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Flatgeobuf - pyogrio spatial index perf benchmark
Raw
.gitattributes
# GitHub syntax highlighting
pixi.lock linguist-language=YAML
Raw
.gitignore
# pixi environments
.pixi
*.geojson.zip
*.fgb
Raw
README.md

Benchmarking FlatGeobuf read with spatial filter

Results

Pyogrio Fiona
With index 4.59 ms 85.2 ms
NO index 9.14 s 4.59 s
Entire file 21.4 s 8 min 30 s

Reproduction

Clone this repo:

git clone https://gist.github.com/6c50cd0a947e0f91a17108a829dab7e4.git flatgeobuf-spatial-index-bench
cd flatgeobuf-spatial-index-bench

Download data:

wget https://usbuildingdata.blob.core.windows.net/usbuildings-v2/California.geojson.zip

Create FlatGeobuf file with spatial index

./.pixi/env/bin/ogr2ogr \
    -lco SPATIAL_INDEX=YES \
    California_index.fgb /vsizip/California.geojson.zip

Create FlatGeobuf file without spatial index

./.pixi/env/bin/ogr2ogr \
    -lco SPATIAL_INDEX=NO \
    California_no_index.fgb /vsizip/California.geojson.zip

Run bench.ipy:

> ./.pixi/env/bin/ipython -i bench.ipy
Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:33:12) [Clang 15.0.7 ]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.15.0 -- An enhanced Interactive Python. Type '?' for help.


Reading indexed FlatGeobuf file with pyogrio:
4.59 ms ± 44.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)


Reading NOT-indexed FlatGeobuf file with pyogrio:
9.14 s ± 104 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)


Reading entire FlatGeobuf file with pyogrio:
CPU times: user 17.8 s, sys: 2.93 s, total: 20.7 s
Wall time: 21.4 s


Reading indexed FlatGeobuf file with fiona:
85.2 ms ± 1.1 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)


Reading NOT-indexed FlatGeobuf file with fiona:
4.59 s ± 14.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)


Reading entire FlatGeobuf file with fiona:
CPU times: user 8min 2s, sys: 22 s, total: 8min 24s
Wall time: 8min 30s
Raw
bench.ipy
import geopandas as gpd
# A small area in San Francisco
bbox = -122.429402, 37.767819, -122.393809, 37.792812
print("\n\nReading indexed FlatGeobuf file with pyogrio:")
%timeit _ = gpd.read_file('California_index.fgb', bbox=bbox, engine="pyogrio")
print("\n\nReading NOT-indexed FlatGeobuf file with pyogrio:")
%timeit _ = gpd.read_file('California_no_index.fgb', bbox=bbox, engine="pyogrio")
print("\n\nReading entire FlatGeobuf file with pyogrio:")
%time _ = gpd.read_file('California_no_index.fgb', engine="pyogrio")
print("\n\nReading indexed FlatGeobuf file with fiona:")
%timeit _ = gpd.read_file('California_index.fgb', bbox=bbox, engine="fiona")
print("\n\nReading NOT-indexed FlatGeobuf file with fiona:")
%timeit _ = gpd.read_file('California_no_index.fgb', bbox=bbox, engine="fiona")
print("\n\nReading entire FlatGeobuf file with fiona:")
%time _ = gpd.read_file('California_no_index.fgb', engine="fiona")
Raw
pixi.lock
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Raw
pixi.toml
[project]
name = "flatgeobuf-spatial-index-bench"
version = "0.1.0"
description = "Add a short description here"
authors = ["Kyle Barron <kyle@developmentseed.org>"]
channels = ["conda-forge"]
platforms = ["osx-arm64"]
[tasks]
[dependencies]
python = "3.11.*"
libgdal = "3.7.1.*"
geopandas = "0.13.2.*"
fiona = "1.9.4.*"
pyogrio = "0.6.0.*"
ipykernel = "6.25.1.*"
ipython = "8.15.0.*"
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