void testrft(FILE *fp,real ***grid,int nx,int ny,int nz,gmx_bool bFirst)
{
#ifdef USE_SGI_FFT
#ifdef GMX_DOUBLE
static double *coeff;
#else
static float *coeff;
#endif
static int la1,la2;
#endif
real *cptr;
real *gptr,*fqqq,fg,fac;
int ntot,i,j,k,m,n,ndim[4];
int npppm,job;
ndim[0] = 0;
ndim[1] = nx;
ndim[2] = ny;
ndim[3] = nz;
ntot = nx*ny*nz;
cptr = grid[0][0];
fqqq = &(grid[0][0][0]);
#ifdef USE_SGI_FFT
if (bFirst) {
fprintf(fp,"Going to use SGI optimized FFT routines.\n");
#ifdef GMX_DOUBLE
coeff = dfft3di(nx,ny,nz,NULL);
#else
coeff = sfft3di(nx,ny,nz,NULL);
#endif
bFirst = FALSE;
}
job = 1;
la1 = nx+2;
la2 = ny;
#ifdef GMX_DOUBLE
dzfft3d(job,nx,ny,nz,cptr,la1,la2,coeff);
#else
scfft3d(job,nx,ny,nz,cptr,la1,la2,coeff);
#endif
#else
fourn(fqqq-1,ndim,3,1);
#endif
job = -1;
#ifdef USE_SGI_FFT
#ifdef GMX_DOUBLE
zdfft3d(job,nx,ny,nz,cptr,la1,la2,coeff);
#else
csfft3d(job,nx,ny,nz,cptr,la1,la2,coeff);
#endif
#else
fourn(fqqq-1,ndim,3,-1);
#endif
}
void testfft(FILE *fp,t_complex ***grid,int nx,int ny,int nz,gmx_bool bFirst)
{
#ifdef USE_SGI_FFT
#ifdef GMX_DOUBLE
static zomplex *coeff;
#else
static complex *coeff;
#endif
static int la1,la2;
#endif
t_complex *cptr;
real *gptr,*fqqq,fg,fac;
int ntot,i,j,k,m,n,ndim[4];
int npppm;
ndim[0] = 0;
ndim[1] = nx;
ndim[2] = ny;
ndim[3] = nz;
ntot = nx*ny*nz;
cptr = grid[0][0];
fqqq = &(grid[0][0][0].re);
#ifdef USE_SGI_FFT
if (bFirst) {
fprintf(fp,"Going to use SGI optimized FFT routines.\n");
#ifdef GMX_DOUBLE
coeff = zfft3di(nx,ny,nz,NULL);
#else
coeff = cfft3di(nx,ny,nz,NULL);
#endif
bFirst = FALSE;
}
la1 = nx;
la2 = ny;
#ifdef GMX_DOUBLE
zfft3d(1,nx,ny,nz,(zomplex *)cptr,la1,la2,coeff);
#else
cfft3d(1,nx,ny,nz,(complex *)cptr,la1,la2,coeff);
#endif
#else
fourn(fqqq-1,ndim,3,1);
#endif
#ifdef USE_SGI_FFT
#ifdef GMX_DOUBLE
zfft3d(-1,nx,ny,nz,(zomplex *)cptr,la1,la2,coeff);
#else
cfft3d(-1,nx,ny,nz,(complex *)cptr,la1,la2,coeff);
#endif
#else
fourn(fqqq-1,ndim,3,-1);
#endif
}
int main(void)
{
int isign;
long idum=(-23);
unsigned long i,j,k,l,ndum=2,*nn;
float *data1,*data2;
nn=lvector(1,NDIM);
data1=vector(1,NDAT2);
data2=vector(1,NDAT2);
for (i=1;i<=NDIM;i++) nn[i]=(ndum <<= 1);
for (i=1;i<=nn[3];i++)
for (j=1;j<=nn[2];j++)
for (k=1;k<=nn[1];k++) {
l=k+(j-1)*nn[1]+(i-1)*nn[2]*nn[1];
l=(l<<1)-1;
/* real part of component */
data2[l]=data1[l]=2*ran1(&idum)-1;
/* imaginary part of component */
l++;
data2[l]=data1[l]=2*ran1(&idum)-1;
}
isign=1;
fourn(data2,nn,NDIM,isign);
/* here would be any processing to be done in Fourier space */
isign = -1;
fourn(data2,nn,NDIM,isign);
printf("Double 3-dimensional transform\n\n");
printf("%22s %24s %20s\n",
"Double transf.","Original data","Ratio");
printf("%10s %13s %12s %13s %11s %13s\n\n",
"real","imag.","real","imag.","real","imag.");
for (i=1;i<=4;i++) {
k=2*(j=2*i);
l=k+(j-1)*nn[1]+(i-1)*nn[2]*nn[1];
l=(l<<1)-1;
printf("%12.2f %12.2f %10.2f %12.2f %14.2f %12.2f\n",
data2[l],data2[l+1],data1[l],data1[l+1],
data2[l]/data1[l],data2[l+1]/data1[l+1]);
}
printf("\nThe product of transform lengths is: %4lu\n",nn[1]*nn[2]*nn[3]);
free_vector(data2,1,NDAT2);
free_vector(data1,1,NDAT2);
free_lvector(nn,1,NDIM);
return 0;
}
static void convolveWithGaussian(double *forceMap,int S,int /*s*/)
{
static double *bf = NULL ;
if(bf == NULL)
{
bf = new double[S*S*2] ;
for(int i=0;i<S;++i)
for(int j=0;j<S;++j)
{
int x = (i<S/2)?i:(S-i) ;
int y = (j<S/2)?j:(S-j) ;
// int l=2*(x*x+y*y);
bf[2*(i+S*j)] = log(sqrtf(0.1 + x*x+y*y)); // linear -> derivative is constant
bf[2*(i+S*j)+1] = 0 ;
}
unsigned long nn[2] = {S,S};
fourn(&bf[-1],&nn[-1],2,1) ;
}
unsigned long nn[2] = {S,S};
fourn(&forceMap[-1],&nn[-1],2,1) ;
for(int i=0;i<S;++i)
for(int j=0;j<S;++j)
{
float a = forceMap[2*(i+S*j)]*bf[2*(i+S*j)] - forceMap[2*(i+S*j)+1]*bf[2*(i+S*j)+1] ;
float b = forceMap[2*(i+S*j)]*bf[2*(i+S*j)+1] + forceMap[2*(i+S*j)+1]*bf[2*(i+S*j)] ;
forceMap[2*(i+S*j)] = a ;
forceMap[2*(i+S*j)+1] = b ;
}
fourn(&forceMap[-1],&nn[-1],2,-1) ;
for(int i=0;i<S*S*2;++i)
forceMap[i] /= S*S;
}
void main(){
long fftSize[NSIZES] = /* size of FFTs cols, must be powers of 2 */
{2, 4, 8, 16, 32, 64, 128, 256,
512, 1024, 2048, 4096, 8192, 16384, 32768, 65536,
131072, 262144, 524288, 1048576, 2097152, 4194304, 8388608, 16777216};
Complex *a1;
long isize;
long i1;
long TheErr;
long N;
long M;
long N2 = 16; /* the number of rows in the 3d fft */
long M2;
long N3 = 32; /* the number of pages in the 3d fft */
long M3;
float maxerrifft;
float maxerrfft;
unsigned long nn[3];
unsigned int randseed = 777;
int rannum;
#if macintosh
UnsignedWide TheTime1;
Microseconds(&TheTime1);
randseed = TheTime1.lo;
#endif
printf(" %6d Byte Floats \n", sizeof(a1[0].Re));
printf(" randseed = %10u\n", randseed);
for (isize = 0; isize < NSIZES; isize++){
srand(randseed);
N = fftSize[isize];
M = roundtol(LOG2(N));
N = POW2(M);
M2 = roundtol(LOG2(N2));
N2 = POW2(M2);
M3 = roundtol(LOG2(N3));
N3 = POW2(M3);
printf("ffts size = %5d X%5d X%6d, ", N3, N2, N);
nn[0] = N3;
nn[1] = N2;
nn[2] = N;
TheErr = fft3dInit(M3, M2, M);
if(!TheErr){
a1 = (Complex *) malloc(N3*N2*N*sizeof(Complex) );
if (a1 == 0) TheErr = 2;
}
if(!TheErr){
/* set up a simple test case */
for (i1=0; i1<N3*N2*N; i1++){
rannum = rand();
a1[i1].Re = BIPRAND(rannum);
rannum = rand();
a1[i1].Im = BIPRAND(rannum);
}
/* first use fourn from numerical recipes in C to verify ifft3d */
/* Note their inverse fft is really the conventional forward fft */
fourn((float *)a1-1, nn-1, 3, -1);
ifft3d((float *)a1, M3, M2, M);
maxerrifft = 0;
srand(randseed);
for (i1=0; i1<N3*N2*N; i1++){
rannum = rand();
maxerrifft = fmax(maxerrifft, fabs(BIPRAND(rannum)-a1[i1].Re));
a1[i1].Re = BIPRAND(rannum);
rannum = rand();
maxerrifft = fmax(maxerrifft, fabs(BIPRAND(rannum)-a1[i1].Im));
a1[i1].Im = BIPRAND(rannum);
}
printf("errifft = %4.3e, ", maxerrifft);
/* now use iffts to verify ffts */
ifft3d((float *)a1, M3, M2, M);
fft3d((float *)a1, M3, M2, M);
maxerrfft = 0;
srand(randseed);
for (i1=0; i1<N3*N2*N; i1++){
rannum = rand();
maxerrfft = fmax(maxerrfft, fabs(BIPRAND(rannum)-a1[i1].Re));
rannum = rand();
maxerrfft = fmax(maxerrfft, fabs(BIPRAND(rannum)-a1[i1].Im));
}
printf("errfft = %4.3e\n", maxerrfft);
free(a1);
fft3dFree();
}
else{
if(TheErr==2) printf(" out of memory \n");
else printf(" error \n");
fft3dFree();
}
}
printf(" Done. \n");
return;
}
void rlft3(float ***data, float **speq, unsigned long nn1, unsigned long nn2,
unsigned long nn3, int isign)
{
void fourn(float data[], unsigned long nn[], int ndim, int isign);
void nrerror(char error_text[]);
unsigned long i1,i2,i3,j1,j2,j3,nn[4],ii3;
double theta,wi,wpi,wpr,wr,wtemp;
float c1,c2,h1r,h1i,h2r,h2i;
if (1+&data[nn1][nn2][nn3]-&data[1][1][1] != nn1*nn2*nn3)
nrerror("rlft3: problem with dimensions or contiguity of data array\n");
c1=0.5;
c2 = -0.5*isign;
theta=isign*(6.28318530717959/nn3);
wtemp=sin(0.5*theta);
wpr = -2.0*wtemp*wtemp;
wpi=sin(theta);
nn[1]=nn1;
nn[2]=nn2;
nn[3]=nn3 >> 1;
if (isign == 1) {
fourn(&data[1][1][1]-1,nn,3,isign);
for (i1=1;i1<=nn1;i1++)
for (i2=1,j2=0;i2<=nn2;i2++) {
speq[i1][++j2]=data[i1][i2][1];
speq[i1][++j2]=data[i1][i2][2];
}
}
for (i1=1;i1<=nn1;i1++) {
j1=(i1 != 1 ? nn1-i1+2 : 1);
wr=1.0;
wi=0.0;
for (ii3=1,i3=1;i3<=(nn3>>2)+1;i3++,ii3+=2) {
for (i2=1;i2<=nn2;i2++) {
if (i3 == 1) {
j2=(i2 != 1 ? ((nn2-i2)<<1)+3 : 1);
h1r=c1*(data[i1][i2][1]+speq[j1][j2]);
h1i=c1*(data[i1][i2][2]-speq[j1][j2+1]);
h2i=c2*(data[i1][i2][1]-speq[j1][j2]);
h2r= -c2*(data[i1][i2][2]+speq[j1][j2+1]);
data[i1][i2][1]=h1r+h2r;
data[i1][i2][2]=h1i+h2i;
speq[j1][j2]=h1r-h2r;
speq[j1][j2+1]=h2i-h1i;
} else {
j2=(i2 != 1 ? nn2-i2+2 : 1);
j3=nn3+3-(i3<<1);
h1r=c1*(data[i1][i2][ii3]+data[j1][j2][j3]);
h1i=c1*(data[i1][i2][ii3+1]-data[j1][j2][j3+1]);
h2i=c2*(data[i1][i2][ii3]-data[j1][j2][j3]);
h2r= -c2*(data[i1][i2][ii3+1]+data[j1][j2][j3+1]);
data[i1][i2][ii3]=h1r+wr*h2r-wi*h2i;
data[i1][i2][ii3+1]=h1i+wr*h2i+wi*h2r;
data[j1][j2][j3]=h1r-wr*h2r+wi*h2i;
data[j1][j2][j3+1]= -h1i+wr*h2i+wi*h2r;
}
}
wr=(wtemp=wr)*wpr-wi*wpi+wr;
wi=wi*wpr+wtemp*wpi+wi;
}
}
if (isign == -1)
fourn(&data[1][1][1]-1,nn,3,isign);
}
void rsk_turbdriving_field()
{
int dots, kx, ky, kz, i,l, kmin, kmax, bytes;
int nn[4];
double rcube, rcubehalf, xk, yk, zk, Pk, abs_k;
/* double Ak[2*DOTS*DOTS*DOTS+1], matrix[DOTS][DOTS][DOTS]; */
double *Ak, *matrix;
if(!(Ak = malloc(bytes=sizeof(double)*(2*DOTS*DOTS*DOTS+1))))
{
printf("failed to allocate memory for Ak: %d.\n",bytes);
endrun(2);
}
if(!(matrix = malloc(sizeof(double)*DOTS*DOTS*DOTS)))
{
printf("failed to allocate memory for matrix.\n");
endrun(2);
}
dots = DOTS;
rcube = 2.0;
rcubehalf = rcube/2.0;
kmin = All.kMin;
kmax = All.kMax;
All.DeltaTimeDrv = 0;
/* /\* ---------------------------------------------------------------------*\/ */
ran1(&iiseed);
nn[1] = dots; /* dimensions of array */
nn[2] = dots;
nn[3] = dots;
if(kmin < 1)
kmin = 1;
for (kx = 0; kx < dots; kx++)
{
xk = kx;
if(kx > dots/2)
xk = dots - xk;
for (ky = 0; ky < dots; ky++)
{
yk = ky;
if(ky > dots/2)
yk = dots - yk;
for (kz = 0; kz < dots/2+1; kz++)
{
zk = kz;
abs_k = sqrt(xk*xk + yk*yk + zk*zk);
if((abs_k < kmin) || (abs_k > kmax))
Pk = 0;
else
Pk = 1/pow(abs_k,All.DrvIndx);
gen_Ak(Ak,kx,ky,kz,Pk,dots);
}
}
}
Ak[2*( 0*dots*dots + 0*dots + 0)+1] = 0;
Ak[2*( 0*dots*dots + 0*dots + dots/2)+1] = 0;
Ak[2*( 0*dots*dots + dots/2*dots + 0)+1] = 0;
Ak[2*( 0*dots*dots + dots/2*dots + dots/2)+1] = 0;
Ak[2*(dots/2*dots*dots + 0*dots + 0)+1] = 0;
Ak[2*(dots/2*dots*dots + 0*dots + dots/2)+1] = 0;
Ak[2*(dots/2*dots*dots + dots/2*dots + 0)+1] = 0;
Ak[2*(dots/2*dots*dots + dots/2*dots + dots/2)+1] = 0;
for(i=2*dots*dots*dots;i>0;i--) /* array must start with Ak[1] for fourn */
Ak[i]=Ak[i-1];
fourn(Ak,nn,3,-1);
for(i=1,l=0;i<2*dots*dots*dots;i+=2,l++)
Ak[l] = Ak[i];
l = 0; /* assign the real part to matrix */
for(kz = 0; kz<dots; kz++)
{
for(ky = 0; ky<dots; ky++)
{
for(kx = 0; kx<dots; kx++)
{
/* matrix[kx][ky][kz] = Ak[l]; */
matrix[kx*DOTS*DOTS+ky*DOTS+kz] = Ak[l];
l++;
}
}
}
for(l = 0; l<2*dots*dots*dots+1; l++) /*empty Ak*/
Ak[l] = 0;
if(dots != IFIELDSIZE)
{
if(ThisTask==0)
{
printf("STOP: array sizes do nor agree\n");
printf("dots: %d\n",dots);
printf("ifieldsize: %d\n",IFIELDSIZE);
fflush(stdout);
}
exit(1);
}
if(icomp == 1) /* copy matrix into xmatrix */
{
for(kz = 0; kz<IFIELDSIZE; kz++)
{
for(ky = 0; ky<IFIELDSIZE; ky++)
{
for(kx = 0; kx<IFIELDSIZE; kx++)
{
xmatrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz] = matrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz];
}
}
}
}
if(icomp == 2) /* copy matrix into ymatrix */
{
for(kz = 0; kz<IFIELDSIZE; kz++)
{
for(ky = 0; ky<IFIELDSIZE; ky++)
{
for(kx = 0; kx<IFIELDSIZE; kx++)
{
ymatrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz] = matrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz];
}
}
}
}
if(icomp == 3) /* copy matrix into zmatrix */
{
for(kz = 0; kz<IFIELDSIZE; kz++)
{
for(ky = 0; ky<IFIELDSIZE; ky++)
{
for(kx = 0; kx<IFIELDSIZE; kx++)
{
zmatrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz] = matrix[kx*IFIELDSIZE*IFIELDSIZE+ky*IFIELDSIZE+kz];
}
}
}
}
SysState.EnergyDrv = 0.0;
for(i=0;i<6;i++)
{
SysState.EnergyDrvComp[i] = 0.0;
SysState.EnergyDrv += SysState.EnergyDrvComp[i];
}
/* ende */
free(Ak);
free(matrix);
}
void main(int nar, char* ar[])
{
int i,j,k,l,m, n=0, num, nnn[4];
float*u; // ,*f;
double*f;
parlist par;
FILE *in,*out,*col,*grs;
char name[100];
char buffer[48];
float cpu[2];
clock_t t;
/* set default values */
par.sigma=2; par.seed=200294;
par.dim=intvector(1,3); par.dim[1]=64; par.dim[2]=32; par.dim[3]=16;
empty(&par.inname); empty(&par.outname);
empty(&par.colname); empty(&par.grsname);
par.length=1; par.nongauss=0; par.lo=-4; par.hi=4; par.bins=100;
par.med=0; par.pixel=1; par.normal=1; par.time=0;
/* work through arguments */
while(++n<nar){
if(ar[n][0]=='-'&&ar[n][1]){
switch(ar[n][1]) {
case'0' : par.grsname =READSTR; break;
case'1' : par.colname =READSTR; break;
case'L' : par.length =READINT; break;
case'N' : par.normal =0; break;
case'b' : par.bins =READINT; break;
case'g' : par.nongauss=READINT; break;
case'h' : par.hi =READFLT; break;
case'i' : par.inname =READSTR; break;
case'l' : par.lo =READFLT; break;
case'm' : par.med =READINT; break;
case'o' : par.outname =READSTR; break;
case'p' : par.pixel =READINT; break;
case'r' : par.seed =READINT; break;
case's' : par.sigma =READFLT; break;
case't' : par.time =1; break;
case'x' : par.dim[1] =READINT; break;
case'y' : par.dim[2] =READINT; break;
case'z' : par.dim[3] =READINT; break;
default : Explain(stderr,ar[0],&par);
}
}
else {
Explain(stderr,ar[0],&par);
}
}
par.a=1./(float)par.dim[1]; /* grid constant is used everywhere */
/* allocate some memory */
n=par.dim[1]*par.dim[2]*par.dim[3];
u=vector(0,2*n);
/* open input file and read data */
fileopenr(&in,par.inname);
/* printf("%s"," here 1a \n");
printf("size = %d\n",sizeof(in)); */
if(in) {
//f=vector(0,n);
f=doublevector(0,n);
fread((void*)buffer,sizeof(char),24,in);
if(n!=fread((void*)f,sizeof(double),n,in)) {
fprintf(stderr,"error when reading input!\n");
exit(99);
}
/* printf("f[0] %d\n",&f[0]);
printf("f[0]wert %g\n", f[0]);
printf("f[1]wert %g\n", f[1]);
printf("f[1]wert %g\n", f[2]);
printf("f[1]wert %g\n", f[3]); */
printf("---\n");
//for(i=0;i<n;i++) u[2*i]=f[i],u[2*i+1]=0;
for(i=0;i<n;i++) u[2*i]=(float)f[i],u[2*i+1]=0;
/* printf("u[0] %d\n",&u[0]);
printf("u[0]wert %g\n", u[0]);
printf("f[0] %d\n",&f[0]);
printf("f[0]wert %g\n", f[0]);
printf("u[1] %d\n",&u[1]);
printf("u[1]wert %g\n", u[1]);
printf("f[1] %d\n",&f[1]);
printf("f[1]wert %g\n", f[1]);
printf("%s"," here 1c \n"); */
//free_vector(f,0,n);
free_doublevector(f,0,n);
/* printf("%s"," here 1d \n");
printf("par.sigma = %g\n",par.sigma); */
if(par.sigma>0) fourn(u-1,par.dim,3,1);
}
/* printf("%s"," here 1e \n"); */
fileclose(in);
/* printf("%s"," here 1 \n"); */
/* open output files */
fileopenw(&out,par.outname);
/* printf("%s"," here 2 \n"); */
cpu[0]=cpu[1]=0;
for(num=0; num<par.length; num++) {
/* random field in Fourier space */
if(par.time) t=clock();
if(!in) randomfield(u,&par);
if(par.time) cpu[0]+=(clock()-t)/(float)CLOCKS_PER_SEC;
/* convolution and normalization */
if(par.time) t=clock();
if(par.sigma>0) convolution(u,&par);
if(par.sigma>0) fourn(u-1,par.dim,3,-1);
normalize(u,&par);
if(par.time) cpu[0]+=(clock()-t)/(float)CLOCKS_PER_SEC;
/* printf("%s"," here 2c \n");*/
/* perform statistics */
if(par.time) t=clock();
minkowski(out,u,&par);
if(par.time) cpu[1]+=(clock()-t)/(float)CLOCKS_PER_SEC;
}
/* printf("%s"," here 3 \n"); */
if(par.time)
fprintf(stderr,"CPU: %13s%13s\n"
" %8.2f sec %8.2f sec\n",
"fields","minkowski",cpu[0],cpu[1]);
/* output xpm bitmap data */
fileopenw(&col,par.colname); if(col) picture(1,col,u,&par); fileclose(col);
fileopenw(&grs,par.grsname); if(grs) picture(0,grs,u,&par); fileclose(grs);
/* finish */
fileclose(out);
free_vector(u,0,2*n);
exit(0);
}
/*==============================================================================
* CALC_POTENTIAL:
*
* rho^ = FFT(rho)
* Phi^ = G^ * rho^ ; G^ = -1/k**2 (no adjustment for finite differences)
* Phi = FFT(Phi^)
*
* uses NR routine fourn.c for FFT's
*==============================================================================*/
void fft_potential(flouble *data, long l1dim)
{
FILE *fpout;
double Green, sf, sf2;
double FFTnorm;
double kx, ky, kz, ksquare, kf;
double sin2sfkz, sin2sfky;
long *k;
long k_dim, k_nyq;
long i, l, m, n;
int forward=1, backward=-1;
unsigned long nn[NDIM];
/* dimensions of grid */
nn[0] = l1dim;
nn[1] = l1dim;
nn[2] = l1dim;
k_dim = l1dim;
k_nyq = l1dim/2;
/* this will help extracting information from data^ */
k = (long*) calloc(l1dim,sizeof(long));
for(i=0; i<l1dim; i++)
{
if(i <= k_nyq)
k[i] = i;
else
k[i] = -(l1dim-i);
}
/* fourn normalisation factor */
FFTnorm = (double)pow3(l1dim);
/* fundamental wave in box units: kf = 2*pi */
kf = TWOPI;
/* adjusting the 7-point-difference Green's function */
sf = PI/(double)l1dim/kf;
sf2 = pow2(sf);
/* forward FFT */
fourn(data-1, nn-1, NDIM, forward);
PkSpectrum.time -= time(NULL);
PkSpectrum.time += time(NULL);
/* calculation of gravitational potential */
for(n = 0; n < k_dim; n++)
{
kz = kf * k[n];
sin2sfkz = pow2(sin(sf*kz));
for(m = 0; m < k_dim; m++)
{
ky = kf * k[m];
sin2sfky = pow2(sin(sf*ky));
for(l = 0; l < k_dim; l++)
{
kx = kf * k[l];
/* get k^2 => NOT needed for 7-point difference approximation to Green = -1.0 / ksquare */
/* ksquare = kx * kx + ky * ky + kz * kz; */
/* Green's function */
if (k[l] == 0 && k[m] == 0 && k[n] == 0)
{
Green = 0.0;
}
else
{
/* 7-point difference approximation to Green = -1.0 / ksquare */
Green = -sf2/(pow2(sin(sf*kx))+sin2sfky+sin2sfkz);
}
data[Re(l,m,n,l1dim)] *= Green;
data[Im(l,m,n,l1dim)] *= Green;
}
}
}
/* backward FFT */
fourn(data-1, nn-1, NDIM, backward);
/* normalize FFT output */
for(i=0; i<2*l1dim*l1dim*l1dim; i++)
data[i] /= FFTnorm;
/* delete k-array again */
free(k);
}
int main(int argc, char **argv)
{
fcpx *bufcz, **cmp;
fcpx **sm, **seg_fft, *seg_fftb;
float *dt;
float phase,amplt; /* read these from oct files */
float real,imag; /* calculate these from phase,amplt */
double alpha;
float t1, t2, tmp, peak;
float w[NFFT], amp[NFFT][NFFT];
int width;
int count;
int nlines=0;
int nbytes1,nbytes2;
int phase_int;
int step;
int xw,yh;
int i,j,i1,j1;
int ndim;
int isign;
int ic, lc;
int imax,jmax; /* indices of max power */
/* FILE *int_file, *sm_file;*/
FILE *pha_file, *amp_file, *sm_file, *int_file; /* intfile is temporarily created form amp_file and pha_file */
struct stat *file_stat = malloc(sizeof(struct stat));
fprintf(stdout,"*** power spectrum smoothing of interferogram ***\n");
fprintf(stdout,"*** Original by Zhong Lu ***\n");
fprintf(stdout,"*** thanking C. Werner and R. Goldstein for their advice ***\n");
fprintf(stdout,"*** circa 2000 Tim Wright ***\n");
fprintf(stdout,"*** Modified to work with 8 Bit Phase/Amplitude... ***\n");
fprintf(stdout,"*** Version 3.0 20140530 ***\n");
fprintf(stdout,"*** Kurt Feigl to record gradients ***\n");
if(argc != 6){
/* fprintf(stderr,"\nusage: %s <ifm> <sm-ifm> <width> <alpha> \n\n",argv[0]) ;*/
// fprintf(stderr,"\nusage: %s <pha.oct> <amp.oct> <smp.oct> <ncol> <alpha> \n\n",argv[0]) ;
fprintf(stderr,"\nusage: %s <pha.oct> <amp.oct> <smp.oct> <ncol> <alpha> \n\n",argv[0]) ;
fprintf(stderr,"input parameters: \n");
// fprintf(stderr,"pha.oct (Input) Phase (Unsigned 8Bit Integer 0 = -pi; 255 = pi)\n");
fprintf(stderr,"pha.oct (Input) Phase (Unsigned 8Bit Integer -128 = -pi; 127 = pi)\n");
// fprintf(stderr,"amp.oct (Input) Amplitude (Unsigned 8Bit Integer 0 - 255)\n");
/* fprintf(stderr,"ifm (Input)complex interferogram (4-byte for real and 4-byte for imaginary)\n");*/
fprintf(stderr,"smp.oct (Output) Smoothed Phase (Unsigned 8Bit Integer -128 = -pi; 127 = pi)\n");
fprintf(stderr,"ncols (Input) Number of columns in all 3 files (pixels per line);\n");
/* fprintf(stderr,"alpha (Input) Power factor in Goldstein & Werner technique (recommend: 0.0 < 0.7 < 1.0);\n"); */
fprintf(stderr,"alpha (Input) Alpha exponent in Goldstein & Werner technique (recommend: 0.0 < 0.7 < 1.0);\n");
exit(-1);
}
pha_file = fopen(argv[1],"rb");
if (pha_file == NULL){fprintf(stderr,"cannot open phase file: %s\n",argv[1]); exit(-1);}
amp_file = fopen(argv[2],"rb");
if (amp_file == NULL){fprintf(stderr,"cannot open amplitude file: %s\n",argv[1]); exit(-1);}
sm_file = fopen(argv[3],"w");
if (sm_file == NULL){fprintf(stderr,"cannot create smoothed interferogram file: %s\n",argv[2]); exit(-1);}
int_file = fopen("temp.cr4","wb");
if (int_file == NULL){fprintf(stderr,"cannot create temp complex file: temp.cr4\n"); exit(-1);}
sscanf(argv[4],"%d",&width);
sscanf(argv[5],"%lf",&alpha);
/* Work out number of lines in file and check that the files are the same size */
stat(argv[1],file_stat);
nbytes1=(int)file_stat->st_size;
fprintf (stderr, "nbytes1 = %d\n",nbytes1);
stat(argv[2],file_stat);
nbytes2=(int)file_stat->st_size;
fprintf (stderr, "nbytes2 = %d\n",nbytes2);
if (nbytes1==nbytes2) {
nlines=(int)(nbytes1/width);
}
else {
fprintf(stderr, "\t Amplitude and Phase Files are different sizes\n");
exit(-1);
}
/* fseek(int_file, 0L, 2);
nlines=(int)ftell(int_file)/(width*2*sizeof(float));
rewind(int_file);*/
step = STEP;
fprintf(stderr, "Input parameters:\n");
fprintf(stderr, "\tInput Phase: %s\n", argv[1]);
fprintf(stderr, "\tInput Amplitude: %s\n", argv[2]);
fprintf(stderr, "\tSmoothed phase: %s\n", argv[3]);
fprintf(stderr, "\tPower spectrum alpha: %f\n", alpha);
fprintf(stderr, "\tFFT window size: %d\n", NFFT);
fprintf(stderr, "\tImage width: %d\n", width);
fprintf(stderr, "\tImage length: %d\n", nlines);
xw=width;
yh=nlines;
fprintf(stdout,"\tarray width, height: %5d %5d\n",xw,yh);
cmp = alloc_2d_c(0, nlines-1, 0,width-1);
sm = alloc_2d_c(0,nlines-1, 0,width);
if (cmp == NULL || sm == NULL) {fprintf(stderr, "failure to allocate space for cmp and sm buffers\n"); exit(-1);}
seg_fftb = (fcpx *)malloc(sizeof(fcpx)*NFFT*NFFT);
if(seg_fftb == NULL){fprintf(stderr,"failure to allocate space for complex data\n"); exit(-1);}
seg_fft = (fcpx **)malloc(sizeof(fcpx *)*NFFT);
if(seg_fft == NULL){fprintf(stderr,"failure to allocate space for complex data pointers\n"); exit(-1);}
bufcz = (fcpx *)malloc(sizeof(fcpx)*width);
if(bufcz == NULL){fprintf(stderr,"failure to allocate space for input line buffer\n"); exit(-1);}
for(i=0; i < NFFT; i++)seg_fft[i] = seg_fftb + i*NFFT;
for(i=0; i < nlines; i++){
for(j=0; j < width; j++){
sm[i][j].re=0.0; sm[i][j].im=0.0;
}
}
for(j=0; j < width; j++){bufcz[j].re=0.; bufcz[j].im=0.;}
for (i=0; i <= NFFT/2-1; i++) {
w[i] = 2.0*(i+1)/(float)NFFT;
w[NFFT-i-1]=w[i];
}
for (i=0; i < NFFT; i++)
for (j=0; j < NFFT; j++)wf[i][j] = w[i]*w[j];
/* Merge amp and phase into "temp.cr4" */
count=0;
while (count < nbytes1) {
phase = (float)fgetc(pha_file);
amplt = (float)fgetc(amp_file);
// if (phase==0&&lt!=0) phase=1;
// real = (amplt/255)*cos(phase*2*PI/255);
// imag = (amplt/255)*sin(phase*2*PI/255);
if (amplt==0) phase=0;
real = (amplt/256)*cos(phase*2*PI/256);
imag = (amplt/256)*sin(phase*2*PI/256);
fwrite (&real, sizeof(float),1,int_file);
fwrite (&imag, sizeof(float),1,int_file);
count ++;
}
printf("\n Created temporary Complex File: temp.cr4\n");
/* Close file for writing and reopen for reading */
fclose (int_file);
fclose (pha_file);
fclose (amp_file);
int_file = fopen("temp.cr4","r");
if (int_file == NULL){fprintf(stderr,"cannot create temp complex file: temp.cr4\n"); exit(-1);}
fseek(int_file, 0, 0);
for (i=0; i < yh; i ++)
fread((char *)cmp[i], sizeof(fcpx), width, int_file);
#if 1
fprintf(stderr, "Please wait, I am filtering the noisy ifms\n");
fprintf(stderr, "I am slow, but you will like the results\n\n");
lc=0;
/* loop over patches with overlap by step */
for (i=-NFFT+step; i <= yh-step; i += step){
for (j=-NFFT+step; j < width-step; j += step){
dt=(float *)&seg_fft[0][0];
ic = 0;
for (i1=0; i1 < NFFT; i1++){
for (j1=0; j1 < NFFT; j1++){
/* pad with zeros */
if ( (i+i1) < 0 || (i+i1) >= yh || (j+j1) < 0 || (j+j1) >= width ) {
dt[ic++] = 0.0;
dt[ic++] = 0.0;
}
else {
/* normalize magnitude to unity */
t1 = cmp[i+i1][j+j1].re;
t2 = cmp[i+i1][j+j1].im;
tmp = sqrt(t1*t1 + t2*t2);
if (tmp != 0.0) {
dt[ic++]=t1/tmp;
dt[ic++]=t2/tmp;
}
else {
dt[ic++]=0.0;
dt[ic++]=0.0;
}
}
}
}
/* Fourier transform */
ndim=2, isign=1, nfft[1]=NFFT, nfft[2]=NFFT, nfft[0]=0;
fourn(dt-1, nfft, ndim, isign);
/* look for maximum spectral amplitude, a.k.a. power */
peak = 0.0;
for (i1=0; i1 < NFFT; i1++){
for (j1=0; j1 < NFFT; j1++){
/* calculate power */
tmp = sqrt(seg_fft[i1][j1].re*seg_fft[i1][j1].re + seg_fft[i1][j1].im*seg_fft[i1][j1].im);
/* if power is greater than peak, then update peak */
if (peak < tmp) {
peak = tmp;
printf("%3d %3d %5d %5d %12.4e %12.4e %12.4e\n",i1,j1,i,j,seg_fft[i1][j1].re,seg_fft[i1][j1].im,tmp);
}
/* record power */
amp[i1][j1] = tmp;
}
}
/* replace spectral value by amplified value */
if (peak != 0.0) {
for (i1=0; i1 < NFFT; i1++){
for (j1=0; j1 < NFFT; j1++){
seg_fft[i1][j1].re = (float)(seg_fft[i1][j1].re*pow((amp[i1][j1]/peak), alpha)/(float)NFFT);
seg_fft[i1][j1].im = (float)(seg_fft[i1][j1].im*pow((amp[i1][j1]/peak), alpha)/(float)NFFT);
}
}
}
/* inverse Fourier transform */
isign=-1;
fourn(dt-1, nfft, ndim, isign);
for (i1=0; i1 < NFFT; i1++){
for (j1=0; j1 < NFFT; j1++){
tmp = sqrt(seg_fft[i1][j1].re*seg_fft[i1][j1].re + seg_fft[i1][j1].im*seg_fft[i1][j1].im);
seg_fft[i1][j1].re = (float)(seg_fft[i1][j1].re*wf[i1][j1]/tmp);
seg_fft[i1][j1].im = (float)(seg_fft[i1][j1].im*wf[i1][j1]/tmp);
}
}
/* replace phase value with filtered (smoothed) value */
for (i1=0; i1 < NFFT; i1++){
for (j1=0; j1 < NFFT; j1++){
/* check that pixel is not in the padded area */
if ( (i+i1) >= 0 && (i+i1) < yh && (j+j1) >= 0 && (j+j1) < width && cmp[i1+i][j1+j].re != 0.0 && cmp[i1+i][j1+j].im != 0.0 ) {
sm[i1+i][j1+j].re += seg_fft[i1][j1].re;
sm[i1+i][j1+j].im += seg_fft[i1][j1].im;
}
}
}
}
lc += step;
fprintf(stderr, "processing line: %5d\r", i);
}
/* Close file for reading and reopen for writing !! There's probably a more elegant solution but this works !! */
fclose (int_file);
int_file = fopen("temp.cr4","w");
if (int_file == NULL){fprintf(stderr,"cannot rewrite temp complex file: temp.cr4\n"); exit(-1);}
/* Write temporary complex output file */
fprintf(stderr, "writing output image \n");
for (i=0; i < yh ; i++)
fwrite((char *)sm[i], sizeof(fcpx), width, int_file);
/* Once more...Close for writing and reopen for reading */
fclose (int_file);
int_file = fopen("temp.cr4","rb");
if (int_file == NULL){fprintf(stderr,"cannot create temp complex file: temp.cr4\n"); exit(-1);}
/* Convert complex array into octal and write Smoothed Phase File */
count = 0;
while (count < nbytes1) {
fread(&real, sizeof(float),1,int_file);
fread(&imag, sizeof(float),1,int_file);
// /* Changed to deal with diapason nulls (phase==0) properly */
// phase_int = (int)(ROUND((255*atan2(imag,real)/2/PI)));
// if (atan2(imag,real)==0) phase_int=0;
// else if (phase_int==0&&atan2(imag,real)>0) phase_int++;
// else if (phase_int==0&&atan2(imag,real)<0) phase_int--;
// while (phase_int > 255) phase_int -=255;
// while (phase_int < 0) phase_int +=255;
/* Changed to deal with diapason nulls (phase==0) properly */
/* 20140530 use 256 */
phase_int = (int)(ROUND((256*atan2(imag,real)/2/PI)));
if (atan2(imag,real)==0) phase_int=0;
else if (phase_int==0&&atan2(imag,real)>0) phase_int++;
else if (phase_int==0&&atan2(imag,real)<0) phase_int--;
while (phase_int > 127) phase_int -=256;
while (phase_int < -128) phase_int +=256;
fputc(phase_int, sm_file);
count ++;
}
printf("\n finished***\n");
#endif
system("rm temp.cr4");
fclose (int_file);
fclose (sm_file);
return(0);
}
