Merge branch 'master' of https://code.it4i.cz/bes0030/4Neuro.git

CMakeLists.txt

@@ -26,27 +26,37 @@ endif (NOT CMAKE_BUILD_TYPE)
 # funroll-all-loops a bez prepinace
 
 set(standard "-std=f2008")
+get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
+
+if (WITH_TIME_PROFILING)
+    add_definitions(-DTIME_PROFILING)
+endif()
+
+message ("Fortran compiler name: " ${Fortran_COMPILER_NAME})
+message ("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
+message ("Fortran compiler: " ${Fortran_COMPILER_NAME})
+message ("Build type:" ${CMAKE_BUILD_TYPE})
 
 if (Fortran_COMPILER_NAME MATCHES "gfortran.*")
   # gfortran
-  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-loops -fno-f2c -O3 ${standard}")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g ${standard}")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-loops -fno-f2c -O3 ${standard} -cpp")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g ${standard} -cpp")
 elseif (Fortran_COMPILER_NAME MATCHES "ifort.*")
   # ifort (untested)
-  set (CMAKE_Fortran_FLAGS_RELEASE "-f77rtl -O3 ${standard}")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-f77rtl -O0 -g ${standard}")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-f77rtl -O3 ${standard} -cpp")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-f77rtl -O0 -g ${standard} -cpp")
 elseif (Fortran_COMPILER_NAME MATCHES "g77")
   # g77
-  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-loops -fno-f2c -O3 -m32 ${standard}")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g -m32 ${standard}")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-loops -fno-f2c -O3 -m32 ${standard} -cpp")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-fno-f2c -O0 -g -m32 ${standard} -cpp")
 else (Fortran_COMPILER_NAME MATCHES "gfortran.*")
-  message ("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
-  message ("Fortran compiler: " ${Fortran_COMPILER_NAME})
   message ("No optimized Fortran compiler flags are known, we just try -O2...")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O2 ${standard}")
-  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g ${standard}")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-O2 ${standard} -cpp")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g ${standard} -cpp")
 endif (Fortran_COMPILER_NAME MATCHES "gfortran.*")
 
+#(Fortran_COMPILER_NAME MATCHES "gfortran.*")
+
 #----------------#
 # User variables #
 #----------------#

build.sh

 #!/bin/bash
 
+#------------#------------------------------------------------------------
+# Parameters #
+#------------#
+
+# Build type (Release/Debug)
+BUILD_TYPE=Debug
+
+# Turn of/off time profiling (1/0)
+WITH_TIME_PROFILING=0
+
+#-------------------------------------------------------------------------
+
 echo "Creating folder 'build'...";
 mkdir -p build/lib;
 echo "Folder 'build' was created'";
 
 cd build;
-cmake ..;
-make && echo "Installation complete." || exit -1;
+cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DWITH_TIME_PROFILING:BOOLEAN=${WITH_TIME_PROFILING} ..
+make VERBOSE=1 && echo "Build complete." || exit -1;
 #make install;
 

src/CMakeLists.txt

 project(Modules)
 enable_language(Fortran)
 
-set(standard "-std=f2008")
-set(CMAKE_Fortran_FLAGS "${standard}")
-
 add_library(neuron_dummy_m SHARED neuron_dummy_m.f90)
 set_target_properties(neuron_dummy_m PROPERTIES LINKER_LANGUAGE Fortran)
 

src/connection_m.f90

 !> Module containing classes representing connections (synapses)
 !! in neural networks.
 !!
-!! It uses `neural_t` class.
+!! It uses `neuron_t` class.
 !!
 !! @author Martin Beseda
 !! @author Martin Mrovec
 !! @date 2017
-!! @todo Implement destructor
-!! @todo Comment constructor
+!! @todo Change generating random connection weights from uniform to Gaussian distribution
 module connection_m
-    ! TODO Implement destructor
     use neuron_dummy_m
 
     implicit none
@@ -21,7 +19,7 @@ module connection_m
     !------------------!
 
     !> Represents a connection between two neurons.
-    type, abstract :: connection_t
+    type :: connection_t
         private 
 
         class(neuron_t), pointer :: input_neuron   !< Pointer to an input neuron
@@ -33,11 +31,15 @@ module connection_m
         !> Initializes the common connection_t class components
         !! 'input_neuron', 'output_neuron' and 'weight'.
         !! I.e. serves similarly to an abstract constructor.
+        !! @param input_neuron Pointer to the input neuron (instance of neuron_t)
+        !! @param output_neuron Pointer to the output neuron (instance of neuron_t)
+        !! @param weight Weight of the connection (real number)
         procedure, private :: init_components   => init_components_impl
 
-        !procedure          :: destroy_instance  => destroy_instance_impl
-
-        !final, deferred    :: destructor
+        !> Nullifies pointers to input and output neurons, so they
+        !! don't get destroyed when the connection_t instance is 
+        !! deallocated.
+        procedure, private :: nullify_pointers  => nullify_pointers_impl
 
         !> Adds a given value to the current weight of the  
         !! connection.
@@ -56,6 +58,9 @@ module connection_m
         !! @return Weight of the connection (type real)
         procedure          :: get_weight        => get_weight_impl
 
+        !> Desctructor for instances of the class connection_t
+        final              :: destroy_connection
+
     end type connection_t
 
     !> Represents a connection between two neurons.
@@ -68,14 +73,36 @@ module connection_m
         !! input neuron state * weight)
         !! to an output neuron.
         procedure :: pass_signal => pass_signal_impl
+
     end type interval_connection_t
 
     !------------!------------------------------------------------------------------------------
     ! Interfaces !
     !------------!
+    interface connection_t
+        !> Constructor of connection_t class
+        !! @param input_neuron Pointer to the input neuron (instance of neuron_t)
+        !! @param output_neuron Pointer to the output neuron (instance of neuron_t)
+        module procedure :: new_connection_2
+
+        !> Constructor of connection_t class
+        !! @param input_neuron Pointer to the input neuron (instance of neuron_t)
+        !! @param output_neuron Pointer to the output neuron (instance of neuron_t)
+        !! @param weight Weight of the connection (real number)
+        module procedure :: new_connection_3
+    end interface connection_t
+
     interface interval_connection_t
         !> Constructor of interval_connection_t class
-        module procedure :: new_interval_connection
+        !! @param input_neuron Pointer to the input neuron (instance of neuron_t)
+        !! @param output_neuron Pointer to the output neuron (instance of neuron_t)
+        module procedure :: new_interval_connection_2 
+ 
+        !> Constructor of interval_connection_t class
+        !! @param input_neuron Pointer to the input neuron (instance of neuron_t)
+        !! @param output_neuron Pointer to the output neuron (instance of neuron_t)
+        !! @param weight Weight of the connection (real number) 
+        module procedure :: new_interval_connection_3
     end interface interval_connection_t
 
     contains
@@ -83,38 +110,66 @@ module connection_m
         ! Method implementations !
         ! -----------------------!
 
-        !subroutine destroy_instance_impl(this)
-        !    class(connection_t), pointer, intent(out) :: this
-
-        !    deallocate(this)
-        !end subroutine destroy_instance_impl
-
         !--------------------!
         ! class connection_t !
         !--------------------!
+        function new_connection_2(input_neuron, output_neuron) result(new_obj)
+            type(neuron_t), pointer, intent(in)      :: input_neuron
+            type(neuron_t), pointer, intent(in)      :: output_neuron
+            real                                     :: weight
+            type(connection_t), pointer              :: new_obj
+
+            allocate(new_obj)
+
+            ! todo change to random numbers from Gaussian distribution
+            call random_seed()
+            call random_number(weight)
+
+            call new_obj%init_components(input_neuron, output_neuron, weight)
+        end function new_connection_2
+      
+
+        function new_connection_3(input_neuron, output_neuron, weight) result(new_obj)
+            type(neuron_t), pointer, intent(in)      :: input_neuron
+            type(neuron_t), pointer, intent(in)      :: output_neuron
+            real, intent(in)                         :: weight
+            type(connection_t), pointer              :: new_obj
+
+            allocate(new_obj)
+
+            call new_obj%init_components(input_neuron, output_neuron, weight)
+        end function new_connection_3
+
         subroutine init_components_impl(this, input_neuron, output_neuron, weight) 
             class(connection_t), intent(inout) :: this
             type(neuron_t), pointer            :: input_neuron
             type(neuron_t), pointer            :: output_neuron
             real, intent(in)                   :: weight
 
-        !DEC$ IF DEFINED TIME_PROFILING
+#ifdef TIME_PROFILING
             real                               :: t1, t2 !< Variables used for time measurement
             call cpu_time(t1)
-        !DEC$ ENDIF
+#endif
 
             this%input_neuron  => input_neuron
             this%output_neuron => output_neuron
             this%weight        = weight
 
 
-        !DEC$ IF DEFINED TIME_PROFILING
+#ifdef TIME_PROFILING
             call cpu_time(t2)
             write(*, "(A)") '+----------------+'
             write(*, "(A, E15.7, A)") '| TIME PROFILING | Function init_components() was running for ', t2-t1, 's.'
             write(*, "(A)") '+----------------+'
-        !DEC$ ENDIF
+#endif
         end subroutine init_components_impl
+            
+        subroutine nullify_pointers_impl(this)
+            class(connection_t), intent(inout) :: this
+
+            nullify(this%input_neuron)
+            nullify(this%output_neuron)
+        end subroutine nullify_pointers_impl
 
         subroutine adjust_weight_impl(this, added_value)
             class(connection_t), intent(inout) :: this
@@ -123,6 +178,12 @@ module connection_m
             this%weight = this%weight + added_value 
         end subroutine adjust_weight_impl
 
+        subroutine destroy_connection(this)
+            type(connection_t), intent(inout) :: this
+
+            call this%nullify_pointers()
+        end subroutine destroy_connection
+
         !-----------------------------!
         ! class interval_connection_t !
         !-----------------------------!
@@ -135,16 +196,31 @@ module connection_m
         !--------------!------------------------------------------------------------------------
         ! Constructors !
         !--------------!
-        function new_interval_connection(input_neuron, output_neuron, weight) result(ret_obj)
+        function new_interval_connection_2(input_neuron, output_neuron) result(new_obj)
+            type(neuron_t), pointer              :: input_neuron
+            type(neuron_t), pointer              :: output_neuron
+            real                                 :: weight
+            type(interval_connection_t), pointer :: new_obj
+
+            allocate(new_obj)
+
+            ! todo change to random numbers from Gaussian distribution
+            call random_seed()
+            call random_number(weight)
+
+            call new_obj%init_components(input_neuron, output_neuron, weight)
+        end function new_interval_connection_2
+
+        function new_interval_connection_3(input_neuron, output_neuron, weight) result(new_obj)
             type(neuron_t), pointer              :: input_neuron
             type(neuron_t), pointer              :: output_neuron
             real, intent(in)                     :: weight
-            type(interval_connection_t), pointer :: ret_obj
+            type(interval_connection_t), pointer :: new_obj
 
-            allocate(ret_obj)
+            allocate(new_obj)
 
-            call ret_obj%init_components(input_neuron, output_neuron, weight)
-        end function new_interval_connection
+            call new_obj%init_components(input_neuron, output_neuron, weight)
+        end function new_interval_connection_3
 
         !-------------------!-------------------------------------------------------------------
         ! Getters & Setters !

src/connection_test.f90

@@ -26,6 +26,9 @@ program connection_test
     print *, 'Assignment was successful.'
 
     print *, 'Creating an instance of the class interval_connection_t...'
+    !con => interval_connection_t(input_neuron=n1_p, &
+    !                             output_neuron=n2_p,&
+    !                             weight=5.25)
     con => interval_connection_t(n1_p, n2_p, 5.25)
     print *, 'The instance of the class interval_connection_t was created successfully.'
 
@@ -80,6 +83,8 @@ program connection_test
         stop -1
     end if
 
+    deallocate(con)
+
     print *, '+-------------------------------------------------------------+'
     print *, '| ALL TESTS OF THE MODULE CONNECTION_M WERE RUN SUCCESSFULLY. |'
     print *, '+-------------------------------------------------------------+'