void caffe_cpu_fft<float>(const int howmany, const int n, const float* x, complex<float>* y) {
/* FFTW plan handle */
fftwf_plan hplan = 0;
const float *in = x;
fftwf_complex *out = reinterpret_cast<fftwf_complex *>(y);
int Ni[] = {n};
int No[] = {n/2+1};
hplan = fftwf_plan_many_dft_r2c(1, Ni, howmany,
const_cast<float *>(in), Ni, 1, n,
out, No, 1, n/2+1,
FFTW_ESTIMATE);
if (0 == hplan) goto failed;
fftwf_execute(hplan);
fftwf_destroy_plan(hplan);
failed:
return;
}
OptFFT::OptFFT(const size_t maxDataSize)
{
assert( maxDataSize % OVERLAPSAMPLES == 0 );
// DOUBLE
//m_pIn = static_cast<double*>( fftw_malloc(sizeof(double) * FRAMESIZE) );
//m_pOut = static_cast<fftw_complex*>( fftw_malloc(sizeof(fftw_complex) * (FRAMESIZE/2 + 1)) );
//m_p = fftw_plan_dft_r2c_1f(FRAMESIZE, m_pIn, m_pOut, FFTW_ESTIMATE); // FFTW_ESTIMATE or FFTW_MEASURE
// FLOAT
// m_pIn = static_cast<float*>( fftwf_malloc(sizeof(float) * FRAMESIZE) );
// m_pOut = static_cast<fftwf_complex*>( fftwf_malloc(sizeof(fftwf_complex) * (FRAMESIZE/2 + 1)) );
//// in destroyed when line executed
//m_p = fftwf_plan_dft_r2c_1d(FRAMESIZE, m_pIn, m_pOut, FFTW_ESTIMATE); // FFTW_ESTIMATE or FFTW_MEASURE
//-----------------------------------------------------------------
int numSamplesPerFrame = FRAMESIZE;
int numSamplesPerFrameOut = FRAMESIZE/2+1;
m_maxFrames = static_cast<int> ( (maxDataSize - FRAMESIZE) / OVERLAPSAMPLES + 1 );
m_pIn = static_cast<float*> ( fftwf_malloc(sizeof(float) * (numSamplesPerFrame * m_maxFrames) ) );
if ( !m_pIn )
{
ostringstream oss;
oss << "fftwf_malloc failed on m_pIn. Trying to allocate <"
<< sizeof(float) * (numSamplesPerFrame * m_maxFrames)
<< "> bytes";
throw std::runtime_error(oss.str());
}
m_pOut = static_cast<fftwf_complex*>( fftwf_malloc(sizeof(fftwf_complex) * (numSamplesPerFrameOut* m_maxFrames) ) );
if ( !m_pOut )
{
ostringstream oss;
oss << "fftwf_malloc failed on m_pOut. Trying to allocate <"
<< sizeof(fftwf_complex) * (numSamplesPerFrameOut* m_maxFrames)
<< "> bytes";
throw std::runtime_error(oss.str());
}
// in destroyed when line executed
m_p = fftwf_plan_many_dft_r2c(1, &numSamplesPerFrame, m_maxFrames,
m_pIn, &numSamplesPerFrame, 1, numSamplesPerFrame,
m_pOut, &numSamplesPerFrameOut,
1, numSamplesPerFrameOut,
FFTW_ESTIMATE | FFTW_DESTROY_INPUT);
if ( !m_p )
throw std::runtime_error ("fftwf_plan_many_dft_r2c failed");
double base = exp( log( static_cast<double>(MAXFREQ) / static_cast<double>(MINFREQ) ) /
static_cast<double>(Filter::NBANDS)
);
m_powTable.resize( Filter::NBANDS+1 );
for ( unsigned int i = 0; i < Filter::NBANDS + 1; ++i )
m_powTable[i] = static_cast<unsigned int>( (pow(base, static_cast<double>(i)) - 1.0) * MINCOEF );
m_pFrames = new float*[m_maxFrames];
if ( !m_pFrames )
{
ostringstream oss;
oss << "Allocation failed on m_pFrames. Trying to allocate <"
<< sizeof(float*) * m_maxFrames
<< "> bytes";
throw std::runtime_error(oss.str());
}
for (int i = 0; i < m_maxFrames; ++i)
{
m_pFrames[i] = new float[Filter::NBANDS];
if ( !m_pFrames[i] )
throw std::runtime_error("Allocation failed on m_pFrames");
}
}
int main(int argc, char* argv[])
{
bool verb, pow2;
char key[7], *mode;;
int n1, n2, n1padded, n2padded, num, dim, n[SF_MAX_DIM], npadded[SF_MAX_DIM], ii[SF_MAX_DIM];
int i, j, i1, i2, index, nw, iter, niter, nthr, *pad;
float thr, pclip, normp;
float *dobs_t, *thresh, *mask;
fftwf_complex *mm, *dd, *dobs;
fftwf_plan fft1, ifft1, fftrem, ifftrem;/* execute plan for FFT and IFFT */
sf_file in, out, Fmask; /* mask and I/O files*/
sf_init(argc,argv); /* Madagascar initialization */
in=sf_input("in"); /* read the data to be interpolated */
out=sf_output("out"); /* output the reconstructed data */
Fmask=sf_input("mask"); /* read the (n-1)-D mask for n-D data */
if(!sf_getbool("verb",&verb)) verb=false;
/* verbosity */
if(!sf_getbool("pow2",&pow2)) pow2=false;
/* round up the length of each axis to be power of 2 */
if (!sf_getint("niter",&niter)) niter=100;
/* total number of iterations */
if (!sf_getfloat("pclip",&pclip)) pclip=10.;
/* starting data clip percentile (default is 10)*/
if ( !(mode=sf_getstring("mode")) ) mode = "exp";
/* thresholding mode: 'hard', 'soft','pthresh','exp';
'hard', hard thresholding; 'soft', soft thresholding;
'pthresh', generalized quasi-p; 'exp', exponential shrinkage */
if (pclip <=0. || pclip > 100.) sf_error("pclip=%g should be > 0 and <= 100",pclip);
if (!sf_getfloat("normp",&normp)) normp=1.;
/* quasi-norm: normp<2 */
for (i=0; i < SF_MAX_DIM; i++) {/* dimensions */
snprintf(key,3,"n%d",i+1);
if (!sf_getint(key,n+i) &&
(NULL == in || !sf_histint(in,key,n+i))) break;
/*( n# size of #-th axis )*/
sf_putint(out,key,n[i]);
}
if (0==i) sf_error("Need n1=");
dim=i;
pad=sf_intalloc (dim);
for (i=0; i<dim; i++) pad[i]=0;
sf_getints("pad",pad,dim); /* number of zeros to be padded for each axis */
n1=n[0];
n2=sf_leftsize(in,1);
for (i=0; i<SF_MAX_DIM; i++) npadded[i]=1;
npadded[0]=n1+pad[0];
n1padded=npadded[0];
n2padded=1;
for (i=1; i<dim; i++){
npadded[i]=n[i]+pad[i];
if (pow2) {/* zero-padding to be power of 2 */
npadded[i]=nextpower2(n[i]);
fprintf(stderr,"n%d=%d n%dpadded=%d\n",i,n[i],i,npadded[i]);
}
n2padded*=npadded[i];
}
nw=npadded[0]/2+1;
num=nw*n2padded;/* data: total number of elements in frequency domain */
/* allocate data and mask arrays */
thresh=(float*) malloc(nw*n2padded*sizeof(float));
dobs_t=(float*) fftwf_malloc(n1padded*n2padded*sizeof(float)); /* time domain observation */
dobs=(fftwf_complex*)fftwf_malloc(nw*n2padded*sizeof(fftwf_complex));/* freq-domain observation */
dd=(fftwf_complex*) fftwf_malloc(nw*n2padded*sizeof(fftwf_complex));
mm=(fftwf_complex*) fftwf_malloc(nw*n2padded*sizeof(fftwf_complex));
if (NULL != sf_getstring("mask")){
mask=sf_floatalloc(n2padded);
} else sf_error("mask needed!");
/* initialize the input data and mask arrays */
memset(dobs_t,0,n1padded*n2padded*sizeof(float));
memset(mask,0,n2padded*sizeof(float));
for (i=0; i<n1*n2; i+=n1){
sf_line2cart(dim,n,i,ii);
j=sf_cart2line(dim,npadded,ii);
sf_floatread(&dobs_t[j], n1, in);
sf_floatread(&mask[j/n1padded], 1, Fmask);
}
/* FFT for the 1st dimension and the remaining dimensions */
fft1=fftwf_plan_many_dft_r2c(1, &n1padded, n2padded, dobs_t, &n1padded, 1, n1padded, dobs, &n1padded, 1, nw, FFTW_MEASURE);
ifft1=fftwf_plan_many_dft_c2r(1, &n1padded, n2padded, dobs, &n1padded, 1, nw, dobs_t, &n1padded, 1, n1padded, FFTW_MEASURE);
fftrem=fftwf_plan_many_dft(dim-1, &npadded[1], nw, dd, &npadded[1], nw, 1, dd, &npadded[1], nw, 1, FFTW_FORWARD, FFTW_MEASURE);
ifftrem=fftwf_plan_many_dft(dim-1, &npadded[1], nw, dd, &npadded[1], nw, 1, dd, &npadded[1], nw, 1, FFTW_BACKWARD, FFTW_MEASURE);
/* transform the data from time domain to frequency domain: dobs_t-->dobs */
fftwf_execute(fft1);
for(i=0; i<num; i++) dobs[i]/=sqrtf(n1padded);
memset(mm,0,num*sizeof(fftwf_complex));
/* Iterative Shrinkage-Thresholding (IST) Algorithm:
mm^{k+1}=T[mm^k+A^* M^* (dobs-M A mm^k)] (M^*=M; Mdobs=dobs)
=T[mm^k+A^*(dobs-M A mm^k)]; (k=0,1,...niter-1)
dd^=A mm^;
*/
for(iter=0; iter<niter; iter++)
{
/* dd<-- A mm^k */
memcpy(dd, mm, num*sizeof(fftwf_complex));
fftwf_execute(ifftrem);
for(i=0; i<num; i++) dd[i]/=sqrtf(n2padded);
/* apply mask: dd<--dobs-M A mm^k=dobs-M dd */
for(i2=0; i2<n2padded; i2++)
for(i1=0; i1<nw; i1++)
{
index=i1+nw*i2;
dd[index]=dobs[index]-mask[i2]*dd[index];
}
/* mm^k += A^*(dobs-M A mm^k); dd=dobs-M A mm^k */
fftwf_execute(fftrem);
for(i=0; i<num; i++) mm[i]+=dd[i]/sqrtf(n2padded);
/* perform thresholding */
for(i=0; i<num; i++) thresh[i]=cabsf(mm[i]);
nthr = 0.5+num*(1.-0.01*pclip); /* round off */
if (nthr < 0) nthr=0;
if (nthr >= num) nthr=num-1;
thr=sf_quantile(nthr, num, thresh);
sf_cpthresh(mm, num, thr, normp, mode);
if (verb) sf_warning("iteration %d;",iter+1);
}
/* frequency--> time domain: dobs-->dobs_t */
memcpy(dd, mm, num*sizeof(fftwf_complex));
fftwf_execute(ifftrem);
for(i=0; i<num; i++) dd[i]/=sqrtf(n2padded);
memcpy(dobs, dd, num*sizeof(fftwf_complex));
fftwf_execute(ifft1);
for(i=0; i<n1padded*n2padded; i++) dobs_t[i]/=sqrtf(n1padded);
for (i=0; i<n1*n2; i+=n1){
sf_line2cart(dim,n,i,ii);
j=sf_cart2line(dim,npadded,ii);
sf_floatwrite(&dobs_t[j],n1,out);
}
free(thresh);
fftwf_free(dobs_t);
fftwf_free(dobs);
fftwf_free(dd);
fftwf_free(mm);
exit(0);
}
int main(int argc, char** argv){
float tr[6];
const float ZAP=32;
const uint64_t TSIZE=18;
const uint64_t zapE=64;
fftwf_init_threads();
fftwf_plan_with_nthreads(omp_get_max_threads());
logmsg("Open file '%s'",argv[1]);
FILE* f = fopen(argv[1],"r");
int hdr_bytes = read_header(f);
const uint64_t nskip = hdr_bytes;
const uint64_t nchan = nchans;
logmsg("Nchan=%"PRIu64", tsamp=%f",nchan,tsamp);
mjk_rand_t *random = mjk_rand_init(12345);
rewind(f);
FILE* of = fopen("clean.fil","w");
uint8_t hdr[nskip];
fread(hdr,1,nskip,f);
fwrite(hdr,1,nskip,of);
const uint64_t nsamp_per_block=round(pow(2,TSIZE));
logmsg("Tblock = %f",nsamp_per_block*tsamp);
mjk_clock_t *t_all = init_clock();
start_clock(t_all);
mjk_clock_t *t_read = init_clock();
mjk_clock_t *t_trns= init_clock();
mjk_clock_t *t_rms = init_clock();
mjk_clock_t *t_fft = init_clock();
mjk_clock_t *t_spec = init_clock();
const uint64_t bytes_per_block = nchan*nsamp_per_block;
uint8_t *buffer = calloc(bytes_per_block,1);
float **data = malloc_2df(nchan,nsamp_per_block);
float **clean = malloc_2df(nchan,nsamp_per_block);
float *bpass = calloc(nchan,sizeof(float));
float *ch_var=NULL;
float *ch_mean=NULL;
float *ch_fft_n=NULL;
float *ch_fft_p=NULL;
logmsg("Planning FFT - this will take a long time the first time it is run!");
start_clock(t_fft);
FILE * wisfile;
if(wisfile=fopen("wisdom.txt","r")){
fftwf_import_wisdom_from_file(wisfile);
fclose(wisfile);
}
const int fftX=nsamp_per_block;
const int fftY=nchan;
const int fftXo=nsamp_per_block/2+1;
float *X = fftwf_malloc(sizeof(float)*fftX);
for (uint64_t i = 0; i < nsamp_per_block ; i++){
X[i]=i;
}
float *tseries = fftwf_malloc(sizeof(float)*fftX);
float complex *fseries = fftwf_malloc(sizeof(float complex)*fftXo);
float *pseries = fftwf_malloc(sizeof(float)*fftXo);
uint8_t *mask = malloc(sizeof(uint8_t)*fftXo);
fftwf_plan fft_1d = fftwf_plan_dft_r2c_1d(fftX,tseries,fseries,FFTW_MEASURE|FFTW_DESTROY_INPUT);
complex float * fftd = fftwf_malloc(sizeof(complex float)*(fftXo*fftY));
fftwf_plan fft_plan = fftwf_plan_many_dft_r2c(
1,&fftX,fftY,
data[0] ,&fftX,1,fftX,
fftd ,&fftXo,1,fftXo,
FFTW_MEASURE|FFTW_PRESERVE_INPUT);
logmsg("Planning iFFT - this will take a long time the first time it is run!");
fftwf_plan ifft_plan = fftwf_plan_many_dft_c2r(
1,&fftX,fftY,
fftd ,&fftXo,1,fftXo,
clean[0] ,&fftX,1,fftX,
FFTW_MEASURE|FFTW_PRESERVE_INPUT);
if(!fft_plan){
logmsg("Error - could not do FFT plan");
exit(2);
}
wisfile=fopen("wisdom.txt","w");
fftwf_export_wisdom_to_file(wisfile);
fclose(wisfile);
stop_clock(t_fft);
logmsg("T(planFFT)= %.2lfs",read_clock(t_fft));
reset_clock(t_fft);
float min_var=1e9;
float max_var=0;
float min_fft_n=1e9;
float max_fft_n=0;
float min_fft_p=1e9;
float max_fft_p=0;
float min_mean=1e9;
float max_mean=0;
uint64_t nblocks=0;
uint64_t totread=0;
while(!feof(f)){
nblocks++;
ch_var = realloc(ch_var,nchan*nblocks*sizeof(float));
ch_mean = realloc(ch_mean,nchan*nblocks*sizeof(float));
ch_fft_n = realloc(ch_fft_n,nchan*nblocks*sizeof(float));
ch_fft_p = realloc(ch_fft_p,nchan*nblocks*sizeof(float));
start_clock(t_read);
uint64_t read = fread(buffer,1,bytes_per_block,f);
stop_clock(t_read);
if (read!=bytes_per_block){
nblocks--;
break;
}
totread+=read;
logmsg("read=%"PRIu64" bytes. T=%fs",read,totread*tsamp/(float)nchan);
uint64_t offset = (nblocks-1)*nchan;
start_clock(t_trns);
// transpose with small blocks in order to increase cache efficiency.
#define BLK 8
#pragma omp parallel for schedule(static,2) shared(buffer,data)
for (uint64_t j = 0; j < nchan ; j+=BLK){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
for (uint64_t k = 0; k < BLK ; k++){
data[j+k][i] = buffer[i*nchan+j+k];
}
}
}
#pragma omp parallel for shared(data)
for (uint64_t j = 0; j < nchan ; j++){
if(j<zapE || (nchan-j) < zapE){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
data[j][i]=ZAP;
}
}
}
if(nblocks==1){
#pragma omp parallel for shared(data,bpass)
for (uint64_t j = 0; j < nchan ; j++){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
bpass[j]+=data[j][i];
}
bpass[j]/=(float)nsamp_per_block;
bpass[j]-=ZAP;
}
}
#pragma omp parallel for shared(data,bpass)
for (uint64_t j = 0; j < nchan ; j++){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
data[j][i]-=bpass[j];
}
}
stop_clock(t_trns);
start_clock(t_rms);
#pragma omp parallel for shared(data,ch_mean,ch_var)
for (uint64_t j = 0; j < nchan ; j++){
float mean=0;
for (uint64_t i = 0; i < nsamp_per_block ; i++){
mean+=data[j][i];
}
mean/=(float)nsamp_per_block;
if(mean > ZAP+5 || mean < ZAP-5){
logmsg("ZAP ch=%"PRIu64,j);
for (uint64_t i = 0; i < nsamp_per_block ; i++){
data[j][i]=ZAP;
}
}
float ss=0;
float x=0;
for (uint64_t i = 0; i < nsamp_per_block ; i++){
x = data[j][i]-mean;
ss+=x*x;
}
float var=ss/(float)nsamp_per_block;
if (var > 0){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
float v = (data[j][i]-mean)/sqrt(var);
if(v > 3 || v < -3){
data[j][i]=mjk_rand_gauss(random)*sqrt(var)+mean;
}
}
}
ch_var[offset+j] = var;
ch_mean[offset+j] = mean;
}
stop_clock(t_rms);
for (uint64_t i = 0; i < nsamp_per_block ; i++){
tseries[i]=0;
}
float tmean=0;
float tvar=0;
float max=0;
float min=1e99;
//#pragma omp parallel for shared(data,tseries)
// NOT THREAD SAFE
for (uint64_t j = 0; j < nchan ; j++){
tmean+=ch_mean[offset+j];
tvar+=ch_var[offset+j];
for (uint64_t i = 0; i < nsamp_per_block ; i++){
tseries[i]+=data[j][i];
if(data[j][i]>max)max=data[j][i];
if(data[j][i]<min)min=data[j][i];
}
}
float ss=0;
float mm=0;
for (uint64_t i = 0; i < nsamp_per_block ; i++){
float x=tseries[i]-tmean;
mm+=tseries[i];
ss+=x*x;
}
float rvar=ss/(float)nsamp_per_block;
logmsg("var=%g tvar=%g",ss/(float)nsamp_per_block,tvar);
logmsg("mean=%g tmean=%g",mm/(float)nsamp_per_block,tmean);
cpgopen("3/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,fftX,tmean-sqrt(tvar)*30,tmean+sqrt(tvar)*30);
cpgbox("ABN",0,0,"ABN",0,0);
cpgline(fftX,X,tseries);
cpgsci(2);
cpgclos();
tr[0] = 0.0 ;
tr[1] = 1;
tr[2] = 0;
tr[3] = 0.5;
tr[4] = 0;
tr[5] = 1;
logmsg("max=%g min=%g",max,min);
cpgopen("4/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nsamp_per_block,0,nchan);
cpgbox("ABN",0,0,"ABN",0,0);
cpggray(*data,nsamp_per_block,nchan,1,nsamp_per_block,1,nchan,tmean/(float)nchan+sqrt(rvar/(float)nchan),tmean/(float)nchan-sqrt(rvar/(float)nchan),tr);
cpgclos();
start_clock(t_fft);
fftwf_execute(fft_1d);
fftwf_execute(fft_plan);
stop_clock(t_fft);
{
float T = sqrt(fftXo*tvar)*12;
logmsg("Zap T=%.2e",T);
float fx[fftXo];
float fT[fftXo];
#pragma omp parallel for shared(fseries,pseries,mask)
for (uint64_t i = 0; i < fftXo ; i++){
mask[i]=1;
}
#pragma omp parallel for shared(fseries,pseries,mask)
for (uint64_t i = 0; i < fftXo ; i++){
pseries[i]=camp(fseries[i]);
fx[i]=i;
float TT = T;
if (i>512)TT=T/2.0;
if(i>32){
fT[i]=TT;
if (pseries[i] > TT) {
mask[i]=0;
}
} else fT[i]=0;
}
uint64_t nmask=0;
for (uint64_t i = 0; i < fftXo ; i++){
if (mask[i]==0){
nmask++;
}
}
logmsg("masked=%d (%.2f%%)",nmask,100*nmask/(float)fftXo);
cpgopen("1/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,fftXo,0,T*10);
cpgbox("ABN",0,0,"ABN",0,0);
cpgline(fftXo,fx,pseries);
cpgsci(2);
cpgline(fftXo,fx,fT);
cpgclos();
}
// exit(1);
start_clock(t_spec);
//FILE* ff=fopen("plot","w");
#pragma omp parallel for shared(fftd,ch_mean,ch_fft_n,ch_fft_p)
for (uint64_t j = 0; j < nchan ; j++){
float var = ch_var[offset+j];
float m=sqrt(var*fftXo/2.0);
float T = sqrt(var*fftXo)*3;
uint64_t n=0;
float p=0;
float complex *fftch = fftd + fftXo*j;
for(uint64_t i = 1; i < fftXo; i++){
if (camp(fftch[i]) > T) {
n++;
p+=camp(fftch[i]);
}
// if(j==512)fprintf(ff,"%f ",camp(fftch[i]));
if(mask[i]==0){
fftch[i]=m*(mjk_rand_gauss(random) + I*mjk_rand_gauss(random));
}
// if(j==512)fprintf(ff,"%f\n",camp(fftch[i]));
}
ch_fft_n[offset+j]=n;
ch_fft_p[offset+j]=p;
}
// fclose(ff);
logmsg("iFFT");
fftwf_execute(ifft_plan);
#pragma omp parallel for schedule(static,2) shared(buffer,clean)
for (uint64_t j = 0; j < nchan ; j+=BLK){
for (uint64_t i = 0; i < nsamp_per_block ; i++){
for (uint64_t k = 0; k < BLK ; k++){
clean[j+k][i]/=(float)fftX;
buffer[i*nchan+j+k] = round(clean[j+k][i]);
}
}
if(j==512){
cpgopen("2/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,fftX,ch_mean[j]-sqrt(ch_var[j])*10,ch_mean[j]+sqrt(ch_var[j])*10);
cpgbox("ABN",0,0,"ABN",0,0);
cpgline(fftX,X,data[j]);
cpgsci(2);
cpgline(fftX,X,clean[j]);
cpgclos();
}
}
fwrite(buffer,1,bytes_per_block,of);
for (uint64_t i = 0; i < nsamp_per_block ; i++){
tseries[i]=0;
}
tmean=0;
tvar=0;
max=0;
min=1e99;
//#pragma omp parallel for shared(clean,tseries)
// NOT THREAD SAFE
for (uint64_t j = 0; j < nchan ; j++){
tmean+=ch_mean[offset+j];
tvar+=ch_var[offset+j];
for (uint64_t i = 0; i < nsamp_per_block ; i++){
tseries[i]+=clean[j][i];
if(clean[j][i]>max)max=clean[j][i];
if(clean[j][i]<min)min=clean[j][i];
}
}
ss=0;
mm=0;
for (uint64_t i = 0; i < nsamp_per_block ; i++){
float x=tseries[i]-tmean;
mm+=tseries[i];
ss+=x*x;
}
rvar=ss/(float)nsamp_per_block;
logmsg("var=%g tvar=%g",ss/(float)nsamp_per_block,tvar);
logmsg("mean=%g tmean=%g",mm/(float)nsamp_per_block,tmean);
cpgopen("5/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,fftX,tmean-sqrt(tvar)*30,tmean+sqrt(tvar)*30);
cpgbox("ABN",0,0,"ABN",0,0);
cpgline(fftX,X,tseries);
cpgsci(2);
cpgclos();
tr[0] = 0.0 ;
tr[1] = 1;
tr[2] = 0;
tr[3] = 0.5;
tr[4] = 0;
tr[5] = 1;
logmsg("max=%g min=%g",max,min);
cpgopen("6/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nsamp_per_block,0,nchan);
cpgbox("ABN",0,0,"ABN",0,0);
cpggray(*clean,nsamp_per_block,nchan,1,nsamp_per_block,1,nchan,tmean/(float)nchan+sqrt(rvar/(float)nchan),tmean/(float)nchan-sqrt(rvar/(float)nchan),tr);
cpgclos();
stop_clock(t_spec);
for (uint64_t j = 0; j < nchan ; j++){
float mean=ch_mean[offset+j];
if (mean > max_mean)max_mean=mean;
if (mean < min_mean)min_mean=mean;
float var=ch_var[offset+j];
if (var > max_var)max_var=var;
if (var < min_var)min_var=var;
float fft_n=ch_fft_n[offset+j];
if (fft_n > max_fft_n)max_fft_n=fft_n;
if (fft_n < min_fft_n)min_fft_n=fft_n;
float fft_p=ch_fft_p[offset+j];
if (fft_p > max_fft_p)max_fft_p=fft_p;
if (fft_p < min_fft_p)min_fft_p=fft_p;
}
}
stop_clock(t_all);
fclose(of);
logmsg("T(all) = %.2lfs",read_clock(t_all));
logmsg("T(read) = %.2lfs",read_clock(t_read));
logmsg("T(trans)= %.2lfs",read_clock(t_trns));
logmsg("T(fft) = %.2lfs",read_clock(t_fft));
logmsg("T(fan) = %.2lfs",read_clock(t_spec));
logmsg("T(rms) = %.2lfs",read_clock(t_rms));
logmsg("T(rest) = %.2lfs",read_clock(t_all)-read_clock(t_read)-read_clock(t_trns)-read_clock(t_rms)-read_clock(t_fft)-read_clock(t_spec));
tr[0] = -tsamp*nsamp_per_block*0.5;
tr[2] = tsamp*nsamp_per_block;
tr[1] = 0;
tr[3] = 0.5;
tr[5] = 0;
tr[4] = 1;
cpgopen("1/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_mean,nchan,nblocks,1,nchan,1,nblocks,max_mean,min_mean,tr);
cpgclos();
cpgopen("2/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_var,nchan,nblocks,1,nchan,1,nblocks,max_var,min_var,tr);
cpgclos();
cpgopen("3/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_fft_n,nchan,nblocks,1,nchan,1,nblocks,max_fft_n,min_fft_n,tr);
cpgclos();
cpgopen("4/xs");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_fft_p,nchan,nblocks,1,nchan,1,nblocks,max_fft_p,min_fft_p,tr);
cpgclos();
cpgopen("mean.ps/vcps");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_mean,nchan,nblocks,1,nchan,1,nblocks,max_mean,min_mean,tr);
cpgclos();
cpgopen("var.ps/vcps");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_var,nchan,nblocks,1,nchan,1,nblocks,max_var,min_var,tr);
cpgclos();
cpgopen("fft_n.ps/vcps");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_fft_n,nchan,nblocks,1,nchan,1,nblocks,max_fft_n,min_fft_n,tr);
cpgclos();
cpgopen("fft_p.ps/vcps");
cpgsvp(0.1,0.9,0.1,0.9);
cpgswin(0,nblocks*tsamp*nsamp_per_block,0,nchan);
cpgbox("ABN",600,10,"ABN",100,1);
cpggray(ch_fft_p,nchan,nblocks,1,nchan,1,nblocks,max_fft_p,min_fft_p,tr);
cpgclos();
fclose(f);
free(buffer);
free_2df(data);
return 0;
}
/* Set up fft plans. Need to have npol, nphase, nchan
* already filled in struct */
int cyclic_init_ffts(struct cyclic_work *w) {
/* Infer lag, harmonic sizes from chan/phase */
w->nlag = w->nchan; // Total number of lags including + and -
w->nharm = w->nphase/2 + 1; // Only DC and positive harmonics
/* Alloc temp arrays for planning */
PS ps;
CS cs;
CC cc;
PC pc;
struct filter_time ft;
struct filter_freq ff;
struct profile_phase pp;
struct profile_harm ph;
ps.npol = cs.npol = cc.npol = pc.npol = w->npol;
ps.nphase = pc.nphase = w->nphase;
ps.nchan = cs.nchan = w->nchan;
cs.nharm = cc.nharm = w->nharm;
cc.nlag = pc.nlag = w->nlag;
cyclic_alloc_ps(&ps);
cyclic_alloc_cs(&cs);
cyclic_alloc_cc(&cc);
cyclic_alloc_pc(&pc);
ft.nlag = w->nlag;
ff.nchan = w->nchan;
pp.nphase = w->nphase;
ph.nharm = w->nharm;
filter_alloc_time(&ft);
filter_alloc_freq(&ff);
profile_alloc_phase(&pp);
profile_alloc_harm(&ph);
/* FFT plans */
int rv=0;
/* ps2cs - r2c fft along phase (fastest) axis */
w->ps2cs = fftwf_plan_many_dft_r2c(1, &w->nphase, w->npol*w->nchan,
ps.data, NULL, 1, w->nphase,
cs.data, NULL, 1, w->nharm,
FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->ps2cs == NULL) rv++;
/* cs2cc - c2c ifft along channel axis */
w->cs2cc = fftwf_plan_many_dft(1, &w->nchan, w->npol*w->nharm,
cs.data, NULL, w->nharm*w->npol, 1,
cc.data, NULL, w->nharm*w->npol, 1,
FFTW_BACKWARD, FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->cs2cc == NULL) rv++;
/* cc2cs - c2c fft along lag axis */
w->cc2cs = fftwf_plan_many_dft(1, &w->nlag, w->npol*w->nharm,
cc.data, NULL, w->nharm*w->npol, 1,
cs.data, NULL, w->nharm*w->npol, 1,
FFTW_FORWARD, FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->cc2cs == NULL) rv++;
/* time2freq, freq2time for filters */
w->time2freq = fftwf_plan_dft_1d(w->nlag, ft.data, ff.data,
FFTW_FORWARD, FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->time2freq == NULL) rv++;
w->freq2time = fftwf_plan_dft_1d(w->nchan, ff.data, ft.data,
FFTW_BACKWARD, FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->freq2time == NULL) rv++;
/* phase2harm, harm2phase for profiles */
w->phase2harm = fftwf_plan_dft_r2c_1d(w->nphase, pp.data, ph.data,
FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->phase2harm == NULL) rv++;
w->harm2phase = fftwf_plan_dft_c2r_1d(w->nphase, ph.data, pp.data,
FFTW_MEASURE | FFTW_PRESERVE_INPUT);
if (w->harm2phase == NULL) rv++;
cyclic_free_ps(&ps);
cyclic_free_cs(&cs);
cyclic_free_cc(&cc);
cyclic_free_pc(&pc);
filter_free_time(&ft);
filter_free_freq(&ff);
profile_free_phase(&pp);
profile_free_harm(&ph);
return(rv);
}
int main(int argc,char *argv[])
{
//this is C, so I have to declare all sorts of variables in advance
//update, I guess it's C++ now so this is a luxury
int i;
int j;
eggname[0]='\0';
//handle the command line options
int onindex;
if(((onindex=handle_options(argc,argv))==-1)||(argc-onindex<0))
{print_usage(); return -1;};
// char *eggname=argv[onindex];
if(eggname[0]=='\0') {
fprintf(stderr,"no input file given, use -i option\n");
return -1;
}
//open the egg
/*
struct egg current;
mBreakEgg(eggname,¤t);
mParseEggHeader(¤t);
sampling_rate_mhz=current.data->sample_rate;
*/
// Monarch *egg=Monarch::OpenForReading(eggname);
// Monarch *egg=Monarch::Open(std::string(eggname),ReadMode);
const Monarch *egg=Monarch::OpenForReading(std::string(eggname));
egg->ReadHeader();
const MonarchHeader *eggheader=egg->GetHeader();
const MonarchRecord *event;
sampling_rate_mhz=eggheader->GetAcquisitionRate();
// printf("record size: %d\n",eggheader->GetRecordSize());
//decide the optimal size for ffts and allocate memory
if(eggheader->GetRecordSize()<(unsigned int)fft_size) {
// if(current.data->record_size<fft_size) {
fprintf(stderr,"fft size larger than record size. make fft size smaller. aborting");
return -1;
}
//nffts_per_event=current.data->record_size/fft_size;
nffts_per_event=eggheader->GetRecordSize()/fft_size;
fft_output_size=fft_size/2+1;
//fft_input=fftwf_alloc_real(fft_size*nffts_per_event);
fft_input=(float*)fftwf_malloc(sizeof(float)*nffts_per_event*fft_size);
//fft_output=fftwf_alloc_complex(fft_size*nffts_per_event);
fft_output=(fftwf_complex*)fftwf_malloc(sizeof(fftwf_complex)*fft_output_size*nffts_per_event);
output_powerspectrum=(double*)malloc(sizeof(double)*fft_output_size);
for(i=0;i<fft_output_size;i++) output_powerspectrum[i]=0;
//create the fft plan
fft_plan=fftwf_plan_many_dft_r2c(1,&fft_size,nffts_per_event,fft_input,NULL,1,fft_size,fft_output,NULL,1,fft_output_size,FFTW_ESTIMATE);
//perform ffts
//int on_event=0;
int nffts_so_far=0;
//while((mHatchNextEvent(¤t)!=1)&&(on_event<=max_number_of_events)) {
//while((event=egg->GetNextEvent())!=NULL&&(on_event<=max_number_of_events)) {
while(egg->ReadRecord()) {
if(on_channel==1)
event=egg->GetRecordSeparateOne();
else
event=egg->GetRecordSeparateTwo();
if(event==NULL) {
fprintf(stderr,"ERROR: event was null. aborting\n");
return -1;
}
//convert data to floats
//for(i=0;i<current.data->record_size;i++)
for(i=0;i<eggheader->GetRecordSize();i++)
//fft_input[i]=(float)(current.data->record[i])-128.0;
fft_input[i]=(float)(event->fData[i])-128.0;
//perform the ffts
fftwf_execute(fft_plan);
//pack in to power spectrum
int on_pt=0;
for(i=0;i<nffts_per_event;i++)
for(j=0;j<fft_output_size;j++) {
output_powerspectrum[j]+=fft_output[on_pt][0]*fft_output[on_pt][0]+fft_output[on_pt][1]*fft_output[on_pt][1];
on_pt++;
}
nffts_so_far+=nffts_per_event;
}
//normalize to power in milliwatts
// each sample * 0.5 (volts fullscale)/255 (levels) /(sqrt(fftlength)
// power *2 (positive and negative freqs) *1000 mW/W / naverages
//1000 (milliwatts/watt) * 0.5 (volts fullscale)/256 (levels) / (sqrt(fft_length)*(number of averages) / 50 ohms
double normalization=2.0*(1000.0*0.5*0.5/(256.0*256.0))*(1.0/(((double)fft_size*fft_size)*((double)nffts_so_far)))/50.0;
for(i=0;i<fft_output_size;i++)
output_powerspectrum[i]*=normalization;
//print out result
if(format=='j') { //ASCII output, JSON
printf("{ \"sampling_rate\": %d , ",sampling_rate_mhz);
printf("\"data\": [");
for(i=0;i<fft_output_size;i++) {
if(i!=0) printf(",");
printf("%g",output_powerspectrum[i]);
}
printf("] }");
} else if(format=='a') {
for(i=0;i<fft_output_size;i++)
printf("%g %g\n",sampling_rate_mhz*((double)i)/((double)(2*fft_output_size)),output_powerspectrum[i]);
} else { //binary
fwrite(output_powerspectrum,sizeof(double),fft_output_size,stdout);
}
//clean up
egg->Close();
fftwf_destroy_plan(fft_plan);
fftwf_free(fft_input);
fftwf_free(fft_output);
free(output_powerspectrum);
//mCleanUp(¤t);
return 0;
}