Source code for torchgeo.datasets.globbiomass
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.
"""GlobBiomass dataset."""
import glob
import os
from collections.abc import Callable, Iterable
from typing import Any, cast
import matplotlib.pyplot as plt
import torch
from matplotlib.figure import Figure
from rasterio.crs import CRS
from .geo import RasterDataset
from .utils import BoundingBox, DatasetNotFoundError, check_integrity, extract_archive
[docs]class GlobBiomass(RasterDataset):
"""GlobBiomass dataset.
The `GlobBiomass dataset <https://doi.pangaea.de/10.1594/PANGAEA.894711>`_
consists of global pixel wise aboveground biomass (AGB) and growth stock
volume (GSV) maps.
Dataset features:
* estimates of AGB and GSV around the world at ~100m per pixel resolution
(45,000x45,0000 px)
* standard error maps of respective measurement at same resolution
Dataset format:
* estimate maps are single-channel
* standard error maps are single-channel
The data can be manually downloaded from `this website
<https://globbiomass.org/wp-content/uploads/GB_Maps/
Globbiomass_global_dataset.html>`_.
If you use this dataset please cite it with the following citation:
* Santoro, M. et al. (2018): GlobBiomass - global datasets of forest biomass.
PANGAEA, https://doi.org/10.1594/PANGAEA.894711
.. versionadded:: 0.3
"""
is_image = False
filename_regex = r"""^
(?P<tile>[0-9A-Z]*)
_(?P<measurement>[a-z]{3})
"""
measurements = ["agb", "gsv"]
md5s = {
"N00E020_agb.zip": "bd83a3a4c143885d1962bde549413be6",
"N00E020_gsv.zip": "da5ddb88e369df2d781a0c6be008ae79",
"N00E060_agb.zip": "85eaca95b939086cc528e396b75bd097",
"N00E060_gsv.zip": "ec84174697c17ca4db2967374446ab30",
"N00E100_agb.zip": "c50c7c996615c1c6f19cb383ef11812a",
"N00E100_gsv.zip": "6e0ff834db822d3710ed40d00a200e8f",
"N00E140_agb.zip": "73f0b44b9e137789cefb711ef9aa281b",
"N00E140_gsv.zip": "43be3dd4563b63d12de006d240ba5edf",
"N00W020_agb.zip": "4fb979732f0a22cc7a2ca3667698084b",
"N00W020_gsv.zip": "ac5bbeedaa0f94a5e01c7a86751d6891",
"N00W060_agb.zip": "59da0b32b08fbbcd2dd76926a849562b",
"N00W060_gsv.zip": "5ca9598f621a7d10ab1d623ee5b44aa6",
"N00W100_agb.zip": "a819b75a39e8d4d37b15745c96ea1e35",
"N00W100_gsv.zip": "71aad3669d522f7190029ec33350831a",
"N00W180_agb.zip": "5a1d7486d8310fbaf4980a76e9ffcd78",
"N00W180_gsv.zip": "274be7dbb4e6d7563773cc302129a9c7",
"N40E020_agb.zip": "38bc7170f94734b365d614a566f872e7",
"N40E020_gsv.zip": "b52c1c777d68c331cc058a273530536e",
"N40E060_agb.zip": "1d94ad59f3f26664fefa4d7308b63f05",
"N40E060_gsv.zip": "3b68786b7641400077ef340a7ef748f4",
"N40E100_agb.zip": "3ccb436047c0db416fb237435645989c",
"N40E100_gsv.zip": "c44efe9e7ce2ae0f2e39b0db10f06c71",
"N40E140_agb.zip": "35ea51da229af1312ba4aaafc0dbd5d6",
"N40E140_gsv.zip": "8431828708c84263a4971a8779864f69",
"N40W020_agb.zip": "38345a1826719301ab1a0251b4835cc2",
"N40W020_gsv.zip": "5e136b7c2f921cd425cb5cc5669e7693",
"N40W060_agb.zip": "e3f54df1d188c0132ecf5aef3dc54ca6",
"N40W060_gsv.zip": "09093d78ffef0220cb459a88e61e3093",
"N40W100_agb.zip": "cc21ce8793e5594dc7a0b45f0d0f1466",
"N40W100_gsv.zip": "21be1398df88818d04dcce422e2010a6",
"N40W140_agb.zip": "64665f53fad7386abb1cf4a44a1c8b1a",
"N40W140_gsv.zip": "b59405219fc807cbe745789fbb6936a6",
"N40W180_agb.zip": "f83ef786da8333ee739e49be108994c1",
"N40W180_gsv.zip": "1f2eb8912b1a204eaeb2858b7e398baa",
"N80E020_agb.zip": "7f7aed44802890672bd908e28eda6f15",
"N80E020_gsv.zip": "6e285eec66306e56dc3a81adc0da2a27",
"N80E060_agb.zip": "55e7031e0207888f25f27efa9a0ab8f4",
"N80E060_gsv.zip": "8d14c7f61ad2aed527e124f9aacae30c",
"N80E100_agb.zip": "562eafd2813ff06e47284c48324bb1c7",
"N80E100_gsv.zip": "73067e0fac442c330ae2294996280042",
"N80E140_agb.zip": "1b51ce0df0dba925c5ef2149bebca115",
"N80E140_gsv.zip": "37ee3047d281fc34fa3a9e024a8317a1",
"N80W020_agb.zip": "60dde6adc0dfa219a34c976367f571c0",
"N80W020_gsv.zip": "b7be4e97bb4179710291ee8dee27f538",
"N80W060_agb.zip": "db7d35d0375851c4a181c3a8fa8b480e",
"N80W060_gsv.zip": "d36ffcf4622348382454c979baf53234",
"N80W100_agb.zip": "c0dbf53e635dabf9a4d7d1756adeda69",
"N80W100_gsv.zip": "abdeaf0d65da1216c326b6d0ce27d61b",
"N80W140_agb.zip": "7719c0efd23cd86215fea0285fd0ea4a",
"N80W140_gsv.zip": "499969bed381197ee9427a2e3f455a2e",
"N80W180_agb.zip": "e3a163d1944e1989a07225d262a01c6f",
"N80W180_gsv.zip": "5d39ec0368cfe63c40c66d61ae07f577",
"S40E140_agb.zip": "263eb077a984117b41cc7cfa0c32915b",
"S40E140_gsv.zip": "e0ffad85fbade4fb711cc5b3c7543898",
"S40W060_agb.zip": "2cbf6858c48f36add896db660826829b",
"S40W060_gsv.zip": "04dbfd4aca0bd2a2a7d8f563c8659252",
"S40W100_agb.zip": "ae89f021e7d9c2afea433878f77d1dd6",
"S40W100_gsv.zip": "b6aa3f276e1b51dade803a71df2acde6",
}
[docs] def __init__(
self,
paths: str | Iterable[str] = "data",
crs: CRS | None = None,
res: float | None = None,
measurement: str = "agb",
transforms: Callable[[dict[str, Any]], dict[str, Any]] | None = None,
cache: bool = True,
checksum: bool = False,
) -> None:
"""Initialize a new Dataset instance.
Args:
paths: one or more root directories to search or files to load
crs: :term:`coordinate reference system (CRS)` to warp to
(defaults to the CRS of the first file found)
res: resolution of the dataset in units of CRS
(defaults to the resolution of the first file found)
measurement: use data from 'agb' or 'gsv' measurement
transforms: a function/transform that takes an input sample
and returns a transformed version
cache: if True, cache file handle to speed up repeated sampling
checksum: if True, check the MD5 of the downloaded files (may be slow)
Raises:
AssertionError: if measurement argument is invalid, or not a str
DatasetNotFoundError: If dataset is not found.
.. versionchanged:: 0.5
*root* was renamed to *paths*.
"""
self.paths = paths
self.checksum = checksum
assert isinstance(measurement, str), "Measurement argument must be a str."
assert (
measurement in self.measurements
), f"You have entered an invalid measurement, please choose one of {self.measurements}."
self.measurement = measurement
self.filename_glob = f"*0_{self.measurement}*.tif"
self.zipfile_glob = f"*0_{self.measurement}.zip"
self._verify()
super().__init__(paths, crs, res, transforms=transforms, cache=cache)
[docs] def __getitem__(self, query: BoundingBox) -> dict[str, Any]:
"""Retrieve image/mask and metadata indexed by query.
Args:
query: (minx, maxx, miny, maxy, mint, maxt) coordinates to index
Returns:
sample at index consisting of measurement mask with 2 channels,
where the first is the measurement and the second the error map
Raises:
IndexError: if query is not found in the index
"""
hits = self.index.intersection(tuple(query), objects=True)
filepaths = cast(list[str], [hit.object for hit in hits])
if not filepaths:
raise IndexError(
f"query: {query} not found in index with bounds: {self.bounds}"
)
measurement_paths = [f for f in filepaths if "err" not in f]
mask = self._merge_files(measurement_paths, query)
std_error_paths = [f for f in filepaths if "err" in f]
std_err_mask = self._merge_files(std_error_paths, query)
mask = torch.cat((mask, std_err_mask), dim=0)
sample = {"mask": mask, "crs": self.crs, "bbox": query}
if self.transforms is not None:
sample = self.transforms(sample)
return sample
def _verify(self) -> None:
"""Verify the integrity of the dataset."""
# Check if the extracted file already exists
if self.files:
return
# Check if the zip files have already been downloaded
assert isinstance(self.paths, str)
pathname = os.path.join(self.paths, self.zipfile_glob)
if glob.glob(pathname):
for zipfile in glob.iglob(pathname):
filename = os.path.basename(zipfile)
if self.checksum and not check_integrity(zipfile, self.md5s[filename]):
raise RuntimeError("Dataset found, but corrupted.")
extract_archive(zipfile)
return
raise DatasetNotFoundError(self)
[docs] def plot(
self,
sample: dict[str, Any],
show_titles: bool = True,
suptitle: str | None = None,
) -> Figure:
"""Plot a sample from the dataset.
Args:
sample: a sample returned by :meth:`__getitem__`
show_titles: flag indicating whether to show titles above each panel
suptitle: optional string to use as a suptitle
Returns:
a matplotlib Figure with the rendered sample
"""
tensor = sample["mask"]
mask = tensor[0, ...]
error_mask = tensor[1, ...]
showing_predictions = "prediction" in sample
if showing_predictions:
pred = sample["prediction"][0, ...]
ncols = 3
else:
ncols = 2
fig, axs = plt.subplots(nrows=1, ncols=ncols, figsize=(ncols * 4, 4))
if showing_predictions:
axs[0].imshow(mask)
axs[0].axis("off")
axs[1].imshow(error_mask)
axs[1].axis("off")
axs[2].imshow(pred)
axs[2].axis("off")
if show_titles:
axs[0].set_title("Mask")
axs[1].set_title("Uncertainty Mask")
axs[2].set_title("Prediction")
else:
axs[0].imshow(mask)
axs[0].axis("off")
axs[1].imshow(error_mask)
axs[1].axis("off")
if show_titles:
axs[0].set_title("Mask")
axs[1].set_title("Uncertainty Mask")
if suptitle is not None:
plt.suptitle(suptitle)
return fig
