From 02e541ea294e5bcc49000576b19297837b6013ac Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 21 Aug 2024 19:16:12 +0100
Subject: [PATCH] feat(vispy): remove no longer needed instanced meshes

---
 pyneuroml/plot/PlotMorphologyVispy.py | 134 --------------------------
 1 file changed, 134 deletions(-)

diff --git a/pyneuroml/plot/PlotMorphologyVispy.py b/pyneuroml/plot/PlotMorphologyVispy.py
index 934f711d..74f8fdaa 100644
--- a/pyneuroml/plot/PlotMorphologyVispy.py
+++ b/pyneuroml/plot/PlotMorphologyVispy.py
@@ -998,140 +998,6 @@ def plot_3D_cell_morphology(
     return meshdata
 
 
-def create_instanced_meshes(meshdata, plot_type, current_view, min_width):
-    """Internal function to plot instanced meshes from mesh data.
-
-    It is more efficient to collect all the segments that require the same
-    cylindrical mesh and to create instanced meshes for them.
-
-    See: https://vispy.org/api/vispy.scene.visuals.html#vispy.scene.visuals.InstancedMesh
-
-    :param meshdata: meshdata to plot: dictionary with:
-        key: (r1, r2, length)
-        value: [(prox, dist, color, offset)]
-    :param plot_type: type of plot
-    :type plot_type: str
-    :param current_view: vispy viewbox to use
-    :type current_view: ViewBox
-    :param min_width: minimum width of tubes
-    :type min_width: float
-    """
-    total_mesh_instances = 0
-    for d, i in meshdata.items():
-        total_mesh_instances += len(i)
-    logger.debug(
-        f"Visualising {len(meshdata.keys())} meshes with {total_mesh_instances} instances"
-    )
-
-    pbar = progressbar.ProgressBar(
-        max_value=total_mesh_instances,
-        widgets=[progressbar.SimpleProgress(), progressbar.Bar(), progressbar.Timer()],
-        redirect_stdout=True,
-    )
-    progress_ctr = 0
-    for d, i in meshdata.items():
-        r1 = float(d[0])
-        r2 = float(d[1])
-        length = float(d[2])
-
-        # actual plotting bits
-        if plot_type == "constant":
-            r1 = min_width
-            r2 = min_width
-
-        if r1 < min_width:
-            r1 = min_width
-        if r2 < min_width:
-            r2 = min_width
-
-        seg_mesh = None
-        # 1: for points, we set the prox/dist to None since they only have
-        # positions.
-        # 2: single compartment cells with r1, r2, and length 0
-        # Note: we can't check if r1 == r2 == length because there
-        # may be cylinders with such a set of parameters
-
-        if r1 == r2 and ((i[0][0] is None and i[0][1] is None) or (length == 0.0)):
-            seg_mesh = create_sphere(9, 9, radius=r1)
-            logger.debug(f"Created spherical mesh template with radius {r1}")
-        else:
-            rows = 2 + int(length / 2)
-            seg_mesh = create_cylindrical_mesh(
-                rows=rows, cols=9, radius=[r1, r2], length=length, closed=True
-            )
-            logger.debug(
-                f"Created cylinderical mesh template with radii {r1}, {r2}, {length}"
-            )
-
-        instance_positions = []
-        instance_transforms = []
-        instance_colors = []
-
-        # if in a notebook, only update once per mesh, but not per mesh
-        # instance
-        if pynml_in_jupyter:
-            pbar.update(progress_ctr)
-
-        for num, im in enumerate(i):
-            # if not in a notebook, update for each mesh instance
-            if not pynml_in_jupyter:
-                pbar.update(progress_ctr)
-
-            progress_ctr += 1
-            prox = im[0]
-            dist = im[1]
-            color = im[2]
-            offset = im[3]
-
-            # points, spherical meshes
-            if prox is not None and dist is not None:
-                orig_vec = [0, 0, length]
-                dir_vector = [dist.x - prox.x, dist.y - prox.y, dist.z - prox.z]
-                k = numpy.cross(orig_vec, dir_vector)
-                mag_k = numpy.linalg.norm(k)
-
-                if mag_k != 0.0:
-                    k = k / mag_k
-                    theta = math.acos(
-                        numpy.dot(orig_vec, dir_vector)
-                        / (numpy.linalg.norm(orig_vec) * numpy.linalg.norm(dir_vector))
-                    )
-                    logger.debug(f"k is {k}, theta is {theta}")
-                    rot_matrix = rotate(math.degrees(theta), k).T
-                    rot_obj = Rotation.from_matrix(rot_matrix[:3, :3])
-                else:
-                    logger.debug("k is [0..], using zeros for rotation matrix")
-                    rot_matrix = numpy.zeros((3, 3))
-                    rot_obj = Rotation.from_matrix(rot_matrix)
-
-                instance_positions.append(
-                    [offset[0] + prox.x, offset[1] + prox.y, offset[2] + prox.z]
-                )
-            else:
-                instance_positions.append(offset)
-                rot_matrix = numpy.zeros((3, 3))
-                rot_obj = Rotation.from_matrix(rot_matrix)
-
-            instance_transforms.append(rot_obj.as_matrix())
-            instance_colors.append(color)
-
-        assert len(instance_positions) == len(instance_transforms)
-        logger.debug(
-            f"Instanced: positions: {instance_positions}, transforms: {instance_transforms}"
-        )
-
-        mesh = InstancedMesh(
-            meshdata=seg_mesh,
-            instance_positions=instance_positions,
-            instance_transforms=instance_transforms,
-            instance_colors=instance_colors,
-            parent=current_view.scene,
-        )
-        # TODO: add a shading filter for light?
-        assert mesh is not None
-    pbar.finish()
-
-
 def plot_3D_schematic(
     cell: Cell,
     segment_groups: typing.Optional[typing.List[SegmentGroup]],