impactmesh 0.1.0__tar.gz

impactmesh-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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impactmesh-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: impactmesh
+Version: 0.1.0
+Summary: ImpactMesh package for mesh-based impact analysis
+Author-email: Benedikt Blumenstiel <benedikt.blumenstiel@ibm.com>, Paul Höhn <paul.hoehn@dlr.com>
+License: Apache-2.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: terratorch>=1.1.1
+Requires-Dist: zarr==2.18.0
+Requires-Dist: numcodecs==0.15.1
+Dynamic: license-file
+
+[![arXiv](https://img.shields.io/badge/arXiv-comming_soon-b31b1b?logo=arxiv)](https://arxiv.org/abs/todo)
+[![HuggingFace](https://img.shields.io/badge/Hugging_Face-IBM--ESA--Geospaital-FFD21E?logo=huggingface)](https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-Fire)
+[![IBMblog](https://img.shields.io/badge/Blog-IBM-0F62FE)](https://research.ibm.com/blog/todo)
+
+# ImpactMesh
+
+ImpactMesh is a large-scale multimodal, multitemporal dataset for flood and wildfire mapping. 
+It combines Sentinel-1 SAR, Sentinel-2 optical imagery, and Copernicus DEM with high-quality annotations from Copernicus EMS. 
+The dataset covers over 400 events globally with four temporal observations per event.
+
+## Dataset
+
+Please find the wildfire subset at https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-Fire and the flood samples at https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-FLood.
+The following map gives an overview of events present in ImpactMesh:
+
+![events_world.png](assets/events_world.png)
+
+This repository provides code to build the pytorch dataloader or directly fine-tune a model with [TerraTorch](https://terrastackai.github.io/terratorch/stable/).
+
+## Setup
+
+Quick start from pypi:
+```shell
+pip install impactmesh
+```
+
+Alternatively create a new environment and install TerraTorch and the package from source:
+```shell
+python -m venv venv
+source venv/bin/activate
+pip install --upgrade pip
+pip install git+https://github.com/terrastackai/terratorch.git@multimodal
+pip install zarr==2.18.0 numcodecs==0.15.1
+pip install -e .
+```
+
+ImpactMesh uses Zarr Version 2.
+
+## Fine-tuning
+
+Run training using on of the configs provided in [configs/](configs).
+```shell
+terratorch fit --config configs/terramind_v1_tiny_impactmesh_fire.yaml
+```
+
+Run the evaluation on the test split.
+```shell
+terratorch test --config configs/terramind_v1_tiny_impactmesh_fire.yaml -- ckpt output/terramind_tiny_impactmesh_fire/1e-4/best_val_loss.ckpt
+```
+
+Run prediction with the following command:
+```shell
+terratorch predict -c configs/terramind_v1_tiny_impactmesh_fire.yaml --ckpt path/to/ckeckpoint.pt --predict_output_dir output/impactmesh_fire_predictions
+
+# TerraTorch automatically uses a tiled inference. It might still lead to OOM errors. In that case, you can use:
+python impactmesh/run_inference.py -c configs/terramind_v1_tiny_impactmesh_fire.yaml --ckpt path/to/ckeckpoint.pt --output_dir output/impactmesh_fire_predictions
+```
+
+## Citation
+
+Our technical report is released soon!
+
+[//]: # (If you use ImpactMesh in your research, please cite the [ImpactMesh]&#40;https://arxiv.org/abs/todo&#41; pre-print.)
+
+[//]: # (```text)
+
+[//]: # (@article{todo})
+
+[//]: # (```)
+
+## Acknowledgement
+
+ImpactMesh was developed as part of the FAST‑EO project funded by the European Space Agency Φ‑Lab (contract #4000143501/23/I‑DT).
+
+Sentinel-2 Level-2A data were downloaded from Microsoft Planetary Computer and are provided under Copernicus Sentinel license conditions (© European Union 2015–2025, ESA) (https://planetarycomputer.microsoft.com/dataset/sentinel-2-l2a).
+
+Sentinel-1 Radiometrically Terrain Corrected (RTC) SAR data were retrieved from Microsoft Planetary Computer (calibrated to GRD and terrain-corrected using PlanetDEM) under Copernicus Sentinel license terms (© European Union 2014–2025) (https://planetarycomputer.microsoft.com/dataset/sentinel-1-rtc).
+
+The DEM data is produced using Copernicus WorldDEM-30 © DLR e.V. 2010-2014 and © Airbus Defence and Space GmbH 2014-2018 provided under COPERNICUS by the European Union and ESA; all rights reserved.
+
+Annotations were sourced from the Copernicus Emergency Management Service (© European Union, 2012–2025), available at https://emergency.copernicus.eu/.
+
+## License
+
+The code and models are release under Apache 2.0. The dataset is released under CC-BY 4.0.

impactmesh-0.1.0/README.md

@@ -0,0 +1,85 @@
+[![arXiv](https://img.shields.io/badge/arXiv-comming_soon-b31b1b?logo=arxiv)](https://arxiv.org/abs/todo)
+[![HuggingFace](https://img.shields.io/badge/Hugging_Face-IBM--ESA--Geospaital-FFD21E?logo=huggingface)](https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-Fire)
+[![IBMblog](https://img.shields.io/badge/Blog-IBM-0F62FE)](https://research.ibm.com/blog/todo)
+
+# ImpactMesh
+
+ImpactMesh is a large-scale multimodal, multitemporal dataset for flood and wildfire mapping. 
+It combines Sentinel-1 SAR, Sentinel-2 optical imagery, and Copernicus DEM with high-quality annotations from Copernicus EMS. 
+The dataset covers over 400 events globally with four temporal observations per event.
+
+## Dataset
+
+Please find the wildfire subset at https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-Fire and the flood samples at https://huggingface.co/datasets/ibm-esa-geospatial/ImpactMesh-FLood.
+The following map gives an overview of events present in ImpactMesh:
+
+![events_world.png](assets/events_world.png)
+
+This repository provides code to build the pytorch dataloader or directly fine-tune a model with [TerraTorch](https://terrastackai.github.io/terratorch/stable/).
+
+## Setup
+
+Quick start from pypi:
+```shell
+pip install impactmesh
+```
+
+Alternatively create a new environment and install TerraTorch and the package from source:
+```shell
+python -m venv venv
+source venv/bin/activate
+pip install --upgrade pip
+pip install git+https://github.com/terrastackai/terratorch.git@multimodal
+pip install zarr==2.18.0 numcodecs==0.15.1
+pip install -e .
+```
+
+ImpactMesh uses Zarr Version 2.
+
+## Fine-tuning
+
+Run training using on of the configs provided in [configs/](configs).
+```shell
+terratorch fit --config configs/terramind_v1_tiny_impactmesh_fire.yaml
+```
+
+Run the evaluation on the test split.
+```shell
+terratorch test --config configs/terramind_v1_tiny_impactmesh_fire.yaml -- ckpt output/terramind_tiny_impactmesh_fire/1e-4/best_val_loss.ckpt
+```
+
+Run prediction with the following command:
+```shell
+terratorch predict -c configs/terramind_v1_tiny_impactmesh_fire.yaml --ckpt path/to/ckeckpoint.pt --predict_output_dir output/impactmesh_fire_predictions
+
+# TerraTorch automatically uses a tiled inference. It might still lead to OOM errors. In that case, you can use:
+python impactmesh/run_inference.py -c configs/terramind_v1_tiny_impactmesh_fire.yaml --ckpt path/to/ckeckpoint.pt --output_dir output/impactmesh_fire_predictions
+```
+
+## Citation
+
+Our technical report is released soon!
+
+[//]: # (If you use ImpactMesh in your research, please cite the [ImpactMesh](https://arxiv.org/abs/todo) pre-print.)
+
+[//]: # (```text)
+
+[//]: # (@article{todo})
+
+[//]: # (```)
+
+## Acknowledgement
+
+ImpactMesh was developed as part of the FAST‑EO project funded by the European Space Agency Φ‑Lab (contract #4000143501/23/I‑DT).
+
+Sentinel-2 Level-2A data were downloaded from Microsoft Planetary Computer and are provided under Copernicus Sentinel license conditions (© European Union 2015–2025, ESA) (https://planetarycomputer.microsoft.com/dataset/sentinel-2-l2a).
+
+Sentinel-1 Radiometrically Terrain Corrected (RTC) SAR data were retrieved from Microsoft Planetary Computer (calibrated to GRD and terrain-corrected using PlanetDEM) under Copernicus Sentinel license terms (© European Union 2014–2025) (https://planetarycomputer.microsoft.com/dataset/sentinel-1-rtc).
+
+The DEM data is produced using Copernicus WorldDEM-30 © DLR e.V. 2010-2014 and © Airbus Defence and Space GmbH 2014-2018 provided under COPERNICUS by the European Union and ESA; all rights reserved.
+
+Annotations were sourced from the Copernicus Emergency Management Service (© European Union, 2012–2025), available at https://emergency.copernicus.eu/.
+
+## License
+
+The code and models are release under Apache 2.0. The dataset is released under CC-BY 4.0.

impactmesh-0.1.0/impactmesh/impactmesh_datamodule.py

@@ -0,0 +1,226 @@
+
+import logging
+import albumentations as A
+import numpy as np
+from pathlib import Path
+from torchgeo.datamodules import NonGeoDataModule
+from .impactmesh_dataset import ImpactMeshDataset
+from terratorch.datamodules.generic_pixel_wise_data_module import Normalize
+from terratorch.datamodules.generic_multimodal_data_module import MultimodalNormalize, wrap_in_compose_is_list
+
+# Dataset statisitcs
+impactmesh_wildfire_means = {
+    "S2L2A": [801.325, 861.655, 991.636, 1019.702, 1366.43, 2000.191, 2255.338, 2354.884, 2481.838, 2747.908, 2185.777, 1495.209],
+    "S1RTC": [-9.838, -15.465],
+    "DEM": [412.745],
+}
+impactmesh_wildfire_stds = {
+    "S2L2A": [1960.514, 1732.936, 1494.812, 1384.473, 1385.129, 1309.367, 1322.601, 1352.448, 1336.39, 2379.374, 1145.593, 991.566],
+    "S1RTC": [3.505, 3.422],
+    "DEM": [354.58],
+}
+
+impactmesh_flood_means = {
+    "S2L2A": [1223.128, 1251.355, 1423.443, 1408.984, 1786.818, 2448.316, 2685.642, 2745.795, 2817.936, 3194.081, 1964.659, 1399.317],
+    "S1RTC": [-9.98, -15.968],
+    "DEM": [141.786],
+}
+impactmesh_flood_stds = {
+    "S2L2A": [2358.709, 2227.598, 2082.363, 2068.519, 2086.682, 2003.085, 2019.494, 2060.309, 2014.732, 2992.644, 1414.951, 1218.357],
+    "S1RTC": [4.24, 4.105],
+    "DEM": [189.363],
+}
+
+
+class ImpactMeshDataModule(NonGeoDataModule):
+    """NonGeo LightningDataModule implementation for ImpactMesh."""
+
+    def __init__(
+        self,
+        data_root: str,
+        batch_size: int = 8,
+        num_workers: int = 0,
+        means: dict[str, list] = None,
+        stds: dict[str, list] = None,
+        train_split: str = None,
+        val_split: str = None,
+        test_split: str = None,
+        predict_split: str = None,
+        modalities: list[str] = None,
+        label_dir: str = "MASK",
+        image_grep: dict[str, str] = None,
+        label_grep: str = None,
+        timesteps: list[int] = None,
+        concat_bands: bool = False,
+        predict_data_root: str = None,
+        train_transform: A.Compose | None | list[A.BasicTransform] = None,
+        val_transform: A.Compose | None | list[A.BasicTransform] = None,
+        test_transform: A.Compose | None | list[A.BasicTransform] = None,
+        no_data_value: float = -9999.,
+        no_data_replace: float = None,
+        rgb_indices: dict[str, list[int]] = None,
+        **kwargs,
+    ) -> None:
+        """
+        Initialize ImpactMeshDataModule.
+
+        Args:
+            data_root (str): Root directory of dataset.
+            batch_size (int): Batch size for DataLoaders. Default is 8.
+            num_workers (int): Number of workers for data loading. Default is 0.
+            means (dict[str, list], optional): Per-modality normalization means. Defaults to dataset statistics.
+            stds (dict[str, list], optional): Per-modality normalization stds. Defaults to dataset statistics.
+            train_split, val_split, test_split, predict_split (str, optional): Split identifiers.
+                Otherwise, run all patches in data_root.
+            modalities (list[str], optional): List of input modalities. Defaults to ["S2L2A", "S1RTC", "DEM"].
+            label_dir (str): Directory name for labels. Default is "MASK".
+            image_grep (dict[str, str], optional): Patterns for image file matching. Default to ImpactMesh pattern.
+            label_grep (str, optional): Pattern for label file matching. Default to ImpactMesh pattern.
+            timesteps (list[int], optional): Temporal indices to include. Defaults to [0, 1, 2, 3].
+            concat_bands (bool): Whether to concatenate bands across modalities. If True, concatenate bands of all
+                modalities, otherwise load samples as dict {<modality>: <torch.tensor>}. Defaults to False.
+            predict_data_root (str, optional): Root for prediction data.
+            train_transform, val_transform, test_transform: List of Albumentations transforms. Defaults to ToTensor.
+            no_data_value (float): Value representing missing data. Default is -9999.
+            no_data_replace (float, optional): Replacement for missing data (NaN and no_data_value). Default is 0.
+            rgb_indices (dict[str, list[int]], optional): RGB band indices per modality.
+            **kwargs: Additional arguments for parent class.
+        """
+        super().__init__(
+            ImpactMeshDataset,
+            batch_size=batch_size,
+            num_workers=num_workers,
+            **kwargs,
+        )
+        self.data_root = Path(data_root)
+        self.train_split = train_split
+        self.val_split = val_split
+        self.test_split = test_split
+        self.predict_split = predict_split
+        self.modalities = modalities or ["S2L2A", "S1RTC", "DEM"]
+        self.label_dir = label_dir
+        self.predict_data_root = predict_data_root
+        if rgb_indices is not None:
+            self.rgb_indices = rgb_indices
+        elif concat_bands:
+            self.rgb_indices = rgb_indices or {"S2L2A": list(range(12)), "S1RTC": [-3, -2], "DEM": [-1]}
+            self.rgb_indices = {m: v for m, v in self.rgb_indices.items() if m in self.modalities}
+        else:
+            self.rgb_indices = rgb_indices or {m: None for m in self.modalities}
+
+        self.image_grep = image_grep or {"S2L2A": "_S2L2A.zarr.zip", "S1RTC": "_S1RTC.zarr.zip", "DEM": "_DEM.tif"}
+        if label_grep is not None:
+            self.label_grep = label_grep
+        elif "flood" in str(self.data_root).lower():
+            self.label_grep = "_annotation_flood.tif"
+        elif "fire" in str(self.data_root).lower():
+            self.label_grep = "_annotation_wildfire.tif"
+        else:
+            raise ValueError(f"Unknown label_grep: {label_grep}. "
+                             f"Specify a label grep or include disaster type in data root {self.data_root}.")
+        self.timesteps = timesteps or [0, 1, 2, 3]
+        self.concat_bands = concat_bands
+        self.no_data_value = no_data_value
+        self.no_data_replace = no_data_replace if no_data_replace is not None else 0
+
+        self.train_transform = wrap_in_compose_is_list(train_transform, image_modalities=self.modalities)
+        self.val_transform = wrap_in_compose_is_list(val_transform, image_modalities=self.modalities)
+        self.test_transform = wrap_in_compose_is_list(test_transform, image_modalities=self.modalities)
+
+        if means is not None and stds is not None:
+            pass
+        elif "flood" in str(self.data_root).lower():
+            means = {m: impactmesh_flood_means[m] for m in self.modalities}
+            stds = {m: impactmesh_flood_stds[m] for m in self.modalities}
+        elif "fire" in str(self.data_root).lower():
+            means = {m: impactmesh_wildfire_means[m] for m in self.modalities}
+            stds = {m: impactmesh_wildfire_stds[m] for m in self.modalities}
+        else:
+            raise ValueError(f"Specify means and std or include disaster type in data root {self.data_root}")
+
+        if self.concat_bands:
+            # Concatenate mean and std values
+            self.means = np.concatenate([means[m] for m in self.modalities]).tolist()
+            self.stds = np.concatenate([stds[m] for m in self.modalities]).tolist()
+
+            self.aug = Normalize(self.means, self.stds)
+        else:
+            # Apply standardization per modality
+            self.means = {m: means[m] for m in means.keys()}
+            self.stds = {m: stds[m] for m in stds.keys()}
+
+            self.aug = MultimodalNormalize(self.means, self.stds)
+
+
+    def setup(self, stage: str) -> None:
+        """Set up datasets.
+
+        Args:
+            stage: Either fit, validate, test, or predict.
+        """
+        if stage in ["fit"]:
+            self.train_dataset = ImpactMeshDataset(
+                data_root=self.data_root,
+                split_file=self.train_split,
+                modalities=self.modalities,
+                label_dir=self.label_dir,
+                image_grep=self.image_grep,
+                label_grep=self.label_grep,
+                timesteps=self.timesteps,
+                concat_bands=self.concat_bands,
+                transform=self.train_transform,
+                no_data_value=self.no_data_value,
+                no_data_replace=self.no_data_replace,
+                rgb_indices=self.rgb_indices,
+                aug=self.aug,
+            )
+        if stage in ["fit", "validate"]:
+            self.val_dataset = ImpactMeshDataset(
+                data_root=self.data_root,
+                split_file=self.val_split,
+                modalities=self.modalities,
+                label_dir=self.label_dir,
+                image_grep=self.image_grep,
+                label_grep=self.label_grep,
+                timesteps=self.timesteps,
+                concat_bands=self.concat_bands,
+                transform=self.val_transform,
+                no_data_value=self.no_data_value,
+                no_data_replace=self.no_data_replace,
+                rgb_indices=self.rgb_indices,
+                aug=self.aug,
+            )
+        if stage in ["test"]:
+            self.test_dataset = ImpactMeshDataset(
+                data_root=self.data_root,
+                split_file=self.test_split,
+                modalities=self.modalities,
+                label_dir=self.label_dir,
+                image_grep=self.image_grep,
+                label_grep=self.label_grep,
+                timesteps=self.timesteps,
+                concat_bands=self.concat_bands,
+                transform=self.test_transform,
+                no_data_value=self.no_data_value,
+                no_data_replace=self.no_data_replace,
+                rgb_indices=self.rgb_indices,
+                aug=self.aug,
+            )
+        if stage in ["predict"]:
+            if self.predict_data_root is None:
+                logging.warning(f"predict_data_root is not specified, using default data_root {self.data_root}.")
+            self.predict_dataset = ImpactMeshDataset(
+                data_root=self.predict_data_root or self.data_root,
+                split_file=self.predict_split,
+                modalities=self.modalities,
+                label_dir=None,
+                image_grep=self.image_grep,
+                label_grep=None,
+                timesteps=self.timesteps,
+                concat_bands=self.concat_bands,
+                transform=self.test_transform,
+                no_data_value=self.no_data_value,
+                no_data_replace=self.no_data_replace,
+                rgb_indices=self.rgb_indices,
+                aug=self.aug,
+            )