From 9fa9ee4b016eb8befae1e087fe66fc80df8f6771 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 1 Sep 2016 15:25:13 +0100
Subject: [PATCH] Fix to ImageWrapper to workaround nibabel truncating trailing
dimensions of lenght 1.
---
fsl/data/imagewrapper.py | 36 +++++++++++++++++++++++++++++-------
1 file changed, 29 insertions(+), 7 deletions(-)
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 6acf0c1ea..79a5b0c37 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -79,7 +79,10 @@ class ImageWrapper(notifier.Notifier):
The ``ImageWrapper`` abstracts away trailing image dimensions of length 1.
This means that if the header for a NIFTI image specifies that the image
has four dimensions, but the fourth dimension is of length 1, you do not
- need to worry about indexing that fourth dimension.
+ need to worry about indexing that fourth dimension. However, all NIFTI
+ images will be presented as having at least three dimensions, so if your
+ image header specifies a third dimension of length 1, you will still
+ need provide an index of 0 for that dimensions, for all data accesses.
*Data range*
@@ -88,7 +91,7 @@ class ImageWrapper(notifier.Notifier):
In order to avoid the computational overhead of calculating the image data
range (its minimum/maximum values) when an image is first loaded in, an
``ImageWrapper`` incrementally updates the known image data range as data
- is accessed. The ``ImageWrapper`` keeps track of the image data _coverage_,
+ is accessed. The ``ImageWrapper`` keeps track of the image data *coverage*,
the portion of the image which has already been considered in the data
range calculation. When data from a region of the image not in the coverage
is accessed, the coverage is expanded to include this region. The coverage
@@ -204,11 +207,11 @@ class ImageWrapper(notifier.Notifier):
.. note:: The ``dataRange`` parameter is intended for situations where
- the image data range is known (e.g. it was calculated
- earlier, and the image is being re-loaded). If a
+ the image data range is known in advance (e.g. it was
+ calculated earlier, and the image is being re-loaded). If a
``dataRange`` is passed in, it will *not* be overwritten by
any range calculated from the data, unless the calculated
- data range is wider than the provided ``dataRange``.
+ data range is wider than the provided ``dataRange``.
"""
if dataRange is None:
@@ -332,6 +335,14 @@ class ImageWrapper(notifier.Notifier):
if isTuple:
sliceobj = sliceTupleToSliceObj(sliceobj)
+ # Truncate some dimensions from the
+ # slice object if it has too many
+ # (e.g. trailing dims of length 1).
+ ndims = len(self.__image.shape)
+
+ if len(sliceobj) > ndims:
+ sliceobj = sliceobj[:ndims]
+
# If the image has not been loaded
# into memory, we can use the nibabel
# ArrayProxy. Otheriwse if it is in
@@ -527,8 +538,19 @@ class ImageWrapper(notifier.Notifier):
log.debug('Getting image data: {}'.format(sliceobj))
- sliceobj = nib.fileslice.canonical_slicers(
- sliceobj, self.__image.shape)
+ if not isinstance(sliceobj, tuple):
+ sliceobj = (sliceobj,)
+
+ # Truncate some dimensions from the
+ # slice object if it has too many
+ # (e.g. trailing dims of length 1).
+ shape = self.__image.shape
+ ndims = len(shape)
+
+ if len(sliceobj) > ndims:
+ sliceobj = sliceobj[:ndims]
+
+ sliceobj = nib.fileslice.canonical_slicers(sliceobj, shape)
# TODO Cache 3D images for large 4D volumes,
# so you don't have to hit the disk?
--
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