Include a new attenuation curve from Salim+18 and update the README_f…

…ull from examples

examples/AGN_MOD.list

@@ -0,0 +1,14 @@
+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

examples/COSMOS.para

@@ -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]

examples/README_full

@@ -1,54 +1,43 @@
 #! /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/'
+# 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
 
 
 
@@ -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
@@ -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
 

ext/README.extinc

@@ -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