fix pydocstyle errors (38d78dec) · Commits · Akke Esa Tapio Viitanen / lsst_inaf_agile

src/lsst_inaf_agile/ananna2022.py

+5 −7

Original line number	Diff line number	Diff line
		@@ -3,9 +3,7 @@
		# Email: akke.viitanen@helsinki.fi
		# Date: 2024-08-01 13:53:22

		"""
		Implements Ananna+2022
		"""
		"""Implement Ananna+ 2022."""

		import matplotlib.pyplot as plt
		import numpy as np
		@@ -69,10 +67,7 @@ parameters = {


		def get_phi_bh(m, m_star, phi_star, alpha, beta, h=1.0, sample=None):
		"""
		Return the Schechter function form of BHMF
		"""

		"""Return the Schechter function form of BHMF."""
		if sample:
		## NOTE: errors for sigma=0.50 case
		# m_star = 10 ** (np.log10(m_star) + np.random.uniform(-0.20, 0.25))
		@@ -94,6 +89,7 @@ def get_phi_bh(m, m_star, phi_star, alpha, beta, h=1.0, sample=None):


		def get_phi_lambda(lambda_edd, lambda_edd_star, xi_star, delta1, epsilon_lambda, h=1.0):
		"""Return phi_lambda following the functional form in Ananna."""
		ratio = lambda_edd / lambda_edd_star
		return (
		np.ma.true_divide(xi_star, np.power(ratio, delta1) + np.power(ratio, delta1 + epsilon_lambda)) * h**3
		@@ -101,6 +97,7 @@ def get_phi_lambda(lambda_edd, lambda_edd_star, xi_star, delta1, epsilon_lambda,


		def get_phi_bh_fig10(m, is_type1=True, is_type2=True, log_ledd_gt=-3, h=1.0):
		"""Get phi_bh from Ananna Fig10."""
		x = np.log10(m)
		y = np.zeros_like(m)

		@@ -116,6 +113,7 @@ def get_phi_bh_fig10(m, is_type1=True, is_type2=True, log_ledd_gt=-3, h=1.0):


		def get_phi_lambda_fig10(lambda_edd, is_type1=True, is_type2=True, log_mbh_gt=6.5, h=1.0):
		"""Get phi_lambda from Ananna Fig10."""
		x = np.log10(lambda_edd)
		y = np.zeros_like(lambda_edd)

src/lsst_inaf_agile/catalog_agn.py

+23 −10

Original line number	Diff line number	Diff line
		@@ -84,6 +84,7 @@ class CatalogAGN:
		filename of the EGG filter database (db.dat)
		catalog: np.ndarray
		catalog data

		"""

		def __init__(
		@@ -125,6 +126,7 @@ class CatalogAGN:
		Returns
		-------
		Value of the column.

		"""
		if key not in self.catalog.dtype.names:
		return self.catalog_galaxy[key]
		@@ -147,6 +149,7 @@ class CatalogAGN:
		Returns
		-------
		List of 4-tuples of column names, types, descriptions, and units.

		"""
		return (
		[
		@@ -306,6 +309,7 @@ class CatalogAGN:
		----------
		Gamma: float
		Assumed power-law index for the band conversion.

		"""
		return np.log10(util.convert_flux(10 ** self["log_FX_2_10"], 2.0, 10.0, 2.0, 7.0, Gamma=Gamma))

		@@ -329,11 +333,13 @@ class CatalogAGN:
		return lusso2010.get_log_l_2500(self["log_L_2_keV"], alpha, beta, scatter)

		def get_is_optical_type2(self, func_get_f_obs=None, use_f_obs_for_ctk_agn=False):
		"""Return boolean vector selecting optical type2 AGN.
		"""
		Return boolean vector selecting optical type2 AGN.

		The optical type2 AGN fraction is evaluated based on Merloni+2014
		assuming obscured fraction as a function of intrinsic X-ray luminosity
		and redshift.

		"""
		select_ctk = self["is_agn_ctk"]
		if func_get_f_obs is None:
		@@ -359,10 +365,12 @@ class CatalogAGN:
		mu_type_2=0.3,
		ebv_ctk=9.0,
		):
		"""Return AGN reddening E(B-V) in ABmag.
		"""
		Return AGN reddening E(B-V) in ABmag.

		The E(B-V) is assumed to be different for type1 and type2 AGN, while
		CTK AGN are assumed to be all type2.

		"""
		type_1_ebv = (np.linspace(0, 1, 101),)
		type_2_ebv = (np.linspace(0, 3, 301),)
		@@ -462,7 +470,8 @@ class CatalogAGN:
		return self["is_agn_ctn"] + self["is_agn_ctk"]

		def get_sed(self, i):
		"""Return an AGN SED.
		"""
		Return an AGN SED.

		Parameters
		----------
		@@ -475,6 +484,7 @@ class CatalogAGN:
		Wavelength in microns.
		flux: array_like
		observer frame flux in microjanskies.

		"""
		filename = f"{self.dirname}/seds/agn-seds-{i}.fits"
		if not os.path.exists(filename):
		@@ -484,7 +494,8 @@ class CatalogAGN:
		return fits["LAMBDA"][0], fits["FLUX"][0]

		def _get_sed(self, i, ratio_max=0.90, dlog_wav=7.65e-4):
		"""Generate an AGN SED.
		"""
		Generate an AGN SED.

		Parameters
		----------
		@@ -494,6 +505,7 @@ class CatalogAGN:
		Maximum allowed ratio flux_agn / flux_total for type2 AGN.
		dlog_wav: float
		SED wavelength resolution in dex.

		"""
		logger.debug(f"Getting AGN SED {i} {self.catalog.size}")

		@@ -568,7 +580,8 @@ class CatalogAGN:
		return agn_sed

		def _get_flux_single(self, my_sed, band, rest_frame, redshift, distance):
		"""Return a single bandbass flux by integrating the SED.
		"""
		Return a single bandbass flux by integrating the SED.

		Take a rest-frame intrinsic SED and integrate it along a filter
		passband. The SED is shifted to either rest-frame (10pc) or observer
		@@ -586,6 +599,7 @@ class CatalogAGN:
		Redshift of the SED
		distance: float
		Distance at which to evaluate the flux.

		"""
		# Get the flux in observed frame or rest frame
		if rest_frame:
		@@ -636,15 +650,12 @@ class CatalogAGN:
		def get_MBH(
		self, sigma_total=0.50, offset=0.00, sigma_intrinsic=False, sigma_observational=None, select=None
		):
		"""Return log10 of the supermassive black hole mass in Msun.
		"""
		Return log10 of the supermassive black hole mass in Msun.

		The MBH is assigned in accordance with the continuity equation after
		which log-normal scatter is added to the final value of the MBH.

		Parameters
		----------
		sigma_total: float
		Magnitude of log-normal scatter in dex.
		"""
		# Get MBH
		log_mbh = get_log_mbh_continuity_new2(self["M"], self["Z"])
		@@ -741,6 +752,7 @@ class CatalogAGN:
		EGG-style passband name.
		mjd: float or array_like or None
		MJD of observation.

		"""
		if mjd is None:
		mjd = util.get_mjd_vec()
		@@ -795,6 +807,7 @@ class CatalogAGN:
		Returns
		-------
		The value of the lightcurve at given MJD in microjanskies.

		"""
		lc = self.get_lightcurve(i, band)
		return np.interp(mjd - mjd0, util.get_mjd_vec(), lc)

src/lsst_inaf_agile/catalog_combined.py

+28 −31

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ class CatalogCombined:
		Single star catalog.
		catalog_binary: catalog_star.CatalogStar or None
		Binary star catalog.

		"""

		def __init__(
		@@ -63,6 +64,7 @@ class CatalogCombined:
		catalog_binary=None,
		sql_query=None,
		):
		"""Initialize CombinedCatalog."""
		self.dirname = dirname
		self.catalog_galaxy = catalog_galaxy
		self.catalog_agn = catalog_agn
		@@ -95,7 +97,7 @@ class CatalogCombined:
		self.write()

		def get_filename(self):
		"""Return the FITS filename of the combined catalog"""
		"""Return the FITS filename of the combined catalog."""
		return f"{self.dirname}/catalog.fits"

		def get_dtype(self):
		@@ -105,6 +107,7 @@ class CatalogCombined:
		Returns
		-------
		List of (name, type) corresponding to the names and types of the columns.

		"""
		dtype = {}
		for catalog in (self.catalog_galaxy, self.catalog_agn, self.catalog_star, self.catalog_binary):
		@@ -121,8 +124,10 @@ class CatalogCombined:

		def get_number_galaxy_star_binary(self):
		"""
		Return the tuple (N_galaxy, N_star, N_binary) where N is the number of
		objects in the combined catalog.
		Return the tuple (N_galaxy, N_star, N_binary).

		N is the number of objects in the combined catalog.

		"""
		return (
		len(self.catalog_galaxy.catalog),
		@@ -132,7 +137,7 @@ class CatalogCombined:

		def get_catalog_combined(self):
		r"""
		Constructs the combined catalog based on the dtype.
		Construct the combined catalog based on the dtype.

		For each column in the catalog, the column is looked for in the
		AGN/galaxy/star/binary catalogs. Upon a match, the corresponding rows
		@@ -146,8 +151,8 @@ class CatalogCombined:
		Returns
		-------
		The combined catalog as a numpy ndarray.
		"""

		"""
		n_galaxy, n_star, n_binary = self.get_number_galaxy_star_binary()
		n_total = n_galaxy + n_star + n_binary
		catalog_combined = np.full(n_total, np.nan, dtype=self.get_dtype())
		@@ -184,10 +189,7 @@ class CatalogCombined:
		return catalog_combined

		def postprocess(self):
		"""
		Adds columns in post-processing
		"""

		"""Add columns in post-processing."""
		for band in self.catalog_galaxy.bands:
		logger.info(f"Postprocessing flux {band}")
		self.catalog_combined[band + "_total"] = self.get_flux_total(band, False)
		@@ -207,8 +209,8 @@ class CatalogCombined:
		- galaxy: sum of galaxy bulge and disk fluxes
		- star: point fluxes
		- binary star: sum of the component point fluxes
		"""

		"""
		# NOTE: override rest-frame behavior as EGG does not have absmags for
		# disk/bulge separately
		keys = ["disk", "bulge", "point"]
		@@ -230,9 +232,7 @@ class CatalogCombined:
		return ret

		def write(self):
		"""
		Writes the combined catalog to a FITS file
		"""
		"""Write the combined catalog to a FITS file."""
		fitsio.write(self.get_filename(), self.catalog_combined, clobber=True)
		return self.catalog_combined

		@@ -246,8 +246,10 @@ class CatalogCombined:
		filename of the sqlite3 database
		name_table: str
		name of the table in the sqlite3 database
		"""
		if_exists: str
		sqlite3 action to handle an existing table

		"""
		import sqlite3

		from astropy.table import Table
		@@ -260,28 +262,23 @@ class CatalogCombined:
		df.to_sql(name_table, con, index=False, if_exists=if_exists, chunksize=1024, method="multi")

		def get_is_galaxy(self):
		"""
		Return boolean vector selecting galaxies
		"""
		"""Return boolean vector selecting galaxies."""
		return np.isfinite(self.catalog_combined["Z"])

		def get_is_star(self):
		"""
		Return boolean vector selecting stars
		"""
		"""Return boolean vector selecting stars."""
		return ~self.get_is_galaxy()

		def get_index_star(self, i):
		"""
		Return the index in the stellar catalog corresponding to 'i' in the
		combined catalog.
		Return the index in the stellar catalog corresponding to 'i' in the combined catalog.

		Parameters
		----------
		i: int
		ID of the truth catalog object
		"""

		"""
		n_galaxy, n_star, n_binary = self.get_number_galaxy_star_binary()

		# Handles single star
		@@ -297,11 +294,12 @@ class CatalogCombined:

		def write_reference_catalog(self, filename: str, maglim: float, selection_band: str):
		"""
		Write a mock LSST reference catalog in CSV format to the given
		'filename'. The reference catalog is cut to brighter than the magnitude
		limit 'maglim' in the band 'selection_band'.
		"""
		Write a mock LSST reference catalog in CSV format to the given 'filename'.

		The reference catalog is cut to brighter than the magnitude limit
		'maglim' in the band 'selection_band'.

		"""
		logger.info("Writing the reference catalog...")
		if os.path.exists(filename):
		logger.info(f"{filename} exists, will not overwrite.")
		@@ -384,9 +382,7 @@ class CatalogCombined:
		return 24.0

		def __getitem__(self, key):
		"""
		Return combined catalog value corresponding to 'key'.
		"""
		"""Return combined catalog value corresponding to 'key'."""
		return self.catalog_combined[key]

		def get_luminosity_function(
		@@ -418,6 +414,8 @@ class CatalogCombined:
		maximum redshift
		select: array_like
		boolean vector for selecting values
		values: array_like
		values to use instead of the value corresponding to 'key'
		nmin: int
		minimum allowed counts per bin
		deredden: bool
		@@ -426,7 +424,6 @@ class CatalogCombined:
		weight LF by occupation fraction

		"""

		# select in redshift
		z = self["Z"]
		if select is None:

src/lsst_inaf_agile/convert_agile_manager.py

+6 −6

Original line number	Diff line number	Diff line
		@@ -3,9 +3,7 @@
		# Email: akke.viitanen@helsinki.fi
		# Date: 2025-09-12 00:39:53

		"""
		Middleware for reference catalog config
		"""
		"""Middleware for reference catalog config."""

		import numpy as np
		import util
		@@ -14,9 +12,11 @@ from lsst.meas.algorithms.convertRefcatManager import ConvertGaiaManager

		class ConvertAgileManager(ConvertGaiaManager):
		"""
		Convert from AGILE to the reference catalog format. This class is
		piggybacking on the existing Gaia converter (proper motions, covariances),
		but only overloads the way fluxes are handled.
		Convert from AGILE to the reference catalog format.

		The class is piggybacking on the existing Gaia converter (proper motions,
		covariances), but only overloads the way fluxes are handled.

		"""

		def _getFluxes(self, input):

src/lsst_inaf_agile/egg.py

+30 −6

Original line number	Diff line number	Diff line
		@@ -3,9 +3,7 @@
		# Email: akke.viitanen@helsinki.fi
		# Date: 2023-04-12 22:44:16

		"""
		Wrapper for calling egg
		"""
		"""Impelement wrapper for calling egg."""

		import logging
		import os
		@@ -26,15 +24,36 @@ if not shutil.which("egg-gencat"):


		class Egg:
		"""
		EGG class.

		Provie a wrapper for the EGG command-line software.

		Attributes
		----------
		egg_kwargs: dict
		list of EGG key value pairs used to construct the EGG command-line arguments.

		Examples
		--------
		>>> # Create an EGG object with 1deg2 area and logM > 9.5 (Chabrier)
		>>> # follow-it by calling egg.run() ...
		>>> egg = Egg({'area': 1, 'mmin': 9.5})

		"""

		def __init__(self, egg_kwargs):
		"""Initialize EGG."""
		self.egg_kwargs = egg_kwargs

		def get_argument_line(self):
		"""Get the EGG argument line for calling it from the terminal."""
		exclude = []
		egg_kwargs = {k: v for k, v in self.egg_kwargs.items()}
		return sorted([f"{k}={str(v)}" for k, v in egg_kwargs.items() if k not in exclude])

		def get_filename(self):
		"""Return an example filename constructed from the kwargs."""
		if "out" in self.egg_kwargs:
		return self.egg_kwargs["out"]

		@@ -46,9 +65,11 @@ class Egg:
		return filename

		def get_area(self):
		"""Return EGG catalog area."""
		return self.egg_kwargs["area"]

		def run(self, overwrite=False):
		"""Run EGG using the kwargs supplied."""
		cmd = " ".join(["egg-gencat"] + self.get_argument_line())
		filename = self.get_filename()
		if not overwrite and os.path.exists(filename):
		@@ -62,7 +83,7 @@ class Egg:
		return os.system(cmd)

		def get_sed(self, i):
		"""Return a EGG SED"""
		"""Return an EGG SED."""
		import fitsio

		dirname = os.path.dirname(self.egg_kwargs["save_sed"])
		@@ -78,6 +99,8 @@ class Egg:
		@staticmethod
		def read(filename):
		"""
		Read an EGG catalog from the filename.

		Note that usually and for small files, loading EGG through
		astropy/fitsio works fine. For large files (n_bands * n_galaxies >= 2
		** 28) these routines fail due to the dtype not fitting into a C
		@@ -90,7 +113,6 @@ class Egg:
		This is a dirty hack, but the alternative is to change completely how
		EGG writes the FITS files.
		"""

		import fitsio
		import numpy as np

		@@ -154,6 +176,7 @@ class Egg:

		@staticmethod
		def get_smf(z, key, filename):
		"""Read an EGG-like stellar mass function from a file."""
		import fitsio
		import numpy as np

		@@ -174,8 +197,8 @@ class Egg:
		Run EGG for the given configuration file.

		Returns the EGG catalog using Egg.read.
		"""

		"""
		logger.info(f"Reading {config}")
		config = ConfigParser()
		config.read("etc/config_egg.ini")
		@@ -186,6 +209,7 @@ class Egg:


		def main():
		"""Run EGG using an example config file."""
		Egg.run_config("etc/config_egg.ini")