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Commit bf578610 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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MNT: Move some functions from imagewrapper over to image - Image to be updated 

to support normalisation of image shape
parent a87fc908
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fsl/data/image.py
+ 112
− 14
View file @ bf578610
......@@ -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`.
......
fsl/data/imagewrapper.py
+ 39
− 117
View file @ bf578610
......@@ -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.
......
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