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5d5638e674
* stat/*: Update functions to take empty matrices Change TorgersonScaling to require an empty matrix. Users who want to reuse data can call Reset now that it is exposed. This function is different than others because the return size is unknown. Forcing the input matrix to be empty makes it clear that the dst matrix will be dynamically resized Fixes #1081.
64 lines
1.8 KiB
Go
64 lines
1.8 KiB
Go
// Copyright ©2019 The Gonum Authors. All rights reserved.
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// Use of this source code is governed by a BSD-style
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// license that can be found in the LICENSE file.
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package layout
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import (
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"gonum.org/v1/gonum/graph"
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"gonum.org/v1/gonum/graph/path"
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"gonum.org/v1/gonum/mat"
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"gonum.org/v1/gonum/spatial/r2"
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"gonum.org/v1/gonum/stat/mds"
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)
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// IsomapR2 implements a graph layout algorithm based on the Isomap
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// non-linear dimensionality reduction method. Coordinates of nodes
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// are computed by finding a Torgerson multidimensional scaling of
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// the shortest path distances between all pairs of node in the graph.
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// The all pair shortest path distances are calculated using the
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// Floyd-Warshall algorithm and so IsomapR2 will not scale to large
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// graphs. Graphs with more than one connected component cannot be
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// laid out by IsomapR2.
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type IsomapR2 struct{}
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// Update is the IsomapR2 spatial graph update function.
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func (IsomapR2) Update(g graph.Graph, layout LayoutR2) bool {
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nodes := graph.NodesOf(g.Nodes())
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v := isomap(g, nodes, 2)
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if v == nil {
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return false
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}
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// FIXME(kortschak): The Layout types do not have the capacity to
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// be cleared in the current API. Is this a problem? I don't know
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// at this stage. It might be if the layout is reused between graphs.
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// Someone may do this.
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for i, n := range nodes {
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layout.SetCoord2(n.ID(), r2.Vec{X: v.At(i, 0), Y: v.At(i, 1)})
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}
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return false
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}
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func isomap(g graph.Graph, nodes []graph.Node, dims int) *mat.Dense {
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p, ok := path.FloydWarshall(g)
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if !ok {
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return nil
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}
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dist := mat.NewSymDense(len(nodes), nil)
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for i, u := range nodes {
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for j, v := range nodes {
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dist.SetSym(i, j, p.Weight(u.ID(), v.ID()))
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}
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}
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var v mat.Dense
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k, _ := mds.TorgersonScaling(&v, nil, dist)
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if k < dims {
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return nil
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}
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return &v
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}
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