"""
CTAO with Gammapy
=================

Access and inspect CTAO data and instrument response functions (IRFs) using Gammapy.

Introduction
------------

The `Cherenkov Telescope Array Observatory (CTAO) <https://www.ctao.org/>`__ is the next generation
ground-based observatory for gamma-ray astronomy. Gammapy is the core
library for the Cherenkov Telescope Array Observatory (CTAO) science tools
(`2017ICRC…35..766D <https://ui.adsabs.harvard.edu/abs/2017ICRC...35..766D>`__
and `CTAO Press
Release <https://www.ctao.org/news/ctao-adopts-the-gammapy-software-package-for-science-analysis/>`__).

CTAO will start taking data in the coming years. For now, to learn how to
analyse CTAO data and to use Gammapy, if you are a member of the CTAO
consortium, you can use the simulated dataset from:

- the CTA first data challenge which ran in 2017 and 2018 (see `here <https://forge.in2p3.fr/projects/data-challenge-1-dc-1/wiki>`__
  for CTAO members)
- the CTAO Science Data Challenge of 2024 (see `here <https://ctaoobservatory.sharepoint.com/:f:/r/sites/share-open-data/Shared%20Documents/Reference%20datasets/Internal%20Science%20Data%20Challenge?csf=1&web=1&e=gNuFzI>`__
  for CTAO members)

Gammapy fully supports the FITS data formats (events, IRFs) used in CTA
1DC and SDC. The XML sky model format is not supported, but are also not needed
to analyse the data, you have to specify your model via the Gammapy YAML
model format, or Python code, as shown below.

You can also use Gammapy to simulate CTAO data and evaluate CTAO performance
using the CTAO response files. Two sets of responses are available for different
array layouts:

- the Omega configuration (prod3b, 2016):  https://zenodo.org/records/5163273,
- the Alpha configuration (prod5, 2021): https://zenodo.org/records/5499840.

They are all fully supported by Gammapy.


Tutorial overview
-----------------

This notebook shows how to access CTAO data and instrument response
functions (IRFs) using Gammapy, and gives some examples how to quick
look the content of CTAO files, especially to see the shape of CTAO IRFs.

At the end of the notebooks, we give several links to other tutorial
notebooks that show how to simulate CTAO data and how to evaluate CTAO
observability and sensitivity, or how to analyse CTAO data.

Note that the FITS data and IRF format currently used by CTAO is the one
documented at https://gamma-astro-data-formats.readthedocs.io/, and is
also used by H.E.S.S. and other Imaging Atmospheric Cherenkov Telescopes
(IACTs). So if you see other Gammapy tutorials using e.g. H.E.S.S.
example data, know that they also apply to CTAO, all you have to do is to
change the loaded data or IRFs to CTAO.

Setup
-----

"""

import os
from pathlib import Path
from astropy import units as u

# %matplotlib inline
import matplotlib.pyplot as plt
from IPython.display import display
from gammapy.data import DataStore, EventList
from gammapy.irf import EffectiveAreaTable2D, load_irf_dict_from_file


######################################################################
# CTA 1DC
# -------
#
# The CTA first data challenge (1DC) ran in 2017 and 2018. It is described
# in detail
# `here <https://forge.in2p3.fr/projects/data-challenge-1-dc-1/wiki>`__
# and a description of the data and how to download it is
# `here <https://forge.in2p3.fr/projects/data-challenge-1-dc-1/wiki#Data-access>`__.
#
# You should download `caldb.tar.gz` (1.2 MB), `models.tar.gz` (0.9
# GB), `index.tar.gz` (0.5 MB), as well as optionally the simulated
# survey data you are interested in: Galactic plane survey `gps.tar.gz`
# (8.3 GB), Galactic center `gc.tar.gz` (4.4 MB), Extragalactic survey
# `egal.tar.gz` (2.5 GB), AGN monitoring `agn.wobble.tar.gz` (4.7 GB).
# After download, follow the instructions how to `untar` the files, and
# set a `CTADATA` environment variable to point to the data.
#
# **For convenience**, since the 1DC data files are large and not publicly
# available to anyone, we have taken a tiny subset of the CTA 1DC data,
# four observations with the southern array from the GPS survey, pointing
# near the Galactic center, and **included them at** `$GAMMAPY_DATA/cta-1dc`.
#
# Files
# ~~~~~
#
# Next we will show a quick overview of the files and how to load them,
# and some quick look plots showing the shape of the CTAO IRFs. How to do
# CTAO simulations and analyses is shown in other tutorials, see links at
# the end of this notebook.
#

# !ls -1 $GAMMAPY_DATA/cta-1dc

# !ls -1 $GAMMAPY_DATA/cta-1dc/data/baseline/gps

# !ls -1 $GAMMAPY_DATA/cta-1dc/caldb/data/cta/1dc/bcf/South_z20_50h

# !ls -1 $GAMMAPY_DATA/cta-1dc/index/gps


######################################################################
# The access to the IRFs files requires to define a `CALDB` environment
# variable. We are going to define it only for this notebook so it won’t
# overwrite the one you may have already defined.
#

os.environ["CALDB"] = os.environ["GAMMAPY_DATA"] + "/cta-1dc/caldb"


######################################################################
# Datastore
# ~~~~~~~~~
#
# You can use the `~gammapy.data.DataStore` to load via the index files
#

data_store = DataStore.from_dir("$GAMMAPY_DATA/cta-1dc/index/gps")
print(data_store)


######################################################################
# If you can’t download the index files, or got errors related to the data
# access using them, you can generate the `~gammapy.data.DataStore` directly from the
# event files.
#

path = Path(os.environ["GAMMAPY_DATA"]) / "cta-1dc/data"
paths = list(path.rglob("*.fits"))
data_store = DataStore.from_events_files(paths)
print(data_store)

data_store.obs_table[["OBS_ID", "GLON_PNT", "GLAT_PNT", "IRF"]]

observation = data_store.obs(110380)
print(observation)


######################################################################
# Events
# ------
#
# We can load events data via the data store and observation, or
# equivalently via the `~gammapy.data.EventList` class by specifying the
# EVENTS filename.
#
# The quick-look `events.peek()` plot below shows that CTAO has a field
# of view of a few degrees, and two energy thresholds, one significantly
# below 100 GeV where the CTAO large-size telescopes (LSTs) detect events,
# and a second one near 100 GeV where the mid-sized telescopes (MSTs)
# start to detect events.
#
# Note that most events are “hadronic background” due to cosmic ray
# showers in the atmosphere that pass the gamma-hadron selection cuts for
# this analysis configuration. Since this is simulated data, column
# `MC_ID` is available that gives an emission component identifier code,
# and the EVENTS header in `events.table.meta` can be used to look up
# which `MC_ID` corresponds to which emission component.
#
# Events can be accessed from the observation object like:

events = observation.events

######################################################################
# Or read directly from an event file:
#

events = EventList.read(
    "$GAMMAPY_DATA/cta-1dc/data/baseline/gps/gps_baseline_110380.fits"
)

######################################################################
# Here we print the data from the first 5 events listed in the table:
#

display(events.table[:5])

######################################################################
# And show a summary plot:
#

events.peek()
plt.show()

######################################################################
# IRFs
# ----
#
# The CTAO instrument response functions (IRFs) are given as FITS files in
# the `caldb` folder, the following IRFs are available:
#
# -  effective area
# -  energy dispersion
# -  point spread function
# -  background
#
# Notes:
#
# -  The IRFs contain the energy and offset dependence of the CTAO response
# -  CTA 1DC was based on an early version of the CTAO FITS responses
#    produced in 2017, improvements have been made since.
# -  The point spread function was approximated by a Gaussian shape
# -  The background is from hadronic and electron air shower events that
#    pass CTAO selection cuts. It was given as a function of field of view
#    coordinates, although it is radially symmetric.
# -  The energy dispersion in CTA 1DC is noisy at low energy, leading to
#    unreliable spectral points for some analyses.
# -  The CTA 1DC response files have the first node at field of view
#    offset 0.5 deg, so to get the on-axis response at offset 0 deg,
#    Gammapy has to extrapolate. Furthermore, because diffuse gamma-rays
#    in the FOV were used to derive the IRFs, and the solid angle at small
#    FOV offset circles is small, the IRFs at the center of the FOV are
#    somewhat noisy. This leads to unstable analysis and simulation issues
#    when using the DC1 IRFs for some analyses.
#

print(observation.aeff)

irf_filename = (
    "$GAMMAPY_DATA/cta-1dc/caldb/data/cta/1dc/bcf/South_z20_50h/irf_file.fits"
)
irfs = load_irf_dict_from_file(irf_filename)
print(irfs)


######################################################################
# Effective area
# ~~~~~~~~~~~~~~
#

# Equivalent alternative way to load IRFs directly
aeff = EffectiveAreaTable2D.read(irf_filename, hdu="EFFECTIVE AREA")
print(aeff)

irfs["aeff"].peek()
plt.show()

# What is the on-axis effective area at 10 TeV?
print(aeff.evaluate(energy_true="10 TeV", offset="0 deg").to("km2"))


######################################################################
# Energy dispersion
# ~~~~~~~~~~~~~~~~~
#

irfs["edisp"].peek()
plt.show()


######################################################################
# Point spread function
# ~~~~~~~~~~~~~~~~~~~~~
#

irfs["psf"].peek()
plt.show()


# %%
# This is how for analysis you could slice out the PSF
# at a given field of view offset
plt.figure(figsize=(8, 5))
irfs["psf"].plot_containment_radius_vs_energy(
    offset=[1] * u.deg, fraction=[0.68, 0.8, 0.95]
)
plt.show()

######################################################################
# Background
# ~~~~~~~~~~
#
# The background is given as a rate in units `MeV-1 s-1 sr-1`.
#

irfs["bkg"].peek()
plt.show()

print(irfs["bkg"].evaluate(energy="3 TeV", fov_lon="1 deg", fov_lat="0 deg"))


######################################################################
# To visualise the background at particular energies:
#

irfs["bkg"].plot_at_energy(
    ["100 GeV", "500 GeV", "1 TeV", "3 TeV", "10 TeV", "100 TeV"]
)
plt.show()

######################################################################
# Source models
# -------------
#
# The 1DC sky model is distributed as a set of XML files, which link
# to numerous other FITS and text files. Gammapy does not natively support this
# XML format. Instead, we use YAML-based model format that improves on the XML format
# by being easier to write and read, add
# relevant information (units for physical quantities), and omit useless
# information (e.g. parameter scales in addition to values).
#
# If you need or prefer to work with the original XML model files, you can use tools like
# `ElementTree <https://docs.python.org/3/library/xml.etree.elementtree.html>`__
# from the Python standard library, or
# `xmltodict <https://github.com/martinblech/xmltodict>`__ installed through
# `pip install xmltodict`. Here’s an example how to load the information
# for a given source, and convert it into the sky model format Gammapy
# understands.
#
# With the following command we can see what the XML file looks like
# (uncomment it if you have installed `xmltodict`).
 
 
# !tail -n 20 $CTADATA/models/models_gps.xml

######################################################################
# Here is an example on how to create a gammapy source model from this

# import xmltodict
# from astropy import units as u
# from gammapy.modeling.models import PowerLawSpectralModel, PointSpatialModel, SkyModel

# # Read XML file
# filename = "$CTADATA/models/models_gps.xml"

# # Access spectrum parameters
# data = xmltodict.parse(open(filename).read())
# source0 = data["source_library"]["source"][0]
# spectrum0 = source0["spectrum"]["parameter"]
# spatial0 = source0["spatialModel"]

# # Printing the type shows we have a point-like model
# print(spatial0['@type'])

# # Helper function to get parameter by name
# def get_param(params, name):
#     for p in params:
#         if p["@name"] == name:
#             return float(p["@value"]) * float(p["@scale"])
#     raise KeyError(f"Parameter '{name}' not found.")

# # Helper to convert parameter value * scale
# par_to_val = lambda par: float(par["@value"]) * float(par["@scale"])

# # Create a spectral model
# spectral_model = PowerLawSpectralModel(
#     amplitude=par_to_val(spectrum0[0]) * u.Unit("cm-2 s-1 MeV-1"),
#     index=par_to_val(spectrum0[1]),
#     reference=par_to_val(spectrum0[2]) * u.Unit("MeV"),
# )
# print(spectral_model)

# # Create the spatial model
# spatial_params = spatial0["parameter"]
# spatial_model = PointSpatialModel(
#     lon_0=get_param(spatial_params, "RA") * u.deg,
#     lat_0=get_param(spatial_params, "DEC") * u.deg,
#     frame="icrs"
# )
# print(spatial_model)

# # Create the SkyModel
# sky_model = SkyModel(spectral_model=spectral_model, spatial_model=spatial_model, name=source0['@name'])
# print(sky_model)


######################################################################
# Latest CTAO performance files
# -----------------------------
#
# CTA 1DC is useful to learn how to analyse CTAO data. But to do
# simulations and studies for CTAO now, you should get the most recent CTAO
# IRFs in FITS format from https://www.ctao.org/for-scientists/performance/.
#
# If you want to use other response files, the following code cells (remove the # to uncomment)
# explain how to proceed. This example is made with the Alpha configuration (Prod5).
#

# !curl -o cta-prod5-zenodo-fitsonly-v0.1.zip https://zenodo.org/records/5499840/files/cta-prod5-zenodo-fitsonly-v0.1.zip
# !unzip cta-prod5-zenodo-fitsonly-v0.1.zip
# !ls fits/

# !tar xf fits/CTA-Performance-prod5-v0.1-South-40deg.FITS.tar.gz -C fits/.
# !ls fits/*.fits.gz

# irfs1 = load_irf_dict_from_file("fits/Prod5-South-40deg-SouthAz-14MSTs37SSTs.180000s-v0.1.fits.gz")
# irfs1["aeff"].plot_energy_dependence()

# irfs2 = load_irf_dict_from_file("fits/Prod5-South-40deg-SouthAz-14MSTs37SSTs.1800s-v0.1.fits.gz")
# irfs2["aeff"].plot_energy_dependence()


######################################################################
# Exercises
# ---------
#
# -  Load the EVENTS file for `obs_id=111159` as a
#    `~gammapy.data.EventList` object.
# -  Use ``EventList.table`` to find the energy, sky coordinate and time of
#    the highest-energy event.
# -  Use `~gammapy.data.EventList.pointing_radec` to find the pointing position of this
#    observation, and use `astropy.coordinates.SkyCoord` methods to find
#    the field of view offset of the highest-energy event.
# -  What is the effective area and PSF 68% containment radius of CTAO at 1
#    TeV for the `South_z20_50h` configuration used for the CTA 1DC
#    simulation?
# -  Get the latest CTAO FITS performance files from
#    https://www.ctao.org/for-scientists/performance/ and run the
#    code example above. Make an effective area ratio plot of 40 deg
#    zenith versus 20 deg zenith for the `South_z40_50h` and
#    `South_z20_50h` configurations.
#


######################################################################
# Next steps
# ----------
#
# -  Learn how to analyse data with
#    :doc:`/tutorials/starting/analysis_1` and
#    :doc:`/tutorials/starting/analysis_2` or any other
#    Gammapy analysis tutorial.
# -  Learn how to evaluate CTAO observability and sensitivity with
#    :doc:`/tutorials/analysis-3d/simulate_3d`,
#    :doc:`/tutorials/analysis-1d/spectrum_simulation`
#    or :doc:`/tutorials/analysis-1d/cta_sensitivity`.
#