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Improved Graph element #2145

Merged
merged 5 commits into from
Nov 23, 2017
Merged

Improved Graph element #2145

merged 5 commits into from
Nov 23, 2017

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philippjfr
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@philippjfr philippjfr commented Nov 23, 2017

Since I started writing the Chord (#2138) and TriMesh (#2143) elements, it's become clear that the Graph element is quite useful as a baseclass for other elements. However currently it isn't as solid, optimized and tested as I'd like it to be, so rather than mixing up a bunch of changes into the Chord and TriMesh PRs I've decided to first build on Graph, ensuring that it is well tested and solid at it's core.

This will improve Graphs in a number of ways:

Graph Element Improvements

  1. Add an optimized pandas based implementation that handles drawing direct edge paths between nodes. The naive implementation relying just on HoloViews functionality is way to slow and this provides a ~100x speedup as long as pandas is installed.
  2. Graphs allowed supplying node information without defining the explicit node positions. This code was brittle and relied on implicit assumptions on the ordering of nodes. I've hardened the exception handling here, being much stricter about how node information is merged and relying on pandas to handle actual merges between node indices.

Graph Plot improvements

  1. The Graph glyphs are now updated in a well defined order, which ensures that explicit paths are re-rendered correctly when updated.
  2. The GraphPlot implementations now support an edge_color_index allowing them to be colored both by categorical attributes (e.g. by their source node) or by a value (e.g. a weight value).
  • Added tests
  • Added documentation

N = len(nodes)
circ = np.pi/N*np.arange(N)*2
x = np.cos(circ)
y = np.sin(circ)
return (x, y, nodes)


def connect_edges_pd(graph):
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Maybe move some of these functions to element.util?

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Yes, sounds good.

@@ -411,6 +412,59 @@ def map_colors(arr, crange, cmap, hex=True):
return arr


def mplcmap_to_palette(cmap, ncolors=None):
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Seems like the right place for these utilities!

g = self.graph4.opts(plot=dict(edge_color_index='Weight'),
style=dict(edge_cmap=['#FFFFFF', '#000000']))
plot = bokeh_renderer.get_plot(g)
print(plot.handles)
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Stray print.

@jlstevens
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Looks good! Other than some very minor comments I posted above, I am happy for you to go ahead and merge once you think it is ready.

@philippjfr
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Yay, even got a gain in coverage. Thanks for the review, merging.

@philippjfr philippjfr merged commit 4c1b01d into master Nov 23, 2017
@philippjfr philippjfr added this to the v1.9.2 milestone Dec 8, 2017
@philippjfr philippjfr deleted the graph_enhancements branch December 18, 2017 15:37
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2 participants