Fixing issues and added further test

tools/psy-maps/psy-maps.xml

@@ -53,8 +53,8 @@
                 </when>
             </conditional>
             <param name="logscale" type="select" label="log scale the data">
-                <option value="True">yes</option>
-                <option value="False" selected="true">no</option>
+                <option value="yes">yes</option>
+                <option value="no" selected="true">no</option>
             </param>
             <param name="projection" type="select">
                 <option value="" selected="true">PlateCarree</option>
@@ -167,6 +167,14 @@
             <param name="colormap" value="RdBu_r" />
             <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/>
         </test>
+        <test>
+            <param name="ifilename" value="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.nc" />
+            <param name="variable" value="chlor_a" />
+            <param name="projection" value="" />
+            <param name="colormap" value="jet" />
+            <param name="logscale" value="yes" />
+            <output name="ofilename" ftype="png" file="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.png" compare="sim_size" delta="1500"/>
+        </test>
     </tests>
     <help><![CDATA[
 

tools/psy-maps/psymap_simple.py

@@ -30,11 +30,14 @@
 import argparse
 import warnings
 from pathlib import Path
+import math
+import xarray
 
 import matplotlib as mpl
 mpl.use('Agg')
 from matplotlib import pyplot  # noqa: I202,E402
 
+import psyplot
 import psyplot.project as psy  # noqa: I202,E402
 from psyplot import rcParams   # noqa: I202,E402
 
@@ -44,15 +47,36 @@ def __init__(self, input, varname, output=None, logscale=False, cmap=None,
                  proj=None, verbose=False, time=None, nrow=None, ncol=None,
                  format=None, title=None):
         self.input = input
+
         self.varname = varname
-        self.proj = proj if proj is not None else "cyl"
+        if proj is None or proj == "":
+            self.proj = "cyl"
+        else:
+            self.proj = proj
         self.cmap = cmap if cmap is not None else "jet"
         self.time = time if time is not None else []
-        self.title = title if title is not None else ""
         self.ncol = int(ncol) if ncol is not None else int(1)
         self.nrow = int(nrow) if nrow is not None else int(1)
+
+        # Open dataset
+        ds = xarray.open_dataset(input)[varname]
+        minv = math.log2(ds.data.min())
+        maxv = math.log2(ds.data.max())
+        if title is not None:
+            self.title = title 
+        else:
+            self.title = ds.long_name
+            if len(self.title) > 60:
+                self.title = ds.standard_name
+        del ds
+
         if logscale:
-            self.bounds = ['log', 2]
+            # Check that data range is sufficient for log scaling
+            if maxv < (minv * (10.0 ** 2.0)):
+                print("Not possible to log scale, switching to linear scale")
+                self.bounds = None
+            else:
+                self.bounds = ['log', 2]
         else:
             self.bounds = None
         if format is None:
@@ -73,30 +97,32 @@ def __init__(self, input, varname, output=None, logscale=False, cmap=None,
             print("nrow: ", self.nrow)
             print("title: ", self.title)
             print("date format: ", self.format)
+            print("logscale: ",self.bounds)
             print("output: ", self.output)
 
     def plot(self):
+        clabel = '{desc}'
         if self.title and self.format:
             title = self.title + "\n" + self.format
         elif not self.title and self.format:
             title = self.format
         elif self.title and not self.format:
             title = self.title
-        else:
-            title = '%(long_name)s'
-
+            clabel = self.title
+
+        # Plot with chosen options
         if self.bounds is None:
             psy.plot.mapplot(self.input, name=self.varname,
                              cmap=self.cmap,
                              projection=self.proj,
                              title=title,
-                             clabel='{desc}')
+                             clabel=clabel)
         else:
             psy.plot.mapplot(self.input, name=self.varname,
                              cmap=self.cmap, bounds = self.bounds,
                              projection=self.proj,
                              title=title,
-                             clabel='{desc}')
+                             clabel=clabel)
 
 
         pyplot.savefig(self.output)
@@ -109,6 +135,7 @@ def multiple_plot(self):
             title = self.format
         else:
             title = self.title + "\n" + self.format
+
         mpl.rcParams['figure.figsize'] = [20, 8]
         mpl.rcParams.update({'font.size': 8})
         rcParams.update({'plotter.maps.grid_labelsize': 8.0})
@@ -166,9 +193,8 @@ def psymap_plot(input, proj, varname, logscale, cmap, output, verbose, time,
         help='Specify which variable to plot (case sensitive)'
     )
     parser.add_argument(
-        "-l", "--logscale",
-        help='Plot the log scaled data',
-        action="store_true"
+        "--logscale",
+        help='Plot the log scaled data'
     )
     parser.add_argument(
         '--cmap',
@@ -208,7 +234,12 @@ def psymap_plot(input, proj, varname, logscale, cmap, output, verbose, time,
         time = []
     else:
         time = list(map(int, args.time.split(",")))
+
+    if args.logscale == 'no':
+        logscale = False
+    else:
+        logscale = True
 
-    psymap_plot(args.input, args.proj, args.varname, args.logscale, args.cmap,
+    psymap_plot(args.input, args.proj, args.varname, logscale, args.cmap,
                 args.output, args.verbose, time,
                 args.nrow, args.ncol, args.format, args.title)