/*!
\page developer_tutorial Libshogun and Developer Tutorial

Shogun is split up into libshogun which contains all the machine learning
algorithms, libshogunui which contains a library for the 'static interfaces',
the static interfaces python, octave, matlab, r and the modular interfaces
python_modular, octave_modular and r_modular (all found in the src/
subdirectory with corresponding name). See src/INSTALL on how to install shogun.

In case one wants to extend shogun the best way is to start using its library.
This can be easily done as a number of examples in examples/libshogun document.

The simplest libshogun based program would be

\verbinclude basic_minimal.cpp

which could be compiled with g++ -lshogun minimal.cpp -o minimal and obviously
does nothing (apart from initializing and destroying a couple of global shogun
objects internally).

In case one wants to redirect shoguns output functions SG_DEBUG(), SG_INFO(),
SG_WARN(), SG_ERROR(), SG_PRINT() etc, one has to pass them to init_shogun() as
parameters like this

\verbatim
void print_message(FILE* target, const char* str)
{
    fprintf(target, "%s", str);
}

void print_warning(FILE* target, const char* str)
{
    fprintf(target, "%s", str);
}

void print_error(FILE* target, const char* str)
{
    fprintf(target, "%s", str);
}

init_shogun(&print_message, &print_warning,
            &print_error);
\endverbatim

To finally see some action one has to include the appropriate header files,
e.g. we create some features and a gaussian kernel

\verbinclude classifier_minimal_svm.cpp

Now you probably wonder why this example does not leak memory. First of all,
supplying pointers to arrays allocated with new[] will make shogun objects own
these objects and will make them take care of cleaning them up on object
destruction. Then, when creating shogun objects they keep a reference counter
internally. Whenever a shogun object is returned or supplied as an argument to
some function its reference counter is increased, for example in the example
above

\verbatim
CLibSVM* svm = new CLibSVM(10, kernel, labels);
\endverbatim

increases the reference count of kernel and labels. On destruction the
reference counter is decreased and the object is freed if the counter is <= 0.

It is therefore your duty to prevent objects from destruction if you keep a
handle to them globally <b>that you still intend to use later</b>. In the example
above accessing labels after the call to SG_UNREF(svm) will cause a
segmentation fault as the Label object was already destroyed in the SVM
destructor. You can do this by SG_REF(obj). To decrement the reference count of
an object, call SG_UNREF(obj) which will also automagically destroy it if the
counter is <= 0 and set obj=NULL only in this case.


Generally, all shogun C++ Objects are prefixed with C, e.g. CSVM and derived from
CSGObject. Since variables in the upper class hierarchy, need to be initialized
upon construction of the object, the constructor of base class needs to be
called in the constructor, e.g. CSVM calls CKernelMachine, CKernelMachine calls
CClassifier which finally calls CSGObject.

For example if you implement your own SVM called MySVM you would in the
constructor do

\verbatim
class MySVM : public CSVM
{
    MySVM( ) : CSVM()
    {

    }

    virtual ~MySVM()
    {

    }
};
\endverbatim

Also make sure that you define the destructor \b virtual.

We are now going to define our own kernel, a linear like kernel defined on
standard double precision floating point vectors. We define it as

\f$k({\bf x}, {\bf x'}) = \sum_{i=1}^D x_i \cdot x'_{D-i+1}\f$

where D is the dimensionality of the data.
To implement this kernel we need to derive a class say CReverseLinearKernel from
CSimpleKernel<float64_t> (for strings it would be CStringKernel, for sparse
features CSparseKernel).

Essentially we only need to overload the CKernel::compute() function with our
own implementation of compute. All the rest gets empty defaults. An example for our compute() function could be


\verbatim
virtual float64_t compute(int32_t idx_a, int32_t idx_b)
{
    int32_t alen, blen;
    bool afree, bfree;

    float64_t* avec= 
        ((CSimpleFeatures<float64_t>*) lhs)->get_feature_vector(idx_a, alen, afree);
    float64_t* bvec=
        ((CSimpleFeatures<float64_t>*) rhs)->get_feature_vector(idx_b, blen, bfree);

    ASSERT(alen==blen);

    float64_t result=0;
    for (int32_t i=0; i<alen; i++)
        result+=avec[i]*bvec[alen-i-1];

    ((CSimpleFeatures<float64_t>*) lhs)->free_feature_vector(avec, idx_a, afree);
    ((CSimpleFeatures<float64_t>*) rhs)->free_feature_vector(bvec, idx_b, bfree);

    return result;
}
\endverbatim

So for two indices idx_a (for vector a) and idx_b (for vector b) we obtain the
corresponding pointers to the feature vectors avec and bvec, do our two line
computation (for loop in the middle) and ``free'' the feature vectors again. It
should be noted that in most cases getting the feature vector is actually a
single memory access operation (and free_feature_vector is a nop in this case).
However, when preprocessor objects are attached to the feature object they
could potentially perform on-the-fly processing operations.

A complete, fully working example could look like this

\verbinclude kernel_revlin.cpp

As you notice only a few other functions are defined returning name of the
object, and object id and allow for loading/saving of kernel initialization
data. No magic really, the same holds when you want to incorporate a new
SVM (derive from CSVM or CLinearClassifier if it is a linear SVM) or create new
feature objects (derive from CFeatures or CSimpleFeatures, CStringFeatures or
CSparseFeatures). For the SVM you would only have to override the CSVM::train()
function, parameter settings like epsilon, C  and evaluating SVMs is done
naturally by the CSVM base class.

In case you would want to integrate this into shoguns
modular interfaces, all you have to do is to put this class in a header file
and to include the header file in the corresponding .i file (in this case
src/modular/Kernel.i). It is easies to search for a similarly wrapped object
and just fill in the same three lines: in the %{ %} block (that is ignored by
swig - the program we use to generate the modular python/octave interface
wrappers)

\verbatim
%{
#include <shogun/kernel/ReverseLinearKernel.h>
%}
\endverbatim

then remove the C prefix (if you had one)

\verbatim
%rename(ReverseLinearKernel) CReverseLinearKernel;
\endverbatim

and finally tell swig to wrap all functions found in the header

\verbatim
%include <shogun/kernel/ReverseLinearKernel.h>
\endverbatim

In case you got your object working we will happily integrate it into shogun
provided you follow a number of basic coding conventions detailed in \subpage devel (see
FORMATTING for formatting instructions, MACROS on how to use and name macros,
TYPES on which types to use, FUNCTIONS on how functions should look like and
NAMING CONVENTIONS for the naming scheme. Note that in case you change the API
in a way that breaks ABI compatibility you need to increase the major number of
the libshogun soname (see \subpage soname ).

*/
