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salim+18 and README_full #15

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salim+18 and README_full #15

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14 changes: 14 additions & 0 deletions examples/AGN_MOD.list
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SALVATO09/BQSO1_template_norm.sed A
SALVATO09/I22491_template_norm.sed A
SALVATO09/M82_template_norm.sed A
SALVATO09/Mrk231_template_norm.sed A
SALVATO09/QSO1_template_norm.sed A
SALVATO09/QSO2_template_norm.sed A
SALVATO09/Sey18_template_norm.sed A
SALVATO09/Sey2_template_norm.sed A
SALVATO09/Spi4_template_norm.sed A
SALVATO09/TQSO1_template_norm.sed A
SALVATO09/hybrid_gal20_agn80.sed A
SALVATO09/hybrid_gal50_agn50.sed A
SALVATO09/hybrid_gal80_agn20.sed A
SALVATO09/QSO_High_lum_DR2-032_t0_ext.spec A
2 changes: 1 addition & 1 deletion examples/COSMOS.para
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Expand Up @@ -102,7 +102,7 @@ ZPHOTLIB CE_COSMOS,STAR_COSMOS,QSO_COSMOS # Library used for Chi2 (max:3)
#------------------ Output catalog Name ---------------------------------
CAT_OUT zphot.out # Output catalog (-> working directory)
PARA_OUT $LEPHAREDIR/examples/output.para # Ouput parameters (full path)
VERBOSE NO # Display the templates/objects which are computed
VERBOSE YES # Display the templates/objects which are computed
PDZ_TYPE BAY_ZG # PDZ in output [def-BAY]. BAY_ZG sum all probabilities at a given z. MIN_ZG takes exp(-chi2_min/2) at a given z, with chi2_min the minimum chi2 at this z.
# You can add and combine BAY_ZG,BAY_ZQ,MIN_ZG,MIN_ZQ,MASS,SFR,SSFR,AGE
PDZ_OUT test # root of the pdz output files [def-NONE]
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132 changes: 70 additions & 62 deletions examples/README_full
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#! /bin/csh


# Location of the code
export LEPHAREDIR='/home/oilbert/LEPHARE/'
# Where to store the libraries (if not created with the make file, you must have a $LEPHAREWORK/filt, $LEPHAREWORK/lib_bin, $LEPHAREWORK/lib_mag
# Indicate the directory containing all the LePHARE data, as the templates/filters/attenutation
export LEPHAREDIR='/Users/ilbert/LEPHARE-data/'
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I guess this could be relative to make it run on any system but it is clear this needs to be changed.

# Where to store the libraries created by filter/sedtolib/mag_gal
export LEPHAREWORK='WORK'
# Shift to apply to the photometry (systematic offsets) for zphota
export SHIFT="0.051121,-0.016466,-0.084605,-0.058664,-0.039816,-0.053934,-0.072388,-0.023517,-0.001748,0.013681,-0.036044,0.041802,0.017099,0.006699,0.006539,0.021207,0.063196,0.015433,-0.163286,0.032249,0.039840,0.050121,0.025781,0.012588,0.052423,0.034833,0.018244,-0.024611,0.000000,0.000000"
# Maximum number of threads
export OMP_NUM_THREADS='25'
# Maximum number of threads. Don't put more than available. It could result in a strange behaviour of the code.
export OMP_NUM_THREADS='10'


#############
## LIBRARY

# Read the filters and compile them within one file stored in $WORK/filt
$LEPHAREDIR/bin/filter -c COSMOS.para
# read a second set of filter which could be used to compute predicted magnitudes in some bands not present in the dataset (useful for simulation)
$LEPHAREDIR/bin/filter -c COSMOS.para -FILTER_LIST euclid/EUC_riz.lowres,euclid/EUC_Y.lowres,euclid/EUC_J.lowres,euclid/EUC_H.lowres -FILTER_CALIB 0 -FILTER_FILE filter_add
filter -c COSMOS.para
# Read a second set of filters which could be used to compute predicted magnitudes in some bands not present in the dataset (useful to simulate data)
filter -c COSMOS.para --FILTER_LIST euclid/EUC_riz.lowres,euclid/EUC_Y.lowres,euclid/EUC_J.lowres,euclid/EUC_H.lowres --FILTER_CALIB 0 --FILTER_FILE filter_add

# Case of the galaxy templates used in Ilbert 2013
# Generate the library of predicted magnitudes for galaxy templates
# Case of the COSMOS templates used in Ilbert 2013
# Read the galaxy templates and store them in $WORK/lib_bin
$LEPHAREDIR/bin/sedtolib -c COSMOS.para -t G -GAL_SED COSMOS_MOD.list -GAL_LIB LIB_VISTA
sedtolib -c COSMOS.para -t G --GAL_SED COSMOS_MOD.list --GAL_LIB LIB_VISTA
# Use the galaxy templates + filters to derive a library of predicted magnitudes and store in $WORK/lib_mag
# Case emission lines correlated to UV light + free factor in scaling the lines
$LEPHAREDIR/bin/mag_gal -c COSMOS.para -t G -GAL_LIB_IN LIB_VISTA -GAL_LIB_OUT VISTA_COSMOS_FREE -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.
# Case emission lines correlated to UV light + no free factor in scaling the lines
$LEPHAREDIR/bin/mag_gal -c COSMOS.para -t G -GAL_LIB_IN LIB_VISTA -GAL_LIB_OUT VISTA_COSMOS -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 1.
# Generate emission lines correlated to UV light + free factor in scaling the lines by a factor 2
mag_gal -c COSMOS.para -t G --GAL_LIB_IN LIB_VISTA --GAL_LIB_OUT VISTA_COSMOS_FREE --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.
# Generate emission lines correlated to UV light + no free factor in scaling the lines
mag_gal -c COSMOS.para -t G --GAL_LIB_IN LIB_VISTA --GAL_LIB_OUT VISTA_COSMOS --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 1.

# STAR
# Generate the library of predicted magnitudes for stars
# Read the stellar templates and store them in $WORK/lib_bin
$LEPHAREDIR/bin/sedtolib -c COSMOS.para -t S -STAR_SED STAR_MOD_ALL.list
sedtolib -c COSMOS.para -t S --STAR_SED STAR_MOD_ALL.list
# Use the stellar templates + filters to derive a library of predicted magnitudes and store in $WORK/lib_mag
$LEPHAREDIR/bin/mag_gal -c COSMOS.para -t S -LIB_ASCII YES -STAR_LIB_OUT ALLSTAR_COSMOS
mag_gal -c COSMOS.para -t S --LIB_ASCII YES --STAR_LIB_OUT ALLSTAR_COSMOS

# Generate the library of predicted magnitudes for AGN templates
# AGN from Salvato 2009
# Read the AGN templates and store them in $WORK/lib_bin
$LEPHAREDIR/bin/sedtolib -c COSMOS.para -t Q -QSO_SED $LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list
sedtolib -c COSMOS.para -t Q --QSO_SED AGN_MOD.list
# Use the AGN templates + filters to derive a library of predicted magnitudes and store in $WORK/lib_mag
$LEPHAREDIR/bin/mag_gal -c COSMOS.para -t Q -MOD_EXTINC 0,1000 -EB_V 0.,0.1,0.2,0.3 -EXTINC_LAW SB_calzetti.dat -LIB_ASCII NO


# BC03 library as Ilbert+2015
# Library to derive physical parameters
# Read the galaxy BC03 templates and store them in $WORK/lib_bin
$LEPHAREDIR/bin/sedtolib -c COSMOS.para -t G -GAL_SED BC03COMB_MOD.list -GAL_LIB LIB_COMB -SEL_AGE AGE_BC03COMB.dat
# Use the galaxy BC03 templates + filters to derive a library of predicted magnitudes and store in $WORK/lib_mag
# Use the "physical" recipes to generate the lines
# Add the dust component with one template of Bethermin+12
$LEPHAREDIR/bin/mag_gal -c COSMOS.para -t G -GAL_LIB_IN LIB_COMB -GAL_LIB_OUT BC03_COSMOS -MOD_EXTINC 3,12,3,12 -EXTINC_LAW SB_calzetti.dat,extlaw_0.9.dat -EB_V 0.,0.1,0.2,0.3,0.4,0.5,0.6,0.7 -Z_STEP 0.03,0,6 -EM_LINES PHYS -EM_DISPERSION 0.25,0.5,1,2,4 -ADD_DUSTEM YES
mag_gal -c COSMOS.para -t Q --MOD_EXTINC 0,1000 --EB_V 0.,0.1,0.2,0.3 --EXTINC_LAW SB_calzetti.dat --LIB_ASCII NO



Expand All @@ -58,61 +47,80 @@ $LEPHAREDIR/bin/mag_gal -c COSMOS.para -t G -GAL_LIB_IN LIB_COMB -GAL_LIB_OUT


# Compute the photo-z and derive the adapation of the zero-points
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT zphot_vista_adapt.out -ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT YES
# Compute the photo-z without the adapation of the zero-points and applying the shifts given in keyword
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT zphot_vista_shift.out -ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO -APPLY_SYSSHIFT $SHIFT -PDZ_OUT zphot_vista_shift -PDZ_TYPE BAY_ZG
# No emission lines
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT zphot_vista_noline.out -ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS -ADD_EMLINES 0,0 -AUTO_ADAPT NO -APPLY_SYSSHIFT $SHIFT
# No shifts
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT zphot_vista_noadapt.out -ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT zphot_vista_adapt.out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT YES

# Extract Id*.spec and Id*.chi for few sources
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT zphot_vista_select.out -ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO -APPLY_SYSSHIFT $SHIFT -PDZ_OUT NONE -PDZ_TYPE BAY_ZG -CAT_LINES 12000,12010 -SPEC_OUT YES

# Derive the stellar masses
$LEPHAREDIR/bin/zphota -c COSMOS.para -CAT_IN COSMOS.in -CAT_OUT masses.out -ZPHOTLIB BC03_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO -APPLY_SYSSHIFT $SHIFT -ZFIX YES -PARA_OUT output_mass.para
# Compute the photo-z without the adapation of the zero-points and applying the shifts given in keyword
# Assume that shifts are derived previously. Shifts will be substracted to apparent magnitudes and to be used later using --APPLY_SYSSHIFT $SHIFT (to avoid rerunning auto-adapt)
export SHIFT="0.051121,-0.016466,-0.084605,-0.058664,-0.039816,-0.053934,-0.072388,-0.023517,-0.001748,0.013681,-0.036044,0.041802,0.017099,0.006699,0.006539,0.021207,0.063196,0.015433,-0.163286,0.032249,0.039840,0.050121,0.025781,0.012588,0.052423,0.034833,0.018244,-0.024611,0.000000,0.000000"
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT zphot_vista_shift.out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO --APPLY_SYSSHIFT $SHIFT --PDZ_OUT zphot_vista_shift --PDZ_TYPE BAY_ZG

# Test with no emission lines
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT zphot_vista_noline.out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS --ADD_EMLINES 0,0 --AUTO_ADAPT NO --APPLY_SYSSHIFT $SHIFT

#######################################################
# FIGURES
#######################################################
# Test with no offsets from auto-adapt
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT zphot_vista_noadapt.out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO

# Extract Id*.spec and Id*.chi for few sources
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT zphot_vista_select.out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO --APPLY_SYSSHIFT $SHIFT --PDZ_OUT NONE --PDZ_TYPE BAY_ZG --CAT_LINES 12000,12010 --SPEC_OUT YES

# Diadgnostics on the photo-z quality
# FIGURES
# Diagnostics on the photo-z quality
# results in figuresLPZ.pdf
python figuresLPZ.py zphot_vista_adapt.out

# Diadgnostics on the physical parameter quality
# results in figuresLPP.pdf
python figuresLPP.py masses.out

# Plot the best-fit templates
# Results in MULTISPEC.pdf
python spec.py Id*spec -d pdf



#################
###################################################
# PHYSICAL PARAMETERS
###################################################


# Generate the library of predicted magnitudes for galaxy templates to be used for physical parameters
# BC03 library
# Library to derive physical parameters
# Read the galaxy BC03 templates and store them in $WORK/lib_bin
sedtolib -c COSMOS.para -t G --GAL_SED BC03COMB_MOD.list --GAL_LIB LIB_COMB --SEL_AGE AGE_BC03COMB.dat
# Use the galaxy BC03 templates + filters to derive a library of predicted magnitudes and store in $WORK/lib_mag
# Example with a larger dz=0.03 step to save speed
# Use the "physical" recipes to generate the lines
# Add the dust component with one template of Bethermin+12
mag_gal -c COSMOS.para -t G --GAL_LIB_IN LIB_COMB --GAL_LIB_OUT BC03_COSMOS --MOD_EXTINC 0,12,0,12,0,12 --EXTINC_LAW SB_calzetti.dat,extlaw_0.9.dat,salim18.dat --EB_V 0.,0.1,0.2,0.3,0.4,0.5,0.6,0.7 --Z_STEP 0.03,0,6 --EM_LINES PHYS --EM_DISPERSION 1 --ADD_DUSTEM YES

# Derive the stellar masses. Can be done with BC03 templates.
zphota -c COSMOS.para --CAT_IN COSMOS.in --CAT_OUT masses.out --ZPHOTLIB BC03_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO --APPLY_SYSSHIFT $SHIFT --ZFIX YES --PARA_OUT output_mass.para

# FIGURES
# Diagnostics on the physical parameter quality
# results in figuresLPP.pdf
python figuresLPP.py masses.out



######################################
# LIR
# Far IR
#######################################################

# Filters including the FIR
$LEPHAREDIR/bin/filter -c HERSCHEL.para
filter -c HERSCHEL.para

#IR library from Dale
$LEPHAREDIR/bin/sedtolib -c HERSCHEL.para -t G -GAL_SED DALE.list -GAL_LIB LIB_DALE
$LEPHAREDIR/bin/mag_gal -c HERSCHEL.para -t G -GAL_LIB_IN LIB_DALE -GAL_LIB_OUT DALE_COSMOS -MOD_EXTINC 0,0
sedtolib -c HERSCHEL.para -t G --GAL_SED DALE.list --GAL_LIB LIB_DALE
mag_gal -c HERSCHEL.para -t G --GAL_LIB_IN LIB_DALE --GAL_LIB_OUT DALE_COSMOS --MOD_EXTINC 0,0

# BC03 SED
$LEPHAREDIR/bin/sedtolib -c HERSCHEL.para -t G -GAL_SED BC03COMB_MOD.list -GAL_LIB LIB_BC03CAL -SEL_AGE AGE_BC03COMB.dat
$LEPHAREDIR/bin/mag_gal -c HERSCHEL.para -t G -GAL_LIB_IN LIB_BC03CAL -GAL_LIB_OUT BC_COSMOS -MOD_EXTINC 1,14,1,14 -EXTINC_LAW SB_calzetti.dat,extlaw_0.9.dat -EB_V 0.,0.1,0.2,0.3,0.4,0.5,0.6,0.7
sedtolib -c HERSCHEL.para -t G --GAL_SED BC03COMB_MOD.list --GAL_LIB LIB_BC03CAL --SEL_AGE AGE_BC03COMB.dat
mag_gal -c HERSCHEL.para -t G --GAL_LIB_IN LIB_BC03CAL --GAL_LIB_OUT BC_COSMOS --MOD_EXTINC 1,14,1,14 --EXTINC_LAW SB_calzetti.dat,extlaw_0.9.dat --EB_V 0.,0.1,0.2,0.3,0.4,0.5,0.6,0.7

# Fit in FIR
$LEPHAREDIR/bin/zphota -c HERSCHEL.para -CAT_IN MIPS.in -CAT_OUT lumFIR.out -ZPHOTLIB BC_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO -ZFIX YES -FIR_LIB DALE_COSMOS -FIR_SUBSTELLAR YES -FIR_FREESCALE YES -FIR_CONT 8257536
zphota -c HERSCHEL.para --CAT_IN MIPS.in --CAT_OUT lumFIR.out --ZPHOTLIB BC_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO --ZFIX YES --FIR_LIB DALE_COSMOS --FIR_SUBSTELLAR YES --FIR_FREESCALE YES --FIR_CONT 8257536

# Fit in FIR with SED in output
$LEPHAREDIR/bin/zphota -c HERSCHEL.para -CAT_IN MIPS.in -CAT_OUT testFIR.out -ZPHOTLIB BC_COSMOS -ADD_EMLINES 0,100 -AUTO_ADAPT NO -ZFIX YES -FIR_LIB DALE_COSMOS -FIR_SUBSTELLAR YES -FIR_FREESCALE YES -FIR_CONT 8257536 -CAT_LINES 11980,12010 -SPEC_OUT YES
zphota -c HERSCHEL.para --CAT_IN MIPS.in --CAT_OUT testFIR.out --ZPHOTLIB BC_COSMOS --ADD_EMLINES 0,100 --AUTO_ADAPT NO --ZFIX YES --FIR_LIB DALE_COSMOS --FIR_SUBSTELLAR YES --FIR_FREESCALE YES --FIR_CONT 8257536 --CAT_LINES 11980,12010 --SPEC_OUT YES

# Plot the best-fit templates
# Results in MULTISPEC.pdf
Expand All @@ -125,7 +133,7 @@ python spec.py Id*spec -d pdf
#########################################################


$LEPHAREDIR/bin/filter -c COSMOS.para -FILTER_LIST cosmos/u_cfht.lowres,cosmos/B_subaru.lowres,cosmos/V_subaru.lowres,cosmos/r_subaru.lowres,cosmos/i_subaru.lowres,cosmos/suprime_FDCCD_z.res,vista/Y.lowres,vista/J.lowres,vista/H.lowres,vista/K.lowres -FILTER_CALIB 0 -FILTER_FILE filter_extinc
filter -c COSMOS.para --FILTER_LIST cosmos/u_cfht.lowres,cosmos/B_subaru.lowres,cosmos/V_subaru.lowres,cosmos/r_subaru.lowres,cosmos/i_subaru.lowres,cosmos/suprime_FDCCD_z.res,vista/Y.lowres,vista/J.lowres,vista/H.lowres,vista/K.lowres --FILTER_CALIB 0 --FILTER_FILE filter_extinc
# Read the filters and compute extinctions
$LEPHAREDIR/bin/filter_extinc -c COSMOS.para -FILTER_FILE filter_extinc.dat
filter_extinc -c COSMOS.para --FILTER_FILE filter_extinc.dat

5 changes: 4 additions & 1 deletion ext/README.extinc
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Expand Up @@ -25,12 +25,15 @@
SB_calzetti_bump3.dat

#
# Added dust law
# Added dust laws

extlaw_0.9.dat
was created in Arnouts+2013


salim18.dat
added the low mass high-z analog from Salim+2018

#
# The atmospheric extinction curves for other purposes
There are also atmospheric extinctions from La Silla (ESO) and CTIO
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