Merge pull request #44 from pakozm/devel

Devel merge with Master

CHANGELIST.md

@@ -4,6 +4,22 @@ ChangeList
 Master branch release
 ---------------------
 
+- Solved bug at `Matrix<T>::select(...)` C++ method. The matrix offset wasn't be
+  added to the resulting matrix offset.
+- Solved bug at `SlidingWindow::setAtWindow(...)` C++ method. The matrix offset
+  wasn't be added to the computed window position.
+- Solved bug at `buffered_memory.h`. Such bug introduces an early stop when
+  reading matrices, ignoring the last lines of files.
+- Added `DEPENDENCIES-INSTALLER.sh`.
+- Added syntactic sugar for `matrix:slice(...)` method: `m("1:2","3:4")` or
+  `m({1,2},{3,4})`, like in Matlab or Octave.
+- Solved problem with `rlcompleter`, which didn't work properly when loaded as a
+  Lua module.
+- Modified `configure.sh` to inform about any error during Lua building.
+- Loadable modules are working on MacOs X.
+- Added `matrix.svd` and `matrix.diagonalize`.
+- Added `stats.pca`, `stats.mean_centered`, `stats.pca_whitening`.
+
 v0.3.0-beta relase
 ------------------
 

DEPENDENCIES-INSTALLER.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+UNAME=`uname`
+echo "System: $UNAME"
+if [ $UNAME = "Linux" ]; then
+    if [ `which apt-get` ]; then
+	apt-get install libz-dev libreadline-dev libblas-dev libatlas-dev libpng12-dev libtiff-dev liblua5.2-dev ||
+	(echo "ERROR INSTALLING DEPENDENCIES" && exit 10)
+    else
+	echo "Error, impossible to install dependencies, this script only works with apt-get"
+	exit 10
+    fi
+elif [ $UNAME = "Darwin" ]; then
+    if [ `which port` ]; then
+	port install zlib readline libpng tiff findutils ||
+	(echo "ERROR INSTALLING DEPENDENCIES" && exit 10)
+	echo "This script will change the default system BSD find by GNU find"
+	echo "BSD find will be renamed as bfind"
+	if [ ! -e /usr/find/bfind ]; then
+	    mv /usr/bin/find /usr/find/bfind
+	else
+	    rm -f /usr/bin/find
+	fi
+	ln -s `which gfind` /usr/bin/find
+    else
+	echo "Error, impossible to install dependencies, this scripts needs MacPorts"
+	exit 10
+    fi
+else
+    echo "Error, impossible to install dependencies, not recognized system: $UNAME"
+    exit 10
+fi
+exit 0

README.md

@@ -4,9 +4,11 @@ April-ANN
 Requirements
 ------------
 
-Requires the following libraries. Versions are only orientative, it could work with older and newer versions.
+Requires the following libraries. Versions are only orientative, it could work
+with older and newer versions whenver the API was compatible.
 
 - GNU C++ compiler (g++): v 4.7.2
+- Only in Linux systems: Lua 5.2 headers to tell April-ANN the default system path for Lua modules (`lua5.2-deb-multiarch.h` header).
 - BLAS implementation: ATLAS (v. 3), Intel MKL (v. 10.3.6), MacOS Accelerate Framework
 - Threads posix (pthread)
 - Readline (libreadline)
@@ -21,6 +23,11 @@ The following libreries are recommended, but optional:
 For perform computation on GPU, this optional library:
 - [OPTIONAL] CUDA and CUBLAS: release 4.2.6
 
+It is possible to install dependencies in Linux (via apt-get) and in MacOS X
+(via MacPorts) running:
+
+- `$ sudo ./DEPENDENCIES-INSTALLER.sh`
+
 Compilation
 -----------
 
@@ -141,12 +148,33 @@ you can use this bibitem:
 
 ```bibtex
 @misc{aprilann,
-        Author = {Francisco Zamora-Mart\'inez and Salvador Espa\~na-Boquera and Jorge Gorbe-Moya and Joan Pastor-Pellicer and Adrian Palacios},
-        Note = {{https://github.com/pakozm/april-ann}},
-        Title = {{April-ANN toolkit, A Pattern Recognizer In Lua with Artificial Neural Networks}},
-        Year = {2013}}
+  Author = {Francisco Zamora-Mart\'inez and Salvador Espa\~na-Boquera and
+	        Jorge Gorbe-Moya and Joan Pastor-Pellicer and Adrian Palacios},
+  Note = {{https://github.com/pakozm/april-ann}},
+  Title = {{April-ANN toolkit, A Pattern Recognizer In Lua with Artificial Neural Networks}},
+  Year = {2013}}
 ```
 
+Publications
+------------
+
+List of research papers which uses this tool:
+
+- Francisco Zamora-Martínez, Pablo Romeu, Paloma Botella-Rocamora, and Juan
+  Pardo. [Towards Energy Efficiency: Forecasting Indoor Temperature via Multivariate Analysis](http://www.mdpi.com/1996-1073/6/9/4639).
+  *Energies*, 6(9):4639-4659, 2013.
+
+- Pablo Romeu, Francisco Zamora-Martinez, Paloma Botella, and Juan Pardo.
+  [Time-Series Forecasting of Indoor Temperature Using Pre-trained Deep Neural Networks](http://dx.doi.org/10.1007/978-3-642-40728-4_57).
+  In *ICANN*, pages 451-458. 2013.
+
+- Joan Pastor-Pellicer, Francisco Zamora-Martinez, Salvador España-Boquera, and M.J. Castro-Bleda.
+  [F-Measure as the error function to train Neural Networks](http://dx.doi.org/10.1007/978-3-642-38679-4).
+  In *Advances in Computational Intelligence, IWANN, part I*, LNCS, pages 376-384. Springer, 2013.
+
+- F. Zamora-Martínez, Pablo Romeu, Juan Pardo, and Daniel Tormo.
+  Some empirical evaluations of a temperature forecasting module based on Artificial Neural Networks for a domotic home environment.
+  In *IC3K - KDIR*, pages 206-211, 2012.
 
 Packages
 --------
@@ -193,10 +221,18 @@ Doxygen documentation
 LINUX installation
 ------------------
 
-Install g++, libatlas-dev, libreadline-dev, libpng-dev, libtiff-dev, libz-dev, libopenmp-dev.
+Install g++, libatlas-dev, libreadline-dev, libpng-dev, libtiff-dev, libz-dev,
+libopenmp-dev or execute: `$ sudo ./DEPENDENCIES-INSTALLER.sh`
 
 MAC OS X installation
 ---------------------
 
-- Install libpng, from (sourceforge)[http://sourceforge.net/projects/libpng/files/]. Follow INSTALL information.
-- Install findutils, from (GNU)[http://ftp.gnu.org/pub/gnu/findutils/]. Follow INSTALL instructions. Execute `./configure --prefix=/usr` in order to substitute BSD find of your MacOS.
+Via MacPorts:
+
+- Install [MacPorts](http://www.macports.org/)
+- Execute `$ sudo ./DEPENDENCIES-INSTALLER.sh`
+
+Or manually:
+
+- Install libpng, from [sourceforge](http://sourceforge.net/projects/libpng/files/). Follow INSTALL information.
+- Install findutils, from [GNU](http://ftp.gnu.org/pub/gnu/findutils/). Follow INSTALL instructions. Execute `./configure --prefix=/usr` in order to substitute BSD find of your MacOS.

binding/bind_templates/luabind_template.cc

@@ -175,6 +175,8 @@ void lua_push$$ClassName$$(lua_State *L, $$ClassName$$ *obj){
 #include "luabindmacros.h"
 
 int lua_new_$$ClassName$$_$$FILENAME2$$(lua_State *L) {
+        // stops garbage collector to avoid problems with reference counting
+        lua_gc(L, LUA_GCSTOP, 0);
 	lua_remove(L,1);  // primer parametro es la metatabla __call(table,...)
 	$$ClassName$$ UNUSED *obj = 0;
 	DEBUG("lua_new_$$ClassName$$ (begin)");
@@ -184,10 +186,14 @@ int lua_new_$$ClassName$$_$$FILENAME2$$(lua_State *L) {
         if (luabind_num_returned_values != 1) {
           LUABIND_ERROR("constructors must return 1 (and only 1) value");
         }
+	// restart the garbage collector
+        lua_gc(L, LUA_GCRESTART, 0);
 	return luabind_num_returned_values;
 }
 
 int lua_delete_$$ClassName$$_$$FILENAME2$$(lua_State *L){
+  // stops garbage collector to avoid problems with reference counting
+  lua_gc(L, LUA_GCSTOP, 0);
   $$ClassName$$ *obj = lua_rawget$$ClassName$$_$$FILENAME2$$(L,1);
   if (obj != 0) {
     DEBUG_OBJ("lua_delete_$$ClassName$$ (begin)",obj);
@@ -202,6 +208,8 @@ int lua_delete_$$ClassName$$_$$FILENAME2$$(lua_State *L){
   else {
     DEBUG_OBJ("lua_delete_$$ClassName$$ WARNING!! NULL pointer", obj);
   }
+  // restart the garbage collector
+  lua_gc(L, LUA_GCRESTART, 0);
   return 0;
 }
 
@@ -374,6 +382,8 @@ void bindluaopen_$$ClassName$$_$$FILENAME2$$(lua_State *L){
 #include "luabindmacros.h"
 
 int lua_call_$$ClassName$$_$$MethodName$$(lua_State *L){
+  // stops garbage collector to avoid problems with reference counting
+  lua_gc(L, LUA_GCSTOP, 0);
   //Comprobamos que el primer elemento sea el userdata que esperamos
   if (!lua_is$$ClassName$$(L,1)) {
       lua_pushstring(L, "First argument of $$MethodName$$ must be of type "
@@ -389,6 +399,8 @@ int lua_call_$$ClassName$$_$$MethodName$$(lua_State *L){
     $$code$$
       }
   DEBUG_OBJ("lua_call_$$ClassName$$_$$MethodName$$ (end)", obj);
+  // restart the garbage collector
+  lua_gc(L, LUA_GCRESTART, 0);
   return luabind_num_returned_values;
 }
 //LUA end
@@ -401,11 +413,15 @@ int lua_call_$$ClassName$$_$$MethodName$$(lua_State *L){
 int lua_call_class_$$ClassName$$_$$ClassMethodName$$(lua_State *L){
 
 	DEBUG("lua_call_class_$$ClassName$$_$$ClassMethodName$$");
+        // stops garbage collector to avoid problems with reference counting
+        lua_gc(L, LUA_GCSTOP, 0);
         int luabind_num_returned_values = 0;
 	// CODE:
 	{
 	  $$code$$
 	}
+	// restart the garbage collector
+        lua_gc(L, LUA_GCRESTART, 0);
 	return luabind_num_returned_values;
 }
 //LUA end
@@ -419,10 +435,14 @@ int lua_call_class_$$ClassName$$_$$ClassMethodName$$(lua_State *L){
 #include "luabindmacros.h"
 
 static int lua_call_$$string.gsub(func_name,"%p","_")$$(lua_State *L){
+  // stops garbage collector to avoid problems with reference counting
+  lua_gc(L, LUA_GCSTOP, 0);
   lua_remove(L,1);  // primer parametro es la metatabla __call(table,...)
   DEBUG("lua_call_$$string.gsub(func_name,"%p","_")$$ (begin)");
   int luabind_num_returned_values = 0;
   $$code$$
+  // restart the garbage collector
+  lua_gc(L, LUA_GCRESTART, 0);
   DEBUG("lua_call_$$string.gsub(func_name,"%p","_")$$ (end)");
   return luabind_num_returned_values;
 }

binding/formiga.lua

@@ -106,7 +106,7 @@ formiga = {
     CPPcompiler = os.getenv("CXX") or "g++",
     Ccompiler = os.getenv("CC") or "gcc",
     extra_libs = {"-ldl"},
-    shared_extra_libs = {"-shared"},
+    shared_extra_libs = { },
     extra_flags = { string.format("-DGIT_COMMIT=%d", commit_count), },
     language_by_extension = {
       c = "c", cc = "c++", cxx = "c++", CC = "c++", cpp = "c++",

build_NOBLAS_debug.lua

@@ -30,6 +30,7 @@ luapkg{
       "-Wl,-E -ldl"
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_NOBLAS_release.lua

@@ -30,6 +30,7 @@ luapkg{
       "-Wl,-E -ldl"
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_cuda_and_mkl_debug.lua

@@ -8,6 +8,8 @@ luapkg{
   program_name = "april-ann.debug",
   verbosity_level = 0,  -- 0 => NONE, 1 => ONLY TARGETS, 2 => ALL
   packages = packages,
+  version_flags = dofile "VERSION.lua",
+  disclaimer_strings = dofile "DISCLAIMER.lua",
   global_flags = {
     debug="yes",
     use_lstrip = "no",
@@ -24,11 +26,14 @@ luapkg{
       "-msse",
       "-pg",
       "-DNO_POOL",
+      "-DNO_OMP",
+      "-fPIC",
       -- For CUDA
       "-I/usr/local/cuda/include",
       "-L/usr/local/cuda/lib",
     },
     extra_libs={
+      "-fPIC",
       "-pg",
       "-lpthread",
       "-rdynamic",
@@ -43,6 +48,10 @@ luapkg{
       -- For CUBLAS
       "-lcublas",
     },
+    shared_extra_libs={
+      "-shared",
+      "-llua5.2",
+    },
   },
 
   main_package = package{

build_cuda_and_mkl_release.lua

@@ -8,6 +8,8 @@ luapkg{
   program_name = "april-ann",
   verbosity_level = 0,  -- 0 => NONE, 1 => ONLY TARGETS, 2 => ALL
   packages = packages,
+  version_flags = dofile "VERSION.lua",
+  disclaimer_strings = dofile "DISCLAIMER.lua",
   global_flags = {
     debug="no",
     use_lstrip = "yes",
@@ -24,11 +26,14 @@ luapkg{
       "-msse",
       "-DNDEBUG",
       "-DNO_POOL",
+      "-DNO_OMP",
+      "-fPIC",
       -- For CUDA
       "-I/usr/local/cuda/include",
       "-L/usr/local/cuda/lib",
     },
     extra_libs={
+      "-fPIC",
       "-lpthread",
       "-rdynamic",
       -- For Intel MKL :)
@@ -42,6 +47,10 @@ luapkg{
       -- For CUBLAS
       "-lcublas",
     },
+    shared_extra_libs={
+      "-shared",
+      "-llua5.2",
+    },
   },
 
   main_package = package{

build_debug.lua

@@ -34,6 +34,7 @@ luapkg{
       "-llapack_atlas",
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_debug_macosx.lua

@@ -37,6 +37,8 @@ luapkg{
       "-fPIC",
     },
     shared_extra_libs={
+     "-flat_namespace",
+     "-bundle",
       assert(io.popen("pkg-config --libs 'lua >= 5.2'"):read("*l"))
     },
   },

build_mkl_debug.lua

@@ -43,6 +43,7 @@ luapkg{
       "-liomp5"
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_mkl_release.lua

@@ -41,6 +41,7 @@ luapkg{
       "-liomp5",
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_release.lua

@@ -33,6 +33,7 @@ luapkg{
       "-llapack_atlas",
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

build_release_macosx.lua

@@ -35,6 +35,8 @@ luapkg{
       "-fPIC",
     },
     shared_extra_libs={
+     "-flat_namespace",
+     "-bundle",
       assert(io.popen("pkg-config --libs 'lua >= 5.2'"):read("*l"))
     },
   },

build_release_pi.lua

@@ -32,6 +32,7 @@ luapkg{
       "-llapack_atlas",
     },
     shared_extra_libs={
+      "-shared",
       "-llua5.2",
     },
   },

configure.sh

@@ -5,9 +5,10 @@ if [ -z $APRILANN_CONFIGURED ]; then
 #export LUA_PATH="`pwd`""/binding/?.lua;?"
 fi
 export LUA_DIR="`pwd`"/lua/lua-5.2.2
-make -C $LUA_DIR
-make -C $LUA_DIR install
-make -C "`pwd`"/lua/lstrip
+(make -C $LUA_DIR            &&
+ make -C $LUA_DIR install    &&
+ make -C "`pwd`"/lua/lstrip) ||
+(echo "Error building Lua!!!" && exit -1)
 if [ -z $APRIL_EXEC ]; then
     export APRIL_EXEC=`pwd`/bin/april-ann
 fi

lua/lua-5.2.2/src/Makefile

@@ -49,7 +49,7 @@ ALL_A= $(LUA_A)
 
 # Targets start here.
 DetectOS:
-	-@make $(UNAME)
+	@make $(UNAME)
 
 Linux: linux