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Source code for torchgeo.datasets.cms_mangrove_canopy

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

"""CMS Global Mangrove Canopy dataset."""

import glob
import os
from typing import Any, Callable, Dict, Optional

import matplotlib.pyplot as plt
from rasterio.crs import CRS

from .geo import RasterDataset
from .utils import check_integrity, extract_archive


class CMSGlobalMangroveCanopy(RasterDataset):
    """CMS Global Mangrove Canopy dataset.

    The `CMS Global Mangrove Canopy dataset
    <https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1665>`_
    consists of a single band map at 30m resolution of either aboveground biomass (agb),
    basal area weighted height (hba95), or maximum canopy height (hmax95).

    The dataset needs to be manually dowloaded from the above link, where you can make
    an account and subsequently download the dataset.

    .. versionadded:: 0.3
    """

    is_image = False

    filename_regex = r"""^
        (?P<mangrove>[A-Za-z]{8})
        _(?P<variable>[a-z0-9]*)
        _(?P<country>[A-Za-z][^.]*)
    """

    zipfile = "CMS_Global_Map_Mangrove_Canopy_1665.zip"
    md5 = "3e7f9f23bf971c25e828b36e6c5496e3"

    all_countries = [
        "AndamanAndNicobar",
        "Angola",
        "Anguilla",
        "AntiguaAndBarbuda",
        "Aruba",
        "Australia",
        "Bahamas",
        "Bahrain",
        "Bangladesh",
        "Barbados",
        "Belize",
        "Benin",
        "Brazil",
        "BritishVirginIslands",
        "Brunei",
        "Cambodia",
        "Cameroon",
        "CarribeanCaymanIslands",
        "China",
        "Colombia",
        "Comoros",
        "CostaRica",
        "Cote",
        "CoteDivoire",
        "CotedIvoire",
        "Cuba",
        "DemocraticRepublicOfCongo",
        "Djibouti",
        "DominicanRepublic",
        "EcuadorWithGalapagos",
        "Egypt",
        "ElSalvador",
        "EquatorialGuinea",
        "Eritrea",
        "EuropaIsland",
        "Fiji",
        "Fiji2",
        "FrenchGuiana",
        "FrenchGuyana",
        "FrenchPolynesia",
        "Gabon",
        "Gambia",
        "Ghana",
        "Grenada",
        "Guadeloupe",
        "Guam",
        "Guatemala",
        "Guinea",
        "GuineaBissau",
        "Guyana",
        "Haiti",
        "Hawaii",
        "Honduras",
        "HongKong",
        "India",
        "Indonesia",
        "Iran",
        "Jamaica",
        "Japan",
        "Kenya",
        "Liberia",
        "Macau",
        "Madagascar",
        "Malaysia",
        "Martinique",
        "Mauritania",
        "Mayotte",
        "Mexico",
        "Micronesia",
        "Mozambique",
        "Myanmar",
        "NewCaledonia",
        "NewZealand",
        "Newzealand",
        "Nicaragua",
        "Nigeria",
        "NorthernMarianaIslands",
        "Oman",
        "Pakistan",
        "Palau",
        "Panama",
        "PapuaNewGuinea",
        "Peru",
        "Philipines",
        "PuertoRico",
        "Qatar",
        "ReunionAndMauritius",
        "SaintKittsAndNevis",
        "SaintLucia",
        "SaintVincentAndTheGrenadines",
        "Samoa",
        "SaudiArabia",
        "Senegal",
        "Seychelles",
        "SierraLeone",
        "Singapore",
        "SolomonIslands",
        "Somalia",
        "Somalia2",
        "Soudan",
        "SouthAfrica",
        "SriLanka",
        "Sudan",
        "Suriname",
        "Taiwan",
        "Tanzania",
        "Thailand",
        "TimorLeste",
        "Togo",
        "Tonga",
        "TrinidadAndTobago",
        "TurksAndCaicosIslands",
        "Tuvalu",
        "UnitedArabEmirates",
        "UnitedStates",
        "Vanuatu",
        "Venezuela",
        "Vietnam",
        "VirginIslandsUs",
        "WallisAndFutuna",
        "Yemen",
    ]

    measurements = ["agb", "hba95", "hmax95"]

[docs] def __init__( self, root: str = "data", crs: Optional[CRS] = None, res: Optional[float] = None, measurement: str = "agb", country: str = all_countries[0], transforms: Optional[Callable[[Dict[str, Any]], Dict[str, Any]]] = None, cache: bool = True, checksum: bool = False, ) -> None: """Initialize a new Dataset instance. Args: root: root directory where dataset can be found 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: which of the three measurements, 'agb', 'hba95', or 'hmax95' country: country for which to retrieve data 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: FileNotFoundError: if no files are found in ``root`` RuntimeError: if dataset is missing or checksum fails AssertionError: if country or measurement arg are not str or invalid """ self.root = root self.checksum = checksum assert isinstance(country, str), "Country argument must be a str." assert ( country in self.all_countries ), "You have selected an invalid country, please choose one of {}".format( self.all_countries ) self.country = country assert isinstance(measurement, str), "Measurement must be a string." assert ( measurement in self.measurements ), "You have entered an invalid measurement, please choose one of {}.".format( self.measurements ) self.measurement = measurement self.filename_glob = f"**/Mangrove_{self.measurement}_{self.country}*" self._verify() super().__init__(root, crs, res, transforms, cache)
def _verify(self) -> None: """Verify the integrity of the dataset. Raises: RuntimeError: if dataset is missing or checksum fails """ # Check if the extracted files already exist pathname = os.path.join(self.root, "**", self.filename_glob) if glob.glob(pathname): return # Check if the zip file has already been downloaded pathname = os.path.join(self.root, self.zipfile) if os.path.exists(pathname): if self.checksum and not check_integrity(pathname, self.md5): raise RuntimeError("Dataset found, but corrupted.") self._extract() return raise RuntimeError( f"Dataset not found in `root={self.root}` " "either specify a different `root` directory or make sure you " "have manually downloaded the dataset as instructed in the documentation." ) def _extract(self) -> None: """Extract the dataset.""" pathname = os.path.join(self.root, self.zipfile) extract_archive(pathname)
[docs] def plot( self, sample: Dict[str, Any], show_titles: bool = True, suptitle: Optional[str] = None, ) -> plt.Figure: """Plot a sample from the dataset. Args: sample: a sample returned by :meth:`RasterDataset.__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 """ mask = sample["mask"].squeeze() ncols = 1 showing_predictions = "prediction" in sample if showing_predictions: pred = sample["prediction"].squeeze() 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(pred) axs[1].axis("off") if show_titles: axs[0].set_title("Mask") axs[1].set_title("Prediction") else: axs.imshow(mask) axs.axis("off") if show_titles: axs.set_title("Mask") if suptitle is not None: plt.suptitle(suptitle) return

© Copyright 2021, Microsoft Corporation. Revision 44fa4132.

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