From a4a8a86ed3d134367d7fe8be1b9feb4da5f531fe Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Mon, 29 Feb 2016 01:44:56 +0100
Subject: [PATCH 01/11] Replace lists by numpy array in projection

---
 lib/mpl_toolkits/mplot3d/art3d.py | 63 +++++++++++--------------------
 1 file changed, 21 insertions(+), 42 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index b8a4619959ef..fe82e418b55a 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -224,16 +224,10 @@ def do_3d_projection(self, renderer):
         '''
         Project the points according to renderer matrix.
         '''
-        xyslist = [
-            proj3d.proj_trans_points(points, renderer.M) for points in
-            self._segments3d]
-        segments_2d = [list(zip(xs, ys)) for (xs, ys, zs) in xyslist]
+        xys = proj3d.proj_trans_points(self._segments3d, renderer.M)
+        segments_2d = xys[0:1, :]
         LineCollection.set_segments(self, segments_2d)
-
-        # FIXME
-        minz = 1e9
-        for (xs, ys, zs) in xyslist:
-            minz = min(minz, min(zs))
+        minz = np.min(xys[2, :])
         return minz
 
     def draw(self, renderer, project=False):
@@ -551,30 +545,15 @@ def set_zsort(self, zsort):
 
     def get_vector(self, segments3d):
         """Optimize points for projection"""
-        si = 0
-        ei = 0
-        segis = []
-        points = []
-        for p in segments3d:
-            points.extend(p)
-            ei = si+len(p)
-            segis.append((si, ei))
-            si = ei
-
-        if len(segments3d) > 0 :
-            xs, ys, zs = list(zip(*points))
-        else :
-            # We need this so that we can skip the bad unpacking from zip()
-            xs, ys, zs = [], [], []
-
-        ones = np.ones(len(xs))
-        self._vec = np.array([xs, ys, zs, ones])
-        self._segis = segis
+        xys = segments3d.reshape((-1, 3)).T
+        ones = np.ones(xys.shape[1])
+        self._vec = np.vstack([xys, ones])
 
     def set_verts(self, verts, closed=True):
         '''Set 3D vertices.'''
         self.get_vector(verts)
         # 2D verts will be updated at draw time
+        # XXX Is this line useful?
         PolyCollection.set_verts(self, [], closed)
 
     def set_verts_and_codes(self, verts, codes):
@@ -601,6 +580,9 @@ def set_sort_zpos(self,val):
         self._sort_zpos = val
         self.stale = True
 
+    from profilehooks import profile
+
+    #@profile
     def do_3d_projection(self, renderer):
         '''
         Perform the 3D projection for this object.
@@ -610,9 +592,9 @@ def do_3d_projection(self, renderer):
             self.update_scalarmappable()
             self._facecolors3d = self._facecolors
 
-        txs, tys, tzs = proj3d.proj_transform_vec(self._vec, renderer.M)
-        xyzlist = [(txs[si:ei], tys[si:ei], tzs[si:ei])
-                   for si, ei in self._segis]
+        # XXX proj_transform_vec can work with arrays only
+        xys = np.array(proj3d.proj_transform_vec(self._vec, renderer.M))
+        xyzlist = np.transpose(xys.T.reshape((-1, 3, 3)), axes=[0, 2, 1])
 
         # This extra fuss is to re-order face / edge colors
         cface = self._facecolors3d
@@ -626,24 +608,21 @@ def do_3d_projection(self, renderer):
 
         # if required sort by depth (furthest drawn first)
         if self._zsort:
-            indices = range(len(xyzlist))
-            z_segments_2d = [(self._zsortfunc(zs), list(zip(xs, ys)), fc, ec,
-                              idx) for (xs, ys, zs), fc, ec, idx in
-                             zip(xyzlist, cface, cedge, indices)]
-            z_segments_2d.sort(key=lambda x: x[0], reverse=True)
+            z_argsort = np.argsort(
+                self._zsortfunc(xyzlist[:, 2, :], axis=1))[::-1]
         else:
             raise ValueError("whoops")
 
-        segments_2d = [s for z, s, fc, ec, idx in z_segments_2d]
+        segments_2d = np.transpose(xyzlist[z_argsort, 0:2, :], axes=[0, 2, 1])
         if self._codes3d is not None:
-            codes = [self._codes3d[idx] for z, s, fc, ec, idx in z_segments_2d]
+            codes = self._codes3d[z_argsort]
             PolyCollection.set_verts_and_codes(self, segments_2d, codes)
         else:
             PolyCollection.set_verts(self, segments_2d)
 
-        self._facecolors2d = [fc for z, s, fc, ec, idx in z_segments_2d]
+        self._facecolors2d = cface[z_argsort]
         if len(self._edgecolors3d) == len(cface):
-            self._edgecolors2d = [ec for z, s, fc, ec, idx in z_segments_2d]
+            self._edgecolors2d = cedge[z_argsort]
         else:
             self._edgecolors2d = self._edgecolors3d
 
@@ -652,11 +631,11 @@ def do_3d_projection(self, renderer):
             zvec = np.array([[0], [0], [self._sort_zpos], [1]])
             ztrans = proj3d.proj_transform_vec(zvec, renderer.M)
             return ztrans[2][0]
-        elif tzs.size > 0 :
+        elif xys[2].size > 0 :
             # FIXME: Some results still don't look quite right.
             #        In particular, examine contourf3d_demo2.py
             #        with az = -54 and elev = -45.
-            return np.min(tzs)
+            return np.min(xys[2])
         else :
             return np.nan
 

From 3d295afbf760f61e443b91001460fa5d61a7c5ef Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Mon, 29 Feb 2016 01:55:47 +0100
Subject: [PATCH 02/11] Remove profiling code

---
 lib/mpl_toolkits/mplot3d/art3d.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index fe82e418b55a..67c7e8647a8c 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -580,9 +580,6 @@ def set_sort_zpos(self,val):
         self._sort_zpos = val
         self.stale = True
 
-    from profilehooks import profile
-
-    #@profile
     def do_3d_projection(self, renderer):
         '''
         Perform the 3D projection for this object.

From 5239e1ae407f59b575fe10dcf61eea968ad00134 Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Mon, 29 Feb 2016 10:52:51 +0100
Subject: [PATCH 03/11] Vectorize output of proj_transform_vec

---
 lib/mpl_toolkits/mplot3d/art3d.py  | 48 ++++++++++++++++--------------
 lib/mpl_toolkits/mplot3d/proj3d.py | 20 +++++++------
 2 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index 67c7e8647a8c..b8cd2061b694 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -127,8 +127,8 @@ def set_3d_properties(self, zs=0, zdir='z'):
 
     def draw(self, renderer):
         xs3d, ys3d, zs3d = self._verts3d
-        xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
-        self.set_data(xs, ys)
+        xyz = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
+        self.set_data(xyz[0], xyz[1])
         lines.Line2D.draw(self, renderer)
         self.stale = False
 
@@ -271,11 +271,11 @@ def get_facecolor(self):
     def do_3d_projection(self, renderer):
         s = self._segment3d
         xs, ys, zs = list(zip(*s))
-        vxs, vys,vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
-        self._path2d = mpath.Path(list(zip(vxs, vys)))
+        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        self._path2d = mpath.Path(vxyzis[0:2].T)
         # FIXME: coloring
         self._facecolor2d = self._facecolor3d
-        return min(vzs)
+        return min(vxyzis[2])
 
     def draw(self, renderer):
         Patch.draw(self, renderer)
@@ -299,11 +299,11 @@ def set_3d_properties(self, path, zs=0, zdir='z'):
     def do_3d_projection(self, renderer):
         s = self._segment3d
         xs, ys, zs = list(zip(*s))
-        vxs, vys,vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
-        self._path2d = mpath.Path(list(zip(vxs, vys)), self._code3d)
+        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
         # FIXME: coloring
         self._facecolor2d = self._facecolor3d
-        return min(vzs)
+        return min(vxyzis[2])
 
 def get_patch_verts(patch):
     """Return a list of vertices for the path of a patch."""
@@ -379,21 +379,21 @@ def set_3d_properties(self, zs, zdir):
 
     def do_3d_projection(self, renderer):
         xs, ys, zs = self._offsets3d
-        vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
 
-        fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
+        fcs = (zalpha(self._facecolor3d, vxyzis[2]) if self._depthshade else
                self._facecolor3d)
         fcs = mcolors.to_rgba_array(fcs, self._alpha)
         self.set_facecolors(fcs)
 
-        ecs = (zalpha(self._edgecolor3d, vzs) if self._depthshade else
+        ecs = (zalpha(self._edgecolor3d, vxyzis[2]) if self._depthshade else
                self._edgecolor3d)
         ecs = mcolors.to_rgba_array(ecs, self._alpha)
         self.set_edgecolors(ecs)
-        PatchCollection.set_offsets(self, list(zip(vxs, vys)))
+        PatchCollection.set_offsets(self, vxyzis[0:2].T)
 
-        if vzs.size > 0:
-            return min(vzs)
+        if len(vxyzis) > 0:
+            return min(vxyzis[2])
         else:
             return np.nan
 
@@ -447,22 +447,22 @@ def set_3d_properties(self, zs, zdir):
 
     def do_3d_projection(self, renderer):
         xs, ys, zs = self._offsets3d
-        vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
 
-        fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
+        fcs = (zalpha(self._facecolor3d, vxyzis[2]) if self._depthshade else
                self._facecolor3d)
         fcs = mcolors.to_rgba_array(fcs, self._alpha)
         self.set_facecolors(fcs)
 
-        ecs = (zalpha(self._edgecolor3d, vzs) if self._depthshade else
+        ecs = (zalpha(self._edgecolor3d, vxyzis[2]) if self._depthshade else
                self._edgecolor3d)
         ecs = mcolors.to_rgba_array(ecs, self._alpha)
         self.set_edgecolors(ecs)
-        PathCollection.set_offsets(self, list(zip(vxs, vys)))
+        PathCollection.set_offsets(self, vxyzis[0:2].T)
 
-        if vzs.size > 0 :
-            return min(vzs)
-        else :
+        if len(vxyzis) > 0:
+            return min(vxyzis[2])
+        else:
             return np.nan
 
 
@@ -545,7 +545,10 @@ def set_zsort(self, zsort):
 
     def get_vector(self, segments3d):
         """Optimize points for projection"""
+        # Segments 3d are given in shape (n_segments, 3, 3)
+        # Flatten them
         xys = segments3d.reshape((-1, 3)).T
+        # Add a fourth dimension with only ones
         ones = np.ones(xys.shape[1])
         self._vec = np.vstack([xys, ones])
 
@@ -589,8 +592,7 @@ def do_3d_projection(self, renderer):
             self.update_scalarmappable()
             self._facecolors3d = self._facecolors
 
-        # XXX proj_transform_vec can work with arrays only
-        xys = np.array(proj3d.proj_transform_vec(self._vec, renderer.M))
+        xys = proj3d.proj_transform_vec(self._vec, renderer.M)
         xyzlist = np.transpose(xys.T.reshape((-1, 3, 3)), axes=[0, 2, 1])
 
         # This extra fuss is to re-order face / edge colors
diff --git a/lib/mpl_toolkits/mplot3d/proj3d.py b/lib/mpl_toolkits/mplot3d/proj3d.py
index 404d21e79bb0..7ab465f6a9b4 100755
--- a/lib/mpl_toolkits/mplot3d/proj3d.py
+++ b/lib/mpl_toolkits/mplot3d/proj3d.py
@@ -156,20 +156,22 @@ def persp_transformation(zfront, zback):
 
 def proj_transform_vec(vec, M):
     vecw = np.dot(M, vec)
-    w = vecw[3]
-    # clip here..
-    txs, tys, tzs = vecw[0]/w, vecw[1]/w, vecw[2]/w
-    return txs, tys, tzs
+    vecw /= vecw[3]
+    return vecw[0:3]
 
 def proj_transform_vec_clip(vec, M):
     vecw = np.dot(M, vec)
-    w = vecw[3]
+    # Determine clipping before rescaling
+    tis = np.logical_and(vecw[0] >= 0, vecw[0] <= 1,
+                         vecw[1] >= 0, vecw[1] <= 1)
     # clip here..
-    txs, tys, tzs = vecw[0]/w, vecw[1]/w, vecw[2]/w
-    tis = (vecw[0] >= 0) * (vecw[0] <= 1) * (vecw[1] >= 0) * (vecw[1] <= 1)
+    # Can anybody comment on this piece of code? I don't understand it...
     if np.sometrue(tis):
-        tis =  vecw[1] < 1
-    return txs, tys, tzs, tis
+        tis = vecw[1] < 1
+    vecw /= vecw[3]
+    # Integrating tis in the numpy array for optimization purposes
+    vecw[3, :] = tis
+    return vecw
 
 def inv_transform(xs, ys, zs, M):
     iM = linalg.inv(M)

From 7285fed2c454ebec019d38b08b2edf38f29c4ebf Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Mon, 29 Feb 2016 11:38:50 +0100
Subject: [PATCH 04/11] Reach vectorized projection functions directly

---
 lib/mpl_toolkits/mplot3d/art3d.py  | 148 ++++++++++++++---------------
 lib/mpl_toolkits/mplot3d/axes3d.py |  10 +-
 lib/mpl_toolkits/mplot3d/proj3d.py |   3 +
 3 files changed, 77 insertions(+), 84 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index b8cd2061b694..b32b2f39268c 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -115,14 +115,10 @@ def set_3d_properties(self, zs=0, zdir='z'):
         xs = self.get_xdata()
         ys = self.get_ydata()
 
-        try:
-            # If *zs* is a list or array, then this will fail and
-            # just proceed to juggle_axes().
-            zs = float(zs)
-            zs = [zs for x in xs]
-        except TypeError:
-            pass
-        self._verts3d = juggle_axes(xs, ys, zs, zdir)
+        if not iterable(zs):
+            zs = np.ones(len(xs)) * zs
+        xyz = np.asarray([xs, ys, zs])
+        self._verts3d = juggle_axes(xyz, zdir)
         self.stale = True
 
     def draw(self, renderer):
@@ -143,15 +139,17 @@ def line_2d_to_3d(line, zs=0, zdir='z'):
 def path_to_3d_segment(path, zs=0, zdir='z'):
     '''Convert a path to a 3D segment.'''
 
-    if not iterable(zs):
-        zs = np.ones(len(path)) * zs
+    # Pre allocate memory
+    seg3d = np.ones((3, len(path)))
 
-    seg = []
+    # Works either if zs is array or scalar
+    seg3d[2] *= zs
+       
     pathsegs = path.iter_segments(simplify=False, curves=False)
-    for (((x, y), code), z) in zip(pathsegs, zs):
-        seg.append((x, y, z))
-    seg3d = [juggle_axes(x, y, z, zdir) for (x, y, z) in seg]
-    return seg3d
+    for i, ((x, y), code) in enumerate(pathsegs):
+        seg3d[0:2, i] = x, y
+    seg3d = juggle_axes(seg3d, zdir)
+    return seg3d.T
 
 def paths_to_3d_segments(paths, zs=0, zdir='z'):
     '''
@@ -164,22 +162,24 @@ def paths_to_3d_segments(paths, zs=0, zdir='z'):
     segments = []
     for path, pathz in zip(paths, zs):
         segments.append(path_to_3d_segment(path, pathz, zdir))
-    return segments
+    return np.asarray(segments)
 
 def path_to_3d_segment_with_codes(path, zs=0, zdir='z'):
     '''Convert a path to a 3D segment with path codes.'''
+    # Pre allocate memory
+    # XXX should we consider a 4d array?
+    seg3d = np.ones((3, len(path)))
 
-    if not iterable(zs):
-        zs = np.ones(len(path)) * zs
+    # Works either if zs is array or scalar
+    seg3d[2] *= zs
 
-    seg = []
-    codes = []
     pathsegs = path.iter_segments(simplify=False, curves=False)
-    for (((x, y), code), z) in zip(pathsegs, zs):
-        seg.append((x, y, z))
-        codes.append(code)
-    seg3d = [juggle_axes(x, y, z, zdir) for (x, y, z) in seg]
-    return seg3d, codes
+    codes = np.empty(len(path))
+    for i, ((x, y), code) in enumerate(pathsegs):
+        seg3d[0:2, i] = x, y
+        codes[i] = code
+    seg3d = juggle_axes(seg3d, zdir)
+    return seg3d.T, codes
 
 def paths_to_3d_segments_with_codes(paths, zs=0, zdir='z'):
     '''
@@ -195,7 +195,7 @@ def paths_to_3d_segments_with_codes(paths, zs=0, zdir='z'):
         segs, codes = path_to_3d_segment_with_codes(path, pathz, zdir)
         segments.append(segs)
         codes_list.append(codes)
-    return segments, codes_list
+    return np.asarray(segments), np.asarray(codes_list)
 
 class Line3DCollection(LineCollection):
     '''
@@ -224,10 +224,16 @@ def do_3d_projection(self, renderer):
         '''
         Project the points according to renderer matrix.
         '''
-        xys = proj3d.proj_trans_points(self._segments3d, renderer.M)
-        segments_2d = xys[0:1, :]
+        shape = self._segments3d.shape
+        segments3d = np.transpose(self._segments3d, axes=[2, 0, 1])
+        segments3d = np.lib.pad(
+            segments3d, ((0, 1), (0, 0), (0, 0)),
+            'constant', constant_values=1)
+        xys = proj3d.proj_transform_vec(segments3d.reshape(4, -1), renderer.M)
+        xys = np.reshape(xys.T, shape)
+        segments_2d = xys[:, :, 0:2]
         LineCollection.set_segments(self, segments_2d)
-        minz = np.min(xys[2, :])
+        minz = np.min(xys[:, :, 2])
         return minz
 
     def draw(self, renderer, project=False):
@@ -255,11 +261,8 @@ def __init__(self, *args, **kwargs):
         self.set_3d_properties(zs, zdir)
 
     def set_3d_properties(self, verts, zs=0, zdir='z'):
-        if not iterable(zs):
-            zs = np.ones(len(verts)) * zs
-
-        self._segment3d = [juggle_axes(x, y, z, zdir) \
-                for ((x, y), z) in zip(verts, zs)]
+        verts = np.vstack(verts, np.ones(len(verts)) * zs)
+        self._segment3d = juggle_axes(verts, zdir)
         self._facecolor3d = Patch.get_facecolor(self)
 
     def get_path(self):
@@ -269,9 +272,9 @@ def get_facecolor(self):
         return self._facecolor2d
 
     def do_3d_projection(self, renderer):
-        s = self._segment3d
-        xs, ys, zs = list(zip(*s))
-        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        # pad ones
+        s = np.vstack(self._segment3d, np.ones(self._segment3d.shape[1]))
+        vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T)
         # FIXME: coloring
         self._facecolor2d = self._facecolor3d
@@ -297,9 +300,9 @@ def set_3d_properties(self, path, zs=0, zdir='z'):
         self._code3d = path.codes
 
     def do_3d_projection(self, renderer):
-        s = self._segment3d
-        xs, ys, zs = list(zip(*s))
-        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        # pad ones
+        s = np.vstack(self._segmenta3d, np.ones(self._segment3d.shape[1]))
+        vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
         # FIXME: coloring
         self._facecolor2d = self._facecolor3d
@@ -366,20 +369,16 @@ def set_3d_properties(self, zs, zdir):
         # Force the collection to initialize the face and edgecolors
         # just in case it is a scalarmappable with a colormap.
         self.update_scalarmappable()
-        offsets = self.get_offsets()
-        if len(offsets) > 0:
-            xs, ys = list(zip(*offsets))
-        else:
-            xs = []
-            ys = []
-        self._offsets3d = juggle_axes(xs, ys, np.atleast_1d(zs), zdir)
+        offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
+        self._offsets3d = juggle_axes(offsets, zdir)
         self._facecolor3d = self.get_facecolor()
         self._edgecolor3d = self.get_edgecolor()
         self.stale = True
 
     def do_3d_projection(self, renderer):
-        xs, ys, zs = self._offsets3d
-        vxyzis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
+        # pad ones
+        s = np.vstack(self._offsets3d, np.ones(self._offsets3d.shape[1]))
+        vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
 
         fcs = (zalpha(self._facecolor3d, vxyzis[2]) if self._depthshade else
                self._facecolor3d)
@@ -434,13 +433,8 @@ def set_3d_properties(self, zs, zdir):
         # Force the collection to initialize the face and edgecolors
         # just in case it is a scalarmappable with a colormap.
         self.update_scalarmappable()
-        offsets = self.get_offsets()
-        if len(offsets) > 0:
-            xs, ys = list(zip(*offsets))
-        else:
-            xs = []
-            ys = []
-        self._offsets3d = juggle_axes(xs, ys, np.atleast_1d(zs), zdir)
+        offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
+        self._offsets3d = juggle_axes(offsets, zdir)
         self._facecolor3d = self.get_facecolor()
         self._edgecolor3d = self.get_edgecolor()
         self.stale = True
@@ -545,12 +539,13 @@ def set_zsort(self, zsort):
 
     def get_vector(self, segments3d):
         """Optimize points for projection"""
-        # Segments 3d are given in shape (n_segments, 3, 3)
-        # Flatten them
-        xys = segments3d.reshape((-1, 3)).T
+        # Segments 3d are given in shape (n_segments, segsize, 3)
+        self._segsize = segments3d.shape[1]
+        # Flatten
+        xyz = segments3d.T.reshape((3, -1))
         # Add a fourth dimension with only ones
-        ones = np.ones(xys.shape[1])
-        self._vec = np.vstack([xys, ones])
+        ones = np.ones(xyz.shape[1])
+        self._vec = np.vstack([xyz, ones])
 
     def set_verts(self, verts, closed=True):
         '''Set 3D vertices.'''
@@ -593,8 +588,9 @@ def do_3d_projection(self, renderer):
             self._facecolors3d = self._facecolors
 
         xys = proj3d.proj_transform_vec(self._vec, renderer.M)
-        xyzlist = np.transpose(xys.T.reshape((-1, 3, 3)), axes=[0, 2, 1])
-
+        xys = np.reshape(xys, (3, self._segsize, -1))
+        xyzlist = xys.T
+        
         # This extra fuss is to re-order face / edge colors
         cface = self._facecolors3d
         cedge = self._edgecolors3d
@@ -608,11 +604,11 @@ def do_3d_projection(self, renderer):
         # if required sort by depth (furthest drawn first)
         if self._zsort:
             z_argsort = np.argsort(
-                self._zsortfunc(xyzlist[:, 2, :], axis=1))[::-1]
+                self._zsortfunc(xyzlist[:, :, 2], axis=1))[::-1]
         else:
             raise ValueError("whoops")
 
-        segments_2d = np.transpose(xyzlist[z_argsort, 0:2, :], axes=[0, 2, 1])
+        segments_2d = xyzlist[z_argsort, :, 0:2]
         if self._codes3d is not None:
             codes = self._codes3d[z_argsort]
             PolyCollection.set_verts_and_codes(self, segments_2d, codes)
@@ -693,39 +689,39 @@ def poly_collection_2d_to_3d(col, zs=0, zdir='z'):
     col.set_verts_and_codes(segments_3d, codes)
     col.set_3d_properties()
 
-def juggle_axes(xs, ys, zs, zdir):
+def juggle_axes(xyz, zdir):
     """
     Reorder coordinates so that 2D xs, ys can be plotted in the plane
     orthogonal to zdir. zdir is normally x, y or z. However, if zdir
     starts with a '-' it is interpreted as a compensation for rotate_axes.
     """
     if zdir == 'x':
-        return zs, xs, ys
+        return xyz[[2, 0, 1]]
     elif zdir == 'y':
-        return xs, zs, ys
+        return xyz[[0, 2, 1]]
     elif zdir[0] == '-':
-        return rotate_axes(xs, ys, zs, zdir)
+        return rotate_axes(xyz, zdir)
     else:
-        return xs, ys, zs
+        return xyz
 
-def rotate_axes(xs, ys, zs, zdir):
+def rotate_axes(xyz, zdir):
     """
     Reorder coordinates so that the axes are rotated with zdir along
     the original z axis. Prepending the axis with a '-' does the
     inverse transform, so zdir can be x, -x, y, -y, z or -z
     """
     if zdir == 'x':
-        return ys, zs, xs
+        return xyz[[1, 2, 0]]
     elif zdir == '-x':
-        return zs, xs, ys
+        return xyz[[2, 0, 1]]
 
     elif zdir == 'y':
-        return zs, xs, ys
+        return xyz[[2, 0, 1]]
     elif zdir == '-y':
-        return ys, zs, xs
+        return xyz[[1, 2, 0]]
 
     else:
-        return xs, ys, zs
+        return xyz
 
 def iscolor(c):
     try:
diff --git a/lib/mpl_toolkits/mplot3d/axes3d.py b/lib/mpl_toolkits/mplot3d/axes3d.py
index b4c422803626..d6581e25fe1e 100755
--- a/lib/mpl_toolkits/mplot3d/axes3d.py
+++ b/lib/mpl_toolkits/mplot3d/axes3d.py
@@ -2340,15 +2340,9 @@ def bar(self, left, height, zs=0, zdir='z', *args, **kwargs):
             if 'alpha' in kwargs:
                 p.set_alpha(kwargs['alpha'])
 
-        if len(verts) > 0 :
-            # the following has to be skipped if verts is empty
-            # NOTE: Bugs could still occur if len(verts) > 0,
-            #       but the "2nd dimension" is empty.
-            xs, ys = list(zip(*verts))
-        else :
-            xs, ys = [], []
+        verts = np.vstack(verts, verts_zs)
 
-        xs, ys, verts_zs = art3d.juggle_axes(xs, ys, verts_zs, zdir)
+        xs, ys, verts_zs = art3d.juggle_axes(verts, zdir)
         self.auto_scale_xyz(xs, ys, verts_zs, had_data)
 
         return patches
diff --git a/lib/mpl_toolkits/mplot3d/proj3d.py b/lib/mpl_toolkits/mplot3d/proj3d.py
index 7ab465f6a9b4..eb9b8c6e0dba 100755
--- a/lib/mpl_toolkits/mplot3d/proj3d.py
+++ b/lib/mpl_toolkits/mplot3d/proj3d.py
@@ -214,6 +214,9 @@ def proj_points(points, M):
     return list(zip(*proj_trans_points(points, M)))
 
 def proj_trans_points(points, M):
+    """
+    Apply transformation matrix M on a set of points
+    """
     xs, ys, zs = list(zip(*points))
     return proj_transform(xs, ys, zs, M)
 

From 328c2f4435fec294ef04c18ae1f0f169e6332c2e Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Wed, 2 Mar 2016 11:35:59 +0100
Subject: [PATCH 05/11] Address comments

---
 lib/mpl_toolkits/mplot3d/art3d.py  | 67 +++++++++++++++++++++++-------
 lib/mpl_toolkits/mplot3d/axes3d.py |  2 +-
 2 files changed, 52 insertions(+), 17 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index b32b2f39268c..c8e29bd2985f 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -118,7 +118,7 @@ def set_3d_properties(self, zs=0, zdir='z'):
         if not iterable(zs):
             zs = np.ones(len(xs)) * zs
         xyz = np.asarray([xs, ys, zs])
-        self._verts3d = juggle_axes(xyz, zdir)
+        self._verts3d = juggle_axes_vec(xyz, zdir)
         self.stale = True
 
     def draw(self, renderer):
@@ -148,7 +148,7 @@ def path_to_3d_segment(path, zs=0, zdir='z'):
     pathsegs = path.iter_segments(simplify=False, curves=False)
     for i, ((x, y), code) in enumerate(pathsegs):
         seg3d[0:2, i] = x, y
-    seg3d = juggle_axes(seg3d, zdir)
+    seg3d = juggle_axes_vec(seg3d, zdir)
     return seg3d.T
 
 def paths_to_3d_segments(paths, zs=0, zdir='z'):
@@ -178,7 +178,7 @@ def path_to_3d_segment_with_codes(path, zs=0, zdir='z'):
     for i, ((x, y), code) in enumerate(pathsegs):
         seg3d[0:2, i] = x, y
         codes[i] = code
-    seg3d = juggle_axes(seg3d, zdir)
+    seg3d = juggle_axes_vec(seg3d, zdir)
     return seg3d.T, codes
 
 def paths_to_3d_segments_with_codes(paths, zs=0, zdir='z'):
@@ -226,10 +226,10 @@ def do_3d_projection(self, renderer):
         '''
         shape = self._segments3d.shape
         segments3d = np.transpose(self._segments3d, axes=[2, 0, 1])
-        segments3d = np.lib.pad(
-            segments3d, ((0, 1), (0, 0), (0, 0)),
-            'constant', constant_values=1)
-        xys = proj3d.proj_transform_vec(segments3d.reshape(4, -1), renderer.M)
+        segments3d = segments3d.reshape((3, -1))
+        # Pad ones
+        segments3d = np.vstack([segments3d, np.ones((1, segments3d.shape[1]))])
+        xys = proj3d.proj_transform_vec(segments3d, renderer.M)
         xys = np.reshape(xys.T, shape)
         segments_2d = xys[:, :, 0:2]
         LineCollection.set_segments(self, segments_2d)
@@ -261,8 +261,8 @@ def __init__(self, *args, **kwargs):
         self.set_3d_properties(zs, zdir)
 
     def set_3d_properties(self, verts, zs=0, zdir='z'):
-        verts = np.vstack(verts, np.ones(len(verts)) * zs)
-        self._segment3d = juggle_axes(verts, zdir)
+        verts = np.vstack([verts, np.ones(len(verts)) * zs])
+        self._segment3d = juggle_axes_vec(verts, zdir)
         self._facecolor3d = Patch.get_facecolor(self)
 
     def get_path(self):
@@ -273,7 +273,7 @@ def get_facecolor(self):
 
     def do_3d_projection(self, renderer):
         # pad ones
-        s = np.vstack(self._segment3d, np.ones(self._segment3d.shape[1]))
+        s = np.vstack([self._segment3d, np.ones(self._segment3d.shape[1])])
         vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T)
         # FIXME: coloring
@@ -370,7 +370,7 @@ def set_3d_properties(self, zs, zdir):
         # just in case it is a scalarmappable with a colormap.
         self.update_scalarmappable()
         offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
-        self._offsets3d = juggle_axes(offsets, zdir)
+        self._offsets3d = juggle_axes_vec(offsets, zdir)
         self._facecolor3d = self.get_facecolor()
         self._edgecolor3d = self.get_edgecolor()
         self.stale = True
@@ -434,7 +434,7 @@ def set_3d_properties(self, zs, zdir):
         # just in case it is a scalarmappable with a colormap.
         self.update_scalarmappable()
         offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
-        self._offsets3d = juggle_axes(offsets, zdir)
+        self._offsets3d = juggle_axes_vec(offsets, zdir)
         self._facecolor3d = self.get_facecolor()
         self._edgecolor3d = self.get_edgecolor()
         self.stale = True
@@ -539,6 +539,7 @@ def set_zsort(self, zsort):
 
     def get_vector(self, segments3d):
         """Optimize points for projection"""
+        segments3d = np.asarray(segments3d)
         # Segments 3d are given in shape (n_segments, segsize, 3)
         self._segsize = segments3d.shape[1]
         # Flatten
@@ -590,7 +591,7 @@ def do_3d_projection(self, renderer):
         xys = proj3d.proj_transform_vec(self._vec, renderer.M)
         xys = np.reshape(xys, (3, self._segsize, -1))
         xyzlist = xys.T
-        
+
         # This extra fuss is to re-order face / edge colors
         cface = self._facecolors3d
         cedge = self._edgecolors3d
@@ -689,7 +690,22 @@ def poly_collection_2d_to_3d(col, zs=0, zdir='z'):
     col.set_verts_and_codes(segments_3d, codes)
     col.set_3d_properties()
 
-def juggle_axes(xyz, zdir):
+def juggle_axes(xs, ys, zs, zdir):
+    """
+    Reorder coordinates so that 2D xs, ys can be plotted in the plane
+    orthogonal to zdir. zdir is normally x, y or z. However, if zdir
+    starts with a '-' it is interpreted as a compensation for rotate_axes.
+    """
+    if zdir == 'x':
+        return zs, xs, ys
+    elif zdir == 'y':
+        return xs, zs, ys
+    elif zdir[0] == '-':
+        return rotate_axes(xs, ys, zs, zdir)
+    else:
+        return xs, ys, zs
+
+def juggle_axes_vec(xyz, zdir):
     """
     Reorder coordinates so that 2D xs, ys can be plotted in the plane
     orthogonal to zdir. zdir is normally x, y or z. However, if zdir
@@ -700,11 +716,30 @@ def juggle_axes(xyz, zdir):
     elif zdir == 'y':
         return xyz[[0, 2, 1]]
     elif zdir[0] == '-':
-        return rotate_axes(xyz, zdir)
+        return rotate_axes_vec(xyz, zdir)
     else:
         return xyz
 
-def rotate_axes(xyz, zdir):
+def rotate_axes(xs, ys, zs, zdir):
+    """
+    Reorder coordinates so that the axes are rotated with zdir along
+    the original z axis. Prepending the axis with a '-' does the
+    inverse transform, so zdir can be x, -x, y, -y, z or -z
+    """
+    if zdir == 'x':
+        return ys, zs, xs
+    elif zdir == '-x':
+        return zs, xs, ys
+
+    elif zdir == 'y':
+        return zs, xs, ys
+    elif zdir == '-y':
+        return ys, zs, xs
+
+    else:
+        return xs, ys, zs
+
+def rotate_axes_vec(xyz, zdir):
     """
     Reorder coordinates so that the axes are rotated with zdir along
     the original z axis. Prepending the axis with a '-' does the
diff --git a/lib/mpl_toolkits/mplot3d/axes3d.py b/lib/mpl_toolkits/mplot3d/axes3d.py
index d6581e25fe1e..3fedd0e2b335 100755
--- a/lib/mpl_toolkits/mplot3d/axes3d.py
+++ b/lib/mpl_toolkits/mplot3d/axes3d.py
@@ -2342,7 +2342,7 @@ def bar(self, left, height, zs=0, zdir='z', *args, **kwargs):
 
         verts = np.vstack(verts, verts_zs)
 
-        xs, ys, verts_zs = art3d.juggle_axes(verts, zdir)
+        xs, ys, verts_zs = art3d.juggle_axes_vec(verts, zdir)
         self.auto_scale_xyz(xs, ys, verts_zs, had_data)
 
         return patches

From a973da8086e5f1607646087535da49b081669d8b Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Thu, 3 Mar 2016 10:29:06 +0100
Subject: [PATCH 06/11] More fixes

---
 lib/mpl_toolkits/mplot3d/art3d.py  | 2 +-
 lib/mpl_toolkits/mplot3d/axes3d.py | 2 +-
 lib/mpl_toolkits/mplot3d/proj3d.py | 3 +--
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index c8e29bd2985f..244bac393d6b 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -261,7 +261,7 @@ def __init__(self, *args, **kwargs):
         self.set_3d_properties(zs, zdir)
 
     def set_3d_properties(self, verts, zs=0, zdir='z'):
-        verts = np.vstack([verts, np.ones(len(verts)) * zs])
+        verts = np.hstack([verts, np.ones((len(verts), 1)) * zs])
         self._segment3d = juggle_axes_vec(verts, zdir)
         self._facecolor3d = Patch.get_facecolor(self)
 
diff --git a/lib/mpl_toolkits/mplot3d/axes3d.py b/lib/mpl_toolkits/mplot3d/axes3d.py
index 3fedd0e2b335..2410d8d6d7df 100755
--- a/lib/mpl_toolkits/mplot3d/axes3d.py
+++ b/lib/mpl_toolkits/mplot3d/axes3d.py
@@ -2340,7 +2340,7 @@ def bar(self, left, height, zs=0, zdir='z', *args, **kwargs):
             if 'alpha' in kwargs:
                 p.set_alpha(kwargs['alpha'])
 
-        verts = np.vstack(verts, verts_zs)
+        verts = np.hstack([verts, np.asarray(verts_zs)[:, np.newaxis]])
 
         xs, ys, verts_zs = art3d.juggle_axes_vec(verts, zdir)
         self.auto_scale_xyz(xs, ys, verts_zs, had_data)
diff --git a/lib/mpl_toolkits/mplot3d/proj3d.py b/lib/mpl_toolkits/mplot3d/proj3d.py
index eb9b8c6e0dba..a96955c3a96d 100755
--- a/lib/mpl_toolkits/mplot3d/proj3d.py
+++ b/lib/mpl_toolkits/mplot3d/proj3d.py
@@ -162,8 +162,7 @@ def proj_transform_vec(vec, M):
 def proj_transform_vec_clip(vec, M):
     vecw = np.dot(M, vec)
     # Determine clipping before rescaling
-    tis = np.logical_and(vecw[0] >= 0, vecw[0] <= 1,
-                         vecw[1] >= 0, vecw[1] <= 1)
+    tis = (vecw[0] >= 0) * (vecw[0] <= 1) * (vecw[1] >= 0) * (vecw[1] <= 1)
     # clip here..
     # Can anybody comment on this piece of code? I don't understand it...
     if np.sometrue(tis):

From 14853d0a5097633ef1847abdfd4a3f03d1999c50 Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Thu, 3 Mar 2016 10:48:22 +0100
Subject: [PATCH 07/11] Fix rotation of axes

---
 lib/mpl_toolkits/mplot3d/axes3d.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/axes3d.py b/lib/mpl_toolkits/mplot3d/axes3d.py
index 2410d8d6d7df..6571277d7b34 100755
--- a/lib/mpl_toolkits/mplot3d/axes3d.py
+++ b/lib/mpl_toolkits/mplot3d/axes3d.py
@@ -2342,9 +2342,9 @@ def bar(self, left, height, zs=0, zdir='z', *args, **kwargs):
 
         verts = np.hstack([verts, np.asarray(verts_zs)[:, np.newaxis]])
 
-        xs, ys, verts_zs = art3d.juggle_axes_vec(verts, zdir)
+        xs, ys, verts_zs = art3d.juggle_axes_vec(verts.T, zdir)
         self.auto_scale_xyz(xs, ys, verts_zs, had_data)
-
+        
         return patches
 
     def bar3d(self, x, y, z, dx, dy, dz, color=None,

From c4de0478db70fc22110128357421b0182bc2c2fd Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Wed, 8 Jun 2016 14:12:46 +0200
Subject: [PATCH 08/11] Fix some failures

---
 lib/mpl_toolkits/mplot3d/art3d.py  | 4 ++--
 lib/mpl_toolkits/mplot3d/axes3d.py | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index 244bac393d6b..3e1192eb55e6 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -233,7 +233,7 @@ def do_3d_projection(self, renderer):
         xys = np.reshape(xys.T, shape)
         segments_2d = xys[:, :, 0:2]
         LineCollection.set_segments(self, segments_2d)
-        minz = np.min(xys[:, :, 2])
+        minz = np.min(xys[:, :, 2]) if xys.size > 0 else 1e9
         return minz
 
     def draw(self, renderer, project=False):
@@ -262,7 +262,7 @@ def __init__(self, *args, **kwargs):
 
     def set_3d_properties(self, verts, zs=0, zdir='z'):
         verts = np.hstack([verts, np.ones((len(verts), 1)) * zs])
-        self._segment3d = juggle_axes_vec(verts, zdir)
+        self._segment3d = juggle_axes_vec(verts.T, zdir)
         self._facecolor3d = Patch.get_facecolor(self)
 
     def get_path(self):
diff --git a/lib/mpl_toolkits/mplot3d/axes3d.py b/lib/mpl_toolkits/mplot3d/axes3d.py
index 6571277d7b34..cbcb9ace7794 100755
--- a/lib/mpl_toolkits/mplot3d/axes3d.py
+++ b/lib/mpl_toolkits/mplot3d/axes3d.py
@@ -2340,11 +2340,11 @@ def bar(self, left, height, zs=0, zdir='z', *args, **kwargs):
             if 'alpha' in kwargs:
                 p.set_alpha(kwargs['alpha'])
 
-        verts = np.hstack([verts, np.asarray(verts_zs)[:, np.newaxis]])
+        verts = np.vstack([list(zip(*verts)), verts_zs])
 
-        xs, ys, verts_zs = art3d.juggle_axes_vec(verts.T, zdir)
+        xs, ys, verts_zs = art3d.juggle_axes_vec(verts, zdir)
         self.auto_scale_xyz(xs, ys, verts_zs, had_data)
-        
+
         return patches
 
     def bar3d(self, x, y, z, dx, dy, dz, color=None,

From 63159615ca443d2e6be51fb5e9f28eeeeda42438 Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Wed, 8 Jun 2016 22:54:29 +0200
Subject: [PATCH 09/11] Use a contiguous representation in memory and views for
 the segments

---
 lib/mpl_toolkits/mplot3d/art3d.py | 77 ++++++++++++++++++++-----------
 1 file changed, 50 insertions(+), 27 deletions(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index 3e1192eb55e6..f244051519d7 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -217,23 +217,39 @@ def set_segments(self, segments):
         '''
         Set 3D segments
         '''
-        self._segments3d = np.asanyarray(segments)
+        self._seg_sizes = [len(c) for c in segments]
+        self._segments3d = []
+        if len(segments) > 0:
+            # Store the points in a single array for easier projection
+            n_segments = np.sum(self._seg_sizes)
+            # Put all segments in a big array
+            self._segments3d_data = np.vstack(segments)
+            # Add a fourth dimension for quaternions
+            self._segments3d_data = np.hstack([self._segments3d_data,
+                                               np.ones((n_segments, 1))])
+
+            # For coveniency, store a view of the array in the original shape
+            cum_s = 0
+            for s in self._seg_sizes:
+                self._segments3d.append(
+                    self._segments3d_data[cum_s:cum_s + s, :3])
+                cum_s += s
         LineCollection.set_segments(self, [])
 
     def do_3d_projection(self, renderer):
         '''
         Project the points according to renderer matrix.
         '''
-        shape = self._segments3d.shape
-        segments3d = np.transpose(self._segments3d, axes=[2, 0, 1])
-        segments3d = segments3d.reshape((3, -1))
-        # Pad ones
-        segments3d = np.vstack([segments3d, np.ones((1, segments3d.shape[1]))])
-        xys = proj3d.proj_transform_vec(segments3d, renderer.M)
-        xys = np.reshape(xys.T, shape)
-        segments_2d = xys[:, :, 0:2]
+        if len(self._segments3d) == 0:
+            return 1e9
+        xys = proj3d.proj_transform_vec(self._segments3d_data.T, renderer.M).T
+        segments_2d = []
+        cum_s = 0
+        for s in self._seg_sizes:
+            segments_2d.append(xys[cum_s:cum_s + s, :2])
+            cum_s += s
         LineCollection.set_segments(self, segments_2d)
-        minz = np.min(xys[:, :, 2]) if xys.size > 0 else 1e9
+        minz = np.min(xys[:, 2])
         return minz
 
     def draw(self, renderer, project=False):
@@ -301,7 +317,7 @@ def set_3d_properties(self, path, zs=0, zdir='z'):
 
     def do_3d_projection(self, renderer):
         # pad ones
-        s = np.vstack(self._segmenta3d, np.ones(self._segment3d.shape[1]))
+        s = np.vstack(self._segments3d, np.ones(self._segments3d.shape[1]))
         vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
         # FIXME: coloring
@@ -433,8 +449,10 @@ def set_3d_properties(self, zs, zdir):
         # Force the collection to initialize the face and edgecolors
         # just in case it is a scalarmappable with a colormap.
         self.update_scalarmappable()
-        offsets = np.vstack(self.get_offsets(), np.ones(len(verts)) * zs)
-        self._offsets3d = juggle_axes_vec(offsets, zdir)
+        offsets = self.get_offsets()
+        offsets = np.hstack([offsets,
+                             (np.ones(len(offsets)) * zs)[:, np.newaxis]])
+        self._offsets3d = juggle_axes_vec(offsets, zdir).T
         self._facecolor3d = self.get_facecolor()
         self._edgecolor3d = self.get_edgecolor()
         self.stale = True
@@ -539,14 +557,16 @@ def set_zsort(self, zsort):
 
     def get_vector(self, segments3d):
         """Optimize points for projection"""
-        segments3d = np.asarray(segments3d)
-        # Segments 3d are given in shape (n_segments, segsize, 3)
-        self._segsize = segments3d.shape[1]
-        # Flatten
-        xyz = segments3d.T.reshape((3, -1))
-        # Add a fourth dimension with only ones
-        ones = np.ones(xyz.shape[1])
-        self._vec = np.vstack([xyz, ones])
+
+        self._seg_sizes = [len(c) for c in segments3d]
+        self._vec = []
+        if len(segments3d) > 0:
+            # Store the points in a single array for easier projection
+            n_segments = np.sum(self._seg_sizes)
+            # Put all segments in a big array
+            self._vec = np.vstack(segments3d)
+            # Add a fourth dimension for quaternions
+            self._vec = np.hstack([self._vec, np.ones((n_segments, 1))]).T
 
     def set_verts(self, verts, closed=True):
         '''Set 3D vertices.'''
@@ -574,7 +594,7 @@ def set_3d_properties(self):
         self._alpha3d = PolyCollection.get_alpha(self)
         self.stale = True
 
-    def set_sort_zpos(self,val):
+    def set_sort_zpos(self, val):
         '''Set the position to use for z-sorting.'''
         self._sort_zpos = val
         self.stale = True
@@ -588,9 +608,12 @@ def do_3d_projection(self, renderer):
             self.update_scalarmappable()
             self._facecolors3d = self._facecolors
 
-        xys = proj3d.proj_transform_vec(self._vec, renderer.M)
-        xys = np.reshape(xys, (3, self._segsize, -1))
-        xyzlist = xys.T
+        xys = proj3d.proj_transform_vec(self._vec, renderer.M).T
+        xyzlist = []
+        cum_s = 0
+        for s in self._seg_sizes:
+            xyzlist.append(xys[cum_s:cum_s + s, :3])
+            cum_s += s
 
         # This extra fuss is to re-order face / edge colors
         cface = self._facecolors3d
@@ -605,11 +628,11 @@ def do_3d_projection(self, renderer):
         # if required sort by depth (furthest drawn first)
         if self._zsort:
             z_argsort = np.argsort(
-                self._zsortfunc(xyzlist[:, :, 2], axis=1))[::-1]
+                [self._zsortfunc(xyz[:, 2]) for xyz in xyzlist])[::-1]
         else:
             raise ValueError("whoops")
 
-        segments_2d = xyzlist[z_argsort, :, 0:2]
+        segments_2d = [xyzlist[i][:, 0:2] for i in z_argsort]
         if self._codes3d is not None:
             codes = self._codes3d[z_argsort]
             PolyCollection.set_verts_and_codes(self, segments_2d, codes)

From bb948bb619b990003670b1afc22c80045e6a14ac Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Tue, 20 Sep 2016 10:37:46 +0200
Subject: [PATCH 10/11] Fix bug in PathPatch

---
 lib/mpl_toolkits/mplot3d/art3d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index f244051519d7..d4970998d3c1 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -317,7 +317,7 @@ def set_3d_properties(self, path, zs=0, zdir='z'):
 
     def do_3d_projection(self, renderer):
         # pad ones
-        s = np.vstack(self._segments3d, np.ones(self._segments3d.shape[1]))
+        s = np.vstack(self._segment3d, np.ones(self._segment3d.shape[1]))
         vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
         # FIXME: coloring
@@ -349,6 +349,7 @@ def pathpatch_2d_to_3d(pathpatch, z=0, zdir='z'):
     pathpatch.__class__ = PathPatch3D
     pathpatch.set_3d_properties(mpath, z, zdir)
 
+
 class Patch3DCollection(PatchCollection):
     '''
     A collection of 3D patches.

From e6211bd1768dbfe0eebd54ae82a03bc78ef6fae6 Mon Sep 17 00:00:00 2001
From: Alexandre Abraham <abraham.alexandre@gmail.com>
Date: Tue, 20 Sep 2016 16:12:54 +0200
Subject: [PATCH 11/11] Fix vstack bug

---
 lib/mpl_toolkits/mplot3d/art3d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/mpl_toolkits/mplot3d/art3d.py b/lib/mpl_toolkits/mplot3d/art3d.py
index d4970998d3c1..ba395fa46c1a 100755
--- a/lib/mpl_toolkits/mplot3d/art3d.py
+++ b/lib/mpl_toolkits/mplot3d/art3d.py
@@ -317,7 +317,7 @@ def set_3d_properties(self, path, zs=0, zdir='z'):
 
     def do_3d_projection(self, renderer):
         # pad ones
-        s = np.vstack(self._segment3d, np.ones(self._segment3d.shape[1]))
+        s = np.vstack([self._segment3d, np.ones(self._segment3d.shape[1])])
         vxyzis = proj3d.proj_transform_vec_clip(s, renderer.M)
         self._path2d = mpath.Path(vxyzis[0:2].T, self._code3d)
         # FIXME: coloring