From 7bdc10725bbd12f4a329e5c294fc3d96404d0feb Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 11 Feb 2025 12:01:14 +0000
Subject: [PATCH] ENH: Add support for "scaled" coordinate system to getAffine
- scaled voxels without L/R flip.
---
fsl/data/image.py | 80 +++++++++++++++++++++++++++++------------------
1 file changed, 50 insertions(+), 30 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 2d698177..354be148 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -210,8 +210,12 @@ class Nifti(notifier.Notifier, meta.Meta):
- The ``fsl`` coordinate system, where voxel coordinates are scaled by
the ``pixdim`` values in the NIFTI header, and the X axis is inverted
- if the voxel-to-world affine has a positive determinant.
+ if the voxel-to-world affine has a positive determinant. The
+ coordinates ``(0, 0, 0)`` correspond to the corner of voxel
+ ``(0, 0, 0)``.
+ - The ``scaled`` coordinate system, where voxel coordinates are scaled by
+ the ``pixdim`` values in the NIFTI header.
The :meth:`getAffine` method is a simple means of acquiring an affine
which will transform between any of these coordinate systems.
@@ -435,7 +439,7 @@ class Nifti(notifier.Notifier, meta.Meta):
def generateAffines(voxToWorldMat, shape, pixdim):
"""Called by :meth:`__init__`, and the :meth:`voxToWorldMat` setter.
Generates and returns a dictionary containing affine transformations
- between the ``voxel``, ``fsl``, and ``world`` coordinate
+ between the ``voxel``, ``fsl``, ``scaled``, and ``world`` coordinate
systems. These affines are accessible via the :meth:`getAffine`
method.
@@ -454,29 +458,43 @@ class Nifti(notifier.Notifier, meta.Meta):
import numpy.linalg as npla
- affines = {}
- shape = list(shape[ :3])
- pixdim = list(pixdim[:3])
- voxToScaledVoxMat = np.diag(pixdim + [1.0])
- isneuro = npla.det(voxToWorldMat) > 0
+ affines = {}
+ shape = list(shape[ :3])
+ pixdim = list(pixdim[:3])
+ voxToScaledMat = np.diag(pixdim + [1.0])
+ voxToFSLMat = np.array(voxToScaledMat)
+ isneuro = npla.det(voxToWorldMat) > 0
if isneuro:
- x = (shape[0] - 1) * pixdim[0]
- flip = affine.scaleOffsetXform([-1, 1, 1],
- [ x, 0, 0])
- voxToScaledVoxMat = affine.concat(flip, voxToScaledVoxMat)
-
- affines['fsl', 'fsl'] = np.eye(4)
- affines['voxel', 'voxel'] = np.eye(4)
- affines['world', 'world'] = np.eye(4)
- affines['voxel', 'world'] = voxToWorldMat
- affines['world', 'voxel'] = affine.invert(voxToWorldMat)
- affines['voxel', 'fsl'] = voxToScaledVoxMat
- affines['fsl', 'voxel'] = affine.invert(voxToScaledVoxMat)
- affines['fsl', 'world'] = affine.concat(affines['voxel', 'world'],
- affines['fsl', 'voxel'])
- affines['world', 'fsl'] = affine.concat(affines['voxel', 'fsl'],
- affines['world', 'voxel'])
+ x = (shape[0] - 1) * pixdim[0]
+ flip = affine.scaleOffsetXform([-1, 1, 1],
+ [ x, 0, 0])
+ voxToFSLMat = affine.concat(flip, voxToFSLMat)
+
+ affines['voxel', 'voxel'] = np.eye(4)
+ affines['voxel', 'scaled'] = voxToFSLMat
+ affines['voxel', 'fsl'] = voxToScaledMat
+ affines['voxel', 'world'] = voxToWorldMat
+
+ affines['scaled', 'scaled'] = np.eye(4)
+ affines['scaled', 'voxel'] = affine.invert(voxToScaledMat)
+ affines['scaled', 'fsl'] = affine.concat(affines['voxel', 'fsl'],
+ affines['scaled', 'voxel'])
+ affines['scaled', 'world'] = affine.concat(affines['voxel', 'world'],
+ affines['scaled', 'voxel'])
+
+ affines['fsl', 'fsl'] = np.eye(4)
+ affines['fsl', 'voxel'] = affine.invert(voxToFSLMat)
+ affines['fsl', 'scaled'] = affine.invert(affines['scaled', 'fsl'])
+ affines['fsl', 'world'] = affine.concat(affines['voxel', 'world'],
+ affines['fsl', 'voxel'])
+
+ affines['world', 'world'] = np.eye(4)
+ affines['world', 'voxel'] = affine.invert(voxToWorldMat)
+ affines['world', 'scaled'] = affine.concat(affines['voxel', 'scaled'],
+ affines['world', 'voxel'])
+ affines['world', 'fsl'] = affine.concat(affines['voxel', 'fsl'],
+ affines['world', 'voxel'])
return affines, isneuro
@@ -515,9 +533,9 @@ class Nifti(notifier.Notifier, meta.Meta):
return from_, to
if from_ is not None: froms = [from_]
- else: froms = ['voxel', 'fsl', 'world']
+ else: froms = ['voxel', 'scaled', 'fsl', 'world']
if to is not None: tos = [to]
- else: tos = ['voxel', 'fsl', 'world']
+ else: tos = ['voxel', 'scaled', 'fsl', 'world']
for from_, to in it.product(froms, tos):
@@ -590,7 +608,7 @@ class Nifti(notifier.Notifier, meta.Meta):
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))
+ else: raise RuntimeError(f'Unrecognised header: {self.header}')
@property
@@ -724,6 +742,8 @@ class Nifti(notifier.Notifier, meta.Meta):
sform/qform
- ``'fsl'``: The FSL coordinate system (scaled voxels, with a
left-right flip if the sform/qform has a positive determinant)
+ - ``'scaled'``: Scaled voxel coordinate system (equivalent to
+ ``'fsl'`` without the flip).
:arg from_: Source coordinate system
:arg to: Destination coordinate system
@@ -732,11 +752,11 @@ class Nifti(notifier.Notifier, meta.Meta):
from_ = from_.lower()
to = to .lower()
- if from_ not in ('voxel', 'fsl', 'world') or \
- to not in ('voxel', 'fsl', 'world'):
+ if from_ not in ('voxel', 'scaled', 'fsl', 'world') or \
+ to not in ('voxel', 'scaled', 'fsl', 'world'):
raise ValueError('Invalid source/reference spaces: "{}" -> "{}".'
- 'Recognised spaces are "voxel", "fsl", and '
- '"world"'.format(from_, to))
+ 'Recognised spaces are "voxel", "fsl", "scaled", '
+ 'and "world"'.format(from_, to))
return np.copy(self.__affines[from_, to])
--
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