{ "__type": "IngestedDoc", "__tag": 4010, "_content": { "Notes": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Strong", "__tag": 4048, "children": [ { "__type": "Text", "__tag": 4046, "value": "Array API Standard Support" } ] } ] }, { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "CrossRef", "__tag": 4002, "value": "to_tree", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:to_tree" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " has experimental support for Python Array API Standard compatible backends in addition to NumPy. Please consider testing these features by setting an environment variable " }, { "__type": "InlineCode", "__tag": 4051, "value": "SCIPY_ARRAY_API=1" }, { "__type": "Text", "__tag": 4046, "value": " and providing CuPy, PyTorch, JAX, or Dask arrays as array arguments. The following combinations of backend and device (or other capability) are supported." } ] }, { "__type": "Code", "__tag": 4050, "value": "==================== ==================== ====================\nLibrary CPU GPU\n==================== ==================== ====================\nNumPy ✅ n/a \nCuPy n/a ✅ \nPyTorch ✅ ✅ \nJAX ⚠️ no JIT ⚠️ no JIT \nDask ⚠️ computes graph n/a \n==================== ==================== ====================", "execution_status": null }, { "__type": "Blockquote", "__tag": 4059, "children": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "See " }, { "__type": "InlineRole", "__tag": 4003, "value": "dev-arrayapi", "domain": null, "role": "ref", "inventory": null }, { "__type": "Text", "__tag": 4046, "value": " for more information." } ] } ] } ], "title": [], "level": 0, "target": null }, "Warns": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Raises": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Yields": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Methods": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Returns": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Parameters", "__tag": 4026, "children": [ { "__type": "DocParam", "__tag": 4016, "name": "tree", "annotation": "ClusterNode or tuple (ClusterNode, list of ClusterNode)", "desc": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "If " }, { "__type": "InlineCode", "__tag": 4051, "value": "rd" }, { "__type": "Text", "__tag": 4046, "value": " is False, a " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": ". If " }, { "__type": "InlineCode", "__tag": 4051, "value": "rd" }, { "__type": "Text", "__tag": 4046, "value": " is True, a list of length " }, { "__type": "InlineCode", "__tag": 4051, "value": "2*n - 1" }, { "__type": "Text", "__tag": 4046, "value": ", with " }, { "__type": "InlineCode", "__tag": 4051, "value": "n" }, { "__type": "Text", "__tag": 4046, "value": " the number of samples. See the description of " }, { "__type": "ParamRef", "__tag": 4071, "name": "rd" }, { "__type": "Text", "__tag": 4046, "value": " above for more details." } ] } ] } ] } ], "title": [], "level": 0, "target": null }, "Summary": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "Convert a linkage matrix into an easy-to-use tree object." } ] } ], "title": [], "level": 0, "target": null }, "Receives": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Warnings": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Attributes": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null }, "Parameters": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Parameters", "__tag": 4026, "children": [ { "__type": "DocParam", "__tag": 4016, "name": "Z", "annotation": "ndarray", "desc": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "The linkage matrix in proper form (see the " }, { "__type": "InlineRole", "__tag": 4003, "value": "linkage", "domain": null, "role": null, "inventory": null }, { "__type": "Text", "__tag": 4046, "value": " function documentation)." } ] } ] }, { "__type": "DocParam", "__tag": 4016, "name": "rd", "annotation": "bool, optional", "desc": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "When False (default), a reference to the root " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " object is returned. Otherwise, a tuple " }, { "__type": "InlineCode", "__tag": 4051, "value": "(r, d)" }, { "__type": "Text", "__tag": 4046, "value": " is returned. " }, { "__type": "InlineCode", "__tag": 4051, "value": "r" }, { "__type": "Text", "__tag": 4046, "value": " is a reference to the root node while " }, { "__type": "InlineCode", "__tag": 4051, "value": "d" }, { "__type": "Text", "__tag": 4046, "value": " is a list of " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " objects - one per original entry in the linkage matrix plus entries for all clustering steps. If a cluster id is less than the number of samples " }, { "__type": "InlineCode", "__tag": 4051, "value": "n" }, { "__type": "Text", "__tag": 4046, "value": " in the data that the linkage matrix describes, then it corresponds to a singleton cluster (leaf node). See " }, { "__type": "InlineRole", "__tag": 4003, "value": "linkage", "domain": null, "role": null, "inventory": null }, { "__type": "Text", "__tag": 4046, "value": " for more information on the assignment of cluster ids to clusters." } ] } ] } ] } ], "title": [], "level": 0, "target": null }, "Extended Summary": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "The reference to the root " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " object is returned (by default)." } ] }, { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Text", "__tag": 4046, "value": "Each " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " object has a " }, { "__type": "InlineCode", "__tag": 4051, "value": "left" }, { "__type": "Text", "__tag": 4046, "value": ", " }, { "__type": "InlineCode", "__tag": 4051, "value": "right" }, { "__type": "Text", "__tag": 4046, "value": ", " }, { "__type": "InlineCode", "__tag": 4051, "value": "dist" }, { "__type": "Text", "__tag": 4046, "value": ", " }, { "__type": "InlineCode", "__tag": 4051, "value": "id" }, { "__type": "Text", "__tag": 4046, "value": ", and " }, { "__type": "InlineCode", "__tag": 4051, "value": "count" }, { "__type": "Text", "__tag": 4046, "value": " attribute. The left and right attributes point to ClusterNode objects that were combined to generate the cluster. If both are None then the " }, { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, { "__type": "Text", "__tag": 4046, "value": " object is a leaf node, its count must be 1, and its distance is meaningless but set to 0." } ] }, { "__type": "Paragraph", "__tag": 4045, "children": [ { "__type": "Emphasis", "__tag": 4047, "children": [ { "__type": "Text", "__tag": 4046, "value": "Note: This function is provided for the convenience of the library\nuser. ClusterNodes are not used as input to any of the functions in this\nlibrary." } ] } ] } ], "title": [], "level": 0, "target": null }, "Other Parameters": { "__type": "Section", "__tag": 4015, "children": [], "title": [], "level": 0, "target": null } }, "_ordered_sections": [ "Summary", "Extended Summary", "Parameters", "Attributes", "Methods", "Returns", "Yields", "Receives", "Other Parameters", "Raises", "Warns", "Warnings", "Notes" ], "item_file": "/scipy/cluster/hierarchy.py", "item_line": 1395, "item_type": "function", "aliases": [ "scipy.cluster.hierarchy.to_tree" ], "example_section_data": { "__type": "Section", "__tag": 4015, "children": [ { "__type": "Code", "__tag": 4050, "value": "import numpy as np\nfrom scipy.cluster import hierarchy\nrng = np.random.default_rng()\nx = rng.random((5, 2))\nZ = hierarchy.linkage(x)\nhierarchy.to_tree(Z)\nrootnode, nodelist = hierarchy.to_tree(Z, rd=True)\nrootnode\nlen(nodelist)\n", "execution_status": "success" } ], "title": [], "level": 0, "target": null }, "see_also": [ { "__type": "SeeAlsoItem", "__tag": 4028, "name": { "__type": "CrossRef", "__tag": 4002, "value": "ClusterNode", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:ClusterNode" }, "kind": "module" }, "descriptions": [], "type": "func" }, { "__type": "SeeAlsoItem", "__tag": 4028, "name": { "__type": "CrossRef", "__tag": 4002, "value": "is_valid_linkage", "reference": { "__type": "LocalRef", "__tag": 4022, "kind": "module", "path": "scipy.cluster.hierarchy:is_valid_linkage" }, "kind": "module" }, "descriptions": [], "type": "func" }, { "__type": "SeeAlsoItem", "__tag": 4028, "name": { "__type": "CrossRef", "__tag": 4002, "value": "linkage", "reference": { "__type": "RefInfo", "__tag": 4000, "module": "current-module", "version": "current-version", "kind": "to-resolve", "path": "linkage" }, "kind": "module" }, "descriptions": [], "type": "func" } ], "signature": { "__type": "SignatureNode", "__tag": 4029, "kind": "function", "parameters": [ { "__type": "SigParam", "__tag": 4030, "name": "Z", "annotation": { "__type": "Empty", "__tag": 4031 }, "kind": "POSITIONAL_OR_KEYWORD", "default": { "__type": "Empty", "__tag": 4031 } }, { "__type": "SigParam", "__tag": 4030, "name": "rd", "annotation": { "__type": "Empty", "__tag": 4031 }, "kind": "POSITIONAL_OR_KEYWORD", "default": "False" } ], "return_annotation": { "__type": "Empty", "__tag": 4031 }, "target_name": "to_tree" }, "references": null, "qa": "scipy.cluster.hierarchy:to_tree", "arbitrary": [], "local_refs": [ "Z", "rd", "tree" ] }