Source code for torchgeo.datasets.eddmaps

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

"""Dataset for EDDMapS."""

import os
import sys
from typing import Any

import numpy as np
import pandas as pd
from import CRS

from .geo import GeoDataset
from .utils import BoundingBox, disambiguate_timestamp

[docs]class EDDMapS(GeoDataset): """Dataset for EDDMapS. `EDDMapS <>`__, Early Detection and Distribution Mapping System, is a web-based mapping system for documenting invasive species and pest distribution. Launched in 2005 by the Center for Invasive Species and Ecosystem Health at the University of Georgia, it was originally designed as a tool for state Exotic Pest Plant Councils to develop more complete distribution data of invasive species. Since then, the program has expanded to include the entire US and Canada as well as to document certain native pest species. EDDMapS query results can be downloaded in CSV, KML, or Shapefile format. This dataset currently only supports CSV files. If you use an EDDMapS dataset in your research, please cite it like so: * EDDMapS. *YEAR*. Early Detection & Distribution Mapping System. The University of Georgia - Center for Invasive Species and Ecosystem Health. Available online at; last accessed *DATE*. .. versionadded:: 0.3 """ res = 0 _crs = CRS.from_epsg(4326) # Lat/Lon
[docs] def __init__(self, root: str = "data") -> None: """Initialize a new Dataset instance. Args: root: root directory where dataset can be found Raises: FileNotFoundError: if no files are found in ``root`` """ super().__init__() self.root = root filepath = os.path.join(root, "mappings.csv") if not os.path.exists(filepath): raise FileNotFoundError(f"Dataset not found in `root={self.root}`") # Read CSV file data = pd.read_csv( filepath, engine="c", usecols=["ObsDate", "Latitude", "Longitude"] ) # Convert from pandas DataFrame to rtree Index i = 0 for date, y, x in data.itertuples(index=False, name=None): # Skip rows without lat/lon if np.isnan(y) or np.isnan(x): continue if not pd.isna(date): mint, maxt = disambiguate_timestamp(date, "%m-%d-%y") else: mint, maxt = 0, sys.maxsize coords = (x, x, y, y, mint, maxt) self.index.insert(i, coords) i += 1
[docs] def __getitem__(self, query: BoundingBox) -> dict[str, Any]: """Retrieve metadata indexed by query. Args: query: (minx, maxx, miny, maxy, mint, maxt) coordinates to index Returns: sample of metadata at that index Raises: IndexError: if query is not found in the index """ hits = self.index.intersection(tuple(query), objects=True) bboxes = [hit.bbox for hit in hits] if not bboxes: raise IndexError( f"query: {query} not found in index with bounds: {self.bounds}" ) sample = {"crs":, "bbox": bboxes} return sample

© Copyright 2021, Microsoft Corporation. Revision 6694cbd4.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: stable
On Read the Docs
Project Home

Free document hosting provided by Read the Docs.


Access comprehensive developer documentation for PyTorch

View Docs


Get in-depth tutorials for beginners and advanced developers

View Tutorials


Find development resources and get your questions answered

View Resources