MNT: Apply same minor optimisations to other im* scripts - avoid expensive imports

fsl/scripts/imglob.py

@@ -11,7 +11,6 @@ NIFTI/ANALYZE image files.
 
 import                   sys
 import                   glob
-import itertools      as it
 import fsl.utils.path as fslpath
 
 
@@ -30,7 +29,7 @@ exts   = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.hdr.gz']
 """List of supported image file extensions. """
 
 
-groups = [('.hdr',    '.img'), ('.hdr.gz', '.img.gz')]
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
 """List of known image file groups (image/header file pairs). """
 
 

fsl/scripts/imln.py

@@ -17,19 +17,22 @@ to NIFTI image files.
 import os.path        as op
 import                   os
 import                   sys
-import                   warnings
-
 import fsl.utils.path as fslpath
 
 
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.data.image as fslimage
-
+# The lists below are defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
 
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
-"""List of file extensions that are supported by ``imln``. """
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
 
 
 usage = """
@@ -50,8 +53,8 @@ def main(argv=None):
         return 1
 
     target, linkbase = argv
-    target           = fslpath.removeExt(target,   ALLOWED_EXTENSIONS)
-    linkbase         = fslpath.removeExt(linkbase, ALLOWED_EXTENSIONS)
+    target           = fslpath.removeExt(target,   exts)
+    linkbase         = fslpath.removeExt(linkbase, exts)
 
     # Target must exist, so we can
     # infer the correct extension(s).
@@ -59,8 +62,8 @@ def main(argv=None):
     # (e.g. a.img without a.hdr).
     try:
         targets = fslpath.getFileGroup(target,
-                                       allowedExts=ALLOWED_EXTENSIONS,
-                                       fileGroups=fslimage.FILE_GROUPS,
+                                       allowedExts=exts,
+                                       fileGroups=groups,
                                        unambiguous=True)
     except Exception as e:
         print(f'Error: {e}')
@@ -70,7 +73,7 @@ def main(argv=None):
         if not op.exists(target):
             continue
 
-        ext  = fslpath.getExt(target, ALLOWED_EXTENSIONS)
+        ext  = fslpath.getExt(target, exts)
         link = f'{linkbase}{ext}'
 
         try:

fsl/scripts/imrm.py

@@ -13,22 +13,22 @@ import itertools      as it
 import os.path        as op
 import                   os
 import                   sys
-import                   warnings
-
 import fsl.utils.path as fslpath
 
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.data.image as fslimage
-
 
 usage = """Usage: imrm <list of image names to remove>
 NB: filenames can be basenames or not
 """.strip()
 
 
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+# This list is defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
 """List of file extensions that are removed by ``imrm``. """
 
 
@@ -42,9 +42,9 @@ def main(argv=None):
         print(usage)
         return 1
 
-    prefixes = [fslpath.removeExt(p, ALLOWED_EXTENSIONS) for p in argv]
+    prefixes = [fslpath.removeExt(p, exts) for p in argv]
 
-    for prefix, ext in it.product(prefixes, ALLOWED_EXTENSIONS):
+    for prefix, ext in it.product(prefixes, exts):
 
         path = f'{prefix}{ext}'
 

fsl/scripts/imtest.py

@@ -11,18 +11,22 @@ not, without having to know the file suffix (.nii, .nii.gz, etc).
 
 import os.path        as op
 import                   sys
-import                   warnings
-
 import fsl.utils.path as fslpath
 
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.data.image as fslimage
 
+# The lists below are defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
 
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
-"""List of file extensions that are supported by ``imln``. """
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
 
 
 def main(argv=None):
@@ -38,7 +42,7 @@ def main(argv=None):
         print('0')
         return 0
 
-    path = fslpath.removeExt(argv[0], ALLOWED_EXTENSIONS)
+    path = fslpath.removeExt(argv[0], exts)
     path = op.realpath(path)
 
     # getFileGroup will raise an error
@@ -47,8 +51,8 @@ def main(argv=None):
     # image) does not exist
     try:
         fslpath.getFileGroup(path,
-                             allowedExts=ALLOWED_EXTENSIONS,
-                             fileGroups=fslimage.FILE_GROUPS,
+                             allowedExts=exts,
+                             fileGroups=groups,
                              unambiguous=True)
         print('1')
     except fslpath.PathError:

fsl/scripts/remove_ext.py

@@ -6,22 +6,22 @@
 #
 
 
-import sys
-import warnings
-
+import                   sys
 import fsl.utils.path as fslpath
 
-# See atlasq.py for explanation
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=FutureWarning)
-    import fsl.data.image as fslimage
-
 
 usage = """Usage: remove_ext <list of image paths to remove extension from>
 """.strip()
 
 
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+# This list is defined in the
+# fsl.data.image class, but are duplicated
+# here for performance (to avoid import of
+# nibabel/numpy/etc).
+exts = ['.nii.gz', '.nii',
+        '.img',    '.hdr',
+        '.img.gz', '.hdr.gz',
+        '.mnc',    '.mnc.gz']
 """List of file extensions that are removed by ``remove_ext``. """
 
 
@@ -40,7 +40,7 @@ def main(argv=None):
     removed = []
 
     for path in argv:
-        removed.append(fslpath.removeExt(path, ALLOWED_EXTENSIONS))
+        removed.append(fslpath.removeExt(path, exts))
 
     print(' '.join(removed))