520 lines
18 KiB
C

/*
* This file is part of the loccorr project.
* Copyright 2021 Edward V. Emelianov <edward.emelianoff@gmail.com>.
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
// FOR MEDIATOR:
// Copyright (c) 2011 ashelly.myopenid.com under <http://www.opensource.org/licenses/mit-license>
// TODO: resolve problem with borders
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <usefull_macros.h>
#include "imagefile.h"
#include "median.h"
#define ELEM_SWAP(a, b) {register Imtype t = a; a = b; b = t;}
#define PIX_SORT(a, b) {if (p[a] > p[b]) ELEM_SWAP(p[a], p[b]);}
static Imtype opt_med2(Imtype *p){
return (p[0] + p[1]) * 0.5;
}
static Imtype opt_med3(Imtype *p){
PIX_SORT(0, 1); PIX_SORT(1, 2); PIX_SORT(0, 1);
return(p[1]) ;
}
static Imtype opt_med4(Imtype *p){
PIX_SORT(0, 2); PIX_SORT(1, 3);
PIX_SORT(0, 1); PIX_SORT(2, 3);
return(p[1] + p[2]) * 0.5;
}
static Imtype opt_med5(Imtype *p){
PIX_SORT(0, 1); PIX_SORT(3, 4); PIX_SORT(0, 3);
PIX_SORT(1, 4); PIX_SORT(1, 2); PIX_SORT(2, 3) ;
PIX_SORT(1, 2);
return(p[2]) ;
}
// even values are from "FAST, EFFICIENT MEDIAN FILTERS WITH EVEN LENGTH WINDOWS", J.P. HAVLICEK, K.A. SAKADY, G.R.KATZ
static Imtype opt_med6(Imtype *p){
PIX_SORT(1, 2); PIX_SORT(3, 4);
PIX_SORT(0, 1); PIX_SORT(2, 3); PIX_SORT(4, 5);
PIX_SORT(1, 2); PIX_SORT(3, 4);
PIX_SORT(0, 1); PIX_SORT(2, 3); PIX_SORT(4, 5);
PIX_SORT(1, 2); PIX_SORT(3, 4);
return ( p[2] + p[3] ) * 0.5;
}
static Imtype opt_med7(Imtype *p){
PIX_SORT(0, 5); PIX_SORT(0, 3); PIX_SORT(1, 6);
PIX_SORT(2, 4); PIX_SORT(0, 1); PIX_SORT(3, 5);
PIX_SORT(2, 6); PIX_SORT(2, 3); PIX_SORT(3, 6);
PIX_SORT(4, 5); PIX_SORT(1, 4); PIX_SORT(1, 3);
PIX_SORT(3, 4); return (p[3]);
}
// optimal Batcher's sort for 8 elements (http://myopen.googlecode.com/svn/trunk/gtkclient_tdt/include/fast_median.h)
static Imtype opt_med8(Imtype *p){
PIX_SORT(0, 4); PIX_SORT(1, 5); PIX_SORT(2, 6);
PIX_SORT(3, 7); PIX_SORT(0, 2); PIX_SORT(1, 3);
PIX_SORT(4, 6); PIX_SORT(5, 7); PIX_SORT(2, 4);
PIX_SORT(3, 5); PIX_SORT(0, 1); PIX_SORT(2, 3);
PIX_SORT(4, 5); PIX_SORT(6, 7); PIX_SORT(1, 4);
PIX_SORT(3, 6);
return(p[3] + p[4]) * 0.5;
}
static Imtype opt_med9(Imtype *p){
PIX_SORT(1, 2); PIX_SORT(4, 5); PIX_SORT(7, 8);
PIX_SORT(0, 1); PIX_SORT(3, 4); PIX_SORT(6, 7);
PIX_SORT(1, 2); PIX_SORT(4, 5); PIX_SORT(7, 8);
PIX_SORT(0, 3); PIX_SORT(5, 8); PIX_SORT(4, 7);
PIX_SORT(3, 6); PIX_SORT(1, 4); PIX_SORT(2, 5);
PIX_SORT(4, 7); PIX_SORT(4, 2); PIX_SORT(6, 4);
PIX_SORT(4, 2); return(p[4]);
}
static Imtype opt_med16(Imtype *p){
PIX_SORT(0, 8); PIX_SORT(1, 9); PIX_SORT(2, 10); PIX_SORT(3, 11);
PIX_SORT(4, 12); PIX_SORT(5, 13); PIX_SORT(6, 14); PIX_SORT(7, 15);
PIX_SORT(0, 4); PIX_SORT(1, 5); PIX_SORT(2, 6); PIX_SORT(3, 7);
PIX_SORT(8, 12); PIX_SORT(9, 13); PIX_SORT(10, 14); PIX_SORT(11, 15);
PIX_SORT(4, 8); PIX_SORT(5, 9); PIX_SORT(6, 10); PIX_SORT(7, 11);
PIX_SORT(0, 2); PIX_SORT(1, 3); PIX_SORT(4, 6); PIX_SORT(5, 7);
PIX_SORT(8, 10); PIX_SORT(9, 11); PIX_SORT(12, 14); PIX_SORT(13, 15);
PIX_SORT(2, 8); PIX_SORT(3, 9); PIX_SORT(6, 12); PIX_SORT(7, 13);
PIX_SORT(2, 4); PIX_SORT(3, 5); PIX_SORT(6, 8); PIX_SORT(7, 9);
PIX_SORT(10, 12); PIX_SORT(11, 13); PIX_SORT(0, 1); PIX_SORT(2, 3);
PIX_SORT(4, 5); PIX_SORT(6, 7); PIX_SORT(8, 9); PIX_SORT(10, 11);
PIX_SORT(12, 13); PIX_SORT(14, 15); PIX_SORT(1, 8); PIX_SORT(3, 10);
PIX_SORT(5, 12); PIX_SORT(7, 14); PIX_SORT(5, 8); PIX_SORT(7, 10);
return (p[7] + p[8]) * 0.5;
}
static Imtype opt_med25(Imtype *p){
PIX_SORT(0, 1) ; PIX_SORT(3, 4) ; PIX_SORT(2, 4) ;
PIX_SORT(2, 3) ; PIX_SORT(6, 7) ; PIX_SORT(5, 7) ;
PIX_SORT(5, 6) ; PIX_SORT(9, 10) ; PIX_SORT(8, 10) ;
PIX_SORT(8, 9) ; PIX_SORT(12, 13); PIX_SORT(11, 13) ;
PIX_SORT(11, 12); PIX_SORT(15, 16); PIX_SORT(14, 16) ;
PIX_SORT(14, 15); PIX_SORT(18, 19); PIX_SORT(17, 19) ;
PIX_SORT(17, 18); PIX_SORT(21, 22); PIX_SORT(20, 22) ;
PIX_SORT(20, 21); PIX_SORT(23, 24); PIX_SORT(2, 5) ;
PIX_SORT(3, 6) ; PIX_SORT(0, 6) ; PIX_SORT(0, 3) ;
PIX_SORT(4, 7) ; PIX_SORT(1, 7) ; PIX_SORT(1, 4) ;
PIX_SORT(11, 14); PIX_SORT(8, 14) ; PIX_SORT(8, 11) ;
PIX_SORT(12, 15); PIX_SORT(9, 15) ; PIX_SORT(9, 12) ;
PIX_SORT(13, 16); PIX_SORT(10, 16); PIX_SORT(10, 13) ;
PIX_SORT(20, 23); PIX_SORT(17, 23); PIX_SORT(17, 20) ;
PIX_SORT(21, 24); PIX_SORT(18, 24); PIX_SORT(18, 21) ;
PIX_SORT(19, 22); PIX_SORT(8, 17) ; PIX_SORT(9, 18) ;
PIX_SORT(0, 18) ; PIX_SORT(0, 9) ; PIX_SORT(10, 19) ;
PIX_SORT(1, 19) ; PIX_SORT(1, 10) ; PIX_SORT(11, 20) ;
PIX_SORT(2, 20) ; PIX_SORT(2, 11) ; PIX_SORT(12, 21) ;
PIX_SORT(3, 21) ; PIX_SORT(3, 12) ; PIX_SORT(13, 22) ;
PIX_SORT(4, 22) ; PIX_SORT(4, 13) ; PIX_SORT(14, 23) ;
PIX_SORT(5, 23) ; PIX_SORT(5, 14) ; PIX_SORT(15, 24) ;
PIX_SORT(6, 24) ; PIX_SORT(6, 15) ; PIX_SORT(7, 16) ;
PIX_SORT(7, 19) ; PIX_SORT(13, 21); PIX_SORT(15, 23) ;
PIX_SORT(7, 13) ; PIX_SORT(7, 15) ; PIX_SORT(1, 9) ;
PIX_SORT(3, 11) ; PIX_SORT(5, 17) ; PIX_SORT(11, 17) ;
PIX_SORT(9, 17) ; PIX_SORT(4, 10) ; PIX_SORT(6, 12) ;
PIX_SORT(7, 14) ; PIX_SORT(4, 6) ; PIX_SORT(4, 7) ;
PIX_SORT(12, 14); PIX_SORT(10, 14); PIX_SORT(6, 7) ;
PIX_SORT(10, 12); PIX_SORT(6, 10) ; PIX_SORT(6, 17) ;
PIX_SORT(12, 17); PIX_SORT(7, 17) ; PIX_SORT(7, 10) ;
PIX_SORT(12, 18); PIX_SORT(7, 12) ; PIX_SORT(10, 18) ;
PIX_SORT(12, 20); PIX_SORT(10, 20); PIX_SORT(10, 12) ;
return (p[12]);
}
#undef PIX_SORT
#define PIX_SORT(a, b) {if (a > b) ELEM_SWAP(a, b);}
/**
* quick select - algo for approximate median calculation for array idata of size n
*/
static Imtype quick_select(Imtype *idata, int n){
int low, high;
int median;
int middle, ll, hh;
Imtype *arr = MALLOC(Imtype, n);
memcpy(arr, idata, n*sizeof(Imtype));
low = 0 ; high = n-1 ; median = (low + high) / 2;
for(;;){
if(high <= low) // One element only
break;
if(high == low + 1){ // Two elements only
PIX_SORT(arr[low], arr[high]) ;
break;
}
// Find median of low, middle and high Imtypes; swap into position low
middle = (low + high) / 2;
PIX_SORT(arr[middle], arr[high]) ;
PIX_SORT(arr[low], arr[high]) ;
PIX_SORT(arr[middle], arr[low]) ;
// Swap low Imtype (now in position middle) into position (low+1)
ELEM_SWAP(arr[middle], arr[low+1]) ;
// Nibble from each end towards middle, swapping Imtypes when stuck
ll = low + 1;
hh = high;
for(;;){
do ll++; while (arr[low] > arr[ll]);
do hh--; while (arr[hh] > arr[low]);
if(hh < ll) break;
ELEM_SWAP(arr[ll], arr[hh]) ;
}
// Swap middle Imtype (in position low) back into correct position
ELEM_SWAP(arr[low], arr[hh]) ;
// Re-set active partition
if (hh <= median) low = ll;
if (hh >= median) high = hh - 1;
}
Imtype ret = arr[median];
FREE(arr);
return ret;
}
#undef PIX_SORT
#undef ELEM_SWAP
/**
* calculate median of array idata with size n
*/
Imtype calc_median(Imtype *idata, int n){
if(!idata || n < 1){
WARNX("calc_median(): wrong dta"); return 0.;
}
typedef Imtype (*medfunc)(Imtype *p);
medfunc fn = NULL;
const medfunc fnarr[] = {opt_med2, opt_med3, opt_med4, opt_med5, opt_med6,
opt_med7, opt_med8, opt_med9};
if(n == 1) return *idata;
if(n < 10) fn = fnarr[n - 1];
else if(n == 16) fn = opt_med16;
else if(n == 25) fn = opt_med25;
if(fn){
return fn(idata);
}else{
return quick_select(idata, n);
}
}
#define ImtypeLess(a,b) ((a)<(b))
#define ImtypeMean(a,b) (((a)+(b))/2)
typedef struct Mediator_t{
Imtype* data; // circular queue of values
int* pos; // index into `heap` for each value
int* heap; // max/median/min heap holding indexes into `data`.
int N; // allocated size.
int idx; // position in circular queue
int ct; // count of Imtypes in queue
} Mediator;
/*--- Helper Functions ---*/
#define minCt(m) (((m)->ct-1)/2) //count of Imtypes in minheap
#define maxCt(m) (((m)->ct)/2) //count of Imtypes in maxheap
//returns 1 if heap[i] < heap[j]
inline int mmless(Mediator* m, int i, int j){
return ImtypeLess(m->data[m->heap[i]],m->data[m->heap[j]]);
}
//swaps Imtypes i&j in heap, maintains indexes
inline int mmexchange(Mediator* m, int i, int j){
int t = m->heap[i];
m->heap[i] = m->heap[j];
m->heap[j] = t;
m->pos[m->heap[i]] = i;
m->pos[m->heap[j]] = j;
return 1;
}
//swaps Imtypes i&j if i<j; returns true if swapped
inline int mmCmpExch(Mediator* m, int i, int j){
return (mmless(m,i,j) && mmexchange(m,i,j));
}
//maintains minheap property for all Imtypes below i/2.
void minSortDown(Mediator* m, int i){
for(; i <= minCt(m); i*=2){
if(i>1 && i < minCt(m) && mmless(m, i+1, i)) ++i;
if(!mmCmpExch(m,i,i/2)) break;
}
}
//maintains maxheap property for all Imtypes below i/2. (negative indexes)
void maxSortDown(Mediator* m, int i){
for(; i >= -maxCt(m); i*=2){
if(i<-1 && i > -maxCt(m) && mmless(m, i, i-1)) --i;
if(!mmCmpExch(m,i/2,i)) break;
}
}
//maintains minheap property for all Imtypes above i, including median
//returns true if median changed
int minSortUp(Mediator* m, int i){
while (i > 0 && mmCmpExch(m, i, i/2)) i /= 2;
return (i == 0);
}
//maintains maxheap property for all Imtypes above i, including median
//returns true if median changed
int maxSortUp(Mediator* m, int i){
while (i < 0 && mmCmpExch(m, i/2, i)) i /= 2;
return (i == 0);
}
/*--- Public Interface ---*/
//creates new Mediator: to calculate `nImtypes` running median.
//mallocs single block of memory, caller must free.
Mediator* MediatorNew(int nImtypes){
int size = sizeof(Mediator) + nImtypes*(sizeof(Imtype)+sizeof(int)*2);
Mediator* m = malloc(size);
m->data = (Imtype*)(m + 1);
m->pos = (int*) (m->data + nImtypes);
m->heap = m->pos + nImtypes + (nImtypes / 2); //points to middle of storage.
m->N = nImtypes;
m->ct = m->idx = 0;
while (nImtypes--){ //set up initial heap fill pattern: median,max,min,max,...
m->pos[nImtypes] = ((nImtypes+1)/2) * ((nImtypes&1)? -1 : 1);
m->heap[m->pos[nImtypes]] = nImtypes;
}
return m;
}
//Inserts Imtype, maintains median in O(lg nImtypes)
void MediatorInsert(Mediator* m, Imtype v){
int isNew=(m->ct<m->N);
int p = m->pos[m->idx];
Imtype old = m->data[m->idx];
m->data[m->idx]=v;
m->idx = (m->idx+1) % m->N;
m->ct+=isNew;
if(p>0){ //new Imtype is in minHeap
if (!isNew && ImtypeLess(old,v)) minSortDown(m,p*2);
else if (minSortUp(m,p)) maxSortDown(m,-1);
}else if (p<0){ //new Imtype is in maxheap
if (!isNew && ImtypeLess(v,old)) maxSortDown(m,p*2);
else if (maxSortUp(m,p)) minSortDown(m, 1);
}else{ //new Imtype is at median
if (maxCt(m)) maxSortDown(m,-1);
if (minCt(m)) minSortDown(m, 1);
}
}
//returns median Imtype (or average of 2 when Imtype count is even)
Imtype MediatorMedian(Mediator* m){
Imtype v = m->data[m->heap[0]];
if ((m->ct&1) == 0) v = ImtypeMean(v, m->data[m->heap[-1]]);
return v;
}
// median + min/max
Imtype MediatorStat(Mediator* m, Imtype *minval, Imtype *maxval){
Imtype v= m->data[m->heap[0]];
if ((m->ct&1) == 0) v = ImtypeMean(v, m->data[m->heap[-1]]);
Imtype min = v, max = v;
int i;
for(i = -maxCt(m); i < 0; ++i){
int v = m->data[m->heap[i]];
if(v < min) min = v;
}
*minval = min;
for(i = 1; i <= minCt(m); ++i){
int v = m->data[m->heap[i]];
if(v > max) max = v;
}
*maxval = max;
return v;
}
/**
* filter image by median (seed*2 + 1) x (seed*2 + 1)
*/
Image *get_median(const Image *img, int seed){
if(seed < 1) return NULL;
size_t w = img->width, h = img->height;
Image *out = Image_sim(img);
Imtype *med = out->data, *inputima = img->data;
size_t blksz = seed * 2 + 1, fullsz = blksz * blksz;
#ifdef EBUG
double t0 = dtime();
#endif
OMP_FOR(shared(inputima, med))
for(size_t x = seed; x < w - seed; ++x){
size_t xx, yy, xm = x + seed + 1, y, ymax = blksz - 1, xmin = x - seed;
Mediator* m = MediatorNew(fullsz);
// initial fill
for(yy = 0; yy < ymax; ++yy)
for(xx = xmin; xx < xm; ++xx)
MediatorInsert(m, inputima[xx + yy*w]);
ymax = 2*seed*w;
xmin += ymax;
xm += ymax;
ymax = h - seed;
size_t medidx = x + seed * w;
for(y = seed; y < ymax; ++y, xmin += w, xm += w, medidx += w){
for(xx = xmin; xx < xm; ++xx)
MediatorInsert(m, inputima[xx]);
med[medidx] = MediatorMedian(m);
}
FREE(m);
}
Image_minmax(out);
DBG("time for median filtering %zdx%zd of image %zdx%zd: %gs", blksz, blksz, w, h,
dtime() - t0);
return out;
}
/**
* @brief get_stat - calculate floating statistics in (seed*2+1)^2
* @param in (i) - input image
* @param seed - radius of box
* @param mean (o) - mean by box (excluding borders)
* @param std (o) - STD by box (excluding borders)
* @retur 0 if error
*/
int get_stat(const Image *in, int seed, Image **mean, Image **std){
if(!in) return 0;
if(seed < 1 || seed > (in->width - 1)/2 || seed > (in->height - 1)/2) return 0;
#ifdef EBUG
double t0 = dtime();
#endif
Image *M = NULL, *S = NULL;
if(mean) M = Image_sim(in);
if(std) S = Image_sim(in);
int ymax = in->height - seed, xmax = in->width - seed;
int hsz = (seed*2 + 1), sz = hsz * hsz, w = in->width;
OMP_FOR()
for(int y = seed; y < ymax; ++y){ // dumb calculations
int startidx = y*w + seed;
Imtype *om = (M) ? &M->data[startidx] : NULL;
Imtype *os = (S) ? &S->data[startidx] : NULL;
for(int x = seed; x < xmax; ++x){
Imtype sum = 0, sum2 = 0;
int yb = y + seed + 1, xm = x - seed;
for(int yy = y - seed; yy < yb; ++yy){
Imtype *ptr = &in->data[yy * w + xm];
for(int xx = 0; xx < hsz; ++xx){
Imtype d = *ptr++;
sum += d;
sum2 += d*d;
}
}
//DBG("sum=%g, sum2=%g, sz=%d", sum, sum2, sz);
sum /= sz;
if(om){
*om++ = sum;
//DBG("mean (%d, %d): %g", x, y, sum);
}
if(os) *os++ = sqrt(sum2/sz - sum*sum);
}
}
if(mean){
Image_minmax(M);
*mean = M;
}
if(std){
Image_minmax(S);
*std = S;
}
DBG("time for mean/sigma computation: %gs", dtime() - t0);
return 1;
}
/**
* @brief calc_background - Simple background calculation by histogram
* @param img (i) - input image (here will be modified its top2proc field)
* @param bk (o) - background value
* @return 0 if error
*/
int calc_background(Image *img, Imtype *bk){
if(img->maxval - img->minval < DBL_EPSILON){
WARNX("Zero image!");
return 0;
}
int w = img->width, h = img->height, wh = w*h;
Imtype min = img->minval, ampl = img->maxval - min;
int histogram[256] = {0};
//DBG("min: %g, max: %g, ampl: %g", min, img->maxval, ampl);
#pragma omp parallel
{
int histogram_private[256] = {0};
#pragma omp for nowait
for(int i = 0; i < wh; ++i){
int newval = (int)((((img->data[i]) - min)/ampl)*255. + 0.5);
++histogram_private[newval];
}
#pragma omp critical
{
for(int i=0; i<256; ++i) histogram[i] += histogram_private[i];
}
}
int modeidx = 0, modeval = 0;
for(int i = 0; i < 256; ++i)
if(modeval < histogram[i]){
modeval = histogram[i];
modeidx = i;
}
//DBG("Mode=%g @ idx%d (N=%d)", ((Imtype)modeidx / 255.)*ampl, modeidx, modeval);
/*
int diff[256] = {0};
for(int i = 1; i < 255; ++i) diff[i] = (histogram[i+1]-histogram[i-1])/2;
if(modeidx == 0) modeidx = 1;
if(modeidx > 253) return NULL; // very bad image: overilluminated
int borderidx = modeidx;
green("1\n");
for(int i = modeidx; i < 255; ++i){ // search bend-point by first derivate
printf("%d: %d, %d\n", i, diff[i], diff[i+1]);
if(diff[i] >= 0 && diff[i+1] >=0){
borderidx = i; break;
}
}
*/
int diff2[256] = {0};
for(int i = 2; i < 254; ++i) diff2[i] = (histogram[i+2]+histogram[i-2]-2*histogram[i])/4;
if(modeidx < 2) modeidx = 2;
if(modeidx > 253) return 0; // very bad image: overilluminated
int borderidx = modeidx;
// green("2\n");
for(int i = modeidx; i < 254; ++i){ // search bend-point by second derivate
// printf("%d: %d, %d\n", i, diff2[i], diff2[i+1]);
if(diff2[i] <= 0 && diff2[i+1] <=0){
borderidx = i; break;
}
}
//DBG("borderidx=%d -> %d", borderidx, (borderidx+modeidx)/2);
//borderidx = (borderidx + modeidx) / 2;
Imtype borderval = ((Imtype)borderidx / 255.)*ampl + min;
if(bk) *bk = borderval;
//green("HISTO:\n");
//for(int i = 0; i < 256; ++i) printf("%d:\t%d\t%d\n", i, histogram[i], diff2[i]);
// calculate values of upper 2% border
#if 0
Image *out = Image_sim(img);
//DBG("found border: %g @ %d", borderval, borderidx);
OMP_FOR()
for(int i = 0; i < wh; ++i){
register Imtype val = img->data[i];
if(val > borderval) out->data[i] = val - borderval;
}
Image_minmax(out);
#endif
return 1;
}