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Add the EnviroAtlas dataset (#364)
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* Add dataset

* Add dataset to docs

* Tests for enviroatlas

* Test coverage

* Added numpy type

* Added plotting

* Code review changes

* Propagating code review comments to Chesapeake
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@calebrob6
calebrob6 authored Jan 28, 2022
1 parent 57981c8 commit d4c8a4b
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5 changes: 5 additions & 0 deletions docs/api/datasets.rst
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Expand Up @@ -37,6 +37,11 @@ Cropland Data Layer (CDL)

.. autoclass:: CDL

EnviroAtlas
^^^^^^^^^^^

.. autoclass:: EnviroAtlas

Landsat
^^^^^^^

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305 changes: 305 additions & 0 deletions tests/data/enviroatlas/data.py
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#!/usr/bin/env python3

# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.

import os
import shutil
from typing import Any, Dict

import fiona
import fiona.transform
import numpy as np
import rasterio
import shapely.geometry
from rasterio.crs import CRS
from rasterio.transform import Affine
from torchvision.datasets.utils import calculate_md5

suffix_to_key_map = {
"a_naip": "naip",
"b_nlcd": "nlcd",
"c_roads": "roads",
"d_water": "water",
"d1_waterways": "waterways",
"d2_waterbodies": "waterbodies",
"e_buildings": "buildings",
"h_highres_labels": "lc",
"prior_from_cooccurrences_101_31": "prior",
"prior_from_cooccurrences_101_31_no_osm_no_buildings": "prior_no_osm_no_buildings",
}

layer_data_profiles: Dict[str, Dict[Any, Any]] = {
"a_naip": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 4,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "pixel",
},
"data_type": "continuous",
"vals": (4, 255),
},
"b_nlcd": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15],
},
"c_roads": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [0, 1],
},
"d1_waterways": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [0, 1],
},
"d2_waterbodies": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [0, 1],
},
"d_water": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [0, 1],
},
"e_buildings": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [0, 1],
},
"h_highres_labels": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 1,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "categorical",
"vals": [10, 20, 30, 40, 70],
},
"prior_from_cooccurrences_101_31": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 5,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "continuous",
"vals": (0, 225),
},
"prior_from_cooccurrences_101_31_no_osm_no_buildings": {
"profile": {
"driver": "GTiff",
"dtype": "uint8",
"nodata": None,
"count": 5,
"crs": CRS.from_epsg(26914),
"blockxsize": 512,
"blockysize": 512,
"tiled": True,
"compress": "deflate",
"interleave": "band",
},
"data_type": "continuous",
"vals": (0, 220),
},
}

tile_list = [
"pittsburgh_pa-2010_1m-train_tiles-debuffered/4007925_se",
"austin_tx-2012_1m-test_tiles-debuffered/3009726_sw",
]


def write_data(path: str, profile: Dict[Any, Any], data_type: Any, vals: Any) -> None:
assert all(key in profile for key in ("count", "height", "width", "dtype"))
with rasterio.open(path, "w", **profile) as dst:
size = (profile["count"], profile["height"], profile["width"])
dtype = np.dtype(profile["dtype"])
if data_type == "continuous":
data = np.random.randint(vals[0], vals[1] + 1, size=size, dtype=dtype)
elif data_type == "categorical":
data = np.random.choice(vals, size=size).astype(dtype)
else:
raise ValueError(f"{data_type} is not recognized")
dst.write(data)


def generate_test_data(root: str) -> str:
"""Creates test data archive for the EnviroAtlas dataset and returns its md5 hash.
Args:
root (str): Path to store test data
Returns:
str: md5 hash of created archive
"""
size = (64, 64)
folder_path = os.path.join(root, "enviroatlas_lotp")

if not os.path.exists(folder_path):
os.makedirs(folder_path)

for prefix in tile_list:
for suffix, data_profile in layer_data_profiles.items():

img_path = os.path.join(folder_path, f"{prefix}_{suffix}.tif")
img_dir = os.path.dirname(img_path)
if not os.path.exists(img_dir):
os.makedirs(img_dir)

data_profile["profile"]["height"] = size[0]
data_profile["profile"]["width"] = size[1]
data_profile["profile"]["transform"] = Affine(
1.0, 0.0, 608170.0, 0.0, -1.0, 3381430.0
)

write_data(
img_path,
data_profile["profile"],
data_profile["data_type"],
data_profile["vals"],
)

# build the spatial index
schema = {
"geometry": "Polygon",
"properties": {
"split": "str",
"naip": "str",
"nlcd": "str",
"roads": "str",
"water": "str",
"waterways": "str",
"waterbodies": "str",
"buildings": "str",
"lc": "str",
"prior_no_osm_no_buildings": "str",
"prior": "str",
},
}
with fiona.open(
os.path.join(folder_path, "spatial_index.geojson"),
"w",
driver="GeoJSON",
crs="EPSG:3857",
schema=schema,
) as dst:
for prefix in tile_list:

img_path = os.path.join(folder_path, f"{prefix}_a_naip.tif")
with rasterio.open(img_path) as f:
geom = shapely.geometry.mapping(shapely.geometry.box(*f.bounds))
geom = fiona.transform.transform_geom(
f.crs.to_string(), "EPSG:3857", geom
)

row = {
"geometry": geom,
"properties": {
"split": prefix.split("/")[0].replace("_tiles-debuffered", "")
},
}
for suffix, data_profile in layer_data_profiles.items():
key = suffix_to_key_map[suffix]
row["properties"][key] = f"{prefix}_{suffix}.tif"
dst.write(row)

# Create archive
archive_path = os.path.join(root, "enviroatlas_lotp")
shutil.make_archive(archive_path, "zip", root_dir=root, base_dir="enviroatlas_lotp")
shutil.rmtree(folder_path)
md5: str = calculate_md5(archive_path + ".zip")
return md5


if __name__ == "__main__":
md5_hash = generate_test_data(os.getcwd())
print(md5_hash)
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