From e20fff6eea2f4729bf6ab1243d9c690d4763e6b9 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 17 Aug 2016 11:58:12 +0100
Subject: [PATCH] Nifti1 renamed to Nifti. Intent is to have it support both
Nifti1 and Nifti2.
---
fsl/data/constants.py | 4 ++--
fsl/data/image.py | 50 ++++++++++++++++++++---------------------
fsl/data/tensorimage.py | 4 ++--
3 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/fsl/data/constants.py b/fsl/data/constants.py
index 8e56778bc..bb26977d1 100644
--- a/fsl/data/constants.py
+++ b/fsl/data/constants.py
@@ -20,8 +20,8 @@ voxel or world space:
ORIENT_UNKNOWN
-These constants relate to the *space* in which a NIFTI1 image is assumed to be
-(i.e. the transformed coordinate space); they are defined in the NIFTI1
+These constants relate to the *space* in which a NIFTI image is assumed to be
+(i.e. the transformed coordinate space); they are defined in the NIFTI
specification:
.. autosummary::
diff --git a/fsl/data/image.py b/fsl/data/image.py
index a4e210b67..696ebd855 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -5,11 +5,11 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""This module provides the :class:`Nifti1` and :class:`Image` classes, for
-representing 3D/4D NIFTI1 images. The ``nibabel`` package is used for file
+"""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:: Currently, only NIFTI1 images are supported.
+.. note:: Support for ANALYZE75 and NIFTI2 images has not been tested.
It is very easy to load a NIFTI image::
@@ -49,15 +49,15 @@ import fsl.data.imagewrapper as imagewrapper
log = logging.getLogger(__name__)
-class Nifti1(object):
- """The ``Nifti1`` class is intended to be used as a base class for
- things which either are, or are associated with, a NIFTI1 image.
- The ``Nifti1`` class is intended to represent information stored in
- the header of a NIFTI1 file - if you want to load the data from
+class Nifti(object):
+ """The ``Nifti`` class is intended to be used as a base class for
+ things which either are, or are associated with, a NIFTI image.
+ The ``Nifti`` class is intended to represent information stored in
+ the header of a NIFTI file - if you want to load the data from
a file, use the :class:`Image` class instead.
- When a ``Nifti1`` instance is created, it adds the following attributes
+ When a ``Nifti`` instance is created, it adds the following attributes
to itself:
@@ -78,13 +78,13 @@ class Nifti1(object):
.. note:: The ``shape`` attribute may not precisely match the image shape
- as reported in the NIFTI1 header, because trailing dimensions of
+ as reported in the NIFTI header, because trailing dimensions of
size 1 are squeezed out. See the :meth:`__determineShape` and
:meth:`mapIndices` methods.
"""
def __init__(self, header):
- """Create a ``Nifti1`` object.
+ """Create a ``Nifti`` object.
:arg header: A :class:`nibabel.nifti1.Nifti1Header` to be used as
the image header.
@@ -112,7 +112,7 @@ class Nifti1(object):
def __determineTransform(self, header):
"""Called by :meth:`__init__`. Figures out the voxel-to-world
coordinate transformation matrix that is associated with this
- ``Nifti1`` instance.
+ ``Nifti`` instance.
"""
# We have to treat FSL/FNIRT images
@@ -135,7 +135,7 @@ class Nifti1(object):
# n.b. For images like this, nibabel returns
# a scaling matrix where the centre voxel
# corresponds to world location (0, 0, 0).
- # This goes against the NIFTI1 spec - it
+ # This goes against the NIFTI spec - it
# should just be a straight scaling matrix.
elif header['qform_code'] == 0 or header['sform_code'] == 0:
pixdims = header.get_zooms()
@@ -211,7 +211,7 @@ class Nifti1(object):
def getXFormCode(self, code=None):
- """This method returns the code contained in the NIFTI1 header,
+ """This method returns the code contained in the NIFTI header,
indicating the space to which the (transformed) image is oriented.
The ``code`` parameter may be either ``sform`` (the default) or
@@ -259,7 +259,7 @@ class Nifti1(object):
@memoize.Instanceify(memoize.memoize)
def isNeurological(self):
- """Returns ``True`` if it looks like this ``Nifti1`` object is in
+ """Returns ``True`` if it looks like this ``Nifti`` object is in
neurological orientation, ``False`` otherwise. This test is purely
based on the determinant of the voxel-to-mm transformation matrix -
if it has a positive determinant, the image is assumed to be in
@@ -316,13 +316,13 @@ class Nifti1(object):
return code
-class Image(Nifti1, notifier.Notifier):
- """Class which represents a 3D/4D NIFTI1 image. Internally, the image
+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`.
- In addition to the attributes added by the :meth:`Nifti1.__init__` method,
+ In addition to the attributes added by the :meth:`Nifti.__init__` method,
the following attributes/properties are present on an ``Image`` instance
as properties (https://docs.python.org/2/library/functions.html#property):
@@ -485,7 +485,7 @@ class Image(Nifti1, notifier.Notifier):
else:
name = 'Nibabel image'
- Nifti1.__init__(self, nibImage.get_header())
+ Nifti.__init__(self, nibImage.get_header())
self.name = name
self.__dataSource = dataSource
@@ -572,7 +572,7 @@ class Image(Nifti1, notifier.Notifier):
else: drange = self.__imageWrapper.dataRange
# Fall back to the cal_min/max
- # fields in the NIFTI1 header
+ # fields in the NIFTI header
# if we don't yet know anything
# about the image data range.
if drange[0] is None or drange[1] is None:
@@ -760,11 +760,11 @@ below.
"""
-EXTENSION_DESCRIPTIONS = ['Compressed NIFTI1 images',
- 'NIFTI1 images',
+EXTENSION_DESCRIPTIONS = ['Compressed NIFTI images',
+ 'NIFTI images',
'ANALYZE75 images',
- 'NIFTI1/ANALYZE75 headers',
- 'Compressed NIFTI1/ANALYZE75 images',
+ 'NIFTI/ANALYZE75 headers',
+ 'Compressed NIFTI/ANALYZE75 images',
'Compressed images']
"""Descriptions for each of the extensions in :data:`ALLOWED_EXTENSIONS`. """
@@ -816,7 +816,7 @@ def addExt(prefix, mustExist=True):
def loadIndexedImageFile(filename):
"""Loads the given image file using ``nibabel`` and ``indexed_gzip``.
- Returns a tuple containing the ``Nifti1Image``, and the open
+ Returns a tuple containing the ``nibabel.Nifti1Image``, and the open
``IndexedGzipFile`` handle.
"""
diff --git a/fsl/data/tensorimage.py b/fsl/data/tensorimage.py
index 0cee5380c..013d1df54 100644
--- a/fsl/data/tensorimage.py
+++ b/fsl/data/tensorimage.py
@@ -87,7 +87,7 @@ def isPathToTensorData(path):
return getTensorDataPrefix(path) is not None
-class TensorImage(fslimage.Nifti1):
+class TensorImage(fslimage.Nifti):
"""The ``TensorImage`` class is able to load and encapsulate the diffusion
tensor data generated by the FSL ``dtifit`` tool.
"""
@@ -133,7 +133,7 @@ class TensorImage(fslimage.Nifti1):
self.__l2 = fslimage.Image(paths['l2'])
self.__l3 = fslimage.Image(paths['l3'])
- fslimage.Nifti1.__init__(self, self.__l1.header)
+ fslimage.Nifti.__init__(self, self.__l1.header)
l1dir = op.abspath(op.dirname(paths['l1']))
--
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