diff --git a/fsl/data/image.py b/fsl/data/image.py
index 68ca3a39e241589aa481e960e119be89e458d1c4..0a776b8d1cc49bec7eafe17ba510c715a0bde7a4 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -136,7 +136,9 @@ class Nifti(notifier.Notifier, meta.Meta):
object.
``shape`` A list/tuple containing the number of voxels along
- each image dimension.
+ each image dimension - see notes below.
+
+ ``realShape`` A list/tuple containing the actual image data shape.
``pixdim`` A list/tuple containing the length of one voxel
along each image dimension.
@@ -163,8 +165,11 @@ class Nifti(notifier.Notifier, meta.Meta):
The ``shape`` attribute may not precisely match the image shape as
reported in the NIFTI header, because trailing dimensions of size 1 are
- squeezed out. See the :meth:`__determineShape` and :meth:`mapIndices`
- methods.
+ squeezed out. See the :meth:`__determineShape` method and the
+ :func:`canonicalSliceObj` function. The actual image data shape can be
+ queried via the :meth:`realShape` property. Note also that the
+ :class:`Image` class expects data access to be with respect to the adjusted
+ shape, not the real shape.
**Affine transformations**
@@ -569,6 +574,12 @@ class Nifti(notifier.Notifier, meta.Meta):
return tuple(self.__shape)
+ @property
+ def realShape(self):
+ """Returns a tuple containing the image data shape. """
+ return tuple(self.__origShape)
+
+
@property
def ndim(self):
"""Returns the number of dimensions in this image. This number may not
@@ -738,18 +749,9 @@ class Nifti(notifier.Notifier, meta.Meta):
return self.getAffine('fsl', 'voxel')
+ @deprecated.deprecated('3.9.0', '4.0.0', 'Use canonicalSliceObj instead')
def mapIndices(self, sliceobj):
- """Adjusts the given slice object so that it may be used to index the
- underlying ``nibabel`` NIFTI image object.
-
- See the :meth:`__determineShape` method.
-
- :arg sliceobj: Something that can be used to slice a
- multi-dimensional array, e.g. ``arr[sliceobj]``.
- """
-
- # How convenient - nibabel has a function
- # that does the dirty work for us.
+ """Deprecated - use :func:`canonicalSliceObj` instead. """
return fileslice.canonical_slicers(sliceobj, self.__origShape)
@@ -1554,6 +1556,102 @@ def canonicalShape(shape):
return shape
+def isValidFancySliceObj(sliceobj, shape):
+ """Returns ``True`` if the given ``sliceobj`` is a valid and fancy slice
+ object.
+
+ ``nibabel`` refers to slice objects as "fancy" if they comprise anything
+ but tuples of integers and simple ``slice`` objects. The ``Image`` class
+ supports an additional type of "fancy" slicing, where the ``sliceobj`` is
+ a boolean ``numpy`` array of the same shape as the image.
+
+ This function returns ``True`` if the given ``sliceobj`` adheres to these
+ requirements, ``False`` otherwise.
+ """
+
+ # We only support boolean numpy arrays
+ # which have the same shape as the image
+ return (isinstance(sliceobj, np.ndarray) and
+ sliceobj.dtype == bool and
+ np.prod(sliceobj.shape) == np.prod(shape))
+
+
+def canonicalSliceObj(sliceobj, shape):
+ """Returns a canonical version of the given ``sliceobj``. See the
+ ``nibabel.fileslice.canonical_slicers`` function.
+ """
+
+ # Fancy slice objects must have
+ # the same shape as the data
+ if isValidFancySliceObj(sliceobj, shape):
+ return sliceobj.reshape(shape)
+
+ else:
+
+ if not isinstance(sliceobj, tuple):
+ sliceobj = (sliceobj,)
+
+ if len(sliceobj) > len(shape):
+ sliceobj = sliceobj[:len(shape)]
+
+ return nib.fileslice.canonical_slicers(sliceobj, shape)
+
+
+def expectedShape(sliceobj, shape):
+ """Given a slice object, and the shape of an array to which
+ that slice object is going to be applied, returns the expected
+ shape of the result.
+
+ .. note:: It is assumed that the ``sliceobj`` has been passed through
+ the :func:`canonicalSliceObj` function.
+
+ :arg sliceobj: Something which can be used to slice an array
+ of shape ``shape``.
+
+ :arg shape: Shape of the array being sliced.
+
+ :returns: A tuple containing:
+
+ - Expected number of dimensions of the result
+
+ - Expected shape of the result (or ``None`` if
+ ``sliceobj`` is fancy).
+ """
+
+ if isValidFancySliceObj(sliceobj, shape):
+ return 1, None
+
+ # Truncate some dimensions from the
+ # slice object if it has too many
+ # (e.g. trailing dims of length 1).
+ elif len(sliceobj) > len(shape):
+ sliceobj = sliceobj[:len(shape)]
+
+ # Figure out the number of dimensions
+ # that the result should have, given
+ # this slice object.
+ expShape = []
+
+ for i in range(len(sliceobj)):
+
+ # Each dimension which has an
+ # int slice will be collapsed
+ if isinstance(sliceobj[i], int):
+ continue
+
+ start = sliceobj[i].start
+ stop = sliceobj[i].stop
+
+ if start is None: start = 0
+ if stop is None: stop = shape[i]
+
+ stop = min(stop, shape[i])
+
+ expShape.append(stop - start)
+
+ return len(expShape), expShape
+
+
def loadMetadata(image):
"""Searches for and loads any sidecar JSON files associated with the given
:class:`.Image`.
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 196110fcf52de6044452d628b968460d14f85fac..4e6710db90e898c34374d19c4312cf8895b3fb7f 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -45,10 +45,9 @@ import collections
import collections.abc as abc
import itertools as it
-import numpy as np
-import nibabel as nib
-
+import numpy as np
+import fsl.data.image as fslimage
import fsl.utils.deprecated as deprecated
import fsl.utils.notifier as notifier
import fsl.utils.naninfrange as nir
@@ -732,112 +731,29 @@ class ImageWrapper(notifier.Notifier):
self.__updateDataRangeOnWrite(slices, values)
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to fsl.data.image')
def isValidFancySliceObj(sliceobj, shape):
- """Returns ``True`` if the given ``sliceobj`` is a valid and fancy slice
- object.
-
- ``nibabel`` refers to slice objects as "fancy" if they comprise anything
- but tuples of integers and simple ``slice`` objects. The ``ImageWrapper``
- class supports one type of "fancy" slicing, where the ``sliceobj`` is a
- boolean ``numpy`` array of the same shape as the image.
-
- This function returns ``True`` if the given ``sliceobj`` adheres to these
- requirements, ``False`` otherwise.
- """
-
- # We only support boolean numpy arrays
- # which have the same shape as the image
- return (isinstance(sliceobj, np.ndarray) and
- sliceobj.dtype == bool and
- np.prod(sliceobj.shape) == np.prod(shape))
+ """Deprecated - moved to :mod:`fsl.data.image`."""
+ return fslimage.isValidFancySliceObj(sliceobj, shape)
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to fsl.data.image')
def canonicalSliceObj(sliceobj, shape):
- """Returns a canonical version of the given ``sliceobj``. See the
- ``nibabel.fileslice.canonical_slicers`` function.
- """
-
- # Fancy slice objects must have
- # the same shape as the data
- if isValidFancySliceObj(sliceobj, shape):
- return sliceobj.reshape(shape)
-
- else:
-
- if not isinstance(sliceobj, tuple):
- sliceobj = (sliceobj,)
+ """Deprecated - moved to :mod:`fsl.data.image`."""
+ return fslimage.canonicalSliceObj(sliceobj, shape)
- if len(sliceobj) > len(shape):
- sliceobj = sliceobj[:len(shape)]
- return nib.fileslice.canonical_slicers(sliceobj, shape)
-
-
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to fsl.data.image')
def expectedShape(sliceobj, shape):
- """Given a slice object, and the shape of an array to which
- that slice object is going to be applied, returns the expected
- shape of the result.
-
- .. note:: It is assumed that the ``sliceobj`` has been passed through
- the :func:`canonicalSliceObj` function.
-
- :arg sliceobj: Something which can be used to slice an array
- of shape ``shape``.
-
- :arg shape: Shape of the array being sliced.
-
- :returns: A tuple containing:
+ """Deprecated - moved to :mod:`fsl.data.image`."""
+ return fslimage.expectedShape(sliceobj, shape)
- - Expected number of dimensions of the result
- - Expected shape of the result (or ``None`` if
- ``sliceobj`` is fancy).
- """
-
- if isValidFancySliceObj(sliceobj, shape):
- return 1, None
-
- # Truncate some dimensions from the
- # slice object if it has too many
- # (e.g. trailing dims of length 1).
- elif len(sliceobj) > len(shape):
- sliceobj = sliceobj[:len(shape)]
-
- # Figure out the number of dimensions
- # that the result should have, given
- # this slice object.
- expShape = []
-
- for i in range(len(sliceobj)):
-
- # Each dimension which has an
- # int slice will be collapsed
- if isinstance(sliceobj[i], int):
- continue
-
- start = sliceobj[i].start
- stop = sliceobj[i].stop
-
- if start is None: start = 0
- if stop is None: stop = shape[i]
-
- stop = min(stop, shape[i])
-
- expShape.append(stop - start)
-
- return len(expShape), expShape
-
-
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def sliceObjToSliceTuple(sliceobj, shape):
- """Turns an array slice object into a tuple of (low, high) index
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Turns an array slice object into a tuple of (low, high) index
pairs, one pair for each dimension in the given shape
:arg sliceobj: Something which can be used to slice an array of shape
@@ -876,10 +792,11 @@ def sliceObjToSliceTuple(sliceobj, shape):
return tuple(indices)
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def sliceTupleToSliceObj(slices):
- """Turns a sequence of (low, high) index pairs into a tuple of array
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Turns a sequence of (low, high) index pairs into a tuple of array
``slice`` objects.
:arg slices: A sequence of (low, high) index pairs.
@@ -893,10 +810,11 @@ def sliceTupleToSliceObj(slices):
return tuple(sliceobj)
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def adjustCoverage(oldCoverage, slices):
- """Adjusts/expands the given ``oldCoverage`` so that it covers the
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Adjusts/expands the given ``oldCoverage`` so that it covers the
given set of ``slices``.
:arg oldCoverage: A ``numpy`` array of shape ``(2, n)`` containing
@@ -943,10 +861,11 @@ return code for the :func:`sliceOverlap` function.
"""
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def sliceOverlap(slices, coverage):
- """Determines whether the given ``slices`` overlap with the given
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Determines whether the given ``slices`` overlap with the given
``coverage``.
:arg slices: A sequence of (low, high) index pairs, assumed to cover
@@ -1012,10 +931,11 @@ def sliceOverlap(slices, coverage):
elif np.all(overlapStates == OVERLAP_ALL): return OVERLAP_ALL
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def sliceCovered(slices, coverage):
- """Returns ``True`` if the portion of the image data calculated by
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Returns ``True`` if the portion of the image data calculated by
the given ``slices` has already been calculated, ``False`` otherwise.
:arg slices: A sequence of (low, high) index pairs, assumed to cover
@@ -1046,10 +966,11 @@ def sliceCovered(slices, coverage):
return True
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def calcExpansion(slices, coverage):
- """Calculates a series of *expansion* slices, which can be used to expand
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Calculates a series of *expansion* slices, which can be used to expand
the given ``coverage`` so that it includes the given ``slices``.
:arg slices: Slices that the coverage needs to be expanded to cover.
@@ -1218,10 +1139,11 @@ def calcExpansion(slices, coverage):
return volumes, expansions
-@deprecated.deprecated('3.9.0', '4.0.0',
- 'The imagewrapper module been migrated to FSLeyes')
+@deprecated.deprecated('3.9.0', '4.0.0', 'Moved to FSLeyes')
def collapseExpansions(expansions, numDims):
- """Scans through the given list of expansions (each assumed to pertain
+ """Deprecated - the imagewrapper has been moved to FSLeyes.
+
+ Scans through the given list of expansions (each assumed to pertain
to a single 3D image), and combines any which cover the same
image area, and cover adjacent volumes.