RAIL_Lephare example on LSST data

Author: Raphael Shirley, Edited by Tianqing Zhang

Last successfully run: May 16, 2025

This example notebook uses synthetic data produced by PZFlow in combination with several predefined SED templates and filter definition files.

NOTE: this notebook takes a lot of memory and may not be able to run on your laptop

Note: If you’re planning to run this in a notebook, you may want to use interactive mode instead. See LePhare_LSST.ipynb in the interactive_examples/estimation_examples/ folder for a version of this notebook in interactive mode.

from rail.estimation.algos.lephare import LephareInformer, LephareEstimator
import numpy as np
import tables_io
import lephare as lp
from rail.core.stage import RailStage
from rail.core.data import TableHandle
from rail.utils.path_utils import RAILDIR

import matplotlib.pyplot as plt
import os

LEPHAREDIR is being set to the default cache directory which is being created at:
/home/runner/.cache/lephare/data
More than 1Gb may be written there.
LEPHAREWORK is being set to the default cache directory:
/home/runner/.cache/lephare/work

Here we load previously created synthetic data

trainFile = os.path.join(RAILDIR, 'rail/examples_data/testdata/output_table_conv_train.hdf5')
testFile = os.path.join(RAILDIR, 'rail/examples_data/testdata/output_table_conv_test.hdf5')
traindata_io = tables_io.read(trainFile)
testdata_io = tables_io.read(testFile)

Retrieve all the required filter and template files

One could add or take out bandpasses by editing the configuration file.

lephare_config_file = os.path.join(RAILDIR, 'rail/examples_data/estimation_data/data/lsst.para')
lephare_config = lp.read_config(lephare_config_file)

lp.data_retrieval.get_auxiliary_data(keymap=lephare_config)

Number of keywords read in the config file: 86

Registry file downloaded and saved as data_registry.txt.

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Created directory: /home/runner/.cache/lephare/data/ext
Created directory: /home/runner/.cache/lephare/data/sed/STAR
Created directory: /home/runner/.cache/lephare/data/filt/lsst
Created directory: /home/runner/.cache/lephare/data/sed/QSO/SALVATO09
Created directory: /home/runner/.cache/lephare/data/sed/STAR/WD
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Created directory: /home/runner/.cache/lephare/data/sed/GAL/COSMOS_SED
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Created directory: /home/runner/.cache/lephare/data/sed/STAR/BD
Created directory: /home/runner/.cache/lephare/data/examples
Created directory: /home/runner/.cache/lephare/data/sed/STAR/LAGET
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We use the inform stage to create the library of SEDs with various redshifts, extinction parameters, and reddening values. This typically takes ~3-4 minutes.

inform_lephare = LephareInformer.make_stage(
    name="inform_Lephare",
    nondetect_val=np.nan,
    model="lephare.pkl",
    hdf5_groupname="",
    # Use a sparse redshift grid to speed up the notebook
    zmin=0,
    zmax=3,
    nzbins=31,
    lephare_config = lephare_config # this is important if you want to modify your default setup with the parameter file
)
inform_lephare.inform(traindata_io)

Inserting handle into data store.  input: None, inform_Lephare
rail_lephare is setting the Z_STEP config to 0.1,0.0,3.0 based on the informer params.
User defined LEPHAREDIR is set. Code runs depend on all required
auxiliary data being present at /home/runner/.cache/lephare/data.
User defined LEPHAREWORK is set. All intermediate files will be written to:
 /home/runner/.cache/lephare/runs/inform_Lephare
# NAME                        IDENT      Lbda_mean Lbeff(Vega)       FWHM     AB-cor    TG-cor      VEGA M_sun(AB)   CALIB      Lb_eff    Fac_corr
total_u.pb                    1             0.3717      0.3767      0.0446    0.6034   -0.2606  -20.8561    6.2709       0      0.3703      1.0000
total_g.pb                    2             0.4844      0.4746      0.1423   -0.0854   -0.2506  -20.7225    5.0868       0      0.4767      1.0000
total_r.pb                    3             0.6249      0.6162      0.1383    0.1515    0.2644  -21.5241    4.6488       0      0.6194      1.0000
total_i.pb                    4             0.7579      0.7517      0.1278    0.3729    0.5879  -22.1705    4.5353       0      0.7539      1.0000
total_z.pb                    5             0.8692      0.8670      0.1047    0.5178    0.7624  -22.6171    4.5165       0      0.8669      1.0000
total_y.pb                    6             0.9768      0.9732      0.0898    0.5512    0.7770  -22.9043    4.5084       0      0.9744      1.0000
#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file     :
# Library type     : STAR
# STAR_SED    :/home/runner/.cache/lephare/data/sed/STAR/STAR_MOD_ALL.list
# STAR_LIB    :LSST_STAR_BIN
# STAR_LIB doc:/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_STAR_BIN.doc
# STAR_FSCALE :0.0000
#######################################
Number of SED in the list 254

WRONG NUMBER OF ARGUMENTS FOR OPTION MOD_EXTINC
We have 2 instead of 8
Use default value 0,0 for all filters
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file     :
# Filter file     : filter_lsst
# Magnitude type     : AB
# COSMOLOGY   :70.0000,0.3000,0.7000
# STAR_LIB_IN    :/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_STAR_BIN(.doc & .bin)
# STAR_LIB_OUT   :/home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_STAR_MAG(.doc & .bin)
# LIB_ASCII   YES
# CREATION_DATE Mon Jun  1 15:08:37 2026
#############################################
#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file     :
# Library type     : GAL
# GAL_SED    :/home/runner/.cache/lephare/data/sed/GAL/COSMOS_SED/COSMOS_MOD.list
# GAL_LIB    :LSST_GAL_BIN
# GAL_LIB doc:/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_GAL_BIN.doc
# GAL_LIB phys:/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_GAL_BIN.phys
# SEL_AGE    :none
# GAL_FSCALE :1.0000
# AGE_RANGE   0.0000 15000000000.0000
#######################################
Number of SED in the list 31
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file     :
# Filter file     : filter_lsst
# Magnitude type     : AB
# GAL_LIB_IN    :/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_GAL_BIN(.doc & .bin)
# GAL_LIB_OUT   :/home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_GAL_MAG(.doc & .bin)
# Z_STEP   :0.0100 0.0000 7.0000
# COSMOLOGY   :70.0000,0.3000,0.7000
# EXTINC_LAW   :SMC_prevot.dat SB_calzetti.dat SB_calzetti_bump1.dat SB_calzetti_bump2.dat
# MOD_EXTINC   :18 26 26 33 26 33 26 33
# EB_V   :0.0000 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.5000
# EM_LINES   EMP_UV
# EM_DISPERSION   0.5000,0.7500,1.0000,1.5000,2.0000,
# LIB_ASCII   YES
# CREATION_DATE Mon Jun  1 15:08:38 2026
#############################################

#######################################
# It s translating SEDs to binary library #
# with the following options :
# Config file     :
# Library type     : QSO
# QSO_SED    :/home/runner/.cache/lephare/data/sed/QSO/SALVATO09/AGN_MOD.list
# QSO_LIB    :LSST_QSO_BIN
# QSO_LIB doc:/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_QSO_BIN.doc
# QSO_FSCALE :1.0000
#######################################
Number of SED in the list 30
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :
# Config file     :
# Filter file     : filter_lsst
# Magnitude type     : AB
# QSO_LIB_IN    :/home/runner/.cache/lephare/runs/inform_Lephare/lib_bin/LSST_QSO_BIN(.doc & .bin)
# QSO_LIB_OUT   :/home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_QSO_MAG(.doc & .bin)
# Z_STEP   :0.0100 0.0000 7.0000
# COSMOLOGY   :70.0000,0.3000,0.7000
# EXTINC_LAW   :SB_calzetti.dat
# MOD_EXTINC   :0 1000
# EB_V   :0.0000 0.1000 0.2000 0.3000 # LIB_ASCII   YES
# CREATION_DATE Mon Jun  1 15:52:28 2026
#############################################

Using user columns from input table assuming they are in the standard order.
Processing 70 objects with 6 bands
#######################################
# PHOTOMETRIC REDSHIFT with OPTIONS   #
# Config file            :
# CAT_IN                 : undefined
# CAT_OUT                : zphot.out
# CAT_LINES              : 0 1000000000
# PARA_OUT               : /home/runner/.cache/lephare/data/examples/output.para
# INP_TYPE               : M
# CAT_FMT[0:MEME 1:MMEE] : 0
# CAT_MAG                : AB
# ZPHOTLIB               : LSST_STAR_MAG LSST_GAL_MAG LSST_QSO_MAG
# FIR_LIB                :
# FIR_LMIN               : 7.000000
# FIR_CONT               : -1.000000
# FIR_SCALE              : -1.000000
# FIR_FREESCALE          : YES
# FIR_SUBSTELLAR         : NO
# ERR_SCALE              : 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000
# ERR_FACTOR             : 1.500000
# GLB_CONTEXT            : 63
# FORB_CONTEXT           : -1
# DZ_WIN                 : 1.000000
# MIN_THRES              : 0.020000
# MAG_ABS                : -24.000000 -5.000000
# MAG_ABS_AGN            : -30.000000 -10

.000000
# MAG_REF                : 3
# NZ_PRIOR               : -1 -1
# Z_INTERP               : YES
# Z_METHOD               : BEST
# MABS_METHOD            : 1
# MABS_CONTEXT           : 63
# MABS_REF               : 1
# AUTO_ADAPT             : NO
# ADAPT_BAND             : 5
# ADAPT_LIM              : 1.500000 23.000000
# ADAPT_ZBIN             : 0.010000 6.000000
# ZFIX                   : NO
# SPEC_OUT               : NO
# CHI_OUT                : NO
# PDZ_OUT                : test
#######################################
Reading input librairies ...
Read lib
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_QSO_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_QSO_MAG.bin
 Done with the library reading with 84120 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_GAL_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_GAL_MAG.bin
 Done with the library reading with 1044490 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_STAR_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_STAR_MAG.bin
 Done with the library reading with 1044744 SED read.
Read lib out
Read filt
# NAME                        IDENT      Lbda_mean Lbeff(Vega)       FWHM     AB-cor      VEGA   CALIB    Fac_corr
total_u.pb                    1             0.3717      0.3767      0.0446    0.6034  -20.8600       0      1.0000
total_g.pb                    2             0.4844      0.4746      0.1423   -0.0854  -20.7200       0      1.0000
total_r.pb                    3             0.6249      0.6162      0.1383    0.1515  -21.5200       0      1.0000
total_i.pb                    4             0.7579      0.7517      0.1278    0.3729  -22.1700       0      1.0000
total_z.pb                    5             0.8692      0.8670      0.1047    0.5178  -22.6200       0      1.0000
total_y.pb                    6             0.9768      0.9732      0.0898    0.5512  -22.9000       0      1.0000
Offsets from auto-adapt: 0.0,0.0,0.0,0.0,0.0,0.0

Inserting handle into data store.  model_inform_Lephare: inprogress_lephare.pkl, inform_Lephare

<rail.core.data.ModelHandle at 0x7f6c8d0a3580>

Now we take the sythetic test data, and find the best fits from the library. This results in a PDF, zmode, and zmean for each input test data. Takes ~2 minutes to run on 1500 inputs.

estimate_lephare = LephareEstimator.make_stage(
    name="test_Lephare",
    nondetect_val=np.nan,
    model=inform_lephare.get_handle("model"),
    hdf5_groupname="",
    aliases=dict(input="test_data", output="lephare_estim"),
)

lephare_estimated = estimate_lephare.estimate(testdata_io)

Inserting handle into data store.  test_data: None, test_Lephare
Inserting handle into data store.  model_inform_Lephare: <class 'rail.core.data.ModelHandle'> lephare.pkl, (wd), test_Lephare
User defined LEPHAREDIR is set. Code runs depend on all required
auxiliary data being present at /home/runner/.cache/lephare/data.
User defined LEPHAREWORK is set. All intermediate files will be written to:
 /home/runner/.cache/lephare/runs/inform_Lephare
Process 0 running estimator on chunk 0 - 1,500
Using user columns from input table assuming they are in the standard order.
Processing 1500 objects with 6 bands
#######################################
# PHOTOMETRIC REDSHIFT with OPTIONS   #
# Config file            :
# CAT_IN                 : undefined
# CAT_OUT                : zphot.out
# CAT_LINES              : 0 1000000000
# PARA_OUT               : /home/runner/.cache/lephare/data/examples/output.para
# INP_TYPE               : M
# CAT_FMT[0:MEME 1:MMEE] : 0
# CAT_MAG                : AB
# ZPHOTLIB               : LSST_STAR_MAG LSST_GAL_MAG LSST_QSO_MAG
# FIR_LIB                :
# FIR_LMIN               : 7.000000
# FIR_CONT               : -1.000000
# FIR_SCALE              : -1.000000
# FIR_FREESCALE          : YES
# FIR_SUBSTELLAR         : NO
# ERR_SCALE              : 0.020000 0.020000 0.020000 0.020000 0.020000 0.020000
# ERR_FACTOR             : 1.500000
# GLB_CONTEXT            : 63
# FORB_CONTEXT           : -1
# DZ_WIN                 : 1.000000
# MIN_THRES              : 0.020000
# MAG_ABS                : -24.000000 -5.000000
# MAG_ABS_AGN            : -30.000000 -10

AUTO_ADAPT is set to YES. Computing offsets.

.000000
# MAG_REF                : 3
# NZ_PRIOR               : -1 -1
# Z_INTERP               : YES
# Z_METHOD               : BEST
# MABS_METHOD            : 1
# MABS_CONTEXT           : 63
# MABS_REF               : 1
# AUTO_ADAPT             : NO
# ADAPT_BAND             : 5
# ADAPT_LIM              : 1.500000 23.000000
# ADAPT_ZBIN             : 0.010000 6.000000
# ZFIX                   : NO
# SPEC_OUT               : NO
# CHI_OUT                : NO
# PDZ_OUT                : test
#######################################
Reading input librairies ...
Read lib
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_QSO_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_QSO_MAG.bin
 Done with the library reading with 84120 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_GAL_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_GAL_MAG.bin
 Done with the library reading with 1044490 SED read.
Number of keywords to be read in the doc: 13
Number of keywords read at the command line (excluding -c config): 0
Reading keywords from /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_STAR_MAG.doc
Number of keywords read in the config file: 16
Keyword NUMBER_ROWS not provided
Keyword NUMBER_SED not provided
Keyword Z_FORM not provided
Reading library: /home/runner/.cache/lephare/runs/inform_Lephare/lib_mag/LSST_STAR_MAG.bin
 Done with the library reading with 1044744 SED read.
Read lib out
Read filt
# NAME                        IDENT      Lbda_mean Lbeff(Vega)       FWHM     AB-cor      VEGA   CALIB    Fac_corr
total_u.pb                    1             0.3717      0.3767      0.0446    0.6034  -20.8600       0      1.0000
total_g.pb                    2             0.4844      0.4746      0.1423   -0.0854  -20.7200       0      1.0000
total_r.pb                    3             0.6249      0.6162      0.1383    0.1515  -21.5200       0      1.0000
total_i.pb                    4             0.7579      0.7517      0.1278    0.3729  -22.1700       0      1.0000
total_z.pb                    5             0.8692      0.8670      0.1047    0.5178  -22.6200       0      1.0000
total_y.pb                    6             0.9768      0.9732      0.0898    0.5512  -22.9000       0      1.0000
# Offsets added to the modeled magnitudes (or substracted to the observed): 0.0,0.0,0.0,0.0,0.0,0.0

Source 113 // Band 0 removed to improve the chi2, with old and new chi2 1703.4709 470.1358
Source 425 // Band 5 removed to improve the chi2, with old and new chi2 1233.4035 0.0636
Source 449 // Band 0 removed to improve the chi2, with old and new chi2 1769.2671 535.9139
Source 449 // Band 1 removed to improve the chi2, with old and new chi2 1769.2671 229.0725
Source 492 // Band 1 removed to improve the chi2, with old and new chi2 3289.6386 2056.3348
Source 492 // Band 0 removed to improve the chi2, with old and new chi2 3289.6386 823.0952
Source 789 // Band 5 removed to improve the chi2, with old and new chi2 1213.6508 1.6393
Source 898 // Band 1 removed to improve the chi2, with old and new chi2 2183.3132 1054.9139
Source 898 // Band 0 removed to improve the chi2, with old and new chi2 2183.3132 0.1236
Source 1140 // Band 5 removed to improve the chi2, with old and new chi2 566.6393 0.3919
Source 1160 // Band 1 removed to improve the chi2, with old and new chi2 2671.9901 1439.0446
Source 1160 // Band 0 removed to improve the chi2, with old and new chi2 2671.9901 206.3085
Source 1251 // Band 2 removed to improve the chi2, with old and new chi2 3699.9761 2466.6396
Source 1251 // Band 1 removed to improve the chi2, with old and new chi2 3699.9761 1233.3106
Source 1302 // Band 5 removed to improve the chi2, with old and new chi2 1236.4347 3.1435
Source 1427 // Band 5 removed to improve the chi2, with old and new chi2 1151.7123 0.0561
Source 1451 // Band 5 removed to improve the chi2, with old and new chi2 1227.1517 0.0000

Inserting handle into data store.  output_test_Lephare: inprogress_output_test_Lephare.hdf5, test_Lephare

An example lephare PDF and comparison to the true value

indx = 0
zgrid = np.linspace(0,3,31)
plt.plot(zgrid, np.squeeze(lephare_estimated.data[indx].pdf(zgrid)), label='Estimated PDF')
plt.axvline(x=testdata_io['redshift'][indx], color='r', label='True redshift')
plt.legend()
plt.xlabel('z')
plt.show()

More example fits

indxs = [8, 16, 32, 64, 128, 256, 512, 1024]
zgrid = np.linspace(0,3,31)
fig, axs = plt.subplots(2,4, figsize=(20,6))
for i, indx in enumerate(indxs):
    ax = axs[i//4, i%4]
    ax.plot(zgrid, np.squeeze(lephare_estimated.data[indx].pdf(zgrid)), label='Estimated PDF')
    ax.axvline(x=testdata_io['redshift'][indx], color='r', label='True redshift')
    ax.set_xlabel('z')

Histogram of the absolute difference between lephare estimate and true redshift

estimate_diff_from_truth = np.abs(lephare_estimated.data.ancil['zmode'] - testdata_io['redshift'])

plt.figure()
plt.hist(estimate_diff_from_truth, 100)
plt.xlabel('abs(z_estimated - z_true)')
plt.show()

Let’s compare the estimated median redshift vs. the true redshift in a scatter plot.

truez = testdata_io['redshift']

plt.figure(figsize=(8,8))
plt.scatter(truez, lephare_estimated.data.median(), s=3)
plt.plot([-1,3],[-1,3], 'k--')
plt.xlim([-0.1,3])
plt.ylim([-0.1,3])

plt.xlabel("redshift", fontsize=12)
plt.ylabel("z mode", fontsize=12)

Text(0, 0.5, 'z mode')