From cc7d74761cf1e01b903894b6a3947bb57636575d Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 7 Nov 2023 16:59:14 +0000
Subject: [PATCH 1/3] feat(connectivity-plots): move matrix plot to new
 sub-module

---
 pyneuroml/plot/Connectivity.py | 35 ++++++++++++++++++++++++++++++++++
 pyneuroml/pynml.py             | 17 ++---------------
 2 files changed, 37 insertions(+), 15 deletions(-)
 create mode 100644 pyneuroml/plot/Connectivity.py

diff --git a/pyneuroml/plot/Connectivity.py b/pyneuroml/plot/Connectivity.py
new file mode 100644
index 00000000..e2878c88
--- /dev/null
+++ b/pyneuroml/plot/Connectivity.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+"""
+Connectivity plotting methods
+
+File: pyneuroml/plot/Connectivity.py
+
+Copyright 2023 NeuroML contributors
+"""
+
+import logging
+
+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...")
diff --git a/pyneuroml/pynml.py b/pyneuroml/pynml.py
index 703e5402..82603364 100644
--- a/pyneuroml/pynml.py
+++ b/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:

From f8c4fe4ec87bdc289f06e55d0808a5a0c72b74a6 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 7 Nov 2023 17:03:52 +0000
Subject: [PATCH 2/3] wip: chord-diagram implementation using mne

https://mne.tools/mne-connectivity/stable/auto_examples/mne_inverse_label_connectivity.html#make-a-connectivity-plot
---
 pyneuroml/plot/Connectivity.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pyneuroml/plot/Connectivity.py b/pyneuroml/plot/Connectivity.py
index e2878c88..a70cad9a 100644
--- a/pyneuroml/plot/Connectivity.py
+++ b/pyneuroml/plot/Connectivity.py
@@ -33,3 +33,12 @@ def plot_connectivity_matrix(filename, level):
     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
+    """
+    pass

From 088fa8a6028e7ebbdf71dba92e6da4c35da50e4c Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 7 Nov 2023 18:04:47 +0000
Subject: [PATCH 3/3] wip: chord diagram

---
 pyneuroml/plot/Connectivity.py | 15 ++++++++++++++-
 tests/plot/test_plot.py        | 12 ++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/pyneuroml/plot/Connectivity.py b/pyneuroml/plot/Connectivity.py
index a70cad9a..4be44abc 100644
--- a/pyneuroml/plot/Connectivity.py
+++ b/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)
diff --git a/tests/plot/test_plot.py b/tests/plot/test_plot.py
index b14a8181..02fda544 100644
--- a/tests/plot/test_plot.py
+++ b/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()