diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..58fd487 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +# Ignore GeoPackage file used in conversion to GeoParquet +*.gpkg* diff --git a/scripts/README.md b/scripts/README.md index c157a28..f0c3c7d 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -6,7 +6,17 @@ The scripts in this directory use [Poetry](https://github.com/python-poetry/poet To install Poetry, follow the Poetry [installation guide](https://python-poetry.org/docs/#installation). -To install from the lockfile, run `poetry install`. To update the lockfile (such as when you add a new dependency) run `poetry update`. +To install from the lockfile: + +``` +poetry install +``` + +To update the lockfile (such as when you add a new dependency): + +``` +poetry update +``` To run a script, prefix it with `poetry run`. For example: @@ -15,3 +25,22 @@ poetry run python update_example_schemas.py ``` Using `poetry run` ensures that you're running the python script using _this_ local environment, not your global environment. + +### nz-building-outlines to Parquet + +```bash +poetry run python write_nz_building_outline.py \ + --input nz-building-outlines.gpkg \ + --output nz-building-outlines.parquet \ + --compression SNAPPY +``` + +#### Recompile pygeos + +Poetry doesn't currently have a way to force installing a package from source. +To make the script run faster, you can reinstall pygeos manually in the +virtualenv: + +``` +poetry run pip install -U --force-reinstall pygeos --no-binary pygeos +``` diff --git a/scripts/poetry.lock b/scripts/poetry.lock index 184fad5..318b044 100644 --- a/scripts/poetry.lock +++ b/scripts/poetry.lock @@ -1,3 +1,369 @@ +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asttokens" +version = "2.0.5" +description = "Annotate AST trees with source code positions" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +six = "*" + +[package.extras] +test = ["astroid", "pytest"] + +[[package]] +name = "attrs" +version = "21.4.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "black" +version = "22.3.0" +description = "The uncompromising code formatter." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +click = ">=8.0.0" +mypy-extensions = ">=0.4.3" +pathspec = ">=0.9.0" +platformdirs = ">=2" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} +typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} + +[package.extras] +colorama = ["colorama (>=0.4.3)"] +d = ["aiohttp (>=3.7.4)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] +uvloop = ["uvloop (>=0.15.2)"] + +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." 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b/scripts/write_nz_building_outline.py new file mode 100644 index 0000000..0ca1053 --- /dev/null +++ b/scripts/write_nz_building_outline.py @@ -0,0 +1,208 @@ +import json +import sys +from enum import Enum +from pathlib import Path +from typing import Any, Dict, List + +import click +import geopandas as gpd +import numpy as np +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +import pygeos +from numpy.typing import NDArray + +GEOPARQUET_VERSION = "0.4.0" +AVAILABLE_COMPRESSIONS = ["NONE", "SNAPPY", "GZIP", "BROTLI", "LZ4", "ZSTD"] + +PygeosGeometryArray = NDArray[pygeos.Geometry] + + +class PathType(click.Path): + """A Click path argument that returns a pathlib Path, not a string""" + + def convert(self, value, param, ctx): + return Path(super().convert(value, param, ctx)) + + +class GeometryType(int, Enum): + """Pygeos (GEOS) geometry type mapping + From https://pygeos.readthedocs.io/en/latest/geometry.html?highlight=type#pygeos.geometry.get_type_id + """ + + Missing = -1 + Point = 0 + LineString = 1 + LinearRing = 2 + Polygon = 3 + MultiPoint = 4 + MultiLinestring = 5 + MultiPolygon = 6 + GeometryCollection = 7 + + +def parse_to_pygeos(df: gpd.GeoDataFrame) -> Dict[str, PygeosGeometryArray]: + """Parse to pygeos geometry array + + This is split out from _create_metadata so that we don't have to create the pygeos + array twice: once for converting to wkb and another time for metadata handling. + """ + geometry_columns: Dict[str, PygeosGeometryArray] = {} + for col in df.columns[df.dtypes == "geometry"]: + geometry_columns[col] = df[col].array.data + + return geometry_columns + + +def _create_metadata( + df: gpd.GeoDataFrame, geometry_columns: Dict[str, PygeosGeometryArray] +) -> Dict[str, Any]: + """Create and encode geo metadata dict. + + Parameters + ---------- + df : GeoDataFrame + + Returns + ------- + dict + """ + + # Construct metadata for each geometry + column_metadata = {} + for col, geometry_array in geometry_columns.items(): + geometry_type = get_geometry_type(geometry_array) + bbox = list(pygeos.total_bounds(geometry_array)) + + series = df[col] + column_metadata[col] = { + "encoding": "WKB", + "geometry_type": geometry_type, + "crs": series.crs.to_json_dict() if series.crs else None, + # We don't specify orientation for now + # "orientation" + "edges": "planar", + "bbox": bbox, + # I don't know how to get the epoch from a pyproj CRS, and if it's relevant + # here + # "epoch": + } + + return { + "version": GEOPARQUET_VERSION, + "primary_column": df._geometry_column_name, + "columns": column_metadata, + # "creator": {"library": "geopandas", "version": geopandas.__version__}, + } + + +def get_geometry_type(pygeos_geoms: PygeosGeometryArray) -> List[str]: + type_ids = pygeos.get_type_id(pygeos_geoms) + unique_type_ids = set(type_ids) + + geom_type_names: List[str] = [] + for type_id in unique_type_ids: + geom_type_names.append(GeometryType(type_id).name) + + return geom_type_names + + +def encode_metadata(metadata: Dict) -> bytes: + """Encode metadata dict to UTF-8 JSON string + + Parameters + ---------- + metadata : dict + + Returns + ------- + UTF-8 encoded JSON string + """ + # Remove unnecessary whitespace in JSON metadata + # https://stackoverflow.com/a/33233406 + return json.dumps(metadata, separators=(',', ':')).encode("utf-8") + + +def cast_dtypes(df: gpd.GeoDataFrame) -> gpd.GeoDataFrame: + """ + Note: This is specific to the nz-building-outlines data + See reference here: + https://nz-buildings.readthedocs.io/en/latest/published_data.html#table-nz-building-outlines + """ + # Double checks + assert df["building_id"].min() >= np.iinfo(np.int32).min + assert df["building_id"].max() <= np.iinfo(np.int32).max + df["building_id"] = df["building_id"].astype(np.int32) + + assert df["capture_source_id"].min() >= np.iinfo(np.int32).min + assert df["capture_source_id"].max() <= np.iinfo(np.int32).max + df["capture_source_id"] = df["capture_source_id"].astype(np.int32) + + for date_col in ["capture_source_from", "capture_source_to", "last_modified"]: + df[date_col] = pd.to_datetime(df[date_col], format="%Y-%m-%d") + + return df + + +def geopandas_to_arrow(df: gpd.GeoDataFrame) -> pa.Table: + geometry_columns = parse_to_pygeos(df) + geo_metadata = _create_metadata(df, geometry_columns) + + df = pd.DataFrame(df) + for col, geometry_array in geometry_columns.items(): + df[col] = pygeos.to_wkb(geometry_array) + + table = pa.Table.from_pandas(df, preserve_index=False) + + metadata = table.schema.metadata + metadata.update({b"geo": encode_metadata(geo_metadata)}) + return table.replace_schema_metadata(metadata) + + +@click.command() +@click.option( + "-i", + "--input", + type=PathType(exists=True, file_okay=True, dir_okay=False, readable=True), + help="Path to input nz-building-outlines.gpkg", + required=True, +) +@click.option( + "--layer-name", + type=str, + required=False, + help="Name of layer within GeoPackage", + show_default=True, + default="nz_building_outlines", +) +@click.option( + "-o", + "--output", + type=PathType(file_okay=True, dir_okay=False, writable=True), + help="Path to output Parquet file.", + required=True, +) +@click.option( + "--compression", + type=click.Choice(AVAILABLE_COMPRESSIONS, case_sensitive=False), + default="SNAPPY", + help="Compression codec to use when writing to Parquet.", + show_default=True, +) +def main(input: Path, layer_name: str, output: Path, compression: str): + print("Starting to read geopackage", file=sys.stderr) + df = gpd.read_file(input, layer=layer_name) + print("Finished reading geopackage", file=sys.stderr) + df = cast_dtypes(df) + + print("Starting conversion to Arrow", file=sys.stderr) + arrow_table = geopandas_to_arrow(df) + print("Finished conversion to Arrow", file=sys.stderr) + print("Starting write to Parquet", file=sys.stderr) + pq.write_table(arrow_table, output, compression=compression) + print("Finished write to Parquet", file=sys.stderr) + + +if __name__ == "__main__": + main()