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Open and Plot Shapefiles in Python

Overview

Teaching: 20 min
Exercises: 10 min
Questions
  • How can I distinguish between and visualize point, line and polygon vector data?

Objectives
  • Know the difference between point, line, and polygon vector elements.

  • Load point, line, and polygon shapefiles with geopandas.

  • Access the attributes of a spatial object with geopandas.

Things You’ll Need To Complete This Episode

See the lesson homepage for detailed information about the software, data, and other prerequisites you will need to work through the examples in this episode.

Starting with this episode, we will be moving from working with raster data to working with vector data. In this episode, we will open and plot point, line and polygon vector data stored in shapefile format in R. These data refer to the NEON Harvard Forest field site, which we have been working with in previous episodes. In later episodes, we will learn how to work with raster and vector data together and combine them into a single plot.

Import Shapefiles

We will use the geopandas package to work with vector data in Python. We will also use the rioxarray.

import geopandas as gpd

The shapefiles that we will import are:

The first shapefile that we will open contains the boundary of our study area (or our Area Of Interest or AOI, hence the name aoi_boundary). To import shapefiles we use the geopandas function read_file().

Let’s import our AOI:

aoi_boundary_HARV = gpd.read_file(
  "data/NEON-DS-Site-Layout-Files/HARV/HarClip_UTMZ18.shp")

Shapefile Metadata & Attributes

When we import the HarClip_UTMZ18 shapefile layer into Python (as our aoi_boundary_HARV object) it comes in as a DataFrame, specifically a GeoDataFrame. read_file() also automatically stores geospatial information about the data. We are particularly interested in describing the format, CRS, extent, and other components of the vector data, and the attributes which describe properties associated with each individual vector object.

Data Tip

The Explore and Plot by Shapefile Attributes episode provides more information on both metadata and attributes and using attributes to subset and plot data.

Spatial Metadata

Key metadata for all shapefiles include:

  1. Object Type: the class of the imported object.
  2. Coordinate Reference System (CRS): the projection of the data.
  3. Extent: the spatial extent (i.e. geographic area that the shapefile covers) of the shapefile. Note that the spatial extent for a shapefile represents the combined extent for all spatial objects in the shapefile.

Each GeoDataFrame has a "geometry" column that contains geometries. In the case of our aoi_boundary_HARV, this geometry is represented by a shapely.geometry.Polygon object. geopandas uses the shapely library to represent polygons, lines, and points, so the types are inherited from shapely.

We can view shapefile metadata using the .crs, .bounds and .type attributes. First, let’s view the geometry type for our AOI shapefile. To view the geometry type, we use the pandas method .type function on the GeoDataFrame, aoi_boundary_HARV.

aoi_boundary_HARV.type
shapely.geometry.polygon.Polygon

To view the CRS metadata:

aoi_boundary_HARV.crs
{'init': 'epsg:32618'}
import earthpy
earthpy.epsg['32618']
'+proj=utm +zone=18 +datum=WGS84 +units=m +no_defs'

Our data in the CRS UTM zone 18N. The CRS is critical to interpreting the object’s extent values as it specifies units. To find the extent of our AOI in the projected coordinates, we can use the .bounds() function:

aoi_boundary_HARV.bounds
            minx          miny           maxx          maxy
0  732128.016925  4.713209e+06  732251.102892  4.713359e+06

The spatial extent of a shapefile or shapely spatial object represents the geographic “edge” or location that is the furthest north, south east and west. Thus is represents the overall geographic coverage of the spatial object. Image Source: National Ecological Observatory Network (NEON).

Extent image

We can convert these coordinates to a bounding box or acquire the index the dataframe to access the geometry. Either of these polygons can be used to clip rasters (more on that later).

Reading a Shapefile from a csv

So far we have been loading file formats that were specifically built to hold spatial information. But often, point data is stored in table format, with a column for the x coordinates and a column for the y coordinates. The easiest way to get this type of data into a GeoDataFrame is with the geopandas function geopandas.points_from_xy, which takes list-like sequences of x and y coordinates. In this case, we can get these list-like sequences from columns of a pandas DataFrame that we get from read_csv.

# we get the projection of the point data from our Canopy Height Model, 
# after examining the pandas DataFrame and seeing that the CRSs are the same
import rioxarray
CHM_HARV <-
  rioxarray.open("data/NEON-DS-Airborne-Remote-Sensing/HARV/CHM/HARV_chmCrop.tif")

# plotting locations in CRS coordinates using CHM_HARV's CRS
plot_locations_HARV =
  pd.read_csv("data/NEON-DS-Site-Layout-Files/HARV/HARV_PlotLocations.csv")
plot_locations_HARV = gpd.GeoDataFrame(plot_locations_HARV, 
                    geometry=gpd.points_from_xy(plot_locations_HARV.easting, plot_locations_HARV.northing), 
                    crs=CHM_HARV.rio.crs)

Plotting a Shapefile

Any GeoDataFrame can be plotted in CRS units to view the shape of the object with .plot().

aoi_boundary_HARV.plot()

We can customize our boundary plot by setting the figsize, edgecolor, and color. Making some polygons transparent will come in handy when we need to add multiple spatial datasets to a single plot.

aoi_boundary_HARV.plot(figsize=(5,5), edgecolor="purple", facecolor="None")

Under the hood, geopandas is using matplotlib to generate this plot. In the next episode we will see how we can add DataArrays and other shapefiles to this plot to start building an informative map of our area of interest.

Spatial Data Attributes

We introduced the idea of spatial data attributes in an earlier lesson. Now we will explore how to use spatial data attributes stored in our data to plot different features.

Challenge: Import Line and Point Shapefiles

Using the steps above, import the HARV_roads and HARVtower_UTM18N layers into Python using geopandas. Name the HARV_roads shapefile as the variable lines_HARV and the HARVtower_UTM18N shapefile point_HARV.

Answer the following questions:

  1. What type of Python spatial object is created when you import each layer?

  2. What is the CRS and extent (bounds) for each object?

  3. Do the files contain points, lines, or polygons?

  4. How many spatial objects are in each file?

Answers

First we import the data:

lines_HARV = gpd.read_file("data/NEON-DS-Site-Layout-Files/HARV/HARV_roads.shp")
point_HARV = gpd.read_file("data/NEON-DS-Site-Layout-Files/HARV/HARVtower_UTM18N.shp")

Then we check the types:

lines_HARV.type
point_HARV.type

We also check the CRS and extent of each object:

print(lines_HARV.crs)
print(point_HARV.bounds)
print(lines_HARV.crs)
print(point_HARV.bounds)

To see the number of objects in each file, we can look at the output from when we print the results in a Jupyter notebook of call len() on a GeoDataFrame. lines_HARV contains 13 features (all lines) and point_HARV contains only one point.

Key Points

  • Shapefile metadata include geometry type, CRS, and extent.

  • Load spatial objects into Python with the geopandas.read_file() method.

  • Spatial objects can be plotted directly with geopandas.GeoDataFrame.plot().