Example notebook, minor fixes, docs

.gitignore

@@ -1,7 +1,10 @@
-#### Øyvind's:
+#### Custom
 
 misc/laura/
 docs/build/
+docs/example_notebooks_basic_example/test_data/.mat
+docs/example_notebooks_basic_example/test_data/.nc
+
 tests/test_data/*.mat
 examples/
 graphics/

README.md

@@ -3,11 +3,9 @@
 ![](docs/images/logos_illustrations/kobbe_header.png)
 
 
-Version 0.0.1: *Under development.*
+Version 0.1: *In development.*
 
 
-Overview
---------
 #### [Documentation page](https://kobbe.readthedocs.io/) *(in development)*
 
 
@@ -19,25 +17,3 @@ the ocean surface.
 
 ![](docs/images/logos_illustrations/sea_ice_illustration.png)
 
-
-_____
-
-  ### **GOAL:**
-
-  **Easy and explicit post-processing to obtain scientific-quality estimates of:**
-
-  - **Sea ice draft**
-  - **Sea ice drift velocity**
-  - **Upper ocean current velocity**
-______
-
-
-Inputs to the process are:
-
-- *.mat* files exported by Norteks [SignatureDeployment](https://www.nortekgroup.com/software) software *(required)*
-- Time series of atmospheric pressure during the deployment *(strongly
-  recommended)*
-- Time series of ocean temperature/salinity in the upper ocean *(recommended)*
-- Magnetic declination correction (single value or time series) *(necessary for
-  correct velocity directions)*
-______

docs/example_notebooks/basic_example/test_data/S100812A002_AeN_M1_1.mat

@@ -0,0 +1 @@
+../../../../tests/test_data/S100812A002_AeN_M1_1.mat

docs/example_notebooks/basic_example/test_data/S100812A002_AeN_M1_2.mat

@@ -0,0 +1 @@
+../../../../tests/test_data/S100812A002_AeN_M1_2.mat

docs/requirements.txt

@@ -1,3 +1,4 @@
 sphinx>=5.0.0
 myst-parser>=0.18.0
+nbsphinx
 git+https://github.com/oyvfoss/kobbe.git#egg=kobbe

docs/source/conf.py

@@ -25,7 +25,8 @@
               'sphinx.ext.coverage',
               'sphinx.ext.napoleon',
               'myst_parser',
-              'sphinx.ext.mathjax',]  # For LaTeX support]
+              'sphinx.ext.mathjax',
+              'nbsphinx']  # For LaTeX support]
 
 
 myst_enable_extensions = [

docs/source/index.rst

@@ -1,7 +1,7 @@
 ``kobbe``
 ---------
 
-*Post-processing of ice and ocean data from Nortek Signature ADCPs*
+*Post-processing of ice and ocean data from Nortek Signature ADCPs in Python*
 
 Preliminary documentation page.
 
@@ -13,4 +13,5 @@ ____
     pipeline/pipeline
     functions/functions
 
+- `Example notebook <notebooks/Example_notebook_Sig500_ice_draft.ipynb>`_
 - `Source code GitHub repository <https://github.com/oyvfoss/kobbe>`_

docs/source/notebooks/Example_notebook_Sig500_ice_draft.ipynb

@@ -0,0 +1 @@
+../../example_notebooks/basic_example/Example notebook for Sig500 ice draft.ipynb

src/kobbe/calc.py

@@ -205,7 +205,8 @@ def footprint(signature: Union[xr.Dataset, str],
 
     Examples
     --------
-    >>> ds = xr.Dataset(attrs={"instrument": "Signature500", "depth": (["time"], [50, 60, 55])})
+    >>> ds = xr.Dataset(attrs={"instrument": "Signature500",
+                        "depth": (["time"], [50, 60, 55])})
     >>> footprint(ds)
     Beam width at surface: 2.5 m.
     For depth 55.0 m and beam width angle 2.9 degrees (Signature500).

src/kobbe/icedraft.py

@@ -12,7 +12,7 @@
 from kobbe import append
 import xarray as xr
 from typing import Tuple
-
+import pandas as pd
 
 def calculate_draft(
     ds: xr.Dataset,
@@ -374,9 +374,27 @@ def get_open_water_surface_depth_LP(
     # 5. Smooth with running mean
     RS = runningstat(owds_med_daily_interp, run_window_days)
 
-    # Export filtered, ensemble median, daily averaged, smoothed daily owsd.
+    # Store filtered, ensemble median, daily averaged, smoothed daily owsd.
     # Also daily time array (td+0.5) of the midpoint of the daily estimates.
-    return RS["mean"], time_daily + 0.5
+    RS_mean = RS["mean"]
+    timestamp_day = time_daily + 0.5
+
+    # 6. Forward and backward fill if we have Nans at the start
+    #    or end (using nice pandas functionlity for this)
+
+    if np.isnan(RS_mean).any():
+
+        # Create a DataFrame
+        df_RS = pd.DataFrame(
+            {'timestamp_day': timestamp_day, 'RS_mean': RS_mean})
+
+        # Use ffill and bfill
+        df_RS['RS_mean'] = df_RS['RS_mean'].ffill().bfill()
+
+        # Convert the filled RS_mean column back to a NumPy array
+        RS_mean = df_RS['RS_mean'].to_numpy()
+
+    return RS_mean, timestamp_day
 
 
 ###########
@@ -743,7 +761,7 @@ def compare_open_water_correction(
             leg = axn.legend(ncol=3, fontsize=10, loc=1,
                              bbox_to_anchor=(0.7, 0.1))
             # Set the legend symbols to 100% opacity and make them bigger
-            for legend_handle in leg.legendHandles:
+            for legend_handle in leg.legend_handles:
                 legend_handle.set_alpha(1.0)
                 legend_handle._sizes = [50]
             axn.grid()

src/kobbe/load.py

@@ -901,7 +901,7 @@ def to_nc(
                 "SEA_ICE_DRAFT_LE",
                 "SEA_ICE_DRAFT_MEDIAN_LE",
                 "SEA_ICE_DRAFT_AST",
-                "SEA_ICE_DRAFT_LE",
+                "SEA_ICE_DRAFT_MEDIAN_AST",
             ]
         if icevel:
             varlist += ["uice", "vice", "Uice", "Vice"]