Merge branch 'main' into main

.github/workflows/deploy.yaml

@@ -21,7 +21,7 @@ jobs:
       - name: Build project
         run: python3 -m build
       - name: Upload artifacts
-        uses: actions/upload-artifact@v4.5.0
+        uses: actions/upload-artifact@v4.6.0
         with:
           name: pypi-dist
           path: dist/

.github/workflows/tests.yaml

@@ -34,8 +34,6 @@ jobs:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ runner.arch }}-Python-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements/required.txt', 'requirements/datasets.txt', 'requirements/tests.txt') }}
         if: ${{ runner.os != 'macOS' }}
-      - name: Setup headless display for pyvista
-        uses: pyvista/setup-headless-display-action@v3
       - name: Install pip dependencies
         if: steps.cache.outputs.cache-hit != 'true'
         run: |
@@ -68,8 +66,6 @@ jobs:
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ runner.arch }}-Python-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements/min-reqs.old') }}
-      - name: Setup headless display for pyvista
-        uses: pyvista/setup-headless-display-action@v3
       - name: Install pip dependencies
         if: steps.cache.outputs.cache-hit != 'true'
         run: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.0
+    rev: v0.9.1
     hooks:
       - id: ruff
         types_or:
@@ -28,7 +28,6 @@ repos:
           - numpy>=1.22
           - pillow>=10.4.0
           - pytest>=6.1.2
-          - pyvista>=0.34.2
           - scikit-image>=0.22.0
           - torch>=2.3
           - torchmetrics>=0.10

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

docs/conf.py

@@ -115,7 +115,6 @@
     'numpy': ('https://numpy.org/doc/stable/', None),
     'python': ('https://docs.python.org/3', None),
     'lightning': ('https://lightning.ai/docs/pytorch/stable/', None),
-    'pyvista': ('https://docs.pyvista.org/version/stable/', None),
     'rasterio': ('https://rasterio.readthedocs.io/en/stable/', None),
     'rtree': ('https://rtree.readthedocs.io/en/stable/', None),
     'segmentation_models_pytorch': ('https://smp.readthedocs.io/en/stable/', None),

docs/tutorials/transforms.ipynb

@@ -707,7 +707,7 @@
     "sample = dataset[idx]\n",
     "rgb = sample['image'][0, 1:4]\n",
     "image = T.ToPILImage()(rgb)\n",
-    "print(f\"Class Label: {dataset.classes[sample['label']]}\")\n",
+    "print(f'Class Label: {dataset.classes[sample[\"label\"]]}')\n",
     "image.resize((256, 256), resample=Image.BILINEAR)"
    ]
   },

experiments/torchgeo/run_resisc45_experiments.py

@@ -38,7 +38,7 @@ def do_work(work: 'Queue[str]', gpu_idx: int) -> bool:
     for model, lr, loss, weights in itertools.product(
         model_options, lr_options, loss_options, weight_options
     ):
-        experiment_name = f"{model}_{lr}_{loss}_{weights.replace('_', '-')}"
+        experiment_name = f'{model}_{lr}_{loss}_{weights.replace("_", "-")}'
 
         output_dir = os.path.join('output', 'resisc45_experiments')
         log_dir = os.path.join(output_dir, 'logs')

experiments/torchgeo/run_so2sat_byol_experiments.py

@@ -39,7 +39,7 @@ def do_work(work: 'Queue[str]', gpu_idx: int) -> bool:
     for model, lr, loss, weights, bands in itertools.product(
         model_options, lr_options, loss_options, weight_options, bands_options
     ):
-        experiment_name = f"{model}_{lr}_{loss}_byol_{bands}-{weights.split('/')[-2]}"
+        experiment_name = f'{model}_{lr}_{loss}_byol_{bands}-{weights.split("/")[-2]}'
 
         output_dir = os.path.join('output', 'so2sat_experiments')
         log_dir = os.path.join(output_dir, 'logs')

experiments/torchgeo/run_so2sat_experiments.py

@@ -38,7 +38,7 @@ def do_work(work: 'Queue[str]', gpu_idx: int) -> bool:
     for model, lr, loss, weights in itertools.product(
         model_options, lr_options, loss_options, weight_options
     ):
-        experiment_name = f"{model}_{lr}_{loss}_{weights.replace('_', '-')}"
+        experiment_name = f'{model}_{lr}_{loss}_{weights.replace("_", "-")}'
 
         output_dir = os.path.join('output', 'so2sat_experiments')
         log_dir = os.path.join(output_dir, 'logs')

experiments/torchgeo/run_so2sat_seed_experiments.py

@@ -39,7 +39,7 @@ def do_work(work: 'Queue[str]', gpu_idx: int) -> bool:
     for model, lr, loss, weights, seed in itertools.product(
         model_options, lr_options, loss_options, weight_options, seeds
     ):
-        experiment_name = f"{model}_{lr}_{loss}_{weights.replace('_', '-')}_{seed}"
+        experiment_name = f'{model}_{lr}_{loss}_{weights.replace("_", "-")}_{seed}'
 
         output_dir = os.path.join('output', 'so2sat_seed_experiments')
         log_dir = os.path.join(output_dir, 'logs')

pyproject.toml

@@ -93,8 +93,6 @@ datasets = [
     "pandas[parquet]>=2",
     # pycocotools 2.0.7+ required for wheels
     "pycocotools>=2.0.7",
-    # pyvista 0.34.2+ required to avoid ImportError in CI
-    "pyvista>=0.34.2",
     # scikit-image 0.19+ required for Python 3.10 wheels
     "scikit-image>=0.19",
     # scipy 1.7.2+ required for Python 3.10 wheels
@@ -115,8 +113,8 @@ docs = [
 style = [
     # mypy 0.900+ required for pyproject.toml support
     "mypy>=0.900",
-    # ruff 0.8+ required for removal of ANN101, ANN102
-    "ruff>=0.8",
+    # ruff 0.9+ required for 2025 style guide
+    "ruff>=0.9",
 ]
 tests = [
     # nbmake 1.3.3+ required for variable mocking

requirements/datasets.txt

@@ -1,9 +1,8 @@
 # datasets
 h5py==3.12.1
 laspy==2.5.4
-opencv-python==4.10.0.84
+opencv-python==4.11.0.86
 pandas[parquet]==2.2.3
 pycocotools==2.0.8
-pyvista==0.44.2
 scikit-image==0.25.0
-scipy==1.15.0
+scipy==1.15.1

requirements/min-reqs.old

@@ -27,10 +27,8 @@ laspy==2.0.0
 opencv-python==4.5.4.58
 pycocotools==2.0.7
 pyarrow==15.0.0  # Remove when we upgrade min version of pandas to `pandas[parquet]>=2`
-pyvista==0.34.2
 scikit-image==0.19.0
 scipy==1.7.2
-vtk==9.3.1  # PyVista is not yet compatible with VTK 9.4+
 
 # tests
 pytest==7.3.0

requirements/required.txt

@@ -1,11 +1,11 @@
 # setup
-setuptools==75.6.0
+setuptools==75.8.0
 
 # install
 einops==0.8.0
 fiona==1.10.1
-kornia==0.7.4
-lightly==1.5.15
+kornia==0.8.0
+lightly==1.5.16
 lightning[pytorch-extra]==2.5.0.post0
 matplotlib==3.10.0
 numpy==2.2.1

requirements/style.txt

@@ -1,3 +1,3 @@
 # style
 mypy==1.14.1
-ruff==0.8.5
+ruff==0.9.2

tests/data/inria/data.py

@@ -68,9 +68,9 @@ def generate_test_data(root: str, n_samples: int = 2) -> str:
         lbl = np.random.randint(2, size=size, dtype=dtype)
         timg = np.random.randint(dtype_max, size=size, dtype=dtype)
 
-        img_path = os.path.join(img_dir, f'austin{i+1}.tif')
-        lbl_path = os.path.join(lbl_dir, f'austin{i+1}.tif')
-        timg_path = os.path.join(timg_dir, f'austin{i+10}.tif')
+        img_path = os.path.join(img_dir, f'austin{i + 1}.tif')
+        lbl_path = os.path.join(lbl_dir, f'austin{i + 1}.tif')
+        timg_path = os.path.join(timg_dir, f'austin{i + 10}.tif')
 
         write_data(img_path, img, driver, crs, transform)
         write_data(lbl_path, lbl, driver, crs, transform)

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/data/seasonet/data.py

@@ -63,7 +63,7 @@
         os.remove(archive)
 
     for grid, comp in zip(grids, name_comps):
-        file_name = f"{comp[0]}_{''.join(comp[1:8])}_{'_'.join(comp[8:])}"
+        file_name = f'{comp[0]}_{"".join(comp[1:8])}_{"_".join(comp[8:])}'
         dir = os.path.join(season, f'grid{grid}', file_name)
         os.makedirs(dir)
 

tests/data/ssl4eo_benchmark_landsat/data.py

@@ -193,7 +193,7 @@ def create_tarballs(directories: str) -> None:
     # mask directory cdl
     mask_keep = ['tm_toa', 'etm_sr', 'oli_sr']
     mask_filenames = {
-        f"ssl4eo_l_{key.split('_')[0]}_cdl": val
+        f'ssl4eo_l_{key.split("_")[0]}_cdl': val
         for key, val in filenames.items()
         if key in mask_keep
     }
@@ -203,7 +203,7 @@ def create_tarballs(directories: str) -> None:
 
     # mask directory nlcd
     mask_filenames = {
-        f"ssl4eo_l_{key.split('_')[0]}_nlcd": val
+        f'ssl4eo_l_{key.split("_")[0]}_nlcd': val
         for key, val in filenames.items()
         if key in mask_keep
     }