Alex G Rice

Dev Blog of a software engineer with passion for geography and GIS

A points in polygons spatial join for Rust and WebAssembly

November 12, 2019

A tour of GIS Spatial Joins, Rust language development, and WebAssembly.

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Background

I first encountered a very slow spatial join while working on the final project for my Geographic Information Systems graduate certificate from Penn State. The class was GEOG486: Cartography and Visualization. I was creating a map of all the lightning strikes in New Mexico over a 12 year period, aggregated into hex-bins. That’s about 10 million points and a thousand hex-bins. Using ESRI ArcMap, the spatial join took ~45 minutes on a desktop workstation. I thought “Wow! Why is that so slow?” My deliverable for that capstone project is a PDF map, which you can download here.

Cartography

More recently working at Descartes Labs we were developing a JavaScript app for lightweight GIS analysis in browser. One of the features was a points-in-polygons (PIP) join. It worked fine, but when we tried a data file with complex polygon geometries, the app grinded to a halt for several minutes. Very slow spatial join strikes again! 👻

Let us dig into this particular type of “contains” spatial join and see why it can be such a performance hit.

Visual Explanation

Spatial Join

Given a collection of Points, and a collection of Polygons (left), return the set of Points which are contained by the Polygons (right). It is something you can do visually without even thinking, but computationally it is more complex than you might think.

Ray Cast Algorithm

A common algorithm for deciding whether a point is contained in a polygon is the raycast algorithm:

Raycast Test Melchoir CC BY-SA 3.0

One simple way of finding whether the point is inside or outside a simple polygon is to test how many times a ray, starting from the point and going in any fixed direction, intersects the edges of the polygon. If the point is on the outside of the polygon the ray will intersect its edge an even number of times. If the point is on the inside of the polygon then it will intersect the edge an odd number of times. Wikipedia

It should be apparent that this algorithm is sensitive to the complexity of the polygons. The more edges and holes, the more expensive it is to test each polygon against each point.

Learning Rust is a Journey

Rust Rust is a new programming language from Mozilla. Rust 1.0 was released in 2015. The 2018 edition of Rust focused on the developer experience and tooling. Rust is being used for everything: traditional systems programming, microservices, databases, network servers, embedded devices, distributed systems, and surprisingly, web app development too because of its suitability to target WebAssembly (WASM).

In the late 90’s I attempted to learn C / C++ but never got very far with it, because I did not have the determination and patience. Simply put, once I experienced crashing and memory corruption I sought out safer alternatives like Java, C#, and Python.

But today Rust claims to offer something pretty appealing: Performance, Reliability and Productivity. Its borrow checking compiler and lifetimes annotation syntax is new and innovative. It also takes ideas from other modern languages, such as OCaml, F#, and Haskell (the ML language family) as well as C++.

I wanted to try out these claims for myself. I have read some Rust books, and done some coding exercises, so I decided this would be a good first project:

  1. Implement a points-in-polygons (PIP) spatial join in Rust.
  2. Compile it to WASM.
  3. Benchmark its performance compared with a popular JavaScript library.

Dancing With The Borrow Checker

Rust has a significant learning curve. In my opinion though it is not as tough as C / C++. The beauty of the Rust developer experience is how the compiler (rustc), package manager (cargo), and linter (clippy) all combine to make a consistent environment that is always pushing you forward and helping you write better code. It is really a joy to use. Yes, sometimes you have to “battle” (I prefer to think of it as “dance”) with the borrow checker and solve puzzles about ownership vs references. Sometimes it is maddening. But in the end, once something compiles, you will have a great degree of confidence that your code is going to do exactly what you expect it to, and do it efficiently.

I intend to show in this article that it is feasible for a Rust beginner to:

  • Create something that compiles and runs reliably
  • Has unit tests
  • Runs much faster than a scripting language

Define The Function Signature

Turf.js is a popular open source package for geospatial analysis for browsers and Node.js. One of Turf’s functions is pointsWithinPolygon. Let us call that the reference implementation. The function signature is, according to Turf’s docs:

points (Feature|FeatureCollection <Point>) // Points as input search
polygon (FeatureCollection|Geometry|Feature<(Polygon|MultiPolygon)>) // Points must be within these (Multi)Polygon(s)
returns FeatureCollection<Point> //  points that land within at least one polygon

For this exercise, I simplified that to:

points (FeatureCollection<Point>)
polygons (FeatureCollection<(Polygon|MultiPolygon)>)
returns FeatureCollection<Point>

Translated from JavaScript to Rust, the function signature is therefore:

pub fn points_within_polygons(
    points: FeatureCollection,
    polygons: FeatureCollection,
) -> Option<FeatureCollection>

Notice the return type is Option. Rust has enumerated types, and in this example it can return None or Some(FeatureCollection). If no points are matched, it is clear what happens in the Rust code: None is returned. Consider the JavaScript function, what happens if no points are matched? An empty FeatureCollection is created?

Also notice the Rust types are relaxed on the points and polygons parameters. In GeoRust the FeatureCollection type is considered as the serialization format (part of the GeoJson spec). There is no way I could find to express exactly FeatureCollection<(Polygon|MultiPolygon)> as the Turf.js docs are suggesting.

However, in Rust, we can pattern match the data at runtime and extract only the features we are interested in: Points, Polygons and MultiPolygons.

Pick a Data Set

  • Points dataset: I randomly generated sets of 10, 100 and 1,000 points in decimal degrees and wrote them to files as a GeoJson FeatureCollection. I wrote a tiny Rust program to do that.
  • Polygons dataset: I chose the Natural Earth datasets ne_110m_land and ne_10m_land. This was convenient because it comes with multiple levels of simplification and many people are familiar with this reference data. I chose the 1:110m and 1:10m for this exercise. Recall the Visual Explanation above? Those polygons are the Natural Earth land vector data:

Spatial Join

Test Driven Development (TDD)

Having identified the reference implementation (Turf.js’s pointsWithinPolygon function) and our two inputs to the function, next I wrote a small TypeScript module to run in Node.js and call Turf.js and print out the results. I saved these to geojson files into tests/fixtures/natural-earth/. Now there are 6 test cases which we will benchmark against later. Simple and Complex polygons, and 3 sizes of Point collections (10, 100 and 1,000).

tests/fixtures/natural-earth
├── ne_10m_land.geojson
├── ne_10m_land_points10_result.geojson
├── ne_10m_land_points100_result.geojson
├── ne_10m_land_points1000_result.geojson
├── ne_110m_land.geojson
├── ne_110m_land_points10_result.geojson
├── ne_110m_land_points100_result.geojson
├── ne_110m_land_points1000_result.geojson
├── points-10.geojson
├── points-100.geojson
├── points-1000.geojson
└── README.txt

Here is an excerpt of one of the unit tests in Rust. Notice the pattern match at the end:

// Excerpt of tests/natural_earth.rs
#[test]
fn natural_earth_test_complex_polygons() {
    let points_data = fs::read_to_string([FIXTURES_PATH, "points-10.geojson"].concat())
        .expect(READ_FILE_FAIL_MSG);
    let points_geojson = points_data.parse::<GeoJson>().unwrap();
    let points_fc = common::feature_collection(points_geojson);
    let polygons_data = fs::read_to_string([FIXTURES_PATH, "ne_10m_land.geojson"].concat())
        .expect(READ_FILE_FAIL_MSG);
    let polygons_geojson = polygons_data.parse::<GeoJson>().unwrap();
    let polygons_fc = common::feature_collection(polygons_geojson);
    let expect_pretty_printed =
        fs::read_to_string([FIXTURES_PATH, "ne_10m_land_points10_result.geojson"].concat())
            .expect(READ_FILE_FAIL_MSG);
    let expect_geojson = expect_pretty_printed.parse::<GeoJson>().unwrap();
    let expect_str = expect_geojson.to_string();
    let maybe_result_fc = points_within_polygons(points_fc, polygons_fc);
    match maybe_result_fc {
        Some(feature_collection) => {
            // features may be returned in different order, so assert on the
            // geojson encoding length. (you can also view the geojsons for
            // comparison)
            let result_str = feature_collection.to_string();
            assert_eq!(expect_str.len(), result_str.len());
        }
        None => panic!("expect result to be FeatureCollection"),
    }
}

Rust Implementation

Of interest is the pattern matching, and converting between GeoJson types and Geo types. It was a pain point learning how to translate into GeoRust native types in and out of GeoJson. However, the heavy lifting of the function contains() was already implemented in GeoRust geo crate, so the task was mostly translating between types, and enumerating through the FeatureCollections.

The complete source code is in Github, please see the Links section. The section Next Steps and Optimizations lists some outstanding TODO items as well as ideas for optimizing this function.

// Excerpt of src/lib.rs
pub fn points_within_polygons(
  points_fc: geojson::FeatureCollection,
  polygons_fc: geojson::FeatureCollection,
) -> Option<geojson::FeatureCollection> {
  let polygon_geometries = geometries_with_bounds(polygons_fc);
  let contained_point_features: Vec<_> = points_fc
    .features
    .into_iter()
    .filter(|point_feature| match &point_feature.geometry {
      None => false,
      Some(geojson_geometry) => match &geojson_geometry.value {
        geojson::Value::Point(point_type) => {
          let point_geometry = create_geo_point::<f64>(&point_type);
          let point_is_contained = polygon_geometries.iter().any(|geometry_with_bounds| {
            match &geometry_with_bounds.geometry {
              Geometry::Polygon(polygon) => polygon.contains(&point_geometry),
              Geometry::MultiPolygon(multi_polygon) => multi_polygon.contains(&point_geometry),
              _ => false,
            }
          });
          point_is_contained
        }
        _ => false,
      },
    })
    .collect();
  if contained_point_features.is_empty() {
    None
  } else {
    let result = geojson::FeatureCollection {
      bbox: None,
      features: contained_point_features,
      foreign_members: None,
    };
    Some(result)
  }
}

WASM bindings

Rust’s wasm-bindgen and wasm-pack tools were easy to use and they just worked. Here is is the Rust function binding my Rust library to JavaScript:

// Excerpt of wasm/src/lib.rs
#[wasm_bindgen]
pub fn points_within_polygons(points: JsValue, polygons: JsValue) -> JsValue {
    utils::set_panic_hook();
    let points_geojson: GeoJson = points.into_serde().unwrap();
    let polygons_geojson: GeoJson = polygons.into_serde().unwrap();
    let points_fc = feature_collection(points_geojson);
    let polygons_fc = feature_collection(polygons_geojson);
    let opt_feature_collection = lib_points_within_polygons(points_fc, polygons_fc);
    match opt_feature_collection {
        Some(feature_collection) => JsValue::from_serde(&feature_collection).unwrap(),
        None => JsValue::from_bool(false),
    }
}

Benchmark module in TypeScript

// Excerpt of js/benchmark.ts
import * as benchmark from 'benchmark';
import { pointsWithinPolygon } from '@turf/turf';
import { readFileSync } from 'fs';
import { points_within_polygons as wasmPointsWithinPolygons } from 'points-within-polygons-wasm';

const suite = new benchmark.Suite;
const pointsFeatureCollection_10 = JSON.parse(readFileSync('./fixtures/natural-earth/points-10.geojson').toString());
const pointsFeatureCollection_100 = JSON.parse(readFileSync('./fixtures/natural-earth/points-100.geojson').toString());
const pointsFeatureCollection_1000 = JSON.parse(readFileSync('./fixtures/natural-earth/points-1000.geojson').toString());
const simplePolygonsFeatureCollection = JSON.parse(readFileSync('./fixtures/natural-earth/ne_110m_land.geojson').toString());
const complexPolygonsFeatureCollection = JSON.parse(readFileSync('./fixtures/natural-earth/ne_10m_land.geojson').toString());
const turfMsg = 'turf.js/pointsWithinPolygon on';
const wasmMsg = 'rust-wasm pointsWithinPolgons on';
suite
    .add(`${turfMsg} simple polygons x 10 points`, () => {
        pointsWithinPolygon(pointsFeatureCollection_10, simplePolygonsFeatureCollection);
    })
    .add(`${wasmMsg} simple polygons x 10 points`, () => {
        wasmPointsWithinPolygons(pointsFeatureCollection_10, simplePolygonsFeatureCollection);
    })
    // ... all the other combinations
    .add(`${turfMsg} complex polygons x 1000 points`, () => {
        pointsWithinPolygon(pointsFeatureCollection_1000, complexPolygonsFeatureCollection);
    })
    .add(`${wasmMsg} complex polygons x 1000 points`, () => {
        wasmPointsWithinPolygons(pointsFeatureCollection_1000, complexPolygonsFeatureCollection);
    })
    .on('cycle', function (event) {
        console.log(String(event.target));
    })
    .run();

Benchmark Results

More operations per second (ops/sec) is better! Each operation is one function call to perform a spatial join.

Benchmark1

Benchmark2

Test System: Node.js v12.13 - OS X - 2.6 GHz Intel Core i5

Observations

  1. Rust WASM is faster in 5/6 of the benchmarks.
  2. Rust WASM exhibits greater performance, relative to Turf.js, the more points its tasked with. Notice the Y-Axis is Log Scale, and the red and blue lines are diverging, not parallel, as the number of points increases.
  3. Turf.js was faster for one out of the six benchmarks: 10 points and Complex polygons. I have a theory (untested) that is because of the cost of serializing the GeoJson to send it to the WASM module. WASM’s native types consist of just integers and float numbers. I believe byte arrays can also be efficiently transferred across the WASM boundary. Everything else has to be serialized. In fact, for each points_in_polygons function call, there are 6 geojson serialization/de-serialization steps!

Serialize All The Things

Flowchart

As suggested above in the discussion some use cases might not see any performance gains with WASM if the cost of serialization is greater than the benefits gained by doing the computation in WASM.

That said, WASM brings other benefits such as predictable behavior, no garbage collection hiccups, and a fast-loading binary format. Rust of course brings its type safety and other developer benefits.

Next Steps and Future Optimizations

Bounding Box Checking

GeoJson Features have an optional bbox property. The Turf.js function checks for that and does an early-out optimization if a point is not within the bbox of a polygon. In my Rust implementation I did not do that, yet. This does not affect the benchmarks shown above because the reference polygon dataset does not include bounding boxes. Checking for the bounding rectangle in the Rust points_within_polygons() seems to be a necessary next step to make it a drop-in replacement for the Turf.js function.

API Design

My Rust function “asks for more ownership than it needs”. That terminology came from Matt Brubeck (@mbrubeck) on the Rust Users Forum. That is, it takes ownership of the points and polygons parameters. This is in large part because of some of the 3rd party functions I used, e.g. the geo_geojson crate also ask to take ownership. This bubbled up to my function signature. This is apparently not unheard of in Rust, and it seems to me that it violates the dependency inversion principle (abstractions should not depend on details). It may just be a fact of life in the Rust borrow checker’s world. In any case, I want to rewrite my function so its signature takes just references. There may need to be lifetime annotations added as well…

// Improved fn signature?
pub fn points_within_polygons(
  points: &FeatureCollection,
  polygons: &FeatureCollection,
) -> Option<FeatureCollection>

Add a R-Tree Spatial Index

In practice, just discovering which points are contained might not actually be that useful. Typically in a GIS workflow one will want to aggregate the points into buckets aka bins. This is commonly seen as a Choropleth Map.

Stuart Lynn (@stuartlynn) co-incidentally is working on a similar project using Rust and WASM. It takes points as CSV and aggregates them into GeoJson polygons. It has a cool user interface/demo, and he used the rstar crate for an r*-tree spatial index. I hope to learn from @stuartlynn’s code and see if the rstar crate can be used in my function and then see how it effects the benchmarks.

Parallelize Using WebWorkers and/or GPU

The Point-in-Polygon (PIP) test is suitable for parallelization on GPU or on WebWorker. This is one of several publications about it: Speeding up Large-Scale Point-in-Polygon Test Based Spatial Join on GPUs.

The upcoming WebGPU standard may offer general purpose GPU compute capabilities that would fit this use case in the browser.

Thanks

One of Rust’s strengths is its Community. I have felt welcomed on the Users Forum, GitHub and Discord chat. The developer experience is a big part of what defines Rust. Cheers to the GeoRust developers, and the individuals I mentioned above.

Links

https://github.com/guidorice/points-within-polygons

https://github.com/guidorice/random-geojson-points

https://www.rust-lang.org/

https://github.com/georust

https://rustwasm.github.io/wasm-pack/

https://rustwasm.github.io/docs/book/

https://github.com/stuartlynn/wasm_geo_agg

http://www.naturalearthdata.com/

http://turfjs.org/

https://webassembly.org/

https://www-cs.ccny.cuny.edu/~jzhang/papers/pipsp_tr.pdf

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