option(EXCLUDE_FROM_INSTALL "exclude-from-install" OFF)
+option(BUILD_PYTHON_BINDING "build-python" ON)
 
 #setup the default build flags
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ")
@@ -137,6 +140,11 @@ add_library(${GRT_LIB_NAME}
             ${GRT_HEADERS}
 )
 
+message(STATUS "Build Python bindings: ${BUILD_PYTHON_BINDING}")
+if( BUILD_PYTHON_BINDING )
+    add_subdirectory(python)
+endif()
+
 #Add the options for what should be installed (when the user runs: sudo make install)
 if(NOT EXCLUDE_FROM_INSTALL)
 	install(

build/cmake-modules/FindNumpy.cmake

@@ -0,0 +1,62 @@
+# - Find the NumPy libraries
+# This module finds if NumPy is installed, and sets the following variables
+# indicating where it is.
+#
+# TODO: Update to provide the libraries and paths for linking npymath lib.
+#
+#  NUMPY_FOUND               - was NumPy found
+#  NUMPY_VERSION             - the version of NumPy found as a string
+#  NUMPY_VERSION_MAJOR       - the major version number of NumPy
+#  NUMPY_VERSION_MINOR       - the minor version number of NumPy
+#  NUMPY_VERSION_PATCH       - the patch version number of NumPy
+#  NUMPY_VERSION_DECIMAL     - e.g. version 1.6.1 is 10601
+#  NUMPY_INCLUDE_DIR         - path to the NumPy include files
+
+unset(NUMPY_VERSION)
+unset(NUMPY_INCLUDE_DIR)
+
+if(PYTHONINTERP_FOUND)
+    execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+            "import numpy as n; print(n.__version__); print(n.get_include());"
+            RESULT_VARIABLE __result
+            OUTPUT_VARIABLE __output
+            OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+    if(__result MATCHES 0)
+        string(REGEX REPLACE ";" "\\\\;" __values ${__output})
+        string(REGEX REPLACE "\r?\n" ";"    __values ${__values})
+        list(GET __values 0 NUMPY_VERSION)
+        list(GET __values 1 NUMPY_INCLUDE_DIR)
+
+        string(REGEX MATCH "^([0-9])+\\.([0-9])+\\.([0-9])+" __ver_check "${NUMPY_VERSION}")
+        if(NOT "${__ver_check}" STREQUAL "")
+            set(NUMPY_VERSION_MAJOR ${CMAKE_MATCH_1})
+            set(NUMPY_VERSION_MINOR ${CMAKE_MATCH_2})
+            set(NUMPY_VERSION_PATCH ${CMAKE_MATCH_3})
+            math(EXPR NUMPY_VERSION_DECIMAL
+                    "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
+            string(REGEX REPLACE "\\\\" "/"  NUMPY_INCLUDE_DIR ${NUMPY_INCLUDE_DIR})
+        else()
+            unset(NUMPY_VERSION)
+            unset(NUMPY_INCLUDE_DIR)
+            message(STATUS "Requested NumPy version and include path, but got instead:\n${__output}\n")
+        endif()
+    endif()
+else()
+    message(STATUS "To find NumPy Python interpretator is required to be found.")
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(NumPy REQUIRED_VARS NUMPY_INCLUDE_DIR NUMPY_VERSION
+        VERSION_VAR   NUMPY_VERSION)
+
+if(NUMPY_FOUND)
+    message(STATUS "NumPy ver. ${NUMPY_VERSION} found (include: ${NUMPY_INCLUDE_DIR})")
+endif()
+
+unset(__result)
+unset(__output)
+unset(__error_value)
+unset(__values)
+unset(__ver_check)
+unset(__error_value)

build/python/CMakeLists.txt

@@ -0,0 +1,47 @@
+
+if (APPLE) # Assume homebrew
+    file(GLOB SWIG_EXECUTABLE /usr/local/Cellar/swig/*/bin/swig)
+    if (NOT EXISTS ${SWIG_EXECUTABLE})
+        message(FATAL_ERROR "Cannot find homebrew SWIG v3 in /usr/local/Cellar/swig/")
+    endif()
+    message(STATUS "Found swig executable: ${SWIG_EXECUTABLE}")
+endif()
+find_package(SWIG 3 REQUIRED)
+INCLUDE(${SWIG_USE_FILE})
+
+find_package(PythonLibs 3 REQUIRED)
+include_directories(${PYTHON_INCLUDE_DIRS})
+message(STATUS "Found python: ${PYTHON_INCLUDE_DIRS} ${PYTHON_LIBRARIES}")
+
+if (APPLE) # Assume homebrew
+    set(PYTHONINTERP_FOUND YES)
+    set(PYTHON_EXECUTABLE /usr/local/bin/python3)
+    if (NOT EXISTS ${PYTHON_EXECUTABLE})
+        message(FATAL_ERROR "Cannot find homebrew Python v3 in ${PYTHON_EXECUTABLE}")
+    endif()
+    message(STATUS "Found Python 3 executable: ${PYTHON_EXECUTABLE}")
+else()
+    find_package(PythonInterp 3)
+endif()
+find_package(Numpy REQUIRED)
+if (NOT IS_DIRECTORY ${NUMPY_INCLUDE_DIR})
+    message(FATAL_ERROR "Cannot find Numpy")
+endif()
+include_directories(${NUMPY_INCLUDE_DIR})
+
+
+include_directories(${GRT_SRC_DIR})
+
+add_compile_options(-Wno-deprecated)
+
+set_property(SOURCE GRT.i PROPERTY CPLUSPLUS ON)
+set_property(SOURCE GRT.i PROPERTY SWIG_FLAGS -Wall -verbose -py3)
+swig_add_library(GRT LANGUAGE python SOURCES GRT.i)
+
+swig_link_libraries(GRT ${PYTHON_LIBRARIES} ${GRT_LIB_NAME} )
+
+# Copy python examples files
+file(GLOB PYTHON_EXAMPLES
+        "${CMAKE_CURRENT_SOURCE_DIR}/*.py"
+        )
+file(COPY ${PYTHON_EXAMPLES} DESTINATION ".")