From 1f55df41bc5e3e263b5046f099ab0e060bf3e6d4 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 11 Feb 2025 12:30:10 +0000
Subject: [PATCH] MNT: Deprecate unfortunately named voxToScaledVoxMat and
scaledVoxToVoxMat methods
---
fsl/data/image.py | 11 +++++++----
fsl/transform/flirt.py | 12 ++++++------
2 files changed, 13 insertions(+), 10 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 4cd9d02a..54d74cfa 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -815,9 +815,10 @@ class Nifti(notifier.Notifier, meta.Meta):
@property
+ @deprecated.deprecated('3.22.0', '4.0.0', 'Use getAffine instead')
def voxToScaledVoxMat(self):
- """Returns a transformation matrix which transforms from voxel
- coordinates into scaled voxel coordinates, with a left-right flip
+ """Returns a transformation matrix which transforms from ``voxel``
+ coordinates into ``fsl`` coordinates, with a left-right flip
if the image appears to be stored in neurological order.
See http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#What_is_the\
@@ -828,9 +829,11 @@ class Nifti(notifier.Notifier, meta.Meta):
@property
+ @deprecated.deprecated('3.22.0', '4.0.0', 'Use getAffine instead')
def scaledVoxToVoxMat(self):
- """Returns a transformation matrix which transforms from scaled voxels
- into voxels, the inverse of the :meth:`voxToScaledVoxMat` transform.
+ """Returns a transformation matrix which transforms from ``fsl``
+ coordinates into ``voxel`` coordinates, the inverse of the
+ :meth:`voxToScaledVoxMat` transform.
"""
return self.getAffine('fsl', 'voxel')
diff --git a/fsl/transform/flirt.py b/fsl/transform/flirt.py
index 5acd4b6f..a5ac25c0 100644
--- a/fsl/transform/flirt.py
+++ b/fsl/transform/flirt.py
@@ -138,15 +138,15 @@ def sformToFlirtMatrix(srcImage, refImage, srcXform=None):
:attr:`.Nifti.voxToWorldMat`
"""
- srcScaledVoxToVoxMat = srcImage.scaledVoxToVoxMat
- srcVoxToWorldMat = srcImage.voxToWorldMat
- refWorldToVoxMat = refImage.worldToVoxMat
- refVoxToScaledVoxMat = refImage.voxToScaledVoxMat
+ srcFSLToVoxMat = srcImage.getAffine('fsl', 'voxel')
+ srcVoxToWorldMat = srcImage.getAffine('voxel', 'world')
+ refWorldToVoxMat = refImage.getAffine('world', 'voxel')
+ refVoxToFSLMat = refImage.getAffine('voxel', 'fsl')
if srcXform is not None:
srcVoxToWorldMat = srcXform
- return concat(refVoxToScaledVoxMat,
+ return concat(refVoxToFSLMat,
refWorldToVoxMat,
srcVoxToWorldMat,
- srcScaledVoxToVoxMat)
+ srcFSLToVoxMat)
--
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