6

Geopandas

Lab Ob jective: Geopandas is a package designed to organize and manipulate geographic data,

It combines the data manipulation tools from Pandas and the geometric capabilities of the Shapely

package. In this lab, we explore the basic data structures of GeoSeries and GeoDataFrames and their

functionalities.

Installation
Geopandas is a new package designed to combine the functionalities of Pandas and Shapely, a package
used for geometric manipulation. Using Geopandas with geographic data is very useful as it allows
the user to not only compare numerical data, but geometric attributes. Since Geopandas is currently
under development, the installation procedure requires that all dependencies are up to date. While
possible to install Geopandas through pip using
>>> pip install geopandas

it is not recommended. You can view the warnings here https://geopandas.org/install.

html.
To install Geopandas through Conda, the recommended day, run the following code.
>>> conda install geopandas
>>> conda install -c conda-forge gdal

A particular package needed for Geopandas is Fiona. Geopandas will not run without the
correct version of this package. To check the current version of Fiona that is installed, run the
following code. If the version is not at least 1.7.13, update Fiona.
# Check version of Fiona
>>> conda list fiona

# Update Fiona if necessary

>>> pip install fiona --upgrade

1
2 Lab 6. Geopandas

GeoSeries
A GeoSeries is a Pandas Series where each entry is a set of geometric objects. There are three classes
of geometric objects inherited from the Shapely package:
1. Points / Multi-Points
2. Lines / Multi-Lines
3. Polygons / Multi-Polygons
A point is used to identify objects like coordinates, where there is one small instance of the object. A
line could be used to describe a road. A polygon could be used to identify regions, such as a country.
Multipoints, multilines, and multipolygons contain lists of points, lines, and polygons, respectively.
Since each object in the GeoSeries is also a Shapely object, the GeoSeries inherits many meth-
ods and attributes of Shapely objects. Some of the key attributes and methods are listed in Table 6.1.
These attributes and methods can be used to calculate distances, nd the sizes of countries, and de-
termine whether coordinates are within country's boundaries. The example below uses the attribute
bounds to nd the maximum and minimum coordinates of Egypt in a built-in GeoDataFrame.

Method/Attribute Description
distance(other) returns minimum distance from GeoSeries to other
contains(other) returns True if shape contains other
intersects(other) returns True if shape intersects other
area returns shape area
convex_hull returns convex shape around all points in the object

Table 6.1: Attributes and Methods for GeoSeries

>>> import geopandas as gpd

>>> world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))
# Get GeoSeries for Egypt
>>> egypt = world[world['name']=='Egypt']

# Find bounds of Egypt

>>> egypt.bounds
minx miny maxx maxy
47 24.70007 22.0 36.86623 31.58568

Creating GeoDataFrames
The main structure used in GeoPandas is a GeoDataFrame, which is similar to a Pandas DataFrame.
A GeoDataFrame has one special column called geometry. This GeoSeries column is used when a
spatial method, like distance(), is used on the GeoDataFrame.
To make a GeoDataFrame, rst create a Pandas DataFrame. At least one of the columns
in the DataFrame should contain geometric information. Convert a column containing geometric
information to a GeoSeries using the apply method. At this point, the Pandas DataFrame can be
cast as a GeoDataFrame. When creating a GeoDataFrame, if more than one column has geometric
data, assign which column will be the geometry using the set_geometry() method.
 3

>>> import pandas as pd

>>> import geopandas as gpd
>>> from shapely.geometry import Point, Polygon

# Create a Pandas DataFrame

>>> df = pd.DataFrame({'City': ['Seoul', 'Lima', 'Johannesburg'],
... 'Country': ['South Korea', 'Peru', 'South Africa'],
... 'Latitude': [37.57, -12.05, -26.20],
... 'Longitude': [126.98, -77.04, 28.04]})

# Create geometry column

>>> df['Coordinates'] = list(zip(df.Longitude, df.Latitude))

# Make geometry column Shapely objects

>>> df['Coordinates'] = df['Coordinates'].apply(Point)

# Cast as GeoDataFrame
>>> gdf = gpd.GeoDataFrame(df, geometry='Coordinates')

# Display the GeoDataFrame

>>> gdf
City Country Latitude Longitude Coordinates
0 Seoul South Korea 37.57 126.98 POINT (126.98000 37.57000)
1 Lima Peru -12.05 -77.04 POINT (-77.04000 -12.05000)
2 Johannesburg South Africa -26.20 28.04 POINT (28.04000 -26.20000)

# Create a polygon with all three cities as points

>>> city_polygon = Polygon(list(zip(df.Longitude, df.Latitude)))

Note
Longitude is the angular measurement starting at the Prime Meridian, 0°, and going to 180°
to the east and −180° to the west. Latitude is the angle between the equatorial plane and
the normal line at a given point; a point along the Equator has latitude 0, the North Pole has
latitude +90° or 90°N , and the South Pole has latitude −90° or 90°S .

Plotting GeoDataFrames
Information from a GeoDataFrame is plotted based on the geometry column. Data points are dis-
played as geometry objects. The following example plots the shapes in the world GeoDataFrame.

# Plot world GeoDataFrame

>>> world.plot()
4 Lab 6. Geopandas

75

50

25

25

50

75

150 100 50 0 50 100 150

Figure 6.1: World map

Multiple GeoDataFrames can be plotted at once. This can be done by by setting one Geo-
DataFrame as the base of the plot and ensuring that each layer uses the same axes. In the follow-
ing example, a GeoDataFrame containing the coordinates of world airports is plotted on top of a
GeoDataFrame containing the polygons of country boundaries, resulting in a world map of airport
locations.

# Set outline of world countries as base

>>> fig,ax = plt.subplots(figsize=(10,7), ncols=1, nrows=1)
>>> base = world.boundary.plot(edgecolor='black', ax=ax, linewidth=1)

# Plot airports on world map

>>> airports.plot(ax=base, marker='o', color='green', markersize=1)
>>> ax.set_xlabel('Longitude')
>>> ax.set_ylabel('Latitude')
>>> ax.set_title('World Airports')
 5

World Airports
75

50

25
Latitude

25

50

75

150 100 50 0 50 100 150

Longitude

Figure 6.2: Airport map

Problem 1. Read in the le airports.csv as a Pandas DataFrame. Create three convex
hulls around the three sets of airports listed below. This can be done by passing in lists of the
airports' coordinates to a shapely.geometry.Polygon object.
Create a new GeoDataFrame with these three Polygons as entries. Plot this GeoDataFrame
on top of an outlined world map.
ˆ Maio Airport, Scatsta Airport, Stokmarknes Skagen Airport, Bekily Airport, K. D.
Matanzima Airport, RAF Ascension Island
ˆ Oiapoque Airport, Maio Airport, Zhezkazgan Airport, Walton Airport, RAF Ascension
Island, Usiminas Airport, Piloto Osvaldo Marques Dias Airport
ˆ Zhezkazgan Airport, Khanty Mansiysk Airport, Novy Urengoy Airport, Kalay Airport,
Biju Patnaik Airport, Walton Airport

Working with GeoDataFrames

As previously mentioned, GeoDataFrames contain many of the functionalities of Pandas DataFrames.
For example, to create a new column, dene a new column name in the GeoDataFrame with the
needed information for each GeoSeries.
# Create column in the world GeoDataFrame for gdp_per_capita
>>> world['gdp_per_cap'] = world.gdp_md_est / world.pop_est

GeoDataFrames can utilize many Pandas functionalities, and they can also be parsed by geo-
metric manipulations. For example, a useful way to index GeoDataFrames is with the cx indexer.
This splits the GeoDataFrame by the coordinates of each geometric object. It is used by calling the
method cx on a GeoDataFrame, followed by a slicing argument, where the rst element refers to the
longitude and the second refers to latitude.
6 Lab 6. Geopandas

# Create a GeoDataFrame containing the northern hemisphere

>>> north = world.cx[:, 0:]

# Create a GeoDataFrame containing the southeastern hemisphere

>>> south_east = world.cx[0:, :0]

GeoSeries in a GeoDataFrame can also be dissolved, or merged, together into one GeoSeries
based on their geometry data. For example, all countries on one continent could be merged to create
a GeoSeries containing the information of that continent. The method designed for this is called
dissolve. It receives two parameters, by and aggfunc. by indicates which column to dissolve along,
and aggfunc tells how to combine the information in all other columns. The default aggfunc is first
, which returns the rst application entry. In the following example, we use sum as the aggfunc so
that each continent is the combination of its countries.
>>> world = world[['continent', 'geometry', 'gdp_per_cap']]

# Dissolve world GeoDataFrame by continent

>>> continent = world.dissolve(by = 'continent', aggfunc='sum')

Projections
When plotting, GeoPandas uses the CRS (coordinate reference system) of a GeoDataFrame. This
reference system informs how coordinates should be spaced on a plot. GeoPandas accepts many
dierent CRSs, and references to them can be found at www.spatialreference.org. Two of the
most commonly used CRSs are EPSG:4326 and EPSG:3395. EPSG:4326 uses the standard latitude-
longitude projection used by GPS. EPSG:3395, also known as Mercator, is the standard navigational
projection.
When creating a new GeoDataFrame, it is important to set the crs attribute of the Geo-
DataFrame. This allows the plot to be shown correctly. GeoDataFrames being layered need to have
the same CRS. To change the CRS, use the method to_crs().
# Check CRS of world GeoDataFrame
>>> print(world.crs)
epsg:4326

# Change CRS of world to Mercator

# inplace=True ensures that we modify world instead of returning a copy
>>> world.to_crs(3395, inplace=True)
>>> print(world.crs)
epsg:3395

GeoDataFrames can also be plotted using the values in the the other attributes of the GeoSeries.
The map plots the color of each geometry object according to the value of the column selected. This
is done by passing in the parameter column into the plot() method.
>>> fig, ax = plt.subplots(1, figsize=(10,4))
# Plot world based on gdp
 7

>>> world.plot(column='gdp_md_est', cmap='OrRd', legend=True, ax=ax)

>>> ax.set_title('World Map based on GDP')
>>> ax.set_xlabel('Longitude')
>>> ax.set_ylabel('Latitude')
>>> plt.show()

World Map based on GDP 1e7

2.00
75
1.75
50
1.50
25
1.25
Latitude

0
1.00
25 0.75
50 0.50
75 0.25

150 100 50 0 50 100 150

Longitude

Figure 6.3: World Map Based on GDP

Problem 2. Use the command geopandas.read_file('county_data.gpkg') to create a Geo-

DataFrame of information about US counties.a Each county's shape is stored in the geometry
column. Use this to plot all US counties two times, rst using the default CRS and then using
EPSG:5071.
Next, create a new GeoDataFrame that merges all counties within a single state. Drop
regions with the following STATEFP codes: 02, 15, 60, 66, 69, 72, 78. Plot this GeoDataFrame
to see an outline of all 48 contiguous states. Ensure a CRS of EPSG:5071.
a Source: http://www2.census.gov/geo/tiger/GENZ2016/shp/cb_2016_us_county_5m.zip

Merging GeoDataFrames
Just as multiple Pandas DataFrames can be merged, multiple GeoDataFrames can be merged with
attribute joins or spatial joins. An attribute join is similar to a merge in Pandas. It combines two
GeoDataFrames on a column (not the geometry column) and then combines the rest of the data into
one GeoDataFrame.
>>> world = gpd.read_file(geopandas.datasets.get_path('naturalearth_lowres'))
>>> cities = gpd.read_file(geopandas.datasets.get_path('naturalearth_cities'))

# Create subsets of the world and cities GeoDataFrames

8 Lab 6. Geopandas

>>> world = world[['continent', 'name', 'iso_a3']]

>>> cities = cities[['name', 'iso_a3']]

# Merge the GeoDataFrames on their iso_a3 code

>>> countries = world.merge(cities, on='iso_a3')

A spatial join merges two GeoDataFrames based on their geometry data. The function used
for this is sjoin. sjoin accepts two GeoDataFrames and then direction on how to merge. It is
imperative that two GeoDataFrames have the same CRS. In the example below, we merge using an
inner join with the option intersects. The inner join means that we will only use keys in the
intersection of both geometry columns, and we will retain only the left geometry column. intersects
tells the GeoDataFrames to merge on GeoSeries that intersect each other. Other options include
contains and within.

# Combine countries and cities on their geographic location

>>> countries = gpd.sjoin(world, cities, how='inner', op='intersects')

Problem 3. Load in the le nytimes.csva as a DataFrame. This le includes county-level
data for the cumulative cases and deaths of Covid-19 in the US, starting with the rst case in
Snohomish County, Washington, on January 21, 2020. Begin by converting the date column
into a DatetimeIndex.
Next, use county FIPS codes to merge your GeoDataFrame from Problem 2 with the
DataFrame you just created. A FIPS code is a 5-digit unique identier for geographic locations.
Ignore rows in the Covid-19 DataFrame with unknown FIPS codes as well as all data from
Hawaii and Alaska.
Note that the fips column of the Covid-19 DataFrame stores entries as oats, but the
county GeoDataFrame stores FIPS codes as strings, with the rst two digits in the STATEFP
column and the last three in the COUNTYFP column.
Once you have completed the merge, plot the cases from March 21, 2020 on top of your
state outline map from Problem 2, using the CRS of EPSG:5071. Finally, print out the name
of the county with the most cases on March 21, 2020 along with its case count.
a Source: https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv

Logarithmic Plotting Techniques

The color scheme of a graph can also help to communicate information clearly. A good list of
available colormaps can be found at https://matplotlib.org/3.2.1/gallery/color/colormap_
reference.html. Note also that you can reverse any colormap by adding _r to the end. The
following example demonstrates some plotting features, using country GDP as in Figure 6.3.
>>> fig, ax = plt.subplots(figsize=(15,7), ncols=1, nrows=1)
>>> world.plot(column='gdp_md_est', cmap='plasma_r',
... ax=ax, legend=True, edgecolor='gray')

# Add title and remove axis tick marks

 9

>>> ax.set_title('GDP on Linear Scale')

>>> ax.set_yticks([])
>>> ax.set_xticks([])
>>> plt.show()

GDP on Linear Scale 1e7

2.00
1.75
1.50
1.25
1.00
0.75
0.50
0.25

Figure 6.4: World map showing country GDP

Sometimes data can be much more informative when plotted on a logarithmic scale. See how
the world map changes when we add a norm argument in the code below. Depending on the purpose
of the graph, Figure 6.5 may be more informative than Figure 6.4.

>>> from matplotlib.colors import LogNorm

>>> from matplotlib.cm import ScalarMappable
>>> fig, ax = plt.subplots(figsize=(15,6), ncols=1, nrows=1)

# Set the norm using data bounds

>>> data = world.gdp_md_est
>>> norm = LogNorm(vmin=min(data), vmax=max(data))

# Plot the graph using the norm

>>> world.plot(column='gdp_md_est', cmap='plasma_r', ax=ax,
... edgecolor='gray', norm=norm)

# Create a custom colorbar

>>> cbar = fig.colorbar(ScalarMappable(norm=norm, cmap='plasma_r'),
... ax=ax, orientation='horizontal', pad=0, label='GDP')

>>> ax.set_title('Country Area on a Log Scale')

>>> ax.set_yticks([])
>>> ax.set_xticks([])
>>> plt.show()
10 Lab 6. Geopandas

GDP on a Log Scale

102 103 104 105 106 107

GDP

Figure 6.5: World map showing country GDP using a log scale

Problem 4. As in Problem 3, plot your state outline map from Problem 2 on top of a map of
the Covid-19 cases from March 21, 2020. This time, however, use a log scale. Use EPSG:5071 for
the CRS. Pick a good colormap (the counties with the most cases should generally be darkest)
and be sure to display a colorbar.

Problem 5. In this problem, you will create an animation of the spread of Covid-19 through
US counties from January 21, 2020 to June 21, 2020. Use a log scale and a good colormap, and
be sure that you're using the same norm and colorbar for the whole animation. Use EPSG:5071
for the projection.
As a reminder, below is a summary of what you will need in order to animate this map.
You may also nd it helpful to refer to the animation section included with the Volume 4 lab
manual.
1. Set up your gure and norm. Be sure to use the highest case count for your vmax so that
the scale remains uniform.
2. Write your update function. This should plot the cases from a given day.
3. Set up your colorbar. Do this outside the update function to avoid adding a new colorbar
each day.
 11

4. Create the animation. Check to make sure everything displays properly before you save
it.
5. Save the animation.
6. Display the animation.