Merge branch 'rf/nifti-xform-template-other' into 'master'

Rf/nifti xform template other

See merge request fsl/fslpy!337

CHANGELOG.rst

@@ -3,6 +3,18 @@ order.
 
 
 
+3.9.2 (Friday 20th May 2022)
+----------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Added the :data:`.NIFTI_XFORM_TEMPLATE_OTHER` identifier, an extension to the
+  NIfTI standard (!337).
+
+
 3.9.1 (Friday 13th May 2022)
 ----------------------------
 

fsl/data/constants.py

@@ -30,6 +30,7 @@ specification:
    NIFTI_XFORM_ALIGNED_ANAT
    NIFTI_XFORM_TALAIRACH
    NIFTI_XFORM_MNI_152
+   NIFTI_XFORM_TEMPLATE_OTHER
 """
 
 
@@ -81,7 +82,14 @@ NIFTI_XFORM_MNI_152      = 4
 """MNI 152 normalized coordinates."""
 
 
-NIFTI_XFORM_ANALYZE      = 5
+NIFTI_XFORM_TEMPLATE_OTHER = 5
+"""Coordinates aligned to some template that is not MNI152 or Talairach.
+
+See https://www.nitrc.org/forum/message.php?msg_id=26394 for details.
+ """
+
+
+NIFTI_XFORM_ANALYZE      = 6
 """Code which indicates that this is an ANALYZE image, not a NIFTI image. """
 
 

fsl/data/image.py

@@ -825,6 +825,7 @@ class Nifti(notifier.Notifier, meta.Meta):
                     - :data:`~.constants.NIFTI_XFORM_ALIGNED_ANAT`
                     - :data:`~.constants.NIFTI_XFORM_TALAIRACH`
                     - :data:`~.constants.NIFTI_XFORM_MNI_152`
+                    - :data:`~.constants.NIFTI_XFORM_TEMPLATE_OTHER`
                     - :data:`~.constants.NIFTI_XFORM_ANALYZE`
         """
 
@@ -852,8 +853,9 @@ class Nifti(notifier.Notifier, meta.Meta):
             if   sform_code != constants.NIFTI_XFORM_UNKNOWN: code = sform_code
             elif qform_code != constants.NIFTI_XFORM_UNKNOWN: code = qform_code
 
-        # Invalid values
-        if code not in range(5):
+        # Invalid code (the maxmimum NIFTI_XFORM_*
+        # code value is 5 at present)
+        if code not in range(6):
             code = constants.NIFTI_XFORM_UNKNOWN
 
         return int(code)

fsl/wrappers/wrapperutils.py

@@ -259,8 +259,9 @@ def applyArgStyle(style=None,
     conventions, e.g. ``-a val``, ``--arg=val``, ``-a val1 val2``,
     ``--arg=val1,val2``.
 
-    The ``style`` and ``valsep`` (and ``charstyle`` and ``charsep``) arguments
-    control how key-value pairs are converted into command-line options:
+    The ``style`` and ``valsep`` options (and ``charstyle`` and ``charsep``,
+    for single-character/short arguments) control how key-value pairs are
+    converted into command-line options:
 
 
     =========  ==========  ===========================
@@ -323,11 +324,15 @@ def applyArgStyle(style=None,
                     one of ``' '``, ``','`` or ``'"'``. Defaults to ``' '``
                     if ``'=' not in style``, ``','`` otherwise.
 
-    :arg singlechar_args: If ``True``, equivalent to ``charstyle='-'``.
+    :arg singlechar_args: If ``True``, equivalent to ``charstyle='-'``. This
+                          argument remains for compatibility, but may be
+                          removed in a future version.
 
     :arg kwargs: Arguments to be converted into command-line options.
 
-    :returns:    A list containing the generated command-line options.
+    :returns:    A sequence containing the generated command-line options, the
+                 same as what ``shlex.split`` would generate for a properly
+                 quoted string.
     """
 
     if style is None:
@@ -373,13 +378,7 @@ def applyArgStyle(style=None,
         if style in ('--', '--='): return f'--{arg}'
         else:                      return f'-{arg}'
 
-    # Formt the argument value. Always returns
-    # a sequence. We don't add quotes around
-    # values - instead we just ensure that
-    # arguments+values are grouped correctly in
-    # the final result (the same as what
-    # shlex.split would generate for a properly
-    # quoted string).
+    # Formt the argument value.
     def fmtval(val, sep):
         if isinstance(val, abc.Sequence) and (not isinstance(val, str)):
             val = [str(v) for v in val]
@@ -389,7 +388,7 @@ def applyArgStyle(style=None,
         else:
             return [str(val)]
 
-    # Format the argument and value together.
+    # Combine the argument and value together.
     # val is assumed to be a sequence.
     def fmtargval(arg, val, style):
         # if '=' in style, val will