Update timeseries plots to resolve issue with some fields (#539)

* Update the timeseries plots to accurately extract data from log files.  Also add an option to plot SST from the python plotting script.  This addresses issue #538

* Fix 2 typos

* Remove SST and arwt tot mass from list of fields to plot

configuration/scripts/timeseries.csh

@@ -13,9 +13,9 @@ endif
 set basename = `echo $1 | sed -e 's#/$##' | sed -e 's/^\.\///'`
 
 # Set x-axis limits
-  # Manuallyl set x-axis limits
+  # Manually set x-axis limits
 #set xrange = 'set xrange ["19980101":"19981231"]'
-  # Let gnuplot determine x-alis limits
+  # Let gnuplot determine x-axis limits
 set xrange = ''
 
 # Determine if BASELINE dataset exists
@@ -59,8 +59,10 @@ endif
 
 # Loop through each field and create the plot
 foreach field ($fieldlist:q)
+  # Add backslashes before (, ), and ^ for grep searches
+  set search_name = "`echo '$field' | sed 's/(/\\(/' | sed 's/)/\\)/' | sed 's/\^/\\^/'`"
   set fieldname = `echo "$field" | sed -e 's/([^()]*)//g'`
-  set search = "'$fieldname'\|istep1"
+  set search = "'$search_name'\|istep1"
   rm -f data.txt
   foreach line ("`egrep $search $logfile`")
     if ("$line" =~ *"istep1"*) then

configuration/scripts/timeseries.py

@@ -53,7 +53,7 @@ def get_data(logfile,field):
     # Build the regular expression to extract the data
     field_regex = field.replace('(','\(').replace('^','\^').replace(')','\)')
     number_regex = '[-+]?\d+\.?\d+([eE][-+]?\d+)?'
-    my_regex = '{}\s+=\s+({})\s+({})'.format(field_regex,number_regex,number_regex)
+    my_regex = '^{}\s+=\s+({})\s+({})'.format(field_regex,number_regex,number_regex)
 
     dtg = []
     arctic = []
@@ -95,9 +95,10 @@ def plot_timeseries(log, field, dtg, arctic, antarctic, expon, dtg_base=None, ar
     Plot the timeseries data from the CICE log file
     '''
 
-    casename = os.path.abspath(log).rstrip('/').rstrip('/logs').split('/')[-1]
+    import re
+    casename = re.sub(r"/logs", "", os.path.abspath(log).rstrip('/')).split('/')[-1]
     if base_dir:
-        base_casename = os.path.abspath(base_dir).rstrip('/').rstrip('/logs').split('/')[-1]
+        base_casename = re.sub(r"/logs", "", os.path.abspath(base_dir).rstrip('/')).split('/')[-1]
 
     # Load the plotting libraries, but set the logging level for matplotlib
     # to WARNING so that matplotlib debugging info is not printed when running