Source code for torchgeo.datasets.nasa_marine_debris
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.
"""NASA Marine Debris dataset."""
import os
from typing import Callable, Optional
import matplotlib.pyplot as plt
import numpy as np
import rasterio
import torch
from matplotlib.figure import Figure
from torch import Tensor
from torchvision.utils import draw_bounding_boxes
from .geo import NonGeoDataset
from .utils import check_integrity, download_radiant_mlhub_collection, extract_archive
[docs]class NASAMarineDebris(NonGeoDataset):
"""NASA Marine Debris dataset.
The `NASA Marine Debris <https://mlhub.earth/data/nasa_marine_debris>`__
dataset is a dataset for detection of floating marine debris in satellite imagery.
Dataset features:
* 707 patches with 3 m per pixel resolution (256x256 px)
* three spectral bands - RGB
* 1 object class: marine_debris
* images taken by Planet Labs PlanetScope satellites
* imagery taken from 2016-2019 from coasts of Greece, Honduras, and Ghana
Dataset format:
* images are three-channel geotiffs in uint8 format
* labels are numpy files (.npy) containing bounding box (xyxy) coordinates
* additional: images in jpg format and labels in geojson format
If you use this dataset in your research, please cite the following paper:
* https://doi.org/10.34911/rdnt.9r6ekg
.. note::
This dataset requires the following additional library to be installed:
* `radiant-mlhub <https://pypi.org/project/radiant-mlhub/>`_ to download the
imagery and labels from the Radiant Earth MLHub
.. versionadded:: 0.2
"""
collection_ids = ["nasa_marine_debris_source", "nasa_marine_debris_labels"]
directories = ["nasa_marine_debris_source", "nasa_marine_debris_labels"]
filenames = ["nasa_marine_debris_source.tar.gz", "nasa_marine_debris_labels.tar.gz"]
md5s = ["fe8698d1e68b3f24f0b86b04419a797d", "d8084f5a72778349e07ac90ec1e1d990"]
class_label = "marine_debris"
[docs] def __init__(
self,
root: str = "data",
transforms: Optional[Callable[[dict[str, Tensor]], dict[str, Tensor]]] = None,
download: bool = False,
api_key: Optional[str] = None,
checksum: bool = False,
verbose: bool = False,
) -> None:
"""Initialize a new NASA Marine Debris Dataset instance.
Args:
root: root directory where dataset can be found
transforms: a function/transform that takes input sample and its target as
entry and returns a transformed version
download: if True, download dataset and store it in the root directory
api_key: a RadiantEarth MLHub API key to use for downloading the dataset
checksum: if True, check the MD5 of the downloaded files (may be slow)
verbose: if True, print messages when new tiles are loaded
"""
self.root = root
self.transforms = transforms
self.download = download
self.api_key = api_key
self.checksum = checksum
self.verbose = verbose
self._verify()
self.files = self._load_files()
[docs] def __getitem__(self, index: int) -> dict[str, Tensor]:
"""Return an index within the dataset.
Args:
index: index to return
Returns:
data and labels at that index
"""
image = self._load_image(self.files[index]["image"])
boxes = self._load_target(self.files[index]["target"])
sample = {"image": image, "boxes": boxes}
# Filter invalid boxes
w_check = (sample["boxes"][:, 2] - sample["boxes"][:, 0]) > 0
h_check = (sample["boxes"][:, 3] - sample["boxes"][:, 1]) > 0
indices = w_check & h_check
sample["boxes"] = sample["boxes"][indices]
if self.transforms is not None:
sample = self.transforms(sample)
return sample
[docs] def __len__(self) -> int:
"""Return the number of data points in the dataset.
Returns:
length of the dataset
"""
return len(self.files)
def _load_image(self, path: str) -> Tensor:
"""Load a single image.
Args:
path: path to the image
Returns:
the image
"""
with rasterio.open(path) as f:
array = f.read()
tensor = torch.from_numpy(array).float()
return tensor
def _load_target(self, path: str) -> Tensor:
"""Load the target bounding boxes for a single image.
Args:
path: path to the labels
Returns:
the target boxes
"""
array = np.load(path)
# boxes contain unecessary value of 1 after xyxy coords
array = array[:, :4]
tensor = torch.from_numpy(array)
return tensor
def _load_files(self) -> list[dict[str, str]]:
"""Load a image and label files.
Returns:
list of dicts containing image and label files
"""
image_root = os.path.join(self.root, self.directories[0])
target_root = os.path.join(self.root, self.directories[1])
image_folders = sorted(
f for f in os.listdir(image_root) if not f.endswith("json")
)
files = []
for folder in image_folders:
files.append(
{
"image": os.path.join(image_root, folder, "image_geotiff.tif"),
"target": os.path.join(
target_root,
folder.replace("source", "labels"),
"pixel_bounds.npy",
),
}
)
return files
def _verify(self) -> None:
"""Verify the integrity of the dataset.
Raises:
RuntimeError: if ``download=False`` but dataset is missing or checksum fails
"""
# Check if the files already exist
exists = [
os.path.exists(os.path.join(self.root, directory))
for directory in self.directories
]
if all(exists):
return
# Check if zip file already exists (if so then extract)
exists = []
for filename, md5 in zip(self.filenames, self.md5s):
filepath = os.path.join(self.root, filename)
if os.path.exists(filepath):
if self.checksum and not check_integrity(filepath, md5):
raise RuntimeError("Dataset checksum mismatch.")
exists.append(True)
extract_archive(filepath)
else:
exists.append(False)
if all(exists):
return
# Check if the user requested to download the dataset
if not self.download:
raise RuntimeError(
"Dataset not found in `root` directory and `download=False`, "
"either specify a different `root` directory or use `download=True` "
"to automatically download the dataset."
)
# Download and extract the dataset
for collection_id in self.collection_ids:
download_radiant_mlhub_collection(collection_id, self.root, self.api_key)
for filename, md5 in zip(self.filenames, self.md5s):
filepath = os.path.join(self.root, filename)
if self.checksum and not check_integrity(filepath, md5):
raise RuntimeError("Dataset checksum mismatch.")
extract_archive(filepath)
[docs] def plot(
self,
sample: dict[str, Tensor],
show_titles: bool = True,
suptitle: Optional[str] = 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
"""
ncols = 1
sample["image"] = sample["image"].byte()
image = sample["image"]
if "boxes" in sample and len(sample["boxes"]):
image = draw_bounding_boxes(image=sample["image"], boxes=sample["boxes"])
image = image.permute((1, 2, 0)).numpy()
if "prediction_boxes" in sample and len(sample["prediction_boxes"]):
ncols += 1
preds = draw_bounding_boxes(
image=sample["image"], boxes=sample["prediction_boxes"]
)
preds = preds.permute((1, 2, 0)).numpy()
fig, axs = plt.subplots(ncols=ncols, figsize=(ncols * 10, 10))
if ncols < 2:
axs.imshow(image)
axs.axis("off")
if show_titles:
axs.set_title("Ground Truth")
else:
axs[0].imshow(image)
axs[0].axis("off")
axs[1].imshow(preds)
axs[1].axis("off")
if show_titles:
axs[0].set_title("Ground Truth")
axs[1].set_title("Predictions")
if suptitle is not None:
plt.suptitle(suptitle)
return fig
