[JOSS Review] Minor issues

[zexinyang]

Hi @gattia and @siavashk,

This is part of the JOSS review process. I found two minor issues after testing your PyCPD package. Could you please address them?

• Found an error when running python examples/fish_deformable_3D_register_with_subset_of_points.py:

Traceback (most recent call last):
  File "examples/fish_deformable_3D_register_with_subset_of_points.py", line 55, in <module>
    main()
  File "examples/fish_deformable_3D_register_with_subset_of_points.py", line 43, in main
    YT = reg.transform_point_cloud(Y=Y)
  File "/home/geo3d/miniconda3/envs/joss-pycpd/lib/python3.8/site-packages/pycpd/deformable_registration.py", line 68, in transform_point_cloud
    return Y + np.dot(self.G, self.W)
ValueError: operands could not be broadcast together with shapes (182,3) (91,3)

This error also failed the pytest:

============================= test session starts ==============================
platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/geo3d/Zexin/project/pycpd
collected 7 items                                                              

testing/affine_test.py ..                                                [ 28%]
testing/deformable_test.py ..F                                           [ 71%]
testing/rigid_test.py ..                                                 [100%]

=================================== FAILURES ===================================
_______________________________ test_3D_low_rank _______________________________

    def test_3D_low_rank():
        fish_target = np.loadtxt('data/fish_target.txt')
        X1 = np.zeros((fish_target.shape[0], fish_target.shape[1] + 1))
        X1[:, :-1] = fish_target
        X2 = np.ones((fish_target.shape[0], fish_target.shape[1] + 1))
        X2[:, :-1] = fish_target
        X = np.vstack((X1, X2))
    
        fish_source = np.loadtxt('data/fish_source.txt')
        Y1 = np.zeros((fish_source.shape[0], fish_source.shape[1] + 1))
        Y1[:, :-1] = fish_source
        Y2 = np.ones((fish_source.shape[0], fish_source.shape[1] + 1))
        Y2[:, :-1] = fish_source
        Y = np.vstack((Y1, Y2))
    
        reg = DeformableRegistration(**{'X': X, 'Y': Y, 'low_rank': True})
        TY, _ = reg.register()
        assert_array_almost_equal(TY, X, decimal=0)
    
        rand_pts = np.random.randint(Y.shape[0], size=int(Y.shape[0]/2))
>       TY2 = reg.transform_point_cloud(Y=Y[rand_pts, :])

testing/deformable_test.py:56: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pycpd.deformable_registration.DeformableRegistration object at 0x7f5ff28b62b0>
Y = array([[-0.28181282, -0.79432332,  1.        ],
       [-0.37639549, -0.58040108,  1.        ],
       [-0.91641226,  ...1006222,  1.        ],
       [-0.10490431, -0.60374743,  1.        ],
       [-0.50945755,  0.00261754,  1.        ]])

    def transform_point_cloud(self, Y=None):
        """
        Update a point cloud using the new estimate of the deformable transformation.
    
        """
        if Y is None:
            self.TY = self.Y + np.dot(self.G, self.W)
            return
        else:
>           return Y + np.dot(self.G, self.W)
E           ValueError: operands could not be broadcast together with shapes (91,3) (182,3)

../../../miniconda3/envs/joss-pycpd/lib/python3.8/site-packages/pycpd/deformable_registration.py:68: ValueError
=========================== short test summary info ============================
FAILED testing/deformable_test.py::test_3D_low_rank - ValueError: operands co...
========================= 1 failed, 6 passed in 0.43s ==========================

• A few warnings can be fixed by replacing is not with !=:

/home/geo3d/Zexin/project/pycpd/pycpd/rigid_registration.py:45: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if R is not None and (R.ndim is not 2 or R.shape[0] is not self.D or R.shape[1] is not self.D or not is_positive_semi_definite(R)):
/home/geo3d/Zexin/project/pycpd/pycpd/rigid_registration.py:49: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if t is not None and (t.ndim is not 2 or t.shape[0] is not 1 or t.shape[1] is not self.D):
/home/geo3d/Zexin/project/pycpd/pycpd/rigid_registration.py:49: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if t is not None and (t.ndim is not 2 or t.shape[0] is not 1 or t.shape[1] is not self.D):
/home/geo3d/Zexin/project/pycpd/pycpd/affine_registration.py:30: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if B is not None and (B.ndim is not 2 or B.shape[0] is not self.D or B.shape[1] is not self.D or not is_positive_semi_definite(B)):
/home/geo3d/Zexin/project/pycpd/pycpd/affine_registration.py:34: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if t is not None and (t.ndim is not 2 or t.shape[0] is not 1 or t.shape[1] is not self.D):
/home/geo3d/Zexin/project/pycpd/pycpd/affine_registration.py:34: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if t is not None and (t.ndim is not 2 or t.shape[0] is not 1 or t.shape[1] is not self.D):