def fftvec(vec):
"""
performs a fft on a vector with 3 components in the first index position
This is really just a wrapper for fft, fftn and their inverses
"""
try:
from anfft import fft, fftn
fft_type = 1
except:
# print "Could not import anfft, importing scipy instead."
#Update 9/18/2013 -- numpy with mkl is way faster than scipy
import mkl
mkl.set_num_threads(8)
from numpy.fft import fft, fftn
fft_type = 0
if force_gpu:
fft_type = 2 #set gpu fft's manually -- not sure what a automatic way would look like
from numpy import complex64, shape, array, empty
if vec.ndim > 2:
if vec.shape[0] == 3:
# "Vector": first index has size 3 so fft the other columns
if fft_type==1:
return array([fftn(i,measure=True) for i in vec]).astype(complex64)
# result = empty(vec.shape, dtype=complex64)
# result[0] = fftn(vec[0], measure=True).astype(complex64)
# result[1] = fftn(vec[1], measure=True).astype(complex64)
# result[2] = fftn(vec[2], measure=True).astype(complex64)
# return result
elif fft_type==0:
return fftn(vec, axes=range(1,vec.ndim)).astype(complex64)
elif fft_type==2:
# return array([gpu_fft(i) for i in vec.astype(complex64)])
result = empty(vec.shape, dtype=complex64)
result[0] = gpu_fft(vec[0].copy())
result[1] = gpu_fft(vec[1].copy())
result[2] = gpu_fft(vec[2].copy())
return result
else: # "Scalar", fft the whole thing
if fft_type==1:
return fftn(vec,measure=True).astype(complex64)
elif fft_type==0:
return fftn(vec).astype(complex64)
elif fft_type==2:
return gpu_fft(vec.copy())
elif vec.ndim == 1: #Not a vector, so use fft
if fft_type==1:
return fft(vec,measure = True).astype(complex64)
elif fft_type==0:
return fft(vec).astype(complex64)
elif fft_type==2:
return gpu_fft(vec.astype(complex64))
else:
#0th index is 3, so its a vector
#return fft(vec, axis=1).astype(complex64)
return array([fft(i) for i in vec])
def fft_fftn(*args, **kwargs):
"""Call the core fft library function fftn.
If the anfft library is used, enable 'measure' optimization.
"""
if using_fft_library == "anfft":
return fft.fftn(*args, measure=True, **kwargs)
else:
return fft.fftn(*args, **kwargs)
def do_fft(self, signal_matrix):
"""
Maybe zero-padding is necessary, it could be done with:
fftn(signal_matrix, [next pow of 2, next pow of 2, next pow of 2])
"""
if self.fft_module == 'anfft':
return anfft.fftn(signal_matrix)
else:
return np.fft.fftn(signal_matrix)
def digthis(region_coeff):
# for i in range(0,len(ra_sam)):
# image[x_sam[i].round(),y_sam[i].round()]=flux_sam[i]+(10**region_coeff[0])# adding background level to the pixels
#print region_coeff
# if (np.any(region_coeff)>3 or np.any(region_coeff<-10)):
if (np.any(abs(region_coeff-desired)>1.5)):
return -np.inf
# if (np.any(abs(region_coeff[faint]-desired[faint])>1)):
# return -np.inf
# for qq in index_photo_z:
#image[x_cat_photo_z[qq].round(),y_cat_photo_z[qq].round()]=(10**region_coeff[pp]) # because the zero's index is used for background.
for qq in izip(sam_corresponding_index[desired_index],cat_corresponding_index[desired_index]):
yo,xo=wcs_pacs160.wcs_sky2pix(cat.ra[qq[1]],cat.dec[qq[1]],0)
xn,yn = ZOOM*(xo-xc_orig)+xc_expanded,ZOOM*(yo-yc_orig)+yc_expanded
pacs160_image[xn[0],yn[0]]=0
pp=0
for qq in izip(sam_corresponding_index[desired_index],cat_corresponding_index[desired_index]):
yo,xo=wcs_pacs160.wcs_sky2pix(cat.ra[qq[1]],cat.dec[qq[1]],0)
xn,yn = ZOOM*(xo-xc_orig)+xc_expanded,ZOOM*(yo-yc_orig)+yc_expanded
pacs160_image[xn[0],yn[0]]=pacs160_image[xn[0],yn[0]]+(10**region_coeff[pp])
pp+=1
# chi2[pp]=np.log(np.interp(region_coeff[pp+1],np.log10(bins),pdffile[qq,:]/pdffile[qq,:].max()) ) # this is -chi2/2 in fact that we retrun.
# return len((chi2==-np.inf).nonzero()[0]*(-1e6)
image_p = hconvolve.padzero2d_i(pacs160_image, r, c)
fftimage = anfft.fftn(image_p)*fftkernel# * anfft.fftn(kernel_p)
test_k_temp = anfft.ifftn(fftimage)[:r1,:c1].real
test_k = interpolation.zoom(test_k_temp,1./ZOOM)/normfactor
test_chi2=0
for i in range(x_min,x_max):
for j in range(y_min,y_max):
test_chi2+=(test_k[i,j]-herschel[i,j])**2/(RMS_pacs160[i,j]**2)
print >>chi2file, -1*(test_chi2/2)
print -1*(test_chi2/2)
return -1*(test_chi2/2)#+chi2.sum()
def explorefluxes(region_coeff):
#weak prior of 3 dex wide on each source is imposed to limit the exploration of walkers with that plausible range.
if (np.any(abs(region_coeff - desired) > 1.5)):
return -np.inf
#at each step the pixels that contain the sources of interest is set to zero.
for qq in izip(sam_corresponding_index[desired_index],
cat_corresponding_index[desired_index]):
yo, xo = wcs_pacs160.wcs_sky2pix(cat.ra[qq[1]], cat.dec[qq[1]], 0)
xn, yn = ZOOM * (xo - xc_orig) + xc_expanded, ZOOM * (
yo - yc_orig) + yc_expanded
pacs160_image[xn[0], yn[0]] = 0
# Pixel values are set to the sources fluxes guesses by the walkers at each step
pp = 0
for qq in izip(sam_corresponding_index[desired_index],
cat_corresponding_index[desired_index]):
yo, xo = wcs_pacs160.wcs_sky2pix(cat.ra[qq[1]], cat.dec[qq[1]], 0)
xn, yn = ZOOM * (xo - xc_orig) + xc_expanded, ZOOM * (
yo - yc_orig) + yc_expanded
pacs160_image[xn[0], yn[0]] += (10**region_coeff[pp])
pp += 1
#convolution is performed after sources are put in their relevent pixel
image_p = hconvolve.padzero2d_i(pacs160_image, r,
c) # taking the FFT of the image
fftimage = anfft.fftn(image_p) * fftkernel # mutiply by FFT of Kernel
test_k_temp = anfft.ifftn(
fftimage
)[:r1, :c1].real # Inverse FFT the result and take the real part
test_k = interpolation.zoom(
test_k_temp,
1. / ZOOM) / normfactor # zoom out by the factor PSF was zoomed in
#compute the chi2 at each step
test_chi2 = 0
for i in range(x_min, x_max):
for j in range(y_min, y_max):
test_chi2 += (test_k[i, j] -
herschel[i, j])**2 / (RMS_pacs160[i, j]**2)
print -1 * (test_chi2 / 2)
return -1 * (test_chi2 / 2)
def diffusion_omega(dt, omega, args):
'''
d(omega)/dt = nu*((omega)_xx + (omega)_yy) - mu*omega
=> d(omega)Hat/(omega)Hat = -nu*(k_x^2 + k_y^2)*dt - mu*dt
=> (omega)Hat = e^(-nu*|k|^2 - mu)dt*(omega)Hat_0
Dynamic viscosity nu = 0.01 for now
'''
omegaHat = anfft.fftn(omega,2, measure=True);
[xVal,yVal] = shape(omegaHat);
omegaHat[xVal/6:5*xVal/6,yVal/6:5*yVal/6] = 0;
k = array(range(N), dtype=complex128) - N/2;
k = ifftshift(k);
[KX, KY] = meshgrid(k,k);
mu = 0.0001;
mask = zeros(N);
for i in arange(N/100):
mask[i] = 1;
mask[N-i-1] = 1;
[dragx,dragy] = meshgrid(mask,mask);
# delsq = -(KX*KX + KY*KY)
delsq = -(pow(KX,6) + pow(KY,6))
omegasq = sqrt(sum(omega*omega)/(N*N));
if (args == 0):
nu = omegasq/pow(N,4);
else:
nu = args;
# print 'viscosity=',nu;
delsq = (nu*delsq - mu*(dragy + dragx))*dt;
multiplier = exp(delsq);
omegaHat = omegaHat*multiplier;
return (real(anfft.ifftn(omegaHat,2)), nu);
xn,yn = ZOOM*(xo-xc_orig)+xc_expanded,ZOOM*(yo-yc_orig)+yc_expanded
pacs160_image[xn[0],yn[0]]+=pacs160_sam[i[0]]
#===================================
r1, c1 = pacs160_image.shape
r2, c2 = kernel_pacs160_zoom2.shape
if r2 % 2 == 0:
r = r1 + r2/2
else:
r = r1 + (r2 + 1) / 2
if c2 % 2 == 0:
c = c1 + c2/2 + 1
else:
c = c1 + (c2 + 1) / 2
kernel_p = hconvolve.padzero2d_k(kernel_pacs160_zoom2, r, c)
fftkernel=anfft.fftn(kernel_p)
#===================================
#bins=np.logspace(-10,3,49)
chi2=np.zeros(len(index_photo_z))
#chi2file_gt_4=open('./chi2file_gt_4_38_sources_correct.txt', 'w+')
#chi2file_gt_4=open('./chi2file_testing.txt', 'w+')
chi2file=open('./chi2file_4.5_gt_1_np_inf_65_sources_startingattrueflux_sgima0.4.txt','w+')
def digthis(region_coeff):
# for i in range(0,len(ra_sam)):
# image[x_sam[i].round(),y_sam[i].round()]=flux_sam[i]+(10**region_coeff[0])# adding background level to the pixels
#print region_coeff
# if (np.any(region_coeff)>3 or np.any(region_coeff<-10)):
if (np.any(abs(region_coeff-desired)>1.5)):
return -np.inf
# if (np.any(abs(region_coeff[faint]-desired[faint])>1)):
def get_dft(array, ndim=None):
array = array.astype(TYPE)
result = anfft.fftn(array, ndim, measure=True)
return result
def fftn(A,shape=None): if shape != None: A = _checkffttype(A) A = procrustes(A,target=shape,side='after',padval=0) return _anfft.fftn(A,measure=True)
xn, yn = ZOOM * (xo - xc_orig) + xc_expanded, ZOOM * (
yo - yc_orig) + yc_expanded
pacs160_image[xn[0], yn[0]] = pacs160_sam[i[0]]
#===================================
r1, c1 = pacs160_image.shape
r2, c2 = kernel_pacs160_zoom2.shape
if r2 % 2 == 0:
r = r1 + r2 / 2
else:
r = r1 + (r2 + 1) / 2
if c2 % 2 == 0:
c = c1 + c2 / 2 + 1
else:
c = c1 + (c2 + 1) / 2
kernel_p = hconvolve.padzero2d_k(kernel_pacs160_zoom2, r, c)
fftkernel = anfft.fftn(kernel_p)
#===================================
image_p = hconvolve.padzero2d_i(pacs160_image, r, c)
fftimage = anfft.fftn(image_p) * fftkernel # * anfft.fftn(kernel_p)
image_conv = anfft.ifftn(fftimage)[:r1, :c1].real
image_blk = interpolation.zoom(image_conv, 1. / ZOOM) / normfactor
final = image_blk + noise_pacs160
pyfits.writeto(
'/astro/ferguson1/safar/SAMS/simulated_images/simulated_pacs160_with_photo_z_zoom2_new_correct_ID.fits',
final, header_pacs160)
def get_dft(array, ndim=None):
array = array.astype(TYPE)
result = anfft.fftn(array, ndim, measure=True)
return result
def fftn(A, shape=None):
if shape != None:
A = _checkffttype(A)
A = procrustes(A, target=shape, side='after', padval=0)
return _anfft.fftn(A, measure=True)
def fft2(A):
return _anfft.fftn(_checkffttype(A), measure=True)