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Issue/8/improve informer and estimator parameter setting (#10)
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* Estimator runs but bugs remain

zmode doesnt seem to be added to output.
Still questions over what stages should go in the inform or estimate stage

* Estimator runs through goldenspike notebook

Still issues with params. Performance seems comparable to BPZ. Added example notebook.

* Moved params into class config object

This allows overwriting through the inform or estimate init

---------

Co-authored-by: Raphael Shirley <[email protected]>
Co-authored-by: drewoldag <[email protected]>
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@raphaelshirley @drewoldag
3 people authored Apr 5, 2024
1 parent 7760d56 commit 9e01da0
Showing 1 changed file with 82 additions and 37 deletions.
119 changes: 82 additions & 37 deletions src/rail/estimation/algos/lephare.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from rail.estimation.estimator import CatEstimator, CatInformer
from rail.core.common_params import SHARED_PARAMS
from ceci.config import StageParameter as Param
import os
import lephare as lp
import numpy as np
Expand All @@ -9,7 +10,7 @@
class LephareInformer(CatInformer):
"""Inform stage for LephareEstimator
This class will set templates and filters required for photoz estimation
This class will set templates and filters required for photoz estimation.
"""

name = "LephareInformer"
Expand All @@ -24,16 +25,63 @@ class LephareInformer(CatInformer):
err_bands=SHARED_PARAMS,
ref_band=SHARED_PARAMS,
redshift_col=SHARED_PARAMS,
lephare_config_file=Param(
str,
"{}/{}".format(os.path.dirname(os.path.abspath(__file__)), "lsst.para"),
msg="Path to the lephare config in .para format",
),
star_sed=Param(
str,
"$LEPHAREDIR/examples/STAR_MOD_ALL.list",
msg="Path to text file containing list of star SED templates",
),
qso_sed=Param(
str,
"$LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list",
msg="Path to text file containing list of galaxy SED templates",
),
gal_sed=Param(
str,
"$LEPHAREDIR/examples/COSMOS_MOD.list",
msg="Path to text file containing list of quasar SED templates",
),
star_mag_dict=Param(
dict,
dict(
lib_ascii="YES",
),
msg="Dictionary of values sent to MagGal for stars",
),
gal_mag_dict=Param(
dict,
dict(
lib_ascii="YES",
mod_extinc="18,26,26,33,26,33,26,33",
extinc_law=(
"SMC_prevot.dat,SB_calzetti.dat,"
"SB_calzetti_bump1.dat,SB_calzetti_bump2.dat"
),
em_lines="EMP_UV",
em_dispersion="0.5,0.75,1.,1.5,2.",
),
msg="Dictionary of values sent to MagGal for galaxies",
),
qso_mag_dict=Param(
dict,
dict(
lib_ascii="YES",
mod_extinc="0,1000",
eb_v="0.,0.1,0.2,0.3",
extinc_law="SB_calzetti.dat",
),
msg="Dictionary of values sent to MagGal for quasars",
),
)

def __init__(self, args, comm=None):
"""Init function, init config stuff (COPIED from rail_bpz)"""
CatInformer.__init__(self, args, comm=comm)
# Default local parameters
self.config_file = "{}/{}".format(
os.path.dirname(os.path.abspath(__file__)), "lsst.para"
)
self.lephare_config = lp.read_config(self.config_file)
self.lephare_config = lp.read_config(self.config["lephare_config_file"])

def _set_config(self, lephare_config):
"""Update the lephare config
Expand All @@ -48,7 +96,7 @@ def _set_config(self, lephare_config):
def _create_filter_library(self):
"""Make the filter library files in lephare format"""
# load filters from config file
filterLib = lp.FilterSvc.from_config(self.config_file)
filterLib = lp.FilterSvc.from_config(self.config["lephare_config_file"])
# Get location to store filter files
filter_output = os.path.join(
os.environ["LEPHAREWORK"], "filt", self.lephare_config["FILTER_FILE"].value
Expand All @@ -64,9 +112,9 @@ def _create_sed_library(self):
We separately create the star, quasar and galaxy libraries.
"""
sedlib = lp.Sedtolib(config_keymap=self.lephare_config)
sedlib.run(typ="STAR", star_sed="$LEPHAREDIR/examples/STAR_MOD_ALL.list")
sedlib.run(typ="QSO", qso_sed="$LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list")
sedlib.run(typ="GAL", gal_sed="$LEPHAREDIR/examples/COSMOS_MOD.list")
sedlib.run(typ="STAR", star_sed=self.config["star_sed"])
sedlib.run(typ="GAL", gal_sed=self.config["gal_sed"])
sedlib.run(typ="QSO", qso_sed=self.config["qso_sed"])

def _create_mag_library(self):
"""Make the magnitudes library file in lephare format.
Expand All @@ -76,31 +124,15 @@ def _create_mag_library(self):
TODO: replace hardcoded config options with class config options.
"""
maglib = lp.MagGal(config_keymap=self.lephare_config)
maglib.run(typ="STAR", lib_ascii="YES")
maglib.run(
typ="QSO",
lib_ascii="YES",
mod_extinc="0,1000",
eb_v="0.,0.1,0.2,0.3",
extinc_law="SB_calzetti.dat",
)
maglib.run(
typ="GAL",
lib_ascii="YES",
mod_extinc="18,26,26,33,26,33,26,33",
extinc_law=(
"SMC_prevot.dat,SB_calzetti.dat,"
+ "SB_calzetti_bump1.dat,SB_calzetti_bump2.dat"
),
em_lines="EMP_UV",
em_dispersion="0.5,0.75,1.,1.5,2.",
)
maglib.run(typ="STAR", **self.config["star_mag_dict"])
maglib.run(typ="GAL", **self.config["gal_mag_dict"])
maglib.run(typ="QSO", **self.config["qso_mag_dict"])

def run(self):
"""Run rail_lephare inform stage.
This is the basic informer which takes the config and templates and
makes the inputs required for the run.
This informer takes the config and templates and makes the inputs
required for the run.
In addition to the three lephare stages making the filter, sed, and
magnitude libraries we also do some tasks required by all rail inform
Expand All @@ -124,7 +156,7 @@ def run(self):
self.szs = training_data[self.config.redshift_col]

# Give principle inform config 'model' to instance.
self.model = dict(config_file=self.config_file)
self.model = dict(lephare_config_file=self.config["lephare_config_file"])
self.add_data("model", self.model)


Expand All @@ -145,10 +177,27 @@ class LephareEstimator(CatEstimator):
ref_band=SHARED_PARAMS,
err_bands=SHARED_PARAMS,
redshift_col=SHARED_PARAMS,
lephare_config_file=Param(
str,
"{}/{}".format(os.path.dirname(os.path.abspath(__file__)), "lsst.para"),
msg="Path to the lephare config in .para format",
),
)

def __init__(self, args, comm=None):
CatEstimator.__init__(self, args, comm=comm)
self.lephare_config = lp.read_config(self.config["lephare_config_file"])
self.photz = lp.PhotoZ(self.lephare_config)

def _estimate_pdf(self, onesource):
"""Return the pdf of a single source.
Do we want to resample on RAIL z grid?
"""
# Check this is the best way to access pdf
pdf = onesource.pdfmap[11] # 11 = Bayesian galaxy redshift
# return the PDF as an array alongside lephare native zgrid
return np.array(pdf.vPDF), np.array(pdf.xaxis)

# Default local parameters
self.config_file = "{}/{}".format(
Expand Down Expand Up @@ -189,9 +238,6 @@ def _process_chunk(self, start, end, data, first):
pdfs = [] # np.zeros((ng, nz))
zmode = np.zeros(ng)
zmean = np.zeros(ng)
# What are tb and todds?
# tb = np.zeros(ng)
# todds = np.zeros(ng)
zgrid = self.zgrid

# Loop over all ng galaxies!
Expand Down Expand Up @@ -220,8 +266,7 @@ def _process_chunk(self, start, end, data, first):
for i in range(ng):
pdf, zgrid = self._estimate_pdf(photozlist[i])
pdfs.append(pdf)
# Take median incase multiple probability densities are equal
# TODO: why is that happening?
# Take median in case multiple probability densities are equal
zmode[i] = np.median(
zgrid[np.where(pdfs[i] == np.max(pdfs[i]))[0].astype(int)]
)
Expand Down

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