From 93253ce6703398e319c66b7ff0dfd5a34b34b951 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Mon, 10 Feb 2025 17:46:50 +0000
Subject: [PATCH 1/2] fix(morph-plot): handle files with single point cell
 types

If a file contains the definition of a point cell type, for example,
`IafTauRefCell`, we should still be able to plot the file, even if its
only a single circle/sphere. Until now, we only handled files if they
had multi-compartmental `Cell` or `Morphology` instances, and the
plotter would crash for files that had other point cell types.
---
 pyneuroml/plot/PlotMorphology.py      | 2 +-
 pyneuroml/plot/PlotMorphologyVispy.py | 8 ++++++--
 pyneuroml/utils/__init__.py           | 9 ++++++---
 pyneuroml/utils/plot.py               | 3 +--
 4 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/pyneuroml/plot/PlotMorphology.py b/pyneuroml/plot/PlotMorphology.py
index e42a9b4c..543c7e37 100644
--- a/pyneuroml/plot/PlotMorphology.py
+++ b/pyneuroml/plot/PlotMorphology.py
@@ -483,7 +483,7 @@ def plot_2D(
             radius = pop_id_vs_radii[pop_id] if pop_id in pop_id_vs_radii else 10
             color = pop_id_vs_color[pop_id] if pop_id in pop_id_vs_color else None
 
-            if cell is None:
+            if cell is None or not isinstance(cell, Cell):
                 plot_2D_point_cells(
                     offset=pos,
                     plane2d=plane2d,
diff --git a/pyneuroml/plot/PlotMorphologyVispy.py b/pyneuroml/plot/PlotMorphologyVispy.py
index 7848e112..9c338230 100644
--- a/pyneuroml/plot/PlotMorphologyVispy.py
+++ b/pyneuroml/plot/PlotMorphologyVispy.py
@@ -607,6 +607,9 @@ def plot_interactive_3D(
         # other networks
         else:
             plottable_nml_model = nml_model
+
+        logger.debug(plottable_nml_model.info(show_contents=True))
+
     # what did we get?
     else:
         raise ValueError(f"Could not process argument: {nml_model}")
@@ -671,7 +674,7 @@ def plot_interactive_3D(
     else:
         cell = list(pop_id_vs_cell.values())[0]
 
-        if cell is not None:
+        if cell is not None and isinstance(cell, Cell):
             view_min, view_max = get_cell_bound_box(cell)
         else:
             logger.debug("Got a point cell")
@@ -790,7 +793,8 @@ def plot_interactive_3D(
             except AttributeError:
                 logging.debug(f"Plotting a point cell at {pos}")
 
-            if cell is None:
+            # a point cell component type
+            if cell is None or not isinstance(cell, Cell):
                 meshdata.append(
                     (
                         f"{radius:.1f}",
diff --git a/pyneuroml/utils/__init__.py b/pyneuroml/utils/__init__.py
index 5a7dd075..e2afdb38 100644
--- a/pyneuroml/utils/__init__.py
+++ b/pyneuroml/utils/__init__.py
@@ -97,8 +97,12 @@ def extract_position_info(
     cell_elements = []
     popElements = []
 
-    cell_elements.extend(nml_model.cells)
-    cell_elements.extend(nml_model.cell2_ca_poolses)
+    members = nml_model.info(show_contents=True, return_format="dict")
+
+    for member, mdict in members.items():
+        if "cell" in mdict["type"].lower():
+            cell_elements.extend(mdict["members"])
+    # cell_elements.extend(nml_model.cell2_ca_poolses)
 
     # if there are no cells, look at morphologies
     if len(cell_elements) == 0:
@@ -715,7 +719,6 @@ def get_model_file_list(
             lems_def_dir = get_model_file_list(inc, filelist, rootdir, lems_def_dir)
 
     elif rootfile.endswith(".sedml"):
-
         try:
             import libsedml
         except ModuleNotFoundError:
diff --git a/pyneuroml/utils/plot.py b/pyneuroml/utils/plot.py
index 5ba53f90..499993a2 100644
--- a/pyneuroml/utils/plot.py
+++ b/pyneuroml/utils/plot.py
@@ -351,7 +351,6 @@ def load_minimal_morphplottable__model(
     model_members = list(vars(nml_model).keys())
     required_members = [
         "id",
-        "cells",
         "morphology",
         "cell2_ca_poolses",
         "networks",
@@ -359,7 +358,7 @@ def load_minimal_morphplottable__model(
         "includes",
     ]
     for m in model_members:
-        if m not in required_members:
+        if m not in required_members and "cells" not in m:
             setattr(nml_model, m, None)
             logger.debug(f"Dropped {m}")
 

From 7bc3b1b8d8762fb29be72a84781aab8e1aaa27fb Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 12 Feb 2025 17:41:06 +0000
Subject: [PATCH 2/2] fix(morph-plotter): ignore exception for an empty list

---
 pyneuroml/utils/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pyneuroml/utils/__init__.py b/pyneuroml/utils/__init__.py
index e2afdb38..6580132f 100644
--- a/pyneuroml/utils/__init__.py
+++ b/pyneuroml/utils/__init__.py
@@ -101,7 +101,10 @@ def extract_position_info(
 
     for member, mdict in members.items():
         if "cell" in mdict["type"].lower():
-            cell_elements.extend(mdict["members"])
+            try:
+                cell_elements.extend(mdict["members"])
+            except TypeError:
+                pass
     # cell_elements.extend(nml_model.cell2_ca_poolses)
 
     # if there are no cells, look at morphologies