Unverified Commit 7c4adfd8 authored by Akke Viitanen's avatar Akke Viitanen
Browse files

use read_fits from utilities

parent 72545af3

.pre-commit-config.yaml

+1 −0
Original line number Diff line number Diff line
@@ -99,6 +99,7 @@ repos: 
            "-D", # Flag to override settings in conf.py

            #"exclude_patterns=notebooks/*,_build", # Exclude notebooks and build dir from pre-commit

            "exclude_patterns=_build", # Exclude notebooks and build dir from pre-commit

            "-j 4", # Use multiple threads

          ]

    # Run unit tests, verify that they pass. Note that coverage is run against

    # the ./src directory here because that is what will be committed. In the

src/lsst_inaf_agile/catalog_agn.py

+2 −2
Original line number Diff line number Diff line
@@ -191,7 +191,7 @@ class CatalogAGN: 
        filename = f"{self.dirname}/agn.fits"

        if os.path.exists(filename) and not overwrite:

            logger.info(f"Returning an existing AGN catalog {filename}")

            return fitsio.read(filename)

            return util.read_fits(filename)



        logger.info(f"Creating the AGN catalog {filename}")

        self.catalog = np.empty_like(self.catalog_galaxy["ID"], dtype=self.get_dtype())
@@ -446,7 +446,7 @@ class CatalogAGN: 
        if not os.path.exists(filename):

            return None



        fits = fitsio.read(filename)

        fits = util.read_fits(filename)

        return fits["LAMBDA"][0], fits["FLUX"][0]



    def _get_sed(self, i, ratio_max: float = 0.90, dlog_wav: float = 7.65e-4):

src/lsst_inaf_agile/catalog_galaxy.py

+3 −1
Original line number Diff line number Diff line
@@ -40,7 +40,9 @@ class CatalogGalaxy: 
            util.create_directory(filename)

            fitsio.write(filename, self.catalog, clobber=True)



        self.catalog = fitsio.read(filename)

        from lsst_inaf_agile.util import read_fits



        self.catalog = read_fits(filename)

        return self.catalog



    @staticmethod

src/lsst_inaf_agile/catalog_star.py

+12 −4
Original line number Diff line number Diff line
@@ -8,7 +8,6 @@ 
import logging

import os



import fitsio

import numpy as np

import pyvo as vo

from astropy import constants
@@ -92,8 +91,7 @@ class CatalogStar: 
    def get_stars(self, selection="rmag", maglim=28, fbin=1.0):

        """Query NOIRlab to retrieve the stellar catalogs from LSST-SIM."""

        if os.path.exists(self.filename):

            logger.info(f"Reading {self.filename}")

            return fitsio.read(self.filename)

            return util.read_fits(self.filename)



        table = "lsst_sim.simdr2"

        if self.is_binary:
@@ -118,7 +116,15 @@ class CatalogStar: 
        tap_service = vo.dal.TAPService("https://datalab.noirlab.edu/tap")

        tap_results = tap_service.search(query)

        table = tap_results.to_table()



        import warnings



        from astropy.units import UnitsWarning



        with warnings.catch_warnings():

            warnings.simplefilter("ignore", UnitsWarning)

            table.write(self.filename)



        return table



    def is_cepheid(self, i):
@@ -155,9 +161,11 @@ class CatalogStar: 
            lc = self.get_lightcurve_mjd_binary(*args)

            return self.catalog[f"{band}_point"][i] if lc is None else lc



        # Handle cepheids

        if self.is_cepheid(i):

            return self.get_lightcurve_mjd_cepheid(*args)



        # Handle LPVs

        if self.is_lpv(i):

            return self.get_lightcurve_mjd_lpv(*args, self.is_c_rich(i))

src/lsst_inaf_agile/egg.py

+2 −5
Original line number Diff line number Diff line
@@ -82,14 +82,12 @@ class Egg: 


    def get_sed(self, i):

        """Return an EGG SED."""

        import fitsio



        dirname = os.path.dirname(self.egg_kwargs["save_sed"])

        fname = f"{dirname}/egg-seds-{i}.fits"

        try:

            if not os.path.exists(fname):

                os.system(f"egg-getsed seds={dirname}/egg-seds.dat id={i}")

            return fitsio.read(fname)

            return util.read_fits(fname)

        except FileNotFoundError:

            logger.warning("Could not find galaxy sed")

            return None
@@ -176,10 +174,9 @@ 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



        smf = fitsio.read(filename)

        smf = util.read_fits(filename)

        i = None

        for _i, (zlo, zhi) in enumerate(smf["ZB"][0].T):

            if zlo <= z < zhi: