From e30514af2579c311aa351c539e15d4d029f785ff Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 5 Jan 2017 14:18:44 +0000
Subject: [PATCH] Nifti class explicitly supports ANALYZE images
---
fsl/data/constants.py | 4 +++
fsl/data/image.py | 81 ++++++++++++++++++++++++++++++++++---------
2 files changed, 69 insertions(+), 16 deletions(-)
diff --git a/fsl/data/constants.py b/fsl/data/constants.py
index bb26977d1..d257945ec 100644
--- a/fsl/data/constants.py
+++ b/fsl/data/constants.py
@@ -81,6 +81,10 @@ NIFTI_XFORM_MNI_152 = 4
"""MNI 152 normalized coordinates."""
+NIFTI_XFORM_ANALYZE = 5
+"""Code which indicates that this is an ANALYZE image, not a NIFTI image. """
+
+
# NIFTI file intent codes
NIFTI_INTENT_NONE = 0
NIFTI_INTENT_CORREL = 2
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 5f1ad22c4..8a6aa7ae2 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -64,20 +64,52 @@ class Nifti(object):
================= ====================================================
- ``header`` The :mod:`nibabel` NIFTI header object.
+ ``header`` The :mod:`nibabel` NIFTI1/NIFTI2/Analyze 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
- along each image dimension.
+ along each image dimension.
+
``voxToWorldMat`` A 4*4 array specifying the affine transformation
for transforming voxel coordinates into real world
coordinates.
+
``worldToVoxMat`` A 4*4 array specifying the affine transformation
for transforming real world coordinates into voxel
coordinates.
- ``intent`` The NIFTI intent code specified in the header.
+
+ ``intent`` The NIFTI intent code specified in the header (or
+ :attr:`.constants.NIFTI_INTENT_NONE` for Analyze
+ images).
================= ====================================================
+
+ A ``Nifti`` instance expects to be passed either a
+ ``nibabel.nifti1.Nifti1Header`` or a ``nibabel.nifti2.Nifti2Header``, but
+ can als encapsulate a ``nibabel.analyze.AnalyzeHeader``. In this case:
+
+ - The image voxel orientation is assumed to be R->L, P->A, I->S.
+
+ - The affine will be set to a diagonal matrix with the header pixdims as
+ its elements (with the X pixdim negated), and an offset specified by
+ the ANALYZE ``origin`` fields. Construction of the affine is handled
+ by ``nibabel``.
+
+ - The :meth:`niftiVersion` method will return ``0``.
+
+ - The :meth:`getXFormCode` method will return
+ :attr:`.constants.NIFTI_XFORM_ANALYZE`.
+
+
+ .. warning:: The ``header`` field may either be a ``nifti1``, ``nifti2``,
+ or ``analyze`` header object. Make sure to take this into
+ account if you are writing code that should work with all
+ three. Use the :meth:`niftiVersion` property if you need to
+ know what type of image you are dealing with.
+
.. note:: The ``shape`` attribute may not precisely match the image shape
as reported in the NIFTI header, because trailing dimensions of
@@ -85,19 +117,22 @@ class Nifti(object):
:meth:`mapIndices` methods.
"""
+
def __init__(self, header):
"""Create a ``Nifti`` object.
- :arg header: A :class:`nibabel.nifti1.Nifti1Header` or
- :class:`nibabel.nifti2.Nifti2Header` to be used as the
- image header.
+ :arg header: A :class:`nibabel.nifti1.Nifti1Header`,
+ :class:`nibabel.nifti2.Nifti2Header`, or
+ ``nibabel.analyze.AnalyzeHeader`` 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):
+ # and Nifti1Header a sub-class of AnalyzeHeader,
+ # so we only need to test for the latter.
+ if not isinstance(header, nib.analyze.AnalyzeHeader):
raise ValueError('Unrecognised header: {}'.format(header))
header = header.copy()
@@ -121,14 +156,21 @@ class Nifti(object):
@property
def niftiVersion(self):
- """Returns the NIFTI file version - either ``1`` or ``2``. """
+ """Returns the NIFTI file version:
+
+ - ``0`` for ANALYZE
+ - ``1`` for NIFTI1
+ - ``2`` for NIFTI2
+ """
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
+ # nib.Nifti2 is a subclass of Nifti1,
+ # and Nifti1 a subclass of Analyze,
+ # so we have to check in order
+ if isinstance(self.header, nib.nifti2.Nifti2Header): return 2
+ elif isinstance(self.header, nib.nifti1.Nifti1Header): return 1
+ elif isinstance(self.header, nib.analyze.AnalyzeHeader): return 0
else: raise RuntimeError('Unrecognised header: {}'.format(self.header))
@@ -138,12 +180,15 @@ class Nifti(object):
coordinate transformation matrix that is associated with this
``Nifti`` instance.
"""
-
+
# We have to treat FSL/FNIRT images
# specially, as FNIRT clobbers the
# sform section of the NIFTI header
# to store other data.
intent = header.get('intent_code', -1)
+ qform = header.get('qform_code', -1)
+ sform = header.get('sform_code', -1)
+
if intent in (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
constants.FSL_DCT_COEFFICIENTS,
@@ -161,12 +206,12 @@ class Nifti(object):
# corresponds to world location (0, 0, 0).
# This goes against the NIFTI spec - it
# should just be a straight scaling matrix.
- elif header['qform_code'] == 0 and header['sform_code'] == 0:
+ elif qform == 0 and sform == 0:
pixdims = header.get_zooms()
voxToWorldMat = transform.scaleOffsetXform(pixdims, 0)
# Otherwise we let nibabel decide
- # which transform to use.
+ # which transform to use.
else:
voxToWorldMat = np.array(header.get_best_affine())
@@ -238,8 +283,12 @@ class Nifti(object):
- :data:`~.constants.NIFTI_XFORM_ALIGNED_ANAT`
- :data:`~.constants.NIFTI_XFORM_TALAIRACH`
- :data:`~.constants.NIFTI_XFORM_MNI_152`
+ - :data:`~.constants.NIFTI_XFORM_ANALYZE`
"""
+ if self.niftiVersion == 0:
+ return constants.NIFTI_XFORM_ANALYZE
+
if code == 'sform' : code = 'sform_code'
elif code == 'qform' : code = 'qform_code'
elif code is not None:
--
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