Add config file for BGC scripts, prevent -inf when taking log10, savi…

…ng regional figures in main figures dir

diagnostics/biogeochemistry/NWA12/chl_eval_regional.py

@@ -140,7 +140,7 @@ def plot_chl_regional(pp_root, label, config, dev):
     cbar.set_ticks([0.25, 0.5, 1, 2, 4, 8])
     cbar.set_ticklabels([0.25, 0.5, 1, 2, 4, 8])
     logger.info("Saving figure")
-    save_figure('regional_chl', label=label)
+    save_figure('regional_chl', label=label, output_dir = "../figures")
 
 
 if __name__ == '__main__':

diagnostics/biogeochemistry/chl_eval.py

@@ -1,7 +1,7 @@
 """
 Compare model surface chla with data from occci-v6.0.
 How to use:
-python chl_eval.py -p /archive/acr/fre/NWA/2023_04/NWA12_COBALT_2023_04_kpo4-coastatten-physics/gfdl.ncrc5-intel22-prod -c ../physics/config.yaml
+python chl_eval.py -p /archive/acr/fre/NWA/2023_04/NWA12_COBALT_2023_04_kpo4-coastatten-physics/gfdl.ncrc5-intel22-prod -c config.yaml
 """
 
 import cartopy.crs as ccrs
@@ -52,7 +52,7 @@ def plot_chl(pp_root, label, config, dev):
     # Flip to right side up.
     # satellite = satellite.isel(lat=slice(None, None, -1))
     log_model = np.log10(np.maximum(model_climo, 1e-14))
-    log_sat = np.log10(satellite)
+    log_sat = np.log10(np.maximum(satellite,1e-14))
     logger.info("SATELITE: %s",satellite)
     logger.info("Successfully opened model grid and calculated climotology")
 

diagnostics/biogeochemistry/config.yaml

@@ -0,0 +1,35 @@
+# ------------- Dataset Locations and Variables ---------------
+model_grid: '../data/geography/ocean_static.nc'
+
+# ------------ Domain and General Plotting Details --------------
+
+# Xlim/ylim to plot
+x: 
+    min: -99
+    max: -35
+
+y:
+    min: 4
+    max: 59
+
+# Projection ( current options are either NorthPolarStereo or PlateCarree )
+projection_grid: 'PlateCarree'
+projection_data: 'PlateCarree'
+
+# Location of skill score annotations in plot
+text_x: -98.5
+text_y: 54
+
+# Space between skill score text
+text_xint: 4 # This is unused if col=1, so it is only included for completeness
+text_yint: 4
+plot_lat: False
+
+# --------------- Script specific settings -----------------
+#  ---- chl_eval settings
+chl_satellite: '/work/acr/occci-v6.0/oc-cci_chl_19970901_20191130_climo.nc'
+chl_start: '1997-09-01'
+chl_end: '2019-11-30'
+chl_ticks: [-4, -2, -1, -0.5, -0.1, 0, 0.1, 0.5, 1, 2, 4]
+chl_ticks_labels: ['-4', '-2', '-0.5', '0', '0.5', '2', '4']
+chl_cbar_ticks: [0.25, 0.5, 1, 2, 4, 8]