wip: chord diagram

pyneuroml/plot/Connectivity.py

@@ -8,6 +8,7 @@
 """
 
 import logging
+import numpy as np
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -41,4 +42,16 @@ def plot_chord_diagram(filename):
     :param filename: name of NeuroML file
     :type filename: str
     """
-    pass
+    from pyneuroml.pynml import read_neuroml2_file
+    from mne_connectivity.viz import plot_connectivity_circle
+
+    doc = read_neuroml2_file(filename)
+
+    nodes = [p.id for p in doc.networks[0].populations]
+    print(f"Nodes for chord diagram are: {nodes}")
+
+    con = []
+    # TODO: logic to get connectivity information
+    print(f"Connecitivity is {con}")
+
+    fix, axes = plot_connectivity_circle(con, nodes)

tests/plot/test_plot.py

@@ -12,6 +12,7 @@
 import pathlib as pl
 
 from pyneuroml.plot import generate_plot, generate_interactive_plot
+from pyneuroml.plot.Connectivity import plot_chord_diagram
 from .. import BaseTestCase
 
 logger = logging.getLogger(__name__)
@@ -86,6 +87,17 @@ def test_generate_interactive_plot(self):
         self.assertIsFile(filename)
         pl.Path(filename).unlink()
 
+    def test_chord_diagram(self):
+        """Test the chord diagram plotter"""
+        filename = "tests/plot/test_chord_diagram.png"
+
+        # remove the file first
+        try:
+            pl.Path(filename).unlink()
+        except FileNotFoundError:
+            pass
+        plot_chord_diagram("./Izh2007Cells.net.nml")
+
 
 if __name__ == "__main__":
     unittest.main()