def structure(radius):
structure = pd.read_table('../MODEL/gas/%s.txt' % radius, sep=" ")
z = structure['z'].values #altitudes in AU.
dz = (structure['z'][10] - structure['z'][11]) * au.to(
'cm'
).value # dz is constant along the vertical, so we only need to compute it at one height.
return structure, dz
def __init__(self,model,dx,nphi=2**12,screen_res=2,\
wavelength=1.3e-3,dpc=8400,rpc=5800,r0 = 'sgra',\
r_outer=10000000,r_inner=12,alpha='kolmogorov',\
anisotropy=2.045,pa=78,match_screen_res=False,live_dangerously=False,think_positive=False):
# set initial members
self.logger = logging.getLogger(self.__class__.__name__)
self.live_dangerously = live_dangerously
self.think_positive = think_positive
self.wavelength = wavelength * 1e-3 # observing wavelength in km
self.dpc = float(dpc) # earth-source distance in pc
self.rpc = float(rpc) # R: source-scatterer distance in pc
self.d = self.dpc - self.rpc # D: earth-scatterer distance in pc
self.m = self.d / self.rpc # magnification factor (D/R)
if r0 == 'sgra':
# major axis (EW) phase coherence length in km
self.r0 = 3136.67 * (1.3e-6 / self.wavelength)
else:
try:
self.r0 = float(r0)
except:
raise ValueError('Bad value for r0')
self.anisotropy = anisotropy # anisotropy for screen = (EW / NS elongation)
self.pa = pa # orientation of major axis, E of N (or CCW of +y)
# Fresnel scale in km
self.rf = sqrt(self.dpc * pc.to(units.km).value /
(2 * pi / self.wavelength) * self.m / (1 + self.m)**2)
# compute pixel scale for image
if match_screen_res:
self.ips = 1
self.screen_dx = screen_res * self.r0
else:
self.screen_dx = screen_res * self.r0 # size of a screen pixel in km
self.ips = int(
ceil(1e-6 * dx * self.d * au.to(units.km).value /
self.screen_dx)) # image pixel / screen pixel
# image arrays
self.dx = 1e6 * self.ips * (self.screen_dx /
(au.to(units.km).value * self.d)
) # image pixel scale in uas
self.nx = int(ceil(model.shape[-1] * dx /
self.dx)) # number of image pixels
self.model = model # source model
self.model_dx = dx # source model resolution
self.iss = np.array([], dtype=np.float64) # scattered image
self.isrc = np.array(
[],
dtype=np.float64) # source image at same scale as scattered image
# screen parameters
if type(nphi) == int:
self.nphi = (nphi, nphi) # size of screen array
else:
self.nphi = nphi
self.nphi = np.asarray(self.nphi)
self.r_inner = r_inner # inner turbulence scale in r0
self.r_outer = r_outer # outer turbulence scale in r0
#self.qmax = 1.*screen_res/r_inner # 1 / inner turbulence scale in pix
#self.qmin = 1.*screen_res/r_outer # 1 / outer tubulence scale in pix
if alpha == 'kolmogorov':
self.alpha = 5. / 3
else:
try:
self.alpha = float(alpha)
except:
raise ValueError('Bad value for alpha')
# use logger to report
self.chatter()
# includes sanity check
self.setModel(self.model,
self.model_dx,
think_positive=self.think_positive)
radii = radii(
) # radii in list, used to loop on radii and define names of columns in (r,z) opacity tables.
X = X() # species names in list, used to loop on species.
gas_opacity_frame = pd.DataFrame()
dust_opacity_frame = pd.DataFrame()
#---------------------------
for radius in radii:
dz = z = Q = 0
tau_m = tau_d = structure = dust_density = 0
#-----extract physical structures and dz-----
structure = pd.read_table('../MODEL/gas/%s.txt' % radius, sep=" ")
z = structure['z'].values #altitudes in AU.
dz = (structure['z'][10] - structure['z'][11]) * au.to(
'cm'
).value # dz is constant along the vertical, so we only need to compute it at one arbitrary height.
#--------------------------------------------
#-----extract dust densities-----
dust_density = pd.read_table('../MODEL/%s/dust_density.in' % radius,
sep=" ")
#print(dust['size1'])
#--------------------------------
#-----extract dust sizes-----
size_table = pd.read_table('../MODEL/%s/sizes.in' % radius,
sep=" ",
index_col=0,
names=['value'])
#print(size.loc['size1'].value)
import pencil as pc
import numpy as np
import math
from astropy.constants import au
#
datadir = '../data'
unit_length = au.to('cm').value
par = pc.read.param(datadir=datadir)
#
# According to the RADMC3D manual, the way the variable coordsystem works is
#
# If coordsystem<100 the coordinate system is cartesian.
# If 100<=coordsystem<200 thecoordinate system is spherical (polar).
# If 200<=coordsystem<300 the coordinate system is cylindrical.
#
xdim = unit_length
print(par.coord_system)
if (par.coord_system == 'cartesian'):
coordsystem = 99
ydim = unit_length
zdim = unit_length
elif (par.coord_system == 'cylindric'):
coordsystem = 200
ydim = 1.
zdim = unit_length
elif (par.coord_system == 'spherical'):
coordsystem = 100
ydim = 1.
zdim = 1.
else:
print("the world is flat and we never got here")
from datetime import datetime
import numpy as np
from numpy import radians
from numpy.testing import TestCase, assert_almost_equal, run_module_suite
from astropy import units
from astropy.constants import au
from poliastro import ephem
AU = au.to(units.km).value
class TestEphem(TestCase):
def test_vallado55(self):
dd = datetime(1994, 5, 20, 20)
a, ecc, inc, omega, argp, nu = ephem.mean_elements(dd, ephem.JUPITER)
assert_almost_equal(a / AU, 5.202895, decimal=3)
assert_almost_equal(ecc, 0.048319, decimal=3)
assert_almost_equal(inc, 0.022770, decimal=4)
assert_almost_equal(omega, 1.753543, decimal=2)
assert_almost_equal(argp, 4.803144, decimal=1)
assert_almost_equal(nu, 3.590915, decimal=1)
if __name__ == '__main__':
run_module_suite()
import pencil as pc
import numpy as np
import math
from astropy.constants import au
#
datadir = '../data'
unit_length=au.to('cm').value
par=pc.read_param(datadir=datadir)
#
# According to the RADMC3D manual, the way the variable coordsystem works is
#
# If coordsystem<100 the coordinate system is cartesian.
# If 100<=coordsystem<200 thecoordinate system is spherical (polar).
# If 200<=coordsystem<300 the coordinate system is cylindrical.
#
xdim=unit_length
print par.coord_system
if (par.coord_system == 'cartesian'):
coordsystem = 99
ydim=unit_length
zdim=unit_length
elif (par.coord_system == 'cylindric'):
coordsystem = 200
ydim=1.
zdim=unit_length
elif (par.coord_system == 'spherical'):
coordsystem = 100
ydim=1.
zdim=1.
else:
print "the world is flat and we never got here"
def __init__(self,model,dx,nphi=2**12,screen_res=2,\
wavelength=1.3e-3,dpc=8400,rpc=5800,r0 = 'sgra',\
r_outer=10000000,r_inner=12,alpha='kolmogorov',\
anisotropy=2.045,pa=78,match_screen_res=False,live_dangerously=False,think_positive=False):
# set initial members
self.logger = logging.getLogger(self.__class__.__name__)
self.live_dangerously = live_dangerously
self.think_positive = think_positive
self.wavelength = wavelength*1e-3 # observing wavelength in km
self.dpc = float(dpc) # earth-source distance in pc
self.rpc = float(rpc) # R: source-scatterer distance in pc
self.d = self.dpc - self.rpc # D: earth-scatterer distance in pc
self.m = self.d/self.rpc # magnification factor (D/R)
if r0 == 'sgra':
# major axis (EW) phase coherence length in km
self.r0 = 3136.67*(1.3e-6/self.wavelength)
else:
try:
self.r0 = float(r0)
except:
raise ValueError('Bad value for r0')
self.anisotropy = anisotropy # anisotropy for screen = (EW / NS elongation)
self.pa = pa # orientation of major axis, E of N (or CCW of +y)
# Fresnel scale in km
self.rf = sqrt(self.dpc*pc.to(units.km).value / (2*pi / self.wavelength) * self.m / (1+self.m)**2)
# compute pixel scale for image
if match_screen_res:
self.ips = 1
self.screen_dx = screen_res * self.r0
else:
self.screen_dx = screen_res * self.r0 # size of a screen pixel in km
self.ips = int(ceil(1e-6*dx*self.d*au.to(units.km).value/self.screen_dx)) # image pixel / screen pixel
# image arrays
self.dx = 1e6 * self.ips * (self.screen_dx / (au.to(units.km).value * self.d)) # image pixel scale in uas
self.nx = int(ceil(model.shape[-1] * dx / self.dx)) # number of image pixels
self.model = model # source model
self.model_dx = dx # source model resolution
self.iss = np.array([],dtype=np.float64) # scattered image
self.isrc = np.array([],dtype=np.float64) # source image at same scale as scattered image
# screen parameters
if type(nphi) == int:
self.nphi = (nphi,nphi) # size of screen array
else:
self.nphi = nphi
self.nphi = np.asarray(self.nphi)
self.r_inner = r_inner # inner turbulence scale in r0
self.r_outer = r_outer # outer turbulence scale in r0
#self.qmax = 1.*screen_res/r_inner # 1 / inner turbulence scale in pix
#self.qmin = 1.*screen_res/r_outer # 1 / outer tubulence scale in pix
if alpha == 'kolmogorov':
self.alpha = 5./3
else:
try:
self.alpha = float(alpha)
except:
raise ValueError('Bad value for alpha')
# use logger to report
self.chatter()
# includes sanity check
self.setModel(self.model,self.model_dx,think_positive=self.think_positive)
