def ferengi_downscale(image_low,z_low,z_high,pix_low,pix_hi,upscale=False,nofluxscale=False,evo=None):
da_in = cosmos.angular_distance(z_low)
da_out = cosmos.angular_distance(z_high)
dl_in=da_in*(1+z_low)**2#cosmos.luminosity_distance(z_low)
dl_out=da_out*(1+z_high)**2#cosmos.luminosity_distance(z_high)
if evo is not None:
evo_fact = evo(0.0,z_high)
else:
evo_fact=1.0
mag_factor = (da_in/da_out)*(pix_low/pix_hi)
if upscale == True:
mag_factor=1./mag_factor
lum_factor = (dl_in/dl_out)**2*(1.+z_high)/(1.+z_low)
if nofluxscale==True:
lum_factor=1.0
N,M = image_low.shape
N_out = int(round(N*mag_factor))
M_out = int(round(M*mag_factor))
img_out = rebin2d(image_low,N_out,M_out,flux_scale=True)
return img_out*lum_factor*evo_fact
def get_luminosity_image(image, z, pixscale):
lum_dist = cosmos.luminosity_distance(z) * Mpc #in cm
ang_dist = cosmos.angular_distance(z) * Mpc ##in cm
pixel_flux = image / (np.pi * hst_rad**2) * (h * c / l_eff)
pixel_lum = pixel_flux * 4 * np.pi * lum_dist**2
pixel_area = (pixscale / (180 / np.pi * 3600) * (ang_dist) *
(1e6 / Mpc))**2 #in pc
lum_density = pixel_lum / pixel_area / solar_lum ## image in L_sun/s/pc^2
return lum_density
def ferengi_transformation_psf(psf_low,psf_high,z_low,z_high,pix_low,pix_high,same_size=None):
""" Compute the transformation psf. Psf_low and psf_high are the low and high redshift PSFs respectively.
Also needed as input paramenters the redshifts (low and high) and pixelscales (low and high).
"""
psf_l = ferengi_psf_centre(psf_low)
psf_h = ferengi_psf_centre(psf_high)
da_in = cosmos.angular_distance(z_low)
da_out = cosmos.angular_distance(z_high)
N,M=psf_l.shape
add=0
out_size = round((da_in/da_out)*(pix_low/pix_high)*(N+add))
while out_size%2==0:
add+=2
psf_l=np.pad(psf_l,1,mode='constant')
out_size = round((da_in/da_out)*(pix_low/pix_high)*(N+add))
if add>N*3:
return -99
## raise ValueError('Enlarging PSF failed!')
psf_l = ferengi_downscale(psf_l,z_low,z_high,pix_low,pix_high,nofluxscale=True)
psf_l = ferengi_psf_centre(psf_l)
# Make the psfs the same size (then center)
psf_l,psf_h=ferengi_make_psf_same(psf_l,psf_h)
psf_l = ferengi_psf_centre(psf_l)
psf_h = ferengi_psf_centre(psf_h)
# NORMALIZATION
psf_l/=np.sum(psf_l)
psf_h/=np.sum(psf_h)
return psf_l,psf_h,ferengi_psf_centre(ferengi_deconvolve(psf_h,psf_l))
def get_luminosity_image(image, z, pixscale, segmap):
lum_dist = cosmos.luminosity_distance(z) * Mpc #in cm
ang_dist = cosmos.angular_distance(z) * Mpc ##in cm
pixel_flux = image / (np.pi * hst_rad**2) * (h * c / l_eff)
pixel_lum = pixel_flux * 4 * np.pi * lum_dist**2
pixel_area = (pixscale / (180 / np.pi * 3600) * (ang_dist) *
(1e6 / Mpc))**2 #in pc
fig, ax = mpl.subplots(1, 2, figsize=(22, 13))
ax[0].hist((pixel_flux[(pixel_flux > 0) * (segmap != 0)]),
bins=50,
histtype='stepfilled',
color='LightSeaGreen')
fig.text(0.30,
0.93,
r"$\sum_{i} F_{i} = %.4e\ \mathrm{ergs\ s^{-1}cm^{-2}}$" %
((np.sum(pixel_flux[(pixel_flux > 0) * (segmap != 0)]))),
fontsize=25,
color='Teal',
weight='bold',
ha='center')
ax[0].set_xlabel(r'$F_{i}\ [\mathrm{ergs\ s^{-1}cm^{-2}}]$')
ax[1].hist(np.log10(pixel_lum[(pixel_lum > 0) * (segmap != 0)] /
solar_lum),
bins=50,
histtype='stepfilled',
color='PowderBlue')
fig.text(
0.70,
0.93,
r"$\log_{10} \left[ \frac{\sum_{i} L_{i}}{L_\odot} \right] = %.4f$" %
(np.log10(
np.sum(pixel_lum[(pixel_lum > 0) * (segmap != 0)]) / solar_lum)),
fontsize=25,
color='SteelBlue',
weight='bold',
ha='center')
ax[1].set_xlabel(r'$\log_{10} \left(L_{i}/L_\odot\right)$')
fig.canvas.mpl_connect('key_press_event', exit_code)
lum_density = pixel_lum / pixel_area / solar_lum ## image in L_sun/s/pc^2
return lum_density
else:
if os.path.isfile('psf.fits'):
sp.call('rm psf.fits',shell=True)
focus_value = get_focus(args.focus,tilename)
psf_dir='/'.join(match_tiles.split('/')[:-1])+'/PSFs'
xc,yc=gfh.get_center_coords(imgname,RA[i],DEC[i])
select_PSF(ID[i],psf_dir,focus_value,xc,yc)
if args.fixthresh:
t = args.threshold
else:
sigma_0=args.sigma0
t = sigma_0 * ((1+Z[i])/(1+4.0))**(-3)
galaxy_sizes,segflag = compute_size(imgname,RA[i],DEC[i],Mag[i],hsize,t,fractions,sblim)
da=cosmos.angular_distance(Z[i],pars=None)*1000
galaxy_physic_sizes = np.array([(N*(args.pixscale**2)*(180/np.pi*3600)**(-2)*(da**2)) for N in galaxy_sizes])
galaxy_physic_sizes[galaxy_physic_sizes<0] = -99.0
if args.verbose:
print(""" threshold = %8.4f @ z = %.3f d_a=%.3f Mpc)
Pixel Sizes %s
Physic Sizes %s
Segmentation Flag %i
"""%(t,Z[i],da/1000.,"\t".join(["%10i"%(s) for s in galaxy_sizes]),"\t".join(["%10.5f"%(s) for s in galaxy_physic_sizes]) ,segflag ))
if not args.nosaving:
table_out.write("%10i\t%12.8f\t%12.8f\t%5.3f\t%2i\t"%(ID[i],RA[i],DEC[i],Z[i],Zflag[i]))
table_out.write("\t".join(["%10.5f"%(s) for s in galaxy_sizes]))
table_out.write("\t")
table_out.write("\t".join(["%10.5f"%(s) for s in galaxy_physic_sizes]))
def find_pairs_and_clumps(image_stamp,redshift,galmag,color,hsize,threshold,fractions,sblimit,pixelscale,zeropoint,ksky=3.0,Areamin=10,Aperture=0.5,no_dilation=True,degrade=None,size=5,safedist=1.0,title=None,plot_results=False,segmap_output=False,erosion=[3],verbose=False,ident=None,zphot_sel=None):
if np.amax(image_stamp)==np.amin(image_stamp):
if verbose:
print("Invalid data values: %.4f,%.4f"%(np.amax(image_stamp),np.amin(image_stamp)))
return {}
dilate = define_structure(size)
sky_med,sky_std = mi.sky_value(image_stamp,ksky)
if degrade is not None:
N,M=image_stamp.shape
image_stamp = mi.rebin2d(image_stamp,int(N/degrade),int(M/degrade),flux_scale=True)
pixelscale*=degrade
if no_dilation:
image_smooth = mi.sci_nd.gaussian_filter(image_stamp,sigma=1.0)
if args.error:
factor=-1.0
else:
factor=1.0
if np.abs(color)<10:
corrected_thresh = color_correction(threshold,color)
new_sblimit = corrected_thresh*sblimit
# if verbose:
# print("K-I=%.4f\t old sb limit = %.5f\t new sb limit = %.5f counts/s/arcsec**2"%(color,threshold*sblimit,new_sblimit))
threshold=corrected_thresh
elif np.abs(color)>10:
if verbose:
print("Invalid color value: %.4f"%color)
return {}
segmap = mi.gen_segmap_sbthresh(factor*(image_smooth-sky_med),hsize,hsize,sblimit,pixelscale,thresh=threshold,Amin=Areamin,all_detection=True)
single_source_map = mi.select_object_map_connected(hsize,hsize,factor*image_smooth,segmap,pixscale=pixelscale,radius=Aperture)
image_smooth,single_source_map,imglag,segflag = mi.image_validation(image_smooth,single_source_map,pixelscale,safedist)
# fig,ax=mpl.subplots(1,3,figsize=(25,10))
# ax[0].imshow(image_smooth)
# ax[1].imshow(segmap)
# ax[2].imshow(single_source_map)
# fig.canvas.mpl_connect('key_press_event',exit_code)
# mpl.show()
if no_dilation:
dilated_map = single_source_map
else:
dilated_map = mi.sci_nd.binary_dilation(single_source_map,structure=dilate).astype(np.int32)
gal_selection,gal_magnitudes = galaxy_map(image_stamp,segmap,zeropoint,sky_med,factor)
ngals=np.amax(gal_selection)
#
FullSet={}
if verbose:
print('Ngals=%i'%ngals)
for i in range(ngals):
GalPositionsBar={}
GalPositionsMax={}
GalMags={}
GalDistances={}
GalSizes={}
single_gal_map=gal_selection.copy()
single_gal_map[gal_selection!=(i+1)]=0
single_gal_map[gal_selection==(i+1)]=1
# fig,ax=mpl.subplots(1,4,figsize=(25,12))
# ax[0].imshow(factor*image_smooth,vmin=0)
# ax[1].imshow(segmap)
# ax[2].imshow(gal_selection)
# ax[3].imshow(single_gal_map)
# fig.canvas.mpl_connect('key_press_event',exit_code)
# mpl.show()
nregs=[]
nregs2=[]
# fractions = [0.2,1.0]#np.linspace(0,1,101)
Xcen,Ycen=mi.barycenter(factor*image_stamp,single_gal_map)
if zphot_sel is None:
prob_dist = 1.0
prob_dist_area = 1.0
else:
GalDists = mi.dist(Ycen,Xcen,zphot_sel[:,0],zphot_sel[:,1])
kmin = np.argmin(GalDists)
dmin = GalDists[kmin]
vpair=500. #km/s
redshift_error = np.sqrt( vpair*vpair + 200*200. + 20000*20000.)/2.9979e5*(1+redshift)
if dmin < 1.0/pixelscale:
z,zl,zu = zphot_sel[kmin,2],zphot_sel[kmin,3],zphot_sel[kmin,4]
prob_dist = probability_zphot(z,zl,zu,redshift-redshift_error,redshift+redshift_error)
else:
prob_dist = -99
if gal_magnitudes[i]<MagCapak[0]:
prob_dist_area=0.0
else:
NCounts = simps(NumCapak[MagCapak<gal_magnitudes[i]],MagCapak[MagCapak<gal_magnitudes[i]])
radius = mi.dist(Ycen,Xcen,hsize,hsize)*pixelscale
prob_dist_area = max(1-NCounts/(3600.*3600.)*radius*radius*np.pi,0)
for f in fractions:
S = get_segmap_level(factor*image_smooth,single_gal_map,f)
clump_map_full,nr= mi.sci_nd.label(S)
clump_map_clean,nr2 = clean_map(clump_map_full,minarea=Areamin)
# fig,ax=mpl.subplots(1,2)
# ax[0].imshow(clump_map_full)
# ax[1].imshow(clump_map_clean)
# mpl.show()
M,Pb,Pm,Sc=get_clump_stats(factor*image_stamp,clump_map_clean,zeropoint)
GalMags[str(f)]=M
GalPositionsBar[str(f)]=Pb
GalPositionsMax[str(f)]=Pm
GalSizes[str(f)]=Sc
nregs.append(nr)
nregs2.append(nr2)
for f in fractions:
FP = GalPositionsBar[str(f)]
nclumps=np.shape(FP)[0]
DistsSingle=np.zeros(nclumps)
for n in range(nclumps):
DistsSingle[n] = pixelscale*np.sqrt((FP[n,0]-Xcen)*(FP[n,0]-Xcen)+(FP[n,1]-Ycen)*(FP[n,1]-Ycen))
GalDistances[f]=DistsSingle
if verbose:
print('\t %i ----> f=%.2f \t nclumps=%i'%(i,f,nclumps))
if verbose:
print(50*'=')
FullSet[i+1]={}
FullSet[i+1]['weight']=[prob_dist,prob_dist_area]
FullSet[i+1]['mags']=GalMags
FullSet[i+1]['posibar']=GalPositionsBar
FullSet[i+1]['posimax']=GalPositionsMax
FullSet[i+1]['dist']=GalDistances
FullSet[i+1]['size']=GalSizes
## Real_Sizes = Sizes - SizesPSF
if plot_results:
print("mag_cat=",galmag)
print('sky median = %.5f +- %.6f'%(sky_med,sky_std))
print("sky_threshold = %.8f (sigma = %.8f)"%(sblimit*threshold,threshold))
print("Redshift = %.4f"%redshift)
# mpl.rcParams['image.cmap']='gist_stern_r'
# mpl.rcParams['axes.labelsize']=12
# mpl.rcParams['xtick.labelsize']=10
# mpl.rcParams['ytick.labelsize']=10
# rad,flux,xc,yc,q,theta = compute_sbprofile(image_smooth-sky_med,single_source_map,pixelscale)
# radPSF,fluxPSF,xcPSF,ycPSF,qPSF,thetaPSF = compute_sbprofile(psf_image-sky_med,single_source_map_psf,pixelscale)
#==============================================================================
# PAPER FIGURE
#==============================================================================
sidecut=40
import matplotlib.colors as mpc
import matplotlib.cm as cm
# from sklearn.cluster import MeanShift, estimate_bandwidth
# from sklearn.datasets.samples_generator import make_blobs
#
# centers = [[1, 1], [-1, -1], [1, -1]]
# X, _ = make_blobs(n_samples=10000, centers=centers, cluster_std=0.6)
figS,axS=mpl.subplots()
dmax = 20/(cosmos.angular_distance(redshift)/(180/np.pi*3600)*1000)
new_image = (factor*image_stamp)
hsize_new = new_image.shape[0]/2
if 'Hband' in args.image:
CMAP='Reds_r'
elif 'Iband' in args.image:
CMAP='YlGnBu_r'
else:
CMAP='viridis'
VMAX = np.amax(new_image[hsize_new-15:hsize_new+15,hsize_new-15:hsize_new+15])
axS.imshow(np.abs(new_image),cmap=CMAP,extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale),vmax=VMAX)
mi.gen_circle(axS,0,0,dmax,color='white',lw=3)
colors = ['gold','lime','red','cyan','cyan',\
'orange','blue','black','yellow','magenta',\
'brown','gray','Olive','OrangeRed','Coral','Yellow','Magenta','Thistle',\
'SpringGreen','Turquoise','RosyBrown','Silver','SlateGray','Black',\
'Aquamarine','LimeGreen','PeachPuff','Lavender','MediumOrchid']
P=np.array([])
for k in range(ngals):
single_gal_map=gal_selection.copy()
single_gal_map[gal_selection!=(k+1)]=0
single_gal_map[gal_selection==(k+1)]=1
gps,nc = detect_all_clumps(FullSet[k+1],np.arange(0.1,0.8,0.1))
P=np.append(P,gps)
Xcen,Ycen=mi.barycenter(new_image,single_gal_map)
GalDists = mi.dist(Ycen,Xcen,zphot_sel[:,0],zphot_sel[:,1])
kmin = np.argmin(GalDists)
dmin = GalDists[kmin]
# vpair=500. #km/s
# z_search = vpair/2.9979e5*(1+redshift)
# z_spec_err = 0.0017*(1+redshift)
# z_phot_err = 0.1*(1+redshift)
# redshift_error = np.sqrt( z_search*z_search + z_spec_err*z_spec_err + z_phot_err*z_phot_err)
vpair=500. #km/s
redshift_error = np.sqrt( vpair*vpair + 200*200. + 20000*20000.)/2.9979e5*(1+redshift)
if dmin < 1.0/pixelscale:
z,zl,zu = zphot_sel[kmin,2],zphot_sel[kmin,3],zphot_sel[kmin,4]
prob_dist = probability_zphot(z,zl,zu,redshift-redshift_error,redshift+redshift_error,plot_results=True)
else:
prob_dist = -99
print('p(z), on this run',prob_dist)
X = pixelscale*(gps[:,1]-hsize_new+0.5)
Y = pixelscale*(gps[:,0]-hsize_new+0.5)
axS.plot(X,Y,'o',mfc='none',mec=colors[k],ms=20,mew=3)
S = get_segmap_level(factor*image_smooth,single_gal_map,1.0)
# mi.draw_border(axS,S,colors[k],extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
NDS = define_structure(3)
axS.contour(mi.sci_nd.binary_dilation(S,structure=NDS).astype(np.int),levels=[0.5],colors=colors[k],linewidths=3.0,extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
for eixo in [axS]:
for t in eixo.xaxis.get_ticklines():
t.set_color('white')
for t in eixo.yaxis.get_ticklines():
t.set_color('white')
for side in ['left','top','bottom','right']:
eixo.spines[side].set_color('white')
P = P.reshape([len(P)/2,2])
ZF=1.30
axS.set_xlim(-hsize_new*pixelscale/ZF,hsize_new*pixelscale/ZF)
axS.set_ylim(-hsize_new*pixelscale/ZF,hsize_new*pixelscale/ZF)
axS.set_xlabel(r'$\Delta \alpha\ [\mathrm{arcsec}]$')
axS.set_ylabel(r'$\Delta \delta\ [\mathrm{arcsec}]$')
# figS.savefig('clumps_first_pass_SingleGalaxy.png')
if args.zphot:
fig2,ax2=mpl.subplots()
for element in zphot_sel:
xc,yc=element[:2]
ax2.plot(xc,yc,'s',mfc='none',mec='k',markersize=12)
for k in range(ngals):
gps,nc = detect_all_clumps(FullSet[k+1],np.arange(0.1,0.8,0.1))
Weights = FullSet[k+1]['weight']
X = gps[:,1]
Y = gps[:,0]
print(X,Y,Weights)
ax2.plot(X,Y,'o',mfc='none',mec=colors[k],ms=20,mew=3)
# figS.savefig('../ClumpyGalaxies/images/clumps_example_SingleGalaxy.pdf')
# figS.savefig('../ClumpyGalaxies/images/clumps_example_SingleGalaxy.png')
fig,ax=mpl.subplots(ngals,3,figsize=(20,18))
ax=ax.reshape(np.size(ax))
mpl.subplots_adjust(wspace=0)
jetcmap = cm.get_cmap('YlGnBu_r', 10) #generate a jet map with 10 values
jet_vals = jetcmap(np.arange(10)) #extract those values as an array
jet_vals[0] = [0., 0, 0., 0.] #change the first value
# new_jet = mpc.LinearSegmentedColormap.from_list("newjet", jet_vals)
for i in range(ngals):
axnum=i*3
single_gal_map=gal_selection.copy()
single_gal_map[gal_selection!=(i+1)]=0
single_gal_map[gal_selection==(i+1)]=1
ax[axnum+1].imshow(new_image,cmap=CMAP,extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
ax[axnum+2].imshow(gal_selection,cmap='viridis',extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
nregs=[]
nregs2=[]
# fractions = [0.2,0.51.0]#np.linspace(0,1,101)
for f in fractions:
S = get_segmap_level(image_smooth,single_gal_map,f)
clump_map_full,nr= mi.sci_nd.label(S)
clump_map_clean,nr2 = clean_map(clump_map_full,minarea=5)
M,P,Pm,Sc=get_clump_stats(factor*image_stamp,clump_map_clean,zeropoint)
nregs.append(nr)
nregs2.append(nr2)
Xcen,Ycen=mi.barycenter(factor*image_stamp,single_gal_map)
ax[axnum+1].set_ylim((Xcen-hsize_new-50)*pixelscale,(Xcen-hsize_new+50)*pixelscale)
ax[axnum+1].set_xlim((Ycen-hsize_new-50)*pixelscale,(Ycen-hsize_new+50)*pixelscale)
mi.gen_circle(ax[axnum+2],(Ycen-hsize_new)*pixelscale,(Xcen-hsize_new)*pixelscale,0.75,color='cyan',lw=2)
# ax[axnum+2].set_ylim((Xcen-hsize_new-50)*pixelscale,(Xcen-hsize_new+50)*pixelscale)
# ax[axnum+2].set_xlim((Ycen-hsize_new-50)*pixelscale,(Ycen-hsize_new+50)*pixelscale)
ax[axnum].plot(np.array(fractions),nregs,'s-',color='DarkRed',label='All Disconnected')
ax[axnum].plot(np.array(fractions),nregs2,'o-',color='Navy',label='A>10pix Disconnected')
for f,c in zip([0.2,0.5,1.0],['red','lime','cyan','gold']):
S = get_segmap_level(image_smooth,single_gal_map,f)
labelmap,nr= mi.sci_nd.label(S)
# ax[axnum+1].hlines(pixelscale*f*((new_image.shape[0]-2*sidecut)/2),-2,-1,color=c,lw=3)
# ax[axnum+1].text(-1.5,pixelscale*f*((new_image.shape[0]-2*sidecut)/2),r'$f=%.2f$'%f,color=c,fontsize=12,va='bottom',ha='center')
ax[axnum].vlines(f,0,nr,color=c,lw=3)
mi.draw_border(ax[axnum+1],S,c,extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
# NDS = define_structure(3)
# ax[axnum].contour(mi.sci_nd.binary_dilation(S,structure=NDS).astype(np.int),levels=[0.5],colors=c,linewidths=3.0,extent=(-hsize_new*pixelscale,hsize_new*pixelscale,-hsize_new*pixelscale,hsize_new*pixelscale))
# for eixo in ax[1:]:
# mi.gen_circle(eixo,hsize_new,hsize_new,(2*hsize/args.size)*args.aperture,color='red')
# eixo.tick_params(labelleft='off',labelbottom='off')
ax[axnum].hlines(1,0,1.1,'k',':')
ax[axnum].set_xlim(0,1.1)
ax[axnum].set_ylim(0,1.4*max(nregs))
ax[axnum].set_xlabel(r'$f$')
ax[axnum].set_ylabel(r'$N_c$')
ax[0].legend(loc='best')
# fig.savefig('clumps_first_pass.png')
fig.canvas.mpl_connect('key_press_event',exit_code)
mpl.show()
sys.exit()
#==============================================================================
# END PAPER FIGURE
#==============================================================================
return FullSet
def rescale_rexc(r_exc,z_low,z_high):
d_low = cosmos.angular_distance(z_low)
d_high = cosmos.angular_distance(z_high)
return r_exc*(d_low/d_high)