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/*
* filters.c
*
* Image filtering
*
* Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2020 Thomas White <taw@physics.org>
* 2013 Anton Barty <anton.barty@desy.de>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <libcrystfel-config.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include <gsl/gsl_statistics_int.h>
#include <gsl/gsl_blas.h>
#include "image.h"
/** \file filters.h */
static void filter_noise_in_panel(float *data, int width, int height)
{
int x, y;
for ( y=0; y<height; y++ ) {
for ( x=0; x<width; x++ ) {
int dx, dy;
float val = data[x+width*y];
/* This isn't really the right thing to do at the edges,
* but this filter is so horrible it's unlikely to matter. */
if ( (x==0) || (x==width-1)
|| (y==0) || (y==height-1) ) {
if ( val < 0 ) {
data[x+width*y] = 0.0;
}
continue;
}
for ( dy=-1; dy<=+1; dy++ ) {
for ( dx=-1; dx<=+1; dx++ ) {
if ( data[(x+dx)+width*(y+dy)] ) val = 0.0;
}
}
data[x+width*y] = val;
}
}
}
void filter_noise(struct image *image)
{
int i;
for ( i=0; i<image->detgeom->n_panels; i++ ) {
struct detgeom_panel *p = &image->detgeom->panels[i];
filter_noise_in_panel(image->dp[i], p->w, p->h);
}
}
/* Force the linker to bring in CBLAS to make GSL happy */
void filters_fudge_gslcblas()
{
STATUS("%p\n", cblas_sgemm);
}
#define SWAP(a,b) { float t=(a);(a)=(b);(b)=t; }
static float kth_smallest(float *a, int n, int k)
{
long l, m;
l = 0;
m = n-1;
while ( l < m ) {
long i, j;
float x;
x=a[k];
i=l;
j=m;
do {
while (a[i]<x) i++;
while (x<a[j]) j--;
if ( i<=j ) {
SWAP(a[i],a[j]);
i++;
j--;
}
} while (i<=j);
if ( j<k ) l = i;
if ( k<i ) m = j;
}
return a[k];
}
#undef SWAP
void filter_median(struct image *image, int size)
{
int counter;
int nn;
float *buffer;
int pn;
if ( size <= 0 ) return;
nn = 2*size+1;
nn = nn*nn;
/* "localBg" is way too big, but guaranteed big enough */
buffer = calloc(nn, sizeof(float));
if ( buffer == NULL ) {
ERROR("Failed to allocate LB buffer.\n");
return;
}
/* Determine local background
* (median over window width either side of current pixel) */
for ( pn=0; pn<image->detgeom->n_panels; pn++ ) {
int fs, ss;
int i;
struct detgeom_panel *p;
float *localBg;
p = &image->detgeom->panels[pn];
localBg = calloc(p->w*p->h, sizeof(float));
if ( localBg == NULL ) {
ERROR("Failed to allocate LB buffer.\n");
return;
}
for ( ss=0; ss<p->h; ss++ ) {
for ( fs=0; fs<p->w; fs++ ) {
int ifs, iss;
counter = 0;
// Loop over median window
for ( iss=-size; iss<=size; iss++ ) {
for ( ifs=-size; ifs<=size; ifs++ ) {
int idx;
if ( (fs+ifs) < 0 ) continue;
if ( (fs+ifs) >= p->w ) continue;
if ( (ss+iss) < 0 ) continue;
if ( (ss+iss) >= p->h ) continue;
idx = fs+ifs + (ss+iss)*p->w;
buffer[counter++] = image->dp[pn][idx];
}
}
// Find median value
localBg[fs+p->w*ss] = kth_smallest(buffer, counter,
counter/2);
}
}
/* Do the background subtraction */
for ( i=0; i<p->w*p->h; i++ ) {
image->dp[pn][i] -= localBg[i];
}
free(localBg);
}
free(buffer);
}
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