Merge branch 'master' into time_series

wildlife-dynamics · Dec 18, 2024 · 62f3ec1 · 62f3ec1
2 parents f972c84 + fbb36b5
commit 62f3ec1
Show file tree

Hide file tree

Showing 18 changed files with 446 additions and 48 deletions.
diff --git a/doc/source/notebooks/01. IO/EarthRanger_IO.ipynb b/doc/source/notebooks/01. IO/EarthRanger_IO.ipynb
@@ -29,7 +29,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/01. IO/GEE_IO.ipynb b/doc/source/notebooks/01. IO/GEE_IO.ipynb
@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/01. IO/Landscape Dynamics Data.ipynb b/doc/source/notebooks/01. IO/Landscape Dynamics Data.ipynb
@@ -29,7 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/02. Relocations & Trajectories/Relocations_and_Trajectories.ipynb b/doc/source/notebooks/02. Relocations & Trajectories/Relocations_and_Trajectories.ipynb
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/03. Home Range & Movescape/EcoGraph.ipynb b/doc/source/notebooks/03. Home Range & Movescape/EcoGraph.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/03. Home Range & Movescape/Elliptical Time Density (ETD).ipynb b/doc/source/notebooks/03. Home Range & Movescape/Elliptical Time Density (ETD).ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/03. Home Range & Movescape/Reduce Regions.ipynb b/doc/source/notebooks/03. Home Range & Movescape/Reduce Regions.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/04. EcoMap & EcoPlot/EcoMap.ipynb b/doc/source/notebooks/04. EcoMap & EcoPlot/EcoMap.ipynb
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/04. EcoMap & EcoPlot/EcoPlot.ipynb b/doc/source/notebooks/04. EcoMap & EcoPlot/EcoPlot.ipynb
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "%pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/05. Environmental Analyses/Landscape Grid.ipynb b/doc/source/notebooks/05. Environmental Analyses/Landscape Grid.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/05. Environmental Analyses/Remote Sensing Time Series Anomaly.ipynb b/doc/source/notebooks/05. Environmental Analyses/Remote Sensing Time Series Anomaly.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/05. Environmental Analyses/Seasonal Calculation.ipynb b/doc/source/notebooks/05. Environmental Analyses/Seasonal Calculation.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/doc/source/notebooks/06. Data Management/Tracking Data Gantt Chart.ipynb b/doc/source/notebooks/06. Data Management/Tracking Data Gantt Chart.ipynb
@@ -29,7 +29,7 @@
    "source": [
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
-    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].14' &> /dev/null"
+    "!pip install 'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].15' &> /dev/null"
    ]
   },
   {

diff --git a/ecoscope/io/earthranger.py b/ecoscope/io/earthranger.py
@@ -13,6 +13,7 @@
     clean_kwargs,
     clean_time_cols,
     dataframe_to_dict,
+    filter_bad_geojson,
     format_iso_time,
     pack_columns,
     to_gdf,
@@ -511,6 +512,9 @@ def get_subjectgroup_observations(
         else:
             subjects = self.get_subjects(subject_group_name=subject_group_name, include_inactive=include_inactive)
 
+        if subjects.empty:
+            return subjects
+
         return self.get_subject_observations(subjects, **kwargs)
 
     def get_event_types(self, include_inactive=False, **addl_kwargs):
@@ -628,9 +632,8 @@ def get_events(
         if not gdf.empty:
             gdf = clean_time_cols(gdf)
             if gdf.loc[0, "location"] is not None:
-                gdf.loc[~gdf["geojson"].isna(), "geometry"] = gpd.GeoDataFrame.from_features(
-                    gdf.loc[~gdf["geojson"].isna(), "geojson"]
-                )["geometry"]
+                gdf = filter_bad_geojson(gdf)
+                gdf["geometry"] = gpd.GeoDataFrame.from_features(gdf["geojson"])["geometry"]
                 gdf.set_geometry("geometry", inplace=True)
                 gdf.set_crs(4326, inplace=True)
             gdf.sort_values("time", inplace=True)
@@ -640,7 +643,9 @@ def get_events(
 
     def get_patrol_types(self):
         df = pd.DataFrame(self._get("activity/patrols/types"))
-        return df.set_index("id")
+        if not df.empty:
+            df = df.set_index("id")
+        return df
 
     def get_patrols(self, since=None, until=None, patrol_type=None, patrol_type_value=None, status=None, **addl_kwargs):
         """
@@ -737,19 +742,20 @@ def get_patrol_events(
 
         events = []
         for _, row in patrol_df.iterrows():
-            if row["patrol_segments"]:
-                for segment in row["patrol_segments"]:
-                    for event in segment.get("events", []):
-                        event["patrol_id"] = row.get("id")
-                        event["patrol_segment_id"] = segment.get("id")
-                        event["patrol_start_time"] = (segment.get("time_range") or {}).get("start_time")
-                        events.append(event)
+            for segment in row.get("patrol_segments", []):
+                for event in segment.get("events", []):
+                    event["patrol_id"] = row.get("id")
+                    event["patrol_segment_id"] = segment.get("id")
+                    event["patrol_start_time"] = (segment.get("time_range") or {}).get("start_time")
+                    events.append(event)
         events_df = pd.DataFrame(events)
         if events_df.empty:
             return events_df
 
+        events_df = filter_bad_geojson(events_df)
         events_df["geometry"] = events_df["geojson"].apply(lambda x: shape(x.get("geometry")))
-        events_df["time"] = events_df["geojson"].apply(lambda x: x.get("properties").get("datetime"))
+        events_df["time"] = events_df["geojson"].apply(lambda x: x.get("properties", {}).get("datetime"))
+        events_df = events_df.loc[events_df["time"].notnull()]
         events_df = clean_time_cols(events_df)
 
         return gpd.GeoDataFrame(events_df, geometry="geometry", crs=4326)
@@ -870,38 +876,43 @@ def get_patrol_observations(self, patrols_df, include_patrol_details=False, **kw
                         until=patrol_end_time,
                         **kwargs,
                     )
-                    if include_patrol_details:
-                        observation["patrol_id"] = patrol["id"]
-                        observation["patrol_title"] = patrol["title"]
-                        observation["patrol_serial_number"] = patrol["serial_number"]
-                        observation["patrol_start_time"] = patrol_start_time
-                        observation["patrol_end_time"] = patrol_end_time
-                        observation["patrol_type"] = patrol_type
-                        observation = (
-                            observation.reset_index()
-                            .merge(
-                                pd.DataFrame(df_pt).add_prefix("patrol_type__"),
-                                left_on="patrol_type",
-                                right_on="id",
-                            )
-                            .drop(
-                                columns=[
-                                    "patrol_type__ordernum",
-                                    "patrol_type__icon_id",
-                                    "patrol_type__default_priority",
-                                    "patrol_type__is_active",
-                                ]
-                            )
-                        )
                     if len(observation) > 0:
                         observation["groupby_col"] = patrol["id"]
+
+                        if include_patrol_details:
+                            observation["patrol_id"] = patrol["id"]
+                            observation["patrol_title"] = patrol["title"]
+                            observation["patrol_serial_number"] = patrol["serial_number"]
+                            observation["patrol_start_time"] = patrol_start_time
+                            observation["patrol_end_time"] = patrol_end_time
+                            observation["patrol_type"] = patrol_type
+                            observation = (
+                                observation.reset_index()
+                                .merge(
+                                    pd.DataFrame(df_pt).add_prefix("patrol_type__"),
+                                    left_on="patrol_type",
+                                    right_on="id",
+                                )
+                                .drop(
+                                    columns=[
+                                        "patrol_type__ordernum",
+                                        "patrol_type__icon_id",
+                                        "patrol_type__default_priority",
+                                        "patrol_type__is_active",
+                                    ]
+                                )
+                            )
+
                         observations.append(observation)
                 except Exception as e:
                     print(
                         f"Getting observations for subject_id={subject_id} start_time={patrol_start_time}"
                         f"end_time={patrol_end_time} failed for: {e}"
                     )
 
+        if not observations:
+            return pd.DataFrame()
+
         df = pd.concat(observations)
         df = clean_time_cols(df)
         df = ecoscope.base.Relocations(df)

diff --git a/ecoscope/io/earthranger_utils.py b/ecoscope/io/earthranger_utils.py
@@ -70,3 +70,7 @@ def pack_columns(dataframe: pd.DataFrame, columns: typing.List):
         dataframe.drop(metadata_cols, inplace=True, axis=1)
         dataframe.rename(columns={"metadata": "additional"}, inplace=True)
     return dataframe
+
+
+def filter_bad_geojson(dataframe: pd.DataFrame):
+    return dataframe[dataframe["geojson"].apply(lambda x: True if isinstance(x, dict) and x.get("geometry") else False)]
diff --git a/tests/sample_data/io/get_events_bad_geojson.feather b/tests/sample_data/io/get_events_bad_geojson.feather