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dcheriandcherian
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Rasterization improvements (#38)
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‎.pre-commit-config.yaml

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- mdformat-black
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- mdformat-myst
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# - repo: https://github.com/kynan/nbstripout
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# rev: 0.8.1
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# hooks:
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# - id: nbstripout
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# args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
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- repo: https://github.com/kynan/nbstripout
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rev: 0.8.1
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hooks:
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- id: nbstripout
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args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.1

‎docs/api.rst

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‎docs/conf.py

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# -- General configuration -----------------------------------------------------
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.viewcode",
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"sphinx.ext.autosummary",
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"sphinx.ext.intersphinx",
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"sphinx.ext.extlinks",
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"numpydoc",
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"sphinx.ext.napoleon",
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"myst_nb",
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"autoapi.extension",
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"sphinx_codeautolink",
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"sphinx_remove_toctrees",
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"sphinxext.opengraph",
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]
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autoapi_dirs = ["../src/rasterix/"]
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autoapi_options = [
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"members",
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"undoc-members",
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"show-inheritance",
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# "show-module-summary",
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"special-members",
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# "imported-members",
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]
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autoapi_ignore = ["*compat*", "*util*"]
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autoapi_add_toctree_entry = False
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autodoc_typehints = "none"
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codeautolink_concat_default = True
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extlinks = {
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"xarray": ("https://docs.xarray.dev/en/stable/", None),
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"xproj": ("https://xproj.readthedocs.io/en/stable/", None),
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"pyproj": ("https://pyproj4.github.io/pyproj/stable/", None),
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"exactextract": ("https://isciences.github.io/exactextract/", None),
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"rasterio": ("https://rasterio.readthedocs.io/en/stable/", None),
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}
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autosummary_generate = True
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autodoc_typehints = "none"
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# Napoleon configurations
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napoleon_google_docstring = False

‎docs/index.md

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caption: Rasterizing
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hidden:
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---
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rasterize/rasterio
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rasterize/geometry_mask
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rasterize/exactextract
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```
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```{toctree}
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---
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caption: Reference
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hidden:
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---
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api.rst
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autoapi/rasterix/index
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```

‎docs/rasterize/exactextract.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "0",
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"metadata": {},
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"source": [
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"# With `exactextract`\n",
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"\n",
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"Rasterix includes dask-aware wrappers for `exactextract.exact_extract`'s coverage estimation."
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]
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},
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{
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"cell_type": "markdown",
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"id": "1",
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"metadata": {},
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"source": [
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"## Read data\n",
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"\n",
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"### Read in some raster data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2",
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"metadata": {},
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"outputs": [],
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"source": [
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"import xarray as xr\n",
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"\n",
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"ds = xr.tutorial.open_dataset(\"eraint_uvz\")\n",
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"ds = ds.rio.write_crs(\"epsg:4326\")\n",
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"ds"
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]
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},
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{
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"cell_type": "markdown",
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"id": "3",
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"metadata": {},
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"source": [
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"### Read in example geometries"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4",
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"metadata": {},
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"outputs": [],
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"source": [
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"import geodatasets\n",
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"import geopandas as gpd\n",
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"\n",
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"world = gpd.read_file(geodatasets.get_path(\"naturalearth land\"))\n",
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"world"
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]
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},
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{
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"cell_type": "markdown",
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"id": "5",
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"metadata": {},
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"source": [
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"## Calculate coverage"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6",
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"metadata": {},
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"outputs": [],
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"source": [
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"from rasterix.rasterize.exact import coverage\n",
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"\n",
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"n = coverage(ds, world[[\"geometry\"]], xdim=\"longitude\", ydim=\"latitude\")\n",
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"n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7",
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"metadata": {},
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"outputs": [],
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"source": [
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"n.isel(geometry=112).plot()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "8",
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"metadata": {},
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"source": [
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"Optionally clip to the `total_bounds` of the geometries passed in"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9",
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"metadata": {},
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"outputs": [],
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"source": [
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"from rasterix.rasterize.exact import coverage\n",
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"\n",
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"coverage(\n",
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" ds,\n",
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" world[[\"geometry\"]].iloc[slice(112, 113)],\n",
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" xdim=\"longitude\",\n",
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" ydim=\"latitude\",\n",
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" clip=True,\n",
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").plot()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "10",
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"metadata": {},
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"source": [
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"Notice that the output data is a `sparse.COO` array with a new dimension `geometry`. The input geometries are propagated as a coordinate variable named `geometry`.\n",
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"\n",
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"Different coverage weights are supported. Extra attributes `units` and `long_name` are assigned as appropriate."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "11",
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"metadata": {},
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"outputs": [],
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"source": [
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"from rasterix.rasterize.exact import coverage\n",
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"\n",
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"n = coverage(ds, world[[\"geometry\"]], xdim=\"longitude\", ydim=\"latitude\", coverage_weight=\"fraction\")\n",
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"n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "12",
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"metadata": {},
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"source": [
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"## Out-of-core support\n",
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"\n",
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"As with other rasterization code, various combinations of chunked and in-memory arrays and geometries are supported."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "13",
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"metadata": {},
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"outputs": [],
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"source": [
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"chunked = ds.chunk({\"latitude\": -1, \"longitude\": 120})\n",
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"d = coverage(chunked, world[[\"geometry\"]], xdim=\"longitude\", ydim=\"latitude\")\n",
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"d"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "14",
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"metadata": {},
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"outputs": [],
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"source": [
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"xr.testing.assert_identical(d, n)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "15",
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"metadata": {},
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"outputs": [],
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"source": [
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"import dask_geopandas as dgpd\n",
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"\n",
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"dd = coverage(\n",
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" ds.chunk({\"latitude\": -1, \"longitude\": 240}),\n",
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" dgpd.from_geopandas(world[[\"geometry\"]], npartitions=3),\n",
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" xdim=\"longitude\",\n",
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" ydim=\"latitude\",\n",
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")\n",
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"dd"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "16",
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"metadata": {},
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"outputs": [],
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"source": [
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"xr.testing.assert_identical(dd, n)"
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]
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}
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],
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"metadata": {
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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