diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index bc7b88c1c146670cafd7799a5366e901ec8e4a79..ce4881625db90f191f964d82c459f4b60ef54a03 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,20 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.21.0 (Tuesday 23rd July 2024)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Behaviour of the ``imcp`` / ``immv`` commands has been adjusted so that
+ when an image file is copied/moved, and converted to a different format
+ (e.g. ``.nii`` to ``.nii.gz``), the image data and header slope/intercept
+ fields are not modified (!462).
+
+
3.20.0 (Wednesday 10th July 2024)
---------------------------------
diff --git a/fsl/tests/__init__.py b/fsl/tests/__init__.py
index a758db12e28746a44d9324a0b8a190590d87239c..2846ee5cc1ece704acd134efcb8f9485966ede77 100644
--- a/fsl/tests/__init__.py
+++ b/fsl/tests/__init__.py
@@ -10,6 +10,7 @@
import os
import sys
import glob
+import hashlib
import shutil
import fnmatch
import logging
@@ -439,3 +440,10 @@ def make_random_mask(filename, shape, xform, premask=None, minones=1):
img.save(filename)
return img
+
+
+def sha256(filename):
+ hashobj = hashlib.sha256()
+ with open(filename, 'rb') as f:
+ hashobj.update(f.read())
+ return hashobj.hexdigest()
diff --git a/fsl/tests/test_dicom.py b/fsl/tests/test_dicom.py
index dfda97f20a2236e8cfe27d3b1c68a0a84a9b71c5..ca68ebd8aae88c12f459f4e7b9a53938f409d709 100644
--- a/fsl/tests/test_dicom.py
+++ b/fsl/tests/test_dicom.py
@@ -151,7 +151,7 @@ def test_scanDir():
datafile = op.join(datadir, 'example_dicom.tbz2')
with tarfile.open(datafile) as f:
- f.extractall()
+ f.extractall(filter='data')
series = fsldcm.scanDir('.')
assert len(series) == 2
diff --git a/fsl/tests/test_immv_imcp.py b/fsl/tests/test_immv_imcp.py
index 7b3e3fcbe900927ef206e7bc5926f609b1797bec..b4b80ffcc882692c50eed1e02e59fcc278e4eedc 100644
--- a/fsl/tests/test_immv_imcp.py
+++ b/fsl/tests/test_immv_imcp.py
@@ -7,22 +7,26 @@
from __future__ import print_function
+import gzip
+import itertools as it
+import os.path as op
+import os
+import shutil
+import tempfile
+from unittest import mock
-import os.path as op
-import os
-import shutil
-import tempfile
-
-import numpy as np
+import numpy as np
import nibabel as nib
-import fsl.utils.imcp as imcp
-import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.utils.tempdir as tempdir
+import fsl.data.image as fslimage
-from fsl.tests import make_random_image
-from fsl.tests import make_dummy_file
-from fsl.tests import looks_like_image
+from fsl.tests import (make_random_image,
+ make_dummy_file,
+ looks_like_image,
+ sha256)
real_print = print
@@ -315,3 +319,60 @@ def test_imcp_shouldPass(move=False):
def test_immv_shouldPass():
test_imcp_shouldPass(move=True)
+
+
+def test_imcp_data_unmodified():
+ """Test that the data in an imcp'd image file is not modified. """
+
+ dtypes = [
+ np.int16,
+ np.int32,
+ np.float32,
+ np.float64]
+
+ slints = [(None, None), (1, 0), (3, 1.5)]
+
+ for dtype, (slope, inter) in it.product(dtypes, slints):
+ with tempdir.tempdir():
+ data = np.random.randint(1, 100, (10, 10, 10)).astype(dtype)
+ hdr = nib.Nifti1Header()
+ hdr.set_data_dtype(dtype)
+ hdr.set_data_shape((10, 10, 10))
+ hdr.set_slope_inter(slope, inter)
+ hdr.set_sform(np.eye(4))
+
+ # write header/data separately, as otherwise
+ # nibabel will automatically rescale the data
+ with open('image.nii', 'wb') as f:
+ hdr.write_to(f)
+ f.write(data.tobytes())
+
+ # Input/output formats the same,
+ # should induce a straight file copy
+ imcp.imcp('image.nii', 'copied.nii', useDefaultExt=False)
+
+ # uncompresed->compressed will cause imcp
+ # to load in the image, rather than doing a
+ # file copy
+ with mock.patch.dict(os.environ, FSLOUTPUTTYPE='NIFTI_GZ'):
+ imcp.imcp('image.nii', 'converted.nii.gz', useDefaultExt=True)
+
+ # copied files should be identical
+ assert sha256('image.nii') == sha256('copied.nii')
+
+ # Converted files should have the same
+ # data, slope, and intercept. Read result
+ # header/data separately to avoid nibabel
+ # auto-rescaling.
+ with gzip.open('converted.nii.gz', 'rb') as f:
+ gothdr = nib.Nifti1Header.from_fileobj(f)
+ databytes = f.read()
+
+ gotdata = np.frombuffer(databytes, dtype=dtype).reshape((10, 10, 10))
+
+ # Data should be binary identical
+ assert np.all(gotdata == data)
+
+ if slope is None: slope = 1
+ if inter is None: inter = 0
+ assert np.all(np.isclose(gothdr.get_slope_inter(), (slope, inter)))
diff --git a/fsl/utils/imcp.py b/fsl/utils/imcp.py
index be4b623938ba6244a83f24eb30972937aa3b5ed4..2cf3651c64887db87e970e6b5072f23b6ce4cc5b 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
diff --git a/fsl/version.py b/fsl/version.py
index d40259f541448c9137101a2669c6adfd55cf14f9..53af914072b527c481c37c0361d962b66d64338a 100644
--- a/fsl/version.py
+++ b/fsl/version.py
@@ -47,7 +47,7 @@ import re
import string
-__version__ = '3.21.0.dev0'
+__version__ = '3.22.0.dev0'
"""Current version number, as a string. """