int sub_image (imageptr iptr, regionptr rptr, imageptr *optr)
{
int nx,ny,nz, nx1,ny1,nz1, ix,iy,iz, ix0,iy0,iz0;
size_t np, np1;
nx = Nx(iptr);
ny = Ny(iptr);
nz = Nz(iptr);
np = nx*ny*nz;
/* grab the bounding box */
ix0 = BLC(rptr)[0];
iy0 = BLC(rptr)[1];
iz0 = BLC(rptr)[2];
nx1 = TRC(rptr)[0] - ix0;
ny1 = TRC(rptr)[1] - iy0;
nz1 = TRC(rptr)[2] - iz0;
np1 = nx1*ny1*nz1;
*optr = (imageptr ) allocate(sizeof(image));
dprintf (DLEV,"copy_image:Allocated image @ %d size=%d * %d * %d",*optr,nx1,ny1,nz1);
Frame(*optr) = (real *) allocate(np1*sizeof(real));
dprintf (DLEV,"Frame allocated @ %d ",Frame(*optr));
Nx(*optr) = nx1;
Ny(*optr) = ny1;
Nz(*optr) = nz1;
Xmin(*optr) = Xmin(iptr) + ix0*Dx(iptr);
Ymin(*optr) = Ymin(iptr) + iy0*Dy(iptr);
Zmin(*optr) = Zmin(iptr) + iz0*Dz(iptr);
Dx(*optr) = Dx(iptr);
Dy(*optr) = Dy(iptr);
Dz(*optr) = Dz(iptr);
Namex(*optr) = mystrcpy(Namex(iptr));
Namey(*optr) = mystrcpy(Namey(iptr));
Namez(*optr) = mystrcpy(Namez(iptr));
Xref(*optr) = Xref(iptr) + ix0;
Yref(*optr) = Yref(iptr) + iy0;
Zref(*optr) = Zref(iptr) + iz0;
for (iz=0; iz<nz1; iz++)
for (iy=0; iy<ny1; iy++)
for (ix=0; ix<nx1; ix++)
CubeValue(*optr,ix,iy,iz) = CubeValue(iptr,ix-ix0,iy-iy0,iz-iy0);
Storage(*optr) = matdef[idef];
Axis(*optr) = Axis(iptr);
set_iarray(*optr);
return 1; /* succes return code */
}
local void object_ferrers(int npars, real *pars)
{
int i,nx = Nx(iptr);
int j,ny = Ny(iptr);
int l, lmax;
real A = 1.0; /* peak */
real h = 1.0; /* size */
real e = 0.0; /* 1-b/a */
real b = 0.0; /* phi */
real p = 1.0; /* power factor */
real x1,y1,x2,y2,x3,y3,r,arg,value;
real amp,phi,sum;
real sinb,cosb;
if (npar > 0) A = pars[0];
if (npar > 1) h = pars[1];
if (npar > 2) e = pars[2];
if (npar > 3) b = pars[3];
if (npar > 4) p = pars[4];
dprintf(0,"ferrers: %g %g %g %g %g\n",A,h,e,b,p);
if (A==0) return;
lmax = Qtotflux ? 2 : 1;
sinb = sin(b*PI/180.0);
cosb = cos(b*PI/180.0);
for (l=0; l<lmax; l++) { /* 1st loop: sum up the flux if in 2nd loop: normalize */
if (l==0)
sum = 0.0;
else {
A /= sum;
dprintf(0,"ferrers: A->%g\n",A);
}
for (j=0; j<ny; j++) {
y1 = (j-center[1])*Dy(iptr) + Ymin(iptr);
for (i=0; i<nx; i++) {
x1 = (i-center[0])*Dx(iptr) + Xmin(iptr);
x2 = -x1*sinp - y1*cosp;
y2 = (x1*cosp - y1*sinp)/cosi;
x3 = x2*cosb - y2*sinb;
y3 = (x2*sinb + y2*cosb)/(1-e);
r = (x3*x3+y3*y3)/(h*h);
value = r < 1 ? A * pow(1.0-r, p) : 0.0;
if (Qtotflux) {
if (l==0)
sum += value;
else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} /* i */
} /* j */
} /* k */
}
local void object_gauss(int npars, real *pars)
{
int i,nx = Nx(iptr);
int j,ny = Ny(iptr);
real A = 1.0;
real h = 1.0;
real x1,y1,x2,y2,r,arg,value;
if (npar > 0) A = pars[0];
if (npar > 1) h = pars[1];
dprintf(0,"gauss: %g %g\n",A,h);
if (A==0) return;
if (Qtotflux) {
A /= (PI*h*h/surface);
dprintf(0,"gauss: A->%g\n",A);
}
for (j=0; j<ny; j++) {
y1 = (j-center[1])*Dy(iptr) + Ymin(iptr);
for (i=0; i<nx; i++) {
x1 = (i-center[0])*Dx(iptr) + Xmin(iptr);
x2 = -x1*sinp - y1*cosp;
y2 = x1*cosp - y1*sinp;
r = sqrt(x2*x2 + sqr(y2/cosi));
arg = r/h;
dprintf(2,"%d %d : %g %g %g %g %g\n",i,j,x1,y1,x2,y2,arg);
value = (arg < 13) ? A * exp(-0.5*arg*arg) : 0.0;
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
}
}
}
void ini_matrix(imageptr *iptr, int nx, int ny)
{
int ix,iy;
printf ("iptr @ %d (sizeof = %d)\n",*iptr,sizeof(image));
if (*iptr==0) {
*iptr = (imageptr ) allocate((sizeof(image)));
printf ("allocated image 'iptr' @ %d\n",*iptr);
Frame(*iptr) = (real *) allocate (nx*ny*sizeof(real));
printf ("Allocated frame @ %d\n",Frame(*iptr));
} else {
printf ("Image already allocated @ %d\n",*iptr);
printf ("with Frame @ %d\n",Frame(*iptr));
}
Nx(*iptr) = nx;
Ny(*iptr) = ny;
Nz(*iptr) = 1;
Xmin(*iptr) = 1.0;
Ymin(*iptr) = 2.0;
Zmin(*iptr) = 3.0;
Dx(*iptr) = 0.1;
Dy(*iptr) = 0.1;
Dz(*iptr) = 0.1;
Namex(*iptr) = NULL; /* no axis names */
Namey(*iptr) = NULL;
Namez(*iptr) = NULL;
Unit(*iptr) = NULL; /* no units */
Mask(*iptr) = NULL;
set_iarray(*iptr);
for (ix=0; ix<nx; ix++)
for (iy=0; iy<ny; iy++)
MapValue(*iptr,ix,iy) = (ix*ny+iy)*0.1;
}
nemo_main()
{
int n = 0;
setparams(); /* set globals */
instr = stropen (infile, "r");
plinit ("***", 0.0, 20.0, 0.0, 20.0); /* init yapp */
while (read_image(instr,&iptr)) { /* loop while more images found */
dprintf(1,"Time= %g MinMax= %g %g\n",Time(iptr),MapMin(iptr),MapMax(iptr));
nx=Nx(iptr);
ny=Ny(iptr);
nz=Nz(iptr);
if (nz > 1) error("Cannot handle 3D images [%d,%d,%d]",nx,ny,nz);
xmin=Xmin(iptr);
ymin=Ymin(iptr);
dx=Dx(iptr);
dy=Dy(iptr);
xsize = nx * dx;
ysize = ny * dy;
if (n>0) {
sleep(1);
plframe();
}
plot_map(); /* plot the map */
n++;
}
plstop(); /* end of yapp */
strclose(instr);
}
void nemo_main ()
{
setparams(); /* set par's in globals */
instr = stropen (infile, "r");
read_image (instr,&iptr);
/* set some global paramters */
nx = Nx(iptr);
ny = Ny(iptr);
nz = Nz(iptr);
xmin = Xmin(iptr);
ymin = Ymin(iptr);
zmin = Zmin(iptr);
dx = Dx(iptr);
dy = Dy(iptr);
dz = Dz(iptr);
if(hasvalue("gauss"))
make_gauss_beam(getparam("dir"));
outstr = stropen (outfile,"w");
if (hasvalue("wiener"))
wiener();
else
smooth_it();
write_image (outstr,iptr);
strclose(instr);
strclose(outstr);
}
local void object_isothermal(int npars, real *pars)
{
int i,nx = Nx(iptr);
int j,ny = Ny(iptr);
int l, lmax;
real A = 1.0; /* peak */
real h = 1.0; /* size */
real p = -0.5; /* power factor */
real x1,y1,x2,y2,x3,y3,r,arg,value;
real amp,phi,sum;
real sinb,cosb;
if (npar > 0) A = pars[0];
if (npar > 1) h = pars[1];
if (npar > 2) p = pars[2];
dprintf(0,"isothermal: %g %g %g \n",A,h,p);
if (A==0) return;
lmax = Qtotflux ? 2 : 1;
for (l=0; l<lmax; l++) { /* 1st loop: sum up the flux if in 2nd loop: normalize */
if (l==0)
sum = 0.0;
else {
A /= sum;
dprintf(0,"isothermal: A->%g\n",A);
}
for (j=0; j<ny; j++) {
y1 = (j-center[1])*Dy(iptr) + Ymin(iptr);
for (i=0; i<nx; i++) {
x1 = (i-center[0])*Dx(iptr) + Xmin(iptr);
x2 = -x1*sinp - y1*cosp;
y2 = (x1*cosp - y1*sinp)/cosi;
r = (x2*x2+y2*y2)/(h*h);
value = A * pow(1.0+r, p);
if (Qtotflux) {
if (l==0)
sum += value;
else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} /* i */
} /* j */
} /* k */
}
int copy_image (imageptr iptr, imageptr *optr)
{
int nx,ny,nz;
size_t np;
nx = Nx(iptr);
ny = Ny(iptr);
nz = Nz(iptr);
np = nx*ny*nz;
*optr = (imageptr ) allocate(sizeof(image));
dprintf (DLEV,"copy_image:Allocated image @ %d size=%d * %d * %d",*optr,nx,ny,nz);
Frame(*optr) = (real *) allocate(np*sizeof(real));
dprintf (DLEV,"Frame allocated @ %d ",Frame(*optr));
Nx(*optr) = nx;
Ny(*optr) = ny;
Nz(*optr) = nz;
Xmin(*optr) = Xmin(iptr);
Ymin(*optr) = Ymin(iptr);
Zmin(*optr) = Zmin(iptr);
Dx(*optr) = Dx(iptr);
Dy(*optr) = Dy(iptr);
Dz(*optr) = Dz(iptr);
Namex(*optr) = mystrcpy(Namex(iptr));
Namey(*optr) = mystrcpy(Namey(iptr));
Namez(*optr) = mystrcpy(Namez(iptr));
Xref(*optr) = Xref(iptr);
Yref(*optr) = Yref(iptr);
Zref(*optr) = Zref(iptr);
Storage(*optr) = matdef[idef];
Axis(*optr) = Axis(iptr);
set_iarray(*optr);
return 1; /* succes return code */
}
std::string LaczeDoGNUPlota::ZapiszUstawienieZakresu(char Os) const
{
ostringstream strm;
float Min, Max;
switch (Os) {
case 'x': Min = Xmin(); Max = Xmax(); break;
case 'y': Min = Ymin(); Max = Ymax(); break;
case 'z': Min = Zmin(); Max = Zmax(); break;
default: cerr << "!!! Blad w 'ZapiszUstawienieZakresu' niedozwolony"
" znak: " << Os << endl;
return "";
}
strm << "set " << Os << "range [" << Min << ":" << Max << "]\n";
return strm.str();
}
int write_image (stream outstr, imageptr iptr)
{
put_history(outstr);
put_set (outstr,ImageTag);
put_set (outstr,ParametersTag);
put_data (outstr,NxTag, IntType, &(Nx(iptr)), 0);
put_data (outstr,NyTag, IntType, &(Ny(iptr)), 0);
put_data (outstr,NzTag, IntType, &(Nz(iptr)), 0);
put_data (outstr,XminTag,RealType, &(Xmin(iptr)), 0);
put_data (outstr,YminTag,RealType, &(Ymin(iptr)), 0);
put_data (outstr,ZminTag,RealType, &(Zmin(iptr)), 0);
put_data (outstr,DxTag, RealType, &(Dx(iptr)), 0);
put_data (outstr,DyTag, RealType, &(Dy(iptr)), 0);
put_data (outstr,DzTag, RealType, &(Dz(iptr)), 0);
put_data (outstr,XrefTag,RealType, &(Xref(iptr)), 0);
put_data (outstr,YrefTag,RealType, &(Yref(iptr)), 0);
put_data (outstr,ZrefTag,RealType, &(Zref(iptr)), 0);
put_data (outstr,MapMinTag, RealType, &(MapMin(iptr)), 0);
put_data (outstr,MapMaxTag, RealType, &(MapMax(iptr)), 0);
put_data (outstr,BeamTypeTag, IntType, &(BeamType(iptr)), 0);
put_data (outstr,BeamxTag, RealType, &(Beamx(iptr)), 0);
put_data (outstr,BeamyTag, RealType, &(Beamy(iptr)), 0);
put_data (outstr,BeamzTag, RealType, &(Beamz(iptr)), 0);
if (Namex(iptr))
put_string (outstr,NamexTag,Namex(iptr));
if (Namey(iptr))
put_string (outstr,NameyTag,Namey(iptr));
if (Namez(iptr))
put_string (outstr,NamezTag,Namez(iptr));
if (Unit(iptr))
put_string (outstr,UnitTag,Unit(iptr));
put_data (outstr,TimeTag, RealType, &(Time(iptr)), 0);
put_string(outstr,StorageTag,matdef[idef]);
put_data (outstr,AxisTag, IntType, &(Axis(iptr)), 0);
put_tes (outstr, ParametersTag);
put_set (outstr,MapTag);
if (Nz(iptr)==1)
put_data (outstr,MapValuesTag,RealType,
Frame(iptr),Nx(iptr),Ny(iptr),0);
else
put_data (outstr,MapValuesTag,RealType,
Frame(iptr),Nx(iptr),Ny(iptr),Nz(iptr),0);
put_tes (outstr, MapTag);
put_tes (outstr, ImageTag);
return 1;
}
local void object_bar(int npars, real *pars)
{
int i,nx = Nx(iptr);
int j,ny = Ny(iptr);
real A = 1.0;
real h = 1.0;
real e = 0.0;
real b = 0.0;
real x1,y1,x2,y2,x3,y3,r,arg,value;
real sinb,cosb,omba;
if (npar > 0) A = pars[0];
if (npar > 1) h = pars[1];
if (npar > 2) e = pars[2];
if (npar > 3) b = pars[3];
dprintf(0,"bar: %g %g %g %g\n",A,h,e,b);
sinb = sin(b*PI/180.0);
cosb = cos(b*PI/180.0);
if (A==0) return;
if (Qtotflux) {
A /= (PI*h*h*(1-e)/surface);
dprintf(0,"bar: A->%g\n",A);
}
dprintf(1,"bar b=%g\n",b);
for (j=0; j<ny; j++) {
y1 = (j-center[1])*Dy(iptr) + Ymin(iptr);
for (i=0; i<nx; i++) {
x1 = (i-center[0])*Dx(iptr) + Xmin(iptr);
x2 = -x1*sinp - y1*cosp;
y2 = (x1*cosp - y1*sinp)/cosi;
x3 = x2*cosb - y2*sinb;
y3 = (x2*sinb + y2*cosb)/(1-e);
r = sqrt(x3*x3+y3*y3);
arg = r/h;
value = (arg < 100) ? A * exp(-arg) : 0.0;
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
}
}
}
void fixheader(imageptr iptr, string options, real t0, real dt)
{
char *ap = allocate(sizeof(options) + sizeof("Attribute") + 10);
sprintf(ap,"Attribute: %s",options);
Namex(iptr) = strdup("Particle");
Xmin(iptr) = 0.0;
Dx(iptr) = 1.0;
Namey(iptr) = strdup(ap);
Ymin(iptr) = 0.0;
Dy(iptr) = 1.0;
Namez(iptr) = strdup("Time");
Zmin(iptr) = t0;
Dz(iptr) = dt;
free(ap);
}
/*
* CREATE_CUBE: create a blank cube Nx by Ny by Nz in size
*/
int create_cube (imageptr *iptr, int nx, int ny, int nz)
{
*iptr = (imageptr ) allocate(sizeof(image));
dprintf (DLEV,"CREATE_CUBE: Allocated image @ cube %d size=%d * %d * %d",
*iptr,nx,ny,nz);
if (*iptr == NULL)
return 0; /* no memory available */
Frame(*iptr) = (real *) allocate(nx*ny*nz*sizeof(real));
dprintf (DLEV,"Frame allocated @ %d ",Frame(*iptr));
Nx(*iptr) = nx; /* cube dimension */
Ny(*iptr) = ny;
Nz(*iptr) = nz;
Xmin(*iptr) = 0.0; /* start lower left corner at 0.0 */
Ymin(*iptr) = 0.0;
Zmin(*iptr) = 0.0;
Xref(*iptr) = 0.0;
Yref(*iptr) = 0.0;
Zref(*iptr) = 0.0;
Dx(*iptr) = 1.0; /* unity pixels */
Dy(*iptr) = 1.0;
Dz(*iptr) = 1.0;
MapMin(*iptr) = 0.0;
MapMax(*iptr) = 0.0;
BeamType(*iptr) = 0;
Beamx(*iptr) = 0.0; /* name beams */
Beamy(*iptr) = 0.0;
Beamz(*iptr) = 0.0;
Namex(*iptr) = NULL; /* no axis names yet */
Namey(*iptr) = NULL;
Namez(*iptr) = NULL;
Unit(*iptr) = NULL; /* no units */
Time(*iptr) = 0.0;
Storage(*iptr) = matdef[idef];
Axis(*iptr) = 0;
Mask(*iptr) = NULL;
set_iarray(*iptr);
return 1; /* succes return code */
}
int create_image (imageptr *iptr, int nx, int ny)
{
*iptr = (imageptr ) allocate(sizeof(image));
dprintf (DLEV,"create_image:Allocated image @ %d size=%d * %d",*iptr,nx,ny);
Frame(*iptr) = (real *) allocate(nx*ny*sizeof(real));
dprintf (DLEV,"Frame allocated @ %d ",Frame(*iptr));
Axis(*iptr) = 0; /* old style axis with no reference pixel */
Nx(*iptr) = nx; /* old style ONE map, no cube */
Ny(*iptr) = ny;
Nz(*iptr) = 1;
Xmin(*iptr) = 0.0; /* start lower left corner at 0.0 */
Ymin(*iptr) = 0.0;
Zmin(*iptr) = 0.0;
Dx(*iptr) = 1.0; /* unity pixels */
Dy(*iptr) = 1.0;
Dz(*iptr) = 1.0;
Xref(*iptr) = 0.0;
Yref(*iptr) = 0.0;
Zref(*iptr) = 0.0;
MapMin(*iptr) = 0.0;
MapMax(*iptr) = 0.0;
BeamType(*iptr) = 0;
Beamx(*iptr) = 0.0; /* name beams */
Beamy(*iptr) = 0.0;
Beamz(*iptr) = 0.0;
Namex(*iptr) = NULL; /* no axis names */
Namey(*iptr) = NULL;
Namez(*iptr) = NULL;
Unit(*iptr) = NULL; /* no units */
Time(*iptr) = 0.0;
Storage(*iptr) = matdef[idef];
Axis(*iptr) = 0;
Mask(*iptr) = NULL;
set_iarray((*iptr));
return 1; /* succes return code */
}
void make_rawheader(FITS *fitsfile, imageptr iptr, bool Qrel)
{
int ndim, n;
double tmpr[3];
ndim = (Nz(iptr) > 1) ? 3 : 2;
n = nemoinpd(getparam("cdelt"),tmpr,3);
if (n == 0) {
Dx(iptr) = 2.0/Nx(iptr);
Dy(iptr) = 2.0/Ny(iptr);
Dz(iptr) = 2.0/Nz(iptr);
} else if (n == 3) {
Dx(iptr) = tmpr[0];
Dy(iptr) = tmpr[1];
Dz(iptr) = tmpr[2];
} else
error("cdelt= needs either 3 or 0 entries");
Xmin(iptr) = 0.0;
Ymin(iptr) = 0.0;
Zmin(iptr) = 0.0;
}
plot_map ()
{
real m_range, brightness, dcm;
real m_min, m_max;
int i, ix, iy;
int cnt; /* counter of pixels */
nsize = Nx(iptr); /* old method forced square .. */
cell = Dx(iptr); /* and forced so for gray scale due to LW mem-problems */
size = nsize*cell;
m_min = MapMin(iptr); /* get min- and max from header */
m_max = MapMax(iptr);
dprintf (1,"Min and max in map from map-header are: %f %f\n",m_min,m_max);
if (mmax==UNDEF) /* reset default autoscales to user supplied if necessary */
mmax=m_max;
if (mmin==UNDEF)
mmin=m_min;
m_range = mmax-mmin;
if (m_range==0) {
mmax=mmin+1.0;
if (gray) warning("%g; Plot-range was zero, mmax increased by 1",mmin);
}
dprintf (1,"User reset Min and max are: %f %f\n",mmin,mmax);
sprintf (plabel,"File: %s",infile); /* filename */
sprintf (clabel,"Contours: %s",cntstr); /* contour levels */
sprintf (glabel,"Gray MinMax: %g %g",mmin,mmax); /* grey scale minmax */
sprintf (tlabel,"Time: %g",Time(iptr)); /* time of orig snapshot */
/* set scales and labels along axes */
if (xplot[0]==UNDEF || xplot[1]==UNDEF) {
xplot[0] = Xmin(iptr) - 0.5*Dx(iptr);
xplot[1] = xplot[0] + Nx(iptr)*Dx(iptr);
}
if (Namex(iptr))
strncpy(xlabel,Namex(iptr),80);
else
strcpy (xlabel,"");
if (yplot[0]==UNDEF || yplot[1]==UNDEF) {
yplot[0] = Ymin(iptr) - 0.5*Dy(iptr);
yplot[1] = yplot[0] + Ny(iptr)*Dy(iptr);
}
if (Namey(iptr))
strncpy(ylabel,Namey(iptr),80);
else
strcpy (ylabel,"");
dprintf (1,"Plotting area x=%f:%f y=%f:%f\n",
xplot[0], xplot[1], yplot[0], yplot[1]);
if (gray) {
/* gray-scale */
dcm = Dx(iptr) / (xplot[1]-xplot[0]) * 16.0;
pl_matrix (Frame(iptr), nx, ny,
xtrans(Xmin(iptr)), ytrans(Ymin(iptr)), dcm , mmin, mmax, power, blankval);
/* color_bar (100.0,500.0,32); */
}
/* OLD ROUTINE, has to call relocate/frame ---> plcontour */
plltype(lwidth,ltype);
if (cmode==0)
contour (Frame(iptr),nx,ny,cntval,ncntval,
Xmin(iptr),
Ymin(iptr),
Xmin(iptr)+(Nx(iptr)-1)*Dx(iptr),
Ymin(iptr)+(Ny(iptr)-1)*Dy(iptr), lineto);
else if (cmode==1)
pl_contour (Frame(iptr),nx,ny,ncntval,cntval);
plltype(1,1);
/* draw axes and their labels */
xaxis ( 2.0, 2.0, 16.0, xplot, -7, xtrans, xlabel);
xaxis ( 2.0,18.0, 16.0, xplot, -7, xtrans, NULL);
yaxis ( 2.0, 2.0, 16.0, yplot, -7, ytrans, ylabel);
yaxis (18.0, 2.0, 16.0, yplot, -7, ytrans, NULL);
pltext (plabel,2.0,18.4, 0.32, 0.0); /* plot header with file name */
pltext (clabel,2.0,19.0, 0.32, 0.0); /* plot header with contour levels */
pltext (glabel,2.0,19.6, 0.32, 0.0); /* plot header with greyscale info */
pltext (tlabel,10.0,19.6,0.32, 0.0); /* time info */
pljust(1);
pltext (headline,10.0,18.4, 0.26, 0.0); /* plot extra user suplied header */
pljust(-1);
}
void nemo_main()
{
stream instr, outstr;
int nx, ny, nz; /* size of scratch map */
int nx1, ny1, nz1, nz2;
int ni, i, ix, iy, iz, iz1;
real dmin, dmax;
imageptr iptr[MAXIM], optr; /* pointer to image */
string flipmode;
instr = stropen(getparam("in"), "r");
outstr = stropen(getparam("out"), "w");
for (i=0; i<MAXIM; i++) { /* loop over all to gather data */
iptr[i] = 0;
if (read_image( instr, &iptr[i]) == 0) break;
nx1 = Nx(iptr[i]);
ny1 = Ny(iptr[i]);
nz1 = Nz(iptr[i]);
dprintf(1,"Image %d: %d x %d x %d\n",i,nx1,ny1,nz1);
if (i==0) {
nx = nx1;
ny = ny1;
nz = nz1;
dmin = MapMin(iptr[i]);
dmax = MapMax(iptr[i]);
} else {
if (nx != nx1) error("size nx: %d != %d",nx,nx1);
if (ny != ny1) error("size ny: %d != %d",ny,ny1);
nz += nz1;
dmin = MIN(dmin,MapMin(iptr[i]));
dmax = MAX(dmax,MapMax(iptr[i]));
}
}
ni = i;
dprintf(0,"Final cube: %d x %d x %d\n",nx,ny,nz);
dprintf(0,"Data min/max: %g %g\n",dmin,dmax);
create_cube(&optr,nx,ny,nz);
MapMin(optr) = dmin;
MapMax(optr) = dmax;
Xmin(optr) = Xmin(iptr[0]);
Ymin(optr) = Ymin(iptr[0]);
Zmin(optr) = Zmin(iptr[0]);
Xref(optr) = Xref(iptr[0]);
Yref(optr) = Yref(iptr[0]);
Zref(optr) = Zref(iptr[0]);
Dx(optr) = Dx(iptr[0]);
Dy(optr) = Dy(iptr[0]);
Dz(optr) = Dz(iptr[0]);
for (i=0, iz=0; i<ni; i++) { /* grab all data in output cube */
nz1 = Nz(iptr[i]);
for (iz1=0; iz1< nz1; iz1++, iz++) {
for (iy=0; iy<ny; iy++) {
for (ix=0; ix<nx; ix++) {
CubeValue(optr,ix,iy,iz) = CubeValue(iptr[i],ix,iy,iz1);
}
}
}
}
write_image(outstr, optr);
}
void make_fitheader(FITS *fitsfile, imageptr iptr, bool Qrel, bool Qout, int axistype,
FLOAT *data_min, FLOAT *data_max)
{
int nz, tmpi, i, j;
real crpix1, crpix2, crpix3;
FLOAT tmpr, cd[3][3];
char cdname[10], ctype[32];
nz = Nz(iptr);
fitrdhdr(fitsfile,"CRVAL1",&tmpr,0.0); Xmin(iptr) = tmpr;
fitrdhdr(fitsfile,"CRVAL2",&tmpr,0.0); Ymin(iptr) = tmpr;
fitrdhdr(fitsfile,"CRVAL3",&tmpr,0.0); Zmin(iptr) = tmpr;
if (Qrel) {
Xmin(iptr) = Ymin(iptr) = Zmin(iptr) = 0.0;
}
fitrdhdr(fitsfile,"CDELT1",&tmpr,1.0); Dx(iptr)=tmpr;
fitrdhdr(fitsfile,"CDELT2",&tmpr,1.0); Dy(iptr)=tmpr;
fitrdhdr(fitsfile,"CDELT3",&tmpr,1.0); Dz(iptr)=tmpr;
for (i=1; i<=3; i++)
for (j=1; j<=3; j++) {
sprintf(cdname,"CD%d_%d",i,j);
fitrdhdr(fitsfile,cdname,&tmpr, (i==j ? 1.0 : 0.0));
dprintf(1,"%s: %g\n",cdname,tmpr);
cd[i-1][j-1] = tmpr;
}
if (fitexhd(fitsfile,"CD1_1")) {
if (fitexhd(fitsfile,"CDELT1"))
warning("CDELT1 as well as CD_1_1 have been specified - using CD");
Dx(iptr) = cd[0][0];
Dy(iptr) = cd[1][1];
Dz(iptr) = cd[2][2];
}
fitrdhdr(fitsfile,"CRPIX1",&tmpr,1.0); crpix1 = tmpr;
fitrdhdr(fitsfile,"CRPIX2",&tmpr,1.0); crpix2 = tmpr;
if (nz>1) {
fitrdhdr(fitsfile,"CRPIX3",&tmpr,1.0); crpix3 = tmpr;
} else
crpix3 = 0.0;
if (!Qout) {
print_axis(1, Nx(iptr), crpix1, Xmin(iptr), Dx(iptr));
print_axis(2, Ny(iptr), crpix2, Ymin(iptr), Dy(iptr));
print_axis(3, Nz(iptr), crpix3, Zmin(iptr), Dz(iptr));
return;
}
if (axistype==0) {
Axis(iptr) = 0;
if (crpix1 != 1.0)
Xmin(iptr) -= (crpix1-1.0)*Dx(iptr);
if (crpix2 != 1.0)
Ymin(iptr) -= (crpix2-1.0)*Dy(iptr);
if (nz>1 && crpix3 != 1.0)
Zmin(iptr) -= (crpix3-1.0)*Dz(iptr);
} else if (axistype==1) {
Axis(iptr) = 1;
Xref(iptr) = crpix1-1;
Yref(iptr) = crpix2-1;
Zref(iptr) = crpix3-1;
} else
error("Illegal axistype=%d",axistype);
fitrdhda(fitsfile,"CTYPE1",ctype,"");
Namex(iptr) = scopy(ctype);
fitrdhda(fitsfile,"CTYPE2",ctype,"");
Namey(iptr) = scopy(ctype);
if (nz>1) {
fitrdhda(fitsfile,"CTYPE3",ctype,"");
Namez(iptr) = scopy(ctype);
}
fitrdhdr(fitsfile,"DATAMIN",&tmpr,0.0);
MapMin(iptr) = *data_min = tmpr;
dprintf(1,"DATAMIN: %g %g\n",*data_min,MapMin(iptr));
fitrdhdr(fitsfile,"DATAMAX",&tmpr,0.0);
MapMax(iptr) = *data_max = tmpr;
dprintf(1,"DATAMAX: %g %g\n",*data_max,MapMax(iptr));
if (fitexhd(fitsfile,"BLANK")) {
dprintf(1,"BLANK keyword exists\n");
fitrdhdi(fitsfile,"BITPIX",&tmpi,-1);
if (tmpi<0) {
warning("FITS keyword BLANK not interpreted - BITPIX<0");
} else {
fitrdhdi(fitsfile,"BLANK",&tmpi,0);
dprintf(1,"BLANK = %d\n",tmpi);
}
}
}
/*
* create a velocity field (GIPSY method)
* 0..nx-1 and 0..ny-1
* start from pixel, work back to gal plane and interpolate
* (a.k.a. retracing method)
*
*/
local void cube_create(stream outstr)
{
int i, j, k, n, nx, ny;
real m_min, m_max, sum;
real den, vel, sig, velk, x;
imageptr vptr;
real f = 4.0;
m_min = HUGE; m_max = -HUGE;
nx = Nx(velptr);
ny = Ny(velptr);
if (!create_cube(&vptr, nx, ny, nz)) /* output data cube */
error("Could not create cube from scratch");
for (j=0; j<ny; j++) /* Loop over all pixels */
for (i=0; i<nx; i++) {
for (k=0; k<nz; k++)
CubeValue(vptr,i,j,k) = undef; /* first set all to 'undefined' */
sum = 0.0;
vel = MapValue(velptr,i,j);
if (denptr) {
den = MapValue(denptr,i,j);
if (den <= 0.0) continue;
} else
den = 1.0;
if (sigptr) {
sig = MapValue(sigptr,i,j);
if (sig < 0.0) continue;
} else
sig = sigdef;
if (sig == 0.0) { /* special case, only populate 1 cell */
k = (int) floor( (vel-zrange[0])/zrange[2] );
if (k<0 || k>nz-1) continue;
CubeValue(vptr,i,j,k) = den;
sum = den;
} else { /* else use a gaussian profile */
for (k=0, velk=zrange[0]+0.5*zrange[2]; k<nz; k++, velk += zrange[2]) {
x = (velk-vel)/sig;
x = ABS(x);
if (x > f) continue;
CubeValue(vptr,i,j,k) = den * exp(-0.5*x*x);
sum += CubeValue(vptr,i,j,k);
}
}
sum = den/sum; /* now normalize the spectrum so the sum is 'den' */
for (k=0; k<nz; k++) {
if (CubeValue(vptr,i,j,k) != undef)
CubeValue(vptr,i,j,k) *= sum;
}
}
n=0;
for (k=0; k<nz; k++) /* get min and max in map */
for (j=0; j<ny; j++)
for (i=0; i<nx; i++)
if (CubeValue(vptr,i,j,k) != undef) {
m_min = MIN(CubeValue(vptr,i,j,k),m_min);
m_max = MAX(CubeValue(vptr,i,j,k),m_max);
} else
n++;
MapMin(vptr) = m_min;
MapMax(vptr) = m_max;
Dx(vptr) = Dx(velptr);
Dy(vptr) = Dy(velptr);
Dz(vptr) = zrange[2];
Xmin(vptr) = Xmin(velptr);
Ymin(vptr) = Ymin(velptr);
Zmin(vptr) = zrange[0];
if (n>0) warning("%d/%d cells with no signal",n,nx*ny*nz);
printf("Min and max in map: %g %g\n",m_min,m_max);
write_image (outstr,vptr);
}
void nemo_main()
{
stream instr, outstr;
int nx, ny, nz, nx1, ny1, nz1;
int axis, mom;
int i,j,k, apeak, cnt;
imageptr iptr=NULL, iptr1=NULL, iptr2=NULL; /* pointer to images */
real tmp0, tmp1, tmp2, tmp00, newvalue, peakvalue, scale, offset;
bool Qpeak;
instr = stropen(getparam("in"), "r");
mom = 0;
axis = 3;
Qpeak = getbparam("peak");
read_image( instr, &iptr);
nx1 = nx = Nx(iptr);
ny1 = ny = Ny(iptr);
nz1 = 1;
nz = Nz(iptr);
outstr = stropen(getparam("out"), "w");
create_cube(&iptr1,nx1,ny1,nz1);
create_cube(&iptr2,nx1,ny1,nz1);
scale = Dz(iptr);
offset = Zmin(iptr);
for(j=0; j<ny; j++)
for(i=0; i<nx; i++) {
tmp0 = tmp00 = tmp1 = tmp2 = 0.0;
cnt = 0;
peakvalue = CubeValue(iptr,i,j,0);
for(k=0; k<nz; k++) {
if (out_of_range(CubeValue(iptr,i,j,k))) continue;
cnt++;
tmp0 += CubeValue(iptr,i,j,k);
tmp00 += sqr(CubeValue(iptr,i,j,k));
if (CubeValue(iptr,i,j,k) > peakvalue) {
apeak = k;
peakvalue = CubeValue(iptr,i,j,k);
}
}
if (cnt==0 || tmp0==0.0) {
newvalue = 0.0;
} else {
if (Qpeak)
newvalue = peakvalue;
else
newvalue = tmp0;
}
CubeValue(iptr1,i,j,1) = newvalue;
}
Xmin(iptr1) = Xmin(iptr);
Ymin(iptr1) = Ymin(iptr);
Zmin(iptr1) = Zmin(iptr) + 0.5*(nz-1)*Dz(iptr);
Dx(iptr1) = Dx(iptr);
Dy(iptr1) = Dy(iptr);
Dz(iptr1) = nz * Dz(iptr);
Namex(iptr1) = Namex(iptr); /* care: we're passing a pointer */
Namey(iptr1) = Namey(iptr);
Namez(iptr1) = Namez(iptr);
write_image(outstr, iptr1);
}
void InitVazimPlanet() {
int i,j,k;
real *field;
real dr, dz;
real r, z, H, r0, rho_o, t;
real rho;
FILE *fo;
real vt, omega;
real *vr;
real *cs;
real md0,nuind,nu0;
real vr0, fac1, fac2;
field = Vx->field_cpu;
vr = Vy->field_cpu;
cs = Energy->field_cpu;
boolean GhostInclude = TRUE;
nuind = 0.5+2*FLARINGINDEX;
nu0 = ALPHA*ASPECTRATIO*ASPECTRATIO;
int begin_k =(GhostInclude ? 0 : NGHZ);
int end_k = Nz+2*NGHZ-begin_k;
int begin_j =(GhostInclude ? 0 : NGHY);
int end_j = Ny+2*NGHY-begin_j;
int begin_i = (GhostInclude ? 0 : NGHX);
int end_i = Nx+2*NGHX-begin_i;
for (k = begin_k; k<end_k; k++) {
for (j = begin_j; j<end_j; j++) {
r = Ymed(j);
// vr0=-1.5*nu0*pow(r,nuind);
// fac1 = pow(YMAX,.5-nuind)*SIGMAIN*YMIN-pow(YMIN,.5-nuind)*SIGMAOUT*YMAX;
//
// fac2 = fac1 + (-pow(YMAX,1-nuind)*SIGMAIN*YMIN+pow(YMIN,1-nuind)*SIGMAOUT*YMAX)/sqrt(r);
// fac1=SIGMAOUT*YMAX/r-SIGMAIN*YMIN/r;
// fac1 /= (sqrt(YMAX) - sqrt(YMIN));
// fac2 = SIGMAIN*YMIN/r + fac1*(sqrt(r)-sqrt(YMIN));
// md0 = 1.5*nu0*fac1;
fac1 = -1.5 * nu0 * pow(r,nuind-1);
for (i = begin_i; i<end_i; i++) {
omega = sqrt(G*MSTAR/r/r/r);
vt = omega*r*sqrt(1.0+pow(ASPECTRATIO,2)*pow(r/R0,2*FLARINGINDEX)*
(2.0*FLARINGINDEX - 1.0 - SIGMASLOPE));
vt -= OMEGAFRAME*r;
field[l] = vt*(1.+ASPECTRATIO*NOISE*(drand48()-.5));
//vr[l] = r*omega*ASPECTRATIO*NOISE*(drand48()-.5);
// vr[l] = -1.5*ALPHA*ASPECTRATIO*ASPECTRATIO*pow(r,-0.5+2*FLARINGINDEX);
vr[l] = -1.5 * ALPHA*ASPECTRATIO*ASPECTRATIO*pow(Ymin(j),2*FLARINGINDEX-0.5);
}
}
}
}
image *xyopen(int *handle, string name, string status, int naxis, int *axes)
{
int i, access;
string read_matdef;
image *iptr;
stream str;
if(naxis>MAXNAXIS)
error("naxis=%d not supported: MAXNAXIS=%d",naxis, MAXNAXIS);
if (first) xy_init();
str = stropen(name,status); /* open file */
switch (*status) {
case 'r': /* "r", "old" */
case 'o':
access = GET;
break;
case 'w': /* "w", "new" */
case 'n':
access = PUT;
break;
default:
error("xyopen: Unsupported mode %s",status);
}
iptr = (imageptr )allocate(sizeof(image)); /* new image */
if(access == GET){
get_history(str);
get_set (str,ImageTag);
get_set (str,ParametersTag);
get_data (str,NxTag,IntType, &(Nx(iptr)), 0);
get_data (str,NyTag,IntType, &(Ny(iptr)), 0);
get_data (str,NzTag,IntType, &(Nz(iptr)), 0);
get_data_coerced (str,XminTag,RealType, &(Xmin(iptr)), 0);
get_data_coerced (str,YminTag,RealType, &(Ymin(iptr)), 0);
get_data_coerced (str,ZminTag,RealType, &(Zmin(iptr)), 0);
get_data_coerced (str,DxTag,RealType, &(Dx(iptr)), 0);
get_data_coerced (str,DyTag,RealType, &(Dy(iptr)), 0);
get_data_coerced (str,DzTag,RealType, &(Dz(iptr)), 0);
get_data_coerced (str,MapMinTag, RealType, &(MapMin(iptr)), 0);
get_data_coerced (str,MapMaxTag, RealType, &(MapMax(iptr)), 0);
get_data (str,BeamTypeTag, IntType, &(BeamType(iptr)), 0);
get_data_coerced (str,BeamxTag, RealType, &(Beamx(iptr)), 0);
get_data_coerced (str,BeamyTag, RealType, &(Beamy(iptr)), 0);
get_data_coerced (str,BeamzTag, RealType, &(Beamz(iptr)), 0);
if (get_tag_ok(str,NamexTag)) /* X-axis name */
Namex(iptr) = get_string(str,NamexTag);
else
Namex(iptr) = NULL;
if (get_tag_ok(str,NameyTag)) /* Y-axis name */
Namey(iptr) = get_string(str,NameyTag);
else
Namey(iptr) = NULL;
if (get_tag_ok(str,NamezTag)) /* Z-axis name */
Namez(iptr) = get_string(str,NamezTag);
else
Namez(iptr) = NULL;
if (get_tag_ok(str,UnitTag)) /* units */
Unit(iptr) = get_string(str,UnitTag);
else
Unit(iptr) = NULL;
read_matdef = get_string(str,StorageTag);
if (!streq(read_matdef,matdef[idef]))
dprintf(0,"read_image: StorageTag = %s, compiled with %s\n",
read_matdef, matdef[idef]);
get_tes(str,ParametersTag);
get_set(str,MapTag);
if(Nz(iptr)<=1)
get_data_set(str,MapValuesTag,RealType,Nx(iptr),Ny(iptr),0);
else
get_data_set(str,MapValuesTag,RealType,Nx(iptr),Ny(iptr),Nz(iptr),0);
for (i=0; i<naxis; i++) axes[i] = 1;
axes[0] = Nx(iptr); axes[1] = Ny(iptr); axes[2] = Nz(iptr);
} else { /* PUT */
Nx(iptr) = Ny(iptr) = Nz(iptr) = 1;
if (naxis>0) Nx(iptr) = axes[0];
if (naxis>1) Ny(iptr) = axes[1];
if (naxis>2) Nz(iptr) = axes[2];
put_history(str);
put_set (str,ImageTag);
put_set (str,ParametersTag);
put_data (str,NxTag, IntType, &(Nx(iptr)), 0);
put_data (str,NyTag, IntType, &(Ny(iptr)), 0);
put_data (str,NzTag, IntType, &(Nz(iptr)), 0);
put_data (str,XminTag,RealType, &(Xmin(iptr)), 0);
put_data (str,YminTag,RealType, &(Ymin(iptr)), 0);
put_data (str,ZminTag,RealType, &(Zmin(iptr)), 0);
put_data (str,DxTag, RealType, &(Dx(iptr)), 0);
put_data (str,DyTag, RealType, &(Dy(iptr)), 0);
put_data (str,DzTag, RealType, &(Dz(iptr)), 0);
put_data (str,MapMinTag, RealType, &(MapMin(iptr)), 0);
put_data (str,MapMaxTag, RealType, &(MapMax(iptr)), 0);
put_data (str,BeamTypeTag, IntType, &(BeamType(iptr)), 0);
put_data (str,BeamxTag, RealType, &(Beamx(iptr)), 0);
put_data (str,BeamyTag, RealType, &(Beamy(iptr)), 0);
put_data (str,BeamzTag, RealType, &(Beamz(iptr)), 0);
if (Namex(iptr))
put_string (str,NamexTag,Namex(iptr));
if (Namey(iptr))
put_string (str,NameyTag,Namey(iptr));
if (Namez(iptr))
put_string (str,NamezTag,Namez(iptr));
if (Unit(iptr))
put_string (str,UnitTag,Unit(iptr));
put_string(str,StorageTag,matdef[idef]);
put_tes(str, ParametersTag);
put_set(str, MapTag);
if(Nz(iptr)<=1)
put_data_set(str,MapValuesTag,RealType,Nx(iptr),Ny(iptr),0);
else
put_data_set(str,MapValuesTag,RealType,Nx(iptr),Ny(iptr),Nz(iptr),0);
}
*handle = -1;
for(i=0; i<MAXOPEN; i++) { /* look for a new table entry */
if(images[i].str == NULL) *handle = i;
}
if(*handle < 0)
error("xyopen: No more free slots; too many open images");
for (i=0; i<MAXNAXIS; i++)
images[*handle].axes[i] = 1;
images[*handle].str = str;
images[*handle].iptr = iptr;
images[*handle].offset = 0;
images[*handle].access = access;
images[*handle].naxis = (Nz(iptr)<=1 ? 2 : 3);
images[*handle].axes[0] = Nx(iptr);
images[*handle].axes[1] = Ny(iptr);
images[*handle].axes[2] = Nz(iptr);
return iptr;
}
void write_fits(string name,imageptr iptr)
{
FLOAT tmpr,xmin[3],xref[3],dx[3],mapmin,mapmax; /* fitsio FLOAT !!! */
FITS *fitsfile;
char *cp, origin[80];
string *hitem, axname[3];
float *buffer, *bp;
int i, j, k, axistype, bitpix, keepaxis[3], nx[3], p[3], nx_out[3], ndim=3;
double bscale, bzero;
if (hasvalue("ndim")) ndim = getiparam("ndim");
nx[0] = Nx(iptr);
nx[1] = Ny(iptr);
nx[2] = Nz(iptr); if (nx[2] <= 0) nx[2] = 1;
xmin[0] = Xmin(iptr)*scale[0];
xmin[1] = Ymin(iptr)*scale[1];
xmin[2] = Zmin(iptr)*scale[2];
dx[0] = Dx(iptr)*scale[0];
dx[1] = Dy(iptr)*scale[1];
dx[2] = Dz(iptr)*scale[2];
xref[0] = Xref(iptr)+1.0;
xref[1] = Yref(iptr)+1.0;
xref[2] = Zref(iptr)+1.0;
axistype = Axis(iptr);
axname[0] = (Namex(iptr) ? Namex(iptr) : xyz[0]);
axname[1] = (Namey(iptr) ? Namey(iptr) : xyz[1]);
axname[2] = (Namez(iptr) ? Namez(iptr) : xyz[2]);
mapmin = MapMin(iptr);
mapmax = MapMax(iptr);
if (Qdummy)
for (i=0; i<3; i++) p[i] = i;
else {
if (Qrefmap) warning("dummy=f and usage of refmap will result in bad headers");
permute(nx,p,3);
dprintf(0,"Reordering axes: %d %d %d\n",p[0],p[1],p[2]);
}
#if 1
for (i=0; i<3; i++) nx_out[i] = nx[p[i]];
/* fix this so CubeValue works */
Nx(iptr) = nx_out[0];
Ny(iptr) = nx_out[1];
Nz(iptr) = nx_out[2];
#else
for (i=0; i<3; i++) nx_out[i] = nx[i];
#endif
sprintf(origin,"NEMO ccdfits %s",getparam("VERSION"));
dprintf(1,"NEMO Image file written to FITS disk file\n");
dprintf(1,"%d %d %d %f %f %f %f %f %f %f %f %f %f %f \n",
nx[0],nx[1],nx[2],xmin[0],xmin[1],xmin[2],dx[0],dx[1],dx[2],xref[0],xref[1],xref[2],
mapmin,mapmax);
dprintf(1,"keepaxis(%d,%d,%d)\n",keepaxis[0],keepaxis[1],keepaxis[2]);
fit_setblocksize(2880*getiparam("blocking"));
bitpix = getiparam("bitpix");
fit_setbitpix(bitpix);
if (bitpix == 16) { /* scale from -2^(bitpix-1) .. 2^(bitpix-1)-1 */
bscale = (mapmax - mapmin) / (2.0*32768.0 - 1.0);
bzero = mapmax - bscale*32767.0;
fit_setscale(bscale,bzero);
} else if (bitpix == 32) {
bscale = (mapmax - mapmin) / (2.0*2147483648.0 - 1.0);
bzero = mapmax - bscale*2147483647.0;
fit_setscale(bscale,bzero);
} else if (bitpix == 8) {
bscale = (mapmax - mapmin) / (2.0*128.0 - 1.0);
bzero = mapmin;
fit_setscale(bscale,bzero);
}
dprintf(1,"bscale,bzero=%g %g\n",bscale,bzero);
fitsfile = fitopen(name,"new",ndim,nx_out);
if (fitsfile==NULL) error("Could not open fitsfile %s for writing\n",name);
if (Qrefmap || Qcrpix) {
fitwrhdr(fitsfile,"CRPIX1",ref_crpix[0]);
fitwrhdr(fitsfile,"CRPIX2",ref_crpix[1]);
if (ndim>2) fitwrhdr(fitsfile,"CRPIX3",ref_crpix[2]);
} else {
if (axistype==1) {
fitwrhdr(fitsfile,"CRPIX1",xref[0]);
fitwrhdr(fitsfile,"CRPIX2",xref[1]);
if (ndim>2) fitwrhdr(fitsfile,"CRPIX3",xref[2]);
} else {
fitwrhdr(fitsfile,"CRPIX1",1.0); /* CRPIX = 1 by Nemo definition */
fitwrhdr(fitsfile,"CRPIX2",1.0);
if (ndim>2) fitwrhdr(fitsfile,"CRPIX3",1.0);
}
}
if (Qrefmap || Qcrval) {
fitwrhdr(fitsfile,"CRVAL1",ref_crval[0]);
fitwrhdr(fitsfile,"CRVAL2",ref_crval[1]);
if (ndim>2) fitwrhdr(fitsfile,"CRVAL3",ref_crval[2]);
} else {
fitwrhdr(fitsfile,"CRVAL1",xmin[p[0]]);
fitwrhdr(fitsfile,"CRVAL2",xmin[p[1]]);
if (ndim>2) fitwrhdr(fitsfile,"CRVAL3",xmin[p[2]]);
}
if (Qcdmatrix) {
fitwrhdr(fitsfile,"CD1_1",dx[p[0]]);
fitwrhdr(fitsfile,"CD2_2",dx[p[1]]);
if (ndim>2) fitwrhdr(fitsfile,"CD3_3",dx[p[2]]);
} else {
if (Qrefmap || Qcdelt) {
fitwrhdr(fitsfile,"CDELT1",ref_cdelt[0]*scale[0]);
fitwrhdr(fitsfile,"CDELT2",ref_cdelt[1]*scale[1]);
if (ndim>2) fitwrhdr(fitsfile,"CDELT3",ref_cdelt[2]*scale[2]);
} else {
fitwrhdr(fitsfile,"CDELT1",dx[p[0]]);
fitwrhdr(fitsfile,"CDELT2",dx[p[1]]);
if (ndim>2) fitwrhdr(fitsfile,"CDELT3",dx[p[2]]);
}
}
if (Qradecvel) {
dprintf(0,"[Axes names written as %s, %s, %s\n",
radeve[p[0]],radeve[p[1]],radeve[p[2]]);
fitwrhda(fitsfile,"CTYPE1",radeve[p[0]]);
fitwrhda(fitsfile,"CTYPE2",radeve[p[1]]);
if (ndim>2) fitwrhda(fitsfile,"CTYPE3",radeve[p[2]]);
} else {
if (Qrefmap) {
fitwrhda(fitsfile,"CTYPE1",ref_ctype[0]);
fitwrhda(fitsfile,"CTYPE2",ref_ctype[1]);
if (ndim>2) fitwrhda(fitsfile,"CTYPE3",ref_ctype[2]);
} else {
fitwrhda(fitsfile,"CTYPE1",axname[p[0]]);
fitwrhda(fitsfile,"CTYPE2",axname[p[1]]);
if (ndim>2) fitwrhda(fitsfile,"CTYPE3",axname[p[2]]);
}
}
fitwrhdr(fitsfile,"DATAMIN",mapmin);
fitwrhdr(fitsfile,"DATAMAX",mapmax);
fitwrhda(fitsfile,"ORIGIN",origin);
cp = getenv("USER"); /* AUTHOR */
if (cp)
fitwrhda(fitsfile,"AUTHOR",cp);
else
fitwrhda(fitsfile,"AUTHOR","NEMO");
if (object) /* OBJECT */
fitwrhda(fitsfile,"OBJECT",object);
if (comment) /* COMMENT */
stuffit(fitsfile,"COMMENT",comment);
if (headline)
stuffit(fitsfile,"COMMENT",headline);
hitem = ask_history(); /* HISTORY */
fitwra(fitsfile,"HISTORY","NEMO: History in reversed order");
for (i=0, cp=hitem[0]; cp != NULL; i++) {
stuffit(fitsfile,"HISTORY",cp);
cp = hitem[i+1];
}
for(i=0; i<nfill; i++) /* debugging header I/O */
fitwra(fitsfile,"COMMENT","Dummy filler space");
buffer = (float *) allocate(nx[p[0]]*sizeof(float));
for (k=0; k<nx_out[2]; k++) { /* loop over all planes */
fitsetpl(fitsfile,1,&k);
for (j=0; j<nx_out[1]; j++) { /* loop over all rows */
for (i=0, bp=buffer; i<nx_out[0]; i++, bp++)
*bp = iscale[0] * CubeValue(iptr,i,j,k) + iscale[1];
fitwrite(fitsfile,j,buffer);
}
}
free(buffer);
fitclose(fitsfile);
}
local void object_spiral(int npars, real *pars)
{
int i,nx = Nx(iptr);
int j,ny = Ny(iptr);
int l, lmax;
real A = 1.0;
real h = 1.0;
real k = 1.0; /* wave number */
real p = 1.0; /* 1/2 power of cos */
real r0 = 0.0; /* starting radius */
real p0 = 0.0; /* starting angle */
int m = 2; /* number of arms */
real x1,y1,x2,y2,x3,y3,r,arg,value;
real amp,phi,sum;
bool Qint, pint;
if (npar > 0) A = pars[0];
if (npar > 1) h = pars[1];
if (npar > 2) k = pars[2];
if (npar > 3) p = pars[3];
if (npar > 4) m = (int) pars[4]; /* note rounding ? */
if (npar > 5) r0 = pars[5];
if (npar > 6) p0 = pars[6];
dprintf(0,"spiral: %g %g %g %g %d %g %g\n",A,h,k,p,m,r0,p0);
if (A==0) return;
p0 *= PI/180.0; /* convert from degrees to radians */
k *= TWO_PI; /* angles are 2.PI.k.r , so absorb 2.PI.k in one */
pint = (int) p;
Qint = (p-pint == 0);
if (Qint)
warning("Integer power p = %d\n",pint);
lmax = Qtotflux ? 2 : 1;
for (l=0; l<lmax; l++) { /* 1st loop: sum up the flux if in 2nd loop: normalize */
if (l==0)
sum = 0.0;
else {
A /= sum;
dprintf(0,"spiral: A->%g\n",A);
}
for (j=0; j<ny; j++) {
y1 = (j-center[1])*Dy(iptr) + Ymin(iptr);
for (i=0; i<nx; i++) {
x1 = (i-center[0])*Dx(iptr) + Xmin(iptr);
x2 = -x1*sinp - y1*cosp;
y2 = (x1*cosp - y1*sinp)/cosi;
r = sqrt(x2*x2+y2*y2);
if (r < r0)
value = 0.0;
else {
/* ? should match this up better so we can connect bar and spiral ? */
phi = atan2(y2,x2) + k*(r-r0) + p0;
if (Qint) {
amp = powi(cos(m*phi),pint); /* these can come out negative for odd p's !! */
} else
amp = powd(cos(m*phi),(double)p);
arg = r/h;
value = (arg < 80) ? A * amp * exp(-arg) : 0.0;
}
if (Qtotflux) {
if (l==0)
sum += value;
else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} else
MapValue(iptr,i,j) = factor*MapValue(iptr,i,j) + value;
} /* i */
} /* j */
} /* k */
}
int read_image (stream instr, imageptr *iptr)
{
string read_matdef;
int nx=0, ny=0, nz=0;
size_t nxyz;
get_history(instr); /* accumulate history */
if (!get_tag_ok (instr,ImageTag))
return 0; /* not an image available */
if (*iptr==NULL) { /* allocate image if neccessary */
*iptr = (imageptr ) allocate(sizeof(image));
dprintf (DLEV,"Allocated image @ %d ",*iptr);
} else {
nx = Nx(*iptr);
ny = Ny(*iptr);
nz = Nz(*iptr);
dprintf (DLEV,"Image %dx%dx%d already allocated @ %d\n",
nx,ny,nz,*iptr);
}
get_set (instr,ImageTag);
get_set (instr,ParametersTag);
get_data (instr,NxTag,IntType, &(Nx(*iptr)), 0);
get_data (instr,NyTag,IntType, &(Ny(*iptr)), 0);
get_data (instr,NzTag,IntType, &(Nz(*iptr)), 0);
if ((nx>0 || ny>0 || nz>0) &&
(nx != Nx(*iptr) || ny != Ny(*iptr) || nz != Nz(*iptr)))
error("Cannot read different sized images in old pointer yet");
if (get_tag_ok(instr,AxisTag))
get_data (instr,AxisTag,IntType, &(Axis(*iptr)), 0);
else
Axis(*iptr) = 0;
if (Axis(*iptr) == 1) {
get_data_coerced (instr,XrefTag,RealType, &(Xref(*iptr)), 0);
get_data_coerced (instr,YrefTag,RealType, &(Yref(*iptr)), 0);
get_data_coerced (instr,ZrefTag,RealType, &(Zref(*iptr)), 0);
} else {
Xref(*iptr) = 0.0;
Yref(*iptr) = 0.0;
Zref(*iptr) = 0.0;
}
get_data_coerced (instr,XminTag,RealType, &(Xmin(*iptr)), 0);
get_data_coerced (instr,YminTag,RealType, &(Ymin(*iptr)), 0);
get_data_coerced (instr,ZminTag,RealType, &(Zmin(*iptr)), 0);
get_data_coerced (instr,DxTag,RealType, &(Dx(*iptr)), 0);
get_data_coerced (instr,DyTag,RealType, &(Dy(*iptr)), 0);
get_data_coerced (instr,DzTag,RealType, &(Dz(*iptr)), 0);
get_data_coerced (instr,MapMinTag, RealType, &(MapMin(*iptr)), 0);
get_data_coerced (instr,MapMaxTag, RealType, &(MapMax(*iptr)), 0);
get_data (instr,BeamTypeTag, IntType, &(BeamType(*iptr)), 0);
get_data_coerced (instr,BeamxTag, RealType, &(Beamx(*iptr)), 0);
get_data_coerced (instr,BeamyTag, RealType, &(Beamy(*iptr)), 0);
get_data_coerced (instr,BeamzTag, RealType, &(Beamz(*iptr)), 0);
if (get_tag_ok(instr,NamexTag)) /* X-axis name */
Namex(*iptr) = get_string(instr,NamexTag);
else
Namex(*iptr) = NULL;
if (get_tag_ok(instr,NameyTag)) /* Y-axis name */
Namey(*iptr) = get_string(instr,NameyTag);
else
Namey(*iptr) = NULL;
if (get_tag_ok(instr,NamezTag)) /* Z-axis name */
Namez(*iptr) = get_string(instr,NamezTag);
else
Namez(*iptr) = NULL;
if (get_tag_ok(instr,UnitTag)) /* units */
Unit(*iptr) = get_string(instr,UnitTag);
else
Unit(*iptr) = NULL;
if (get_tag_ok(instr,TimeTag)) /* time */
get_data_coerced (instr,TimeTag, RealType, &(Time(*iptr)), 0);
else
Time(*iptr) = 0.0;
read_matdef = get_string(instr,StorageTag);
if (!streq(read_matdef,matdef[idef]))
dprintf(0,"read_image: StorageTag = %s, compiled with %s\n",
read_matdef, matdef[idef]);
get_tes (instr,ParametersTag);
get_set (instr,MapTag);
if (Frame(*iptr)==NULL) { /* check if allocated */
nxyz = Nx(*iptr)*Ny(*iptr)*Nz(*iptr);
Frame(*iptr) = (real *) allocate(nxyz * sizeof(real));
dprintf (DLEV,"Frame allocated @ %d ",Frame(*iptr));
} else
dprintf (DLEV,"Frame already allocated @ %d\n",Frame(*iptr));
if (Nz(*iptr)==1)
get_data_coerced (instr,MapValuesTag,RealType, Frame(*iptr),
Nx(*iptr), Ny(*iptr), 0);
else
get_data_coerced (instr,MapValuesTag,RealType, Frame(*iptr),
Nx(*iptr), Ny(*iptr), Nz(*iptr), 0);
get_tes (instr,MapTag);
get_tes (instr,ImageTag);
set_iarray(*iptr);
dprintf (DLEV,"Frame size %d * %d \n",Nx(*iptr), Ny(*iptr));
return 1; /* succes return code */
}
nemo_main()
{
stream denstr, velstr, outstr, tabstr;
real center[2], cospa, sinpa, cosi, sini, cost, costmin, x, y, xt, yt, r, den;
real vr, wt, frang, dx, dy, xmin, ymin, rmin, rmax, ave, tmp, rms;
real sincosi, cos2i, tga, dmin, dmax, dval, dr, area, fsum1, fsum2;
int i, j, k, nx, ny, ir, nring, nundf, nout, nang, nsum;
string outmode;
int mode = -1;
velstr = stropen(getparam("in"),"r");
read_image(velstr,&velptr);
nx = Nx(velptr);
ny = Ny(velptr);
if (hasvalue("out")) {
outmode = getparam("mode");
mode = string_index(outmodes, outmode);
if (mode < 0) error("Illegal mode=%s [%d], valid:",outmode,mode,outmodes);
warning("New out= mode mode=%s [%d]",outmode,mode);
Qout = TRUE;
outstr = stropen(getparam("out"),"w");
copy_image(velptr,&outptr);
}
if (hasvalue("den")) {
Qden = TRUE;
denstr = stropen(getparam("den"),"r");
read_image(denstr,&denptr);
} else if (mode==2)
error("Need den=");
if (hasvalue("tab")) {
Qtab = TRUE;
tabstr = stropen(getparam("tab"),"w");
}
nrad = nemoinpd(getparam("radii"),rad,MAXRING);
if (nrad < 2) error("got no rings (%d), use radii=",nrad);
nring = nrad-1;
if (hasvalue("center")) {
if (nemoinpd(getparam("center"),center,2) != 2)
error("not enuf values for center=, need 2");
xpos = center[0];
ypos = center[1];
} else {
xpos = (Nx(velptr)-1.0)/2.0;
ypos = (Ny(velptr)-1.0)/2.0;
}
pa = getdparam("pa");
inc = getdparam("inc");
vsys = getdparam("vsys");
undf = getdparam("blank");
frang = getdparam("frang");
cospa = cos(pa*PI/180.0);
sinpa = sin(pa*PI/180.0);
sini = sin(inc*PI/180.0);
cosi = cos(inc*PI/180.0);
costmin = sin(frang*PI/180.0);
sincosi = sini*cosi;
cos2i = cosi*cosi;
for (i=0; i<nring; i++)
pixe[i] = vsum[i] = vsqu[i] = wsum[i] = 0;
nundf = nout = nang = 0;
ymin = Ymin(velptr);
xmin = Xmin(velptr);
dx = Dx(velptr); dx = ABS(dx); dx = -dx;
dy = Dy(velptr); dy = ABS(dy);
rmin = -nx*dx*10.0;
rmax = 0.0;
dprintf(0,"Map %d x %d pixels, size %g x %g\n",
Nx(velptr), Ny(velptr), -dx*Nx(velptr), dy*Ny(velptr));
dprintf(0,"Pixel size: %g x %g\n",-dx, dy);
dmin = dmax = vsys;
/* loop over the map, accumulating data for fitting process */
for (j=0; j<ny; j++) {
y = (j-ypos)*dy;
for (i=0; i<nx; i++) {
if (MapValue(velptr,i,j) == undf) {
nundf++;
if (Qout) MapValue(outptr,i,j) = undf;
continue;
}
x = (i-xpos)*dx;
yt = x*sinpa + y*cospa; /* major axis now along Y */
xt = x*cospa - y*sinpa; /* minor axis along X */
xt /= cosi; /* deproject to the circle */
r = sqrt(xt*xt+yt*yt); /* radius in the disk */
rmin = MIN(r,rmin);
rmax = MAX(r,rmax);
ir = ring_index(nrad,rad,r);
dprintf(2,"r=%g ir=%d (x,y)=%g,%g (xt,yt)=%g,%g\n",
r,ir,x,y,xt,yt);
if (ir < 0) {
nout++;
continue;
}
cost = yt/r;
dval = MapValue(velptr,i,j);
if (mode==1)
dval /= r;
else if (mode==2)
dval *= MapValue(denptr,i,j) / r;
if (outptr) {
if (ABS(cost) > costmin) {
MapValue(outptr,i,j) = dval;
if (dval > dmax) dmax = dval;
if (dval < dmin) dmin = dval;
} else {
MapValue(outptr,i,j) = undf;
}
}
/* now some ring accumulation, remnant of the velfit fitting */
if (ABS(cost) > costmin) {
pixe[ir] += 1;
wsum[ir] += 1.0;
vsum[ir] += dval;
vsqu[ir] += dval*dval;
} else
nang++;
} /* i */
} /* j */
/* write output map(s), if needed */
if (Qout) {
dprintf(0,"Data min/max = %g %g\n",dmin,dmax);
MapMin(outptr) = dmin;
MapMax(outptr) = dmax;
write_image(outstr,outptr);
}
/* report on the rings */
if (Qtab) {
fprintf(tabstr,"# r I rms I_sum1 I_sum2 i_ring Npoints\n");
fsum1 = 0.0; /* this will count rings with average values */
fsum2 = 0.0; /* this will count up flux whenever it fell in a ring */
nsum = 0;
for (i=0; i<nring; i++) {
if (wsum[i] == 0.0) continue;
nsum++;
r = 0.5*(rad[i] + rad[i+1]);
dr = rad[i+1] - rad[i];
area = PI*(sqr(rad[i+1]) - sqr(rad[i]));
ave = vsum[i]/wsum[i];
rms = vsqu[i]/wsum[i]-ave*ave;
if (rms < 0) rms=0.0;
rms = sqrt(rms);
fsum1 += ave*area;
fsum2 += vsum[i];
fprintf(tabstr,"%g %g %g %g %g %d %d\n",
r,ave,rms,fsum1,fsum2,i+1,pixe[i]);
}
}
dprintf(0,"Nundf=%d/%d Nout=%d Nang=%d (sum=%d)\n",
nundf,nx*ny,nout,nang,nout+nundf+nang);
dprintf(0,"Rmin/max = %g %g\n",rmin,rmax);
}
void nemo_main()
{
stream instr, outstr;
int nx, ny, nz, mode;
int i,j,k;
imageptr iptr1=NULL, iptr2=NULL, optr; /* pointer to images */
real d1, d2, d3, d4, d5, d6, dx, dy, dz;
bool Qsym = TRUE; /* symmetric derivates w.r.t. pixel point */
match(getparam("mode"),valid_modes,&mode);
if (mode==0) error("Not a valid mode; valid:%s",valid_modes);
dprintf(0,"Image sharpening method #%d\n",mode);
instr = stropen(getparam("in"), "r");
read_image( instr, &iptr1);
nx = Nx(iptr1);
ny = Ny(iptr1);
nz = Nz(iptr1);
dx = Dx(iptr1);
dy = Dy(iptr1);
dz = Dz(iptr1);
if (mode & MODE_DIV || mode & MODE_VORT) {
if (read_image(instr,&iptr2) == 0)
error("No second image found in %s\n",getparam("in"));
if (nx != Nx(iptr2))
error("Second image doesn't match in NX: %d <> %d\n",Nx(iptr2),nx);
if (ny != Ny(iptr2))
error("Second image doesn't match in NY: %d <> %d\n",Ny(iptr2),ny);
if (nz != Nz(iptr2))
error("Second image doesn't match in NZ: %d <> %d\n",Nz(iptr2),nz);
}
outstr = stropen(getparam("out"), "w");
create_cube(&optr,nx,ny,nz);
Dx(optr) = Dx(iptr1);
Dy(optr) = Dy(iptr1);
Dz(optr) = Dz(iptr1);
Xmin(optr) = Xmin(iptr1);
Ymin(optr) = Ymin(iptr1);
Zmin(optr) = Zmin(iptr1);
if (mode & MODE_LAPLACE) {
for (k=1; k<nz-1; k++) {
for (j=1; j<ny-1; j++) {
for (i=1; i<nx-1; i++) {
d1 = CV1(i,j,k) - CV1(i-1,j,k);
d2 = CV1(i,j,k) - CV1(i+1,j,k);
d3 = CV1(i,j,k) - CV1(i,j-1,k);
d4 = CV1(i,j,k) - CV1(i,j+1,k);
d5 = CV1(i,j,k) - CV1(i,j,k-1);
d6 = CV1(i,j,k) - CV1(i,j,k+1);
CVO(i,j,k) = sqrt(d1*d1+d2*d2+d3*d3+d4*d4+d5*d5+d6*d6);
}
CVO(0,j,k) = 0.0;
CVO(nx-1,j,k) = 0.0;
}
for (i=0; i<nx; i++)
CVO(i,0,k) = CVO(i,ny-1,k) = 0.0;
}
for(j=0; j<ny; j++)
for(i=0; i<nx; i++)
CVO(i,j,0) = CVO(i,j,nz-1) = 0.0;
} else if (mode & MODE_DIV || mode & MODE_VORT) {
warning("only 2D implemented");
for (k=0; k<nz; k++) {
for (j=0; j<ny-1; j++) {
for (i=0; i<nx-1; i++) {
if (Qsym) {
if (i>0 && j>0) {
d1 = 0.5*(CV1(i+1,j,k) - CV1(i-1,j,k)); /* dv_x/dx */
d2 = 0.5*(CV1(i,j+1,k) - CV1(i,j-1,k)); /* dv_x/dy */
d3 = 0.5*(CV2(i+1,j,k) - CV2(i-1,j,k)); /* dv_y/dx */
d4 = 0.5*(CV2(i,j+1,k) - CV2(i,j-1,k)); /* dv_y/dy */
} else
d1 = d2 = d3 = d4 = 0.0;
} else {
d1 = CV1(i+1,j,k) - CV1(i,j,k); /* dv_x/dx */
d2 = CV1(i,j+1,k) - CV1(i,j,k); /* dv_x/dy */
d3 = CV2(i+1,j,k) - CV2(i,j,k); /* dv_y/dx */
d4 = CV2(i,j+1,k) - CV2(i,j,k); /* dv_y/dy */
}
if (mode&MODE_DIV)
CVO(i,j,k) = d1/dx + d4/dy;
else if (mode&MODE_VORT)
CVO(i,j,k) = d3/dx - d2/dy;
}
CVO(nx-1,j,k) = 0.0;
}
for (i=0; i<nx; i++) {
CVO(i,ny-1,k) = 0.0;
}
}
} else if (mode & MODE_AREGAN || mode & MODE_PREGAN) {
warning("only 2D implemented");
for (k=0; k<nz; k++) {
for (j=0; j<ny-1; j++) {
for (i=0; i<nx-1; i++) {
d1 = CV1(i,j,k) - CV1(i+1,j,k);
d2 = CV1(i,j+1,k) - CV1(i+1,j+1,k);
d3 = CV1(i,j,k) - CV1(i,j+1,k);
d4 = CV1(i+1,j,k) - CV1(i+1,j+1,k);
if (mode&MODE_AREGAN)
CVO(i,j,k) = sqrt(sqr(d1+d2)+sqr(d3+d4))/2;
else {
if (d3+d4==0.0 && d1+d2==0.0)
CVO(i,j,k) = 0.0;
else
CVO(i,j,k) = atan2(d3+d4,d1+d2) * 180 / PI;
}
}
CVO(nx-1,j,k) = 0.0;
}
for (i=0; i<nx; i++) {
CVO(i,ny-1,k) = 0.0;
}
}
}
write_image(outstr, optr);
}
void nemo_main()
{
stream instr, outstr;
int nx, ny, nz; /* size of scratch map */
int ix, iy, flip;
imageptr iptr=NULL; /* pointer to image */
real tmp, zzz;
string flipmode;
flipmode = getparam("flip");
if (streq(flipmode,"x"))
flip = X;
else if (streq(flipmode,"y"))
flip = Y;
else if (streq(flipmode,"xy"))
flip = XY;
else
error("Illegal flip axis");
instr = stropen(getparam("in"), "r");
outstr = stropen(getparam("out"), "w");
read_image( instr, &iptr);
nx = Nx(iptr);
ny = Ny(iptr);
nz = Nz(iptr);
if(flip==X) {
for (iy=0; iy<ny; iy++) { /* flip in x */
for (ix=0; ix<nx/2; ix++) {
tmp = MapValue(iptr,ix,iy);
zzz = MapValue(iptr,nx-ix-1,iy);
dprintf(1,"%d %d: %f %f\n",ix,iy,tmp,zzz);
MapValue(iptr,ix,iy) = MapValue(iptr,nx-ix-1,iy);
MapValue(iptr,nx-ix-1,iy) = tmp;
}
}
} else if (flip==Y) {
for (iy=0; iy<ny; iy++) { /* flip in y */
for (ix=0; ix<nx/2; ix++) {
tmp = MapValue(iptr,iy,ix);
zzz = MapValue(iptr,iy,nx-ix-1);
dprintf(1,"%d %d: %f %f\n",ix,iy,tmp,zzz);
MapValue(iptr,iy,ix) = MapValue(iptr,iy,nx-ix-1);
MapValue(iptr,iy,nx-ix-1) = tmp;
}
}
} else if (flip==XY) {
for (iy=0; iy<ny; iy++) { /* swap the x and y axes */
for (ix=iy+1; ix<nx; ix++) {
tmp = MapValue(iptr,ix,iy);
dprintf(1,"%d %d: %f \n",ix,iy,tmp);
MapValue(iptr,ix,iy) = MapValue(iptr,iy,ix);
MapValue(iptr,iy,ix) = tmp;
}
}
SWAPR(Xmin(iptr), Ymin(iptr));
SWAPR(Dx(iptr), Dy(iptr));
SWAPS(Namex(iptr), Namey(iptr));
}
write_image(outstr, iptr);
}
void nemo_main()
{
stream instr, outstr;
int nx, ny, nz;
int nstep,nstep1;
int i,j,k, n, n1, i1, j1, m;
int ix[2], iy[2];
imageptr iptr=NULL, optr; /* pointer to images */
real *vals, fraction;
string mode = getparam("mode");
bool Qmedian = (*mode == 'm');
bool Qmean = (*mode == 'a');
nstep = getiparam("nstep");
if (nstep%2 != 1) error("step size %d needs to be odd",nstep);
nstep1 = (nstep-1)/2;
n = getiparam("n");
if (Qmedian)
dprintf(1,"Median filter size %d\n",n);
else if (Qmean)
dprintf(1,"Mean filter size %d\n",n);
else
dprintf(1,"Subtraction filter size %d\n",n);
if (n%2 != 1) error("filter size %d needs to be odd",n);
n1 = (n-1)/2;
vals = (real *) allocate (sizeof(real) * (n*n + 1));
instr = stropen(getparam("in"), "r");
read_image( instr, &iptr);
nx = Nx(iptr);
ny = Ny(iptr);
nz = Nz(iptr);
if (nz > 1) error("Cannot do 3D cubes properly; use 2D");
if (hasvalue("x") && hasvalue("y")) {
get_range("x",ix);
get_range("y",iy);
} else {
ix[0] = 0;
ix[1] = nx-1;
iy[0] = 0;
iy[1] = ny-1;
}
dprintf(1,"Xrange: %d - %d Yrange: %d - %d\n",ix[0],ix[1],iy[0],iy[1]);
outstr = stropen(getparam("out"), "w");
create_cube(&optr,nx,ny,nz);
Dx(optr) = Dx(iptr);
Dy(optr) = Dy(iptr);
Dz(optr) = Dz(iptr);
Xmin(optr) = Xmin(iptr);
Ymin(optr) = Ymin(iptr);
Zmin(optr) = Zmin(iptr);
if (nstep > 1) {
warning("Cheat mode nstep=%d",nstep);
for (j=nstep1; j<ny-nstep1; j+=nstep) {
for (i=nstep1; i<nx-nstep1; i+=nstep) {
if (j<n1 || j >= ny-n1 || j < iy[0] || j > iy[1]) {
CVO(i,j) = CVI(i,j);
continue;
}
if (i<n1 || i >= nx-n1 || i < ix[0] || i > ix[1]) {
CVO(i,j) = CVI(i,j);
continue;
}
m = 0;
for (j1=j-n1; j1<=j+n1; j1++)
for (i1=i-n1; i1<=i+n1; i1++)
vals[m++] = CVI(i1,j1);
CVO(i,j) = median(m,vals,fraction);
for (j1=j-nstep1; j1<=j+nstep1; j1++)
for (i1=i-nstep1; i1<=i+nstep1; i1++)
CVO(i1,j1) = CVO(i,j);
}
}
} else {
for (j=0; j<ny; j++) {
for (i=0; i<nx; i++) {
if (j<n1 || j >= ny-n1 || j < iy[0] || j > iy[1]) {
CVO(i,j) = CVI(i,j);
continue;
}
if (i<n1 || i >= nx-n1 || i < ix[0] || i > ix[1]) {
CVO(i,j) = CVI(i,j);
continue;
}
m = 0;
for (j1=j-n1; j1<=j+n1; j1++)
for (i1=i-n1; i1<=i+n1; i1++)
vals[m++] = CVI(i1,j1);
if (Qmedian)
CVO(i,j) = median(m,vals,fraction);
else if (Qmean)
CVO(i,j) = mean(m,vals,fraction);
else
CVO(i,j) = subtract(m,vals,fraction);
}
}
}
write_image(outstr, optr);
}
void inipotential (int *npar, double par[], char *name)
{
int n;
n = *npar;
if (n>0) omega = par[0]; /* standard pattern speed */
if (n>1) iscale = par[1]; /* scaling factor applied to potential */
if (n>2) { /* alternate definition of center pixel */
xcen = par[2];
if (n>3) ycen = par[3];
else ycen = xcen;
}
if (n>4) { /* alternate definition of pixel size */
dx = par[4];
if (n>5) dy = par[5];
else dy = dx;
}
if (n>6) warning("inipotential(ccd): npar=%d only 6 parameter accepted",n);
/* set some easy to use booleans */
Qcen = n>2; /* if a new center was defined via parameters */
Qdel = n>4; /* if a new pixel size was defined via parameters */
dprintf(1,"INIPOTENTIAL: %s: %s\n",CCD_VERSION,name);
dprintf(1," Parameters: Omega=%g iscale=%g xcen,ycen=%g,%g dx,dy=%g,%g\n",
omega,iscale,xcen,ycen,dx,dy);
potstr = stropen (name, "r"); /* open the image */
read_image (potstr,&iptr); /* read the image */
if (iscale != 1.0) {
int i,j;
for (j=0; j<Ny(iptr); j++)
for (i=0; i<Nx(iptr); i++)
MapValue(iptr,i,j) = MapValue(iptr,i,j) * iscale;
}
nx = Nx(iptr);
ny = Ny(iptr);
if (!Qdel) {
dx = Dx(iptr);
dy = Dy(iptr);
}
idx = 1.0/dx;
idy = 1.0/dy;
if (!Qcen) {
xmin = Xmin(iptr);
ymin = Ymin(iptr);
} else {
xmin = -xcen*dx;
ymin = -ycen*dy;
}
if (idx != idy) {
if (idx == -idy && xmin == -ymin) { /* try and patch it */
idx = -idx;
xmin = -xmin;
warning("Astronomical coordinate convention assumed");
} else
warning("Possible bug when using dx != dy");
}
if (idx<0) warning("1/Dx=%f",idx);
if (idy<0) warning("1/Dy=%f",idy);
xmax = xmin + nx * dx; /* pixel centers */
ymax = ymin + ny * dy;
dprintf(1,"Offset and scale factors: xmin,ymin,1/dx,1/dy=%f %f %f %f\n",
xmin,ymin,idx,idy);
dprintf(1,"Formal full pixel X-range: %g %g\n",xmin-0.5*dx,xmax+0.5*dx);
dprintf(1,"Formal full pixel Y-range: %g %g\n",ymin-0.5*dy,ymax+0.5*dy);
dprintf(1,"Ranges: %g %g %g %g\n",xmin,xmax,ymin,ymax);
par[0] = omega;
}