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cflux_alma.py
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cflux_alma.py
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import numpy as np
import matplotlib.pyplot as plt
from astropy import units
from astropy.io import fits
from photutils import EllipticalAnnulus,CircularAnnulus,EllipticalAperture
from photutils import aperture_photometry
from mcmax3d_analysis.mcmax3d_convolution import convolve_model
import sys
from gofish import imagecube
plt.style.use('fancy')
def image(fits_image,beam_x,beam_y,beam_angle):
############################################################
# Absolute paths to files
path_fits_image='../output/'+fits_image
path_image_file='../Image_alma.out'
path_input_file='../input.dat'
############################################################
# Fetching information
imfile=open(path_image_file).readlines()
for line in imfile:
if line.split('=')[0]=='MCobs:fov':
fov=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:npix':
npix=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:phi':
phi_image=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:theta':
theta=float(line.split('=')[1].split('!')[0])
else:
continue
infile=open(path_input_file).readlines()
for line in infile:
if line.split('=')[0]=='Distance':
d=float(line.split('=')[1])
############################################################
# Derived quantities
pxsize=fov/npix # pixel scale (arcsec/px)
theta=(theta*units.deg).to(units.rad).value # Inclination (rad)
d=(d*units.pc).to(units.au).value # Distance (au)
e=np.sin(theta) # eccentricity of the annulus
############################################################
# Load MCMax3D image
hdulist=fits.open(path_fits_image)
data_mod=hdulist[0].data[0] # mJy/arcsec^2
############################################################
# Convolve?
data_mod=convolve_model(data_mod,fov,npix,beam_x,beam_y,beam_angle) # mJy/arcsec^2
############################################################
# Convertion from mJy/arcsec^2 to mJy/beam
beam_area=np.pi*(beam_x)*(beam_y)/(4*np.log(2))
data_mod=data_mod*beam_area # mJy/beam
print("Maximum value of the density flux in ALMA image (mJy/beam)",data_mod.max())
return data_mod
def radial_profile_gofish(data,disk_inc,disk_pa,d,x0_off,y0_off,lim):
cube=imagecube(data)
xm, ym, dym = cube.radial_profile(inc=disk_inc,
PA=disk_pa,
dist=d,
x0=x0_off,
y0=y0_off)
xm=xm*d
ym=ym # mJy/beam
dym=dym
f=open("../alma_radial_profile_modeled.dat","w")
for (i,j,k) in zip(xm,ym,dym):
if i<=lim:
f.write("%.13e %.13e %.13e \n"%(i,j,k))
f.close()
return None
def radial_profile(data,lim):
############################################################
# Fetching information
imfile=open("../Image_alma.out").readlines()
for line in imfile:
if line.split('=')[0]=='MCobs:fov':
fov=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:npix':
npix=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:phi':
phi_image=float(line.split('=')[1].split('!')[0])
elif line.split('=')[0]=='MCobs:theta':
theta=float(line.split('=')[1].split('!')[0])
else:
continue
infile=open("../input.dat").readlines()
for line in infile:
if line.split('=')[0]=='Distance':
d=float(line.split('=')[1])
############################################################
# Derived quantities
pxsize=fov/npix # pixel scale (arcsec/px)
theta=(theta*units.deg).to(units.rad).value # Inclination (rad)
d=(d*units.pc).to(units.au).value # Distance (au)
e=np.sin(theta) # eccentricity of the annulus
############################################################
# Input params
angle_annulus=0.0
# Determining limit for radial profile
#lim=120.0
linear_lim=2*(lim) # AU
angular_lim=linear_lim/d # rad
angular_lim=(angular_lim*units.rad).to(units.arcsec).value # arcsec
pixel_lim=int(round(angular_lim/pxsize))
xc=0.5*data.shape[0] # Image center in data coordinates
yc=0.5*data.shape[1] # Image center in data coordinates
dr=1.0 # Width of the annulus
a_in_array=[]
for i in np.arange(yc+dr,yc+0.5*pixel_lim,dr):
a_in_array.append(i-xc)
a_out_array=[i+dr for i in a_in_array]
b_out_array=[i*(1-e**2)**0.5 for i in a_out_array]
apertures=[EllipticalAnnulus((yc,xc),a_in=ain,a_out=aout,b_out=bout,theta=angle_annulus)
for (ain,aout,bout) in zip(a_in_array,a_out_array,b_out_array)]
"""
############################################################
# Do a check
a=0.01
vmin_jband=np.percentile(data,a)
vmax_jband=np.percentile(data,100-a)
aperture=apertures[-1]
plt.imshow(data,clim=(vmin_jband,vmax_jband))
plt.title("Image model")
aperture.plot(color='red',lw=1)
plt.show()
print(data.max())
sys.exit()
"""
# Radial distance of each annulus
r_arcsec=[(j+0.5*(i-j))*pxsize for (i,j) in zip(a_out_array,a_in_array)] # arcsec
r_rad=[(i*units.arcsec).to(units.rad).value for i in r_arcsec] # rad
r_au=[(i*d) for i in r_rad] # AU
# Creating numpy arrays
r_au=np.array(r_au)
r_arcsec=np.array(r_arcsec)
phot_table=aperture_photometry(data,apertures)
col_values=[]
for col in phot_table.colnames:
col_values.append(phot_table[col][0])
brightness=[col_values[i] for i in range(3,len(col_values))]
brightness=np.array(brightness)
for i in range(0,len(brightness)):
brightness[i]=brightness[i]/apertures[i].area
rcmin=30.0
rcmax=100.0
bmaxc=[]
for i in range(0,len(r_au)):
if rcmin<=r_au[i]<=rcmax:
bmaxc.append(brightness[i])
bmaxc=np.array(bmaxc)
fac=1/max(bmaxc)
brightness=brightness*fac
"""
############################################################
# Creating brightness profile
fig=plt.figure()
ax=plt.axes()
ax.plot(r_au,brightness/max(brightness),'*')
ax.set_xlabel(r"Projected radial distance (AU)")
ax.set_ylabel("Density flux (mJy/beam)")
ax.set_title("Radial profile model")
plt.show()
sys.exit()
"""
############################################################
# Creating file
file=open('../alma_radial_profile_modeled.dat',"w")
for i in range(0,len(r_au)):
file.write('%.15e %.15e \n'%(r_au[i],brightness[i]))
return None