Merge branch 'develop' into feature/list-of-edge-builders

CHANGELOG.md

@@ -12,6 +12,9 @@ Keep it human-readable, your future self will thank you!
 
 ### Added
 - feat: Define node sets and edges based on an ICON icosahedral mesh (#53)
+- feat: Add support for `post_processors` in the recipe. (#71)
+- feat: Add `RemoveUnconnectedNodes` post processor to clean unconnected nodes in LAM. (#71)
+- feat: Define node sets and edges based on an ICON icosahedral mesh (#53)
 - feat: Support for multiple edge builders between two sets of nodes (#70)
 
 ## [0.4.0 - LAM and stretched graphs](https://github.com/ecmwf/anemoi-graphs/compare/0.3.0...0.4.0) - 2024-11-08

src/anemoi/graphs/create.py

@@ -102,6 +102,32 @@ def clean(self, graph: HeteroData) -> HeteroData:
 
         return graph
 
+    def post_process(self, graph: HeteroData) -> HeteroData:
+        """Allow post-processing of the resulting graph.
+
+        This method applies any configured post-processors to the graph,
+        which can modify or enhance the graph structure or attributes.
+
+        Parameters
+        ----------
+        graph : HeteroData
+            The graph to be post-processed.
+
+        Returns
+        -------
+        HeteroData
+            The post-processed graph.
+
+        Notes
+        -----
+        Post-processors are applied in the order they are specified in the configuration.
+        Each post-processor should implement an `update_graph` method that takes and returns a HeteroData object.
+        """
+        for processor in self.config.get("post_processors", []):
+            graph = instantiate(processor).update_graph(graph)
+
+        return graph
+
     def save(self, graph: HeteroData, save_path: Path, overwrite: bool = False) -> None:
         """Save the generated graph to the output path.
 
@@ -141,6 +167,7 @@ def create(self, save_path: Path | None = None, overwrite: bool = False) -> Hete
         graph = HeteroData()
         graph = self.update_graph(graph)
         graph = self.clean(graph)
+        graph = self.post_process(graph)
 
         if save_path is None:
             LOGGER.warning("No output path specified. The graph will not be saved.")

src/anemoi/graphs/processors/__init__.py

@@ -0,0 +1,3 @@
+from .post_process import RemoveUnconnectedNodes
+
+__all__ = [RemoveUnconnectedNodes]

src/anemoi/graphs/processors/post_process.py

@@ -0,0 +1,149 @@
+# (C) Copyright 2024 Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+
+from __future__ import annotations
+
+import logging
+from abc import ABC
+from abc import abstractmethod
+
+import torch
+from torch_geometric.data import HeteroData
+
+LOGGER = logging.getLogger(__name__)
+
+
+class PostProcessor(ABC):
+
+    @abstractmethod
+    def update_graph(self, graph: HeteroData) -> HeteroData:
+        raise NotImplementedError(f"The {self.__class__.__name__} class does not implement the method update_graph().")
+
+
+class BaseMaskingProcessor(PostProcessor, ABC):
+    """Base class for mask based processor."""
+
+    def __init__(
+        self,
+        nodes_name: str,
+        save_mask_indices_to_attr: str | None = None,
+    ) -> None:
+        self.nodes_name = nodes_name
+        self.save_mask_indices_to_attr = save_mask_indices_to_attr
+        self.mask: torch.Tensor = None
+
+    def removing_nodes(self, graph: HeteroData) -> HeteroData:
+        """Remove nodes based on the mask passed."""
+        for attr_name in graph[self.nodes_name].node_attrs():
+            graph[self.nodes_name][attr_name] = graph[self.nodes_name][attr_name][self.mask]
+
+        return graph
+
+    def create_indices_mapper_from_mask(self) -> dict[int, int]:
+        return dict(zip(torch.where(self.mask)[0].tolist(), list(range(self.mask.sum()))))
+
+    def update_edge_indices(self, graph: HeteroData) -> HeteroData:
+        """Update the edge indices to the new position of the nodes."""
+        idx_mapping = self.create_indices_mapper_from_mask()
+        for edges_name in graph.edge_types:
+            if edges_name[0] == self.nodes_name:
+                graph[edges_name].edge_index[0] = graph[edges_name].edge_index[0].apply_(idx_mapping.get)
+
+            if edges_name[2] == self.nodes_name:
+                graph[edges_name].edge_index[1] = graph[edges_name].edge_index[1].apply_(idx_mapping.get)
+
+        return graph
+
+    @abstractmethod
+    def compute_mask(self, graph: HeteroData) -> torch.Tensor: ...
+
+    def add_attribute(self, graph: HeteroData) -> HeteroData:
+        """Add an attribute of the mask indices as node attribute."""
+        if self.save_mask_indices_to_attr is not None:
+            LOGGER.info(
+                f"An attribute {self.save_mask_indices_to_attr} has been added with the indices to mask the nodes from the original graph."
+            )
+            mask_indices = torch.where(self.mask)[0].reshape((graph[self.nodes_name].num_nodes, -1))
+            graph[self.nodes_name][self.save_mask_indices_to_attr] = mask_indices
+
+        return graph
+
+    def update_graph(self, graph: HeteroData) -> HeteroData:
+        """Post-process the graph.
+
+        Parameters
+        ----------
+        graph: HeteroData
+            The graph to post-process.
+
+        Returns
+        -------
+        HeteroData
+            The post-processed graph.
+        """
+        self.mask = self.compute_mask(graph)
+        LOGGER.info(f"Removing {(~self.mask).sum()} nodes from {self.nodes_name}.")
+        graph = self.removing_nodes(graph)
+        graph = self.update_edge_indices(graph)
+        graph = self.add_attribute(graph)
+        return graph
+
+
+class RemoveUnconnectedNodes(BaseMaskingProcessor):
+    """Remove unconnected nodes in the graph.
+
+    Attributes
+    ----------
+    nodes_name: str
+        Name of the unconnected nodes to remove.
+    ignore: str, optional
+        Name of an attribute to ignore when removing nodes. Nodes with
+        this attribute set to True will not be removed.
+    save_mask_indices_to_attr: str, optional
+        Name of the attribute to save the mask indices. If provided,
+        the indices of the kept nodes will be saved in this attribute.
+
+    Methods
+    -------
+    compute_mask(graph)
+        Compute the mask of the connected nodes.
+    prune_graph(graph, mask)
+        Prune the nodes with the specified mask.
+    add_attribute(graph, mask)
+        Add an attribute of the mask indices as node attribute.
+    update_graph(graph)
+        Post-process the graph.
+    """
+
+    def __init__(
+        self,
+        nodes_name: str,
+        save_mask_indices_to_attr: str | None = None,
+        ignore: str | None = None,
+    ) -> None:
+        super().__init__(nodes_name, save_mask_indices_to_attr)
+        self.ignore = ignore
+
+    def compute_mask(self, graph: HeteroData) -> torch.Tensor:
+        """Compute the mask of connected nodes."""
+        nodes = graph[self.nodes_name]
+        connected_mask = torch.zeros(nodes.num_nodes, dtype=torch.bool)
+
+        if self.ignore is not None:
+            LOGGER.info(f"The nodes with {self.ignore}=True will not be removed.")
+            connected_mask[nodes[self.ignore].bool().squeeze()] = True
+
+        for (source_name, _, target_name), edges in graph.edge_items():
+            if source_name == self.nodes_name:
+                connected_mask[edges.edge_index[0]] = True
+
+            if target_name == self.nodes_name:
+                connected_mask[edges.edge_index[1]] = True
+
+        return connected_mask

tests/conftest.py

@@ -63,6 +63,15 @@ def graph_with_nodes() -> HeteroData:
     return graph
 
 
+@pytest.fixture
+def graph_with_isolated_nodes() -> HeteroData:
+    graph = HeteroData()
+    graph["test_nodes"].x = torch.tensor([[1], [2], [3], [4], [5], [6]])
+    graph["test_nodes"]["mask_attr"] = torch.tensor([[1], [1], [1], [0], [0], [0]], dtype=torch.bool)
+    graph["test_nodes", "to", "test_nodes"].edge_index = torch.tensor([[2, 3, 4], [1, 2, 3]])
+    return graph
+
+
 @pytest.fixture
 def graph_nodes_and_edges() -> HeteroData:
     """Graph with 1 set of nodes and edges."""

tests/processors/test_post_process.py

@@ -0,0 +1,79 @@
+# (C) Copyright 2024 Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+from __future__ import annotations
+
+import pytest
+import torch
+from torch_geometric.data import HeteroData
+
+from anemoi.graphs.processors.post_process import RemoveUnconnectedNodes
+
+
+def test_remove_unconnected_nodes(graph_with_isolated_nodes: HeteroData):
+    processor = RemoveUnconnectedNodes(nodes_name="test_nodes", ignore=None, save_mask_indices_to_attr=None)
+
+    graph = processor.update_graph(graph_with_isolated_nodes)
+
+    assert graph["test_nodes"].num_nodes == 4
+    assert torch.equal(graph["test_nodes"].x, torch.tensor([[2], [3], [4], [5]]))
+    assert "original_indices" not in graph["test_nodes"]
+
+
+def test_remove_unconnected_nodes_with_indices_attr(graph_with_isolated_nodes: HeteroData):
+    processor = RemoveUnconnectedNodes(
+        nodes_name="test_nodes", ignore=None, save_mask_indices_to_attr="original_indices"
+    )
+
+    graph = processor.update_graph(graph_with_isolated_nodes)
+
+    assert graph["test_nodes"].num_nodes == 4
+    assert torch.equal(graph["test_nodes"].x, torch.tensor([[2], [3], [4], [5]]))
+    assert torch.equal(graph["test_nodes", "to", "test_nodes"].edge_index, torch.tensor([[1, 2, 3], [0, 1, 2]]))
+    assert torch.equal(graph["test_nodes"].original_indices, torch.tensor([[1], [2], [3], [4]]))
+
+
+def test_remove_unconnected_nodes_with_ignore(graph_with_isolated_nodes: HeteroData):
+    processor = RemoveUnconnectedNodes(nodes_name="test_nodes", ignore="mask_attr", save_mask_indices_to_attr=None)
+
+    graph = processor.update_graph(graph_with_isolated_nodes)
+
+    assert graph["test_nodes"].num_nodes == 5
+    assert torch.equal(graph["test_nodes"].x, torch.tensor([[1], [2], [3], [4], [5]]))
+    assert torch.equal(graph["test_nodes", "to", "test_nodes"].edge_index, torch.tensor([[2, 3, 4], [1, 2, 3]]))
+
+
+@pytest.mark.parametrize(
+    "nodes_name,ignore,save_mask_indices_to_attr",
+    [
+        ("test_nodes", None, "original_indices"),
+        ("test_nodes", "mask_attr", None),
+        ("test_nodes", None, None),
+    ],
+)
+def test_remove_unconnected_nodes_parametrized(
+    graph_with_isolated_nodes: HeteroData,
+    nodes_name: str,
+    ignore: str | None,
+    save_mask_indices_to_attr: str | None,
+):
+    processor = RemoveUnconnectedNodes(
+        nodes_name=nodes_name, ignore=ignore, save_mask_indices_to_attr=save_mask_indices_to_attr
+    )
+
+    graph = processor.update_graph(graph_with_isolated_nodes)
+
+    assert isinstance(graph, HeteroData)
+    pruned_nodes = 4 if ignore is None else 5
+    assert graph[nodes_name].num_nodes == pruned_nodes
+
+    if save_mask_indices_to_attr:
+        assert save_mask_indices_to_attr in graph[nodes_name]
+        assert graph[nodes_name][save_mask_indices_to_attr].ndim == 2
+    else:
+        assert graph[nodes_name].node_attrs() == graph_with_isolated_nodes[nodes_name].node_attrs()