add dynamic colorbar is plotting and add bottom temp animation

Author: GilesFearon

.github/workflows/postprocess_croco.yml

@@ -146,6 +146,20 @@ jobs:
                 --skip_time 6 \
                 --ref_date '2000-01-01 00:00:00'
           sudo chown somisana:somisana ${{ env.RUN_DIR }}/postprocess/croco_avg_temp_surf.gif
+      - name: animate bottom temperature and currents
+        continue-on-error: true
+        run: |
+          docker run \
+            --rm \
+            -v ${{ env.RUN_DIR }}:/tmp \
+            ghcr.io/saeon/somisana-croco_cli_${{ inputs.BRANCH_REF }}:latest \
+              crocplot \
+                --fname /tmp/output/croco_avg.nc \
+                --level 0 \
+                --gif_out /tmp/postprocess/croco_avg_temp_bot.gif \
+                --skip_time 6 \
+                --ref_date '2000-01-01 00:00:00'
+          sudo chown somisana:somisana ${{ env.RUN_DIR }}/postprocess/croco_avg_temp_bot.gif
       - name: animate 100m temperature and currents
         continue-on-error: true
         run: |

cli.py

@@ -190,10 +190,11 @@ def reformat_gfs_atm_handler(args):
             help='do a plot/animation of a croco output file(s)')
     parser_crocplot.add_argument('--fname', required=True, type=str, help='input native CROCO filename (can handle wildcards to animate over multiple files)')
     parser_crocplot.add_argument('--var', required=False, default='temp', type=str, help='the variable name to plot')
-    parser_crocplot.add_argument('--gif_out', required=True, type=str, help='the output gif filename')
+    parser_crocplot.add_argument('--gif_out', required=False, type=str, help='the output gif filename')
+    parser_crocplot.add_argument('--mp4_out', required=False, type=str, help='the output mp4 filename')
     parser_crocplot.add_argument('--level', required=False, default=None, type=parse_int, help='level to plot. If >=0, then a sigma level is plotted. If <0 then a z level (in m) is plotted. Default behaviour will plot the surface layer')
     parser_crocplot.add_argument('--ticks', required=False, type=parse_list,
-                         default=[12,13,14,15,16,17,18,19,20,21,22], 
+                         default=None, 
                          help='contour ticks to use in plotting the variable')
     parser_crocplot.add_argument('--cbar_label', required=False, default='temperature ($\degree$C)', type=str, help='the label used for the colorbar')
     parser_crocplot.add_argument('--isobaths', required=False, type=parse_list,
@@ -220,7 +221,8 @@ def crocplot_handler(args):
                       add_vectors = True,
                       skip_time = args.skip_time,
                       isobaths=args.isobaths,
-                      gif_out=args.gif_out
+                      gif_out=args.gif_out,
+                      mp4_out=args.mp4_out
                       )
     parser_crocplot.set_defaults(func=crocplot_handler)
 

crocotools_py/plotting.py

@@ -242,15 +242,15 @@ def plot(fname,
         ax=None, # allowing for adding to an existing axis
         var='temp', # croco variable to plot
         grdname=None, # option croco grid file (if grid variables arem't in the croco output file)
-        time=None, # see post.get_var() for 'time' format. If a single value, then a plot is made, if two values, then an animation between those times is made
+        time=slice(None), # see post.get_var() for 'time' format. If a single value, then a plot is made, if two values, then an animation between those times is made
         level=None, # see post.get_var() for 'level' format. Has to be a single value for this function to do a plot
-        ticks = np.linspace(12,22,num=11), # the ticks to plot (should default to None and determine automatically)
+        ticks = None, #np.linspace(12,22,num=11), (gets set automatically if None)
         cmap = 'Spectral_r',
         extents = None, # [lon0,lon1,lat0,lat1] whole domain plotted if None
         ref_date = None, # datetime, from CROCO model setup
         add_cbar = True, # add a colorbar?
         cbar_loc = None, # [left, bottom, width, height] (gets set automatically if None)
-        cbar_label = 'temperature ($\degree$C)',
+        cbar_label = None, # 'temperature ($\degree$C)', we just use 'var' is None
         add_vectors = True, # add vectors?
         scale_uv = None, # define the vector scaling (gets set automatically if None)
         ref_vector = None, # value of reference vector
@@ -260,6 +260,7 @@ def plot(fname,
         isobaths = None, # optional list of isobaths to overlay over plot
         jpg_out=None, # full path to jpg output
         gif_out=None, # full path to gif output
+        mp4_out=None, # option to rather write an mp4
         ):
     '''
     this is a convenience function for doing a quick 2D plot with minimal coding.
@@ -293,7 +294,22 @@ def plot(fname,
     else:
         # this will be an animation, starting with the first time-step
         data_plt=da_var.isel(time=0).values
-        
+    
+    if ticks is None:
+        # get the range of the data to plot (using 5th and 95th percentiles)
+        vmin=np.nanpercentile(da_var, 1)
+        vmax=np.nanpercentile(da_var, 99)
+        # round these to two significant figures
+        vmin=round(vmin, 2 - int(np.floor(np.log10(abs(vmin)))) - 1)
+        vmax=round(vmax, 2 - int(np.floor(np.log10(abs(vmax)))) - 1)
+        num_ticks = 10
+        step = (vmax - vmin) / num_ticks
+        step = round(step, 2 - int(np.floor(np.log10(abs(step)))) - 1)
+        # update vmax based on the rounded step
+        vmax = vmin + num_ticks * step
+        # Generate the ticks using the rounded step size
+        ticks = np.arange(vmin, vmax + step/10, step) # Add a small value to ensure new_vmax is included
+    
     # compute the extents from the grid if not explicitly defined
     if extents is None:
         lon_min = min(np.ravel(lon))
@@ -346,6 +362,8 @@ def plot(fname,
     time_plt = plot_time(ax,time_var[0])
 
     if add_cbar:
+        if cbar_label is None:
+            cbar_label = var
         plot_cbar(ax,var_plt,label=cbar_label,ticks=ticks,loc=cbar_loc,aspect_ratio=aspect_ratio)
 
     if add_vectors:
@@ -417,6 +435,9 @@ def plot_tstep(i):
         if gif_out is not None:
             print('writing '+gif_out)
             anim.save(gif_out, writer='imagemagick')
+        if mp4_out is not None:
+            print('writing '+mp4_out)
+            anim.save(mp4_out, writer="ffmpeg")
 
 def plot_blk(croco_grd, # the croco grid file - needed as not saved in the blk file
         croco_blk_file, # the croco blk file