feat(morph-plot): fix closed cylinder generation

pyneuroml/plot/PlotMorphologyVispy.py

@@ -1405,6 +1405,64 @@ def create_spherical_mesh(
     )
 
 
+@lru_cache(maxsize=100)
+def compute_faces_of_cylindrical_mesh(rows: int, cols: int, closed: bool):
+    """Compute faces for cylindrical meshes
+
+    Since we tend to use a constant set of rows and cols, this function should
+    be called repeatedly with the same values, and thus benefits from caching.
+
+    :param rows: number of rows in mesh
+    :type rows: int
+    :param cols: number of cols in mesh
+    :type cols: int
+    :param closed: toggle whether mesh is closed or open
+    :type closed: bool
+    :returns: numpy array with faces (triplets of vertex indices)
+
+    """
+    faces = numpy.empty((rows * cols * 2, 3), dtype=numpy.uint32)
+    rowtemplate1 = (
+        (numpy.arange(cols).reshape(cols, 1) + numpy.array([[0, 1, 0]])) % cols
+    ) + numpy.array([[0, 0, cols]])
+    logger.debug(f"Template1 is: {rowtemplate1}")
+
+    rowtemplate2 = (
+        (numpy.arange(cols).reshape(cols, 1) + numpy.array([[0, 1, 1]])) % cols
+    ) + numpy.array([[cols, 0, cols]])
+    # logger.debug(f"Template2 is: {rowtemplate2}")
+
+    for row in range(rows):
+        start = row * cols * 2
+        faces[start : start + cols] = rowtemplate1 + row * cols
+        faces[start + cols : start + (cols * 2)] = rowtemplate2 + row * cols
+
+    num_verts = (rows + 1) * cols
+    # used below:
+    # index of center of first cap = num_verts
+    # index of center of second cap = num_verts + 1
+
+    # add extra faces to cover the caps
+    if closed is True:
+        cap1 = numpy.arange(cols).reshape(cols, 1)
+        cap1 = numpy.concatenate(
+            (numpy.full((cols, 1), num_verts), cap1, numpy.roll(cap1, 1)), axis=1
+        )
+        logger.debug(f"cap1 is {cap1}")
+
+        cap2 = numpy.arange(rows * cols, (rows + 1) * cols).reshape(cols, 1)
+        cap2 = numpy.concatenate(
+            (numpy.full((cols, 1), num_verts + 1), cap2, numpy.roll(cap2, 1)), axis=1
+        )
+        logger.debug(f"cap2 is {cap2}")
+
+        faces = numpy.append(faces, cap1, axis=0)
+        faces = numpy.append(faces, cap2, axis=0)
+
+    logger.debug(f"Faces are: {faces}")
+    return faces
+
+
 @lru_cache(maxsize=10000)
 def create_cylindrical_mesh(
     rows: int,
@@ -1456,43 +1514,7 @@ def create_cylindrical_mesh(
         verts = numpy.append(verts, [[0.0, 0.0, 0.0], [0.0, 0.0, length]], axis=0)
     logger.debug(f"Verts are: {verts}")
 
-    # compute faces
-    faces = numpy.empty((rows * cols * 2, 3), dtype=numpy.uint32)
-    rowtemplate1 = (
-        (numpy.arange(cols).reshape(cols, 1) + numpy.array([[0, 1, 0]])) % cols
-    ) + numpy.array([[0, 0, cols]])
-    logger.debug(f"Template1 is: {rowtemplate1}")
-
-    rowtemplate2 = (
-        (numpy.arange(cols).reshape(cols, 1) + numpy.array([[0, 1, 1]])) % cols
-    ) + numpy.array([[cols, 0, cols]])
-    # logger.debug(f"Template2 is: {rowtemplate2}")
-
-    for row in range(rows):
-        start = row * cols * 2
-        faces[start : start + cols] = rowtemplate1 + row * cols
-        faces[start + cols : start + (cols * 2)] = rowtemplate2 + row * cols
-
-    # add extra faces to cover the caps
-    if closed is True:
-        cap1 = (numpy.arange(cols).reshape(cols, 1) + numpy.array([[0, 0, 1]])) % cols
-        cap1[..., 0] = len(verts) - 2
-        logger.debug(f"cap1 is {cap1}")
-
-        cap2_start = rows * cols
-        cap2 = numpy.arange(cols).reshape(cols, 1)
-        logger.info(f"cap2 is {cap2}")
-        cap2 = cap2 + numpy.array([[cap2_start, cap2_start, cap2_start + 1]])
-        logger.info(f"cap2 is {cap2}")
-        cap2 = cap2 % cap2_start + cap2 * int(cap2 / cap2_start - 1)
-        logger.info(f"cap2 is {cap2}")
-        cap2[..., 0] = len(verts) - 1
-        logger.info(f"cap2 is {cap2}")
-
-        faces = numpy.append(faces, cap1, axis=0)
-        faces = numpy.append(faces, cap2, axis=0)
-
-    logger.debug(f"Faces are: {faces}")
+    faces = compute_faces_of_cylindrical_mesh(rows, cols, closed)
 
     return MeshData(vertices=verts, faces=faces)
 
@@ -1568,7 +1590,7 @@ def create_mesh(meshdata, plot_type, current_view, min_width, save_mesh_to):
             seg_mesh = create_cylindrical_mesh(
                 rows=rows, cols=9, radius=(r1, r2), length=length, closed=True
             )
-            logger.info(
+            logger.debug(
                 f"Created cylinderical mesh template with radii {r1}, {r2}, {length}"
             )