Chord diagram and other connectivity plot related refactoring

pyneuroml/plot/Connectivity.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+"""
+Connectivity plotting methods
+
+File: pyneuroml/plot/Connectivity.py
+
+Copyright 2023 NeuroML contributors
+"""
+
+import logging
+import numpy as np
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+def plot_connectivity_matrix(filename, level):
+    """Plot a connectivity matrix
+
+    :param filename: name of NeuroML file
+    :type filename: str
+    :param level: level at which to plot
+    :type level: int
+    """
+    from neuromllite.MatrixHandler import MatrixHandler
+    from neuroml.hdf5.NeuroMLXMLParser import NeuroMLXMLParser
+
+    logger.info("Converting %s to matrix form, level %i" % (filename, level))
+
+    handler = MatrixHandler(level=level, nl_network=None)
+
+    currParser = NeuroMLXMLParser(handler)
+    currParser.parse(filename)
+    handler.finalise_document()
+
+    logger.info("Done with MatrixHandler...")
+
+
+def plot_chord_diagram(filename):
+    """Plot a chord connectivity diagram
+
+    :param filename: name of NeuroML file
+    :type filename: str
+    """
+    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)

pyneuroml/pynml.py

@@ -2312,23 +2312,10 @@ def evaluate_arguments(args):
             exit_on_fail = True
         elif args.matrix:
             confirm_neuroml_file(f)
-            from neuromllite.MatrixHandler import MatrixHandler
-
             level = int(args.matrix[0])
+            from pyneuroml.plot.Connectivity import plot_connectivity_matrix
 
-            logger.info("Converting %s to matrix form, level %i" % (f, level))
-
-            from neuroml.hdf5.NeuroMLXMLParser import NeuroMLXMLParser
-
-            handler = MatrixHandler(level=level, nl_network=None)
-
-            currParser = NeuroMLXMLParser(handler)
-
-            currParser.parse(f)
-
-            handler.finalise_document()
-
-            logger.info("Done with MatrixHandler...")
+            plot_connectivity_matrix(f, level)
 
             exit(0)
         elif args.validate:

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()