From c7d4f6d28f4a1ed12aaa36e47128befaa1fd8a15 Mon Sep 17 00:00:00 2001
From: Kyle Johnsen <johnsenkyle13@gmail.com>
Date: Mon, 25 Jul 2022 16:35:26 -0400
Subject: [PATCH] plot only neurons in lims, fix figargs bug, v0.5.1

---
 cleosim/visualization.py | 13 ++++++++++---
 pyproject.toml           |  2 +-
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/cleosim/visualization.py b/cleosim/visualization.py
index 2f62e16..cc1edc7 100644
--- a/cleosim/visualization.py
+++ b/cleosim/visualization.py
@@ -177,12 +177,20 @@ def _plot(
     neuron_artists = []
     for i in range(len(neuron_groups)):
         ng = neuron_groups[i]
-        args = [ng.x / axis_scale_unit, ng.y / axis_scale_unit, ng.z / axis_scale_unit]
+        xyz = [ng.x / axis_scale_unit, ng.y / axis_scale_unit, ng.z / axis_scale_unit]
+        # mask neurons outside desired lims:
+        for i_dim, lim in enumerate([xlim, ylim, zlim]):
+            if lim is not None:
+                xyz[i_dim] = np.ma.masked_array(
+                    xyz[i_dim],
+                    np.logical_or(xyz[i_dim] < lim[0], xyz[i_dim] > lim[1]),
+                    dtype=float,
+                )
         kwargs = {"label": ng.name, "alpha": _neuron_alpha}
         if colors is not None:
             kwargs["color"] = colors[i]
         kwargs.update(scatterargs)
-        neuron_artists.append(ax.scatter(*args, **kwargs))
+        neuron_artists.append(ax.scatter(*xyz, **kwargs))
         ax.set_xlabel(f"x ({axis_scale_unit._dispname})")
         ax.set_ylabel(f"y ({axis_scale_unit._dispname})")
         ax.set_zlabel(f"z ({axis_scale_unit._dispname})")
@@ -269,5 +277,4 @@ def plot(
         devices,
         invert_z,
         scatterargs,
-        **figargs,
     )
diff --git a/pyproject.toml b/pyproject.toml
index a0579ca..66b3fad 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cleosim"
-version = "0.5.0"
+version = "0.5.1"
 description = "Closed Loop, Electrophysiology, and Optogenetics Simulator: testbed and prototyping kit"
 authors = [
     "Kyle Johnsen <kyle@kjohnsen.org>",