morphology.cpp File Reference

#include "morphology.h"
#include "filters.h"
#include <vector>

Include dependency graph for morphology.cpp:

Go to the source code of this file.

Functions
void	dilate2D_step (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count)
void	erode2D_step (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count)
void	dilate2D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	erode2D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	closing2D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	opening2D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	border (const MultidimArray< double > &img, MultidimArray< double > &border)
void	simplify_border (const MultidimArray< double > &border, MultidimArray< double > &simplified_border)
void	random_convex_hull (const MultidimArray< double > &img, MultidimArray< double > &hull, long N)
void	dilate3D_step (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count)
void	erode3D_step (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count)
void	dilate3D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	erode3D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	closing3D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	opening3D (const MultidimArray< double > &in, MultidimArray< double > &out, int neig, int count, int size)
void	dilate3D (const MultidimArray< double > &in, const MultidimArray< double > &structuringElement, MultidimArray< double > &out)
void	erode3D (const MultidimArray< double > &in, const MultidimArray< double > &structuringElement, MultidimArray< double > &out)
void	sharpening (const MultidimArray< double > &in, double width, double strength, MultidimArray< double > &out)

Function Documentation

dilate2D_step()

void dilate2D_step	(	const MultidimArray< double > &	in,
		MultidimArray< double > &	out,
		int	neig,
		int	count
	)

Definition at line 32 of file morphology.cpp.

{
    double sum = 0;
    double dcount=count;
    for (int i = STARTINGY(in) + 1;i < FINISHINGY(in); i++)
        for (int j = STARTINGX(in) + 1;j < FINISHINGX(in); j++)
        {
            if (A2D_ELEM(in,i, j) == 0)
            {
                // 4-environment
                A2D_ELEM(out, i, j) = 0;
                sum = A2D_ELEM(in,i - 1, j) + A2D_ELEM(in,i + 1, j) +
                      A2D_ELEM(in,i, j - 1) + A2D_ELEM(in,i, j + 1);
                if (sum > dcount)
                { //change the value to foreground
                    A2D_ELEM(out, i, j) = 1;
                }
                else if (neig == 8)
                { //8-environment
                    sum +=A2D_ELEM(in,i - 1, j - 1) + A2D_ELEM(in,i - 1, j + 1) +
                          A2D_ELEM(in,i + 1, j - 1) + A2D_ELEM(in,i + 1, j + 1);
                    if (sum > dcount)
                    { //change the value to foreground
                        A2D_ELEM(out, i, j) = 1;
                    }
                }
            }
            else
            {
                A2D_ELEM(out, i, j) = A2D_ELEM(in,i, j);
            }
        }
}

dilate3D_step()

void dilate3D_step	(	const MultidimArray< double > &	in,
		MultidimArray< double > &	out,
		int	neig,
		int	count
	)

Definition at line 290 of file morphology.cpp.

{
    int sum = 0;
    for (int k = STARTINGZ(in) + 1;k < FINISHINGZ(in); k++)
        for (int i = STARTINGY(in) + 1;i < FINISHINGY(in); i++)
            for (int j = STARTINGX(in) + 1;j < FINISHINGX(in); j++)
            {
                if (A3D_ELEM(in,k, i, j) == 0)
                {
                    // 6-environment
                    A3D_ELEM(out,k, i, j) = 0;
                    sum = (int)(A3D_ELEM(in,k - 1, i, j) + A3D_ELEM(in,k + 1, i, j) +
                            A3D_ELEM(in,k, i - 1, j) + A3D_ELEM(in,k, i + 1, j)
                                + A3D_ELEM(in,k, i, j - 1) + A3D_ELEM(in,k, i, j + 1));
                    if (sum > count)
                    { //change the value to foreground
                        A3D_ELEM(out,k, i, j) = 1;
                    }
                    else if (neig == 18)
                    { //18-environment
                        sum = (int)(sum + A3D_ELEM(in,k - 1, i, j - 1) + A3D_ELEM(in,k - 1, i, j + 1) + A3D_ELEM(in,k + 1, i, j - 1) + A3D_ELEM(in,k + 1, i, j + 1) +
                                    A3D_ELEM(in,k, i + 1, j + 1) + A3D_ELEM(in,k, i + 1, j - 1) + A3D_ELEM(in,k, i - 1, j + 1) + A3D_ELEM(in,k, i - 1, j - 1) +
                                    A3D_ELEM(in,k - 1, i + 1, j) + A3D_ELEM(in,k - 1, i - 1, j) + A3D_ELEM(in,k + 1, i + 1, j) + A3D_ELEM(in,k + 1, i - 1, j));
                        if (sum > count)
                        { //change the value to foreground
                            A3D_ELEM(out,k, i, j) = 1;
                        }
                    }
                    else if (neig == 26)
                    { //26-environment
                        sum = (int)(sum + A3D_ELEM(in,k - 1, i + 1, j + 1) + A3D_ELEM(in,k - 1, i + 1, j - 1) +
                                    A3D_ELEM(in,k - 1, i - 1, j + 1) + A3D_ELEM(in,k - 1, i - 1, j - 1) +
                                    A3D_ELEM(in,k + 1, i + 1, j + 1) + A3D_ELEM(in,k + 1, i + 1, j - 1) +
                                    A3D_ELEM(in,k + 1, i - 1, j + 1) + A3D_ELEM(in,k + 1, i - 1, j - 1));
                        if (sum > count)
                        { //change the value to foreground
                            A3D_ELEM(out,k, i, j) = 1;
                        }
                    }

                }
                else
                {
                    A3D_ELEM(out,k, i, j) = A3D_ELEM(in,k, i, j);
                }
            }
}

erode2D_step()

void erode2D_step	(	const MultidimArray< double > &	in,
		MultidimArray< double > &	out,
		int	neig,
		int	count
	)

Definition at line 67 of file morphology.cpp.

{
    double dcount=count;
    double sum;
    for (int i = STARTINGY(in) + 1;i < FINISHINGY(in); i++)
        for (int j = STARTINGX(in) + 1;j < FINISHINGX(in); j++)
        {
            if (A2D_ELEM(in, i, j) == 1)
            {
                // 4-environment
                A2D_ELEM(out,i, j) = 1;
                sum = A2D_ELEM(in,i - 1, j) + A2D_ELEM(in,i + 1, j) +
                      A2D_ELEM(in, i, j - 1) + A2D_ELEM(in, i, j + 1);
                if ((4 - sum) > dcount)
                { //change the value to background
                    A2D_ELEM(out, i, j) = 0;
                }
                else if (neig == 8)
                { //8-environment
                    sum += A2D_ELEM(in, i - 1, j - 1) + A2D_ELEM(in, i - 1, j + 1) +
                           A2D_ELEM(in, i + 1, j - 1) + A2D_ELEM(in, i + 1, j + 1);
                    if ((neig - sum) > dcount)
                    { //change the value to background
                        A2D_ELEM(out,i, j) = 0;
                    }
                }
            }
            else
            {
                A2D_ELEM(out, i, j) = A2D_ELEM(in, i, j);
            }
        }
}

erode3D_step()

void erode3D_step	(	const MultidimArray< double > &	in,
		MultidimArray< double > &	out,
		int	neig,
		int	count
	)

Definition at line 339 of file morphology.cpp.

{
    int sum = 0;
    for (int k = STARTINGZ(in) + 1;k < FINISHINGZ(in); k++)
        for (int i = STARTINGY(in) + 1;i < FINISHINGY(in); i++)
            for (int j = STARTINGX(in) + 1;j < FINISHINGX(in); j++)
            {
                if (A3D_ELEM(in,k, i, j) == 1)
                {
                    // 6-environment
                    A3D_ELEM(out,k, i, j) = 1;

                    sum = (int)(A3D_ELEM(in,k - 1, i, j) + A3D_ELEM(in,k + 1, i, j) + A3D_ELEM(in,k, i - 1, j) + A3D_ELEM(in,k, i + 1, j)
                                + A3D_ELEM(in,k, i, j - 1) + A3D_ELEM(in,k, i, j + 1));
                    if ((6 - sum) > count)
                    { //change the value to background
                        A3D_ELEM(out,k, i, j) = 0;
                    }
                    else if (neig == 18)
                    { //18-environment
                        sum = (int)(sum + A3D_ELEM(in,k - 1, i, j - 1) + A3D_ELEM(in,k - 1, i, j + 1) + A3D_ELEM(in,k + 1, i, j - 1) + A3D_ELEM(in,k + 1, i, j + 1) +
                                    A3D_ELEM(in,k, i + 1, j + 1) + A3D_ELEM(in,k, i + 1, j - 1) + A3D_ELEM(in,k, i - 1, j + 1) + A3D_ELEM(in,k, i - 1, j - 1) +
                                    A3D_ELEM(in,k - 1, i + 1, j) + A3D_ELEM(in,k - 1, i - 1, j) + A3D_ELEM(in,k + 1, i + 1, j) + A3D_ELEM(in,k + 1, i - 1, j));
                        if ((neig - sum) > count)
                        { //change the value to background
                            A3D_ELEM(out,k, i, j) = 0;
                        }
                    }
                    else if (neig == 26)
                    { //26-environment
                        sum = (int)(sum + A3D_ELEM(in,k - 1, i, j - 1) + A3D_ELEM(in,k - 1, i, j + 1) + A3D_ELEM(in,k + 1, i, j - 1) + A3D_ELEM(in,k + 1, i, j + 1) +
                                    A3D_ELEM(in,k, i + 1, j + 1) + A3D_ELEM(in,k, i + 1, j - 1) + A3D_ELEM(in,k, i - 1, j + 1) + A3D_ELEM(in,k, i - 1, j - 1) +
                                    A3D_ELEM(in,k - 1, i + 1, j) + A3D_ELEM(in,k - 1, i - 1, j) + A3D_ELEM(in,k + 1, i + 1, j) + A3D_ELEM(in,k + 1, i - 1, j) +
                                    A3D_ELEM(in,k - 1, i + 1, j + 1) + A3D_ELEM(in,k - 1, i + 1, j - 1) +
                                    A3D_ELEM(in,k - 1, i - 1, j + 1) + A3D_ELEM(in,k - 1, i - 1, j - 1) +
                                    A3D_ELEM(in,k + 1, i + 1, j + 1) + A3D_ELEM(in,k + 1, i + 1, j - 1) +
                                    A3D_ELEM(in,k + 1, i - 1, j + 1) + A3D_ELEM(in,k + 1, i - 1, j - 1));

                        if ((neig - sum) > count)
                        { //change the value to background
                            A3D_ELEM(out,k, i, j) = 0;
                        }
                    }

                }
                else
                {
                    A3D_ELEM(out,k, i, j) = A3D_ELEM(in,k, i, j);
                }
            }

}