TreeSatAI: Add new dataset (#2402)

* TreeSatAI: Add new dataset

* Add versionadded

* ruff

* mypy fix

* Add docs

* Add test data

* Add zip data

* Add labels zip

* Add tests

* Add data module and tests

* Capitalization is important

* Fix uint casting to float

* Use many-hot encoding to support multilabel classification

* Silence overflow warnings

* Add docs for data module

Author: adamjstewart

docs/api/datamodules.rst

@@ -53,6 +53,7 @@ Dataset,Task,Source,License,# Samples,# Classes,Size (px),Resolution (m),Bands
 `SSL4EO-L Benchmark`_,S,Lansat & CDL,"CC0-1.0",25K,134,264x264,30,MSI
 `SSL4EO-L Benchmark`_,S,Lansat & NLCD,"CC0-1.0",25K,17,264x264,30,MSI
 `SustainBench Crop Yield`_,R,MODIS,"CC-BY-SA-4.0",11k,-,32x32,-,MSI
+`TreeSatAI`_,"C, R, S","Aerial, Sentinel-1/2",CC-BY-4.0,50K,"12, 15, 20","6, 20, 304","0.2, 10","CIR, MSI, SAR"
 `Tropical Cyclone`_,R,GOES 8--16,"CC-BY-4.0","108,110",-,256x256,4K--8K,MSI
 `UC Merced`_,C,USGS National Map,"public domain","2,100",21,256x256,0.3,RGB
 `USAVars`_,R,NAIP Aerial,"CC-BY-4.0",100K,-,-,4,"RGB, NIR"

docs/api/datasets.rst

@@ -0,0 +1,13 @@
+model:
+  class_path: MultiLabelClassificationTask
+  init_args:
+    model: 'resnet18'
+    in_channels: 19
+    num_classes: 15
+    loss: 'bce'
+data:
+  class_path: TreeSatAIDataModule
+  init_args:
+    batch_size: 1
+  dict_kwargs:
+    root: 'tests/data/treesatai'

docs/api/datasets/non_geo_datasets.csv

@@ -0,0 +1,129 @@
+#!/usr/bin/env python3
+
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+import glob
+import json
+import os
+import random
+import shutil
+import zipfile
+
+import numpy as np
+import rasterio
+from rasterio import Affine
+from rasterio.crs import CRS
+
+SIZE = 32
+
+random.seed(0)
+np.random.seed(0)
+
+classes = (
+    'Abies',
+    'Acer',
+    'Alnus',
+    'Betula',
+    'Cleared',
+    'Fagus',
+    'Fraxinus',
+    'Larix',
+    'Picea',
+    'Pinus',
+    'Populus',
+    'Prunus',
+    'Pseudotsuga',
+    'Quercus',
+    'Tilia',
+)
+
+species = (
+    'Acer_pseudoplatanus',
+    'Alnus_spec',
+    'Fagus_sylvatica',
+    'Picea_abies',
+    'Pseudotsuga_menziesii',
+    'Quercus_petraea',
+    'Quercus_rubra',
+)
+
+profile = {
+    'aerial': {
+        'driver': 'GTiff',
+        'dtype': 'uint8',
+        'nodata': None,
+        'width': SIZE,
+        'height': SIZE,
+        'count': 4,
+        'crs': CRS.from_epsg(25832),
+        'transform': Affine(
+            0.19999999999977022, 0.0, 552245.4, 0.0, -0.19999999999938728, 5728215.0
+        ),
+    },
+    's1': {
+        'driver': 'GTiff',
+        'dtype': 'float32',
+        'nodata': -9999.0,
+        'width': SIZE // 16,
+        'height': SIZE // 16,
+        'count': 3,
+        'crs': CRS.from_epsg(32632),
+        'transform': Affine(10.0, 0.0, 552245.0, 0.0, -10.0, 5728215.0),
+    },
+    's2': {
+        'driver': 'GTiff',
+        'dtype': 'uint16',
+        'nodata': None,
+        'width': SIZE // 16,
+        'height': SIZE // 16,
+        'count': 12,
+        'crs': CRS.from_epsg(32632),
+        'transform': Affine(10.0, 0.0, 552241.6565, 0.0, -10.0, 5728211.6251),
+    },
+}
+
+multi_labels = {}
+for split in ['train', 'test']:
+    with open(f'{split}_filenames.lst') as f:
+        for filename in f:
+            filename = filename.strip()
+            for sensor in ['aerial', 's1', 's2']:
+                kwargs = profile[sensor]
+                directory = os.path.join(sensor, '60m')
+                os.makedirs(directory, exist_ok=True)
+                if 'int' in kwargs['dtype']:
+                    Z = np.random.randint(
+                        np.iinfo(kwargs['dtype']).min,
+                        np.iinfo(kwargs['dtype']).max,
+                        size=(kwargs['height'], kwargs['width']),
+                        dtype=kwargs['dtype'],
+                    )
+                else:
+                    Z = np.random.rand(kwargs['height'], kwargs['width'])
+
+                path = os.path.join(directory, filename)
+                with rasterio.open(path, 'w', **kwargs) as src:
+                    for i in range(1, kwargs['count'] + 1):
+                        src.write(Z, i)
+
+            k = random.randrange(1, 4)
+            labels = random.choices(classes, k=k)
+            pcts = np.random.rand(k)
+            pcts /= np.sum(pcts)
+            multi_labels[filename] = list(map(list, zip(labels, map(float, pcts))))
+
+os.makedirs('labels', exist_ok=True)
+path = os.path.join('labels', 'TreeSatBA_v9_60m_multi_labels.json')
+with open(path, 'w') as f:
+    json.dump(multi_labels, f)
+
+for sensor in ['s1', 's2', 'labels']:
+    shutil.make_archive(sensor, 'zip', '.', sensor)
+
+for spec in species:
+    path = f'aerial_60m_{spec}.zip'.lower()
+    with zipfile.ZipFile(path, 'w') as f:
+        for path in glob.iglob(os.path.join('aerial', '60m', f'{spec}_*.tif')):
+            filename = os.path.split(path)[-1]
+            f.write(path, arcname=filename)

tests/conf/treesatai.yaml

@@ -0,0 +1 @@
+{"Picea_abies_3_46636_WEFL_NLF.tif": [["Prunus", 0.20692122963708826], ["Fraxinus", 0.7930787703629117]], "Pseudotsuga_menziesii_1_339575_BI_NLF.tif": [["Tilia", 0.4243067837573989], ["Larix", 0.5756932162426011]], "Quercus_rubra_1_92184_WEFL_NLF.tif": [["Tilia", 0.5816157697641007], ["Fagus", 0.4183842302358993]], "Fagus_sylvatica_9_29995_WEFL_NLF.tif": [["Larix", 1.0]], "Quercus_petraea_5_80549_WEFL_NLF.tif": [["Alnus", 0.5749721529276662], ["Acer", 0.4250278470723338]], "Acer_pseudoplatanus_3_5758_WEFL_NLF.tif": [["Tilia", 0.8430361090251272], ["Larix", 0.1569638909748729]], "Alnus_spec._5_13114_WEFL_NLF.tif": [["Pseudotsuga", 0.17881149698366108], ["Quercus", 0.38732907538618866], ["Cleared", 0.4338594276301503]], "Quercus_petraea_2_84375_WEFL_NLF.tif": [["Acer", 0.3909090505343164], ["Pseudotsuga", 0.2628926194326892], ["Cleared", 0.34619833003299444]], "Picea_abies_2_46896_WEFL_NLF.tif": [["Acer", 0.4953810312272686], ["Fraxinus", 0.0006659055704136941], ["Pinus", 0.5039530632023177]], "Acer_pseudoplatanus_4_6058_WEFL_NLF.tif": [["Tilia", 1.0]]}

tests/data/treesatai/aerial/60m/Acer_pseudoplatanus_3_5758_WEFL_NLF.tif

@@ -0,0 +1 @@
+Acer_pseudoplatanus_4_6058_WEFL_NLF.tif

tests/data/treesatai/aerial/60m/Acer_pseudoplatanus_4_6058_WEFL_NLF.tif

@@ -0,0 +1,9 @@
+Picea_abies_3_46636_WEFL_NLF.tif
+Pseudotsuga_menziesii_1_339575_BI_NLF.tif
+Quercus_rubra_1_92184_WEFL_NLF.tif
+Fagus_sylvatica_9_29995_WEFL_NLF.tif
+Quercus_petraea_5_80549_WEFL_NLF.tif
+Acer_pseudoplatanus_3_5758_WEFL_NLF.tif
+Alnus_spec._5_13114_WEFL_NLF.tif
+Quercus_petraea_2_84375_WEFL_NLF.tif
+Picea_abies_2_46896_WEFL_NLF.tif

tests/data/treesatai/aerial/60m/Alnus_spec._5_13114_WEFL_NLF.tif

@@ -0,0 +1,62 @@
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+import glob
+import os
+import shutil
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import pytest
+import torch.nn as nn
+from pytest import MonkeyPatch
+from torch import Tensor
+
+from torchgeo.datasets import DatasetNotFoundError, TreeSatAI
+
+root = os.path.join('tests', 'data', 'treesatai')
+md5s = {
+    'aerial_60m_acer_pseudoplatanus.zip': '',
+    'labels.zip': '',
+    's1.zip': '',
+    's2.zip': '',
+    'test_filenames.lst': '',
+    'train_filenames.lst': '',
+}
+
+
+class TestTreeSatAI:
+    @pytest.fixture
+    def dataset(self, monkeypatch: MonkeyPatch) -> TreeSatAI:
+        monkeypatch.setattr(TreeSatAI, 'url', root + os.sep)
+        monkeypatch.setattr(TreeSatAI, 'md5s', md5s)
+        transforms = nn.Identity()
+        return TreeSatAI(root, transforms=transforms)
+
+    def test_getitem(self, dataset: TreeSatAI) -> None:
+        x = dataset[0]
+        assert isinstance(x, dict)
+        assert isinstance(x['label'], Tensor)
+        for sensor in dataset.sensors:
+            assert isinstance(x[f'image_{sensor}'], Tensor)
+
+    def test_len(self, dataset: TreeSatAI) -> None:
+        assert len(dataset) == 9
+
+    def test_download(self, dataset: TreeSatAI, tmp_path: Path) -> None:
+        TreeSatAI(tmp_path, download=True)
+
+    def test_extract(self, dataset: TreeSatAI, tmp_path: Path) -> None:
+        for file in glob.iglob(os.path.join(root, '*.*')):
+            shutil.copy(file, tmp_path)
+        TreeSatAI(tmp_path)
+
+    def test_not_downloaded(self, tmp_path: Path) -> None:
+        with pytest.raises(DatasetNotFoundError, match='Dataset not found'):
+            TreeSatAI(tmp_path)
+
+    def test_plot(self, dataset: TreeSatAI) -> None:
+        x = dataset[0]
+        x['prediction'] = x['label']
+        dataset.plot(x)
+        plt.close()

tests/data/treesatai/aerial/60m/Fagus_sylvatica_9_29995_WEFL_NLF.tif

@@ -237,7 +237,7 @@ def test_freeze_backbone(self, model_name: str) -> None:
 
 class TestMultiLabelClassificationTask:
     @pytest.mark.parametrize(
-        'name', ['bigearthnet_all', 'bigearthnet_s1', 'bigearthnet_s2']
+        'name', ['bigearthnet_all', 'bigearthnet_s1', 'bigearthnet_s2', 'treesatai']
     )
     def test_trainer(
         self, monkeypatch: MonkeyPatch, name: str, fast_dev_run: bool

tests/data/treesatai/aerial/60m/Picea_abies_2_46896_WEFL_NLF.tif

@@ -48,6 +48,7 @@
 from .ssl4eo import SSL4EOLDataModule, SSL4EOS12DataModule
 from .ssl4eo_benchmark import SSL4EOLBenchmarkDataModule
 from .sustainbench_crop_yield import SustainBenchCropYieldDataModule
+from .treesatai import TreeSatAIDataModule
 from .ucmerced import UCMercedDataModule
 from .usavars import USAVarsDataModule
 from .utils import MisconfigurationException
@@ -110,6 +111,7 @@
     'SpaceNet6DataModule',
     'SpaceNetBaseDataModule',
     'SustainBenchCropYieldDataModule',
+    'TreeSatAIDataModule',
     'TropicalCycloneDataModule',
     'UCMercedDataModule',
     'USAVarsDataModule',