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Aug 26, 2024
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Create analysis example for pollution data & run black #34

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1c3d9b7
Create analysis example for pollution data
mar3021 Aug 13, 2024
7448f53
Updates to links
mar3021 Aug 13, 2024
027b9ff
Change speed units in outlier filter
mar3021 Aug 26, 2024
2e0c358
Update article reference
mar3021 Aug 26, 2024
72f6e46
Updates to pollution data notebook example
mar3021 Aug 26, 2024
cc3c54b
Delete 2021-01-30_all.csv
mar3021 Aug 26, 2024
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107 changes: 72 additions & 35 deletions 2-analysis-examples/bird-migration.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
"import geopandas as gpd\n",
"import movingpandas as mpd\n",
"import shapely as shp\n",
"import hvplot.pandas \n",
"import hvplot.pandas\n",
"import matplotlib.pyplot as plt\n",
"\n",
"from geopandas import GeoDataFrame, read_file\n",
Expand All @@ -49,11 +49,14 @@
"from urllib.request import urlretrieve\n",
"\n",
"import warnings\n",
"warnings.filterwarnings('ignore')\n",
"\n",
"plot_defaults = {'linewidth':5, 'capstyle':'round', 'figsize':(9,3), 'legend':True}\n",
"opts.defaults(opts.Overlay(active_tools=['wheel_zoom'], frame_width=300, frame_height=500))\n",
"hvplot_defaults = {'tiles':None, 'cmap':'Viridis', 'colorbar':True}\n",
"warnings.filterwarnings(\"ignore\")\n",
"\n",
"plot_defaults = {\"linewidth\": 5, \"capstyle\": \"round\", \"figsize\": (9, 3), \"legend\": True}\n",
"opts.defaults(\n",
" opts.Overlay(active_tools=[\"wheel_zoom\"], frame_width=300, frame_height=500)\n",
")\n",
"hvplot_defaults = {\"tiles\": None, \"cmap\": \"Viridis\", \"colorbar\": True}\n",
"\n",
"mpd.show_versions()"
]
Expand All @@ -72,7 +75,7 @@
"outputs": [],
"source": [
"%%time\n",
"df = read_file('../data/gulls.gpkg')\n",
"df = read_file(\"../data/gulls.gpkg\")\n",
"print(f\"Finished reading {len(df)}\")"
]
},
Expand Down Expand Up @@ -114,7 +117,7 @@
"metadata": {},
"outputs": [],
"source": [
"df['individual-local-identifier'].unique()"
"df[\"individual-local-identifier\"].unique()"
]
},
{
Expand All @@ -130,7 +133,7 @@
"metadata": {},
"outputs": [],
"source": [
"df['individual-local-identifier'].value_counts().plot(kind='bar', figsize=(17,3))"
"df[\"individual-local-identifier\"].value_counts().plot(kind=\"bar\", figsize=(17, 3))"
]
},
{
Expand All @@ -146,7 +149,9 @@
"metadata": {},
"outputs": [],
"source": [
"tc = mpd.TrajectoryCollection(df, 'individual-local-identifier', t='timestamp', min_length=100) \n",
"tc = mpd.TrajectoryCollection(\n",
" df, \"individual-local-identifier\", t=\"timestamp\", min_length=100\n",
")\n",
"tc"
]
},
Expand Down Expand Up @@ -186,7 +191,7 @@
"metadata": {},
"outputs": [],
"source": [
"filtered = tc.filter('individual-local-identifier', '91916A')\n",
"filtered = tc.filter(\"individual-local-identifier\", \"91916A\")\n",
"my_traj = filtered.trajectories[0].copy()\n",
"my_traj.df.head()"
]
Expand All @@ -197,7 +202,7 @@
"metadata": {},
"outputs": [],
"source": [
"my_traj.hvplot(title=f'Movement of {my_traj.id}', line_width=2) "
"my_traj.hvplot(title=f\"Movement of {my_traj.id}\", line_width=2)"
]
},
{
Expand All @@ -215,7 +220,7 @@
"metadata": {},
"outputs": [],
"source": [
"trips_by_year = mpd.TemporalSplitter(filtered).split(mode='year')\n",
"trips_by_year = mpd.TemporalSplitter(filtered).split(mode=\"year\")\n",
"trips_by_year.to_traj_gdf()"
]
},
Expand All @@ -232,7 +237,7 @@
"metadata": {},
"outputs": [],
"source": [
"one_year = trips_by_year.get_trajectory('91916A_2010-12-31 00:00:00')\n",
"one_year = trips_by_year.get_trajectory(\"91916A_2010-12-31 00:00:00\")\n",
"one_year"
]
},
Expand All @@ -251,8 +256,14 @@
"metadata": {},
"outputs": [],
"source": [
"one_year.hvplot(title=f'Movement speed of {one_year.id}', \n",
" line_width=5.0, c='speed', cmap='RdYlGn', colorbar=True, clim=(0,20)) "
"one_year.hvplot(\n",
" title=f\"Movement speed of {one_year.id}\",\n",
" line_width=5.0,\n",
" c=\"speed\",\n",
" cmap=\"RdYlGn\",\n",
" colorbar=True,\n",
" clim=(0, 20),\n",
")"
]
},
{
Expand All @@ -270,8 +281,11 @@
"source": [
"def plot_location_at_timestamp(traj, t, fig_size=250):\n",
" loc = GeoDataFrame([traj.get_row_at(t)])\n",
" return (loc.hvplot(title=str(t), geo=True, tiles='OSM', size=200, color='red') * \n",
" traj.hvplot(line_width=1.0, color='black', tiles=False, width=fig_size, height=fig_size))"
" return loc.hvplot(\n",
" title=str(t), geo=True, tiles=\"OSM\", size=200, color=\"red\"\n",
" ) * traj.hvplot(\n",
" line_width=1.0, color=\"black\", tiles=False, width=fig_size, height=fig_size\n",
" )"
]
},
{
Expand All @@ -280,9 +294,11 @@
"metadata": {},
"outputs": [],
"source": [
"( plot_location_at_timestamp(one_year, datetime(2010,9,1)) + \n",
" plot_location_at_timestamp(one_year, datetime(2010,10,1)) +\n",
" plot_location_at_timestamp(one_year, datetime(2010,11,1)) )"
"(\n",
" plot_location_at_timestamp(one_year, datetime(2010, 9, 1))\n",
" + plot_location_at_timestamp(one_year, datetime(2010, 10, 1))\n",
" + plot_location_at_timestamp(one_year, datetime(2010, 11, 1))\n",
")"
]
},
{
Expand All @@ -302,11 +318,13 @@
" ts = [datetime(year, month, day) for year in traj.df.index.year.unique()]\n",
" return plot_locations_at_timestamps(traj, ts, ax=ax)\n",
"\n",
"def plot_locations_at_timestamps(traj, ts, ax=None): \n",
"\n",
"def plot_locations_at_timestamps(traj, ts, ax=None):\n",
" loc = GeoDataFrame([traj.get_row_at(t) for t in ts])\n",
" loc['date_label'] = loc.index.strftime('%Y-%m-%d')\n",
" return (loc.hvplot(title=f'Movement of {traj.id}', c='date_label', size=200, geo=True, tiles='OSM') *\n",
" traj.hvplot(line_width=1.0, color='black', geo=True, tiles=False) )"
" loc[\"date_label\"] = loc.index.strftime(\"%Y-%m-%d\")\n",
" return loc.hvplot(\n",
" title=f\"Movement of {traj.id}\", c=\"date_label\", size=200, geo=True, tiles=\"OSM\"\n",
" ) * traj.hvplot(line_width=1.0, color=\"black\", geo=True, tiles=False)"
]
},
{
Expand Down Expand Up @@ -334,7 +352,9 @@
"outputs": [],
"source": [
"area_of_interest = Polygon([(30, 25), (50, 25), (50, 15), (30, 15), (30, 25)])\n",
"plotted_area_of_interest = GeoDataFrame(pd.DataFrame([{'geometry': area_of_interest, 'id': 1}]), crs=4326).hvplot(geo=True, color='yellow', alpha=0.5)"
"plotted_area_of_interest = GeoDataFrame(\n",
" pd.DataFrame([{\"geometry\": area_of_interest, \"id\": 1}]), crs=4326\n",
").hvplot(geo=True, color=\"yellow\", alpha=0.5)"
]
},
{
Expand All @@ -347,7 +367,9 @@
"print(f\"Found {len(arrivals)} arrivals\")\n",
"\n",
"for traj in arrivals:\n",
" print(f\"Individual '{traj.df['individual-local-identifier'].iloc[0]}' arrived at {traj.get_start_time()}\")"
" print(\n",
" f\"Individual '{traj.df['individual-local-identifier'].iloc[0]}' arrived at {traj.get_start_time()}\"\n",
" )"
]
},
{
Expand All @@ -356,7 +378,10 @@
"metadata": {},
"outputs": [],
"source": [
"( plot_locations_at_timestamps(my_traj, [traj.get_start_time() for traj in arrivals]) * plotted_area_of_interest )"
"(\n",
" plot_locations_at_timestamps(my_traj, [traj.get_start_time() for traj in arrivals])\n",
" * plotted_area_of_interest\n",
")"
]
},
{
Expand All @@ -376,7 +401,12 @@
"source": [
"year_of_interest = 2010\n",
"trajs_in_aoi = tc.clip(area_of_interest)\n",
"relevant = [ traj for traj in trajs_in_aoi if traj.get_start_time().year <= year_of_interest and traj.get_end_time().year >= year_of_interest]\n",
"relevant = [\n",
" traj\n",
" for traj in trajs_in_aoi\n",
" if traj.get_start_time().year <= year_of_interest\n",
" and traj.get_end_time().year >= year_of_interest\n",
"]\n",
"print(\"Found {} arrivals\".format(len(relevant)))"
]
},
Expand All @@ -387,9 +417,13 @@
"outputs": [],
"source": [
"for traj in relevant:\n",
" print(\"Individual '{}' arrived at {} (duration: {})\".format(\n",
" traj.df['individual-local-identifier'].iloc[0], traj.get_start_time().date(), \n",
" traj.get_end_time()-traj.get_start_time()))"
" print(\n",
" \"Individual '{}' arrived at {} (duration: {})\".format(\n",
" traj.df[\"individual-local-identifier\"].iloc[0],\n",
" traj.get_start_time().date(),\n",
" traj.get_end_time() - traj.get_start_time(),\n",
" )\n",
" )"
]
},
{
Expand All @@ -407,10 +441,12 @@
"metadata": {},
"outputs": [],
"source": [
"my_traj = tc.get_trajectory('91761A')\n",
"segment = my_traj.get_segment_between(datetime(year_of_interest,1,1), datetime(year_of_interest,12,31))\n",
"my_traj = tc.get_trajectory(\"91761A\")\n",
"segment = my_traj.get_segment_between(\n",
" datetime(year_of_interest, 1, 1), datetime(year_of_interest, 12, 31)\n",
")\n",
"\n",
"segment.hvplot(color='black', line_width=1.0) * plotted_area_of_interest "
"segment.hvplot(color=\"black\", line_width=1.0) * plotted_area_of_interest"
]
},
{
Expand All @@ -435,7 +471,8 @@
"1. [Soccer game](soccer-game.ipynb)\n",
"1. [Mars rover & heli](mars-rover.ipynb)\n",
"1. [Ever Given](ever-given.ipynb)\n",
"1. [Iceberg](iceberg.ipynb) "
"1. [Iceberg](iceberg.ipynb)\n",
"1. [Pollution data](pollution-data.ipynb)"
]
}
],
Expand Down
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