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Renaming function create_fake_disk to cube_inject_fakedisk. Code clea…
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…nup to make it more compliant with PEP8

The following modules were modified: phase_function, scattered_light_disk and dust_distribution modules
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@carlos-gg
carlos-gg committed Sep 19, 2018
1 parent bfc6e00 commit f397617
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201 changes: 114 additions & 87 deletions vip_hci/metrics/dust_distribution.py
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Original file line number Diff line number Diff line change
@@ -1,17 +1,18 @@
# -*- coding: utf-8 -*-
"""
Created on Wed May 6 17:07:00 2015
@author: jmilli
"""
import numpy as np

class Dust_distribution:
_author__ = 'Julien Milli'


class Dust_distribution(object):
"""This class represents the dust distribution
"""

def __init__(self,density_dico={'name':'2PowerLaws','ain':5,'aout':-5,\
'a':60,'e':0,'ksi0':1.,'gamma':2.,'beta':1.}):
def __init__(self,density_dico={'name':'2PowerLaws', 'ain':5, 'aout':-5,
'a':60, 'e':0, 'ksi0':1., 'gamma':2.,
'beta':1.}):
"""
Constructor for the Dust_distribution class.
Expand All @@ -20,55 +21,63 @@ def __init__(self,density_dico={'name':'2PowerLaws','ain':5,'aout':-5,\
the midplane, and vertically whenever it drops below 0.5% of the
peak density in the midplane
"""
self.accuracy=5.e-3
if not isinstance(density_dico,dict):
raise TypeError('The parameters describing the dust density distribution must be a Python dictionnary')
self.accuracy = 5.e-3
if not isinstance(density_dico, dict):
errmsg = 'The parameters describing the dust density distribution' \
' must be a Python dictionnary'
raise TypeError(errmsg)
if 'name' not in density_dico.keys():
raise TypeError('The dictionnary describing the dust density distribution must contain the key "name"')
errmsg = 'The dictionnary describing the dust density ' \
'distribution must contain the key "name"'
raise TypeError(errmsg)
self.type = density_dico['name']
if self.type == '2PowerLaws':
self.dust_distribution_calc = DustEllipticalDistribution2PowerLaws(\
self.accuracy,density_dico)
self.dust_distribution_calc = DustEllipticalDistribution2PowerLaws(
self.accuracy, density_dico)
else:
raise TypeError('The only dust distribution implemented so far is the "2PowerLaws"')
errmsg = 'The only dust distribution implemented so far is the' \
' "2PowerLaws"'
raise TypeError(errmsg)

def set_density_distribution(self,density_dico):
"""
Updates the parameters of the density distribution.
Update the parameters of the density distribution.
"""
self.dust_distribution_calc.set_density_distribution(density_dico)

def density_cylindrical(self,r,costheta,z):
def density_cylindrical(self, r, costheta, z):
"""
Returns the particule volume density at r, theta, z
Return the particule volume density at r, theta, z.
"""
return self.dust_distribution_calc.density_cylindrical(r,costheta,z)
return self.dust_distribution_calc.density_cylindrical(r, costheta, z)

def density_cartesian(self,x,y,z):
def density_cartesian(self, x, y, z):
"""
Returns the particule volume density at x,y,z, taking into account the offset
of the disk
Return the particule volume density at x,y,z, taking into account the
offset of the disk.
"""
return self.dust_distribution_calc.density_cartesian(x,y,z)
return self.dust_distribution_calc.density_cartesian(x, y, z)


def print_info(self,pxInAu=None):
def print_info(self, pxInAu=None):
"""
Utility function that displays the parameters of the radial distribution of the dust
Utility function that displays the parameters of the radial distribution
of the dust
Input:
- pxInAu (optional): the pixel size in au
"""
print('----------------------------')
print('Dust distribution parameters')
print('----------------------------')
self.dust_distribution_calc.print_info(pxInAu=None)

self.dust_distribution_calc.print_info(pxInAu)


class DustEllipticalDistribution2PowerLaws:
"""
"""

def __init__(self,accuracy=5.e-3,density_dico={'ain':5,'aout':-5,\
'a':60,'e':0,'ksi0':1.,'gamma':2.,'beta':1.}):
def __init__(self, accuracy=5.e-3, density_dico={'ain':5,'aout':-5,
'a':60,'e':0,'ksi0':1.,
'gamma':2.,'beta':1.}):
"""
Constructor for the Dust_distribution class.
Expand All @@ -84,37 +93,37 @@ def set_density_distribution(self,density_dico):
"""
"""
if 'ksi0' not in density_dico.keys():
ksi0=1.
ksi0 = 1.
else:
ksi0=density_dico['ksi0']
ksi0 = density_dico['ksi0']
if 'beta' not in density_dico.keys():
beta=1.
beta = 1.
else:
beta=density_dico['beta']
beta = density_dico['beta']
if 'gamma' not in density_dico.keys():
gamma=1.
gamma = 1.
else:
gamma=density_dico['gamma']
gamma = density_dico['gamma']
if 'aout' not in density_dico.keys():
aout=-5.
aout = -5.
else:
aout=density_dico['aout']
aout = density_dico['aout']
if 'ain' not in density_dico.keys():
ain=5.
ain = 5.
else:
ain=density_dico['ain']
ain = density_dico['ain']
if 'e' not in density_dico.keys():
e=0.
e = 0.
else:
e=density_dico['e']
e = density_dico['e']
if 'a' not in density_dico.keys():
a=60.
a = 60.
else:
a=density_dico['a']
self.set_vertical_density(ksi0=ksi0,gamma=gamma,beta=beta)
self.set_radial_density(ain=ain,aout=aout,a=a,e=e)
a = density_dico['a']
self.set_vertical_density(ksi0=ksi0, gamma=gamma, beta=beta)
self.set_radial_density(ain=ain, aout=aout, a=a, e=e)

def set_vertical_density(self,ksi0=1.,gamma=2.,beta=1.):
def set_vertical_density(self, ksi0=1., gamma=2., beta=1.):
"""
Sets the parameters of the vertical density function
Expand All @@ -139,12 +148,12 @@ def set_vertical_density(self,ksi0=1.,gamma=2.,beta=1.):
print('Warning the flaring coefficient beta is negative')
print('beta was changed from {0:6.2f} to 0 (flat disk)'.format(beta))
beta = 0.
self.ksi0=float(ksi0)
self.gamma=float(gamma)
self.beta=float(beta)
self.zmax=ksi0*(-np.log(self.accuracy))**(1./gamma)
self.ksi0 = float(ksi0)
self.gamma = float(gamma)
self.beta = float(beta)
self.zmax = ksi0*(-np.log(self.accuracy))**(1./gamma)

def set_radial_density(self,ain=5.,aout=-5.,a=60.,e=0.):
def set_radial_density(self, ain=5., aout=-5., a=60., e=0.):
"""
Sets the parameters of the radial density function
Expand Down Expand Up @@ -179,15 +188,17 @@ def set_radial_density(self,ain=5.,aout=-5.,a=60.,e=0.):
e = 0.99
if a < 0:
raise ValueError('Warning the semi-major axis a is negative')
self.ain=float(ain)
self.aout=float(aout)
self.a=float(a)
self.e=float(e)
self.p=self.a*(1-self.e**2)
self.ain = float(ain)
self.aout = float(aout)
self.a = float(a)
self.e = float(e)
self.p = self.a*(1-self.e**2)
try:
self.rmax=self.a*self.accuracy**(1/self.aout) #maximum distance of integration, AU
if self.ain!=self.aout:
self.apeak = self.a * np.power(-self.ain/self.aout,1./(2.*(self.ain-self.aout)))
# maximum distance of integration, AU
self.rmax = self.a*self.accuracy**(1/self.aout)
if self.ain != self.aout:
self.apeak = self.a * np.power(-self.ain/self.aout,
1./(2.*(self.ain-self.aout)))
else:
self.apeak = self.a
except OverflowError:
Expand All @@ -204,69 +215,85 @@ def set_radial_density(self,ain=5.,aout=-5.,a=60.,e=0.):
raise ZeroDivisionError
self.itiltthreshold = np.rad2deg(np.arctan(self.rmax/self.zmax))

def print_info(self,pxInAu=None):
def print_info(self, pxInAu=None):
"""
Utility function that displays the parameters of the radial distribution of the dust
Utility function that displays the parameters of the radial distribution
of the dust
Input:
- pxInAu (optional): the pixel size in au
"""
if pxInAu is not None:
print('Reference semi-major axis: {0:.1f}au or {1:.1f}px'.format(self.a,self.a/pxInAu))
print('Semi-major axis at maximum dust density: {0:.1f}au or {1:.1f}px (same as ref sma if ain=-aout)'.format(self.apeak,self.apeak/pxInAu))
print('Ellipse p parameter: {0:.1f}au or {1:.1f}px'.format(self.p,self.p/pxInAu))
msg = 'Reference semi-major axis: {0:.1f}au or {1:.1f}px'
print(msg.format(self.a,self.a/pxInAu))
msg2 = 'Semi-major axis at maximum dust density: {0:.1f}au or ' \
'{1:.1f}px (same as ref sma if ain=-aout)'
print(msg2.format(self.apeak,self.apeak/pxInAu))
msg3 = 'Ellipse p parameter: {0:.1f}au or {1:.1f}px'
print(msg3.format(self.p,self.p/pxInAu))
else:
print('Reference semi-major axis: {0:.1f}au'.format(self.a))
print('Semi-major axis at maximum dust density: {0:.1f}au (same as ref sma if ain=-aout)'.format(self.apeak))
msg = 'Semi-major axis at maximum dust density: {0:.1f}au (same ' \
'as ref sma if ain=-aout)'
print(msg.format(self.apeak))
print('Ellipse p parameter: {0:.1f}au'.format(self.p))
print('Ellipticity: {0:.3f}'.format(self.e))
print('Inner slope: {0:.2f}'.format(self.ain))
print('Outer slope: {0:.2f}'.format(self.aout))
if pxInAu is not None:
print('Scale height: {0:.1f}au or {1:.1f}px at {2:.1f}'.format(self.ksi0,self.ksi0/pxInAu,self.a))
msg = 'Scale height: {0:.1f}au or {1:.1f}px at {2:.1f}'
print(msg.format(self.ksi0,self.ksi0/pxInAu,self.a))
else:
print('Scale height: {0:.2f} au at {1:.2f}'.format(self.ksi0,self.a))
print('Scale height: {0:.2f} au at {1:.2f}'.format(self.ksi0,
self.a))
print('Vertical profile index: {0:.2f}'.format(self.gamma))
print('Disc vertical FWHM: {0:.2f} at {1:.2f}'.format(2.*self.ksi0*np.power(np.log10(2.),1./self.gamma),self.a))
msg = 'Disc vertical FWHM: {0:.2f} at {1:.2f}'
print(msg.format(2.*self.ksi0*np.power(np.log10(2.), 1./self.gamma),
self.a))
print('Flaring coefficient: {0:.2f}'.format(self.beta))
print('------------------------------------')
print('Properties for numerical integration')
print('------------------------------------')
print('Requested accuracy {0:.2e}'.format(self.accuracy))
# print('Minimum radius for integration: {0:.2f} au'.format(self.rmin))
print('Maximum radius for integration: {0:.2f} au'.format(self.rmax))
print('Maximum height for integration: {0:.2f} au'.format(self.zmax))
print('Inclination threshold: {0:.2f} degrees'.format(self.itiltthreshold))
print('Maximum height for integration: {0:.2f} au'.format(self.zmax))
msg = 'Inclination threshold: {0:.2f} degrees'
print(msg.format(self.itiltthreshold))
return

def density_cylindrical(self,r,costheta,z):
def density_cylindrical(self, r, costheta, z):
""" Returns the particule volume density at r, theta, z
"""
radial_ratio=r/(self.p/(1-self.e*costheta))
radial_density_term=np.sqrt(2./(np.power(radial_ratio,-2*self.ain)+np.power(radial_ratio,-2*self.aout)))
vertical_density_term=np.exp(-np.power(np.abs(z)/(self.ksi0*np.power(radial_ratio,self.beta)),self.gamma))
radial_ratio = r/(self.p/(1-self.e*costheta))
den = (np.power(radial_ratio, -2*self.ain) +
np.power(radial_ratio,-2*self.aout))
radial_density_term = np.sqrt(2./den)
den2 = (self.ksi0*np.power(radial_ratio,self.beta))
vertical_density_term = np.exp(-np.power(np.abs(z)/den2, self.gamma))
return radial_density_term*vertical_density_term

def density_cartesian(self,x,y,z):
""" Returns the particule volume density at x,y,z, taking into account the offset
of the disk
def density_cartesian(self, x, y, z):
""" Returns the particule volume density at x,y,z, taking into account
the offset of the disk
"""
r=np.sqrt(x**2+y**2)
if r==0:
r = np.sqrt(x**2+y**2)
if r == 0:
costheta=0
else:
costheta=x/r
costheta = x/r
return self.density_cylindrical(r,costheta,z)

if __name__=='__main__':

if __name__ == '__main__':
"""
Main of the class for debugging
"""
test = DustEllipticalDistribution2PowerLaws()
test.set_radial_density(ain=5.,aout=-5.,a=60.,e=0.)
test.set_radial_density(ain=5., aout=-5., a=60., e=0.)
test.print_info()
costheta=0.
z=0.
costheta = 0.
z = 0.
for a in np.linspace(60-5,60+5,11):
t = test.density_cylindrical(a,costheta,z)
print('r={0:.1f} density={1:.4f}'.format(a,t))

t = test.density_cylindrical(a, costheta, z)
print('r={0:.1f} density={1:.4f}'.format(a, t))
5 changes: 2 additions & 3 deletions vip_hci/metrics/fakedisk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,17 +7,16 @@
from __future__ import division, print_function

__author__ = 'Julien Milli @ ESO, Valentin Christiaens @ ULg/UChile'
__all__ = ['create_fakedisk_cube',
__all__ = ['cube_inject_fakedisk',
'cube_inject_trace']

import numpy as np
from scipy import signal
from ..preproc import cube_derotate, frame_shift
from ..var import frame_center
import pdb


def create_fakedisk_cube(fakedisk, angle_list, psf=None, imlib='opencv',
def cube_inject_fakedisk(fakedisk, angle_list, psf=None, imlib='opencv',
interpolation='lanczos4', cxy=None, nproc=1,
border_mode='constant'):
"""
Expand Down
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