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Source code for torchgeo.datasets.idtrees

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

"""IDTReeS dataset."""

import glob
import os
from typing import Any, Callable, Dict, List, Optional, Tuple, cast, overload

import fiona
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import rasterio
import torch
from rasterio.enums import Resampling
from torch import Tensor
from torchvision.ops import clip_boxes_to_image, remove_small_boxes
from torchvision.utils import draw_bounding_boxes

from .geo import NonGeoDataset
from .utils import download_url, extract_archive


class IDTReeS(NonGeoDataset):
    """IDTReeS dataset.

    The `IDTReeS <https://idtrees.org/competition/>`__
    dataset is a dataset for tree crown detection.

    Dataset features:

    * RGB Image, Canopy Height Model (CHM), Hyperspectral Image (HSI), LiDAR Point Cloud
    * Remote sensing and field data generated by the
      `National Ecological Observatory Network (NEON) <https://data.neonscience.org/>`_
    * 0.1 - 1m resolution imagery
    * Task 1 - object detection (tree crown delination)
    * Task 2 - object classification (species classification)
    * Train set contains 85 images
    * Test set (task 1) contains 153 images
    * Test set (task 2) contains 353 images and tree crown polygons

    Dataset format:

    * optical - three-channel RGB 200x200 geotiff
    * canopy height model - one-channel 20x20 geotiff
    * hyperspectral - 369-channel 20x20 geotiff
    * point cloud - Nx3 LAS file (.las), some files contain RGB colors per point
    * shapely files (.shp) containing polygons
    * csv file containing species labels and other metadata for each polygon

    Dataset classes:

    0. ACPE
    1. ACRU
    2. ACSA3
    3. AMLA
    4. BETUL
    5. CAGL8
    6. CATO6
    7. FAGR
    8. GOLA
    9. LITU
    10. LYLU3
    11. MAGNO
    12. NYBI
    13. NYSY
    14. OXYDE
    15. PEPA37
    16. PIEL
    17. PIPA2
    18. PINUS
    19. PITA
    20. PRSE2
    21. QUAL
    22. QUCO2
    23. QUGE2
    24. QUHE2
    25. QULA2
    26. QULA3
    27. QUMO4
    28. QUNI
    29. QURU
    30. QUERC
    31. ROPS
    32. TSCA

    If you use this dataset in your research, please cite the following paper:

    * https://doi.org/10.1101/2021.08.06.453503

    .. versionadded:: 0.2
    """

    classes = {
        "ACPE": "Acer pensylvanicum L.",
        "ACRU": "Acer rubrum L.",
        "ACSA3": "Acer saccharum Marshall",
        "AMLA": "Amelanchier laevis Wiegand",
        "BETUL": "Betula sp.",
        "CAGL8": "Carya glabra (Mill.) Sweet",
        "CATO6": "Carya tomentosa (Lam.) Nutt.",
        "FAGR": "Fagus grandifolia Ehrh.",
        "GOLA": "Gordonia lasianthus (L.) Ellis",
        "LITU": "Liriodendron tulipifera L.",
        "LYLU3": "Lyonia lucida (Lam.) K. Koch",
        "MAGNO": "Magnolia sp.",
        "NYBI": "Nyssa biflora Walter",
        "NYSY": "Nyssa sylvatica Marshall",
        "OXYDE": "Oxydendrum sp.",
        "PEPA37": "Persea palustris (Raf.) Sarg.",
        "PIEL": "Pinus elliottii Engelm.",
        "PIPA2": "Pinus palustris Mill.",
        "PINUS": "Pinus sp.",
        "PITA": "Pinus taeda L.",
        "PRSE2": "Prunus serotina Ehrh.",
        "QUAL": "Quercus alba L.",
        "QUCO2": "Quercus coccinea",
        "QUGE2": "Quercus geminata Small",
        "QUHE2": "Quercus hemisphaerica W. Bartram ex Willd.",
        "QULA2": "Quercus laevis Walter",
        "QULA3": "Quercus laurifolia Michx.",
        "QUMO4": "Quercus montana Willd.",
        "QUNI": "Quercus nigra L.",
        "QURU": "Quercus rubra L.",
        "QUERC": "Quercus sp.",
        "ROPS": "Robinia pseudoacacia L.",
        "TSCA": "Tsuga canadensis (L.) Carriere",
    }
    metadata = {
        "train": {
            "url": "https://zenodo.org/record/3934932/files/IDTREES_competition_train_v2.zip?download=1",  # noqa: E501
            "md5": "5ddfa76240b4bb6b4a7861d1d31c299c",
            "filename": "IDTREES_competition_train_v2.zip",
        },
        "test": {
            "url": "https://zenodo.org/record/3934932/files/IDTREES_competition_test_v2.zip?download=1",  # noqa: E501
            "md5": "b108931c84a70f2a38a8234290131c9b",
            "filename": "IDTREES_competition_test_v2.zip",
        },
    }
    directories = {"train": ["train"], "test": ["task1", "task2"]}
    image_size = (200, 200)

[docs] def __init__( self, root: str = "data", split: str = "train", task: str = "task1", transforms: Optional[Callable[[Dict[str, Tensor]], Dict[str, Tensor]]] = None, download: bool = False, checksum: bool = False, ) -> None: """Initialize a new IDTReeS dataset instance. Args: root: root directory where dataset can be found split: one of "train" or "test" task: 'task1' for detection, 'task2' for detection + classification (only relevant for split='test') 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 checksum: if True, check the MD5 of the downloaded files (may be slow) Raises: ImportError: if laspy or pandas are are not installed """ assert split in ["train", "test"] assert task in ["task1", "task2"] self.root = root self.split = split self.task = task self.transforms = transforms self.download = download self.checksum = checksum self.class2idx = {c: i for i, c in enumerate(self.classes)} self.idx2class = {i: c for i, c in enumerate(self.classes)} self.num_classes = len(self.classes) self._verify() try: import pandas as pd # noqa: F401 except ImportError: raise ImportError( "pandas is not installed and is required to use this dataset" ) try: import laspy # noqa: F401 except ImportError: raise ImportError( "laspy is not installed and is required to use this dataset" ) self.images, self.geometries, self.labels = self._load(root)
[docs] def __getitem__(self, index: int) -> Dict[str, Tensor]: """Return an index within the dataset. Args: index: index to return Returns: data and label at that index """ path = self.images[index] image = self._load_image(path).to(torch.uint8) hsi = self._load_image(path.replace("RGB", "HSI")) chm = self._load_image(path.replace("RGB", "CHM")) las = self._load_las(path.replace("RGB", "LAS").replace(".tif", ".las")) sample = {"image": image, "hsi": hsi, "chm": chm, "las": las} if self.split == "test": if self.task == "task2": sample["boxes"] = self._load_boxes(path) h, w = sample["image"].shape[1:] sample["boxes"], _ = self._filter_boxes( image_size=(h, w), min_size=1, boxes=sample["boxes"], labels=None ) else: sample["boxes"] = self._load_boxes(path) sample["label"] = self._load_target(path) h, w = sample["image"].shape[1:] sample["boxes"], sample["label"] = self._filter_boxes( image_size=(h, w), min_size=1, boxes=sample["boxes"], labels=sample["label"], ) 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.images)
def _load_image(self, path: str) -> Tensor: """Load a tiff file. Args: path: path to .tif file Returns: the image """ with rasterio.open(path) as f: array = f.read(out_shape=self.image_size, resampling=Resampling.bilinear) tensor = torch.from_numpy(array) return tensor def _load_las(self, path: str) -> Tensor: """Load a single point cloud. Args: path: path to .las file Returns: the point cloud """ import laspy las = laspy.read(path) array: "np.typing.NDArray[np.int_]" = np.stack([las.x, las.y, las.z], axis=0) tensor = torch.from_numpy(array) return tensor def _load_boxes(self, path: str) -> Tensor: """Load object bounding boxes. Args: path: path to .tif file Returns: the bounding boxes """ base_path = os.path.basename(path) geometries = cast(Dict[int, Dict[str, Any]], self.geometries) # Find object ids and geometries # The train set geometry->image mapping is contained # in the train/Field/itc_rsFile.csv file if self.split == "train": indices = self.labels["rsFile"] == base_path ids = self.labels[indices]["id"].tolist() geoms = [geometries[i]["geometry"]["coordinates"][0][:4] for i in ids] # The test set has no mapping csv. The mapping is inside of the geometry # properties i.e. geom["property"]["plotID"] contains the RGB image filename # Return all geometries with the matching RGB image filename of the sample else: ids = [ k for k, v in geometries.items() if v["properties"]["plotID"] == base_path ] geoms = [geometries[i]["geometry"]["coordinates"][0][:4] for i in ids] # Convert to pixel coords boxes = [] with rasterio.open(path) as f: for geom in geoms: coords = [f.index(x, y) for x, y in geom] xmin = min(coord[1] for coord in coords) xmax = max(coord[1] for coord in coords) ymin = min(coord[0] for coord in coords) ymax = max(coord[0] for coord in coords) boxes.append([xmin, ymin, xmax, ymax]) tensor = torch.tensor(boxes) return tensor def _load_target(self, path: str) -> Tensor: """Load target label for a single sample. Args: path: path to image Returns: the label """ # Find indices for objects in the image base_path = os.path.basename(path) indices = self.labels["rsFile"] == base_path # Load object labels classes = self.labels[indices]["taxonID"].tolist() labels = [self.class2idx[c] for c in classes] tensor = torch.tensor(labels) return tensor def _load( self, root: str ) -> Tuple[List[str], Optional[Dict[int, Dict[str, Any]]], Any]: """Load files, geometries, and labels. Args: root: root directory Returns: the image path, geometries, and labels """ import pandas as pd if self.split == "train": directory = os.path.join(root, self.directories[self.split][0]) labels: pd.DataFrame = self._load_labels(directory) geoms = self._load_geometries(directory) else: directory = os.path.join(root, self.task) if self.task == "task1": geoms = None labels = None else: geoms = self._load_geometries(directory) labels = None images = glob.glob(os.path.join(directory, "RemoteSensing", "RGB", "*.tif")) return images, geoms, labels def _load_labels(self, directory: str) -> Any: """Load the csv files containing the labels. Args: directory: directory containing csv files Returns: a pandas DataFrame containing the labels for each image """ import pandas as pd path_mapping = os.path.join(directory, "Field", "itc_rsFile.csv") path_labels = os.path.join(directory, "Field", "train_data.csv") df_mapping = pd.read_csv(path_mapping) df_labels = pd.read_csv(path_labels) df_mapping = df_mapping.set_index("indvdID", drop=True) df_labels = df_labels.set_index("indvdID", drop=True) df = df_labels.join(df_mapping, on="indvdID") df = df.drop_duplicates() df.reset_index() return df def _load_geometries(self, directory: str) -> Dict[int, Dict[str, Any]]: """Load the shape files containing the geometries. Args: directory: directory containing .shp files Returns: a dict containing the geometries for each object """ filepaths = glob.glob(os.path.join(directory, "ITC", "*.shp")) i = 0 features: Dict[int, Dict[str, Any]] = {} for path in filepaths: with fiona.open(path) as src: for feature in src: # The train set has a unique id for each geometry in the properties if self.split == "train": features[feature["properties"]["id"]] = feature # The test set has no unique id so create a dummy id else: features[i] = feature i += 1 return features @overload def _filter_boxes( self, image_size: Tuple[int, int], min_size: int, boxes: Tensor, labels: Tensor ) -> Tuple[Tensor, Tensor]: ... @overload def _filter_boxes( self, image_size: Tuple[int, int], min_size: int, boxes: Tensor, labels: None ) -> Tuple[Tensor, None]: ... def _filter_boxes( self, image_size: Tuple[int, int], min_size: int, boxes: Tensor, labels: Optional[Tensor], ) -> Tuple[Tensor, Optional[Tensor]]: """Clip boxes to image size and filter boxes with sides less than ``min_size``. Args: image_size: tuple of (height, width) of image min_size: filter boxes that have any side less than min_size boxes: [N, 4] shape tensor of xyxy bounding box coordinates labels: (Optional) [N,] shape tensor of bounding box labels Returns: a tuple of filtered boxes and labels """ boxes = clip_boxes_to_image(boxes=boxes, size=image_size) indices = remove_small_boxes(boxes=boxes, min_size=min_size) boxes = boxes[indices] if labels is not None: labels = labels[indices] return boxes, labels def _verify(self) -> None: """Verify the integrity of the dataset. Raises: RuntimeError: if ``download=False`` but dataset is missing or checksum fails """ url = self.metadata[self.split]["url"] md5 = self.metadata[self.split]["md5"] filename = self.metadata[self.split]["filename"] directories = self.directories[self.split] # Check if the files already exist exists = [ os.path.exists(os.path.join(self.root, directory)) for directory in directories ] if all(exists): return # Check if zip file already exists (if so then extract) filepath = os.path.join(self.root, filename) if os.path.exists(filepath): extract_archive(filepath) 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 download_url( url, self.root, filename=filename, md5=md5 if self.checksum else None ) filepath = os.path.join(self.root, filename) extract_archive(filepath)
[docs] def plot( self, sample: Dict[str, Tensor], show_titles: bool = True, suptitle: Optional[str] = None, hsi_indices: Tuple[int, int, int] = (0, 1, 2), ) -> plt.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 hsi_indices: tuple of indices to create HSI false color image Returns: a matplotlib Figure with the rendered sample """ assert len(hsi_indices) == 3 def normalize(x: Tensor) -> Tensor: return (x - x.min()) / (x.max() - x.min()) ncols = 3 hsi = normalize(sample["hsi"][hsi_indices, :, :]).permute((1, 2, 0)).numpy() chm = normalize(sample["chm"]).permute((1, 2, 0)).numpy() if "boxes" in sample and len(sample["boxes"]): labels = ( [self.idx2class[int(i)] for i in sample["label"]] if "label" in sample else None ) image = draw_bounding_boxes( image=sample["image"], boxes=sample["boxes"], labels=labels ) image = image.permute((1, 2, 0)).numpy() else: image = sample["image"].permute((1, 2, 0)).numpy() if "prediction_boxes" in sample and len(sample["prediction_boxes"]): ncols += 1 labels = ( [self.idx2class[int(i)] for i in sample["prediction_label"]] if "prediction_label" in sample else None ) preds = draw_bounding_boxes( image=sample["image"], boxes=sample["prediction_boxes"], labels=labels ) preds = preds.permute((1, 2, 0)).numpy() fig, axs = plt.subplots(ncols=ncols, figsize=(ncols * 10, 10)) axs[0].imshow(image) axs[0].axis("off") axs[1].imshow(hsi) axs[1].axis("off") axs[2].imshow(chm) axs[2].axis("off") if ncols > 3: axs[3].imshow(preds) axs[3].axis("off") if show_titles: axs[0].set_title("Ground Truth") axs[1].set_title("Hyperspectral False Color Image") axs[2].set_title("Canopy Height Model") if ncols > 3: axs[3].set_title("Predictions") if suptitle is not None: plt.suptitle(suptitle) return fig
[docs] def plot_las(self, index: int, colormap: Optional[str] = None) -> Any: """Plot a sample point cloud at the index. Args: index: index to plot colormap: a valid matplotlib colormap Returns: a open3d.visualizer.Visualizer object. Use Visualizer.run() to display Raises: ImportError: if open3d is not installed """ try: import open3d # noqa: F401 except ImportError: raise ImportError( "open3d is not installed and is required to plot point clouds" ) import laspy path = self.images[index] path = path.replace("RGB", "LAS").replace(".tif", ".las") las = laspy.read(path) points: "np.typing.NDArray[np.int_]" = np.stack( [las.x, las.y, las.z], axis=0 ).transpose((1, 0)) if colormap: if hasattr(mpl, "colormaps"): cm = mpl.colormaps[colormap] else: cm = plt.cm.get_cmap(colormap) norm = plt.Normalize() colors = cm(norm(points[:, 2]))[:, :3] else: # Some point cloud files have no color->points mapping if hasattr(las, "red"): colors = np.stack([las.red, las.green, las.blue], axis=0) colors = colors.transpose((1, 0)) / 65535 # Default to no colormap if no colors exist in las file else: colors = np.zeros_like(points) pcd = open3d.geometry.PointCloud() pcd.points = open3d.utility.Vector3dVector(points) pcd.colors = open3d.utility.Vector3dVector(colors) vis = open3d.visualization.Visualizer() vis.create_window() vis.add_geometry(pcd) return vis

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