mantpy 0.2.0__py3-none-any.whl

mantpy/__init__.py

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+"""
+Mantpy — a framework for extracellular matrix analysis in spatial omics.
+
+Graph-based analysis of the extracellular matrix and cell--ECM interactions in
+multiplexed imaging and spatial transcriptomics.
+
+Usage
+-----
+    import mantpy as mt
+
+    ic = mt.im.ImageContainer("codex.tif", lazy=True)  # large-image support
+    adata = mt.read_imc(ic, panel=panel, cells=cells)
+    mt.pp.extract_ecm_patches(adata, ic, tiled=True, tile_size=2048)
+    mt.gr.build_cell_graph(adata)
+    mt.gr.build_ecm_graph(adata)
+    mt.gr.build_cell_ecm_graph(adata)
+    mt.tl.interaction_test(adata)
+    mt.pl.cell_ecm_graph(adata)
+"""
+
+from importlib import import_module as _import_module
+from types import ModuleType as _ModuleType
+
+import mantpy.datasets as datasets
+import mantpy.ds as ds
+import mantpy.fetch as fetch
+import mantpy.gr as gr
+import mantpy.im as im
+import mantpy.io as io
+import mantpy.palette as palette
+import mantpy.pp as pp
+import mantpy.style as style
+import mantpy.tl as tl
+from mantpy._version import __version__
+from mantpy.ds import MantpyDataset
+from mantpy.im import ImageContainer
+from mantpy.io import read_codex, read_ecm_image, read_imc, read_imc_folder
+
+
+def __getattr__(name: str) -> _ModuleType:
+    """Load optional and plotting namespaces only when first requested.
+
+    Plotting and optional neural dependencies can import
+    ``matplotlib.pyplot``, which resolves Matplotlib's backend and changes
+    ``rcParams["backend"]``. Keeping them lazy makes the base package import
+    free of plotting-state changes while preserving ``mt.pl`` and ``mt.nn``.
+    """
+    if name in {"nn", "pl"}:
+        module = _import_module(f"mantpy.{name}")
+        globals()[name] = module
+        return module
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+__all__ = [
+    "__version__",
+    "io",
+    "im",
+    "pp",
+    "gr",
+    "tl",
+    "pl",
+    "ds",
+    "datasets",
+    "fetch",
+    "nn",
+    "palette",
+    "style",
+    "read_imc",
+    "read_imc_folder",
+    "read_codex",
+    "read_ecm_image",
+    "ImageContainer",
+    "MantpyDataset",
+]
+
+
+def __dir__() -> list[str]:
+    """List public lazy exports alongside the populated module namespace."""
+    return sorted(set(globals()) | set(__all__))

mantpy/_constants.py

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+CELLTYPE_COL = "cell_type"
+X_COL = "x"
+Y_COL = "y"
+SAMPLE_ID_COL = "sample_id"
+CONDITION_COL = "condition"
+
+SPATIAL_KEY = "spatial"
+RAW_LAYER = "raw"
+
+CELL_GRAPH_KEY = "cell_graph"
+ECM_GRAPH_KEY = "ecm_graph"
+CELL_ECM_GRAPH_KEY = "cell_ecm_graph"
+
+#: squidpy's canonical connectivity slot (``squidpy._constants._pkg_constants
+#: .Key.obsp.spatial_conn``). Every ``sq.gr.*`` function defaults to it, so a
+#: graph published here is visible to the whole squidpy toolchain.
+SQUIDPY_CONN_KEY = "spatial_connectivities"
+
+ECM_PATCHES_KEY = "ecm_patches"
+ECM_CLUSTER_COL = "ecm_cluster"
+ECM_IMAGE_KEY = "ecm_image"
+IMAGE_CONTAINER_KEY = "image_container"
+
+INTERACTION_TEST_KEY = "interaction_test"
+NEIGHBOURHOOD_CLUSTERS_KEY = "neighbourhood_clusters"
+
+MANTPY_UNS_KEY = "mantpy"
+
+NODE_TYPE_CELL = "cell"
+NODE_TYPE_ECM = "ecm"
+
+EDGE_TYPE_CC = "cell-cell"
+EDGE_TYPE_EE = "ecm-ecm"
+EDGE_TYPE_CE = "cell-ecm"

mantpy/_core/__init__.py

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+# Internal modules — not part of the public API.

mantpy/_core/_edges.py

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+"""Edge construction algorithms for spatial graphs.
+
+Internal module — not part of the public API.
+
+All edge-builder functions return a list of (i, j, distance) tuples so callers
+can decide how to weight or threshold them.
+"""
+
+from __future__ import annotations
+
+from collections.abc import Callable
+
+import networkx as nx
+import numpy as np
+
+EdgeList = list[tuple[int, int, float]]
+WeightFn = Callable[[int, int, float], float]
+
+
+def knn_edges(
+    coords: np.ndarray,
+    k: int,
+    Dmax: float | None = None,
+) -> EdgeList:
+    """K-nearest-neighbour edges.
+
+    Parameters
+    ----------
+    coords
+        (N, 2) array of (x, y) coordinates.
+    k
+        Number of neighbours per node.
+    Dmax
+        Maximum allowed distance.  Edges longer than this are pruned.
+
+    Returns
+    -------
+    List of (i, j, distance) tuples (undirected — each edge appears once).
+    """
+    from sklearn.neighbors import NearestNeighbors
+
+    n = len(coords)
+    if n < 2:
+        return []
+
+    k_actual = min(k + 1, n)  # +1 because NearestNeighbors includes self
+    nn = NearestNeighbors(n_neighbors=k_actual, algorithm="ball_tree")
+    nn.fit(coords)
+    distances, indices = nn.kneighbors(coords)
+
+    edges: EdgeList = []
+    seen: set[tuple[int, int]] = set()
+    for i in range(n):
+        for j_pos in range(1, len(indices[i])):
+            j = int(indices[i][j_pos])
+            d = float(distances[i][j_pos])
+            if Dmax is not None and d > Dmax:
+                continue
+            key = (min(i, j), max(i, j))
+            if key not in seen:
+                seen.add(key)
+                edges.append((i, j, d))
+    return edges
+
+
+def delaunay_edges(
+    coords: np.ndarray,
+    Dmax: float | None = None,
+) -> EdgeList:
+    """Delaunay triangulation edges.
+
+    Parameters
+    ----------
+    coords
+        (N, 2) array of (x, y) coordinates.
+    Dmax
+        Maximum allowed distance.
+
+    Returns
+    -------
+    List of (i, j, distance) tuples.
+    """
+    from scipy.spatial import Delaunay
+
+    n = len(coords)
+    if n < 3:
+        return knn_edges(coords, k=min(2, n - 1), Dmax=Dmax)
+
+    tri = Delaunay(coords)
+    edges: EdgeList = []
+    seen: set[tuple[int, int]] = set()
+    for simplex in tri.simplices:
+        for a, b in [(0, 1), (1, 2), (0, 2)]:
+            i, j = int(simplex[a]), int(simplex[b])
+            key = (min(i, j), max(i, j))
+            if key in seen:
+                continue
+            seen.add(key)
+            d = float(np.linalg.norm(coords[i] - coords[j]))
+            if Dmax is not None and d > Dmax:
+                continue
+            edges.append((i, j, d))
+    return edges
+
+
+def radius_edges(
+    coords: np.ndarray,
+    r: float,
+) -> EdgeList:
+    """Radius-based edges: connect all pairs within distance ``r``.
+
+    Parameters
+    ----------
+    coords
+        (N, 2) array of (x, y) coordinates.
+    r
+        Radius threshold.
+
+    Returns
+    -------
+    List of (i, j, distance) tuples.
+    """
+    from sklearn.neighbors import BallTree
+
+    n = len(coords)
+    if n < 2:
+        return []
+
+    tree = BallTree(coords)
+    indices = tree.query_radius(coords, r=r)
+    edges: EdgeList = []
+    seen: set[tuple[int, int]] = set()
+    for i, neighbours in enumerate(indices):
+        for j in neighbours:
+            j = int(j)
+            if j == i:
+                continue
+            key = (min(i, j), max(i, j))
+            if key in seen:
+                continue
+            seen.add(key)
+            d = float(np.linalg.norm(coords[i] - coords[j]))
+            edges.append((i, j, d))
+    return edges
+
+
+def grid_edges(
+    coords: np.ndarray,
+    connectivity: int = 8,
+    spacing: float | None = None,
+) -> EdgeList:
+    """Lattice-connectivity edges for points sampled on a regular grid.
+
+    Designed for ECM patch centroids, which
+    :func:`~mantpy.pp.extract_ecm_patches` places on a regular, non-overlapping
+    grid. Each node connects to its immediate lattice neighbours — either the
+    4-connected von Neumann neighbourhood (orthogonal only) or the 8-connected
+    Moore neighbourhood (orthogonal + diagonal). The grid spacing is inferred
+    from the data, so the construction is **parameter-free**: there is no
+    distance threshold to tune or defend.
+
+    Unlike ``knn_edges(coords, k=8)``, this never produces long edges that reach
+    across gaps in the lattice (e.g. where background patches were dropped) — a
+    node on the edge of a hole simply ends up with fewer neighbours. It is the
+    clean equivalent of "k=8 KNN then cap diagonals", but expressed directly as
+    a grid stencil.
+
+    Parameters
+    ----------
+    coords
+        (N, 2) array of (x, y) coordinates on a regular grid.
+    connectivity
+        ``8`` — Moore neighbourhood (4 orthogonal + 4 diagonal, default).
+        ``4`` — von Neumann neighbourhood (orthogonal only).
+    spacing
+        Grid spacing. ``None`` (default) infers it as the median
+        nearest-neighbour distance, which equals the lattice step for a regular
+        grid and is robust to a few duplicate/short distances.
+
+    Returns
+    -------
+    List of (i, j, distance) tuples (undirected — each edge appears once).
+    """
+    from sklearn.neighbors import BallTree
+
+    if connectivity not in (4, 8):
+        raise ValueError(f"connectivity must be 4 or 8, got {connectivity!r}.")
+
+    n = len(coords)
+    if n < 2:
+        return []
+
+    tree = BallTree(coords)
+    if spacing is None:
+        nn_dist, _ = tree.query(coords, k=2)
+        step = nn_dist[:, 1]
+        step = step[step > 0]
+        if len(step) == 0:
+            return []
+        spacing = float(np.median(step))
+
+    # Pick a query radius strictly between the farthest in-stencil neighbour and
+    # the nearest out-of-stencil one, so only true lattice neighbours connect:
+    #   4-conn: orthogonal (=spacing)        < r < diagonal (=spacing*sqrt2)
+    #   8-conn: diagonal (=spacing*sqrt2)    < r < 2-step orthogonal (=2*spacing)
+    sqrt2 = 2.0**0.5
+    radius = spacing * (2.0 + sqrt2) / 2.0 if connectivity == 8 else spacing * (1.0 + sqrt2) / 2.0
+
+    indices = tree.query_radius(coords, r=radius)
+    edges: EdgeList = []
+    seen: set[tuple[int, int]] = set()
+    for i, neighbours in enumerate(indices):
+        for j in neighbours:
+            j = int(j)
+            if j == i:
+                continue
+            key = (min(i, j), max(i, j))
+            if key in seen:
+                continue
+            seen.add(key)
+            d = float(np.linalg.norm(coords[i] - coords[j]))
+            edges.append((i, j, d))
+    return edges
+
+
+def build_cell_nx_graph(
+    coords: np.ndarray,
+    cell_types: np.ndarray,
+    edges: EdgeList,
+    extra_node_attrs: dict[str, np.ndarray] | None = None,
+    weight_fn: WeightFn | None = None,
+    edge_feat_fn: WeightFn | None = None,
+) -> nx.Graph:
+    """Build a NetworkX graph from cell coordinates and edges.
+
+    Parameters
+    ----------
+    coords
+        (N, 2) array of (x, y) coordinates.
+    cell_types
+        (N,) array of cell-type strings.
+    edges
+        List of (i, j, distance) tuples.
+    extra_node_attrs
+        Optional dict of ``{attr_name: array_of_length_N}`` for additional
+        node attributes (e.g. marker expression).
+    weight_fn
+        Callable ``(i, j, distance) -> float`` for edge weight.
+        Defaults to ``1/distance``.
+    edge_feat_fn
+        Optional callable ``(i, j, distance) -> 1-D float32 array`` for edge
+        feature vectors.  When provided, each edge stores ``feat_fwd`` (i→j)
+        and ``feat_rev`` (j→i) attributes, which ``to_pyg`` exports as
+        ``edge_attr``.
+
+    Returns
+    -------
+    nx.Graph with node attributes: ``node_type``, ``x``, ``y``, ``cell_type``,
+    and edge attributes: ``distance``, ``weight``, ``edge_type``.
+    """
+    from mantpy._constants import EDGE_TYPE_CC, NODE_TYPE_CELL
+
+    if weight_fn is None:
+        weight_fn = lambda i, j, d: 1.0 / d if d > 0 else float("inf")
+
+    G = nx.Graph()
+    for i in range(len(coords)):
+        attrs = {
+            "node_type": NODE_TYPE_CELL,
+            "x": float(coords[i, 0]),
+            "y": float(coords[i, 1]),
+            "cell_type": str(cell_types[i]),
+        }
+        if extra_node_attrs:
+            for k, v in extra_node_attrs.items():
+                attrs[k] = v[i]
+        G.add_node(f"cell_{i}", **attrs)
+
+    for i, j, d in edges:
+        w = weight_fn(i, j, d)
+        eattrs: dict = {"distance": d, "weight": w, "edge_type": EDGE_TYPE_CC}
+        if edge_feat_fn is not None:
+            eattrs["feat_fwd"] = edge_feat_fn(i, j, d)
+            eattrs["feat_rev"] = edge_feat_fn(j, i, d)
+        G.add_edge(f"cell_{i}", f"cell_{j}", **eattrs)
+
+    return G
+
+
+def build_ecm_nx_graph(
+    ecm_patches_df,
+    edges: EdgeList,
+    extra_node_attrs: dict[str, list] | None = None,
+    weight_fn: WeightFn | None = None,
+    edge_feat_fn: WeightFn | None = None,
+) -> nx.Graph:
+    """Build a NetworkX graph from ECM patch nodes and edges.
+
+    Parameters
+    ----------
+    ecm_patches_df
+        DataFrame with ``x``, ``y``, ``ecm_cluster``, and feature columns.
+    edges
+        List of (i, j, distance) tuples.
+    extra_node_attrs
+        Optional additional node attributes.
+    weight_fn
+        Callable ``(i, j, distance) -> float`` for edge weight.
+        Defaults to ``1/distance``.
+    edge_feat_fn
+        Optional callable ``(i, j, distance) -> 1-D float32 array``.
+        When provided, stores ``feat_fwd`` (i→j) and ``feat_rev`` (j→i) on each
+        edge, exported as ``edge_attr`` by ``to_pyg``.
+
+    Returns
+    -------
+    nx.Graph with node attributes: ``node_type``, ``x``, ``y``,
+    ``ecm_cluster``, ``ecm_features``, and any extra attrs.
+    """
+    from mantpy._constants import EDGE_TYPE_EE, NODE_TYPE_ECM
+
+    if weight_fn is None:
+        weight_fn = lambda i, j, d: 1.0 / d if d > 0 else float("inf")
+
+    feat_cols = [c for c in ecm_patches_df.columns if c.startswith("feat_")]
+    G = nx.Graph()
+
+    for i, row in enumerate(ecm_patches_df.itertuples(index=False)):
+        features = [getattr(row, c) for c in feat_cols]
+        attrs = {
+            "node_type": NODE_TYPE_ECM,
+            "x": float(row.x),
+            "y": float(row.y),
+            "ecm_cluster": int(row.ecm_cluster),
+            "ecm_features": features,
+        }
+        if extra_node_attrs:
+            for k, v in extra_node_attrs.items():
+                attrs[k] = v[i]
+        G.add_node(f"ecm_{i}", **attrs)
+
+    for i, j, d in edges:
+        w = weight_fn(i, j, d)
+        eattrs: dict = {"distance": d, "weight": w, "edge_type": EDGE_TYPE_EE}
+        if edge_feat_fn is not None:
+            eattrs["feat_fwd"] = edge_feat_fn(i, j, d)
+            eattrs["feat_rev"] = edge_feat_fn(j, i, d)
+        G.add_edge(f"ecm_{i}", f"ecm_{j}", **eattrs)
+
+    return G
+
+
+def merge_cell_ecm_graphs(
+    cell_graph: nx.Graph,
+    ecm_graph: nx.Graph,
+    cell_coords: np.ndarray,
+    ecm_coords: np.ndarray,
+    Dmax_CE: float | None,
+    k: int,
+    weight_fn: WeightFn | None = None,
+    edge_feat_fn=None,
+    edge_method: str = "knn",
+) -> nx.Graph:
+    """Merge cell and ECM graphs, adding cross edges within ``Dmax_CE``.
+
+    Parameters
+    ----------
+    cell_graph
+        NetworkX graph of cell nodes.
+    ecm_graph
+        NetworkX graph of ECM nodes.
+    cell_coords
+        (N_cells, 2) coordinates.
+    ecm_coords
+        (N_ecm, 2) coordinates.
+    Dmax_CE
+        Maximum cell-ECM distance to add a cross edge.  ``None`` = no limit.
+    k
+        Maximum number of ECM neighbours per cell.
+    weight_fn
+        Callable ``(i, j, distance) -> float`` for cross-edge weight.
+    edge_feat_fn
+        Optional callable ``(ci, ei, distance, *, reverse=False) -> 1-D
+        float32 array`` for cross-edge features. ``ci`` indexes
+        ``cell_coords`` and ``ei`` indexes ``ecm_coords``; the callable is
+        invoked twice per cross edge with ``reverse=False`` for the
+        cell→ECM orientation and ``reverse=True`` for ECM→cell. Custom
+        callables MUST accept the ``reverse`` keyword — passing one that
+        doesn't will raise ``TypeError`` (mantpy's own
+        :func:`mantpy.gr.build_cell_ecm_graph` already wraps user-supplied
+        edge features into a closure that supports it).
+
+    Returns
+    -------
+    nx.Graph with all cell, ECM, and cross edges.
+    """
+    from mantpy._constants import EDGE_TYPE_CE
+
+    if weight_fn is None:
+        weight_fn = lambda i, j, d: 1.0 / d if d > 0 else float("inf")
+
+    G = nx.Graph()
+    G.add_nodes_from(cell_graph.nodes(data=True))
+    G.add_edges_from(cell_graph.edges(data=True))
+    G.add_nodes_from(ecm_graph.nodes(data=True))
+    G.add_edges_from(ecm_graph.edges(data=True))
+
+    if len(cell_coords) == 0 or len(ecm_coords) == 0:
+        return G
+
+    if edge_method == "delaunay":
+        cross_edges = delaunay_edges_bipartite(cell_coords, ecm_coords, Dmax=Dmax_CE)
+    elif edge_method == "knn":
+        cross_edges = knn_edges_bipartite(cell_coords, ecm_coords, k=k, Dmax=Dmax_CE)
+    else:
+        raise ValueError(f"edge_method must be 'knn' or 'delaunay', got {edge_method!r}")
+
+    # Node identity is recovered by name prefix, so the incoming graphs must use
+    # mantpy's own naming. A graph built elsewhere (squidpy, or any networkx
+    # default) has integer node names, which match neither prefix — see below.
+    cell_nodes = [n for n in G.nodes if str(n).startswith("cell_")]
+    ecm_nodes = [n for n in G.nodes if str(n).startswith("ecm_")]
+
+    # Cross-edges are indexed into these lists positionally. If a list is short,
+    # the index is unresolvable: previously we minted an attribute-less
+    # `cell_{ci}`/`ecm_{ei}` placeholder, which silently routed every cross-edge
+    # onto phantom nodes and left the real ones with none — leaving downstream
+    # callers to fail far away with "No cell-ECM edges with signal clusters
+    # found." Fail here instead, where the cause is visible.
+    for name, nodes, coords in (
+        ("cell", cell_nodes, cell_coords),
+        ("ecm", ecm_nodes, ecm_coords),
+    ):
+        if len(nodes) < len(coords):
+            raise ValueError(
+                f"merge_cell_ecm_graphs found {len(nodes)} '{name}_*' nodes but was given "
+                f"{len(coords)} {name} coordinates. Node names must be '{name}_<i>' matching "
+                f"the row order of {name}_coords; graphs built outside mantpy (e.g. by "
+                "sq.gr.spatial_neighbors) use integer names and must be relabelled first — "
+                f"e.g. nx.relabel_nodes(g, {{i: f'{name}_{{i}}' for i in range(g.number_of_nodes())}})."
+            )
+
+    for ci, ei, d in cross_edges:
+        cn = cell_nodes[ci]
+        en = ecm_nodes[ei]
+        w = weight_fn(ci, ei, d)
+        eattrs: dict = {"distance": d, "weight": w, "edge_type": EDGE_TYPE_CE}
+        if edge_feat_fn is not None:
+            # Cross-edge conventions:
+            #   forward  = cell → ecm  (edge_feat_fn expects ci = cell idx, ei = ecm idx)
+            #   reverse  = ecm  → cell (pass reverse=True so the closure swaps which
+            #                           coords array it indexes into)
+            # Custom callables passed in must accept reverse=False/True;
+            # the previous "swap indices" fallback silently returned wrong
+            # values whenever Na != Nb (cell coords and ecm coords differ
+            # in length, which is the normal case).
+            eattrs["feat_fwd"] = edge_feat_fn(ci, ei, d, reverse=False)
+            eattrs["feat_rev"] = edge_feat_fn(ci, ei, d, reverse=True)
+        G.add_edge(cn, en, **eattrs)
+
+    return G
+
+
+def knn_edges_bipartite(
+    coords_a: np.ndarray,
+    coords_b: np.ndarray,
+    k: int,
+    Dmax: float | None = None,
+) -> list[tuple[int, int, float]]:
+    """K-nearest neighbours from set A to set B (directed A→B)."""
+    from sklearn.neighbors import NearestNeighbors
+
+    if len(coords_a) == 0 or len(coords_b) == 0:
+        return []
+
+    k_actual = min(k, len(coords_b))
+    nn = NearestNeighbors(n_neighbors=k_actual, algorithm="ball_tree")
+    nn.fit(coords_b)
+    distances, indices = nn.kneighbors(coords_a)
+
+    edges = []
+    for i in range(len(coords_a)):
+        for pos in range(k_actual):
+            j = int(indices[i][pos])
+            d = float(distances[i][pos])
+            if Dmax is not None and d > Dmax:
+                continue
+            edges.append((i, j, d))
+    return edges
+
+
+def delaunay_edges_bipartite(
+    coords_a: np.ndarray,
+    coords_b: np.ndarray,
+    Dmax: float | None = None,
+) -> list[tuple[int, int, float]]:
+    """Bipartite Delaunay edges between two point sets.
+
+    Runs Delaunay triangulation on the stacked point cloud
+    ``[coords_a; coords_b]`` and keeps only simplex edges that cross the
+    A/B boundary. Returns ``(i_a, i_b, distance)`` tuples indexed into
+    the two input arrays.
+
+    Parameters
+    ----------
+    coords_a
+        ``(Na, 2)`` coordinates for set A.
+    coords_b
+        ``(Nb, 2)`` coordinates for set B.
+    Dmax
+        Optional distance cap. Edges longer than this are pruned.
+    """
+    from scipy.spatial import Delaunay, QhullError
+
+    na = len(coords_a)
+    nb = len(coords_b)
+    if na == 0 or nb == 0:
+        return []
+    if na + nb < 3:
+        return knn_edges_bipartite(coords_a, coords_b, k=min(1, nb), Dmax=Dmax)
+
+    stacked = np.vstack([coords_a, coords_b])
+    try:
+        tri = Delaunay(stacked)
+    except QhullError:
+        return knn_edges_bipartite(coords_a, coords_b, k=min(5, nb), Dmax=Dmax)
+
+    seen: set[tuple[int, int]] = set()
+    edges: list[tuple[int, int, float]] = []
+    for simplex in tri.simplices:
+        pts = [int(p) for p in simplex]
+        for a, b in [(0, 1), (1, 2), (0, 2)]:
+            p, q = pts[a], pts[b]
+            # one endpoint in A (< na), the other in B (>= na)
+            if (p < na) == (q < na):
+                continue
+            if p < na:
+                ia, ib = p, q - na
+            else:
+                ia, ib = q, p - na
+            key = (ia, ib)
+            if key in seen:
+                continue
+            seen.add(key)
+            d = float(np.linalg.norm(coords_a[ia] - coords_b[ib]))
+            if Dmax is not None and d > Dmax:
+                continue
+            edges.append((ia, ib, d))
+    return edges