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