Add DL4GAMAlps dataset #2508

dcodrut · 2025-01-09T13:21:51Z

This PR adds a a Multi-modal Dataset for Glacier Mapping (Segmentation) in the European Alps.

The dataset consists of Sentinel-2 images from 2015 (mainly), 2016 and 2017, and binary segmentation masks for glaciers, based on an inventory built by glaciology experts (Paul et al. 2020).
Given that glacier ice is not always visible in the images, due to seasonal snow, shadow/cloud cover and, most importantly, debris cover, the dataset also includes additional features that can help in the segmentation task.

Here's a sample extracted with the plot function implemented in the dataset:

A preprint is available here that describes in detail how the dataset was constructed.
For a shorter description check also: https://huggingface.co/datasets/dcodrut/dl4gam_alps.

nilsleh

Thanks a lot for the contribution :) I hope this first round of review is able to resolve the import xarray error that is preventing the unit tests from running. Once they are working, will take another look for anything else!

torchgeo/datasets/glacier_mapping_alps.py

dcodrut · 2025-01-09T22:18:07Z

@microsoft-github-policy-service agree

dcodrut · 2025-01-09T22:30:11Z

Thanks a lot for the contribution :) I hope this first round of review is able to resolve the import xarray error that is preventing the unit tests from running. Once they are working, will take another look for anything else!

I hope it will be somehow useful. Happy to contribute and learn new things on the way :)
Thanks for the comments and please let me know if there are additional things I should change.

adamjstewart · 2025-01-11T18:30:27Z

I'm completely fine with adding xarray and netcdf4 as optional dependencies. We've been talking about adding xarray support for a long time. We're still not sure if it will be directly through xarray or something like rioxarray, but that doesn't matter for this PR.

adamjstewart · 2025-01-11T18:30:41Z

Can you resolve the merge conflicts so the tests run?

torchgeo/datasets/glacier_mapping_alps.py

adamjstewart · 2025-01-15T15:51:33Z

Can you resolve the merge conflicts? These requirements files unfortunately get updated a lot, causing merge issues.

adamjstewart

Code looks fantastic, just a few minor formatting comments. Thanks for taking the time to contribute your dataset to TorchGeo, let's hope it makes it easier for people to actually use and do cool science with!

requirements/datasets.txt

torchgeo/datasets/glacier_mapping_alps.py

docs/api/datasets/non_geo_datasets.csv

torchgeo/datasets/dl4gam_alps.py

adamjstewart · 2025-01-25T13:29:15Z

docs/api/datasets/non_geo_datasets.csv

@@ -21,6 +21,7 @@ Dataset,Task,Source,License,# Samples,# Classes,Size (px),Resolution (m),Bands
 `Forest Damage`_,OD,Drone imagery,"CDLA-Permissive-1.0","1,543",4,"1,500x1,500",,RGB
 `GeoNRW`_,S,Aerial,"CC-BY-4.0","7,783",11,"1,000x1,000",1,"RGB, DEM"
 `GID-15`_,S,Gaofen-2,-,150,15,"6,800x7,200",3,RGB
+`DL4GAM Alps`_,S,"Sentinel-2","CC-BY-4.0","2,251 or 11,440","2","256x256","10","MSI"


Confirmed the license

adamjstewart · 2025-01-25T13:31:20Z

pyproject.toml

+    # netcdf4 1.5.4+ required for xarray.open_dataset with engine="netcdf4"
+    "netcdf4>=1.5.4",


Suggested change

# netcdf4 1.5.4+ required for xarray.open_dataset with engine="netcdf4"

"netcdf4>=1.5.4",

# netcdf4 1.5.8+ required for Python 3.10 wheels

"netcdf4>=1.5.8",

Older versions might work, but are annoying to test in CI due to lack of wheels.

adamjstewart · 2025-01-25T13:32:13Z

pyproject.toml

@@ -97,6 +99,8 @@ datasets = [
    "scikit-image>=0.19",
    # scipy 1.7.2+ required for Python 3.10 wheels
    "scipy>=1.7.2",
+    # xarray 2023.9+ required for xarray.open_dataset


Pretty sure xarray.open_dataset existed before 2023, what error do you see for older versions?

adamjstewart · 2025-01-25T13:32:57Z

requirements/datasets.txt

Also need to update requirements/min-reqs.old with the minimum supported versions so we can test those.

adamjstewart · 2025-01-25T13:33:37Z

tests/datasets/test_dl4gam_alps.py

+from torchgeo.datasets import DatasetNotFoundError, DL4GAMAlps
+
+pytest.importorskip('xarray', minversion='2023.9')
+pytest.importorskip('netCDF4', minversion='1.5.4')


Suggested change

pytest.importorskip('netCDF4', minversion='1.5.4')

pytest.importorskip('netCDF4', minversion='1.5.8')

adamjstewart · 2025-01-25T13:34:54Z

torchgeo/datasets/dl4gam_alps.py

+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License.
+
+"""DL4GAMAlps Dataset."""


Are there any plans to release DL4GAM datasets for other locations? If so, we could rename most of these files to dl4gam.py and then have region-specific datasets grouped together.

adamjstewart · 2025-01-25T13:36:55Z

torchgeo/datasets/dl4gam_alps.py

+        'B11',
+        'B12',
+    )
+    rgb_nir_swir_bands = ('B4', 'B3', 'B2', 'B8', 'B11')  # the subset used in our paper


Suggested change

rgb_nir_swir_bands = ('B4', 'B3', 'B2', 'B8', 'B11') # the subset used in our paper

rgb_nir_swir_bands = ('B4', 'B3', 'B2', 'B8', 'B11') # the subset used in the paper

adamjstewart · 2025-01-25T13:40:45Z

torchgeo/datasets/dl4gam_alps.py

+        This dataset requires the following additional libraries to be installed:
+
+        * `xarray <https://pypi.org/project/xarray/>`_
+        * `netcdf4 <https://pypi.org/project/netCDF4/>`_


Technically h5netcdf is also a valid engine

adamjstewart · 2025-01-25T13:42:02Z

torchgeo/datasets/dl4gam_alps.py

+        # convert to torch tensors
+        for k, v in sample.items():
+            sample[k] = torch.from_numpy(v)


We try to avoid dynamic typing, could we convert to torch tensors earlier or have two different dicts?

adamjstewart · 2025-01-25T13:42:56Z

torchgeo/datasets/dl4gam_alps.py

+            a matplotlib Figure with the rendered sample
+        """
+        # we expect the RGB bands to be present
+        assert {'B4', 'B3', 'B2'}.issubset(set(self.bands)), (


See RGBBandsMissingError. Also need to add Raises: to the docstring.

dcodrut added 5 commits January 9, 2025 13:26

add the GlacierMappingAlps dataset class

6eb701d

add doc entry

6c986a1

add dummy data script

c959d46

add dummy data

0e919c6

unit tests

6fa50bc

github-actions bot added documentation Improvements or additions to documentation datasets Geospatial or benchmark datasets testing Continuous integration testing labels Jan 9, 2025

nilsleh requested changes Jan 9, 2025

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nilsleh added this to the 0.7.0 milestone Jan 9, 2025

dcodrut added 2 commits January 9, 2025 22:50

fix doc strings; refactoring

871d080

lazy import for xarray

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github-actions bot added the dependencies Packaging and dependencies label Jan 9, 2025

dcodrut and others added 2 commits January 14, 2025 03:03

Merge branch 'main' into datasets/glaciers_alps

d5413cb

reformat

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nilsleh reviewed Jan 14, 2025

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fix typo

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dcodrut added 6 commits January 19, 2025 22:47

sort alphabetically

b1202fd

add minimum versions

c7ec25c

rename dataset to DL4GAMAlps

4b9ba74

add an earlier import for tests to fail quicker

e9675b1

fix (transforms were not applied)

874409d

doc update

86bb374

dcodrut dismissed adamjstewart’s stale review via 86bb374 January 19, 2025 23:48

dcodrut and others added 2 commits January 20, 2025 05:21

Merge branch 'main' into datasets/glaciers_alps

58de111

set utils.Path as type hint

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dcodrut requested a review from nilsleh January 20, 2025 14:30

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fix typo

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dcodrut dismissed nilsleh’s stale review via 640f72a January 20, 2025 16:38

Merge branch 'main' into datasets/glaciers_alps

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dcodrut changed the title ~~Add GlacierMappingAlps dataset~~ Add DL4GAMAlps dataset Jan 20, 2025

nilsleh requested a review from adamjstewart January 21, 2025 20:31

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Add DL4GAMAlps dataset #2508

Add DL4GAMAlps dataset #2508

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		# netcdf4 1.5.4+ required for xarray.open_dataset with engine="netcdf4"
		"netcdf4>=1.5.4",

	pytest.importorskip('netCDF4', minversion='1.5.4')
	pytest.importorskip('netCDF4', minversion='1.5.8')

	rgb_nir_swir_bands = ('B4', 'B3', 'B2', 'B8', 'B11') # the subset used in our paper
	rgb_nir_swir_bands = ('B4', 'B3', 'B2', 'B8', 'B11') # the subset used in the paper

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adamjstewart commented Jan 15, 2025 •

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