Legacy and 3x2pt compatibility and other fixes

man/add_datavector.man.sh

@@ -97,10 +97,11 @@ function _outputs {
   then
     output="obs_vec"
   else 
-    _message "BV:DATAVEC_TYPE is not set to a known value: ${DATAVEC_TYPE^^} is not one of {COSEBIS,PSI_STATS_GM,PSI_STATS_GG,BANDPOWERS_EE,BANDPOWERS_NE,BANDPOWERS_NN,XIPM,GT,WT}"
+    _message "BV:DATAVEC_TYPE is not set to a known value: ${DATAVEC_TYPE^^} is not one of {COSEBIS,PSI_STATS_GM,PSI_STATS_GG,BANDPOWERS_EE,BANDPOWERS_NE,BANDPOWERS_NN,XIPM,GT,WT,OBS}"
     exit 1
   fi
   #}}}
+  _message "$output"
   echo ${output}
 }
 #}}}

man/calculate_psistats.man.sh

@@ -56,8 +56,11 @@ function _inp_data {
 # Output data {{{ 
 function _outputs { 
   #Data outputs (leave blank if none)
-  output=`_parse_blockvars psi_stats_@BV:MODES@`
-  echo $output
+  # Need to fix this to output gg and gm instad of nn and ne
+  echo psi_stats_gm psi_stats_gg
+  #output=`_parse_blockvars psi_stats_@BV:MODES@`
+  #output=${output,,}
+  #echo $output
 }
 #}}}
 

man/make_cosmosis_nz_3x2pt.man.sh

@@ -0,0 +1,144 @@
+#
+# make_cosmosis_nz.sh Documentation & Housekeeping functions
+#
+
+#Starting Prompt {{{
+function _prompt { 
+  #Check if we do want verbose output
+  if [ "$1" != "0" ] 
+  then
+    _message "@BLU@========================================@DEF@\n"
+    _message "@BLU@== @RED@ Running make_cosmosis_nz_3x2pt.sh Mode @BLU@ ==@DEF@\n"
+    _message "@BLU@========================================@DEF@\n"
+  fi 
+}
+#}}}
+
+#Mode description {{{
+function _description { 
+  echo "#"
+  echo '# Construct an Nz file in the format expected by '
+  echo '# cosmosis'
+  echo "#"
+  echo "# Function takes input data:"
+  echo "# `_inp_data`"
+  echo "#"
+}
+#}}}
+
+# Abort Message {{{
+_abort()
+{
+  #Message to print when script aborts 
+  #$0 is the script that was running when this error occurred
+  _message "@BLU@ An error occured while running:\n@DEF@$0.\n" >&2
+  _message "@BLU@ Check the logging file for this step in:\n" >&2
+  _message "@DEF@@RUNROOT@/@LOGPATH@/\n" >&2
+  exit 1
+}
+trap '_abort' 0
+set -e 
+#}}}
+
+# Input variables {{{ 
+function _inp_var { 
+  #Variable inputs (leave blank if none)
+  echo ALLPATCH BLU BV:MODES BV:NLENSBINS BV:NSMFLENSBINS BV:PATCHLIST BV:TOMOLIMS DATABLOCK DEF PYTHON3BIN RED RUNROOT SCRIPTPATH STORAGEPATH
+} 
+#}}}
+
+# Input data {{{ 
+function _inp_data { 
+  #Data inputs (leave blank if none)
+  outlist=''
+  #input is dynamic, depending on the value of BV:COSMOSIS_PATCHLIST
+  patchvar="@BV:COSMOSIS_PATCHLIST@"
+  patchvar=`_parse_blockvars ${patchvar}`
+  MODES_IN=`_parse_blockvars @BV:MODES@`
+  modes=''
+  if [[ .*\ $MODES_IN\ .* =~ " EE " ]] || [[ .*\ $MODES_IN\ .* =~ " NE " ]]
+  then
+    modes="${modes} source"
+  fi
+  if [[ .*\ $MODES_IN\ .* =~ " NE " ]] || [[ .*\ $MODES_IN\ .* =~ " NN " ]]
+  then
+    modes="${modes} lens"
+  fi
+  if [[ .*\ $MODES_IN\ .* =~ " OBS " ]]
+  then
+    modes="${modes} obs"
+  fi
+  #Define the patches to loop over {{{
+  if [ "${patchvar}" == "ALL" ] || [ "${patchvar}" == "@BV:COSMOSIS_PATCHLIST@" ]
+  then 
+    patchlist=`echo @BV:PATCHLIST@ @ALLPATCH@ @ALLPATCH@comb`
+  else
+    patchlist="${patchvar}"
+  fi 
+  #}}}
+  for mode in ${modes}
+  do
+    for patch in ${patchlist}
+    do
+      #>&2 echo ${patch}
+      outlist="${outlist} cosmosis_neff_${mode} nz_${mode}_${patch}"
+    done
+  done
+  echo ${outlist}
+} 
+#}}}
+
+# Output data {{{ 
+function _outputs { 
+  #Data outputs (leave blank if none)
+  outlist=''
+  patchvar="@BV:COSMOSIS_PATCHLIST@"
+  patchvar=`_parse_blockvars ${patchvar}`
+  MODES_IN=`_parse_blockvars @BV:MODES@`
+  modes=''
+  if [[ .*\ $MODES_IN\ .* =~ " EE " ]] || [[ .*\ $MODES_IN\ .* =~ " NE " ]]
+  then
+    modes="${modes} source"
+  fi
+  if [[ .*\ $MODES_IN\ .* =~ " NE " ]] || [[ .*\ $MODES_IN\ .* =~ " NN " ]]
+  then
+    modes="${modes} lens"
+  fi
+  if [[ .*\ $MODES_IN\ .* =~ " OBS " ]]
+  then
+    modes="${modes} obs"
+  fi
+  #Define the patches to loop over {{{
+  if [ "${patchvar}" == "ALL" ] || [ "${patchvar}" == "@BV:COSMOSIS_PATCHLIST@" ]
+  then
+    patchlist=`echo @BV:PATCHLIST@ @ALLPATCH@ @ALLPATCH@comb`
+  else
+    patchlist="${patchvar}"
+  fi
+  for mode in ${modes}
+  do
+    for patch in ${patchlist}
+    do
+      outlist="${outlist} cosmosis_nz_${mode}_${patch}"
+    done
+  done
+  echo ${outlist}
+} 
+#}}}
+
+# Execution command {{{ 
+function _runcommand { 
+  #Command for running the script 
+  echo bash @RUNROOT@/@SCRIPTPATH@/make_cosmosis_nz_3x2pt.sh
+} 
+#}}}
+
+# Unset Function command {{{ 
+function _unset_functions { 
+  #Remove these functions from the environment
+  unset -f _prompt _description _inp_data _inp_var _abort _outputs _runcommand _unset_functions
+} 
+#}}}
+
+#Additional Functions 
+

scripts/add_gt.sh

@@ -25,7 +25,7 @@ then
   outlist=${file}
 elif [ -d @BV:TREECORRGT@ ]
 then 
-  filelist=`ls @BV:TREECORRGT@/*.asc*`
+  filelist=`ls @BV:TREECORRGT@/*.txt*`
   for file in ${filelist} 
   do 
     cp ${file} @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/gt/${file##*/}

scripts/add_wt.sh

@@ -25,7 +25,7 @@ then
   outlist=${file}
 elif [ -d @BV:TREECORRWT@ ]
 then 
-  filelist=`ls @BV:TREECORRWT@/*.asc*`
+  filelist=`ls @BV:TREECORRWT@/*.txt*`
   for file in ${filelist} 
   do 
     cp ${file} @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/wt/${file##*/}

scripts/add_xipm.sh

@@ -25,7 +25,7 @@ then
   outlist=${file}
 elif [ -d @BV:TREECORRXIPM@ ]
 then 
-  filelist=`ls @BV:TREECORRXIPM@/*.asc*`
+  filelist=`ls @BV:TREECORRXIPM@/*.txt*`
   for file in ${filelist} 
   do 
     cp ${file} @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/xipm/${file##*/}

scripts/calc_smf.py

@@ -140,6 +140,10 @@
     stellar_mass_in = data[stellar_mass_column]
     z_in = data[z_column]
 
+    # Check that data covers min_z, max_z
+    if not np.any((z_in >= min_z) & (z_in <= max_z)):
+        raise ValueError(f"No data in redshift range {min_z} < z < {max_z}")
+
     # We set the possible minimum z to 0.001
     z_min = np.maximum(0.001, min_z)
     # max_z is given as an input, this is the maximum redshift in the stellar mass-redshift bin.
@@ -151,7 +155,6 @@
     # or maximum redshift of the stellar mass-redshift bin
     z_max_i = np.minimum(z_max_bin, z_max)
 
-
     if estimator == 'simple':
         # Comoving distance at z_min and z_max_i in units of Mpc h
         # z_max_i is the maximum redshift at which galaxy i is visible in the sample

scripts/cosmosis_constructor_3x2pt.sh

@@ -43,8 +43,8 @@ zmax_def = 1.2
 nmass_def = 100 ; 200
 logmassmin_def = 9.0
 logmassmax_def = 18.0
-beta_nl = True
-mead2020_corrections = fit_feedback
+nonlinear_mode = bnl
+hmcode_ingredients = fit
 
 SAMPLER_NAME = @BV:SAMPLER@
 RUN_NAME = %(SAMPLER_NAME)s_%(blind)s${CHAINSUFFIX}
@@ -591,7 +591,7 @@ input_section_name = shear_cl
 output_section_name = shear_xi
 
 [xip_conv]
-file = %(CSL_PATH)s/utility/convert_theta/convert_theta.py
+file = %(HMPATH)s/cosmosis_modules/convert_theta/convert_theta.py
 output_units = arcmin
 section_name = shear_xi_plus
 
@@ -704,7 +704,7 @@ cat > @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_con
 [multinest]
 max_iterations=100000
 multinest_outfile_root= %(OUTPUT_FOLDER)s/%(RUN_NAME)s_
-resume=T
+resume=F
 tolerance = 0.01
 constant_efficiency = F
 live_points = 1000
@@ -738,13 +738,13 @@ fast_slow="F"
 n_batch=`echo "@BV:NTHREADS@" | awk '{printf "%d", 4*$1}'`
 cat > @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_sampler.ini <<- EOF
 [nautilus]
-live_points = 4000
+n_live = 4000
 enlarge_per_dim = 1.1
 split_threshold = 100
 n_networks = 8
 n_batch = $n_batch
 filepath = %(OUTPUT_FOLDER)s/run_nautilus.hdf5
-resume = False ; True
+resume =  False ; True
 f_live = 0.01
 discard_exploration = True
 verbose = True
@@ -1062,15 +1062,14 @@ EOF
 fi
 cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_pipe.ini <<- EOF
 extra_output = ${extraparams} ${shifts} ${listparam} ${tpdparams}
-quiet = T
 timing = F ; T
 debug = F
 fast_slow = ${fast_slow}
 first_fast_module = hod ; halo_model_ingredients_halomod
 
 [runtime]
 sampler = %(SAMPLER_NAME)s
-verbosity = quiet
+verbosity = quiet ; normal ; quiet
 pool_stdout = F ; T
 
 [output]
@@ -1215,15 +1214,15 @@ do
 			sets=""
 			if [[ .*\ $MODES\ .* =~ " EE " ]] || [[ .*\ $MODES\ .* =~ " NE " ]]
 			then
-			    sets="${sets} %(redshift_name)s"
+				sets="${sets} %(redshift_name)s"
 			fi
 			if [[ .*\ $MODES\ .* =~ " NE " ]] || [[ .*\ $MODES\ .* =~ " NN " ]]
 			then
-			    sets="${sets} %(redshift_name_lens)s"
+				sets="${sets} %(redshift_name_lens)s"
 			fi
 			if [[ .*\ $MODES\ .* =~ " OBS " ]]
 			then
-			    sets="${sets} %(redshift_name_obs)s"
+				sets="${sets} %(redshift_name_obs)s"
 			fi
 			cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
 			[$module]
@@ -1432,8 +1431,8 @@ do
 
 			if [ "$add_intrinsic" == "True" ]
 			then
-			cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
-			[$module]
+				cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
+				[$module]
 				file= %(HMPATH)s/cosmosis_modules/onepower_interface.py
 				p_mm = ${ee}
 				p_gg = ${nn}
@@ -1445,29 +1444,29 @@ do
 
 				EOF
 			else
-			cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
-			[$module]
+				cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
+				[$module]
 				file= %(HMPATH)s/cosmosis_modules/onepower_interface.py
-			p_mm = ${ee}
-			p_gg = ${nn}
-			p_gm = ${ne}
-			p_gI = False
-			p_mI = False
-			p_II = False
+				p_mm = ${ee}
+				p_gg = ${nn}
+				p_gm = ${ne}
+				p_gI = False
+				p_mI = False
+				p_II = False
 				split_ia = True
 
 				EOF
 			fi
 
 			cat >> @RUNROOT@/@STORAGEPATH@/@DATABLOCK@/cosmosis_inputs/@SURVEY@_CosmoPipe_constructed_other.ini <<- EOF
-			bnl =  %(beta_nl)s
+			nonlinear_mode =  %(nonlinear_mode)s
 			update_bnl = 10
 			poisson_type = constant
 			point_mass = True
 			dewiggle = True
 			response = False
 			output_suffix = onepower
-			use_mead2020_corrections = %(mead2020_corrections)s
+			hmcode_ingredients = %(hmcode_ingredients)s
 
 			log_mass_min = %(logmassmin_def)s
 			log_mass_max = %(logmassmax_def)s