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, ClassVar, cast
import matplotlib.pyplot as plt
import torch
from matplotlib.figure import Figure
from rasterio.crs import CRS
from .errors import DatasetNotFoundError
from .geo import RasterDataset
from .utils import (
BoundingBox,
Path,
check_integrity,
disambiguate_timestamp,
extract_archive,
)
[docs]class GlobBiomass(RasterDataset):
"""GlobBiomass dataset.
The `GlobBiomass <https://doi.pangaea.de/10.1594/PANGAEA.894711>`__ dataset consists
of global pixelwise aboveground biomass (AGB) and growth stock volume (GSV) maps.
Definitions:
* AGB: the mass, expressed as oven-dry weight of the woody parts
(stem, bark, branches and twigs) of all living trees excluding stump and roots.
* GSV: volume of all living trees more than 10 cm in diameter at breast height
measured over bark from ground or stump height to a top stem diameter of 0 cm.
Units:
* AGB: m3/ha
* GSV: tons/ha (i.e., Mg/ha)
Dataset features:
* Global estimates of AGB and GSV at ~100 m per pixel resolution
(45,000 x 45,000 px)
* Per-pixel uncertainty expressed as standard error
Dataset format:
* Estimate maps are single-channel
* Uncertainty 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 in your research, please cite the following dataset:
* https://doi.org/10.1594/PANGAEA.894711
.. versionadded:: 0.3
"""
filename_glob = '*_{}.tif'
filename_regex = r"""
^(?P<tile>[NS][\d]{2}[EW][\d]{3})
_(?P<measurement>(agb|gsv))
"""
mint, maxt = disambiguate_timestamp('2010', '%Y')
is_image = False
dtype = torch.float32 # pixelwise regression
measurements = ('agb', 'gsv')
md5s: ClassVar[dict[str, str]] = {
'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: Path | Iterable[Path] = '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 GlobBiomass 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* is not valid.
DatasetNotFoundError: If dataset is not found.
.. versionchanged:: 0.5
*root* was renamed to *paths*.
"""
assert measurement in self.measurements
self.paths = paths
self.measurement = measurement
self.checksum = checksum
self.filename_glob = self.filename_glob.format(measurement)
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}'
)
mask = self._merge_files(filepaths, query)
std_error_paths = [str(f).replace('.tif', '_err.tif') for f in filepaths]
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, 'bounds': 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 | os.PathLike)
pathname = os.path.join(self.paths, f'*_{self.measurement}.zip')
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
