diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 6c8862394e6cc4b415c5ed8e2208bcab94674c19..f7124b6641a6c8b6613f3f6a10528f667e478f87 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -17,6 +17,16 @@ Added
* New :func:`.affine.rescale` function, for adjusting a scaling matrix.
+Changed
+^^^^^^^
+
+
+* The :class:`.ImageWrapper` now maintains its own image data cache, rather
+ than depending on ``nibabel``.
+* Internal changes to avoid using the deprecated
+ ``nibabel.dataobj_images.DataobjImage.get_data`` method.
+
+
Fixed
^^^^^
diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index d38d2081d744a27c9edd71902fc3f1909dafa6d9..51c750385796b0967a25491e6e28385420a82218 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -36,6 +36,7 @@ import shlex
import logging
import binascii
+import numpy as np
import nibabel as nib
import fsl.utils.tempdir as tempdir
@@ -279,9 +280,11 @@ def loadSeries(series):
# copy images so nibabel no longer
# refs to the files (as they will
- # be deleted), and use get_data()
- # to force-load the image data.
- images = [nib.Nifti1Image(i.get_data(), None, i.header)
+ # be deleted), and force-load the
+ # the image data into memory (to
+ # avoid any disk accesses due to
+ # e.g. memmap)
+ images = [nib.Nifti1Image(np.asanyarray(i.dataobj), None, i.header)
for i in images]
return [DicomImage(i, series, dcmdir, name=desc) for i in images]
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 39f1f7facdd789e197340177f8e73dea77507c31..46fb47f813b3dbca90888a45a3a01245f635a350 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1204,6 +1204,9 @@ class Image(Nifti):
@property
def nibImage(self):
"""Returns a reference to the ``nibabel`` NIFTI image instance.
+ Note that if the image data has been modified through this ``Image``,
+ it will be out of sync with what is returned by the ``nibabel`` object,
+ until a call to :meth:`save` is made.
"""
return self.__nibImage
@@ -1387,6 +1390,21 @@ class Image(Nifti):
os.close(tmphd)
try:
+ # First of all, the nibabel object won't know
+ # about any image data modifications, so if
+ # any have occurred, we need to create a new
+ # nibabel image using the data managed by the
+ # imagewrapper, and the old header.
+ #
+ # Assuming here that analyze/nifti1/nifti2
+ # nibabel classes have an __init__ which
+ # expects (data, affine, header)
+ if not self.saveState:
+ self.__nibImage = type(self.__nibImage)(self[:],
+ None,
+ self.header)
+ self.header = self.__nibImage.header
+
nib.save(self.__nibImage, tmpfname)
# nibabel should close any old
@@ -1395,6 +1413,8 @@ class Image(Nifti):
self.__nibImage = None
self.header = None
+ # Copy to final destination,
+ # and reload from there
imcp.imcp(tmpfname, filename, overwrite=True)
self.__nibImage = nib.load(filename)
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 8afcccacf7ad3e9b4e6ce035aabffa6393d4cf70..b7d5b3577c903a9bf434d14cbc8647a243c4bfd2 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -76,8 +76,7 @@ class ImageWrapper(notifier.Notifier):
- The image data is not modified (via :meth:`__setitem__`.
If any of these conditions do not hold, the image data will be loaded into
- memory and accessed directly, via the ``nibabel.Nifti1Image.get_data``
- method.
+ memory and accessed directly.
*Image dimensionality*
@@ -218,7 +217,11 @@ class ImageWrapper(notifier.Notifier):
self.reset(dataRange)
- if loadData:
+ # We keep an internal ref to
+ # the data numpy array if/when
+ # it is loaded in memory
+ self.__data = None
+ if loadData or image.in_memory:
self.loadData()
if threaded:
@@ -232,6 +235,7 @@ class ImageWrapper(notifier.Notifier):
the :class:`.TaskThread` is stopped.
"""
self.__image = None
+ self.__data = None
if self.__taskThread is not None:
self.__taskThread.stop()
self.__taskThread = None
@@ -377,16 +381,11 @@ class ImageWrapper(notifier.Notifier):
"""Forces all of the image data to be loaded into memory.
.. note:: This method will be called by :meth:`__init__` if its
- ``loadData`` parameter is ``True``.
+ ``loadData`` parameter is ``True``. It will also be called
+ on all write operations (see :meth:`__setitem__`).
"""
-
- # If the data is not already loaded, this will
- # cause nibabel to load it. By default, nibabel
- # will cache the numpy array that contains the
- # image data, so subsequent calls to this
- # method will not overwrite any changes that
- # have been made to the data array.
- self.__image.get_data()
+ if self.__data is None:
+ self.__data = np.asanyarray(self.__image.dataobj)
def __getData(self, sliceobj, isTuple=False):
@@ -407,14 +406,7 @@ class ImageWrapper(notifier.Notifier):
# ArrayProxy. Otheriwse if it is in
# memory, we can access it directly.
#
- # Furthermore, if it is in memory and
- # has been modified, the ArrayProxy
- # will give us out-of-date values (as
- # the ArrayProxy reads from disk). So
- # we have to read from the in-memory
- # array to get changed values.
- #
- # Finally, note that if the caller has
+ # Note also that if the caller has
# given us a 'fancy' slice object (a
# boolean numpy array), but the image
# data is not in memory, we can't access
@@ -422,8 +414,8 @@ class ImageWrapper(notifier.Notifier):
# (the dataobj attribute) cannot handle
# fancy indexing. In this case an error
# will be raised.
- if self.__image.in_memory: return self.__image.get_data()[sliceobj]
- else: return self.__image.dataobj[ sliceobj]
+ if self.__data is not None: return self.__data[ sliceobj]
+ else: return self.__image.dataobj[sliceobj]
def __imageIsCovered(self):
@@ -444,18 +436,18 @@ class ImageWrapper(notifier.Notifier):
_, expansions = calcExpansion(slices, self.__coverage)
expansions = collapseExpansions(expansions, self.__numRealDims - 1)
- log.debug('Updating image {} data range [slice: {}] '
- '(current range: [{}, {}]; '
- 'number of expansions: {}; '
- 'current coverage: {}; '
- 'volume ranges: {})'.format(
- self.__name,
- slices,
- self.__range[0],
- self.__range[1],
- len(expansions),
- self.__coverage,
- self.__volRanges))
+ log.debug('Updating image %s data range [slice: %s] '
+ '(current range: [%s, %s]; '
+ 'number of expansions: %s; '
+ 'current coverage: %s; '
+ 'volume ranges: %s)',
+ self.__name,
+ slices,
+ self.__range[0],
+ self.__range[1],
+ len(expansions),
+ self.__coverage,
+ self.__volRanges)
# As we access the data for each expansions,
# we want it to have the same dimensionality
@@ -507,12 +499,12 @@ class ImageWrapper(notifier.Notifier):
if any((oldmin is None, oldmax is None)) or \
not np.all(np.isclose([oldmin, oldmax], [newmin, newmax])):
- log.debug('Image {} range changed: [{}, {}] -> [{}, {}]'.format(
- self.__name,
- oldmin,
- oldmax,
- newmin,
- newmax))
+ log.debug('Image %s range changed: [%s, %s] -> [%s, %s]',
+ self.__name,
+ oldmin,
+ oldmax,
+ newmin,
+ newmax)
self.notify()
@@ -591,15 +583,15 @@ class ImageWrapper(notifier.Notifier):
slices = np.array(slices.T, dtype=np.uint32)
slices = tuple(it.chain(map(tuple, slices), [(lowVol, highVol)]))
- log.debug('Image {} data written - clearing known data '
- 'range on volumes {} - {} (write slice: {}; '
- 'coverage: {}; volRanges: {})'.format(
- self.__name,
- lowVol,
- highVol,
- slices,
- self.__coverage[:, :, lowVol:highVol],
- self.__volRanges[lowVol:highVol, :]))
+ log.debug('Image %s data written - clearing known data '
+ 'range on volumes %s - %s (write slice: %s; '
+ 'coverage: %s; volRanges: %s)',
+ self.__name,
+ lowVol,
+ highVol,
+ slices,
+ self.__coverage[:, :, lowVol:highVol],
+ self.__volRanges[lowVol:highVol, :])
for vol in range(lowVol, highVol):
self.__coverage[:, :, vol] = np.nan
@@ -622,7 +614,7 @@ class ImageWrapper(notifier.Notifier):
:arg sliceobj: Something which can slice the image data.
"""
- log.debug('Getting image data: {}'.format(sliceobj))
+ log.debug('Getting image data: %s', sliceobj)
shape = self.__canonicalShape
realShape = self.__image.shape
@@ -721,7 +713,7 @@ class ImageWrapper(notifier.Notifier):
# have any effect.
self.loadData()
- self.__image.get_data()[sliceobj] = values
+ self.__data[sliceobj] = values
self.__updateDataRangeOnWrite(slices, values)
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index a143e06ce1e3ce9a2367444c7e67408459e3cd36..be29b5cad5ed56c789f528b478b19d9823093bb9 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -12,6 +12,7 @@ Freesurfer ``mgh``/``mgz`` image files.
import os.path as op
import six
+import numpy as np
import nibabel as nib
import fsl.utils.path as fslpath
@@ -54,7 +55,7 @@ class MGHImage(fslimage.Image):
name = 'MGH image'
filename = None
- data = image.get_data()
+ data = np.asanyarray(image.dataobj)
xform = image.affine
vox2surf = image.header.get_vox2ras_tkr()
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index c89afb2aadb002e1e6838235578ce124ce4caf41..81fb86826849b6a4eb55c9012f71c0c61cf40cc6 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -952,16 +952,17 @@ def fileOrImage(*args, **kwargs):
# create an independent in-memory
# copy of the image file
- img = nib.load(path, mmap=False)
+ img = nib.load(path, mmap=False)
+ data = np.asanyarray(img.dataobj)
# if any arguments were fsl images,
# that takes precedence.
if fslimage.Image in intypes:
- return fslimage.Image(img.get_data(), header=img.header)
+ return fslimage.Image(data, header=img.header)
# but if all inputs were file names,
# nibabel takes precedence
elif nib.nifti1.Nifti1Image in intypes or len(intypes) == 0:
- return nib.nifti1.Nifti1Image(img.get_data(), None, img.header)
+ return nib.nifti1.Nifti1Image(data, None, img.header)
# this function should not be called
# under any other circumstances
diff --git a/tests/test_dtifit.py b/tests/test_dtifit.py
index 9e9f80ac07808fc5343ebabae4e3e974e5162225..00fc058ffca6dabc4f70a0e15459748681d0d539 100644
--- a/tests/test_dtifit.py
+++ b/tests/test_dtifit.py
@@ -169,12 +169,12 @@ def test_DTIFitTensor():
l2file = op.join(testdir, 'dti_L2.nii')
l3file = op.join(testdir, 'dti_L3.nii')
- v1 = tests.make_random_image(v1file, (5, 5, 5, 3)).get_data()
- v2 = tests.make_random_image(v2file, (5, 5, 5, 3)).get_data()
- v3 = tests.make_random_image(v3file, (5, 5, 5, 3)).get_data()
- l1 = tests.make_random_image(l1file, (5, 5, 5)) .get_data()
- l2 = tests.make_random_image(l2file, (5, 5, 5)) .get_data()
- l3 = tests.make_random_image(l3file, (5, 5, 5)) .get_data()
+ v1 = np.asanyarray(tests.make_random_image(v1file, (5, 5, 5, 3)).dataobj)
+ v2 = np.asanyarray(tests.make_random_image(v2file, (5, 5, 5, 3)).dataobj)
+ v3 = np.asanyarray(tests.make_random_image(v3file, (5, 5, 5, 3)).dataobj)
+ l1 = np.asanyarray(tests.make_random_image(l1file, (5, 5, 5)) .dataobj)
+ l2 = np.asanyarray(tests.make_random_image(l2file, (5, 5, 5)) .dataobj)
+ l3 = np.asanyarray(tests.make_random_image(l3file, (5, 5, 5)) .dataobj)
dtiobj = dtifit.DTIFitTensor(testdir)
diff --git a/tests/test_ensure.py b/tests/test_ensure.py
index 961377d39b841b52cb6d804deff119021edd526c..a8ce2e68bec571c5f3dde218ade22355e51cf664 100644
--- a/tests/test_ensure.py
+++ b/tests/test_ensure.py
@@ -27,7 +27,7 @@ def test_ensureIsImage():
for l in loaded:
assert isinstance(l, nib.nifti1.Nifti1Image)
- assert np.all(img.get_data() == l.get_data())
+ assert np.all(np.asanyarray(img.dataobj) == np.asanyarray(l.dataobj))
l = None
loaded = None
diff --git a/tests/test_image.py b/tests/test_image.py
index 3bb77d01a3d8f6e7d559fc79796db7097c04615e..e12c6acb7dd2b829a588b13551949e83d4bb9e43 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -823,7 +823,7 @@ def _test_Image_changeData(imgtype):
img.register('name3', onDataRange, 'dataRange')
# Calculate the actual data range
- data = img.nibImage.get_data()
+ data = np.asanyarray(img.nibImage.dataobj)
dmin = data.min()
dmax = data.max()
drange = dmax - dmin
@@ -1098,14 +1098,16 @@ def _test_Image_save(imgtype):
# Load the image back in
img2 = fslimage.Image(img.dataSource)
- assert img.saveState
- assert img.dataSource == expDataSource
+ assert img2.saveState
+ assert img2.dataSource == expDataSource
- if imgtype > 0:
- assert np.all(np.isclose(img.voxToWorldMat, xform))
+ for i in (img, img2):
+ if imgtype > 0:
+ assert np.all(np.isclose(i.voxToWorldMat, xform))
- for (x, y, z), v in zip(rvoxs, rvals):
- assert np.isclose(img[x, y, z], v)
+ for (x, y, z), v in zip(rvoxs, rvals):
+ assert np.isclose(i[x, y, z], v)
+ img = None
img2 = None
@@ -1135,7 +1137,7 @@ def _test_Image_init_xform(imgtype):
# an image created off a
# header should have
# identical sform/qform
- fimg = fslimage.Image(img.get_data(), header=img.header)
+ fimg = fslimage.Image(np.asanyarray(img.dataobj), header=img.header)
fsform, fsform_code = fimg.header.get_sform(True)
fqform, fqform_code = fimg.header.get_qform(True)
@@ -1153,7 +1155,7 @@ def _test_Image_init_xform(imgtype):
# set to that xform,
# qform to None, and
# and codes set to (s2, q0)
- fimg = fslimage.Image(img.get_data(), xform=sform)
+ fimg = fslimage.Image(np.asanyarray(img.dataobj), xform=sform)
fsform, fsform_code = fimg.header.get_sform(True)
fqform, fqform_code = fimg.header.get_qform(True)
@@ -1174,7 +1176,7 @@ def _test_Image_init_xform(imgtype):
rxform = affine.compose(np.random.random(3),
np.random.random(3),
np.random.random(3))
- fimg = fslimage.Image(img.get_data(),
+ fimg = fslimage.Image(np.asanyarray(img.dataobj),
header=img.header,
xform=rxform)
diff --git a/tests/test_imagewrapper.py b/tests/test_imagewrapper.py
index fc78da8460f3f1d7ed20364206d3ef12cbae0934..868245fefd24738197b47c2eab4e3214ffc28837 100644
--- a/tests/test_imagewrapper.py
+++ b/tests/test_imagewrapper.py
@@ -790,7 +790,7 @@ def _test_ImageWrapper_write_out(niters, seed, threaded):
wrapper[tuple(sliceobjs)] = newData
_ImageWraper_busy_wait(wrapper)
- expLo, expHi = coverageDataRange(img.get_data(), cov, slices)
+ expLo, expHi = coverageDataRange(np.asanyarray(img.dataobj), cov, slices)
newLo, newHi = wrapper.dataRange
# print('Old range: {} - {}'.format(clo, chi))
@@ -917,10 +917,10 @@ def _test_ImageWrapper_write_in_overlap(niters, seed, threaded):
print('Expected range: {} - {}'.format(expLo, expHi))
print('New range: {} - {}'.format(newLo, newHi))
- print('Slice min/max: {} - {}'.format(img.get_data()[tuple(sliceobjs)].min(),
- img.get_data()[tuple(sliceobjs)].max()))
- print('Data min/max: {} - {}'.format(img.get_data().min(),
- img.get_data().max()))
+ print('Slice min/max: {} - {}'.format(np.asanyarray(img.dataobj)[tuple(sliceobjs)].min(),
+ np.asanyarray(img.dataobj)[tuple(sliceobjs)].max()))
+ print('Data min/max: {} - {}'.format(np.asanyarray(img.dataobj).min(),
+ np.asanyarray(img.dataobj).max()))
assert np.all(newCov == expCov)
diff --git a/tests/test_immv_imcp.py b/tests/test_immv_imcp.py
index dd1273d78e162a3ee96638cfba4b12850d1b080f..3e324841a118b16482d314251384188b78ad614b 100644
--- a/tests/test_immv_imcp.py
+++ b/tests/test_immv_imcp.py
@@ -14,6 +14,7 @@ import os
import shutil
import tempfile
+import numpy as np
import nibabel as nib
import fsl.utils.imcp as imcp
@@ -31,7 +32,7 @@ def print(*args, **kwargs):
def makeImage(filename):
- return hash(make_random_image(filename).get_data().tobytes())
+ return hash(np.asanyarray(make_random_image(filename).dataobj).tobytes())
def checkImageHash(filename, datahash):
@@ -39,7 +40,7 @@ def checkImageHash(filename, datahash):
"""
img = nib.load(filename)
- assert hash(img.get_data().tobytes()) == datahash
+ assert hash(np.asanyarray(img.dataobj).tobytes()) == datahash
def checkFilesToExpect(files, outdir, outputType, datahashes):
diff --git a/tests/test_mghimage.py b/tests/test_mghimage.py
index f34f635c17759eb9803d34c0405d4a2d93e4a9eb..e2ad7739f4796b41297090d09882d0ef5cac6dfe 100644
--- a/tests/test_mghimage.py
+++ b/tests/test_mghimage.py
@@ -31,7 +31,7 @@ def test_MGHImage():
v2s = nbimg.header.get_vox2ras_tkr()
w2s = affine.concat(v2s, affine.invert(nbimg.affine))
- assert np.all(np.isclose(img[:], nbimg.get_data()))
+ assert np.all(np.isclose(img[:], np.asanyarray(nbimg.dataobj)))
assert np.all(np.isclose(img.voxToWorldMat, nbimg.affine))
assert np.all(np.isclose(img.voxToSurfMat, v2s))
assert np.all(np.isclose(img.surfToVoxMat, affine.invert(v2s)))
@@ -44,7 +44,7 @@ def test_MGHImage():
# Load from an in-memory nibabel object
img = fslmgh.MGHImage(nbimg)
- assert np.all(np.isclose(img[:], nbimg.get_data()))
+ assert np.all(np.isclose(img[:], np.asanyarray(nbimg.dataobj)))
assert np.all(np.isclose(img.voxToWorldMat, nbimg.affine))
assert img.dataSource is None
assert img.mghImageFile is None
diff --git a/tests/test_scripts/test_fsl_apply_x5.py b/tests/test_scripts/test_fsl_apply_x5.py
index dbe2bd3a7ec6cfae76fbb07e8a7e663fc5b135ab..49b9908061f20ea678d889dcad4c5fe46e407454 100644
--- a/tests/test_scripts/test_fsl_apply_x5.py
+++ b/tests/test_scripts/test_fsl_apply_x5.py
@@ -44,7 +44,7 @@ def test_help():
-def test_linear():
+def test_linear(seed):
with tempdir.tempdir():
src2ref = _random_affine()
@@ -65,7 +65,7 @@ def test_linear():
assert np.all(np.isclose(result.data, expect))
-def test_nonlinear():
+def test_nonlinear(seed):
with tempdir.tempdir():
src2ref = _random_affine()
@@ -92,7 +92,7 @@ def test_nonlinear():
assert np.all(np.isclose(result, expect))
-def test_linear_altref():
+def test_linear_altref(seed):
with tempdir.tempdir():
src2ref = affine.scaleOffsetXform([1, 1, 1], [5, 5, 5])
@@ -119,7 +119,7 @@ def test_linear_altref():
assert np.all(result.data == expect)
-def test_nonlinear_altref():
+def test_nonlinear_altref(seed):
with tempdir.tempdir():
src2ref = affine.scaleOffsetXform([1, 1, 1], [5, 5, 5])
@@ -149,7 +149,7 @@ def test_nonlinear_altref():
assert np.all(result.data == expect)
-def test_linear_altsrc():
+def test_linear_altsrc(seed):
with tempdir.tempdir():
src2ref = _random_affine()
@@ -198,7 +198,7 @@ def test_linear_altsrc():
assert np.all(np.isclose(outoff.data, expoff))
-def test_nonlinear_altsrc():
+def test_nonlinear_altsrc(seed):
with tempdir.tempdir():
src2ref = _random_affine()
@@ -252,13 +252,20 @@ def test_nonlinear_altsrc():
assert outhi .sameSpace(ref)
assert outoff.sameSpace(ref)
- # We get boundary issues just at the first
- # voxel, so I'm masking that voxel out
- for img in (out, outlo, outhi, outoff,
- exp, explo, exphi, expoff):
- img[0, 0, 0] = 0
-
- assert np.all(np.isclose(out .data, exp))
- assert np.all(np.isclose(outlo .data, explo))
- assert np.all(np.isclose(outhi .data, exphi))
- assert np.all(np.isclose(outoff.data, expoff))
+ # We get boundary cropping,
+ # so ignore edge slices
+ out = out .data[1:-1, 1:-1, 1:-1]
+ outlo = outlo .data[1:-1, 1:-1, 1:-1]
+ outhi = outhi .data[1:-1, 1:-1, 1:-1]
+ outoff = outoff.data[1:-1, 1:-1, 1:-1]
+ exp = exp[ 1:-1, 1:-1, 1:-1]
+ explo = explo[ 1:-1, 1:-1, 1:-1]
+ exphi = exphi[ 1:-1, 1:-1, 1:-1]
+ expoff = expoff[ 1:-1, 1:-1, 1:-1]
+
+ tol = dict(atol=1e-3, rtol=1e-3)
+
+ assert np.all(np.isclose(out, exp, **tol))
+ assert np.all(np.isclose(outlo, explo, **tol))
+ assert np.all(np.isclose(outhi, exphi, **tol))
+ assert np.all(np.isclose(outoff, expoff, **tol))
diff --git a/tests/test_scripts/test_immv_imcp.py b/tests/test_scripts/test_immv_imcp.py
index 607a7da5d761d69c824f5d85f27751b8bf5a395d..582a23d7c74f3ac53025fcafa51e579d33ff3cc4 100644
--- a/tests/test_scripts/test_immv_imcp.py
+++ b/tests/test_scripts/test_immv_imcp.py
@@ -11,6 +11,7 @@ import tempfile
import pytest
+import numpy as np
import nibabel as nib
from fsl.utils.tempdir import tempdir
@@ -269,7 +270,7 @@ def test_imcp_script_shouldPass(move=False):
for inf in infiles:
img = nib.load(op.join(tindir, inf),
mmap=False)
- imghash = hash(img.get_data().tobytes())
+ imghash = hash(np.asanyarray(img.dataobj).tobytes())
img = None
imageHashes.append(imghash)
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 601e9f8ffa25a423d05ae26360708f11ad7eab88..9e1d5d6a82c56801a60918801c28bfeb81f4e825 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -231,8 +231,8 @@ def test_fileOrImage():
@wutils.fileOrImage('img1', 'img2', 'output')
def func(img1, **kwargs):
- img1 = nib.load(img1).get_data()
- img2 = nib.load(kwargs['img2']).get_data()
+ img1 = np.asanyarray(nib.load(img1).dataobj)
+ img2 = np.asanyarray(nib.load(kwargs['img2']).dataobj)
output = nib.nifti1.Nifti1Image(img1 * img2, np.eye(4))
nib.save(output, kwargs['output'])
@@ -247,43 +247,43 @@ def test_fileOrImage():
# file file file
func('img1.nii', img2='img2.nii', output='output.nii')
- assert np.all(nib.load('output.nii').get_data() == expected)
+ assert np.all(np.asanyarray(nib.load('output.nii').dataobj) == expected)
os.remove('output.nii')
# file file array
result = func('img1.nii', img2='img2.nii', output=wutils.LOAD)['output']
- assert np.all(result.get_data() == expected)
+ assert np.all(np.asanyarray(result.dataobj) == expected)
# file array file
func('img1.nii', img2=img2, output='output.nii')
- assert np.all(nib.load('output.nii').get_data() == expected)
+ assert np.all(np.asanyarray(nib.load('output.nii').dataobj) == expected)
os.remove('output.nii')
# file array array
result = func('img1.nii', img2=img2, output=wutils.LOAD)['output']
- assert np.all(result.get_data() == expected)
+ assert np.all(np.asanyarray(result.dataobj) == expected)
# array file file
func(img1, img2='img2.nii', output='output.nii')
- assert np.all(nib.load('output.nii').get_data() == expected)
+ assert np.all(np.asanyarray(nib.load('output.nii').dataobj) == expected)
os.remove('output.nii')
# array file array
result = func(img1, img2='img2.nii', output=wutils.LOAD)['output']
- assert np.all(result.get_data() == expected)
+ assert np.all(np.asanyarray(result.dataobj) == expected)
# array array file
func(img1, img2=img2, output='output.nii')
- assert np.all(nib.load('output.nii').get_data() == expected)
+ assert np.all(np.asanyarray(nib.load('output.nii').dataobj) == expected)
os.remove('output.nii')
# array array array
result = func(img1, img2=img2, output=wutils.LOAD)['output']
- assert np.all(result.get_data() == expected)
+ assert np.all(np.asanyarray(result.dataobj) == expected)
# in-memory image, file, file
result = func(img3, img2='img2.nii', output='output.nii')
- assert np.all(nib.load('output.nii').get_data() == expected)
+ assert np.all(np.asanyarray(nib.load('output.nii').dataobj) == expected)
os.remove('output.nii')
# fslimage, file, load
@@ -307,7 +307,7 @@ def test_fileOrImage():
# nib.image, nib.image, load
result = func(img1, img2=img2, output=wutils.LOAD)['output']
assert isinstance(result, nib.nifti1.Nifti1Image)
- assert np.all(result.get_data()[:] == expected)
+ assert np.all(np.asanyarray(result.dataobj)[:] == expected)
def test_fileOrThing_sequence():
@@ -357,7 +357,7 @@ def test_fileOrThing_outprefix():
@wutils.fileOrImage('img', outprefix='output_base')
def basefunc(img, output_base):
- img = nib.load(img).get_data()
+ img = np.asanyarray(nib.load(img).dataobj)
out1 = nib.nifti1.Nifti1Image(img * 5, np.eye(4))
out2 = nib.nifti1.Nifti1Image(img * 10, np.eye(4))
@@ -368,31 +368,31 @@ def test_fileOrThing_outprefix():
with tempdir.tempdir() as td:
img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
- exp1 = img.get_data() * 5
- exp2 = img.get_data() * 10
+ exp1 = np.asanyarray(img.dataobj) * 5
+ exp2 = np.asanyarray(img.dataobj) * 10
nib.save(img, 'img.nii')
basefunc('img.nii', 'myout')
- assert np.all(nib.load('myout_times5.nii.gz') .get_data() == exp1)
- assert np.all(nib.load('myout_times10.nii.gz').get_data() == exp2)
+ assert np.all(np.asanyarray(nib.load('myout_times5.nii.gz') .dataobj) == exp1)
+ assert np.all(np.asanyarray(nib.load('myout_times10.nii.gz').dataobj) == exp2)
cleardir(td, 'myout*')
basefunc(img, 'myout')
- assert np.all(nib.load('myout_times5.nii.gz') .get_data() == exp1)
- assert np.all(nib.load('myout_times10.nii.gz').get_data() == exp2)
+ assert np.all(np.asanyarray(nib.load('myout_times5.nii.gz') .dataobj) == exp1)
+ assert np.all(np.asanyarray(nib.load('myout_times10.nii.gz').dataobj) == exp2)
cleardir(td, 'myout*')
res = basefunc(img, 'myout', myout_times5=wutils.LOAD)
- assert np.all(res['myout_times5'].get_data() == exp1)
+ assert np.all(np.asanyarray(res['myout_times5'].dataobj) == exp1)
cleardir(td, 'myout*')
res = basefunc(img, 'myout', myout_times10=wutils.LOAD)
- assert np.all(res['myout_times10'].get_data() == exp2)
+ assert np.all(np.asanyarray(res['myout_times10'].dataobj) == exp2)
cleardir(td, 'myout*')
res = basefunc(img, 'myout', myout=wutils.LOAD)
- assert np.all(res['myout_times5'] .get_data() == exp1)
- assert np.all(res['myout_times10'].get_data() == exp2)
+ assert np.all(np.asanyarray(res['myout_times5'] .dataobj) == exp1)
+ assert np.all(np.asanyarray(res['myout_times10'].dataobj) == exp2)
cleardir(td, 'myout*')
@@ -402,7 +402,7 @@ def test_fileOrThing_outprefix_differentTypes():
def func(img, outpref):
img = nib.load(img)
- img = nib.nifti1.Nifti1Image(img.get_data() * 2, np.eye(4))
+ img = nib.nifti1.Nifti1Image(np.asanyarray(img.dataobj) * 2, np.eye(4))
text = '1234567890'
nib.save(img, '{}_image.nii.gz' .format(outpref))
@@ -412,23 +412,23 @@ def test_fileOrThing_outprefix_differentTypes():
with tempdir.tempdir() as td:
img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
- expi = img.get_data() * 2
+ expi = np.asanyarray(img.dataobj) * 2
expt = '1234567890'
func(img, 'myout')
- assert np.all(nib.load('myout_image.nii.gz') .get_data() == expi)
+ assert np.all(np.asanyarray(nib.load('myout_image.nii.gz') .dataobj) == expi)
with open('myout_text.txt', 'rt') as f:
assert f.read().strip() == expt
cleardir(td, 'myout*')
res = func(img, 'myout', myout_image=wutils.LOAD)
assert list(res.keys()) == ['myout_image']
- assert np.all(res['myout_image'].get_data() == expi)
+ assert np.all(np.asanyarray(res['myout_image'].dataobj) == expi)
cleardir(td, 'myout*')
res = func(img, 'myout', myout=wutils.LOAD)
assert list(res.keys()) == ['myout_image']
- assert np.all(res['myout_image'].get_data() == expi)
+ assert np.all(np.asanyarray(res['myout_image'].dataobj) == expi)
cleardir(td, 'myout*')
res = func(img, 'myout', myout_text=wutils.LOAD)
@@ -445,8 +445,8 @@ def test_fileOrThing_outprefix_directory():
@wutils.fileOrImage('img', outprefix='outpref')
def func(img, outpref):
img = nib.load(img)
- img2 = nib.nifti1.Nifti1Image(img.get_data() * 2, np.eye(4))
- img4 = nib.nifti1.Nifti1Image(img.get_data() * 4, np.eye(4))
+ img2 = nib.nifti1.Nifti1Image(np.asanyarray(img.dataobj) * 2, np.eye(4))
+ img4 = nib.nifti1.Nifti1Image(np.asanyarray(img.dataobj) * 4, np.eye(4))
outdir = op.abspath('{}_imgs'.format(outpref))
@@ -457,8 +457,8 @@ def test_fileOrThing_outprefix_directory():
with tempdir.tempdir() as td:
img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
- exp2 = img.get_data() * 2
- exp4 = img.get_data() * 4
+ exp2 = np.asanyarray(img.dataobj) * 2
+ exp4 = np.asanyarray(img.dataobj) * 4
res = func(img, 'myout')
assert len(res) == 0
@@ -469,17 +469,17 @@ def test_fileOrThing_outprefix_directory():
res = func(img, 'myout', myout_imgs=wutils.LOAD)
assert len(res) == 2
- assert np.all(res[op.join('myout_imgs', 'img2')].get_data() == exp2)
- assert np.all(res[op.join('myout_imgs', 'img4')].get_data() == exp4)
+ assert np.all(np.asanyarray(res[op.join('myout_imgs', 'img2')].dataobj) == exp2)
+ assert np.all(np.asanyarray(res[op.join('myout_imgs', 'img4')].dataobj) == exp4)
res = func(img, 'myout', **{op.join('myout_imgs', 'img2') : wutils.LOAD})
assert len(res) == 1
- assert np.all(res[op.join('myout_imgs', 'img2')].get_data() == exp2)
+ assert np.all(np.asanyarray(res[op.join('myout_imgs', 'img2')].dataobj) == exp2)
res = func(img, 'myout', **{op.join('myout_imgs', 'img') : wutils.LOAD})
assert len(res) == 2
- assert np.all(res[op.join('myout_imgs', 'img2')].get_data() == exp2)
- assert np.all(res[op.join('myout_imgs', 'img4')].get_data() == exp4)
+ assert np.all(np.asanyarray(res[op.join('myout_imgs', 'img2')].dataobj) == exp2)
+ assert np.all(np.asanyarray(res[op.join('myout_imgs', 'img4')].dataobj) == exp4)
os.mkdir('foo')
res = func(img, op.join('foo', 'myout'))
@@ -492,8 +492,8 @@ def test_fileOrThing_outprefix_directory():
os.mkdir('foo')
res = func(img, op.join('foo', 'myout'), **{op.join('foo', 'myout') : wutils.LOAD})
assert len(res) == 2
- assert np.all(res[op.join('foo', 'myout_imgs', 'img2')].get_data() == exp2)
- assert np.all(res[op.join('foo', 'myout_imgs', 'img4')].get_data() == exp4)
+ assert np.all(np.asanyarray(res[op.join('foo', 'myout_imgs', 'img2')].dataobj) == exp2)
+ assert np.all(np.asanyarray(res[op.join('foo', 'myout_imgs', 'img4')].dataobj) == exp4)
def test_chained_fileOrImageAndArray():
@@ -503,7 +503,7 @@ def test_chained_fileOrImageAndArray():
image = nib.load(image)
array = np.loadtxt(array)
- outimg = nib.nifti1.Nifti1Image(image.get_data() * 2, np.eye(4))
+ outimg = nib.nifti1.Nifti1Image(np.asanyarray(image.dataobj) * 2, np.eye(4))
np.savetxt(outarray, array * 2)
outimg.to_filename(outimage)
@@ -511,7 +511,7 @@ def test_chained_fileOrImageAndArray():
image = nib.nifti1.Nifti1Image(np.array([[1, 2], [ 3, 4]]), np.eye(4))
array = np.array([[5, 6, 7, 8]])
- expimg = nib.nifti1.Nifti1Image(image.get_data() * 2, np.eye(4))
+ expimg = nib.nifti1.Nifti1Image(np.asanyarray(image.dataobj) * 2, np.eye(4))
exparr = array * 2
with tempdir.tempdir():
@@ -520,31 +520,31 @@ def test_chained_fileOrImageAndArray():
np.savetxt('array.txt', array)
func('image.nii', 'array.txt', 'outimg.nii', 'outarr.txt')
- assert np.all(nib.load('outimg.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('outimg.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('outarr.txt') == exparr)
func('image.nii', array, 'outimg.nii', 'outarr.txt')
- assert np.all(nib.load('outimg.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('outimg.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('outarr.txt') == exparr)
func( image, 'array.txt', 'outimg.nii', 'outarr.txt')
- assert np.all(nib.load('outimg.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('outimg.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('outarr.txt') == exparr)
func( image, array, 'outimg.nii', 'outarr.txt')
- assert np.all(nib.load('outimg.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('outimg.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('outarr.txt') == exparr)
res = func(image, array, wutils.LOAD, 'outarr.txt')
- assert np.all(res['outimage'].get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(res['outimage'].dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('outarr.txt') == exparr)
res = func(image, array, 'outimg.nii', wutils.LOAD)
- assert np.all(nib.load('outimg.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('outimg.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(res['outarray'] == exparr)
res = func(image, array, wutils.LOAD, wutils.LOAD)
- assert np.all(res['outimage'].get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(res['outimage'].dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(res['outarray'] == exparr)
@@ -561,7 +561,7 @@ def test_fileOrThing_chained_outprefix():
image = nib.load(image)
array = np.loadtxt(array)
- outimg = nib.nifti1.Nifti1Image(image.get_data() * 2, np.eye(4))
+ outimg = nib.nifti1.Nifti1Image(np.asanyarray(image.dataobj) * 2, np.eye(4))
outarr = array * 2
np.savetxt('{}_array.txt'.format(out), outarr)
@@ -570,17 +570,17 @@ def test_fileOrThing_chained_outprefix():
image = nib.nifti1.Nifti1Image(np.array([[1, 2], [ 3, 4]]), np.eye(4))
array = np.array([[5, 6, 7, 8]])
- expimg = nib.nifti1.Nifti1Image(image.get_data() * 2, np.eye(4))
+ expimg = nib.nifti1.Nifti1Image(np.asanyarray(image.dataobj) * 2, np.eye(4))
exparr = array * 2
with tempdir.tempdir():
func(image, array, 'myout')
- assert np.all(nib.load('myout_image.nii').get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(nib.load('myout_image.nii').dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(np.loadtxt('myout_array.txt') == exparr)
res = func(image, array, wutils.LOAD)
- assert np.all(res['out_image'].get_data() == expimg.get_data())
+ assert np.all(np.asanyarray(res['out_image'].dataobj) == np.asanyarray(expimg.dataobj))
assert np.all(res['out_array'] == exparr)