Merge pull request #589 from British-Oceanographic-Data-Centre/develop

Tidegauge and Profile tutorials refresh

Author: jpolton

CITATION.cff

@@ -37,6 +37,6 @@ authors:
  - family-names: "Gorman"
    given-names: "Luke"
    orcid: "https://orcid.org/0000-0002-2414-4311"
-title: "British-Oceanographic-Data-Centre/COAsT: v3.1.0"
-version: v3.1.1
-date-released: 2022-09-22
+title: "British-Oceanographic-Data-Centre/COAsT: v3.1.2"
+version: v3.1.2
+date-released: 2022-10-20

coast/data/tidegauge.py

@@ -971,7 +971,7 @@ def _read_bodc_data(fn_bodc, date_start=None, date_end=None, header_length: int
     ###                ~            Plotting             ~                     ###
     ##############################################################################
 
-    def plot_timeseries(self, id, var_list=["ssh"], date_start=None, date_end=None, plot_line=False):
+    def plot_timeseries(self, var_list=["ssh"], date_start=None, date_end=None, plot_line=False):
         """
         Quick plot of time series stored within object's dataset
         Parameters
@@ -992,9 +992,10 @@ def plot_timeseries(self, id, var_list=["ssh"], date_start=None, date_end=None,
             var_list = [var_list]
 
         for var_str in var_list:
-            dim_str = self.dataset[var_str].dims[0]
-            x = np.array(self.dataset[dim_str])
-            y = np.array(self.dataset[var_str])
+            # dim_str = self.dataset[var_str].dims[0]  # commented out: could pull wrong dimensio
+            # x = np.array(self.dataset[dim_str])  # return indices, not coordinate values
+            x = np.array(self.dataset["time"])
+            y = np.array(self.dataset[var_str].squeeze())
 
             # Use only values between stated dates
             start_index = 0
@@ -1019,7 +1020,20 @@ def plot_timeseries(self, id, var_list=["ssh"], date_start=None, date_end=None,
         plt.legend(var_list)
         # Title and axes
         plt.xlabel("Date")
-        plt.title("Site: " + self.dataset.site_name)
+
+        try:
+            self.dataset.id_name
+        except AttributeError:
+            try:
+                self.dataset.site_name
+            except AttributeError:
+                title_str = ""
+            else:
+                title_str = f"Site: {self.dataset.site_name}"
+        else:
+            title_str = f"Site: {self.dataset.id_name}"
+
+        plt.title(title_str)
 
         return fig, ax
 
@@ -1057,19 +1071,22 @@ def plot_on_map_multiple(cls, tidegauge_list, color_var_str=None):
         Y = []
         C = []
         for tg in tidegauge_list:
-            X.append(tg.dataset.longitude)
-            Y.append(tg.dataset.latitude)
+            X.append(tg.dataset.longitude.values)
+            Y.append(tg.dataset.latitude.values)
             if color_var_str is not None:
                 C.append(tg.dataset[color_var_str].values)
 
+        X = np.hstack(X)
+        Y = np.hstack(Y)
         title = ""
         if color_var_str is None:
             fig, ax = plot_util.geo_scatter(X, Y, title=title)
         else:
+            C = np.hstack(C)
             fig, ax = plot_util.geo_scatter(X, Y, title=title, c=C)
 
-        ax.set_xlim((min(X) - 10, max(X) + 10))
-        ax.set_ylim((min(Y) - 10, max(Y) + 10))
+        ax.set_xlim((np.min(X) - 10, np.max(X) + 10))
+        ax.set_ylim((np.min(Y) - 10, np.max(Y) + 10))
         return fig, ax
 
     ##############################################################################

coast/diagnostics/profile_analysis.py

@@ -385,9 +385,15 @@ def interpolate_vertical(cls, profile, new_depth, interp_method="linear", print_
                 # Get arrays to interpolate
                 interpx = profile.depth.values
                 interpy = profile[vv].values
+                if interpx.shape != interpy.shape:
+                    continue
 
                 # Remove NaNs
                 xnans = np.isnan(interpx)
+                try:
+                    ynans = np.isnan(interpy)
+                except:
+                    debug(f"Issue with vv: {vv}")
                 ynans = np.isnan(interpy)
                 xynans = np.logical_or(xnans, ynans)
                 interpx = interpx[~xynans]

coast/diagnostics/tidegauge_analysis.py

@@ -257,8 +257,8 @@ def threshold_statistics(cls, dataset, thresholds=np.arange(-0.4, 2, 0.1), peak_
                     # NTR: Threshold Frequency (Peaks)
                     ds_thresh["peak_count_" + vv][pp, nn] = np.sum(pk_values >= threshn)
 
-                    # NTR: Threshold integral (Time over threshold)
-                    ds_thresh["time_over_threshold_" + vv][pp, nn] = np.sum(data_pp >= threshn)
+                    # NTR: Threshold integral (Timestamps over threshold)
+                    ds_thresh["time_over_threshold_" + vv][pp, nn] = np.sum(data_pp >= threshn)  # sum of booleans
 
                     # NTR: Number of daily maxima over threshold
                     ds_thresh["dailymax_count_" + vv][pp, nn] = np.sum(ds_daily_max.values >= threshn)

environment.yml

@@ -6,8 +6,8 @@ channels:
 dependencies:
   - python==3.8.10
   - pip>=22.2.2
-  - cartopy>=0.20.2
-  - gsw>=3.4.0
+  - cartopy>=0.21.0
+  - gsw==3.4.0
   - pip:
     - numpy==1.22.3
     - dask==2022.3.0
@@ -16,7 +16,7 @@ dependencies:
     - matplotlib>=3.5.3
     - netCDF4==1.5.8
     - scipy>=1.8.0
-    - gsw>=3.4.0
+    - gsw==3.4.0
     - utide>=0.3.0
     - scikit-learn>=1.0.2
     - scikit-image>=0.19.2