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A python package for modeling and analysing transit light-curves.
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README.md

PyLightcurve

A python package for modeling and analysing transit light-curves.

  • Easy search for parameters of current exoplanets.
  • Calculation of limb darkening coefficients.
  • Calculation of exoplanetary orbits.
  • Calculation of transit models.
  • Flexible fitting of transit light-curves.

This module makes use of:

Installation

For the latest stable version 2.3.2, open a terminal and type pip install pylightcurve.

For the new (under development) version 3.0.0, download this repo, unzip and type python setup.py install.

Usage

The code in the examples below can be found in the example/example.py file in this repo.

>>> import pylightcurve as plc
>>> import matplotlib.pyplot as plt
>>> import numpy as np

>>> plt.ion()
plc.find_oec_parameters(target)

Returns the following stellar and transit parameters: planet oec name, logarithmic stellar surface gravity, stellar effective temperature, stellar metallicity, planetary radius relative to teh stellar radius, planetary bolometric emission relative o the stellar bolometric emision, orbital period, orbital semi-major axis relative to the stellar radius, orbital eccentricity, orbital inclination, orbital argument of periastron, transit mid-time.

Note: The database is automatically updated on a daily basis if internet access is available.

  • target
    Name of the planet (str).

For example, we can find the parameters of HD209458b:

>>> (planet, stellar_logg, stellar_temperature, stellar_metallicity, rp_over_rs, fp_over_fs, 
     period, sma_over_rs, eccentricity, inclination, periastron, mid_time) = plc.find_oec_parameters('hd209458b')

>>> print (planet, stellar_logg, stellar_temperature, stellar_metallicity, rp_over_rs, fp_over_fs, 
           period, sma_over_rs, eccentricity, inclination, periastron, mid_time)
('HD 209458 b', 4.375254713815686, 6075.0, 0.02, 0.12035170971037652, 5.1956599618667065e-05, 3.52474859, 
 8.8593557009493, 0.0004, 86.59, 0.0, 2451370.048)
plc.clablimb(method, stellar_logg, stellar_temperature, stellar_metallicity, photometric_filter, stellar_model='ATLAS')

Returns a list of limb darkening coefficients.

  • method
    Limb darkening law (str, 'claret' is the only one currently supported).

  • stellar_logg
    Logarithmic stellar surface gravity (float, in cm/s/s).

  • stellar_temperature
    Stellar effective temperature (float, in Kelvin).

  • stellar_metallicity
    Stellar metallicity (float, dex Fe/H).

  • photometric_filter
    Photometric band of the observation (str, available filters: 'B', 'C', 'H', 'I', 'J', 'K', 'Kp', 'R', 'S1', 'S2', 'S3', 'S4', 'U', 'V', 'b', 'g,', 'i,', 'r,', 'u', 'u,', 'v', 'y', 'z,').

For example, we can calculate the limb darkening coefficients for the claret law for HD209458b in the optical band:

>>> limb_darkening_coefficients = plc.clablimb('claret', stellar_logg, stellar_temperature, 
                                               stellar_metallicity, 'V')

>>> print limb_darkening_coefficients
[ 0.38606363  0.58637444 -0.19471546 -0.00559748]
plc.exoplanet_orbit(period, sma_over_rs, eccentricity, inclination, periastron, mid_time, time_array)

Returns the position vector of the planet in a coordinate system with the parent star at (x,y,z) = (0,0,0), the observer at (x,y,z) = (+inf,0,0) and the z-axis perpendicular to the plane of reference.

  • period
    Orbital period (float, in days).

  • sma_over_rs
    Orbital semi-major axis relative to the stellar radius (float, no units).

  • eccentricity
    Orbital eccentricity (float, no units).

  • inclination
    Orbital inclination (float, in degrees).

  • periastron
    Orbital argument of periastron (float, in degrees).

  • mid_time
    Transit mid-time (float, in days).

  • time_array
    A time sequence (numpy array, in days).

For example, we can calculate the position vector of HD209458b from 2 hours before the mid-transit to 2 hours after the mid-transit with a frequency of 1 point per minute:

>>> time_array = np.arange(mid_time - 2.0 / 24.0, mid_time + 2.0 / 24.0, 1.0 / 60.0 / 24.0)

>>> (position_x, position_y, position_z) = plc.exoplanet_orbit(period, sma_over_rs, eccentricity, inclination, 
                                                               periastron, mid_time, time_array)
                                    
>>> plt.subplot(3,1,1)
>>> plt.plot(time_array, position_x, 'ko', ms=3)
>>> plt.ylabel('x (R star)')
>>> plt.subplot(3,1,2)
>>> plt.plot(time_array, position_y, 'ko', ms=3)
>>> plt.ylabel('y (R star)')
>>> plt.subplot(3,1,3)
>>> plt.plot(time_array, position_z, 'ko', ms=3)
>>> plt.ylabel('z (R star)')
>>> plt.xlabel('time (days)')
plc.transit_projected_distance(period, sma_over_rs, eccentricity, inclination, periastron, mid_time, time_array, precision=3)

Returns the projected distance between the planet and its parent star. When the planet is further than the star, the values returned are negative.

  • period
    Orbital period (float, in days).

  • sma_over_rs
    Orbital semi-major axis relative to the stellar radius (float, no units).

  • eccentricity
    Orbital eccentricity (float, no units).

  • inclination
    Orbital inclination (float, in degrees).

  • periastron
    Orbital argument of periastron (float, in degrees).

  • mid_time
    Transit mid-time (float, in days).

  • time_array
    A time sequence (numpy array, in days).

For example, we can calculate the projected distance of HD209458b from its host star from 2 hours before the mid-transit to 2 hours after the mid-transit with a frequency of 1 point per minute:

>>> z_over_rs = plc.transit_projected_distance(period, sma_over_rs, eccentricity, inclination, periastron,
                                               mid_time, time_array)

>>> plt.plot(time_array, z_over_rs, 'ko', ms=3)
>>> plt.axhline(1, color='k', ls='--')
>>> plt.text(0.5 * (plt.xlim()[1] + plt.xlim()[0]), 0.99, 'transit', ha='center', va='top')
>>> plt.xlabel('time (days)')
>>> plt.ylabel('projected distance (R star)')
plc.transit_flux_drop(method, limb_darkening_coefficients, rp_over_rs, z_over_rs, precision=3)

Returns the observed stellar flux as a function of time - i.e. the transit light-curve.

  • method
    Limb darkening law (str, available methods: 'claret', 'quad', 'sqrt' or 'linear').

  • limb_darkening_coefficients
    A list containing the limb darkening coefficients. The list should contain 1 element if the method used is the 'linear', 2 if the method used is the 'quad' or teh 'sqrt', and 4 if the method used is the 'claret'.

  • rp_over_rs
    Planetary radius relative to the stellar radius (float, no units)

  • z_over_rs
    Projected distance between the planet and its parent star relative to the stellar radius (numpy array, no units).

  • precision
    The level of the numerical precision for the calculation (int, 0 to 6, default value is 3).

For example, we can calculate the transit light-curve of HD209458b from 2 hours before the mid-transit to 2 hours after the mid-transit with a frequency of 1 point per minute:

>>> flux_drop = plc.transit_flux_drop('claret', limb_darkening_coefficients, rp_over_rs, z_over_rs)

>>> plt.plot(time_array, flux_drop, 'ko', ms=3)
>>> plt.ylim(plt.ylim()[0], 1.001)
>>> plt.xlabel('time (days)')
>>> plt.ylabel('observed flux (%)')
plc.transit(method, limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, eccentricity, inclination, periastron, mid_time, time_array, precision=3)

Returns the transit light-curve, directly from the orbital parameters.

  • method
    Limb darkening law (str, available methods: 'claret', 'quad', 'sqrt' or 'linear').

  • limb_darkening_coefficients
    A list containing the limb darkening coefficients. The list should contain 1 element if the method used is the 'linear', 2 if the method used is the 'quad' or teh 'sqrt', and 4 if the method used is the 'claret'.

  • rp_over_rs
    Planetary radius relative to the stellar radius (float, no units)

  • period
    Orbital period (float, in days).

  • sma_over_rs
    Orbital semi-major axis relative to the stellar radius (float, no units).

  • eccentricity
    Orbital eccentricity (float, no units).

  • inclination
    Orbital inclination (float, in degrees).

  • periastron
    Orbital argument of periastron (float, in degrees).

  • mid_time
    Transit mid-time (float, in days).

  • time_array
    A time sequence (numpy array, in days).

  • precision
    The level of the numerical precision for the calculation (int, 0 to 6, default value is 3).

For example, we can calculate the transit light-curve of HD209458b from 2 hours before the mid-transit to 2 hours after the mid-transit with a frequency of 1 point per minute:

>>> transit_light_curve = plc.transit('claret', limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, 
                                      eccentricity, inclination, periastron, mid_time, time_array)

>>> plt.plot(time_array, transit_light_curve, 'ko', ms=3)
>>> plt.ylim(plt.ylim()[0], 1.001)
>>> plt.xlabel('time (days)')
>>> plt.ylabel('observed flux (%)')
plc.transit_integrated(method, limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, eccentricity, inclination, periastron, mid_time, time_array, exp_time, time_factor, precision=3)

Returns the exposure-integrated transit light-curve, directly from the orbital parameters.

  • method
    Limb darkening law (str, available methods: 'claret', 'quad', 'sqrt' or 'linear').

  • limb_darkening_coefficients
    A list containing the limb darkening coefficients. The list should contain 1 element if the method used is the 'linear', 2 if the method used is the 'quad' or teh 'sqrt', and 4 if the method used is the 'claret'.

  • rp_over_rs
    Planetary radius relative to the stellar radius (float, no units)

  • period
    Orbital period (float, in days).

  • sma_over_rs
    Orbital semi-major axis relative to the stellar radius (float, no units).

  • eccentricity
    Orbital eccentricity (float, no units).

  • inclination
    Orbital inclination (float, in degrees).

  • periastron
    Orbital argument of periastron (float, in degrees).

  • mid_time
    Transit mid-time (float, in days).

  • time_array
    A time sequence (numpy array, in days).

  • exp_time
    Exposure time (float, in seconds).

  • time_factor
    Number of sub-exposures to be calculated per exposure (int, no units).

  • precision
    The level of the numerical precision for the calculation (int, 0 to 6, default value is 3).

For example, we can calculate the transit light-curve of HD209458b from 2 hours before the mid-transit to 2 hours after the mid-transit with a frequency of 1 point per minute, assuming an exposure time of 30 seconds which is divided into 10 sub-exposures:

>>> transit_light_curve = plc.transit_integrated('claret', limb_darkening_coefficients, rp_over_rs, period, 
                                                 sma_over_rs, eccentricity, inclination, periastron, mid_time, 
                                                 time_array, 30, 10)

>>> plt.plot(time_array, transit_light_curve, 'ko', ms=3)
>>> plt.ylim(plt.ylim()[0], 1.001)
>>> plt.xlabel('time (days)')
>>> plt.ylabel('observed flux (%)')
plc.TransitAndPolyFitting(data, method, limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, eccentricity, inclination, periastron, mid_time, iterations, walkers, burn, precision=3, exp_time=0, time_factor=1, fit_first_order=False, fit_second_order=False, fit_rp_over_rs=False, fit_period=False, fit_sma_over_rs=False, fit_eccentricity=False, fit_inclination=False, fit_periastron=False, fit_mid_time=False, counter=True, counter_window=False):

Offers a range of options for fitting observed transit light-curves, simultaneously with a second-order polynomial de-trending function.

  • data
    A list containing the input data sets. Each element in the list is a list of 3 arrays, representing the time (in Heliocentric Julian Date), the stellar flux and the uncertainty in the stellar flux example: data=[[time_0, flux_0, error_0], [time_1, flux_1, error_1], [time_2, flux_2, error_2]]

  • method
    Limb darkening law (str, available methods: 'claret', 'quad', 'sqrt' or 'linear').

  • limb_darkening_coefficients
    A list containing the limb darkening coefficients. The list should contain 1 element if the method used is the 'linear', 2 if the method used is the 'quad' or teh 'sqrt', and 4 if the method used is the 'claret'. To fit for the limb darkening coefficients set limb_darkening_coefficients='fit'.

  • rp_over_rs
    Initial value for the planetary radius relative to the stellar radius (float, no units)

  • period
    Initial value for the orbital period (float, in days).

  • sma_over_rs
    Initial value for the orbital semi-major axis relative to the stellar radius (float, no units).

  • eccentricity
    Initial value for the orbital eccentricity (float, no units).

  • inclination
    Initial value for the orbital inclination (float, in degrees).

  • periastron
    Initial value for the orbital argument of periastron (float, in degrees).

  • mid_time
    Initial value for the transit mid-time (float, in days).

  • time_array
    A time sequence (numpy array, in days).

  • iterations
    Number of total mcmc iterations (int, no units).

  • walkers
    Number of walkers, as defined in the emcee package (int, no units).

  • burn
    Number of iterations to be excluded from the beginning of the chains (int, no units).

  • precision
    The level of the numerical precision for the calculation (int, 0 to 6, default value is 3).

  • exp_time
    Exposure time (float, in seconds, default value is 0).

  • time_factor
    Number of sub-exposures to be calculated per exposure (int, no units, default value is 1).

  • fit_first_order
    Flag for including a first order time-dependent de-trending factor (bool, default value is False).

  • fit_second_order
    Flag for including a second order time-dependent de-trending factor (bool, default value is False).

  • fit_rp_over_rs
    A 2-element list containing the lower and upper limits for fitting the planetary radius relative to the stellar radius. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_period
    A 2-element list containing the lower and upper limits for fitting the orbital period. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_sma_over_rs
    A 2-element list containing the lower and upper limits for fitting the orbital semi-major axis relative to the stellar radius. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_eccentricity
    A 2-element list containing the lower and upper limits for fitting the orbital eccentricity. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_inclination
    A 2-element list containing the lower and upper limits for fitting the orbital inclination. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_periastron
    A 2-element list containing the lower and upper limits for fitting the orbital argument of periastron. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • fit_mid_time
    A 2-element list containing the lower and upper limits for fitting the the transit mid-time. To avoid fitting set fit_rp_over_rs=False. Default value is False.

  • counter
    Flag for printing a counter of the completed iterations (bool, default value is True).

  • counter_window=False
    Flag for showing a counter of the completed iterations in an additional Tk window (bool, default value is False).

plc.TransitAndPolyFitting methods:
.run_mcmc()

Sets up and runs the mcmc.

.save_all(export_file)

Saves all the mcmc results (including the chains) in the form of a pickle file.

  • export_file
    File to be created (str).
.save_results(export_file)

Saves the final values and uncertainties of the fitted parameters in the form of a txt file.

  • export_file
    File to be created (str).
.plot_corner(export_file)

Plots the correlations between the fitted parameters.

  • export_file
    File to be created (str).
.plot_traces(export_file)

Plots the mcmc chains of the fitted parameters.

  • export_file
    File to be created (str).
.plot_models(export_file)

Plots the original data and the full model fitted. A prefix is added to indicate the different data sets (set_1, set_2, etc.).

  • export_file
    File to be created (str).
.plot_detrended_models(export_file)

Plots the data corrected by the de-trending function and the transit model fitted. A prefix is added to indicate the different data sets (set_1, set_2, etc.).

  • export_file
    File to be created (str).

In the following example we will create 3 simulated observations of HD209458b, with an exposure time of 2 minutes and additional second-order time-dependent systematics, and fit them using the plc.TransitAndPolyFitting class. To avoid an extremely slow process, we will use a time factor of 2 for the fitting, while we will use a time factor of 120 to create the simulated observations:

>>> time_array = np.arange(mid_time + 10.0 * period - 0.11, mid_time + 10.0 * period + 0.11, 2.0 / 60.0 / 24.0)
>>> flux_array = plc.transit_integrated('claret', limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, 
                                        eccentricity, inclination, periastron, mid_time, time_array, 120, 120, 
                                        precision=6)
>>> systematics_array = 1.2 * (1 + 0.013 * (time_array - time_array[0]) + 
                               0.03 * ((time_array - time_array[0]) ** 2))
>>> error_array = np.random.normal(0, 0.002, len(time_array))

>>> time0 = time_array
>>> flux0 = flux_array * systematics_array + error_array
>>> error0 = np.ones_like(error_array) * np.std(error_array)

>>> time_array = np.arange(mid_time + 25.0 * period - 0.13, mid_time + 25.0 * period + 0.13, 2.0 / 60.0 / 24.0)
>>> flux_array = plc.transit_integrated('claret', limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, 
                                        eccentricity, inclination, periastron, mid_time, time_array, 120, 120, 
                                        precision=6)
>>> systematics_array = 3.6 * (1 - 0.02 * (time_array - time_array[0]) + 
                               0.05 * ((time_array - time_array[0]) ** 2))
>>> error_array = np.random.normal(0, 0.005, len(time_array))

>>> time1 = time_array
>>> flux1 = flux_array * systematics_array + error_array
>>> error1 = np.ones_like(error_array) * np.std(error_array)

>>> time_array = np.arange(mid_time + 31.0 * period - 0.115, mid_time + 31.0 * period + 0.115, 2.0 / 60.0 / 24.0)
>>> flux_array = plc.transit_integrated('claret', limb_darkening_coefficients, rp_over_rs, period, sma_over_rs, 
                                        eccentricity, inclination, periastron, mid_time, time_array, 120, 120, 
                                        precision=6)
>>> systematics_array = 0.75 * (1 - 0.01 * (time_array - time_array[0]) 
                                + 0.0001 * ((time_array - time_array[0]) ** 2))
>>> error_array = np.random.normal(0, 0.0009, len(time_array))

>>> time2 = time_array
>>> flux2 = flux_array * systematics_array + error_array
>>> error2 = np.ones_like(error_array) * np.std(error_array)

>>> plt.close('all')
>>> plt.ioff()

>>> fitting = plc.TransitAndPolyFitting(
        data=[[time0, flux0, error0], [time1, flux1, error1], [time2, flux2, error2]],
        method='claret',
        limb_darkening_coefficients=limb_darkening_coefficients,
        rp_over_rs=rp_over_rs,
        period=period,
        sma_over_rs=sma_over_rs,
        eccentricity=eccentricity,
        inclination=inclination,
        periastron=periastron,
        mid_time=mid_time,
        iterations=150000,
        walkers=50,
        burn=50000,
        precision=3,
        time_factor=2,
        exp_time=120,
        fit_first_order=True,
        fit_second_order=True,
        fit_rp_over_rs=[rp_over_rs / 2.0, rp_over_rs * 2.0],
        fit_period=[period / 2.0, period * 2.0],
        fit_sma_over_rs=[sma_over_rs / 2, sma_over_rs * 2.0],
        fit_inclination=[70, 90],
        fit_mid_time=[mid_time - 0.1, mid_time + 0.1])

>>> fitting.run_mcmc()

>>> fitting.save_all('simulation_data_base.pickle')
>>> fitting.save_results('simulation_results.txt')
>>> fitting.plot_corner('simulation_correlations.pdf')
>>> fitting.plot_traces('simulation_traces.pdf')
>>> fitting.plot_models('simulation_full_models.pdf')
>>> fitting.plot_detrended_models('simulation_detrended_models.pdf')

Licence

MIT License

Copyright (c) 2016-2019 Angelos Tsiaras, Konstantinos Karpouzas and Ryan Varley

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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