Merge pull request #8 from Dawars/python3

Merging the PR onto develop instead of master because some extra work is needed to complete this feature.

Makefile

@@ -52,14 +52,15 @@ $(tmpdirbuild)/package_creation: $(tmpdirbuild)
 	@echo "********"
 	@echo "********"
 	@echo "\033[0m"
-	@virtualenv --system-site-packages $(venv_dir)
+	@virtualenv --system-site-packages $(venv_dir) -p python3
 	@ . $(activate) && pip install --upgrade pip
 	@ . $(activate) && pip install --upgrade virtualenv
 	@ . $(activate) && pip install nose2
 	@ . $(activate) && echo `which pip` && pip -V
 	@ . $(activate) && pip install --upgrade setuptools && echo `which pip` && pip -V
 	@ . $(activate) && pip install --upgrade wheel && echo `which pip` && pip -V
-	@ . $(activate) && pip install numpy scipy pyopengl pillow pyzmq pyyaml && echo `which pip` && pip -V
+	@ . $(activate) && pip install numpy
+	@ . $(activate) && pip install scipy pyopengl pillow pyzmq pyyaml && echo `which pip` && pip -V
 	####### PACKAGE: creating SDIST target
 	@echo "\033[0;33m----- [" ${package_name} "] Creating the source distribution\033[0m"
 	@ . $(activate) && python setup.py sdist

mesh/colors.py

@@ -28,7 +28,7 @@ def main():
                 g = int(reg.group(2)) / 255.
                 b = int(reg.group(3)) / 255.
                 d = reg.group(4)
-                print "'%s': np.array([%.2f, %.2f, %.2f])," % (d, r, g, b)
+                print("'%s': np.array([%.2f, %.2f, %.2f])," % (d, r, g, b))
             line = fp.readline()
 
 

mesh/landmarks.py

@@ -47,7 +47,7 @@ def landm_xyz(self, ordering=None):
 def recompute_landmark_indices(self, landmark_fname=None, safe_mode=True):
     filtered_landmarks = dict(filter(lambda e, : e[1] != [0.0, 0.0, 0.0], self.landm_raw_xyz.items()) if (landmark_fname and safe_mode) else self.landm_raw_xyz.items())
     if len(filtered_landmarks) != len(self.landm_raw_xyz):
-        print "WARNING: %d landmarks in file %s are positioned at (0.0, 0.0, 0.0) and were ignored" % (len(self.landm_raw_xyz) - len(filtered_landmarks), landmark_fname)
+        print("WARNING: %d landmarks in file %s are positioned at (0.0, 0.0, 0.0) and were ignored" % (len(self.landm_raw_xyz) - len(filtered_landmarks), landmark_fname))
 
     self.landm = {}
     self.landm_regressors = {}
@@ -85,7 +85,7 @@ def set_landmarks_from_raw(self, landmarks):
     if np.all(map(lambda x: hasattr(x, "__iter__") and len(x) == 3, landmarks.values())):
         landmarks = dict((i, np.array(l)) for i, l in landmarks.items())
         self.set_landmarks_from_xyz(landmarks)
-    elif np.all(map(lambda x: isinstance(x, (int, long)), landmarks.values())):
+    elif np.all(map(lambda x: isinstance(x, int), landmarks.values())):
         self.landm = landmarks
         self.recompute_landmark_xyz()
     else:

mesh/lines.py

@@ -5,7 +5,7 @@
 # See file LICENSE.txt for full license details.
 
 import numpy as np
-import colors
+from . import colors
 
 
 class Lines(object):

mesh/mesh.py

@@ -13,10 +13,12 @@
 
 
 import os
+from functools import reduce
+
 import numpy as np
 
-import colors
-import search
+from . import colors
+from . import search
 
 try:
     from .serialization import serialization
@@ -153,7 +155,7 @@ def jet(v):
                 result[result < 0.0] = 0.0
                 return row(result)
             color = col(color)
-            color = np.concatenate([jet(color[i]) for i in xrange(color.size)], axis=0)
+            color = np.concatenate([jet(color[i]) for i in range(color.size)], axis=0)
 
         return np.ones_like(arr) * color
 

mesh/meshviewer.py

@@ -90,8 +90,8 @@
 
 # this block is below the previous one to make my linter happy
 if __package__ is None:
-    print "this file cannot be executed as a standalone python module"
-    print "python -m psbody.mesh.%s arguments" % (os.path.splitext(os.path.basename(__file__))[0])
+    print("this file cannot be executed as a standalone python module")
+    print("python -m psbody.mesh.%s arguments" % (os.path.splitext(os.path.basename(__file__))[0]))
     sys.exit(-1)
 
 
@@ -110,10 +110,10 @@ def _test_for_opengl():
         # from OpenGL.GLUT import glutInit
         glutInit()
     except Exception as e:
-        print >> sys.stderr, e
-        print 'failure'
+        print(e, file=sys.stderr)
+        print('failure')
     else:
-        print 'success'
+        print('success')
 
 
 test_for_opengl_cached = None
@@ -129,12 +129,12 @@ def test_for_opengl():
     if test_for_opengl_cached is None:
         p = _run_self(["TEST_FOR_OPENGL"], stderr=subprocess.PIPE)
         p.wait()
-        line = '\n'.join(p.stdout.readlines())
+        line = ''.join(str(p.stdout.readlines()))
         test_for_opengl_cached = 'success' in line
         if not test_for_opengl_cached:
-            print 'OpenGL test failed: '
-            print '\tstdout:', line
-            print '\tstderr:', '\n'.join(p.stderr.readlines())
+            print('OpenGL test failed: ')
+            print('\tstdout:', line)
+            print('\tstderr:', '\n'.join(p.stderr.readlines()))
     return test_for_opengl_cached
 
 
@@ -311,7 +311,7 @@ class MeshViewerLocal(object):
     managed = {}
 
     def __new__(cls, titlebar, uid, shape, keepalive, window_width, window_height):
-        assert(uid is None or isinstance(uid, str) or isinstance(uid, unicode))
+        assert(uid is None or isinstance(uid, str))
 
         if uid == 'stack':
             uid = ''.join(traceback.format_list(traceback.extract_stack()))
@@ -325,7 +325,7 @@ def __new__(cls, titlebar, uid, shape, keepalive, window_width, window_height):
         result.p = _run_self([titlebar, str(shape[0]), str(shape[1]), str(window_width), str(window_height)])
 
         line = result.p.stdout.readline()
-        current_port = re.match('<PORT>(.*?)</PORT>', line)
+        current_port = re.match('<PORT>(.*?)</PORT>', line.decode(sys.stdout.encoding))
         if not current_port:
             raise Exception("MeshViewer remote appears to have failed to launch")
         current_port = int(current_port.group(1))
@@ -870,7 +870,7 @@ def __init__(self,
 
         # Print out our port so that our client can connect to us with it. Flush stdout immediately; otherwise
         # our client could wait forever.
-        print '<PORT>%d</PORT>\n' % (port,)
+        print('<PORT>%d</PORT>\n' % (port,))
         sys.stdout.flush()
 
         self.arcball = ArcBallT(width, height)
@@ -1109,7 +1109,7 @@ def handle_request(self, request):
             mv.autorecenter = obj
             self.need_redraw = True
         elif label == 'titlebar':
-            assert(isinstance(obj, str) or isinstance(obj, unicode))
+            assert(isinstance(obj, str))
             self.titlebar = obj
             glutSetWindowTitle(obj)
         elif label == 'lighting_on':
@@ -1119,7 +1119,7 @@ def handle_request(self, request):
             glClearColor(obj[0], obj[1], obj[2], 1.0)
             self.need_redraw = True
         elif label == 'save_snapshot':  # redraws for itself
-            assert(isinstance(obj, str) or isinstance(obj, unicode))
+            assert(isinstance(obj, str))
             self.snapshot(obj)
         elif label == 'get_keypress':
             self.keypress_port = obj
@@ -1213,7 +1213,7 @@ def init_opengl(self):
                              height=int(sys.argv[5]))
 
     else:
-        print "#" * 10
-        print 'Usage:'
-        print "python -m %s.%s arguments" % (__package__, os.path.splitext(os.path.basename(__file__))[0])
+        print("#" * 10)
+        print('Usage:')
+        print("python -m %s.%s arguments" % (__package__, os.path.splitext(os.path.basename(__file__))[0]))
         sys.exit(-1)

mesh/search.py

@@ -21,17 +21,18 @@
 class AabbTree(object):
     """Encapsulates an AABB (Axis Aligned Bounding Box) Tree"""
     def __init__(self, m):
-        import spatialsearch
+        from . import spatialsearch
+        # this shit return NULL
         self.cpp_handle = spatialsearch.aabbtree_compute(m.v.astype(np.float64).copy(order='C'), m.f.astype(np.uint32).copy(order='C'))
 
     def nearest(self, v_samples, nearest_part=False):
         "nearest_part tells you whether the closest point in triangle abc is in the interior (0), on an edge (ab:1,bc:2,ca:3), or a vertex (a:4,b:5,c:6)"
-        import spatialsearch
+        from . import spatialsearch
         f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
         return (f_idxs, f_part, v) if nearest_part else (f_idxs, v)
 
     def nearest_alongnormal(self, points, normals):
-        import spatialsearch
+        from . import spatialsearch
         distances, f_idxs, v = spatialsearch.aabbtree_nearest_alongnormal(self.cpp_handle,
                                                                           points.astype(np.float64),
                                                                           normals.astype(np.float64))
@@ -57,20 +58,20 @@ def nearest_vertices(self, v_samples):
 class CGALClosestPointTree(object):
     """Encapsulates an AABB (Axis Aligned Bounding Box) Tree """
     def __init__(self, m):
-        import spatialsearch
+        from . import spatialsearch
         self.v = m.v
         n = m.v.shape[0]
         faces = np.vstack([np.array(range(n)), np.array(range(n)) + n, np.array(range(n)) + 2 * n]).T
         eps = 0.000000000001
         self.cpp_handle = spatialsearch.aabbtree_compute(np.vstack([m.v + eps * np.array([1.0, 0.0, 0.0]), m.v + eps * np.array([0.0, 1.0, 0.0]), m.v - eps * np.array([1.0, 1.0, 0.0])]).astype(np.float64).copy(order='C'), faces.astype(np.uint32).copy(order='C'))
 
     def nearest(self, v_samples):
-        import spatialsearch
+        from . import spatialsearch
         f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
         return (f_idxs.flatten(), (np.sum(((self.v[f_idxs.flatten()] - v_samples) ** 2.0), axis=1) ** 0.5).flatten())
 
     def nearest_vertices(self, v_samples):
-        import spatialsearch
+        from . import spatialsearch
         f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
         return self.v[f_idxs.flatten()]
 
@@ -79,11 +80,11 @@ class AabbNormalsTree(object):
     def __init__(self, m):
         # the weight of the normals cosine is proportional to the std of the vertices
         # the best point can be translated up to 2*eps because of the normals
-        import aabb_normals
+        from . import aabb_normals
         eps = 0.1  # np.std(m.v)#0
         self.tree_handle = aabb_normals.aabbtree_n_compute(m.v, m.f.astype(np.uint32).copy(), eps)
 
     def nearest(self, v_samples, n_samples):
-        import aabb_normals
+        from . import aabb_normals
         closest_tri, closest_p = aabb_normals.aabbtree_n_nearest(self.tree_handle, v_samples, n_samples)
         return (closest_tri, closest_p)

mesh/serialization/serialization.py

@@ -14,7 +14,6 @@
 
 from ..errors import SerializationError
 
-
 """
 serialization.py
 
@@ -26,6 +25,7 @@
            'set_landmark_indices_from_ppfile', 'set_landmark_indices_from_lmrkfile',
            'load_from_ply', 'load_from_file']
 
+
 # import os.path
 
 
@@ -74,7 +74,7 @@ def load_from_obj(self, filename):
                     currLandm = line[1]
                 elif line[0] == 'mtllib':
                     self.materials_filepath = os.path.join(os.path.dirname(filename), line[1])
-                    self.materials_file = file(self.materials_filepath, 'r').readlines()
+                    self.materials_file = open(self.materials_filepath, 'r').readlines()
 
     self.v = np.array(v)
     self.f = np.array(f) - 1
@@ -149,7 +149,8 @@ def write_face_to_obj_file(face_index, obj_file):
             if not hasattr(self, 'fn'):
                 self.reset_face_normals()
             normal_indices = self.fn[face_index][::ff] + 1
-            obj_file.write('f %d/%d/%d %d/%d/%d  %d/%d/%d\n' % tuple(np.array([vertex_indices, texture_indices, normal_indices]).T.flatten()))
+            obj_file.write('f %d/%d/%d %d/%d/%d  %d/%d/%d\n' % tuple(
+                np.array([vertex_indices, texture_indices, normal_indices]).T.flatten()))
         elif hasattr(self, 'fn'):
             normal_indices = self.fn[face_index][::ff] + 1
             obj_file.write('f %d//%d %d//%d  %d//%d\n' % tuple(np.array([vertex_indices, normal_indices]).T.flatten()))
@@ -272,7 +273,9 @@ def write_three_json(self, filename, name=""):
     mesh_data["vertices"] = self.v.flatten().tolist()
     mesh_data["normals"] = self.vn.flatten().tolist()
     mesh_data["uvs"] = [np.array([[vt[0], vt[1]] for vt in self.vt]).flatten().tolist()]
-    mesh_data["faces"] = np.array([[42, self.f[i][0], self.f[i][1], self.f[i][2], 0, self.ft[i][0], self.ft[i][1], self.ft[i][2], self.fn[i][0], self.fn[i][1], self.fn[i][2]] for i in range(len(self.f))]).flatten().tolist()
+    mesh_data["faces"] = np.array([[42, self.f[i][0], self.f[i][1], self.f[i][2], 0, self.ft[i][0], self.ft[i][1],
+                                    self.ft[i][2], self.fn[i][0], self.fn[i][1], self.fn[i][2]] for i in
+                                   range(len(self.f))]).flatten().tolist()
 
     json_or_js_file = open(filename, 'w')
     json_or_js_file.write(json.dumps(mesh_data, indent=4))
@@ -422,13 +425,19 @@ def load_from_file(self, filename, use_cpp=True):
 
 
 def load_from_ply(self, filename):
-    import plyutils
+    from os.path import abspath, dirname, join
+
+    test_data_folder = abspath(join(dirname(__file__), '..', 'data', 'unittest'))
+
+    from psbody.mesh.serialization import plyutils
     try:
         res = plyutils.read(filename)
-    except plyutils.error, e:
-        raise SerializationError(e.message)
+    except plyutils.error as e:
+        raise SerializationError(e)
+
     self.v = np.array(res['pts']).T.copy()
     self.f = np.array(res['tri']).T.copy()
+
     if 'color' in res:
         self.set_vertex_colors(np.array(res['color']).T.copy() / 255)
     if 'normals' in res:

mesh/src/aabb_normals.cpp

@@ -35,18 +35,27 @@ static PyMethodDef SpatialsearchMethods[] = {
     {NULL, NULL, 0, NULL}        /* Sentinel */
 };
 
+static struct PyModuleDef moduleDef =
+{
+    PyModuleDef_HEAD_INIT,
+    "aabb_normals", /* name of module */
+    "",          /* module documentation, may be NULL */
+    -1,          /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */
+    SpatialsearchMethods
+};
 
-
-PyMODINIT_FUNC
-initaabb_normals(void)
+PyMODINIT_FUNC PyInit_aabb_normals(void)
 {
-    (void) Py_InitModule("aabb_normals", SpatialsearchMethods);
+    PyObject *module = PyModule_Create(&moduleDef);
+
     import_array();
+
+    return module;
 }
 
-void aabb_tree_destructor(void *ptr)
+void aabb_tree_destructor(PyObject *ptr)
 {
-    TreeAndTri* search = (TreeAndTri*)ptr;
+    TreeAndTri* search = (TreeAndTri*) PyCapsule_GetPointer(ptr, NULL);
     delete search;
 }
 
@@ -90,8 +99,8 @@ aabbtree_normals_compute(PyObject *self, PyObject *args)
     {
       TreeAndTri* search = new TreeAndTri(m_mesh_tri,m_mesh_points,eps,T,P);
 
-      PyObject* result = PyCObject_FromVoidPtr((void*)search, aabb_tree_destructor);
-      return Py_BuildValue("N", result);
+      PyObject* result = PyCapsule_New((void*)search, NULL, aabb_tree_destructor);
+      return result;
     }
     catch (mesh_aabb_tree_error&)
     {
@@ -107,7 +116,7 @@ aabbtree_normals_nearest(PyObject *self, PyObject *args)
     if (!PyArg_ParseTuple(args, "OOO", &py_tree, &py_v, &py_n))
         return NULL;
 
-    TreeAndTri *search = (TreeAndTri *)PyCObject_AsVoidPtr(py_tree);
+    TreeAndTri *search = (TreeAndTri *) PyCapsule_GetPointer(py_tree, NULL);
 
     npy_intp* v_dims = PyArray_DIMS(py_v);
     npy_intp* n_dims = PyArray_DIMS(py_n);
@@ -174,7 +183,7 @@ aabbtree_normals_selfintersects(PyObject *self, PyObject *args)
     if (!PyArg_ParseTuple(args, "O", &py_tree))
         return NULL;
 
-    TreeAndTri *search = (TreeAndTri *)PyCObject_AsVoidPtr(py_tree);
+    TreeAndTri *search = (TreeAndTri *) PyCapsule_GetPointer(py_tree, NULL);
 
     for(Iterator it=search->triangles.begin();it!=search->triangles.end();++it)
         if(search->tree.do_intersect(*it))