minor fixes for conventions

src/geometry/basic_utils.py

@@ -1,6 +1,9 @@
-from . import GeometryConstants, contract, np, new_contract
+from .constants import GeometryConstants
+from contracts import contract, new_contract
+import numpy as np
 import warnings
 
+
 new_contract('R1', 'array[1]')
 new_contract('R2', 'array[2]')
 new_contract('R3', 'array[3]')

src/geometry/manifolds/__init__.py

@@ -1,5 +1,4 @@
-import numpy as np
-from contracts import contract, check, new_contract
+from contracts import new_contract
 from .. import assert_allclose, logger
 
 from .exceptions import DoesNotBelong

src/geometry/manifolds/embedding_relations.py

@@ -1,5 +1,5 @@
 from . import (DifferentiableManifold, SO3, SO2, R1, R2, R3, SE2, SE3, S2, S1,
-    T1, T2, T3, so2, so3, se2, se3, np, Tran2, tran2, tran3, Tran3, tran1)
+    T1, T2, T3, so2, so3, se2, se3, Tran2, tran2, tran3, Tran3, tran1)
 from .. import (S1_project_from_S2, S2_from_S1, S1_project_from_R2,
     S2_project_from_R3, se2_from_so2, so2_project_from_se2, se3_from_so3,
     so3_project_from_se3, SE3_from_SO3, SE2_from_SO2, SO2_project_from_SE2,
@@ -10,6 +10,7 @@
     SE3_from_SE2, SO2_from_angle, angle_from_SO2)
 from geometry.spheres import normalize_pi
 
+import numpy as np
 
 def embedding(small, big, embed_in, project_from, desc=None):
     DifferentiableManifold.embedding(small, big, embed_in, project_from,
@@ -24,6 +25,31 @@ def isomorphism(A, B, a_to_b, b_to_a, desc=None):
 def identity(x):
     return x
 
+def tran1_project_from_tran2(b):
+    return np.array([[0, b[0, -1]],
+                    [0, 0]])
+
+
+def tran2_from_tran1(b):
+    return np.array([[0, 0, b[0, -1]],
+                      [0, 0, 0],
+                      [0, 0, 0]])
+
+
+def tran2_project_from_se2(b):
+    return np.array([[0, 0, b[0, -1]],
+                     [0, 0, b[1, -1]],
+                     [0, 0, 0]])
+
+
+def tran3_project_from_se3(b):
+    return np.array([[0, 0, 0, b[0, -1]],
+                     [0, 0, 0, b[1, -1]],
+                     [0, 0, 0, b[2, -1]],
+                     [0, 0, 0, 0]])
+
+
+
 
 embedding(R1, R2, lambda a: np.array([a[0], 0]),
               lambda b: np.array([b[0]]))
@@ -82,16 +108,6 @@ def T1_from_SO2(y):
 embedding(T3, R3, identity, lambda x: T3.normalize(x))
 
 
-def tran1_project_from_tran2(b):
-    return np.array([[0, b[0, -1]],
-                    [0, 0]])
-
-
-def tran2_from_tran1(b):
-    return np.array([[0, 0, b[0, -1]],
-                      [0, 0, 0],
-                      [0, 0, 0]])
-
 embedding(tran1, tran2, tran2_from_tran1, tran1_project_from_tran2)
 
 
@@ -103,18 +119,6 @@ def tran2_from_tran1(b):
                                          [0, 0, b[1, -1]],
                                          [0, 0, 0]]))
 
-
-def tran2_project_from_se2(b):
-    return np.array([[0, 0, b[0, -1]],
-                     [0, 0, b[1, -1]],
-                     [0, 0, 0]])
-
-
-def tran3_project_from_se3(b):
-    return np.array([[0, 0, 0, b[0, -1]],
-                     [0, 0, 0, b[1, -1]],
-                     [0, 0, 0, b[2, -1]],
-                     [0, 0, 0, 0]])
 
 embedding(tran2, se2, identity, tran2_project_from_se2)
 

src/geometry/manifolds/product_manifold.py

@@ -1,4 +1,6 @@
-from . import DifferentiableManifold, contract, np
+from . import DifferentiableManifold
+from contracts import contract
+import numpy as np
 
 __all__ = ['ProductManifold']
 

src/geometry/manifolds/special_euclidean_group.py

@@ -1,8 +1,9 @@
-from . import DifferentiableManifold, MatrixLieGroup, SO, se, R, contract, np
+from . import DifferentiableManifold, MatrixLieGroup, SO, se, R
 from .. import (SE3_from_SE2, assert_allclose, pose_from_rotation_translation,
     rotation_translation_from_pose, extract_pieces, se2_from_SE2, SE2_from_se2,
     SE2_from_translation_angle)
-from contracts import describe_type
+from contracts import contract, describe_type
+import numpy as np
 
 __all__ = ['SE_group']
 

src/geometry/manifolds/special_orthogonal_group.py

@@ -1,7 +1,9 @@
-from . import DifferentiableManifold, MatrixLieGroup, np, S2, so, contract
+from . import DifferentiableManifold, MatrixLieGroup, S2, so
 from .. import (assert_allclose, rot2d, random_rotation,
     axis_angle_from_rotation, rotation_from_axis_angle)
 from contracts import check
+from contracts import contract
+import numpy as np
 
 
 class SO_group(MatrixLieGroup):

src/geometry/manifolds/sphere.py

@@ -1,9 +1,12 @@
-from . import DifferentiableManifold, np, contract, check
+from . import DifferentiableManifold
 from .. import (any_orthogonal_direction, geodesic_distance_on_sphere,
     random_direction, normalize_length, normalize_length_or_zero,
     rotation_from_axis_angle, rot2d)
+from contracts import contract, check
 from numpy.core.numeric import outer
+import numpy as np
 
+__all__ = ['Sphere', 'Sphere1']
 
 class Sphere(DifferentiableManifold):
     ''' These are hyperspheres of unit radius. '''

src/geometry/manifolds/tangent_bundle.py

@@ -1,4 +1,7 @@
-from . import DifferentiableManifold, contract
+from . import DifferentiableManifold
+from contracts import contract
+
+__all__ = ['TangentBundle']
 
 
 class TangentBundle(DifferentiableManifold):
@@ -25,7 +28,7 @@ def belongs_ts(self, bv):
         # XXX: can we make it recursive?
         raise ValueError('Not supported')
 
-    def project_ts(self, bv): # TODO: test
+    def project_ts(self, bv):  # TODO: test
         # XXX: can we make it recursive?
         raise ValueError('Not supported')
 

src/geometry/mds_algos.py

@@ -1,9 +1,11 @@
-from . import (best_similarity_transform, contract, np, assert_allclose,
+from . import (best_similarity_transform, assert_allclose,
     project_vectors_onto_sphere, eigh)
 from contracts import check_multiple
 import itertools
 from geometry.formatting import formatm
 from geometry import logger
+from contracts import contract
+import numpy as np
 
 
 @contract(S='array[KxN]', returns='array[NxN](>=0)')

src/geometry/poses.py

@@ -1,7 +1,8 @@
 from . import (angle_from_rot2d, rotz, axis_angle_from_rotation, hat_map_2d,
-     contract, assert_allclose, np, rot2d, new_contract,
-    check_SO, check_skew_symmetric, expm, logm)
-from geometry.constants import GeometryConstants
+    assert_allclose, rot2d, new_contract, check_SO, check_skew_symmetric, expm, logm)
+from .constants import GeometryConstants
+from contracts import contract
+import numpy as np
 
 
 def check_SE(M):

src/geometry/poses_embedding.py

@@ -1,5 +1,7 @@
+import numpy as np
+from contracts import contract
 from . import (SE3_from_rotation_translation, combine_pieces, extract_pieces,
-    contract, np, SE2_from_rotation_translation, rotation_translation_from_SE2,
+    SE2_from_rotation_translation, rotation_translation_from_SE2,
     rotation_translation_from_SE3, hat_map, map_hat_2d, SO2_project_from_SO3,
     so2_project_from_so3, so3_from_so2)
 
@@ -67,23 +69,23 @@ def R3_project_from_SE3(b):
 
 @contract(returns='se3', a='se2')
 def se3_from_se2(a):
-    W, v, zero, one = extract_pieces(a) #@UnusedVariable
+    W, v, zero, one = extract_pieces(a)  # @UnusedVariable
     W = so3_from_so2(W)
     v = np.array([v[0], v[1], 0])
     return combine_pieces(W, v, v * 0, 0)
 
 
 @contract(returns='SE2', b='SE3')
 def SE2_project_from_SE3(b):
-    R, t, zero, one = extract_pieces(b) #@UnusedVariable
+    R, t, zero, one = extract_pieces(b)  # @UnusedVariable
     R = SO2_project_from_SO3(R)
     t = t[0:2]
     return combine_pieces(R, t, t * 0, 1)
 
 
 @contract(returns='se2', b='se3')
 def se2_project_from_se3(b):
-    W, v, zero, one = extract_pieces(b) #@UnusedVariable
+    W, v, zero, one = extract_pieces(b)  # @UnusedVariable
     W = so2_project_from_so3(W)
     v = v[0:2]
     return combine_pieces(W, v, v * 0, 0)

src/geometry/rotations.py

@@ -1,10 +1,13 @@
-''' Contains all about rotation matrices, quaternions, and various conversions.
+''' 
+    Contains all about rotation matrices, quaternions, and various conversions.
 
-     conventions: q=( a + bi + cj + dk), with a>0
+    conventions: q=( a + bi + cj + dk), with a>0
 '''
-from . import (assert_allclose, new_contract, contract, safe_arccos, np,
+from . import (assert_allclose, safe_arccos,
     default_axis, normalize_length)
 import itertools
+from contracts import contract, new_contract
+import numpy as np
 
 
 new_contract('unit_quaternion', 'array[4], unit_length')
@@ -17,7 +20,7 @@
 def check_SO(x):
     ''' Checks that the given value is a rotation matrix of arbitrary size. '''
     check_orthogonal(x)
-    determinant = np.linalg.det(x * 1.0) # XXX: voodoo
+    determinant = np.linalg.det(x * 1.0)  # XXX: voodoo
     # lapack_lite.LapackError: 
     # Parameter a has non-native byte order in lapack_lite.dgetrf
     assert_allclose(determinant, 1.0)
@@ -28,7 +31,7 @@ def check_orthogonal(x):
     ''' Check that the argument is an orthogonal matrix. '''
     N = x.shape[0]
     I = np.eye(N)
-    rtol = 10E-10 # XXX:
+    rtol = 10E-10  # XXX:
     atol = 10E-7  # XXX:
     assert_allclose(I, np.dot(x, x.T), rtol=rtol, atol=atol)
     assert_allclose(I, np.dot(x.T, x), rtol=rtol, atol=atol)
@@ -48,7 +51,7 @@ def check_skew_symmetric(x):
             if i < j:
                 continue
             if x[i, j] != -x[j, i]:
-                raise ValueError('Expected skew symmetric, but ' +
+                raise ValueError('Expected skew symmetric, but ' + 
                                  'a[%d][%d] = %f, a[%d][%d] = %f' % \
                                  (i, j, x[i, j], j, i, x[j, i]))
 
@@ -103,8 +106,8 @@ def hat_map_2d(omega):
 def map_hat_2d(W):
     return W[1, 0]
 
-rot2d = SO2_from_angle # TODO: deprecated 
-rot2d_from_angle = SO2_from_angle# TODO: deprecated 
+rot2d = SO2_from_angle  # TODO: deprecated 
+rot2d_from_angle = SO2_from_angle  # TODO: deprecated 
 angle_from_rot2d = angle_from_SO2
 
 
@@ -159,7 +162,7 @@ def geodesic_distance_for_rotations(R1, R2):
     
     '''
     R = np.dot(R1, R2.T)
-    axis1, angle1 = axis_angle_from_rotation(R) #@UnusedVariable
+    axis1, angle1 = axis_angle_from_rotation(R)  # @UnusedVariable
     return angle1
 
 
@@ -226,7 +229,7 @@ def quaternion_from_rotation(R):
     rr = 1 + R[u, u] - R[v, v] - R[w, w]
     assert rr >= 0
     r = np.sqrt(rr)
-    if r == 0: # TODO: add tolerance
+    if r == 0:  # TODO: add tolerance
         return quaternion_from_axis_angle(default_axis(), 0.0)
     else:
         q0 = (R[w, v] - R[v, w]) / (2 * r)
@@ -268,7 +271,7 @@ def axis_angle_from_quaternion(q):
         This is the inverse of :py:func:`quaternion_from_axis_angle`.
     '''
     angle = 2 * safe_arccos(q[0])
-    if angle == 0: # XXX: use tolerance
+    if angle == 0:  # XXX: use tolerance
         axis = default_axis()
     else:
         axis = q[1:] / np.sin(angle / 2)
@@ -343,7 +346,7 @@ def rotation_from_axis_angle2(axis, angle):
 
 @contract(x_axis='direction', vector_on_xy_plane='direction',
           returns='rotation_matrix')
-def rotation_from_axes_spec(x_axis, vector_on_xy_plane): # TODO: docs
+def rotation_from_axes_spec(x_axis, vector_on_xy_plane):  # TODO: docs
     """ 
         Creates a rotation matrix from the axes. 
         ``x_axis`` is the new direction of the (1,0,0) vector

src/geometry/rotations_embedding.py

@@ -1,6 +1,9 @@
-from . import (map_hat_2d, contract, np, angle_from_rot2d,
+from . import (map_hat_2d, angle_from_rot2d,
     rotation_from_axis_angle, hat_map, rot2d)
 
+from contracts import contract
+import numpy as np
+
 
 @contract(returns='SO3', a='SO2')
 def SO3_from_SO2(a):
@@ -13,7 +16,7 @@ def SO2_project_from_SO3(b):
     direction = np.array([1, 0, 0])
     vector = np.dot(b, direction)
     n = np.linalg.norm(vector)
-    atol = 1e-8 # XXX: make common
+    atol = 1e-8  # XXX: make common
     if n < atol:
         return rot2d(0)
     else: