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EMReadApplication.hpp
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Sat, Nov 16, 11:38

EMReadApplication.hpp
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#ifndef EMREADAPPLICATION_HPP
#define EMREADAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <string>
/*!
* \brief The EMReadApplication class is a wrapper around an EMRead
* instance creating an autonomous application to classify data by directly
* passing all the options and parameters from the command line.
*/
class EMReadApplication: public ApplicationInterface
{
public:
EMReadApplication() = delete ;
EMReadApplication(const EMReadApplication& app) = delete ;
/*!
* \brief Constructs an object from the command line
* options.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
*/
EMReadApplication(int argn, char** argv) ;
/*!
* \brief Runs the application. The data are classified
* using the given settings and the posterior probability
* matrix is returned through the stdout.
* The matrix is a 4D matrix with dimensions :
* regions, class, shift flip.
* \return an exit code EXIT_SUCCESS or EXIT_FAILURE
* to return to the OS.
*/
virtual int run() override ;
private:
/*!
* \brief Parses the program command line options and
* sets the object field accordingly.
* If the help option is detected, the "runnable"
* field is set to false and subsequent calls to
* run() will produce nothing.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
* \throw std::invalid_argument if an error is found
* in the program options.
*/
void parseOptions(int argn, char** argv) ;
/*!
* \brief the paths to the file containing the read
* density data.
*/
std::string file_read ;
/*!
* \brief the path to the file in which the probability
* matrix will be saved.
*/
std::string file_out ;
/*!
* \brief the number of classes to partition the data into.
*/
size_t n_class ;
/*!
* \brief the number of iterations allowed.
*/
size_t n_iter ;
/*!
* \brief the shifting freedom.
*/
size_t n_shift ;
/*!
* \brief whether flipping freedom is allowed.
*/
bool flip ;
/*!
* \brief the number of threads.
*/
size_t n_threads ;
/*!
* \brief a seed to initialise the random number generator.
*/
std::string seed ;
/*!
* \brief a flag indicating whether the core of run() can be
* run or not.
*/
bool runnable ;
} ;
#endif // EMREADAPPLICATION_HPP

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