Overview

Teaching: 30 min
Exercises: 0 min
Questions
  • What is GeoPandas?

  • What functionality and advantages does GeoPandas offer over other Python geospatial tools?

  • What geospatial storage, analytical and plotting capabilities does it include?

  • What is its relationship to Pandas?

Objectives
  • Learn to use GeoPandas by reading from common vector geospatial formats (shape files, GeoJSON, etc), PostGIS databases, and from geospatial data generated on the fly.

  • Learn to leverage Pandas functionality in GeoPandas, for effective, mixed attribute-based and geospatial analyses.

  • Learn about common geospatial operations, including reprojection, spatial joins, and overlays.

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GeoPandas: Pandas + geometry data type + custom geo goodness

1. Background

GeoPandas adds a spatial geometry data type to Pandas and enables spatial operations on these types, using shapely. GeoPandas leverages Pandas together with several core open source geospatial packages and practices to provide a uniquely simple and convenient framework for handling geospatial feature data, operating on both geometries and attributes jointly, and as with Pandas, largely eliminating the need to iterate over features (rows). Also as with Pandas, it adds a very convenient and fine-tuned plotting method, and read/write methods that handle multiple file and “serialization” formats.

Additional Notes

GeoPandas is still young, but it builds on mature and stable and widely used packages (Pandas, shapely, etc). Expect kinks and continued growth!

When should you use GeoPandas?

When it may not be the best tool?

2. Set up packages and data file path

We’ll use these throughout the rest of the tutorial.

%matplotlib inline

import os

import matplotlib.pyplot as plt
# The two statemens below are used mainly to set up a plotting
# default style that's better than the default from matplotlib
import seaborn as sns
plt.style.use('bmh')

from shapely.geometry import Point
import pandas as pd
import geopandas as gpd
from geopandas import GeoSeries, GeoDataFrame

data_pth = "../data"

3. GeoSeries: The geometry building block

Like a Pandas Series, a GeoSeries is the building block for the more broadly useful and powerful GeoDataFrame that we’ll focus on in this tutorial. Here we’ll take a bit of time to examine a GeoSeries.

A GeoSeries is made up of an index and a GeoPandas geometry data type. This data type is a shapely.geometry object, and therefore inherits their attributes and methods such as area, bounds, distance, etc.

GeoPandas has six classes of geometric objects, corresponding to the three basic single-entity geometric types and their associated homogeneous collections of multiples entities:

A GeoSeries is then a list of geometry objects and their associated index values.

Entries (rows) in a GeoSeries can store different geometry types

GeoPandas does not constrain the geometry column to be of the same geometry type. This can lead to unexpected problems if you’re not careful! Specially if you’re used to thinking of a GIS file format like shape files, which store a single geometry type. Also beware that certain export operations (say, to shape files …) will fail if the list of geometry objects is heterogeneous.

But enough theory! Let’s get our hands dirty (so to speak) with code. We’ll start by illustrating how GeoSeries are constructured.

Create a GeoSeries from a list of shapely Point objects constructed directly from WKT text (though you will rarely need this raw approach)

from shapely.wkt import loads

GeoSeries([loads('POINT(1 2)'), loads('POINT(1.5 2.5)'), loads('POINT(2 3)')])
0        POINT (1 2)
1    POINT (1.5 2.5)
2        POINT (2 3)
dtype: object

Create a GeoSeries from a list of shapely Point objects

Then enhance it with a crs and plot it.

gs = GeoSeries([Point(-120, 45), Point(-121.2, 46), Point(-122.9, 47.5)])
gs
0        POINT (-120 45)
1      POINT (-121.2 46)
2    POINT (-122.9 47.5)
dtype: object
type(gs), len(gs)
(geopandas.geoseries.GeoSeries, 3)

A GeoSeries (and a GeoDataframe) can store a CRS implicitly associated with the geometry column. This is useful as essential spatial metadata and for transformation (reprojection) to another CRS.

gs.crs = {'init': 'epsg:4326'}

The plot method accepts standard matplotlib.pyplot style options, and can be tweaked like any other matplotlib figure.

gs.plot(marker='*', color='red', markersize=12, figsize=(4, 4))
plt.xlim([-123, -119.8])
plt.ylim([44.8, 47.7]);

png

Let’s get a bit fancier, as a stepping stone to GeoDataFrames. First, we’ll define a simple dictionary of lists, that we’ll use again later.

data = {'name': ['a', 'b', 'c'],
        'lat': [45, 46, 47.5],
        'lon': [-120, -121.2, -122.9]}

Note this convenient, compact approach to create a list of Point shapely objects out of X & Y coordinate lists:

geometry = [Point(xy) for xy in zip(data['lon'], data['lat'])]
geometry
[<shapely.geometry.point.Point at 0x7fad03574c10>,
 <shapely.geometry.point.Point at 0x7fad03574110>,
 <shapely.geometry.point.Point at 0x7facf5b13e10>]

We’ll wrap up by creating a GeoSeries where we explicitly define the index values.

gs = GeoSeries(geometry, index=data['name'])
gs
a        POINT (-120 45)
b      POINT (-121.2 46)
c    POINT (-122.9 47.5)
dtype: object

4. GeoDataFrames: The real power tool.

Additional notes

Start with a simple, manually constructed illustration

We’ll build on the GeoSeries examples. Let’s reuse the data dictionary we defined earlier, this time to create a DataFrame.

df = pd.DataFrame(data)
df


lat lon name
0 45.0 -120.0 a
1 46.0 -121.2 b
2 47.5 -122.9 c


Now we use the DataFrame and the “list-of-shapely-Point-objects” approach to create a GeoDataFrame. Note the use of two GeoDataFrame attribute columns, which are just two simple Pandas Series.

geometry = [Point(xy) for xy in zip(df['lon'], df['lat'])]
gdf = GeoDataFrame(df, geometry=geometry)

There’s nothing new to visualize, but this time we’re using the plot method from a GeoDataFrame, not from a GeoSeries. They’re not exactly the same thing under the hood.

gdf.plot(marker='*', color='green', markersize=6, figsize=(2, 2));

png

FINALLY, we get to work with real data! Load and examine the simple “oceans” shape file

gpd.read_file is the workhorse for reading GIS files. It leverages the fiona package.

oceans = gpd.read_file(os.path.join(data_pth, "oceans.shp"))
oceans.head()


ID Oceans geometry my_polygon
0 1 South Atlantic Ocean POLYGON ((-67.26025728926088 -59.9309210526315... S.Atlantic
1 0 North Pacific Ocean (POLYGON ((180 66.27034771241199, 180 0, 101.1... N.Pacific
2 3 Southern Ocean POLYGON ((180 -60, 180 -90, -180 -90, -180 -60... Southern
3 2 Arctic Ocean POLYGON ((-100.1196521436255 52.89103112710165... Arctic
4 5 Indian Ocean POLYGON ((19.69705552221351 -59.94160091330382... Indian


The crs was read from the shape file’s prj file:

oceans.crs
{'init': u'epsg:4326'}

Now we finally plot a real map (or blobs, depending on your aesthetics), from a dataset that’s global and stored in “geographic” (latitude & longitude) coordinates. It’snot quite the actual ocean shapes defined by coastal boundaries, but bear with me.

oceans.plot();

png

oceans.shp stores both Polygon and Multi-Polygon geometry types (but a Polygon may be viewed as a Multi-Polygon with 1 member). We can get at the geometry types and other geometry properties easily.

oceans.geom_type
0         Polygon
1    MultiPolygon
2         Polygon
3         Polygon
4         Polygon
5    MultiPolygon
6         Polygon
dtype: object
# Beware that these area calculations are in degrees, which is fairly useless
oceans.geometry.area
0     5287.751094
1    11805.894558
2    10822.509589
3     9578.786157
4     9047.879388
5     9640.457926
6     8616.721287
dtype: float64
oceans.geometry.bounds


minx miny maxx maxy
0 -71.183612 -60.000000 28.736134 0.000000
1 -180.000000 0.000000 180.000000 67.479386
2 -180.000000 -90.000000 180.000000 -59.806846
3 -180.000000 47.660532 180.000000 90.000000
4 19.697056 -59.945004 146.991853 37.102940
5 -180.000000 -60.000000 180.000000 2.473291
6 -106.430148 0.000000 45.468236 76.644442


The envelope method returns the bounding box for each polygon. This could be used to create a new spatial column or GeoSeries; directly for plotting; etc.

oceans.envelope.plot();

png

Does it seem weird that some envelope bounding boxes, such as the North Pacific Ocean, span all longitudes? That’s because they’re Multi-Polygons with edges at the ends of the -180 and +180 degree coordinate range.

oceans[oceans['Oceans'] == 'North Pacific Ocean'].plot();

png

Load “Natural Earth” countries dataset, bundled with GeoPandas

Natural Earth is a public domain map dataset available at 1:10m, 1:50m, and 1:110 million scales. Featuring tightly integrated vector and raster data, with Natural Earth you can make a variety of visually pleasing, well-crafted maps with cartography or GIS software.” It (a subset?) comes bundled with GeoPandas and is accessible from the gpd.datasets module. We’ll use it as a helpful global base layer map.

world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))
world.head(2)


continent gdp_md_est geometry iso_a3 name pop_est
0 Asia 22270.0 POLYGON ((61.21081709172574 35.65007233330923,... AFG Afghanistan 28400000.0
1 Africa 110300.0 (POLYGON ((16.32652835456705 -5.87747039146621... AGO Angola 12799293.0


Its CRS is also EPSG:4326:

world.crs
{'init': u'epsg:4326'}
world.plot();

png

Map plot overlays: Plotting multiple spatial layers

Here’s a compact, quick way of using GeoDataFrame plot method to overlay two GeoDataFrame, while style customizing the styles for each layer.

world.plot(ax=oceans.plot(cmap='Set2', alpha=1), alpha=1);

png

Watch for plotting bug

The oceans polygon boundaries are coming through the world dataset! I’ve looked into this and can’t find a solution. I think it’s a bug in the GeoPandas underlying plotting library or plotting approach.

We can also compose the plot using conventional matplotlib steps and options that give us more control.

f, ax = plt.subplots(1, figsize=(10, 5))
# Other nice categorical color maps (cmap) include 'Set2' and 'Set3'
oceans.plot(cmap='Paired', alpha=1, linewidth=0.2, ax=ax)
world.plot(alpha=1, ax=ax)
ax.set_ylim([-100, 100])
ax.set_title('Countries and Ocean Basins')
plt.axis('equal');

png

5. Extras: Reading from other data source types; fancier plotting

Read from remote PostgreSQL/PostGIS database and from an OGC WFS service.

Read PostgreSQL/PostGIS dataset from the Amazon Cloud

Though the fact that it’s on an Amazon Cloud is fairly irrelevant. It could be on a UW server, or on your local computer. The approach is identical.

import json
import psycopg2

First we’ll read the database connection information from a hidden JSON file, to add a level of security and not expose all that information on the github GeoHackWeek repository. This is also a good practice for handling sensitive information.

with open(os.path.join(data_pth, ".db.json")) as f:
    db_conn_dict = json.load(f)

Open the database connection, returning a connection object:

conn = psycopg2.connect(**db_conn_dict)

Now that we’ve used the connection information, we’ll overwrite the user and password keys and print out the dictionary, to give you a look at what needs to be in it:

db_conn_dict['user'] = '*****'
db_conn_dict['password'] = '*****'
db_conn_dict
{u'database': u'geohackweek2016',
 u'host': u'geohackweek2016.czoeuvaufkjq.us-west-2.rds.amazonaws.com',
 u'password': '*****',
 u'port': 5432,
 u'user': '*****'}

Finally, the magic: Read in the world_seas PostGIS dataset (a spatially enabled table in the PostgreSQL database) into a GeoDataFrame, using the opened connection object. Note the use of a simple SQL query string: sql select * from world_seas

seas = GeoDataFrame.from_postgis("select * from world_seas", conn, 
                                 geom_col='geometry', crs={'init': 'epsg:4326'}, 
                                 coerce_float=False)

Limitations in reading from PostGIS

GeoPandas apparently can not automatically read geom_col and crs from PostGIS. They must be specified explicitly. That’s a hassle that hopefully will be fixed in the future. Want to contribute the enhancement??

Close the connection. Clean up after yourself.

conn.close()

Let’s take a look at the GeoDataFrame.

seas.head()


gid name id gazetteer is_generic oceans geometry
0 1 Inner Seas off the West Coast of Scotland 18 4283 False North Atlantic Ocean (POLYGON ((-6.496945454545455 58.0874909090909...
1 2 Mediterranean Sea - Western Basin 28A 4279 False North Atlantic Ocean (POLYGON ((12.4308 37.80325454545454, 12.41498...
2 3 Mediterranean Sea - Eastern Basin 28B 4280 False North Atlantic Ocean (POLYGON ((23.60853636363636 35.60874545454546...
3 4 Sea of Marmara 29 3369 False North Atlantic Ocean (POLYGON ((26.21790909090909 40.05290909090909...
4 5 Black Sea 30 3319 False North Atlantic Ocean (POLYGON ((29.04846363636364 41.25555454545454...


More advanced plotting and data filtering

Color the layer based on one column that aggregates individual polygons; using a categorical map, as before, but explicitly selecting the column (column='oceans') and categorical mapping (categorical=True); dispplaying an auto-generated legend; while displaying all polygon boundaries. “oceans” (ocean basins, actually) contain one or more ‘seas’.

seas.plot(column='oceans', categorical=True, legend=True, figsize=(14,6));

png

Additional plotting examples

See http://darribas.org/gds15/content/labs/lab_04.html for great examples of lots of other cool GeoPandas map plotting tips.

Combine what we’ve learned. A map overlay, using world as a background layer, and filtering seas based on an attribute value (from oceans column) and an auto-derived GeoPandas geometry attribute (area). world is in gray scale, while the filtered seas is in color.

seas_na_arealt1000 = seas[(seas['oceans'] == 'North Atlantic Ocean') 
                          & (seas.geometry.area < 1000)]
seas_na_arealt1000.plot(ax=world.plot(alpha=0.1), cmap='Paired')

# Use the bounds geometry attribute to set a nice
# geographical extent for the plot, based on the filtered GDF
bounds = seas_na_arealt1000.geometry.bounds

plt.xlim([bounds.minx.min()-5, bounds.maxx.max()+5])
plt.ylim([bounds.miny.min()-5, bounds.maxy.max()+5]);

png

Save the filtered seas GeoDataFrame to a shape file

The to_file method uses the fiona package to write to a GIS file. The default driver for output file format is ‘ESRI Shapefile’, but many others are available because fiona leverages GDAL/OGR.

seas_na_arealt1000.to_file(os.path.join(data_pth, "seas_na_arealt1000.shp"))

Read from OGC WFS GeoJSON response into a GeoDataFrame

Use an Open Geospatial Consortium (OGC) Web Feature Service (WFS) request to obtain geospatial data from a remote source. OGC WFS is an open geospatial standard.

We won’t go into all details here about what’s going on. Suffice it to say that we issue an OGC WFS request for all features from the layer named “oa:goainv” found in a GeoServer instance from NANOOS, requesting the response in GeoJSON format. Then we “load” it into a geojson feature object (basically a dictionary) using the geojson package.

The “oa:goainv” layer is a global dataset of monitoring sites and cruises where data relevant to ocean acidification is collected. It’s a work in progress from the Global Ocean Acidification Observation Network (GOA-ON); for additional information see the GOA-ON Data Portal.

import requests
import geojson

wfs_url = "http://data.nanoos.org/geoserver/ows"
params = dict(service='WFS', version='1.0.0', request='GetFeature',
              typeName='oa:goaoninv', outputFormat='json')

r = requests.get(wfs_url, params=params)
wfs_geo = geojson.loads(r.content)

Let’s examine the general characteristics of this GeoJSON object. We’ll take advantage of the __geo_interface__ interface we discussed earlier.

print(type(wfs_geo))
print(wfs_geo.keys())
print(len(wfs_geo.__geo_interface__['features']))
<class 'geojson.feature.FeatureCollection'>
['crs', 'totalFeatures', u'type', 'features']
527

Now we use the from_features constructor method to create a GeoDataFrame, passing to it the features from the __geo_interface__ method.

wfs_gdf = GeoDataFrame.from_features(wfs_geo.__geo_interface__['features'])

Display the values for the last feature, as an example.

wfs_gdf.iloc[-1]
Oceans                                                     South Pacific Ocean
Source_Doc_kml                                                            None
additional_organizations                  Woods Hole Oceanographic Institution
agency                                       National Science Foundation (NSF)
city                                                                          
comments                     The Southern Ocean Apex Surface Mooring is co-...
comments_about_overlaps                                                       
contact_email                                      help@oceanobservatories.org
contact_name                                                                  
country                                                                     US
cruise_id                                                                  NaN
data_url                     https://rawdata.oceanobservatories.org/files/G...
department                                                                    
deploy_date                                                                   
depth_range                                                                   
duration                                                                      
frequency                                                           sub-hourly
geometry                                             POINT (-89.2069 -54.4041)
id                                                                         572
latitude                                                              -54.4041
line_xy                                                                   None
location                                                                      
longitude                                                             -89.2069
method                                                                        
method_documentation                                                          
organization                                    Ocean Observatories Initiative
organization_abbreviation                                                  OOI
overlaps_with                                                                 
parameters                          temperature; salinity; pH; CO2_air; CO2_sw
parameters_planned                                                            
platform_name                GS01SUMO: Global Southern Ocean Apex Surface M...
platform_name_kml                                                         None
platform_type                                                                M
point_xy                                                                  None
project                                                                       
sensors                                                                       
source_doc                                                                 OOI
track_pt_lat                                                              None
track_pt_lon                                                              None
type                                                      Apex Surface Mooring
url                          http://oceanobservatories.org/site/gs01sumo/; ...
Name: 526, dtype: object

Finally, a simple map overlay plot.

wfs_gdf.plot(ax=world.plot(alpha=1), figsize=(10, 6),
             marker='o', color='red', markersize=4);

png

Key Points