From d92f8e0ff8ae89761a61169cb4859a00c1c048da Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 2 Dec 2019 09:36:08 +0000
Subject: [PATCH] BF: Fix up adjust method
---
fsl/data/image.py | 26 +++++++++++++++-----------
fsl/transform/affine.py | 2 +-
2 files changed, 16 insertions(+), 12 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 7eaf53f4f..39f1f7fac 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -864,22 +864,26 @@ class Nifti(notifier.Notifier, meta.Meta):
raise ValueError('Exactly one of pixdim or '
'shape must be specified')
+ if shape is not None: ndim = len(shape)
+ else: ndim = len(pixdim)
+
+ # We only allow adjustment of
+ # the spatial dimensions
+ if ndim != 3:
+ raise ValueError('Three dimensions must be specified')
+
+ oldShape = np.array(self.shape[ :ndim])
+ oldPixdim = np.array(self.pixdim[:ndim])
newShape = shape
newPixdim = pixdim
# if pixdims were specified,
- # convert them into a shape
+ # convert them into a shape,
+ # and vice versa
if newPixdim is not None:
- npixdim = len(newPixdim)
- newPixdim = np.array(newPixdim)
- oldShape = np.array(self.shape[ :npixdim])
- oldPixdim = np.array(self.pixdim[:npixdim])
- newShape = oldShape * (oldPixdim / newPixdim)
-
- # We only allow adjustment of
- # the spatial dimensions
- if len(newShape) != 3:
- raise ValueError('Three dimensions must be specified')
+ newShape = oldShape * (oldPixdim / newPixdim)
+ else:
+ newPixdim = oldPixdim * (oldShape / newShape)
# Rescale the voxel-to-world affine
xform = affine.rescale(oldShape, newShape, origin)
diff --git a/fsl/transform/affine.py b/fsl/transform/affine.py
index 92a16ddd4..c7fb71f2a 100644
--- a/fsl/transform/affine.py
+++ b/fsl/transform/affine.py
@@ -588,7 +588,7 @@ def rmsdev(T1, T2, R=None, xc=None):
def rescale(oldShape, newShape, origin=None):
"""Calculates an affine matrix to use for resampling.
- This function generates an affine transformation matreix that can be used
+ This function generates an affine transformation matrix that can be used
to resample an N-D array from ``oldShape`` to ``newShape`` using, for
example, ``scipy.ndimage.affine_transform``.
--
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