Merge branch 'rel/3.9.5' into 'v3.9'

Rel/3.9.5

See merge request fsl/fslpy!345

CHANGELOG.rst

@@ -2,6 +2,27 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.9.5 (Thursday 2nd June 2022)
+------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Updated the :func:`.ensureIsImage` function to support ``pathlib.Path``
+  objects (!343).
+
+
+Fixed
+^^^^^
+
+
+* Some fixes in the :mod:`.wrappers` module (specifically in the
+  :class:`.FileOrThing` class) to better support ``pathlib.Path`` objects
+  (!343).
+
+
 3.9.4 (Friday 27th May 2022)
 ----------------------------
 
@@ -13,7 +34,6 @@ Changed
 * Changed the behaviour of :meth:`.Image.__getitem__` so that, if image
   data is accessed with a boolean mask array (e.g. ``image[mask > 0]``),
   the image data is loaded into memory (!341).
-* Fixed an issue in the :func:`.func_to_cmd` function (!339).
 
 
 3.9.3 (Friday 27th May 2022)

fsl/utils/ensure.py

@@ -13,6 +13,7 @@ that some condition is met.
    ensureIsImage
 """
 
+import pathlib
 
 import nibabel as nib
 
@@ -22,7 +23,7 @@ import fsl.data.image as fslimage
 def ensureIsImage(img):
     """Ensures that the given ``img`` is an in-memory ``nibabel`` object.
     """
-    if isinstance(img, str):
+    if isinstance(img, (str, pathlib.Path)):
         img = fslimage.addExt(img)
         img = nib.load(img)
     return img

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.9.4'
+__version__ = '3.9.5'
 """Current version number, as a string. """
 
 

fsl/wrappers/__init__.py

@@ -76,6 +76,21 @@ Similarly, we can run a ``fslmaths`` command on in-memory images::
     output = fslmaths(image).mas(mask).bin().run()
 
 
+It is possible to run a Python script in Windows, and call FSL commands which
+are installed in a WSL environment. When specifying inputs/outputs as
+file/directory paths, the safest option is to use ``pathlib.Path`` objects
+to ensure that they are correctly translated bewteen Windows and Linux-style
+paths, e.g.::
+
+    from pathlib import Path
+    from fsl.wrappers import bet
+
+    bet(Path('T1\\T1.nii.gz`), Path('T1_brain'))
+
+If you use strings to specify inputs/outputs, they must be absolute paths, as
+they may otherwise not be translated correctly.
+
+
 If you are *writing* wrapper functions, take a look at the
 :mod:`.wrapperutils` module - it contains several useful functions and
 decorators.

fsl/wrappers/wrapperutils.py

@@ -709,6 +709,7 @@ class FileOrThing:
 
           - The argument value that was passed in
         """
+
         self.__func      = func
         self.__prepIn    = prepIn
         self.__prepOut   = prepOut
@@ -873,6 +874,8 @@ class FileOrThing:
         # accept an output prefix which contains
         # a directory path.
         if prefix is not None:
+            if isinstance(prefix, pathlib.Path):
+                prefix = op.abspath(prefix)
 
             # If prefix is set to LOAD,
             # all generated output files
@@ -965,6 +968,15 @@ class FileOrThing:
         if realPrefix is not None and len(prefixedFiles) == 0:
             allargs[self.__outprefix] = realPrefix
 
+        # Turn any Path objects into absolute path
+        # strings. Don't use Path.resolve(), as it
+        # returns a relative path for non-existent
+        # files/dirs on Windows/certain Python
+        # versions.
+        for k, v in allargs.items():
+            if isinstance(v, pathlib.Path):
+                allargs[k] = op.abspath(v)
+
         args   = [allargs.pop(k) for k in argnames]
         kwargs = allargs
 

tests/test_ensure.py

@@ -5,6 +5,7 @@
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
+import pathlib
 
 import numpy   as np
 import nibabel as nib
@@ -22,8 +23,10 @@ def test_ensureIsImage():
 
         assert ensure.ensureIsImage(img) is img
 
-        loaded = [ensure.ensureIsImage('image.nii'),
-                  ensure.ensureIsImage('image')]
+        loaded = [ensure.ensureIsImage(             'image.nii'),
+                  ensure.ensureIsImage(             'image'),
+                  ensure.ensureIsImage(pathlib.Path('image')),
+                  ensure.ensureIsImage(pathlib.Path('image.nii'))]
 
         for l in loaded:
             assert isinstance(l, nib.nifti1.Nifti1Image)

tests/test_wrappers/test_wrapperutils.py

@@ -475,6 +475,44 @@ def test_fileOrThing_outprefix():
         cleardir(td, 'myout*')
 
 
+def test_fileOrThing_pathlib():
+    @wutils.fileOrImage('img', 'out')
+    def basefunc(img, out):
+        img    = np.asanyarray(nib.load(img).dataobj)
+        outimg = nib.nifti1.Nifti1Image(img * 5,  np.eye(4))
+        nib.save(outimg, out)
+
+    with tempdir.tempdir() as td:
+        img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
+        exp = np.asanyarray(img.dataobj) * 5
+        nib.save(img, 'img.nii')
+
+        basefunc(pathlib.Path('img.nii'), pathlib.Path('output.nii'))
+        assert np.all(np.asanyarray(nib.load('output.nii') .dataobj) == exp)
+
+
+def test_fileOrThing_outprefix_pathlib():
+    @wutils.fileOrImage('img', outprefix='output_base')
+    def basefunc(img, output_base):
+        img = np.asanyarray(nib.load(img).dataobj)
+
+        out1 = nib.nifti1.Nifti1Image(img * 5,  np.eye(4))
+        out2 = nib.nifti1.Nifti1Image(img * 10, np.eye(4))
+
+        nib.save(out1, '{}_times5.nii.gz' .format(output_base))
+        nib.save(out2, '{}_times10.nii.gz'.format(output_base))
+
+    with tempdir.tempdir() as td:
+        img  = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
+        exp1 = np.asanyarray(img.dataobj) * 5
+        exp2 = np.asanyarray(img.dataobj) * 10
+        nib.save(img, 'img.nii')
+
+        basefunc(pathlib.Path('img.nii'), pathlib.Path('myout'))
+        assert np.all(np.asanyarray(nib.load('myout_times5.nii.gz') .dataobj) == exp1)
+        assert np.all(np.asanyarray(nib.load('myout_times10.nii.gz').dataobj) == exp2)
+
+
 def test_fileOrThing_outprefix_differentTypes():
 
     @wutils.fileOrImage('img', outprefix='outpref')