Merge branch 'eurocrops_handlenones' into tutorial_be

docs/api/datasets.rst

@@ -354,6 +354,11 @@ MapInWild
 
 .. autoclass:: MapInWild
 
+MDAS
+^^^^
+
+.. autoclass:: MDAS
+
 Million-AID
 ^^^^^^^^^^^
 

docs/api/datasets/non_geo_datasets.csv

@@ -29,6 +29,7 @@ Dataset,Task,Source,License,# Samples,# Classes,Size (px),Resolution (m),Bands
 `LEVIR-CD+`_,CD,Google Earth,-,985,2,"1,024x1,024",0.5,RGB
 `LoveDA`_,S,Google Earth,"CC-BY-NC-SA-4.0","5,987",7,"1,024x1,024",0.3,RGB
 `MapInWild`_,S,"Sentinel-1/2, ESA WorldCover, NOAA VIIRS DNB","CC-BY-4.0",1018,1,1920x1920,10--463.83,"SAR, MSI, 2020_Map, avg_rad"
+`MDAS`_,S,"Sentinel-1/2,EnMAP,HySpex","CC-BY-SA-4.0",3,20,"100x120, 300x360, 1364x1636, 10000x12000, 15000x18000",0.3--30,HSI
 `Million-AID`_,C,Google Earth,-,1M,51--73,,0.5--153,RGB
 `MMEarth`_,"C, S","Aster, Sentinel, ERA5","CC-BY-4.0","100K--1M",,"128x128 or 64x64",10,MSI
 `NASA Marine Debris`_,OD,PlanetScope,"Apache-2.0",707,1,256x256,3,RGB

tests/data/mdas/data.py

@@ -0,0 +1,161 @@
+#!/usr/bin/env python3
+
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+import hashlib
+import os
+import shutil
+
+import numpy as np
+import rasterio
+from rasterio.crs import CRS
+from rasterio.transform import from_origin
+
+# Set the random seed for reproducibility
+np.random.seed(0)
+
+# Define the root directory, dataset name, subareas, and modalities based on mdas.py
+root_dir = '.'
+ds_root_name = 'Augsburg_data_4_publication'
+subareas = ['sub_area_1', 'sub_area_2', 'sub_area_3']
+modalities = [
+    '3K_DSM',
+    '3K_RGB',
+    'HySpex',
+    'EeteS_EnMAP_10m',
+    'EeteS_EnMAP_30m',
+    'EeteS_Sentinel_2_10m',
+    'Sentinel_1',
+    'Sentinel_2',
+    'osm_buildings',
+    'osm_landuse',
+    'osm_water',
+]
+
+landuse_class_codes = [
+    -2147483647,  # no label
+    7201,  # forest
+    7202,  # park
+    7203,  # residential
+    7204,  # industrial
+    7205,  # farm
+    7206,  # cemetery
+    7207,  # allotments
+    7208,  # meadow
+    7209,  # commercial
+    7210,  # nature reserve
+    7211,  # recreation ground
+    7212,  # retail
+    7213,  # military
+    7214,  # quarry
+    7215,  # orchard
+    7217,  # scrub
+    7218,  # grass
+    7219,  # heath
+]
+
+# Remove existing dummy data if it exists
+dataset_path = os.path.join(root_dir, ds_root_name)
+if os.path.exists(dataset_path):
+    shutil.rmtree(dataset_path)
+
+
+def create_dummy_geotiff(
+    path: str,
+    num_bands: int = 3,
+    width: int = 32,
+    height: int = 32,
+    dtype: np.dtype = np.uint16,
+    binary: bool = False,
+    landuse: bool = False,
+) -> None:
+    """Create a dummy GeoTIFF file."""
+    crs = CRS.from_epsg(32632)
+    transform = from_origin(0, 0, 1, 1)
+
+    if binary:
+        data = np.random.randint(0, 2, size=(num_bands, height, width)).astype(dtype)
+    elif landuse:
+        num_pixels = num_bands * height * width
+        no_label_ratio = 0.1
+        num_no_label = int(no_label_ratio * num_pixels)
+        num_labels = num_pixels - num_no_label
+        landuse_values = np.random.choice(landuse_class_codes[1:], size=num_labels)
+        no_label_values = np.full(num_no_label, landuse_class_codes[0], dtype=dtype)
+        combined = np.concatenate([landuse_values, no_label_values])
+        np.random.shuffle(combined)
+        data = combined.reshape((num_bands, height, width)).astype(dtype)
+    else:
+        # Generate random data for other modalities
+        data = np.random.randint(0, 255, size=(num_bands, height, width)).astype(dtype)
+
+    os.makedirs(os.path.dirname(path), exist_ok=True)
+
+    with rasterio.open(
+        path,
+        'w',
+        driver='GTiff',
+        height=height,
+        width=width,
+        count=num_bands,
+        dtype=dtype,
+        crs=crs,
+        transform=transform,
+    ) as dst:
+        dst.write(data)
+
+
+# Create directory structure and dummy data
+for subarea in subareas:
+    # Format the subarea name for filenames, as in mdas.py _format_subarea method
+    parts = subarea.split('_')
+    subarea_formatted = parts[0] + '_' + parts[1] + parts[2]  # e.g., 'sub_area1'
+
+    subarea_dir = os.path.join(root_dir, ds_root_name, subarea)
+
+    for modality in modalities:
+        filename = f'{modality}_{subarea_formatted}.tif'
+        file_path = os.path.join(subarea_dir, filename)
+
+        if modality in ['osm_buildings', 'osm_water']:
+            create_dummy_geotiff(file_path, num_bands=1, dtype=np.uint8, binary=True)
+        elif modality == 'osm_landuse':
+            create_dummy_geotiff(file_path, num_bands=1, dtype=np.float64, landuse=True)
+        elif modality == 'HySpex':
+            create_dummy_geotiff(file_path, num_bands=368, dtype=np.int16)
+        elif modality in ['EeteS_EnMAP_10m', 'EeteS_EnMAP_30m']:
+            create_dummy_geotiff(file_path, num_bands=242, dtype=np.uint16)
+        elif modality == 'Sentinel_1':
+            create_dummy_geotiff(file_path, num_bands=2, dtype=np.float32)
+        elif modality in ['Sentinel_2', 'EeteS_Sentinel_2_10m']:
+            create_dummy_geotiff(file_path, num_bands=13, dtype=np.uint16)
+        elif modality == '3K_DSM':
+            create_dummy_geotiff(file_path, num_bands=1, dtype=np.float32)
+        elif modality == '3K_RGB':
+            create_dummy_geotiff(file_path, num_bands=3, dtype=np.uint8)
+
+print(f'Dummy MDAS dataset created at {os.path.join(root_dir, ds_root_name)}')
+
+# Create a zip archive of the dataset directory
+zip_filename = f'{ds_root_name}.zip'
+zip_path = os.path.join(root_dir, zip_filename)
+
+shutil.make_archive(
+    base_name=os.path.splitext(zip_path)[0],
+    format='zip',
+    root_dir='.',
+    base_dir=ds_root_name,
+)
+
+
+def calculate_md5(filename: str) -> str:
+    hash_md5 = hashlib.md5()
+    with open(filename, 'rb') as f:
+        for chunk in iter(lambda: f.read(4096), b''):
+            hash_md5.update(chunk)
+    return hash_md5.hexdigest()
+
+
+checksum = calculate_md5(zip_path)
+print(f'MD5 checksum: {checksum}')

tests/datasets/test_mdas.py

@@ -0,0 +1,113 @@
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+import os
+import shutil
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import pytest
+import torch
+import torch.nn as nn
+from _pytest.fixtures import SubRequest
+from pytest import MonkeyPatch
+
+from torchgeo.datasets import MDAS, DatasetNotFoundError
+
+
+class TestMDAS:
+    @pytest.fixture(
+        params=[
+            {'subareas': ['sub_area_1'], 'modalities': ['HySpex']},
+            {
+                'subareas': ['sub_area_1', 'sub_area_2'],
+                'modalities': ['3K_DSM', 'HySpex', 'osm_water'],
+            },
+            {
+                'subareas': ['sub_area_2', 'sub_area_3'],
+                'modalities': [
+                    '3K_DSM',
+                    '3K_RGB',
+                    'HySpex',
+                    'EeteS_EnMAP_10m',
+                    'EeteS_EnMAP_30m',
+                    'EeteS_Sentinel_2_10m',
+                    'Sentinel_2',
+                    'Sentinel_1',
+                    'osm_buildings',
+                    'osm_landuse',
+                    'osm_water',
+                ],
+            },
+        ]
+    )
+    def dataset(
+        self, monkeypatch: MonkeyPatch, tmp_path: Path, request: SubRequest
+    ) -> MDAS:
+        md5 = '99e1744ca6f19aa19a3aa23a2bbf7bef'
+        monkeypatch.setattr(MDAS, 'md5', md5)
+        url = os.path.join('tests', 'data', 'mdas', 'Augsburg_data_4_publication.zip')
+        monkeypatch.setattr(MDAS, 'url', url)
+
+        params = request.param
+        subareas = params['subareas']
+        modalities = params['modalities']
+
+        root = tmp_path
+        transforms = nn.Identity()
+
+        return MDAS(
+            root=root,
+            subareas=subareas,
+            modalities=modalities,
+            transforms=transforms,
+            download=True,
+            checksum=True,
+        )
+
+    def test_getitem(self, dataset: MDAS) -> None:
+        x = dataset[0]
+        assert isinstance(x, dict)
+        for key in dataset.modalities:
+            if key.startswith('osm'):
+                key = f'{key}_mask'
+            else:
+                key = f'{key}_image'
+            assert key in x
+
+        for key, value in x.items():
+            assert isinstance(value, torch.Tensor)
+
+    def test_len(self, dataset: MDAS) -> None:
+        assert len(dataset) == len(dataset.subareas)
+
+    def test_already_downloaded(self, dataset: MDAS) -> None:
+        MDAS(root=dataset.root)
+
+    def test_not_yet_extracted(self, tmp_path: Path) -> None:
+        filename = 'Augsburg_data_4_publication.zip'
+        dir = os.path.join('tests', 'data', 'mdas')
+        shutil.copyfile(
+            os.path.join(dir, filename), os.path.join(str(tmp_path), filename)
+        )
+        MDAS(root=str(tmp_path))
+
+    def test_invalid_subarea(self) -> None:
+        with pytest.raises(AssertionError):
+            MDAS(subareas=['foo'])
+
+    def test_invalid_modality(self) -> None:
+        with pytest.raises(AssertionError):
+            MDAS(modalities=['foo'])
+
+    def test_not_downloaded(self, tmp_path: Path) -> None:
+        with pytest.raises(DatasetNotFoundError, match='Dataset not found'):
+            MDAS(tmp_path)
+
+    def test_plot(self, dataset: MDAS) -> None:
+        dataset.plot(dataset[0], suptitle='Test')
+        plt.close()
+
+    def test_plot_single_sample(self, dataset: MDAS) -> None:
+        dataset.plot(dataset[0], show_titles=False)
+        plt.close()

torchgeo/datasets/__init__.py

@@ -85,6 +85,7 @@
 from .levircd import LEVIRCD, LEVIRCDBase, LEVIRCDPlus
 from .loveda import LoveDA
 from .mapinwild import MapInWild
+from .mdas import MDAS
 from .millionaid import MillionAID
 from .mmearth import MMEarth
 from .naip import NAIP
@@ -159,6 +160,7 @@
     'GBIF',
     'GID15',
     'LEVIRCD',
+    'MDAS',
     'NAIP',
     'NCCM',
     'NLCD',

torchgeo/datasets/eurocrops.py

@@ -205,9 +205,6 @@ def get_label(self, feature: 'fiona.model.Feature') -> int:
         # (Parent code is computed by replacing rightmost non-0 character with 0.)
         hcat_code = feature['properties'][self.label_name]
         if hcat_code is None:
-            print(
-                f"Feature does not contain the label '{self.label_name}'. Skip rendering."
-            )
             return 0
 
         while True: