pathpy
import and plotting fail for (some) netzschleuder dataset
Some of the netzschleuder datasets cannot be imported; others can be imported but cannot be plotted. I'm putting both cases together because the plot likely fails because of something not being set up during import.
For example, "polbooks" can be imported but cannot be plotted
empirical = pp.io.read_netzschleuder_network("polbooks”)
pp.plot(empirical)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[28], line 1
----> 1 pp.plot(empirical)
File /opt/conda/lib/python3.10/site-packages/pathpyG/visualisations/__init__.py:110, in plot(data, kind, **kwargs)
106 raise NotImplementedError
108 filename = kwargs.pop("filename", None)
--> 110 plt = PLOT_CLASSES[kind](data, **kwargs)
111 if filename:
112 plt.save(filename, **kwargs)
File /opt/conda/lib/python3.10/site-packages/pathpyG/visualisations/network_plots.py:125, in NetworkPlot.__init__(self, network, **kwargs)
123 self.network = network
124 self.config = kwargs
--> 125 self.generate()
File /opt/conda/lib/python3.10/site-packages/pathpyG/visualisations/network_plots.py:130, in NetworkPlot.generate(self)
128 """Generate the plot."""
129 self._compute_edge_data()
--> 130 self._compute_node_data()
131 self._compute_layout()
132 self._cleanup_config()
File /opt/conda/lib/python3.10/site-packages/pathpyG/visualisations/network_plots.py:146, in NetworkPlot._compute_node_data(self)
143 categories = {a.replace("node_", "") for a in self.network.node_attrs()}.intersection(attributes)
145 # add node data to data dict
--> 146 self._get_node_data(nodes, attributes, attr, categories)
148 # convert needed attributes to useful values
149 attr["color"] = self._convert_color(attr["color"], mode="node")
File /opt/conda/lib/python3.10/site-packages/pathpyG/visualisations/network_plots.py:176, in NetworkPlot._get_node_data(self, nodes, attributes, attr, categories)
173 # add edge attributes if needed
174 for attribute in attributes:
175 attr[attribute][uid] = (
--> 176 self.network[f"node_{attribute}", uid].item() if attribute in categories else None
177 )
AttributeError: 'list' object has no attribute ‘item'
.
Instead, for "student_cooperation", the import fails.
empirical = pp.io.read_netzschleuder_network("student_cooperation")
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[29], line 1
----> 1 empirical = pp.io.read_netzschleuder_network("student_cooperation") # other networks don t seem to work
2 empirical.mapping = pp.IndexMap(range(empirical.N))
File /opt/conda/lib/python3.10/site-packages/pathpyG/io/netzschleuder.py:458, in read_netzschleuder_network(name, net, ignore_temporal, multiedges, base_url)
455 decompressed = reader.readall()
457 # parse graphtool binary format
--> 458 return parse_graphtool_format(bytes(decompressed))
460 except ModuleNotFoundError:
461 msg = 'Package zstandard is required to decompress graphtool files. Please install module, e.g., using "pip install zstandard.'
File /opt/conda/lib/python3.10/site-packages/pathpyG/io/netzschleuder.py:275, in parse_graphtool_format(data, id_node_attr)
273 for a in edge_attr:
274 if not a.startswith('edge_'):
--> 275 g.data['edge_{0}'.format(a)] = torch.tensor(edge_attr[a], dtype=torch.float).to(config['torch']['device'])
276 for a in graph_attr:
277 g.data[a] = graph_attr[a]
ValueError: too many dimensions 'str'
These are two separate issues:
The failure to plot the polbooks data set is related to the code to plot networks, which seemingly cannot handle some node attributes. I'm including @hackl in the assignee list.
The failure to load the student_cooperation data set is an issue of the code to read the netzschleuder format. I will check how to fix this.
I will look at how to include node attributes in the plot. I think currently, it is not supported because of the new data format used in pathpyG.
