From 64ac4c25c908c13ccdcd7331897a73c31b0f6549 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Sun, 20 Nov 2016 14:11:14 +0000
Subject: [PATCH] Support for NIFTI2
---
fsl/data/image.py | 69 ++++++++++++++++++++++++++++------------
fsl/data/imagewrapper.py | 5 +--
2 files changed, 52 insertions(+), 22 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 1ff4ee748..dbb9d11f4 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -6,10 +6,8 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :class:`Nifti` and :class:`Image` classes, for
-representing 3D/4D NIFI1 images. The ``nibabel`` package is used for file
-I/O.
-
-.. note:: Support for ANALYZE75 and NIFTI2 images has not been tested.
+representing 3D/4D NIFTI1 and NIFTI2 images. The ``nibabel`` package is used
+for file I/O.
It is very easy to load a NIFTI image::
@@ -66,7 +64,7 @@ class Nifti(object):
================= ====================================================
- ``header`` The :mod:`nibabel.Nifti1Header` object.
+ ``header`` The :mod:`nibabel` NIFTI header object.
``shape`` A list/tuple containing the number of voxels along
each image dimension.
``pixdim`` A list/tuple containing the length of one voxel
@@ -90,10 +88,18 @@ class Nifti(object):
def __init__(self, header):
"""Create a ``Nifti`` object.
- :arg header: A :class:`nibabel.nifti1.Nifti1Header` to be used as
- the image header.
+ :arg header: A :class:`nibabel.nifti1.Nifti1Header` or
+ :class:`nibabel.nifti2.Nifti2Header` to be used as the
+ image header.
"""
+ import nibabel as nib
+
+ # Nifti2Header is a sub-class of Nifti1Header,
+ # so we don't need to test for it
+ if not isinstance(header, nib.nifti1.Nifti1Header):
+ raise ValueError('Unrecognised header: {}'.format(header))
+
header = header.copy()
origShape, shape, pixdim = self.__determineShape(header)
@@ -112,6 +118,20 @@ class Nifti(object):
self.voxToWorldMat = voxToWorldMat
self.worldToVoxMat = worldToVoxMat
+
+ @property
+ def niftiVersion(self):
+ """Returns the NIFTI file version - either ``1`` or ``2``. """
+
+ import nibabel as nib
+
+ # nib.Nifti2 is a subclass of Nifti1,
+ # so we have to check it first.
+ if isinstance(self.header, nib.nifti2.Nifti2Header): return 2
+ elif isinstance(self.header, nib.nifti1.Nifti1Header): return 1
+
+ else: raise RuntimeError('Unrecognised header: {}'.format(self.header))
+
def __determineTransform(self, header):
"""Called by :meth:`__init__`. Figures out the voxel-to-world
@@ -185,7 +205,7 @@ class Nifti(object):
def mapIndices(self, sliceobj):
"""Adjusts the given slice object so that it may be used to index the
- underlying ``nibabel.Nifti1Image`` object.
+ underlying ``nibabel`` NIFTI image object.
See the :meth:`__determineShape` method.
@@ -312,9 +332,10 @@ class Nifti(object):
class Image(Nifti, notifier.Notifier):
- """Class which represents a 3D/4D NIFTI image. Internally, the image
- is loaded/stored using a :mod:`nibabel.nifti1.Nifti1Image`, and data
- access managed by a :class:`.ImageWrapper`.
+ """Class which represents a 3D/4D NIFTI image. Internally, the image is
+ loaded/stored using a :mod:`nibabel.nifti1.Nifti1Image` or
+ :mod:`nibabel.nifti2.Nifti2Image`, and data access managed by a
+ :class:`.ImageWrapper`.
In addition to the attributes added by the :meth:`Nifti.__init__` method,
@@ -330,7 +351,7 @@ class Image(Nifti, notifier.Notifier):
file from where it was loaded, or some other string
describing its origin.
- ``nibImage`` A reference to the ``nibabel.Nifti1Image`` object.
+ ``nibImage`` A reference to the ``nibabel`` NIFTI image object.
``saveState`` A boolean value which is ``True`` if this image is
saved to disk, ``False`` if it is in-memory, or has
@@ -380,8 +401,9 @@ class Image(Nifti, notifier.Notifier):
:arg name: A name for the image.
- :arg header: If not ``None``, assumed to be a
- :class:`nibabel.nifti1.Nifti1Header` to be used as the
+ :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.
@@ -454,7 +476,10 @@ class Image(Nifti, notifier.Notifier):
if header is not None: xform = header.get_best_affine()
elif xform is None: xform = np.identity(4)
-
+
+ # We default to NIFTI1 and not
+ # NIFTI2, because the rest of
+ # FSL is not yet NIFTI2 compatible.
nibImage = nib.nifti1.Nifti1Image(image,
xform,
header=header)
@@ -538,7 +563,7 @@ class Image(Nifti, notifier.Notifier):
@property
def nibImage(self):
- """Returns a reference to the ``nibabel.nifti1.Nifti1Image`` instance.
+ """Returns a reference to the ``nibabel`` NIFTI image instance.
"""
return self.__nibImage
@@ -844,7 +869,7 @@ def defaultExt():
def loadIndexedImageFile(filename):
"""Loads the given image file using ``nibabel`` and ``indexed_gzip``.
- Returns a tuple containing the ``nibabel.Nifti1Image``, and the open
+ Returns a tuple containing the ``nibabel`` NIFTI image, and the open
``IndexedGzipFile`` handle.
"""
@@ -853,13 +878,17 @@ def loadIndexedImageFile(filename):
log.debug('Loading {} using indexed gzip'.format(filename))
- fobj = igzip.SafeIndexedGzipFile(
+ # guessed_image_type returns a
+ # ref to one of the Nifti1Image
+ # or Nifti2Image classes.
+ ftype = nib.loadsave.guessed_image_type(filename)
+ fobj = igzip.SafeIndexedGzipFile(
filename=filename,
spacing=4194304,
readbuf_size=1048576)
- fmap = nib.Nifti1Image.make_file_map()
+ fmap = ftype.make_file_map()
fmap['image'].fileobj = fobj
- image = nib.Nifti1Image.from_file_map(fmap)
+ image = ftype.from_file_map(fmap)
return image, fobj
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index a4a08a0ec..cebdfee9e 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -62,7 +62,8 @@ class ImageWrapper(notifier.Notifier):
*In memory or on disk?*
The image data will be kept on disk, and accessed through the
- ``nibabel.Nifti1Image.dataobj`` array proxy, if:
+ ``nibabel.Nifti1Image.dataobj`` (or ``nibabel.Nifti2Image.dataobj``) array
+ proxy, if:
- The ``loadData`` parameter to :meth:`__init__` is ``False``.
- The :meth:`loadData` method never gets called.
@@ -134,7 +135,7 @@ class ImageWrapper(notifier.Notifier):
threaded=False):
"""Create an ``ImageWrapper``.
- :arg image: A ``nibabel.Nifti1Image``.
+ :arg image: A ``nibabel.Nifti1Image`` or ``nibabel.Nifti2Image``.
:arg name: A name for this ``ImageWrapper``, solely used for
debug log messages.
--
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