Eleos - A Python interface to NEMESIS

Please note, this is a WIP project and features may be added/removed at any time. It is absolutely not guarunteed to be backward compatible until it has matured significantly.

Documentation

Documentation can be found on ReadTheDocs here. This is still WIP, full documentation will be added in due course.

Installation

Eleos is available on PyPI so it can be installed as any other Python package. On Unix-like systems:

pip install nemesis_eleos

And on Windows:

py -m pip install nemesis_eleos

While eleos only creates files for, and reads files created by, NEMESIS, it is mandatory to have NEMESIS installed for this package to work. This is primarily due to requiring the utilities Makephase and Normxsc on the PATH. See the NEMESIS GitHub page for full instructions on how to download the software and how to compile it.

This library was built with the intention of running on the University of Leicester’s HPC system ALICE3. Therefore, functions like cores.generate_alice_job and cores.run_alice_job are only guaranteed to work on ALICE3, which uses the SLURM job scheduler. Other HPC facilities will require their own template submission files in data/statics and functions in cores.

Working Directory Structure

This library will function best with the following structure in your working directory:

parent_directory
|-- core_1
|-- core_2
|   ...
generate.py
analyse.py

where parent_directory/ contains a set of cores for a retrieval, core_N/ is the core folder that NEMESIS is run from, generate.py is the code that generates these cores using eleos.cores, and analyse.py is the code that analyses the results using eleos.results. This is only a recommendation, and you can structure your working directories however you like.

Core Generation Example (generate.py)

More examples can be found in the examples/ directory.

The eleos.cores module is designed to be used to generate cores ready for NEMESIS to run. This code generates a core with NH3 and PH3 profiles and three aerosol layers for a JWST NIRSPEC observation of Jupiter. It uses the built-in .ref files, ktables and other miscellaneous NEMESIS input files (available in eleos/data/). Then it generates a submission script for ALICE and submits the job to the scheduler. After the core has successfully run, there will be a selection of summary plots in the parent/core/plots directory.

from eleos import cores, shapes, profiles


# Create a profile to retrieve ammonia - this is parameterised as model 20 in NEMESIS
nh3 = profiles.GasProfile(gas_name="NH3", 
                          shape=shapes.Shape20(
                          knee_pressure=1.0, 
                          tropopause_pressure=0.1,
                          deep_vmr=2e-4, deep_vmr_error=10e-6,
                          fsh=0.2,           fsh_error=0.1))

# Create a profile to retrieve phosphine - this is a simple scaling of the prior distribution
ph3 = profiles.GasProfile(gas_name="PH3", 
                          shape=shapes.Shape2(
                          scale_factor=2, scale_factor_error=0.1))


# Create a Gaussian-shaped cloud layer at 1.2 bar with set optical properties
deep = profiles.AerosolProfile(label="Deep Cloud",
                               retrieve_optical=False,
                               shape=shapes.Shape47(
                               central_pressure=1.23, central_pressure_error=0.04,
                               pressure_width=0.1,    pressure_width_error=0.1,
                               opacity=1.75,          opacity_error=0.5),
                               radius=3.02,           
                               variance=0.5,          
                               real_n=1.3,
                               imag_n=1e-3)

# Create another Gaussian cloud at 0.6 bar and retrieve the optical properties as well (particle radius, variance and imag. refractive index)
main = profiles.AerosolProfile(label="Main Cloud",
                               retrieve_optical=True,
                               shape=shapes.Shape47(
                               central_pressure=0.6,  central_pressure_error=0.01,
                               pressure_width=0.2,    pressure_width_error=0.2,
                               opacity=1.0,           opacity_error=0.5),
                               radius=3.02,           radius_error=0.1,
                               variance=0.1,          variance_error=0.1,
                               real_n=1.3, 
                               imag_n=1e-3,           imag_n_error=1e-3)

# Create an aerosol layer that represents a uniformally distributed haze between 0.5bar and 0.1bar and retrieve the optical properties
haze = profiles.AerosolProfile(label="Haze",
                               retrieve_optical=True,
                               shape=shapes.Shape37(
                               bottom_pressure=0.5, 
                               top_pressure=0.1,
                               opacity=0.25,       opacity_error=0.1),
                               radius=0.34,        radius_error=0.02,
                               variance=0.3,       variance_error=0.3,
                               real_n=1.3,
                               imag_n=1e-3,        imag_n_error=1e-3)

# Set the directory of the core and clear it of any previous retrievals
cd = "example/"
cores.clear_parent_directory(cd)

# Create the NemesisCore object with the profiles we defined
core = cores.NemesisCore(cd,
                         planet="jupiter",
                         instrument_ktables="NIRSPEC",
                         spx_file="example.spx",
                         profiles=[ph3, nh3, deep, main, haze],
                         fmerror_factor=5,
                         num_iterations=20,
                         scattering=True,
                         reference_wavelength=4,
                         min_pressure=1e-3, 
                         max_pressure=10)

# If there is a specific feature at a given wavelength that we want NEMESIS to always fit, we can use the fix_peak method
core.fix_peak(central_wavelength=4.07, width=0.05)

# Create all the files necessary for NEMESIS to run
core.generate_core()

# Run the job on ALICE - this will also run Eleos from the command line to make some summary plots in example/core_1/plots/
cores.generate_alice_job(cd, python_env_name="pythonmain", username="scat2", hours=3)
cores.run_alice_job(cd)

Result Analysis Example (analyse.py)

Once NEMESIS has been run on the core, the eleos.results module is used to analyse the output. This script takes the output of the previous and generates a set of summary tables containing the prior and retrieved values for each parameter, a plot of the retrieved spectrum, and a plot of the aerosol densities.

import matplotlib.pyplot as plt
from eleos import results


# Load the retrieved core as a NemesisResult object
res = results.NemesisResult("example/core_1")

# Get some information about the run
res.print_summary()

# Create two plots
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12,5))

# Plot the retrieved spectrum, and aerosol density as a function of pressure 
res.plot_spectrum(ax=ax1)
res.plot_aerosol_profiles(ax=ax2)

# Save the figure
fig.tight_layout()
fig.savefig("example.png", dpi=500)

Sensitivity Analysis

To determine the effect of each parameter on the spectrum, a sensitivity analysis can be run for a given core. This varies each parameter in each profile by a series of factors (by default 80%, 90%, 95%, 105%, 110%, and 120%) and looks at the relative change in the spectrum compared to not changing anything. To generate the analysis cores we can use the load_from_previous function in eleos.cores to load the core we want to analyse and create_sensitivity_analysis to generate the forward model cores with the tweaked parameters.

from eleos import cores


# Define and clear the new parent directory
cd = "sensitivity/"
# cores.clear_parent_directory(cd)

# Load the previously retrieved core
core = cores.load_from_previous("example/core_1/", cd)

# Create a sensitivity analysis and run it
cores.create_sensitivity_analysis(core)
cores.generate_alice_job(cd, python_env_name="pythonmain", username="scat2", hours=2, memory=1)
cores.run_alice_job(cd)

After all the cores have run, we can use the eleos.results module again to analyse the results.

from eleos import results

cd = "sensitivity/"

sens = results.SensitivityAnalysis(cd)
sens.make_parameters_plot()
sens.savefig("sensitivity.png", dpi=400)

or, alternatively, we can run the equivalent script from the command-line using

python -m eleos --make-sensitivity-summary sensitivity/

Command Line

Eleos can be run at the command line in order to quickly generate summary plots and print a human-readable representation of the.mre file for a core directory using the command

python -m eleos --make-summary path/to/core/directory

At the moment, this only works for cores created by Eleos, as it requires the core.pkl file to be present which contains a serialisation of the NemesisCore object used to create the core. This allows very easy access to all the profiles, shapes, attributes etc… In the future, this restriction might be lifted.

Limitations and future work

Eleos is not and will never be as flexible as NEMESIS. It is intended to provide a framework for automating the boilerplate code used in generating hundreds of consistent cores through a standard interface, without relying on bespoke code to interface with NEMESIS.

Currently, this library only supports Jupiter (although expansion should be fairly easy when providing .ref files), preset k-tables. In the future, these will be relaxed once the basics of the library have been debugged and tested for both forward and retrieval modes.

A big limitation is the lack of TemperatureProfiles. While these have been partially implemented, for my work in the NIR range we keep the temeprature fixed so adding this is not a priority for me. In the future it will be added though!