PyObject *
ImageMap_s (int color, PyObject *args)
{
PyObject *oa=NULL;
PyArrayObject *aa=NULL;
float
*a=NULL,
tr[6], levels[10],
x1=0.0, y1=0.0, x2=0.0, y2=0.0,
fg=0.0, bg=0.0;
int
rn=0, cn=0;
if (!PyArg_ParseTuple(args,"O|ffffff:imagemap_s",
&oa, &fg, &bg, &x1, &y1, &x2, &y2))
return(NULL);
if (!(aa =(PyArrayObject *)tofloatmat(oa, &a, &rn, &cn))) return(NULL);
/* Perform autocalibrations as nesecairy. */
autocal2d(a, rn, cn, &fg, &bg, 5, levels, &x1, &x2, &y1, &y2, tr);
if (color)
cpgimag(a, cn, rn, 0+1, cn, 0+1, rn, bg, fg, tr);
else
cpggray(a, cn, rn, 0+1, cn, 0+1, rn, fg, bg, tr);
Py_DECREF(aa);
PYRN;
}
/*
* Class: pulsarhunter_PgplotInterface
* Method: pggray
* Signature: ([FIIIIIIFFF)V
*/
JNIEXPORT void JNICALL Java_pulsarhunter_PgplotInterface_pggray
(JNIEnv *env, jclass cl, jfloatArray arr, jint idim, jint jdim, jint i1, jint i2, jint j1, jint j2, jfloat fg, jfloat bg, jfloatArray tr){
jfloat* trArr = (*env)->GetFloatArrayElements(env,tr,0);
jfloat* arrArr = (*env)->GetFloatArrayElements(env,arr,0);
cpggray(arrArr,idim,jdim,i1,i2,j1,j2,fg,bg,trArr);
(*env)->ReleaseFloatArrayElements(env,tr,trArr,0);
(*env)->ReleaseFloatArrayElements(env,arr,arrArr,0);
}
static PyObject *
ImageMap(int color, PyObject *args)
{
float fg=0.0, bg=0.0, *a=NULL, *tr=NULL;
int cd=0, rd=0, c1=0, c2=0, r1=0, r2=0, rn=0, cn=0, sz=0;
PyObject *oa = NULL, *ot = NULL;
PyArrayObject *aa = NULL, *at = NULL;
if (!PyArg_ParseTuple(args,"OiiiiiiffO:pggray",
&oa, &cd, &rd, &c1, &c2, &r1, &r2,
&fg, &bg, &ot))
return(NULL);
if (!(aa =(PyArrayObject *)tofloatmat(oa, &a, &rn, &cn))) goto fail;
if (!(at =(PyArrayObject *)tofloatvector(ot, &tr, &sz))) goto fail;
if (sz < 6) {
PyErr_SetString(PpgTYPEErr,"pggray: invalid transform. vactor");
goto fail;
}
if (color)
cpgimag(a, cn, rn, c1+1, c2+1, r1+1, r2+1, bg, fg, tr);
else
cpggray(a, cn, rn, c1+1, c2+1, r1+1, r2+1, fg, bg, tr);
Py_DECREF(aa);
Py_DECREF(at);
PYRN;
fail:
if (aa) { Py_DECREF(aa); }
if (at) { Py_DECREF(at); }
return(NULL);
}
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;
}
