TEST: numpy deprecation warnings

tests/test_atlases_query.py

@@ -85,7 +85,7 @@ def _get_zero_mask(aimg):
         elif isinstance(aimg, fslatlases.ProbabilisticAtlas):
 
             # Keep memory usage down
-            zmask = np.ones(aimg.shape[:3], dtype=np.bool)
+            zmask = np.ones(aimg.shape[:3], dtype=bool)
             for vol in range(aimg.shape[-1]):
                 zmask = np.logical_and(zmask, aimg[..., vol] == 0)
 

tests/test_image_resample.py

@@ -75,7 +75,7 @@ def test_resample(seed):
                    (np.isclose(np.modf(origtestcoords)[0], 0.5)))
             out = np.any(out, axis=1) | (resvals == 0)
 
-            origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
+            origtestcoords = np.array(origtestcoords.round(), dtype=int)
 
             origtestcoords = origtestcoords[~out, :]
             restestcoords  = restestcoords[ ~out, :]
@@ -166,8 +166,8 @@ def test_resampleToPixdims():
 
     img          = fslimage.Image(make_random_image(dims=(10, 10, 10)))
     imglo, imghi = affine.axisBounds(img.shape, img.voxToWorldMat)
-    oldpix       = np.array(img.pixdim, dtype=np.float)
-    oldshape     = np.array(img.shape,  dtype=np.float)
+    oldpix       = np.array(img.pixdim, dtype=float)
+    oldshape     = np.array(img.shape,  dtype=float)
 
     for i, origin in it.product(range(25), ('centre', 'corner')):
 
@@ -215,16 +215,16 @@ def test_resampleToReference2():
     # More specific test - output
     # data gets transformed correctly
     # into reference space
-    img          = np.zeros((5, 5, 5), dtype=np.float)
+    img          = np.zeros((5, 5, 5), dtype=float)
     img[1, 1, 1] = 1
     img          = fslimage.Image(img)
 
     refv2w = affine.scaleOffsetXform([1, 1, 1], [-1, -1, -1])
-    ref    = np.zeros((5, 5, 5), dtype=np.float)
+    ref    = np.zeros((5, 5, 5), dtype=float)
     ref    = fslimage.Image(ref, xform=refv2w)
     res    = resample.resampleToReference(img, ref, order=0)
 
-    exp          = np.zeros((5, 5, 5), dtype=np.float)
+    exp          = np.zeros((5, 5, 5), dtype=float)
     exp[2, 2, 2] = 1
 
     assert np.all(np.isclose(res[0], exp))

tests/test_imagewrapper.py

@@ -1195,7 +1195,7 @@ def test_3D_indexing(shape=None, img=None):
 
     assert type(img[0, 0, 0]) == np.float64
 
-    mask1 = np.zeros(shape, dtype=np.bool)
+    mask1 = np.zeros(shape, dtype=bool)
 
     mask1[0, 0, 0] = True
     mask1[1, 0, 0] = True
@@ -1252,7 +1252,7 @@ def test_3D_4D_indexing():
     assert type(img[0, 0, 0, 0]) == np.float64
     assert type(img[0, 0, 0, :]) == np.float64
 
-    mask = np.zeros(padShape, dtype=np.bool)
+    mask = np.zeros(padShape, dtype=bool)
     mask[0, 0, 0, 0] = True
 
     assert type(img[mask])      == np.ndarray
@@ -1282,13 +1282,13 @@ def test_3D_len_one_indexing(shape=None, img=None):
     assert type(img[0, 0])    == np.ndarray
     assert type(img[0, 0, 0]) == np.float64
 
-    mask = np.zeros(shape[:2], dtype=np.bool)
+    mask = np.zeros(shape[:2], dtype=bool)
     mask[0, 0] = True
 
     assert type(img[mask])      == np.ndarray
     assert      img[mask].shape == (1, )
 
-    mask = np.zeros(shape, dtype=np.bool)
+    mask = np.zeros(shape, dtype=bool)
     mask[0, 0, 0] = True
 
     assert type(img[mask])      == np.ndarray
@@ -1352,7 +1352,7 @@ def test_4D_indexing(shape=None, img=None):
 
     assert type(img[0, 0, 0, 0]) == np.float64
 
-    mask1 = np.zeros(shape, dtype=np.bool)
+    mask1 = np.zeros(shape, dtype=bool)
 
     mask1[0, 0, 0, 0] = True
     mask1[1, 0, 0, 0] = True

tests/test_transform/test_affine.py

@@ -395,7 +395,7 @@ def test_transform():
         mask = np.array([[1, 0, 0, 1],
                          [0, 1, 0, 1],
                          [0, 0, 1, 1],
-                         [0, 0, 0, 1]], dtype=np.bool)
+                         [0, 0, 0, 1]], dtype=bool)
 
         return np.all((xform != 0) == mask)
 

tests/test_transform/test_nonlinear.py

@@ -161,7 +161,7 @@ def test_convertDeformationSpace():
         refcoords = [np.random.randint(0, basefield.shape[0], 5),
                      np.random.randint(0, basefield.shape[1], 5),
                      np.random.randint(0, basefield.shape[2], 5)]
-        refcoords = np.array(refcoords, dtype=np.int).T
+        refcoords = np.array(refcoords, dtype=int).T
         refcoords = affine.transform(refcoords, ref.voxToScaledVoxMat)
         srccoords = basefield.transform(refcoords)