Hypergraph refactor #77
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added tests for different types of hypergraphs
and added fix for negative vertices
| node_size (optional): int | ||
| Change the size of the drawen nodes | ||
| pattern_size (optional): range | ||
| Only draw patterns that are in range of pattern_size | ||
| num_neurons: None or int | ||
| If None, only the neurons that are part of a pattern are shown. If an | ||
| integer is passed, it identifies the total number of recorded neurons | ||
| including non-pattern neurons to be additionally shown in the graph. | ||
| Default: None | ||
| must_involve_neuron (optional) : int | ||
| Highlight pattern which includes neuron x | ||
| node_color (optional) : String | ||
| change the color of the nodes | ||
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| node_linewidth (optional) : int | ||
| change the line width of the nodes |
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I think the order of the individual options seems a bit random. I think users will expect first the options that control what is shown (e.g., number of neurons), then how its shown (e.g., node color).
| plt.show() | ||
| viziphant.patterns.plot_patterns_hypergraph(patterns) | ||
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What was the reason to remove the fig = and plt.show() parts?
| if isinstance(self.vertices[0], int): | ||
| max_vertex = max(max(hyperedge) for hyperedge in self.hyperedges) | ||
| else: | ||
| max_vertex = 0 | ||
| if isinstance(max_vertex, str): | ||
| max_vertex = 0 |
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Can you include comments on the logic of these if statements? Why int and str?
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I assume you need this to get unique IDs for the pseudo vertecies?
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| node_size (optional) : int | ||
| Size of the nodes in the Hypergraphs | ||
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| node_color (optional) : String | ||
| change the color of the nodes | ||
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| node_linewidth (optional) : int | ||
| change the line width of the nodes |
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| node_size (optional) : int | |
| Size of the nodes in the Hypergraphs | |
| node_color (optional) : String | |
| change the color of the nodes | |
| node_linewidth (optional) : int | |
| change the line width of the nodes | |
| node_size (optional) : int | |
| Size of the nodes in the Hypergraphs | |
| node_color (optional) : String | |
| change the color of the nodes | |
| node_linewidth (optional) : int | |
| change the line width of the nodes |
| nx.dijkstra_path_length(graph, 1, 2), nx.dijkstra_path_length(graph, 1, 4) | ||
| ) | ||
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| # Two Hypergraphs with the same data should be equal |
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I think all unit tests should have such a sentence as a comment that briefly outlines the idea of the test.
| # self.spiketrains = elephant.spike_train_generation.compound_poisson_process( | ||
| # rate=5 * pq.Hz, | ||
| # amplitude_distribution=[0] + [0.98] + [0] * 8 + [0.02], | ||
| # t_stop=10 * pq.s, | ||
| # ) | ||
| # self.patterns = elephant.spade.spade( | ||
| # spiketrains=self.spiketrains, | ||
| # binsize=1 * pq.ms, | ||
| # winlen=1, | ||
| # min_spikes=2, | ||
| # n_surr=100, | ||
| # dither=5 * pq.ms, | ||
| # psr_param=[0, 0, 0], | ||
| # output_format="patterns", | ||
| # )["patterns"] |
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Why are these lines commented out -- forgotten or kept for a potential later unit test? In the latter case, please introduce a TODO comment. Otherwise, in the former case, please remove this code.
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