diff --git a/fsl/data/image.py b/fsl/data/image.py
index c6f83c5988b1317ca1e2b691f499d5c339b10d26..c03618d856931ee96c0ab037ba530aa42d4c1a76 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -771,60 +771,64 @@ class Image(Nifti):
calcRange=True,
indexed=False,
threaded=False,
+ dataSource=None,
**kwargs):
"""Create an ``Image`` object with the given image data or file name.
- :arg image: A string containing the name of an image file to load,
- or a :mod:`numpy` array, or a :mod:`nibabel` image
- object.
-
- :arg name: A name for the image.
-
- :arg header: If not ``None``, assumed to be a
- :class:`nibabel.nifti1.Nifti1Header` or
- :class:`nibabel.nifti2.Nifti2Header` to be used as the
- image header. Not applied to images loaded from file,
- or existing :mod:`nibabel` images.
-
- :arg xform: A :math:`4\\times 4` affine transformation matrix
- which transforms voxel coordinates into real world
- coordinates. If not provided, and a ``header`` is
- provided, the transformation in the header is used.
- If neither a ``xform`` nor a ``header`` are provided,
- an identity matrix is used. If both a ``xform`` and a
- ``header`` are provided, the ``xform`` is used in
- preference to the header transformation.
-
- :arg loadData: If ``True`` (the default) the image data is loaded
- in to memory. Otherwise, only the image header
- information is read, and the image data is kept
- from disk. In either case, the image data is
- accessed through an :class:`.ImageWrapper` instance.
- The data may be loaded into memory later on via the
- :meth:`loadData` method.
-
- :arg calcRange: If ``True`` (the default), the image range is
- calculated immediately (vi a call to
- :meth:`calcRange`). Otherwise, the image range is
- incrementally updated as more data is read from memory
- or disk.
-
- :arg indexed: If ``True``, and the file is gzipped, it is opened
- using the :mod:`indexed_gzip` package. Otherwise the
- file is opened by ``nibabel``. Ignored if ``loadData``
- is ``True``.
-
- :arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
- separate thread for data range calculation. Defaults
- to ``False``. Ignored if ``loadData`` is ``True``.
+ :arg image: A string containing the name of an image file to load,
+ or a :mod:`numpy` array, or a :mod:`nibabel` image
+ object.
+
+ :arg name: A name for the image.
+
+ :arg header: If not ``None``, assumed to be a
+ :class:`nibabel.nifti1.Nifti1Header` or
+ :class:`nibabel.nifti2.Nifti2Header` to be used as the
+ image header. Not applied to images loaded from file,
+ or existing :mod:`nibabel` images.
+
+ :arg xform: A :math:`4\\times 4` affine transformation matrix
+ which transforms voxel coordinates into real world
+ coordinates. If not provided, and a ``header`` is
+ provided, the transformation in the header is used.
+ If neither a ``xform`` nor a ``header`` are provided,
+ an identity matrix is used. If both a ``xform`` and a
+ ``header`` are provided, the ``xform`` is used in
+ preference to the header transformation.
+
+ :arg loadData: If ``True`` (the default) the image data is loaded
+ in to memory. Otherwise, only the image header
+ information is read, and the image data is kept
+ from disk. In either case, the image data is
+ accessed through an :class:`.ImageWrapper` instance.
+ The data may be loaded into memory later on via the
+ :meth:`loadData` method.
+
+ :arg calcRange: If ``True`` (the default), the image range is
+ calculated immediately (vi a call to
+ :meth:`calcRange`). Otherwise, the image range is
+ incrementally updated as more data is read from memory
+ or disk.
+
+ :arg indexed: If ``True``, and the file is gzipped, it is opened
+ using the :mod:`indexed_gzip` package. Otherwise the
+ file is opened by ``nibabel``. Ignored if ``loadData``
+ is ``True``.
+
+ :arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
+ separate thread for data range calculation. Defaults
+ to ``False``. Ignored if ``loadData`` is ``True``.
+
+ :arg dataSource: If ``image`` is not a file name, this argument may be
+ used to specify the file from which the image was
+ loaded.
All other arguments are passed through to the ``nibabel.load`` function
(if it is called).
"""
- nibImage = None
- dataSource = None
- fileobj = None
+ nibImage = None
+ fileobj = None
if loadData:
indexed = False
@@ -1132,6 +1136,10 @@ class Image(Nifti):
filename = op.abspath(filename)
+ # make sure the extension is specified
+ if not looksLikeImage(filename):
+ filename = addExt(filename, mustExist=False)
+
log.debug('Saving {} to {}'.format(self.name, filename))
# If this Image is not managing its
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index c1530d493993253962493dd9776611145a888235..ba352c3e64f396b788f9b613383a55cbdb6a49c1 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -19,6 +19,7 @@ import os.path as op
import six
import nibabel as nib
+import fsl.utils.path as fslpath
import fsl.data.image as fslimage
@@ -54,7 +55,7 @@ class MGHImage(fslimage.Image):
name = op.basename(filename)
image = nib.load(image)
else:
- name = None
+ name = 'MGH image'
filename = None
data = image.get_data()
@@ -63,12 +64,26 @@ class MGHImage(fslimage.Image):
fslimage.Image.__init__(self,
data,
xform=affine,
- name=name)
+ name=name,
+ dataSource=filename)
if filename is not None:
self.setMeta('mghImageFile', filename)
+ def save(self, filename=None):
+ """Overrides :meth:`.Image.save`. If a ``filename`` is not provided,
+ converts the original (MGH) file name into a NIFTI filename, before
+ passing it to the :meth:`.Image.save` method.
+ """
+ if filename is None:
+ filename = self.dataSource
+
+ filename = fslpath.removeExt(filename, ALLOWED_EXTENSIONS)
+
+ return fslimage.Image.save(self, filename)
+
+
@property
def mghImageFile(self):
"""If this ``MGHImage`` was loaded from a file, returns the file