Merge branch 'mnt/deprecations' into 'master'

Mnt/deprecations

See merge request fsl/fslpy!286

CHANGELOG.rst

@@ -24,6 +24,9 @@ Deprecated
   ``canHaveGui``, ``inSSHSession``, ``inVNCSession``, ``wxPlatform``,
   ``wxFlavour``, ``glVersion``, ``glRenderer``, and ``glIsSoftwareRenderer``.
   Equivalent functions are being added to the ``fsleyes-widgets`` library.
+* The :mod:`fsl.utils.filetree` package has been deprecated, and will be
+  removed in a future version of ``fslpy`` - it is now published as a separate
+  library on [PyPI](https://pypi.org/project/file-tree/).
 
 
 

fsl/data/imagewrapper.py

@@ -733,7 +733,7 @@ def isValidFancySliceObj(sliceobj, shape):
     # We only support boolean numpy arrays
     # which have the same shape as the image
     return (isinstance(sliceobj, np.ndarray) and
-            sliceobj.dtype == np.bool        and
+            sliceobj.dtype == bool           and
             np.prod(sliceobj.shape) == np.prod(shape))
 
 

fsl/data/mesh.py

@@ -701,7 +701,7 @@ def calcVertexNormals(vertices, indices, fnormals):
                    the mesh.
     """
 
-    vnormals = np.zeros((vertices.shape[0], 3), dtype=np.float)
+    vnormals = np.zeros((vertices.shape[0], 3), dtype=float)
 
     # TODO make fast. I can't figure
     # out how to use np.add.at to

fsl/transform/affine.py

@@ -627,8 +627,8 @@ def rescale(oldShape, newShape, origin=None):
     if origin is None:
         origin = 'centre'
 
-    oldShape = np.array(oldShape, dtype=np.float)
-    newShape = np.array(newShape, dtype=np.float)
+    oldShape = np.array(oldShape, dtype=float)
+    newShape = np.array(newShape, dtype=float)
     ndim     = len(oldShape)
 
     if len(oldShape) != len(newShape):

fsl/utils/filetree/__init__.py

@@ -289,7 +289,7 @@ of the short variable names defined in the
 Running a pipeline on a subset of participants/sessions/runs
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Suppose you want to run your pipeline on a subset of your data while testing. 
+Suppose you want to run your pipeline on a subset of your data while testing.
 You may want to do this if your data has a a hierarchy of variables (e.g. participant, session, run) as in the example below.
 
 ::
@@ -321,3 +321,12 @@ __author__ = 'Michiel Cottaar <Michiel.Cottaar@ndcn.ox.ac.uk>'
 from .filetree import FileTree, register_tree, MissingVariable
 from .parse import tree_directories, list_all_trees
 from .query import FileTreeQuery
+
+import fsl.utils.deprecated as deprecated
+
+deprecated.warn('fsl.utils.filetree',
+                vin='3.6.0',
+                rin='4.0.0',
+                msg='The filetree package is now released as a separate '
+                    'Python library ("file-tree" on PyPi), and will be '
+                    'removed in a future version of fslpy.')

fsl/utils/image/resample.py

@@ -209,7 +209,7 @@ def resample(image,
        np.all(np.isclose(matrix, np.eye(len(newShape) + 1))):
         return data, image.voxToWorldMat
 
-    newShape = np.array(np.round(newShape), dtype=np.int)
+    newShape = np.array(np.round(newShape), dtype=int)
 
     # Apply smoothing if requested,
     # and if not using nn interp