Fix plots

plot_general/plot.sh

 #!/bin/bash
 
-if [ ! -e ../plots/pdf ]; then  mkdir -v ../plots/pdf; fi
-if [ ! -e ../plots/png ]; then  mkdir -v ../plots/png; fi
-if [ ! -e ../plots/svg ]; then  mkdir -v ../plots/svg; fi
+if [ ! -d ../plots/pdf ]; then  mkdir -pv ../plots/pdf; fi
+if [ ! -d ../plots/png ]; then  mkdir -pv ../plots/png; fi
+if [ ! -d ../plots/svg ]; then  mkdir -pv ../plots/svg; fi
+
 
 # create plot(s) for every data.csv found within data folder
 for datafile in ../data/*/data.csv; do
 {
+  echo -e "\n------------------- ${datafile}"
+  test -f ${datafile} || {
+      echo "File  ${datafile}  does not exist, skipping"
+      continue
+  }
   # cut on last "/" to get folder name
   folder=$(echo $datafile | rev | cut -d "/" -f 2- | rev)
+  folder=`dirname ${datafile}`
+  basefile=`basename ${datafile}`
 
   # Clean up any remaining *_plot.csv if there are any. They must be created on the fly.
   if [ -e "${datafile%.csv}_plot.csv" ]; then
@@ -22,9 +30,10 @@ for datafile in ../data/*/data.csv; do
     pushd "$folder"
       ./filter.sh
     popd
+    echo "Filter done"
   else
     # Link from same directory, so use bare file name without path
-    ln -sv "$(echo $datafile | rev | cut -d "/" -f 1 | rev)" "${datafile%.csv}_plot.csv"
+    ln -sv "${basefile}" "${datafile%.csv}_plot.csv"
   fi
 
   # Plotting.
@@ -33,6 +42,9 @@ for datafile in ../data/*/data.csv; do
   # - there is a specific plot.plt already deposited for the specific folder.
 
   if [ ! -e "$folder"/plot.plt ]; then
+    # remove the non-existing file, just to eliminate broken symlinks
+    rm -f "$folder"/plot.plt
+    echo ln -sv "$(pwd)"/plot.plt "$folder"/;
     ln -sv "$(pwd)"/plot.plt "$folder"/;
   fi