From 68b48c48c09a0ec2a4fb1326210f85f72fc2f3bd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Jul 2024 15:18:51 +0100
Subject: [PATCH] MNT: Work-around nibabel auto-rescaling logic so that
data/slope/intercept in imcp'd images is not modified
---
fsl/utils/imcp.py | 26 +++++++++++++++++++++++---
1 file changed, 23 insertions(+), 3 deletions(-)
diff --git a/fsl/utils/imcp.py b/fsl/utils/imcp.py
index be4b62393..2cf3651c6 100644
--- a/fsl/utils/imcp.py
+++ b/fsl/utils/imcp.py
@@ -50,7 +50,8 @@ def imcp(src,
:func:`~fsl.data.image.defaultOutputType`. If the
source file does not have the same type as the default
extension, it will be converted. If ``False``, the
- source file type is not changed.
+ source file type is used, and the destination file type
+ (if specified) is ignored.
:arg move: If ``True``, the files are moved, instead of being
copied. See :func:`immv`.
@@ -143,7 +144,7 @@ def imcp(src,
img = nib.load(src)
- # Force conversion to specific data type if
+ # Force conversion to specific file format if
# necessary. The file format (pair, gzipped
# or not) is taken care of automatically by
# nibabel
@@ -151,7 +152,26 @@ def imcp(src,
elif 'NIFTI2' in destType.name: cls = nib.Nifti2Image
elif 'NIFTI' in destType.name: cls = nib.Nifti1Image
- img = cls(np.asanyarray(img.dataobj), None, header=img.header)
+ # The default behaviour of nibabel when saving
+ # is to rescale the image data to the full range
+ # of the data type, and then set the scl_slope/
+ # inter header fields accordingly. This is highly
+ # disruptive in many circumstances. Fortunately:
+ # - The nibabel ArrayProxy class provides a
+ # get_unscaled method, which allows us to
+ # bypass the rescaling at load time.
+ # - Explicitly setting the slope and intercept
+ # on the header allows us to bypass rescaling
+ # at save time.
+ #
+ # https://github.com/nipy/nibabel/issues/1001
+ # https://neurostars.org/t/preserve-datatype-and-precision-with-nibabel/27641/2
+ slope = img.dataobj.slope
+ inter = img.dataobj.inter
+ data = np.asanyarray(img.dataobj.get_unscaled(),
+ dtype=img.get_data_dtype())
+ img = cls(data, None, header=img.header)
+ img.header.set_slope_inter(slope, inter)
nib.save(img, dest)
# Make sure the image reference is cleared, and
--
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