diff --git a/exoctk/data/throughputs/CHEOPS_CHEOPS.band.txt b/exoctk/data/throughputs/CHEOPS_CHEOPS.band.txt new file mode 100644 index 00000000..dbcf7fa4 --- /dev/null +++ b/exoctk/data/throughputs/CHEOPS_CHEOPS.band.txt @@ -0,0 +1,153 @@ +3400 0.0 +3450 0.005238095238095264 +3500 0.01480331262939965 +3550 0.027784679089026997 +3600 0.048907867494824155 +3650 0.09075569358178082 +3700 0.14814699792960673 +3750 0.2063354037267085 +3800 0.2666418219461706 +3850 0.32336291038154436 +3900 0.37528837622005373 +3950 0.4213250517598327 +4000 0.45859903381642164 +4050 0.49228985507245887 +4100 0.5235362318840523 +4150 0.5538020473889972 +4200 0.5828519668736979 +4250 0.6113084886128296 +4300 0.6393664596273252 +4350 0.6664982746721849 +4400 0.6928557625948901 +4450 0.7192132505175952 +4500 0.7413043478260842 +4550 0.7584726867335548 +4600 0.7756410256410254 +4650 0.789003166483985 +4700 0.801381683108026 +4750 0.813760199732067 +4800 0.8262525879917187 +4850 0.8390062111801245 +4900 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0.02692 +11030 0.025789 +11040 0.024658 +11050 0.023528 +11060 0.022399 +11070 0.021271 +11080 0.020145 +11090 0.019021 +11100 0.017899 +11110 0.016781 +11120 0.015666 +11130 0.014555 +11140 0.013448 +11150 0.012346 +11160 0.011248 +11170 0.010157 +11180 0.0090715 +11190 0.0079924 +11200 0.0069202 +11210 0.005855 +11220 0.0047974 +11230 0.0037476 +11240 0.0027059 +11250 0.0016725 +11260 0.00064763 +11270 0 diff --git a/exoctk/exoctk_app/app_exoctk.py b/exoctk/exoctk_app/app_exoctk.py index 2aca4503..8fa1d905 100644 --- a/exoctk/exoctk_app/app_exoctk.py +++ b/exoctk/exoctk_app/app_exoctk.py @@ -23,6 +23,7 @@ from exoctk.forward_models.forward_models import fortney_grid, generic_grid from exoctk.groups_integrations.groups_integrations import perform_calculation from exoctk.limb_darkening import limb_darkening_fit as lf +from exoctk.limb_darkening import spam from exoctk.modelgrid import ModelGrid from exoctk.phase_constraint_overlap.phase_constraint_overlap import phase_overlap_constraint, calculate_pre_duration from exoctk.throughputs import Throughput @@ -546,6 +547,20 @@ def limb_darkening(): # Load default form form = fv.LimbDarkeningForm() + # Planet properties + planet_properties = ['transit_duration', 'orbital_period', 'rp_rs', 'a_rs', 'inclination', 'eccentricity', 'omega'] + + def empty_fields(form): + form.transit_duration.data = form.transit_duration.data or '' + form.orbital_period.data = form.orbital_period.data or '' + form.rp_rs.data = form.rp_rs.data or '' + form.a_rs.data = form.a_rs.data or '' + form.inclination.data = form.inclination.data or '' + form.eccentricity.data = form.eccentricity.data or '' + form.omega.data = form.omega.data or '' + + return form + # Reload page with stellar data from ExoMAST if form.resolve_submit.data: @@ -557,16 +572,28 @@ def limb_darkening(): form.targname.data = get_canonical_name(form.targname.data) data, target_url = get_target_data(form.targname.data) - # Update the form data + # Update the star data form.feh.data = data.get('Fe/H') form.teff.data = data.get('Teff') form.logg.data = data.get('stellar_gravity') form.target_url.data = str(target_url) + # Update the planet data + form.transit_duration.data = data.get('transit_duration') + form.orbital_period.data = data.get('orbital_period') + form.rp_rs.data = data.get('Rp/Rs') + form.a_rs.data = data.get('a/Rs') + form.inclination.data = data.get('inclination') + form.eccentricity.data = data.get('eccentricity') + form.omega.data = data.get('omega') + except Exception: form.target_url.data = '' form.targname.errors = ["Sorry, could not resolve '{}' in exoMAST.".format(form.targname.data)] + # Ensure planet fields are not None + form = empty_fields(form) + # Send it back to the main page return render_template('limb_darkening.html', form=form) @@ -587,6 +614,9 @@ def limb_darkening(): form.wave_min.data = bandpass.wave_min.value form.wave_max.data = bandpass.wave_max.value + # Ensure planet fields are not None + form = empty_fields(form) + # Send it back to the main page return render_template('limb_darkening.html', form=form) @@ -610,6 +640,9 @@ def limb_darkening(): setattr(form.feh.validators[1], 'max', float(feh_rng[1])) setattr(form.feh.validators[1], 'message', 'Metallicity must be between {} and {}'.format(*feh_rng)) + # Ensure planet fields are not None + form = empty_fields(form) + # Send it back to the main page return render_template('limb_darkening.html', form=form) @@ -647,6 +680,21 @@ def limb_darkening(): for prof in form.profiles.data: ld.calculate(*star_params, prof, mu_min=float(form.mu_min.data), bandpass=bandpass) + # Check if spam coefficients can be calculated + planet_data = {param: getattr(form, param).data for param in planet_properties} + planet_data['Rp/Rs'] = planet_data['rp_rs'] + planet_data['a/Rs'] = planet_data['a_rs'] + spam_calc = all([val is not None and val != '' for key, val in planet_data.items()]) + if spam_calc: + + # Make sure non-linear profile is included for spam calculation if all planet parameters are provided + if '4-parameter' not in form.profiles.data: + ld.calculate(*star_params, '4-parameter', mu_min=float(form.mu_min.data), bandpass=bandpass) + + # Calculate spam coeffs + planet_data = {key: float(val) for key, val in planet_data.items()} + ld.spam(planet_data=planet_data) + # Draw tabbed figure final = ld.plot_tabs() @@ -689,8 +737,41 @@ def limb_darkening(): # Log the successful form inputs log_exoctk.log_form_input(form_input, 'limb_darkening', DB) + # Make a table for each profile with a row for each wavelength bin + profile_spam_tables = '' + spam_file_as_string = '' + if ld.spam_results is not None: + + # Store SPAM tables as string + keep_cols = ['Teff', 'logg', 'FeH', 'profile', 'filter', 'wave_min', 'wave_eff', 'wave_max', 'c1', 'c2'] + print_spam_table = ld.spam_results[[col for col in keep_cols if col in ld.spam_results.colnames]] + spam_file_as_string = '\n'.join(print_spam_table.pformat(max_lines=-1, max_width=-1)) + profile_spam_tables = [] + for profile in list(np.unique(ld.spam_results['profile'])): + + # Make LaTeX for polynomials + latex = lf.ld_profile(profile, latex=True) + poly = '\({}\)'.format(latex).replace('*', '\cdot').replace('\e', 'e') + + # Make the table into LaTeX + table = filter_table(ld.spam_results, profile=profile) + co_cols = [c for c in ld.spam_results.colnames if c.startswith('c') and c not in ['coeffs', 'color']] + table = table[['wave_eff', 'wave_min', 'wave_max'] + co_cols] + table.rename_column('wave_eff', '\(\lambda_\mbox{eff}\hspace{5px}(\mu m)\)') + table.rename_column('wave_min', '\(\lambda_\mbox{min}\hspace{5px}(\mu m)\)') + table.rename_column('wave_max', '\(\lambda_\mbox{max}\hspace{5px}(\mu m)\)') + + # Add the results to the lists + html_table = '\n'.join(table.pformat(max_width=-1, max_lines=-1, html=True)).replace('Limb Darkening Calculator
K
The stellar effective temperature ({{ form.teff.validators[1].min }} - {{ form.teff.validators[1].max }}) + {% for error in form.teff.errors[:1] %} +

{{ error }}

+ {% endfor %}
@@ -55,6 +58,9 @@

Limb Darkening Calculator

dex
The logarithm of the stellar surface gravity ({{ form.logg.validators[1].min }} - {{ form.logg.validators[1].max }}) + {% for error in form.logg.errors[:1] %} +

{{ error }}

+ {% endfor %}
@@ -63,20 +69,96 @@

Limb Darkening Calculator

dex
The logarithm of the stellar metallicity ({{ form.feh.validators[1].min }} - {{ form.feh.validators[1].max }}) + {% for error in form.feh.errors[:1] %} +

{{ error }}

+ {% endfor %}
- {% for error in form.teff.errors[:1] %} + + + +
+
+ +
+ +
+
Transit Duration
+ {{ form.transit_duration(value=form.transit_duration.data, size=10, placeholder="0 - 50", rows=1, class='form-control') }} +
hour
+
+ The transit duration ({{ form.transit_duration.validators[1].min }} - {{ form.transit_duration.validators[1].max }}) + {% for error in form.transit_duration.errors[:1] %}

{{ error }}

{% endfor %} - {% for error in form.logg.errors[:1] %} +
+ +
+
Orbital Period
+ {{ form.orbital_period(value=form.orbital_period.data, size=10, placeholder="0 - 1000", rows=1, class='form-control') }} +
day
+
+ The orbital period ({{ form.orbital_period.validators[1].min }} - {{ form.orbital_period.validators[1].max }}) + {% for error in form.orbital_period.errors[:1] %}

{{ error }}

{% endfor %} - {% for error in form.feh.errors[:1] %} +
+ +
+
\(R_\text{p}/R_\text{*}\)
+ {{ form.rp_rs(value=form.rp_rs.data, size=10, placeholder="0 - 1.0", rows=1, class='form-control') }} +
+
+ The ratio of the planet radius to the stellar radius ({{ form.rp_rs.validators[1].min }} - {{ form.rp_rs.validators[1].max }}) + {% for error in form.rp_rs.errors[:1] %}

{{ error }}

{% endfor %} - {% for error in form.mu_min.errors[:1] %} +
+ +
+
\(a/R_\text{*}\)
+ {{ form.a_rs(value=form.a_rs.data, size=10, placeholder="0 - 1.0", rows=1, class='form-control') }} +
+
+ The ratio of the semi-major axis to the stellar radius ({{ form.a_rs.validators[1].min }} - {{ form.a_rs.validators[1].max }}) + {% for error in form.a_rs.errors[:1] %} +

{{ error }}

+ {% endfor %} +
+ +
+
Inclination
+ {{ form.inclination(value=form.inclination.data, size=10, placeholder="0 - 180", rows=1, class='form-control') }} +
deg
+
+ The inclination of the orbit ({{ form.inclination.validators[1].min }} - {{ form.inclination.validators[1].max }}) + {% for error in form.inclination.errors[:1] %}

{{ error }}

{% endfor %} +
+ +
+
Eccentricity
+ {{ form.eccentricity(value=form.eccentricity.data, size=10, placeholder="0 - 1.0", rows=1, class='form-control') }} +
+
+ The eccentricity of the orbit ({{ form.eccentricity.validators[1].min }} - {{ form.eccentricity.validators[1].max }}) + {% for error in form.eccentricity.errors[:1] %} +

{{ error }}

+ {% endfor %} +
+ +
+
\(\omega \)
+ {{ form.omega(value=form.omega.data, size=10, placeholder="0 - 360", rows=1, class='form-control') }} +
deg
+
+ The longitude of the periapsis ({{ form.omega.validators[1].min }} - {{ form.omega.validators[1].max }}) + {% for error in form.omega.errors[:1] %} +

{{ error }}

+ {% endfor %} +
+
@@ -173,6 +255,9 @@

Limb Darkening Calculator

{% endfor %} + {% for error in form.profiles.errors %} + {{ error }} + {% endfor %}
@@ -181,11 +266,11 @@

Limb Darkening Calculator

The minimum angle to consider when fitting the LD profile + {% for error in form.mu_min.errors[:1] %} +

{{ error }}

+ {% endfor %}
- {% for error in form.profiles.errors %} - {{ error }} - {% endfor %} diff --git a/exoctk/exoctk_app/templates/limb_darkening_results.html b/exoctk/exoctk_app/templates/limb_darkening_results.html index 9eb56c51..196216c6 100644 --- a/exoctk/exoctk_app/templates/limb_darkening_results.html +++ b/exoctk/exoctk_app/templates/limb_darkening_results.html @@ -51,6 +51,36 @@

Input

Models {{ form.modeldir.data }} + {% if spam_table != '' %} + + Transit Duration + {{ form.transit_duration.data }} + + + Orbital Period + {{ form.orbital_period.data }} + + + Rp/R* + {{ form.rp_rs.data }} + + + a/R* + {{ form.a_rs.data }} + + + Inclination + {{ form.inclination.data }} + + + Eccentricity + {{ form.eccentricity.data }} + + + \( \omega \) + {{ form.omega.data }} + + {% endif %} @@ -69,17 +99,27 @@

Result


+

Coefficients

- -
{% for tab in table %} {{ tab|safe }} -
{% endfor %} + {% if spam_table != '' %} +
+

SPAM Coefficients

+
+
+ +
+ {% for tab in spam_table %} + {{ tab|safe }} + {% endfor %} + {% endif %} + diff --git a/exoctk/limb_darkening/__init__.py b/exoctk/limb_darkening/__init__.py index 571b7101..bf0cc6a0 100644 --- a/exoctk/limb_darkening/__init__.py +++ b/exoctk/limb_darkening/__init__.py @@ -1,4 +1,4 @@ """ Package to generate limb darkening coefficients from a grid of model spectra """ -from . import limb_darkening_fit \ No newline at end of file +from . import limb_darkening_fit, spam diff --git a/exoctk/limb_darkening/limb_darkening_fit.py b/exoctk/limb_darkening/limb_darkening_fit.py index 557c385c..a3e137cd 100755 --- a/exoctk/limb_darkening/limb_darkening_fit.py +++ b/exoctk/limb_darkening/limb_darkening_fit.py @@ -5,6 +5,7 @@ spectra """ +from copy import copy import inspect import os import warnings @@ -24,6 +25,7 @@ from .. import modelgrid from .. import utils +from . import spam rc('font', **{'family': 'sans-serif', 'sans-serif': ['Helvetica'], 'size': 16}) rc('text', usetex=True) @@ -121,7 +123,8 @@ class LDC: bp = Filter('WFC3_IR.G141', n_bins=5) ld.calculate(4000, 4.5, 0.0, 'quadratic', bandpass=bp) ld.calculate(4000, 4.5, 0.0, '4-parameter', bandpass=bp) - ld.plot(show=True) + ld.spam(planet_name='WASP-12b', profiles=['quadratic', 'logarithmic']) + ld.plot_tabs(show=True) """ def __init__(self, model_grid='ACES'): """Initialize an LDC object @@ -150,6 +153,10 @@ def __init__(self, model_grid='ACES'): dtypes = ['|S20', float, float, float, '|S20', '|S20', '|S20', object, object, object, np.float16, np.float16, np.float16, object, object, np.float16, object, object, np.float16, object, object, object, '|S20'] self.results = at.Table(names=columns, dtype=dtypes) + # Table for spam results + self.spam_results = None + + # Colors for plotting self.ld_color = {'quadratic': 'blue', '4-parameter': 'red', 'exponential': 'green', 'linear': 'orange', 'square-root': 'cyan', '3-parameter': 'magenta', 'logarithmic': 'pink'} self.count = 1 @@ -514,3 +521,61 @@ def save(self, filepath): # Save to file ii.write(results, filepath, format='fixed_width_two_line') + + def spam(self, planet_name=None, planet_data=None, profiles=['quadratic'], **kwargs): + """ + Calculates SPAM coefficients by transforming non-linear coefficients + + Parameters + ---------- + planet_name: string + The name of the input planet (e.g., 'WASP-19b'); this will be used to query the planet properties from MAST. + planet_data: dict + Dictionary containing the planet properties. Must include 'transit_duration', 'orbital_period' (days), 'Rp/Rs', 'a/Rs', 'inclination' (degrees), 'eccentricity' and 'omega' (degrees) + profiles: sequence + The profiles to calculate, ['quadratic', 'logarithmic', 'square-root'] + """ + # Profiles supported by SPAM transformation code + spam_supported = ['quadratic', 'square-root', 'logarithmic'] + + if not all([profile in spam_supported for profile in profiles]): + raise ValueError("{}: Supported profiles include {}".format(profiles, spam_supported)) + + # Require 4-parameter calculation + if '4-parameter' in self.results['profile']: + + # For each desired profile... + for profile in profiles: + + # Rows of non-linear calculations + nonlin = copy(self.results[self.results['profile'] == '4-parameter']) + + # Update profile + nonlin['profile'] = profile + + # ...and for each wavelength channel... + for row in nonlin: + + # Calculate SPAM coefficients + (c1, c2), properties = spam.transform_coefficients(row['c1'], row['c2'], row['c3'], row['c4'], ld_law=profile, planet_name=planet_name, planet_data=planet_data, **kwargs) + row['c1'], row['c2'] = c1.round(3), c2.round(3) + + # Remove unused columns + omit_cols = ['c3', 'c4', 'e1', 'e2', 'e3', 'e4'] + nonlin = nonlin[[col for col in nonlin.columns if col not in omit_cols]] + + # Add planet properties to table + planet_properties = ['transit_duration', 'orbital_period', 'Rp/Rs', 'a/Rs', 'inclination', 'eccentricity', 'omega'] + for prop in planet_properties: + nonlin.add_column([round(properties[prop], 4)] * len(nonlin), name=prop) + + # Add the results to the spam table + if self.spam_results is None: + self.spam_results = nonlin + else: + self.spam_results = at.vstack([self.spam_results, nonlin]) + + else: + + print("Limb darkening coefficients must first be calculated using the 4-parameter profile to get SPAM coefficient transformations.") + diff --git a/exoctk/limb_darkening/spam.py b/exoctk/limb_darkening/spam.py new file mode 100644 index 00000000..031e5fb2 --- /dev/null +++ b/exoctk/limb_darkening/spam.py @@ -0,0 +1,180 @@ +import numpy as np +from scipy.optimize import minimize + +try: + import batman + +except: + print('Batman library not installed. Install it by doing "pip install batman-package" to use exoctk.limb_darkening.spam.') + +from .. import utils + + +def init_batman(t, ld_law, nresampling=None, etresampling=None): + """ + This function initializes the batman lightcurve generator object. + + Parameters + ---------- + + t: array + Array containing the times at which the lightcurve will be evaluated. Assumes units of days. + ld_law: string + Limb-darkening law used to compute the model. Available ld laws: uniform, linear, quadratic, + logarithmic, exponential, squareroot, nonlinear, power2. + nresampling: int + Number of resampled points in case resampling is wanted. + etresampling: float + Exposure time of the resampling, same units as input time. + + Returns + ------- + + params: batman object + Object containing the parameters of the lightcurve model. + m: batman object + Object that enables the lightcurve calculation. + + """ + + params = batman.TransitParams() + params.t0 = 0. + params.per = 1. + params.rp = 0.1 + params.a = 15. + params.inc = 87. + params.ecc = 0. + params.w = 90. + + if ld_law == 'linear': + params.u = [0.5] + + elif ld_law == 'nonlinear': + params.u = [0.1, 0.1, 0.1, 0.1] + + else: + params.u = [0.1,0.3] + + params.limb_dark = ld_law + + if nresampling is None or etresampling is None: + m = batman.TransitModel(params, t) + + else: + m = batman.TransitModel(params, t, supersample_factor=nresampling, exp_time=etresampling) + + return params, m + + +def spam_objective_function(theta, params, m, params_twop, m_twop): + """ + Objective function that the SPAM algorithm is looking to minimize. + """ + + u1, u2 = theta + params_twop.u = [u1, u2] + + return np.sum((m.light_curve(params) - m_twop.light_curve(params_twop))**2) + + +def transform_coefficients(c1, c2, c3, c4, planet_name=None, planet_data=None, ld_law='quadratic', ndatapoints=1000, method='BFGS', u1_guess=0.5, u2_guess=0.5): + """ + Given a set of non-linear limb-darkening coefficients (c1, c2, c3 and c4) and either a planet name ('planet_name') or a dictionary with + the planet's data ('planet_data'), this function returns the Synthetic-Photometry/Atmosphere-Model (SPAM; https://arxiv.org/abs/1106.4659) + limb-darkening coefficients of the star. + + Reference: + Howarth, I., 2011, "On stellar limb darkening and exoplanetary transits", MNRAS, 418, 1165 + https://ui.adsabs.harvard.edu/abs/2011MNRAS.418.1165H/abstract + + Parameters + ---------- + + c1: float + First limb-darkening coefficient of the non-linear law. + c2: float + Same as c1, but second. + c3: float + Same as c1, but third. + c4: float + Same as c1, but fourth. + planet_name: string + String with the name of the input planet (e.g., 'WASP-19b'); this will be used to query the planet properties from MAST. + planet_data: dict + Dictionary containing the planet properties. In particular, this dictionary should contain the keys + 'transit_duration', 'orbital_period' (days), 'Rp/Rs', 'a/Rs', 'inclination' (degrees), 'eccentricity' and 'omega' (degrees) + for the algorithm to work. Properties in this dictionary take prescedence over the ones retrieved from MAST. + ld_law: string + Limb-darkening law for which SPAM coefficients are wanted. Default is 'quadratic', but can also be 'squareroot' or 'logarithmic'. + ndatapoints: int + Number of datapoints that will be used for the lightcurve simulations to extract back the SPAM coefficients. + method: string + Minimization method to match lightcurves. Default is 'BFGS', but can be any of the ones available for scipy.optimize.minimize. + Details: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html + u1_guess: float + Guess starting value for u1. Default is 0.5 + u2_guess: flat + Guess starting value for u2. Default is 0.5. + + Returns + ------- + + u1: float + The first limb-darkening coefficient of the selected two-parameter law. + u2: flat + Same as u1, but for the second coefficient. + + """ + + planet_properties = ['transit_duration', 'orbital_period', 'Rp/Rs', 'a/Rs', 'inclination', 'eccentricity', 'omega'] + + # Check if planet name is given + if planet_name is not None: + + # If planet_name is given, retrieve MAST properties + mast_planet_data, url = utils.get_target_data(planet_name) + + # Merge the dictionaries, prioritizing the manual input + mast_planet_data.update(planet_data or {}) + planet_data = mast_planet_data + + if planet_data is None: + + raise Exception("User must input either 'planet_name' and/or 'planet_data' for SPAM to work. See details by doing exoctk.limb_darkening.spam.transform_coefficients?.") + + # Check that all properties exist in the input dictionary + missing = [planet_property for planet_property in planet_properties if planet_data.get(planet_property) is None] + if len(missing) > 0: + + # Print current data for user + print('{} properties'.format(planet_name or 'Planet')) + for planet_property in planet_properties: + print('{}: {}'.format(planet_property, planet_data.get(planet_property))) + + raise ValueError("{} missing planet propert{} needed for SPAM to work. Please include this in the 'planet_data' input dictionary".format(len(missing), 'y is' if len(missing) == 1 else 'ies are')) + + # User inputs check done. Now jump into the algorithm. First, define times around transit + times = np.linspace(-planet_data['transit_duration']/2., planet_data['transit_duration']/2., ndatapoints) + + # Now initialize models + params, m = init_batman(times, 'nonlinear') + params_twop, m_twop = init_batman(times, ld_law) + + # Define params according to the planet_data dictionary + for par in [params, params_twop]: + + par.per = planet_data['orbital_period'] + par.rp = planet_data['Rp/Rs'] + par.a = planet_data['a/Rs'] + par.inc = planet_data['inclination'] + par.ecc = planet_data['eccentricity'] + par.w = planet_data['omega'] + + # Set non-linear law coefficients + params.u = [c1, c2, c3, c4] + + # Allright, now given these models, optimize u1 and u2 such that they match as good as possible the lightcurves of + # the non-linear law. We use scipy.optimize for this + results = minimize(spam_objective_function, [u1_guess, u2_guess], args=(params, m, params_twop, m_twop), method=method.lower()) + + return results.x, {prop: val for prop, val in planet_data.items() if prop in planet_properties}