Merge branch 'release/4.0.0'

NEWS

@@ -1,6 +1,6 @@
-2015-01-18 Soeren Sonnenburg <[email protected]>
+2015-01-26 Soeren Sonnenburg <[email protected]>
 
-	* SHOGUN Release version 3.2.1 (libshogun 16.1, data 0.8, parameter 1)
+	* SHOGUN Release version 4.0.0 (libshogun 17.0, data 0.9, parameter 1)
 	* This release features the work of our 8 GSoC 2014 students [student; mentors]:
 	    - OpenCV Integration and Computer Vision Applications [Abhijeet Kislay; Kevin Hughes]
 	    - Large-Scale Multi-Label Classification [Abinash Panda; Thoralf Klein]

src/interfaces/modular/IO.i

@@ -26,6 +26,7 @@
 %rename(SerializableHdf5File) CSerializableHdf5File;
 %rename(SerializableJsonFile) CSerializableJsonFile;
 %rename(SerializableXmlFile) CSerializableXmlFile;
+%rename(NeuralNetworkFileReader) CNeuralNetworkFileReader;
 %rename(SimpleFile) CSimpleFile;
 %rename(MemoryMappedFile) CMemoryMappedFile;
 %rename(VwParser) CVwParser;
@@ -131,6 +132,7 @@ namespace shogun
 %include <shogun/io/SerializableHdf5File.h>
 %include <shogun/io/SerializableJsonFile.h>
 %include <shogun/io/SerializableXmlFile.h>
+%include <shogun/io/NeuralNetworkFileReader.h>
 
 %include <shogun/io/SimpleFile.h>
 %include <shogun/io/MemoryMappedFile.h>

src/interfaces/modular/IO_includes.i

@@ -20,6 +20,7 @@
 #include <shogun/io/SerializableHdf5File.h>
 #include <shogun/io/SerializableJsonFile.h>
 #include <shogun/io/SerializableXmlFile.h>
+#include <shogun/io/NeuralNetworkFileReader.h>
 #include <shogun/io/SimpleFile.h>
 #include <shogun/io/MemoryMappedFile.h>
 %}

src/interfaces/octave_static/OctaveInterface.cpp

@@ -633,8 +633,8 @@ void COctaveInterface::clear_octave_globals()
 
 void COctaveInterface::run_octave_init()
 {
-	char* name=strdup("octave");
-	char* opts=strdup("-q");
+	char* name=get_strdup("octave");
+	char* opts=get_strdup("-q");
 	char* argv[2]={name, opts};
 	octave_main(2,argv,1);
 	free(opts);

src/interfaces/r_static/RInterface.cpp

@@ -18,6 +18,7 @@ extern "C" {
 #include <shogun/lib/ShogunException.h>
 #include <shogun/io/SGIO.h>
 #include <shogun/base/init.h>
+#include <shogun/lib/memory.h>
 
 #ifdef HAVE_PYTHON
 #include "../python_static/PythonInterface.h"
@@ -552,8 +553,8 @@ void CRInterface::run_r_init()
 #ifdef R_HOME_ENV
 	setenv("R_HOME", R_HOME_ENV, 0);
 #endif
-	char* name=strdup("R");
-	char* opts=strdup("-q");
+	char* name=get_strdup("R");
+	char* opts=get_strdup("-q");
 	char* argv[2]={name, opts};
 	Rf_initEmbeddedR(2, argv);
 	free(opts);

src/shogun/io/File.cpp

@@ -185,12 +185,12 @@ CFile::~CFile()
 void CFile::set_variable_name(const char* name)
 {
 	SG_FREE(variable_name);
-	variable_name=strdup(name);
+	variable_name=get_strdup(name);
 }
 
 char* CFile::get_variable_name()
 {
-	return strdup(variable_name);
+	return get_strdup(variable_name);
 }
 
 #define SPARSE_VECTOR_GETTER(type)										\

src/shogun/io/NeuralNetworkFileReader.cpp

@@ -0,0 +1,264 @@
+/*
+ * Copyright (c) 2014, Shogun Toolbox Foundation
+ * All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without 
+ * modification, are permitted provided that the following conditions are met:
+
+ * 1. Redistributions of source code must retain the above copyright notice, 
+ * this list of conditions and the following disclaimer.
+ * 
+ * 2. Redistributions in binary form must reproduce the above copyright notice, 
+ * this list of conditions and the following disclaimer in the documentation 
+ * and/or other materials provided with the distribution.
+ * 
+ * 3. Neither the name of the copyright holder nor the names of its 
+ * contributors may be used to endorse or promote products derived from this 
+ * software without specific prior written permission.
+
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+ * POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * Written (W) 2014 Khaled Nasr
+ */
+
+#include <shogun/lib/config.h>
+#ifdef HAVE_JSON
+
+#include <shogun/io/NeuralNetworkFileReader.h>
+#include <shogun/neuralnets/NeuralNetwork.h>
+#include <shogun/neuralnets/NeuralLayer.h>
+#include <shogun/neuralnets/NeuralInputLayer.h>
+#include <shogun/neuralnets/NeuralLinearLayer.h>
+#include <shogun/neuralnets/NeuralLogisticLayer.h>
+#include <shogun/neuralnets/NeuralSoftmaxLayer.h>
+#include <shogun/neuralnets/NeuralRectifiedLinearLayer.h>
+#include <shogun/lib/DynamicObjectArray.h>
+#include <shogun/lib/SGVector.h>
+
+using namespace shogun;
+
+CNeuralNetwork* CNeuralNetworkFileReader::read_file(const char* file_path)
+{
+	json_object* json_network = json_object_from_file(file_path);
+
+	if (is_error(json_network)) 
+	{
+		SG_ERROR("Error while opening file: %s!\n", file_path);
+		return NULL;
+	}
+
+	CNeuralNetwork* network = parse_network(json_network);
+
+	json_object_put(json_network);
+
+	return network;
+}
+
+CNeuralNetwork* CNeuralNetworkFileReader::read_string(const char* str)
+{
+	json_object* json_network = json_tokener_parse(str);
+
+	if (is_error(json_network)) 
+	{
+		SG_ERROR("Error while parsing the given string\n");
+		return NULL;
+	}
+
+	CNeuralNetwork* network = parse_network(json_network);
+
+	json_object_put(json_network);
+
+	return network;
+}
+
+CNeuralNetwork* CNeuralNetworkFileReader::parse_network(json_object* json_network)
+{
+	CNeuralNetwork* network = new CNeuralNetwork;
+
+	// find the layers
+	json_object_iter iter;
+	json_object* json_layers = NULL;
+	json_object_object_foreachC(json_network, iter)
+	{
+		if (string_equal(iter.key, "layers"))
+			json_layers = iter.val;
+	}
+
+	if (json_layers)
+		network->set_layers(parse_layers(iter.val));
+	else
+		SG_ERROR("No layers found in file\n");
+
+	// set the connections
+	json_object_iter layers_iter;
+	json_object_object_foreachC(json_layers, layers_iter)
+	{
+		json_object_iter layer_iter;
+		json_object_object_foreachC(layers_iter.val, layer_iter)
+		{
+			if (string_equal(layer_iter.key, "inputs"))
+			{
+				int32_t len = json_object_array_length(layer_iter.val);
+
+				for (int32_t i=0; i<len; i++)
+				{
+					const char* input_key = json_object_get_string(
+						json_object_array_get_idx(layer_iter.val, i));
+
+					int32_t from = find_layer_index(json_layers, input_key);
+					int32_t to = find_layer_index(json_layers, layers_iter.key);
+
+					if (from == -1)
+						SG_ERROR("Invalid layer identifier (%s) in layer (%s)\n", 
+							input_key, layers_iter.key);
+
+					network->connect(from, to);
+				}
+			}
+		}
+	}
+
+	// set the training parameters
+	float sigma = 0.01;
+	json_object_object_foreachC(json_network, iter)
+	{
+		if (string_equal(iter.key, "sigma"))
+			sigma = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "optimization_method"))
+		{
+			const char* method = json_object_get_string(iter.val);
+			if (string_equal(method, "NNOM_LBFGS"))
+				network->optimization_method = NNOM_LBFGS;
+			else if (string_equal(method, "NNOM_GRADIENT_DESCENT"))
+				network->optimization_method = NNOM_GRADIENT_DESCENT;
+			else
+				SG_ERROR("Invalid optimization method (%s)\n", method);
+		}
+		else if (string_equal(iter.key, "l2_coefficient"))
+			network->l2_coefficient = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "l1_coefficient"))
+			network->l1_coefficient = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "dropout_hidden"))
+			network->dropout_hidden = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "dropout_input"))
+			network->dropout_input = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "max_norm"))
+			network->max_norm = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "epsilon"))
+			network->epsilon = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "max_num_epochs"))
+			network->max_num_epochs = json_object_get_int(iter.val);
+		else if (string_equal(iter.key, "gd_mini_batch_size"))
+			network->gd_mini_batch_size = json_object_get_int(iter.val);
+		else if (string_equal(iter.key, "gd_learning_rate"))
+			network->gd_learning_rate = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "gd_learning_rate_decay"))
+			network->gd_learning_rate_decay = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "gd_momentum"))
+			network->gd_momentum = json_object_get_double(iter.val);
+		else if (string_equal(iter.key, "gd_error_damping_coeff"))
+			network->gd_error_damping_coeff = json_object_get_double(iter.val);
+
+		else if (!string_equal(iter.key, "layers"))
+			SG_ERROR("Invalid parameter (%s)\n", iter.key);
+	}
+
+	network->initialize(sigma);
+
+	return network;
+}
+
+CDynamicObjectArray* CNeuralNetworkFileReader::parse_layers(
+		json_object* json_layers)
+{	
+	CDynamicObjectArray* layers = new CDynamicObjectArray();
+
+	json_object_iter iter;
+	json_object_object_foreachC(json_layers, iter)
+	{
+		layers->append_element(parse_layer(iter.val));
+	}
+
+	return layers;
+}
+
+CNeuralLayer* CNeuralNetworkFileReader::parse_layer(json_object* json_layer)
+{
+	json_object_iter iter;
+
+	CNeuralLayer* layer = NULL;
+	const char* type = NULL;
+
+	// find the layer type and create a appropriate instance 
+	json_object_object_foreachC(json_layer, iter)
+	{
+		if (string_equal(iter.key, "type"))
+		{	
+			type = json_object_get_string(iter.val);
+
+			if (string_equal(type, "NeuralInputLayer"))
+				layer = new CNeuralInputLayer();
+			else if (string_equal(type, "NeuralLinearLayer"))
+				layer = new CNeuralLinearLayer();
+			else if (string_equal(type, "NeuralLogisticLayer"))
+				layer = new CNeuralLogisticLayer();
+			else if (string_equal(type, "NeuralSoftmaxLayer"))
+				layer = new CNeuralSoftmaxLayer();
+			else if (string_equal(type, "NeuralRectifiedLinearLayer"))
+				layer = new CNeuralRectifiedLinearLayer();
+			else
+				SG_ERROR("Unknown layer type: %s", type);
+		}
+	}
+
+	// fill in the fields
+	json_object_object_foreachC(json_layer, iter)
+	{
+		if(string_equal(iter.key, "num_neurons"))
+		{
+			layer->set_num_neurons(json_object_get_int(iter.val));
+		}
+		else if(string_equal(type,"NeuralInputLayer") && 
+			string_equal(iter.key, "start_index"))
+		{
+			((CNeuralInputLayer*)layer)->set_start_index(
+				json_object_get_int(iter.val));
+		}
+	}
+
+	return layer;
+}
+
+int32_t CNeuralNetworkFileReader::find_layer_index(json_object* json_layers, 
+		const char* layer_key)
+{
+	int32_t index = 0;
+
+	json_object_iter iter;
+	json_object_object_foreachC(json_layers, iter)
+	{
+		if (string_equal(iter.key, layer_key))
+			return index;
+		else
+			index++;
+	}
+
+	return -1;
+}
+
+bool CNeuralNetworkFileReader::string_equal(const char* str1, const char* str2)
+{
+	return (strcmp(str1, str2) == 0);
+}
+
+#endif