source/libtomo/misc/median_filt3d.c
// Copyright (c) 2015, UChicago Argonne, LLC. All rights reserved.
// Copyright 2015. UChicago Argonne, LLC. This software was produced
// under U.S. Government contract DE-AC02-06CH11357 for Argonne National
// Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
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// C-module for median filtration and dezingering (3D and 2D cases)
// Original author: Daniil Kazantsev, Diamond Light Source Ltd.
#include <math.h>
#include <omp.h>
#include <stdlib.h>
#include <string.h>
#include "libtomo/median_filt3d.h"
int floatcomp(const void* elem1, const void* elem2)
{
if(*(const float*)elem1 < *(const float*)elem2)
return -1;
return *(const float*)elem1 > *(const float*)elem2;
}
int uint16comp(const void* elem1, const void* elem2)
{
if(*(const unsigned short*)elem1 < *(const unsigned short*)elem2)
return -1;
return *(const unsigned short*)elem1 > *(const unsigned short*)elem2;
}
void
medfilt3D_float(float* Input, float* Output, int radius, int sizefilter_total,
float mu_threshold, long i, long j, long k, size_t index, size_t dimX,
size_t dimY, size_t dimZ)
{
float* ValVec;
long i_m;
long j_m;
long k_m;
long i1;
long j1;
long k1;
long long counter;
int midval;
size_t index1;
midval = (sizefilter_total / 2);
ValVec = (float*) calloc(sizefilter_total, sizeof(float));
/* filling the allocated vector with the neighbouring values */
counter = 0LL;
for(i_m = -radius; i_m <= radius; i_m++)
{
i1 = i + i_m;
if((i1 < 0) || (i1 >= dimX))
i1 = i;
for(j_m = -radius; j_m <= radius; j_m++)
{
j1 = j + j_m;
if((j1 < 0) || (j1 >= dimY))
j1 = j;
for(k_m = -radius; k_m <= radius; k_m++)
{
k1 = k + k_m;
if((k1 < 0) || (k1 >= dimZ))
k1 = k;
index1 = dimX * dimY * (size_t)k1 + (size_t)j1 * dimX + (size_t)i1;
ValVec[counter] = Input[index1];
counter++;
}
}
}
qsort(ValVec, sizefilter_total, sizeof(float), floatcomp);
if(mu_threshold == 0.0F)
{
/* perform median filtration */
Output[index] = ValVec[midval];
}
else
{
/* perform dezingering */
if(fabsf(Input[index] - ValVec[midval]) >= mu_threshold)
Output[index] = ValVec[midval];
}
free(ValVec);
}
void
medfilt2D_float(float* Input, float* Output, int radius, int sizefilter_total,
float mu_threshold, long i, long j, size_t index, size_t dimX, size_t dimY)
{
float* ValVec;
long i_m;
long j_m;
long i1;
long j1;
long long counter;
int midval;
size_t index1;
midval = (sizefilter_total / 2);
ValVec = (float*) calloc(sizefilter_total, sizeof(float));
/* filling the allocated vector with the neighbouring values */
counter = 0LL;
for(i_m = -radius; i_m <= radius; i_m++)
{
i1 = i + i_m;
if((i1 < 0) || (i1 >= dimX))
i1 = i;
for(j_m = -radius; j_m <= radius; j_m++)
{
j1 = j + j_m;
if((j1 < 0) || (j1 >= dimY))
j1 = j;
index1 = (size_t)(j1) * dimX + (size_t)(i1);
ValVec[counter] = Input[index1];
counter++;
}
}
qsort(ValVec, sizefilter_total, sizeof(float), floatcomp);
if(mu_threshold == 0.0F)
{
/* perform median filtration */
Output[index] = ValVec[midval];
}
else
{
/* perform dezingering */
if(fabsf(Input[index] - ValVec[midval]) >= mu_threshold)
Output[index] = ValVec[midval];
}
free(ValVec);
}
void
medfilt3D_uint16(unsigned short* Input, unsigned short* Output, int radius,
int sizefilter_total, float mu_threshold, long i, long j, long k,
size_t index, size_t dimX, size_t dimY, size_t dimZ)
{
unsigned short* ValVec;
long i_m;
long j_m;
long k_m;
long i1;
long j1;
long k1;
long long counter;
int midval;
size_t index1;
midval = (sizefilter_total / 2);
ValVec = (unsigned short*) calloc(sizefilter_total, sizeof(unsigned short));
/* filling the allocated vector with the neighbouring values */
counter = 0LL;
for(i_m = -radius; i_m <= radius; i_m++)
{
i1 = i + i_m;
if((i1 < 0) || (i1 >= dimX))
i1 = i;
for(j_m = -radius; j_m <= radius; j_m++)
{
j1 = j + j_m;
if((j1 < 0) || (j1 >= dimY))
j1 = j;
for(k_m = -radius; k_m <= radius; k_m++)
{
k1 = k + k_m;
if((k1 < 0) || (k1 >= dimZ))
k1 = k;
index1 = dimX * dimY * (size_t)k1 + (size_t)j1 * dimX + (size_t)i1;
ValVec[counter] = Input[index1];
counter++;
}
}
}
qsort(ValVec, sizefilter_total, sizeof(unsigned short), uint16comp);
if(mu_threshold == 0.0F)
{
/* perform median filtration */
Output[index] = ValVec[midval];
}
else
{
/* perform dezingering */
if(abs(Input[index] - ValVec[midval]) >= mu_threshold)
Output[index] = ValVec[midval];
}
free(ValVec);
}
void
medfilt2D_uint16(unsigned short* Input, unsigned short* Output, int radius,
int sizefilter_total, float mu_threshold, long i, long j, size_t index,
size_t dimX, size_t dimY)
{
unsigned short* ValVec;
long i_m;
long j_m;
long i1;
long j1;
long long counter;
int midval;
size_t index1;
midval = (sizefilter_total / 2);
ValVec = (unsigned short*) calloc(sizefilter_total, sizeof(unsigned short));
/* filling the allocated vector with the neighbouring values */
counter = 0LL;
for(i_m = -radius; i_m <= radius; i_m++)
{
i1 = i + i_m;
if((i1 < 0) || (i1 >= dimX))
i1 = i;
for(j_m = -radius; j_m <= radius; j_m++)
{
j1 = j + j_m;
if((j1 < 0) || (j1 >= dimY))
j1 = j;
index1 = (size_t)(j1) * dimX + (size_t)(i1);
ValVec[counter] = Input[index1];
counter++;
}
}
qsort(ValVec, sizefilter_total, sizeof(unsigned short), uint16comp);
if(mu_threshold == 0.0F)
{
/* perform median filtration */
Output[index] = ValVec[midval];
}
else
{
/* perform dezingering */
if(abs(Input[index] - ValVec[midval]) >= mu_threshold)
Output[index] = ValVec[midval];
}
free(ValVec);
}
DLL int
medianfilter_main_float(float* Input, float* Output, int radius, float mu_threshold,
int ncores, int dimX, int dimY, int dimZ)
{
int sizefilter_total;
int diameter;
long i;
long j;
long k;
size_t index;
size_t totalvoxels;
totalvoxels = (size_t)(dimX) * (size_t)(dimY) * (size_t)(dimZ);
diameter = (2 * radius + 1); /* diameter of the filter's kernel */
/* dealing here with a custom given number of cpu threads */
if(ncores > 0)
{
// Explicitly disable dynamic teams
omp_set_dynamic(0);
// Use a number of threads for all consecutive parallel regions
omp_set_num_threads(ncores);
}
if(dimZ == 0)
/* 2D filtering */
{
sizefilter_total = (int) (powf(diameter, 2));
#pragma omp parallel for shared(Input, Output) private(i, j, index)
for(j = 0; j < dimY; j++)
{
for(i = 0; i < dimX; i++)
{
index = (size_t)(j) * dimX + (size_t)(i);
medfilt2D_float(Input, Output, radius, sizefilter_total, mu_threshold, i,
j, index, (size_t) dimX, (size_t) dimY);
}
}
}
else
/* 3D filtering */
{
sizefilter_total = (int) (powf(diameter, 3));
#pragma omp parallel for shared(Input, Output) private(i, j, k, index)
for(k = 0; k < dimZ; k++)
{
for(j = 0; j < dimY; j++)
{
for(i = 0; i < dimX; i++)
{
index = dimX * dimY * (size_t)(k) + (size_t)(j) * dimX + (size_t)(i);
medfilt3D_float(Input, Output, radius, sizefilter_total, mu_threshold,
i, j, k, index, (size_t) dimX, (size_t) dimY,
(size_t) dimZ);
}
}
}
}
return 0;
}
DLL int
medianfilter_main_uint16(unsigned short* Input, unsigned short* Output, int radius,
float mu_threshold, int ncores, int dimX, int dimY, int dimZ)
{
int sizefilter_total;
int diameter;
long i;
long j;
long k;
size_t index;
size_t totalvoxels;
totalvoxels = (size_t)(dimX) * (size_t)(dimY) * (size_t)(dimZ);
diameter = (2 * radius + 1); /* diameter of the filter's kernel */
/* dealing here with a custom given number of cpu threads */
if(ncores > 0)
{
// Explicitly disable dynamic teams
omp_set_dynamic(0);
// Use a number of threads for all consecutive parallel regions
omp_set_num_threads(ncores);
}
if(dimZ == 0)
/* 2D filtering */
{
sizefilter_total = (int) (powf(diameter, 2));
#pragma omp parallel for shared(Input, Output) private(i, j, index)
for(j = 0; j < dimY; j++)
{
for(i = 0; i < dimX; i++)
{
index = (size_t)(j) * dimX + (size_t)(i);
medfilt2D_uint16(Input, Output, radius, sizefilter_total, mu_threshold, i,
j, index, (size_t) dimX, (size_t) dimY);
}
}
}
else
/* 3D filtering */
{
sizefilter_total = (int) (powf(diameter, 3));
#pragma omp parallel for shared(Input, Output) private(i, j, k, index)
for(k = 0; k < dimZ; k++)
{
for(j = 0; j < dimY; j++)
{
for(i = 0; i < dimX; i++)
{
index = dimX * dimY * (size_t)(k) + (size_t)(j) * dimX + (size_t)(i);
medfilt3D_uint16(Input, Output, radius, sizefilter_total,
mu_threshold, i, j, k, index,(size_t) dimX,
(size_t)dimY, (size_t)dimZ);
}
}
}
}
return 0;
}