MeanShiftFilter Class Reference

#include <mean_shift.h>

Inheritance diagram for MeanShiftFilter:

Collaboration diagram for MeanShiftFilter:

Public Member Functions
void	readParams (XmippProgram *program)
void	apply (MultidimArray< double > &img)
Public Member Functions inherited from XmippFilter
virtual	~XmippFilter ()
virtual void	show ()

Static Public Member Functions
static void	defineParams (XmippProgram *program)

Public Attributes
double	sigma_r
double	sigma_s
int	iters
int	numThreads
bool	fast
bool	save_iters
int	verbose

Detailed Description

Parameters for denoise program

Definition at line 37 of file mean_shift.h.

Member Function Documentation

apply()

void MeanShiftFilter::apply ( MultidimArray< double > &  img )

virtual

Apply the filter

Implements XmippFilter.

Definition at line 313 of file mean_shift.cpp.

{
    MultidimArray<double> output(input);

    auto * th_ids = new pthread_t[numThreads];
    auto * th_args = new ThreadProcessPlaneArgs[numThreads];

    for( int iter = 0 ; iter < iters ; ++iter )
    {
      if (verbose)
        std::cout << formatString("Running iteration %d/%d", iter+1, iters) << std::endl;

        for( int nt = 0; nt < numThreads ; nt++ )
        {
            th_args[nt].myID = nt;
            th_args[nt].numThreads = numThreads;
            th_args[nt].sigma_s = sigma_s;
            th_args[nt].sigma_r = sigma_r;
            th_args[nt].input = &input;
            th_args[nt].output = &output;
            th_args[nt].fast = fast;

            pthread_create( (th_ids+nt), nullptr, thread_process_plane, (void *)(th_args+nt));
        }

        for( int nt = 0; nt < numThreads ; nt++ )
        {
            pthread_join( *(th_ids+nt), nullptr);
        }

        if( save_iters )
        {
            FileName fn_aux = "xxx"; //fixme
            fn_aux = fn_aux.insertBeforeExtension( std::string("_iter_") + integerToString(iter) );

            if (verbose)
              std::cout << "Saving intermidiate file: " << fn_aux << std::endl;

            output.write( fn_aux );
        }

        //update input for next iteration
        input = output;
    }
    delete[] th_ids;
    delete[] th_args;
}

defineParams()

void MeanShiftFilter::defineParams ( XmippProgram *  program )

static

Definition at line 288 of file mean_shift.cpp.

{
    program->addParamsLine("== Mean shift ==");
    program->addParamsLine("[--mean_shift <hr> <hs> <iter=1>] : Filter based on the mean-shift algorithm");
    program->addParamsLine("                                  :+ hs: Sigma for the range domain");
    program->addParamsLine("                                  :+ hr: Sigma for the spatial domain");
    program->addParamsLine("                                  :+ iter: Number of iterations to be used");
    program->addParamsLine("      alias -t;");
    program->addParamsLine("[--thr <n=1>]                     : Number of processing threads");
    program->addParamsLine("[--fast]                          : Use faster processing (avoid gaussian calculations)");
    program->addParamsLine("[--save_iters]                    : Save result image/volume for each iteration");

}

readParams()

void MeanShiftFilter::readParams ( XmippProgram *  program )

virtual

Read params from a program

Reimplemented from XmippFilter.

Definition at line 302 of file mean_shift.cpp.

{
    sigma_r = program->getDoubleParam("--mean_shift", 0);//hr
    sigma_s = program->getDoubleParam("--mean_shift", 1);//hs
    iters = program->getIntParam("--mean_shift", 2);//iters
    fast = program->checkParam("--fast");
    numThreads = program->getIntParam("--thr");
    save_iters = program->checkParam("--save_iters");
    verbose = program->verbose;
}

Member Data Documentation

fast

bool MeanShiftFilter::fast

Definition at line 42 of file mean_shift.h.

iters

int MeanShiftFilter::iters

Definition at line 41 of file mean_shift.h.

numThreads

int MeanShiftFilter::numThreads

Definition at line 41 of file mean_shift.h.

save_iters

bool MeanShiftFilter::save_iters

Definition at line 42 of file mean_shift.h.

sigma_r

double MeanShiftFilter::sigma_r

Definition at line 40 of file mean_shift.h.

sigma_s

double MeanShiftFilter::sigma_s

Definition at line 40 of file mean_shift.h.

verbose

int MeanShiftFilter::verbose

Verbosity used by denoiser. By default will be 0, programs using denoiser should set this

Definition at line 46 of file mean_shift.h.

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The documentation for this class was generated from the following files:

• xmipp/libraries/reconstruction/mean_shift.h
• xmipp/libraries/reconstruction/mean_shift.cpp