Merge branch 'bf/imcp_paths' into 'master'

Bf/imcp paths

See merge request fsl/fslpy!78

CHANGELOG.rst

@@ -11,7 +11,7 @@ Added
 
 * New :mod:`fsl.utils.filetree` package for defining and working with
   file/directory templates.
-* Simple built-in `.deprecated` decorator.
+* Simple built-in :mod:`.deprecated` decorator.
 
 
 Changed
@@ -23,6 +23,14 @@ Changed
   file handles.
 
 
+Fixed
+^^^^^
+
+
+* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions
+  on input arguments.
+
+
 Removed
 ^^^^^^^
 

fsl/data/image.py

@@ -1376,6 +1376,20 @@ def removeExt(filename):
     return fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
 
 
+def fixExt(filename):
+    """Fix the extension of ``filename``.
+
+    For example, if a file name is passed in as ``file.nii.gz``, but the
+    file is actually ``file.nii``, this function will fix the file name.
+
+    If ``filename`` already exists, it is returned unchanged.
+    """
+    if op.exists(filename):
+        return filename
+    else:
+        return addExt(removeExt(filename))
+
+
 def defaultExt():
     """Returns the default NIFTI file extension that should be used.
 

fsl/scripts/imcp.py

@@ -60,6 +60,7 @@ def main(argv=None):
         return 1
 
     try:
+        srcs = [fslimage.fixExt(s) for s in srcs]
         srcs = fslpath.removeDuplicates(
             srcs,
             allowedExts=fslimage.ALLOWED_EXTENSIONS,

fsl/scripts/immv.py

@@ -61,6 +61,7 @@ def main(argv=None):
         return 1
 
     try:
+        srcs = [fslimage.fixExt(s) for s in srcs]
         srcs = fslpath.removeDuplicates(
             srcs,
             allowedExts=fslimage.ALLOWED_EXTENSIONS,

tests/test_image.py

@@ -504,6 +504,31 @@ def test_defaultExt():
         assert fslimage.defaultExt() == e
 
 
+def test_fixExt():
+    with tempdir():
+
+        # error if if file doesn't exist
+        with pytest.raises(fslpath.PathError):
+            fslimage.fixExt('file.nii.gz')
+
+        with open('file.nii', 'w') as f:
+            f.write('1')
+        assert fslimage.fixExt('file.nii.gz') == 'file.nii'
+        assert fslimage.fixExt('file.nii')    == 'file.nii'
+
+        with open('file.nii.gz', 'w') as f:
+            f.write('1')
+
+        assert fslimage.fixExt('file.nii.gz') == 'file.nii.gz'
+        assert fslimage.fixExt('file.nii')    == 'file.nii'
+
+        os.remove('file.nii')
+        os.remove('file.nii.gz')
+        with open('file.nii.gz', 'w') as f:
+            f.write('1')
+        assert fslimage.fixExt('file.nii') == 'file.nii.gz'
+
+
 def  test_Image_orientation_analyze_neuro(): _test_Image_orientation(0, 'neuro')
 def  test_Image_orientation_analyze_radio(): _test_Image_orientation(0, 'radio')
 def  test_Image_orientation_nifti1_neuro():  _test_Image_orientation(1, 'neuro')

tests/test_immv_imcp.py

@@ -20,10 +20,11 @@ import               pytest
 
 import nibabel as nib
 
-import fsl.utils.imcp   as imcp
-import fsl.scripts.imcp as imcp_script
-import fsl.scripts.immv as immv_script
-import fsl.data.image   as fslimage
+from   fsl.utils.tempdir import tempdir
+import fsl.utils.imcp        as imcp
+import fsl.scripts.imcp      as imcp_script
+import fsl.scripts.immv      as immv_script
+import fsl.data.image        as fslimage
 
 from . import make_random_image
 from . import make_dummy_file
@@ -730,3 +731,27 @@ def test_imcp_shouldPass(move=False):
 
 def test_immv_shouldPass():
     test_imcp_shouldPass(move=True)
+
+def test_imcp_badExt():
+    with tempdir():
+
+        with open('file.nii.gz', 'wt') as f:
+            f.write('1')
+
+        result = imcp_script.main(['file.nii', 'dest'])
+
+        assert result == 0
+        assert op.exists('dest.nii.gz')
+
+
+
+def test_immv_badExt():
+    with tempdir():
+
+        with open('file.nii.gz', 'wt') as f:
+            f.write('1')
+
+        result = immv_script.main(['file.nii', 'dest'])
+
+        assert result == 0
+        assert op.exists('dest.nii.gz')