Merge d869818 into d1a6f95

nipy · Feb 23, 2021 · 349eaea · 349eaea
2 parents d1a6f95 + d869818
commit 349eaea
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Showing 6 changed files with 8 additions and 7 deletions.
diff --git a/examples/interfaces/process_ds105.py b/examples/interfaces/process_ds105.py
@@ -204,7 +204,7 @@ def coregister(self, in_prefix=''):
         return in_prefix
 
     def seg_norm(self, in_prefix=''):
-        def_tpms = np.zeros((3,1), dtype=np.object)
+        def_tpms = np.zeros((3,1), dtype=object)
         spm_path = spm_info.spm_path
         def_tpms[0] = pjoin(spm_path, 'tpm', 'grey.nii'),
         def_tpms[1] = pjoin(spm_path, 'tpm', 'white.nii'),

diff --git a/examples/interfaces/process_fiac.py b/examples/interfaces/process_fiac.py
@@ -99,7 +99,7 @@ def coregister(data_def):
 
 
 def segnorm(data_def):
-    def_tpms = np.zeros((3,1), dtype=np.object)
+    def_tpms = np.zeros((3,1), dtype=object)
     spm_path = spm_info.spm_path
     def_tpms[0] = pjoin(spm_path, 'tpm', 'grey.nii'),
     def_tpms[1] = pjoin(spm_path, 'tpm', 'white.nii'),

diff --git a/nipy/core/reference/coordinate_map.py b/nipy/core/reference/coordinate_map.py
@@ -649,7 +649,8 @@ def inverse(self, preserve_dtype=False):
             sym_inv = Matrix(self.affine).inv()
             m_inv = matrix2numpy(sym_inv).astype(aff_dt)
         else: # linalg inverse succeeded
-            if preserve_dtype and aff_dt != np.object: # can we cast back?
+            # Do we need a specific dtype?  Can we cast to this dtype?
+            if preserve_dtype and aff_dt != np.object_:
                 m_inv_orig = m_inv
                 m_inv = m_inv.astype(aff_dt)
                 if not np.allclose(m_inv_orig, m_inv):

diff --git a/nipy/core/reference/coordinate_system.py b/nipy/core/reference/coordinate_system.py
@@ -117,7 +117,7 @@ def __init__(self, coord_names, name='', coord_dtype=np.float):
             raise ValueError('coord_names must have distinct names')
         # verify that the dtype is coord_dtype for sanity
         sctypes = (np.sctypes['int'] + np.sctypes['float'] +
-                   np.sctypes['complex'] + np.sctypes['uint'] + [np.object])
+                   np.sctypes['complex'] + np.sctypes['uint'] + [object])
         coord_dtype = np.dtype(coord_dtype)
         if coord_dtype not in sctypes:
             raise ValueError('Coordinate dtype should be one of %s' % sctypes)

diff --git a/nipy/core/reference/tests/test_coordinate_map.py b/nipy/core/reference/tests/test_coordinate_map.py
@@ -30,7 +30,7 @@
 # Dtypes for testing coordinate map creation / processing
 _SYMPY_SAFE_DTYPES = (np.sctypes['int'] + np.sctypes['uint'] +
                       np.sctypes['float'] + np.sctypes['complex'] +
-                      [np.object])
+                      [object])
 # Sympy <= 1.1 does not handle numpy longcomplex correctly. See:
 # https://github.com/sympy/sympy/pull/12901
 if np.longcomplex in _SYMPY_SAFE_DTYPES:  # Not present for Windows

diff --git a/nipy/core/reference/tests/test_coordinate_system.py b/nipy/core/reference/tests/test_coordinate_system.py
@@ -56,15 +56,15 @@ def test_unique_coord_names():
 def test_dtypes():
     # invalid dtypes
     dtypes = np.sctypes['others']
-    dtypes.remove(np.object)
+    dtypes.remove(object)
     for dt in dtypes:
         assert_raises(ValueError, CoordinateSystem, 'ijk', 'test', dt)
     # compound dtype
     dtype = np.dtype([('field1', '<f8'), ('field2', '<i4')])
     assert_raises(ValueError, CoordinateSystem, 'ijk', 'test', dtype)
     # valid dtypes
     dtypes = (np.sctypes['int'] + np.sctypes['float'] + np.sctypes['complex'] +
-              [np.object])
+              [object])
     for dt in dtypes:
         cs = CoordinateSystem('ij', coord_dtype=dt)
         assert_equal(cs.coord_dtype, dt)