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Memory usage optimisation #26

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merged 2 commits into from
Jan 27, 2025
Merged

Memory usage optimisation #26

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4814838
Modified read_shear_cat to save memory.
sachaguer Jan 24, 2025
cbc094e
Removed unnecessary lines of code.
sachaguer Jan 24, 2025
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7 changes: 2 additions & 5 deletions shear_psf_leakage/rho_tau_cov.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,13 +73,10 @@ def __init__(
#Create treecorr catalogs
self.gal, self.psf, self.psf_error, self.size_error = self.create_treecorr_catalog(cat_gal, cat_psf)

del cat_gal, cat_psf #Free memory from the galaxy and star catalogs.

#Compute the shape noise
self.sigma_e = self.compute_shape_noise(self.gal, self.gal)
self.sigma_psf = self.compute_shape_noise(self.psf, self.psf)
self.sigma_psf_error = self.compute_shape_noise(self.psf_error, self.psf_error)
if self.use_eta:
self.sigma_psf_size_error = self.compute_shape_noise(self.size_error, self.size_error)


#interpolate rho stats
self.rho_0_p_itp = self.build_interpolator(self.psf, self.psf, type='plus')
Expand Down
87 changes: 48 additions & 39 deletions shear_psf_leakage/rho_tau_stat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
"""

from tqdm import tqdm
import warnings

import numpy as np
import matplotlib.pyplot as plt
Expand Down Expand Up @@ -234,7 +235,7 @@ def set_params(self, params=None, output=None):
if output is not None:
self._output = output

def read_shear_cat(self, path_gal, path_psf, hdu=1):
def read_shear_cat(self, path_gal, path_psf, hdu=1, store=False):
"""
read_shear_cat

Expand All @@ -247,18 +248,22 @@ def read_shear_cat(self, path_gal, path_psf, hdu=1):
"""
assert ((path_gal is not None) or (path_psf is not None)), ("Please specify a path for the shear catalog you want to read.")
if path_gal is not None:
self.dat_shear = fits.getdata(path_gal, ext=hdu)
dat_shear = fits.getdata(path_gal, ext=hdu)
return dat_shear
if path_psf is not None:
self.dat_psf = fits.getdata(path_psf, ext=hdu)
dat_psf = fits.getdata(path_psf, ext=hdu)
return dat_psf

def get_cat_fields(self, cat_type, square_size=False):
def get_cat_fields(self, cat, cat_type, square_size=False):
"""
Get Cat Fields

Get catalogue fields for correlation.

Parameters
----------
cat : str
catalogue of galaxies or stars. Type should match the cat_type given in argument.
cat_type : str
catalogue type, allowed are 'gal', 'psf', 'psf_error' or 'psf_size_error'

Expand Down Expand Up @@ -291,48 +296,46 @@ def get_cat_fields(self, cat_type, square_size=False):

if cat_type=="gal":
if self._params["w_col"] is not None:
weights = self.dat_shear[self._params["w_col"]]
weights = cat[self._params["w_col"]]
else:
weights = np.ones_like(ra)
assert self.dat_shear is not None, ("Check you read the shear catalogs correctly.")
ra = self.dat_shear[self._params["ra_col"]]
dec = self.dat_shear[self._params["dec_col"]]
g1 = self.dat_shear[self._params["e1_col"]] - np.average(self.dat_shear[self._params["e1_col"]], weights=weights)
g2 = self.dat_shear[self._params["e2_col"]] - np.average(self.dat_shear[self._params["e2_col"]], weights=weights)
ra = cat[self._params["ra_col"]]
dec = cat[self._params["dec_col"]]
g1 = cat[self._params["e1_col"]] - np.average(cat[self._params["e1_col"]], weights=weights)
g2 = cat[self._params["e2_col"]] - np.average(cat[self._params["e2_col"]], weights=weights)
if self._params.get("R11", None) is not None:
g1 /= self._params["R11"]
if self._params.get("R22", None) is not None:
g2 /= self._params["R22"]
else:
assert self.dat_psf is not None, ("Check you read the shear catalogs correctly.")
#Add a mask?
#mask = (self.dat_psf[self._params["FLAG_PSF_HSM"]]==0) & (self.dat_psf[self._params["FLAG_STAR_HSM"]]==0)
ra = self.dat_psf[self._params["ra_col"]]
dec = self.dat_psf[self._params["dec_col"]]
ra = cat[self._params["ra_col"]]
dec = cat[self._params["dec_col"]]
weights = None

if cat_type=="psf":
g1 = self.dat_psf[self._params["e1_PSF_col"]]# - self.dat_psf[self._params["e1_PSF_col"]].mean()
g2 = self.dat_psf[self._params["e2_PSF_col"]]# - self.dat_psf[self._params["e2_PSF_col"]].mean()
g1 = cat[self._params["e1_PSF_col"]]# - cat[self._params["e1_PSF_col"]].mean()
g2 = cat[self._params["e2_PSF_col"]]# - cat[self._params["e2_PSF_col"]].mean()

elif cat_type=="psf_error":
g1 = (self.dat_psf[self._params["e1_star_col"]] - self.dat_psf[self._params["e1_PSF_col"]])
g1 = (cat[self._params["e1_star_col"]] - cat[self._params["e1_PSF_col"]])
#g1 -= g1.mean()
g2 = (self.dat_psf[self._params["e2_star_col"]] - self.dat_psf[self._params["e2_PSF_col"]])
g2 = (cat[self._params["e2_star_col"]] - cat[self._params["e2_PSF_col"]])
#g2 -= g2.mean()

else:
size_star = self.dat_psf[self._params["star_size"]]**2 if square_size else self.dat_psf[self._params["star_size"]]
size_psf = self.dat_psf[self._params["PSF_size"]]**2 if square_size else self.dat_psf[self._params["PSF_size"]]
size_star = cat[self._params["star_size"]]**2 if square_size else cat[self._params["star_size"]]
size_psf = cat[self._params["PSF_size"]]**2 if square_size else cat[self._params["PSF_size"]]

g1 = self.dat_psf[self._params["e1_star_col"]] * (size_star - size_psf) / size_star
g1 = cat[self._params["e1_star_col"]] * (size_star - size_psf) / size_star
#g1 -= g1.mean()
g2 = self.dat_psf[self._params["e2_star_col"]] * (size_star - size_psf) / size_star
g2 = cat[self._params["e2_star_col"]] * (size_star - size_psf) / size_star
#g2 -= g2.mean()

return ra, dec, g1, g2, weights

def build_catalog(self, cat_type, key, npatch=None, patch_centers=None, square_size=False, mask=False):
def build_catalog(self, cat, cat_type, key, npatch=None, patch_centers=None, square_size=False, mask=False):
"""
build_catalogue

Expand Down Expand Up @@ -360,19 +363,19 @@ def build_catalog(self, cat_type, key, npatch=None, patch_centers=None, square_s
if npatch is None:
npatch = self._params["patch_number"]

ra, dec, g1, g2, weights = self.get_cat_fields(cat_type, square_size)
ra, dec, g1, g2, weights = self.get_cat_fields(cat, cat_type, square_size)

if mask:
flag_psf = self.dat_psf[self._params["PSF_flag"]]
flag_star = self.dat_psf[self._params["star_flag"]]
flag_psf = cat[self._params["PSF_flag"]]
flag_star = cat[self._params["star_flag"]]
mask_arr = (flag_psf==0) & (flag_star==0)
if weights is not None:
weights = weights[mask_arr]
else:
mask_arr = np.array([True for i in ra])

if patch_centers is None:
cat = treecorr.Catalog(
cat_tc = treecorr.Catalog(
ra=ra[mask_arr],
dec=dec[mask_arr],
g1=g1[mask_arr],
Expand All @@ -383,7 +386,7 @@ def build_catalog(self, cat_type, key, npatch=None, patch_centers=None, square_s
npatch=npatch
)
else:
cat = treecorr.Catalog(
cat_tc = treecorr.Catalog(
ra=ra[mask_arr],
dec=dec[mask_arr],
g1=g1[mask_arr],
Expand All @@ -395,7 +398,7 @@ def build_catalog(self, cat_type, key, npatch=None, patch_centers=None, square_s
)

self.catalogs_dict.update(
{key: cat}
{key: cat_tc}
)

def delete_catalog(self, key):
Expand Down Expand Up @@ -515,16 +518,18 @@ def build_cat_to_compute_rho(self, path_cat_star, catalog_id='', square_size=Fal
HDU number of input FITS file, default is 1
"""

self.catalogs.read_shear_cat(path_gal=None, path_psf=path_cat_star, hdu=hdu)
psf_cat = self.catalogs.read_shear_cat(path_gal=None, path_psf=path_cat_star, hdu=hdu)

if self.verbose:
print("Building catalogs...")

self.catalogs.build_catalog(cat_type='psf', key='psf_'+catalog_id, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf', key='psf_'+catalog_id, square_size=square_size, mask=mask)
patch_centers = self.catalogs.catalogs_dict['psf_'+catalog_id].patch_centers
self.catalogs.build_catalog(cat_type='psf_error', key='psf_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf_error', key='psf_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
if self.use_eta:
self.catalogs.build_catalog(cat_type='psf_size_error', key='psf_size_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf_size_error', key='psf_size_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)

del psf_cat

if self.verbose:
print("Catalogs successfully built...")
Expand Down Expand Up @@ -806,29 +811,33 @@ def build_cat_to_compute_tau(self, path_cat, cat_type, catalog_id='', square_siz
"""

if cat_type=="psf":
self.catalogs.read_shear_cat(path_gal=None, path_psf=path_cat, hdu=hdu)
psf_cat = self.catalogs.read_shear_cat(path_gal=None, path_psf=path_cat, hdu=hdu)

if self.verbose:
print("Building catalogs...")

self.catalogs.build_catalog(cat_type='psf', key='psf_'+catalog_id, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf', key='psf_'+catalog_id, square_size=square_size, mask=mask)
patch_centers = self.catalogs.catalogs_dict['psf_'+catalog_id].patch_centers
self.catalogs.build_catalog(cat_type='psf_error', key='psf_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf_error', key='psf_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
if self.use_eta:
self.catalogs.build_catalog(cat_type='psf_size_error', key='psf_size_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)
self.catalogs.build_catalog(cat=psf_cat, cat_type='psf_size_error', key='psf_size_error_'+catalog_id, patch_centers=patch_centers, square_size=square_size, mask=mask)

del psf_cat

else:
self.catalogs.read_shear_cat(path_gal=path_cat, path_psf=None, hdu=hdu)
gal_cat = self.catalogs.read_shear_cat(path_gal=path_cat, path_psf=None, hdu=hdu)

if self.verbose:
print("Building catalog...")

try:
patch_centers = self.catalogs.catalogs_dict['psf_'+catalog_id].patch_centers
except KeyError:
print("Warning, you should build psf catalog before galaxy catalog.")
warnings.warn("You should build psf catalog before galaxy catalog.")
patch_centers = None
self.catalogs.build_catalog(cat_type='gal', key='gal_'+catalog_id, patch_centers=patch_centers)
self.catalogs.build_catalog(cat=gal_cat, cat_type='gal', key='gal_'+catalog_id, patch_centers=patch_centers)

del gal_cat

if self.verbose:
print("Catalogs successfully built...")
Expand Down