Note

Download full notebook here

FAQs

import warnings
warnings.filterwarnings('ignore')
import numpy as np
#picaso
from picaso import justdoit as jdi
from picaso import justplotit as jpi
from bokeh.io import output_notebook
output_notebook()

Loading BokehJS ...

How do I load in target properties from Exo.Mast?

nexsci = jdi.all_planets()

nexsci.head()

	objectid	pl_name	pl_letter	hostid	hostname	hd_name	hip_name	tic_id	disc_pubdate	disc_year	...	cb_flag	pl_angsep	pl_angseperr1	pl_angseperr2	pl_angseplim	pl_angsepformat	pl_angsepstr	pl_angsepsymerr	pl_angsep_reflink	pl_ndispec
0	3.2390	Kepler-1167 b	b	2.136990	Kepler-1167	NaN	NaN	TIC 273875149	2016-05	2016.0	...	0.0	0.0213	NaN	NaN	0.0	NaN	0.0213	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0
1	3.1444	Kepler-1740 b	b	2.433343	Kepler-1740	NaN	NaN	TIC 138479461	2022-02	2021.0	...	0.0	0.0734	NaN	NaN	0.0	NaN	0.0734	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0
2	3.4135	Kepler-1581 b	b	2.442550	Kepler-1581	NaN	NaN	TIC 121215710	2016-05	2016.0	...	0.0	0.1390	NaN	NaN	0.0	NaN	0.1390	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0
3	3.6590	Kepler-644 b	b	2.512738	Kepler-644	NaN	NaN	TIC 271669616	2016-05	2016.0	...	0.0	0.0352	NaN	NaN	0.0	NaN	0.0352	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0
4	3.1575	Kepler-1752 b	b	2.507010	Kepler-1752	NaN	NaN	TIC 417655835	2022-02	2021.0	...	0.0	0.2800	NaN	NaN	0.0	NaN	0.2800	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0

5 rows × 683 columns

nexsci.loc[nexsci['hostname']=='HAT-P-26']

	objectid	pl_name	pl_letter	hostid	hostname	hd_name	hip_name	tic_id	disc_pubdate	disc_year	...	cb_flag	pl_angsep	pl_angseperr1	pl_angseperr2	pl_angseplim	pl_angsepformat	pl_angsepstr	pl_angsepsymerr	pl_angsep_reflink	pl_ndispec
4887	3.1101	HAT-P-26 b	b	2.103496	HAT-P-26	NaN	NaN	TIC 420779000	2011-02	2010.0	...	0.0	0.335	NaN	NaN	0.0	NaN	0.335	NaN	<a refstr=CALCULATED_VALUE href=/docs/pscp_cal...	0.0

1 rows × 683 columns

#first isolate the row
hatp26_row = nexsci.loc[nexsci['hostname']=='HAT-P-26']

#add it to load planet function with opacity
opa = jdi.opannection(wave_range=[1,5])
hatp26 = jdi.load_planet(hatp26_row,opa , st_metfe=0)#hatp26 is misst st_metfe so we must add it as a keyword

Load planet function adds in: - planet properties and stellar properties - parameterized PT profile

That means you still need to add in the chemistry and cloud parameters

absolute_co=0.55#solar
logfeh = 1.5 #10^1.5 ~ 30x solar
hatp26.chemeq_visscher_2121(absolute_co,logfeh) #adds in template chemistry from sonora
df = hatp26.spectrum(opa, calculation='transmission+thermal')

x,y = jdi.mean_regrid(df['wavenumber'], df['fpfs_thermal'],R=150)
plot = [jpi.spectrum(x,y,plot_width=400, y_axis_type='log',y_axis_label='FpFs')]
x,y = jdi.mean_regrid(df['wavenumber'], df['transit_depth'],R=150)
plot += [jpi.spectrum(x,y,plot_width=400,y_axis_label='(Rp/Rs)^2')]

jpi.show(jpi.row(plot))

How do I access the pressure-temperature profile parameterizations?

#start by loading in some template properties
opa = jdi.opannection(wave_range=[1,5])
hatp26_row = nexsci.loc[nexsci['hostname']=='HAT-P-26']
hatp26 = jdi.load_planet(hatp26_row,opa, st_metfe=0)

How do the input parameters effect the parameterization?

fig = [jpi.figure(width=300, height=300, y_axis_type='log', y_range=[100,1e-6],x_range=[400,1700],
                  y_axis_label='Pressure(bars)',x_axis_label='Temperature (K)',
                 title='Effect of logg1')]
colors = jpi.pals.magma(10)
for i, logg1 in enumerate(np.linspace(-2,2,10)):
    hatp26.guillot_pt(576.17, T_int=100, logg1=logg1, logKir=-1.5)
    fig[0].line(hatp26.inputs['atmosphere']['profile']['temperature'],
            hatp26.inputs['atmosphere']['profile']['pressure'],color=colors[i])

fig += [jpi.figure(width=300, height=300, y_axis_type='log', y_range=[100,1e-6],x_range=[400,1700],
                 x_axis_label='Temperature (K)',title='Effect of LogKir')]
for i,logKir in enumerate(np.linspace(-2,2,10)):
    hatp26.guillot_pt(576.17, T_int=100, logg1=-2, logKir=logKir)
    fig[1].line(hatp26.inputs['atmosphere']['profile']['temperature'],
            hatp26.inputs['atmosphere']['profile']['pressure'], color=colors[i])

fig += [jpi.figure(width=300, height=300, y_axis_type='log', y_range=[100,1e-6],x_range=[400,1700],
                 x_axis_label='Temperature (K)',title='Effect of Tint')]
for i,T_int in enumerate(np.linspace(50,300,10)):
    hatp26.guillot_pt(576.17, T_int=T_int, logg1=-2, logKir=-2)
    fig[2].line(hatp26.inputs['atmosphere']['profile']['temperature'],
            hatp26.inputs['atmosphere']['profile']['pressure'], color=colors[i])

jpi.show(jpi.row(fig))

How do I return the output from photon attenuation plot?

#first isolate the row
hatp26_row = nexsci.loc[nexsci['hostname']=='HAT-P-26']

#add it to load planet function with opacity
opa = jdi.opannection(wave_range=[0.3,1])
hatp26 = jdi.load_planet(hatp26_row,opa ,st_metfe=0)
co_absolute = 0.55
logfeh=2
hatp26.chemeq_visscher_2121(co_absolute,logfeh)
df = hatp26.spectrum(opa, calculation='reflected',full_output=True)

plot,wave,at_pressures_gas,at_pressures_cld,at_pressures_ray = jpi.photon_attenuation(df['full_output'],
                                                                                     return_output=True)

#now you can make your own plot!
fig = jpi.figure(y_axis_type='log',y_range=[10,1e-3],height=250, width=500)
for i,iy,ilab in zip([0,1],[at_pressures_gas,at_pressures_ray ], ['Molecular','Rayleigh']):
    x,y = jpi.mean_regrid(1e4/wave,iy, R=150)
    fig.line(1e4/x,y,legend_label=ilab, line_width=4, color=jpi.Colorblind8[i])
jpi.show(fig)

Can I use the phase angle function to specify a non-zero phase for thermal emission?

The phase angle function computes the incoming and outgoing angles. However, non-zero phase functionality is specific to reflected light observations only. This might be confusing because of course it is possible to observe thermal emission of planet at non-zero phase. However, unlike reflected light, thermal emission radiates from the planet in all directions (regardless of phase angle).

Do not force the code to run at non-zero phase angles for thermal emission.

I’m confused about what opacity file to use

Question: I’m confused about the opacity files. Version 1.0 (opacity.db) is the low res version that covers the “useful” wavelengths (0.3 to 14 micron) while version 2.0 has two files that cover the 0.6-6 micron at higher resolution and 4.8-15 micron. What should I download? And once I download it, where do I put them? If it’s just the one file that seems straightforward in terms of where to put it but what happens when there are two files (or all 3) in the same folder?

Answer:

What do I download?

The low sampled files across a large wavelength range, which is on Zenodo as V1 is great for quick calculations that don’t necessarily need to be accurate. For example: proposals, example models, any testing, retrievals on fake data.

However, when comparing to real data, it’s important to use higher sampling. This tutorial shows users estimated sampling errors. Therefore, it is important to have higher sampling files as well. The higher sampling files are located here under V2.

So depending on your use case, the answer might be: download both!

Where do I put all the files?

PICASO uses the function `justdoit.opannection <https://natashabatalha.github.io/picaso/picaso.html#picaso.justdoit.opannection>`__ to grab the opacity file located in the reference directory `opacities <https://github.com/natashabatalha/picaso/tree/master/reference/opacities>`__. In the installation instructions you will notice there is a step to place the zenodo file here. Just for completeness, internally, we specify the name of this file here.

The general recommendation is to keep one “default” file in your reference/opacities folder so that you do not need to worry about always specifying a file when running the code. Then assign one place, easy to locate, where you include the rest of the files. In order to access these will need to point to this file path using the filename_db keyword in opannection.

Has your question not been answered? Feel free to contact us!

Submit an issue on Github: https://github.com/natashabatalha/picaso/issues