diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 3d9e5010821d5ee7cbae1a0b1bd6995948188d51..0f42a87ff36c11f32a0f94e80702127d84b3d0bc 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -9,7 +9,8 @@ to manage data access to ``nibabel`` NIFTI images.
"""
-import logging
+import logging
+import collections
import numpy as np
import nibabel as nib
@@ -38,9 +39,21 @@ class ImageWrapper(notifier.Notifier):
property.
- .. todo:: Figure out if NIFTI2 can be supported as well.
+ The ``ImageWrapper`` class uses the following functions (also defined in
+ this module) to keep track of the portion of the image that has currently
+ been included in the data range calculation:
+
+ .. autosummary::
+ :nosignatures:
+
+ sliceObjToSliceTuple
+ sliceTupleToSliceObj
+ sliceCovered
+ calcSliceExpansion
+ adjustCoverage
"""
+
def __init__(self, image, name=None, loadData=False):
"""Create an ``ImageWrapper``.
@@ -85,7 +98,11 @@ class ImageWrapper(notifier.Notifier):
# been included in the data range calculation, so
# we do not unnecessarily re-calculate ranges on
# the same part of the image.
- self.__sliceCoverage = []
+ self.__coverage = []
+
+ # TODO Use a numpy array of size
+ # (2, [numRealDims - 1], [shape[numRealDims - 1]])
+ # instead of a list of lists
# This is a list of lists of (low, high) pairs,
# one list for each entry in the last dimension
@@ -96,7 +113,7 @@ class ImageWrapper(notifier.Notifier):
for i in range(image.shape[self.__numRealDims - 1]):
cov = [[None, None] for i in range(self.__numRealDims - 1)]
- self.__sliceCoverage.append(cov)
+ self.__coverage.append(cov)
if loadData:
self.loadData()
@@ -128,7 +145,7 @@ class ImageWrapper(notifier.Notifier):
"""
if isTuple:
- sliceobj = sliceTupletoSliceObj(sliceobj)
+ sliceobj = sliceTupleToSliceObj(sliceobj)
# If the image has not been loaded
# into memory, we can use the nibabel
@@ -168,10 +185,10 @@ class ImageWrapper(notifier.Notifier):
self.__name,
self.__range[0],
self.__range[1],
- self.__sliceCoverage))
+ self.__coverage))
volumes, expansions = calcSliceExpansion(slices,
- self.__sliceCoverage,
+ self.__coverage,
self.__numRealDims,
self.__numPadDims)
@@ -190,10 +207,7 @@ class ImageWrapper(notifier.Notifier):
self.__range = (newmin, newmax)
for vol, exp in zip(volumes, expansions):
- self.__sliceCoverage[vol] = adjustSliceCoverage(
- self.__sliceCoverage[vol],
- exp,
- self.__numRealDims)
+ self.__coverage[vol] = adjustCoverage(self.__coverage[vol], exp)
# TODO floating point error
if newmin != oldmin or newmax != oldmax:
@@ -234,7 +248,7 @@ class ImageWrapper(notifier.Notifier):
slices = sliceObjToSliceTuple(sliceobj, self.__image.shape)
if not sliceCovered(slices,
- self.__sliceCoverage,
+ self.__coverage,
self.__image.shape,
self.__numRealDims):
@@ -243,14 +257,25 @@ class ImageWrapper(notifier.Notifier):
return data
-
def sliceObjToSliceTuple(sliceobj, shape):
"""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
+ ``shape``.
+
+ :arg shape: Shape of the array being sliced.
"""
indices = []
+ if not isinstance(sliceobj, collections.Sequence):
+ sliceobj = [sliceobj]
+
+ if len(sliceobj) != len(shape):
+ missing = len(shape) - len(sliceobj)
+ sliceobj = list(sliceobj) + [slice(None) for i in range(missing)]
+
for dim, s in enumerate(sliceobj):
# each element in the slices tuple should
@@ -266,8 +291,11 @@ def sliceObjToSliceTuple(sliceobj, shape):
return tuple(indices)
-def sliceTupletoSliceObj(slices):
- """
+def sliceTupleToSliceObj(slices):
+ """Turns a sequence of (low, high) index pairs into a tuple of array
+ slice objects.
+
+ :arg slices: A sequence of (low, high) index pairs.
"""
sliceobj = []
@@ -278,10 +306,41 @@ def sliceTupletoSliceObj(slices):
return tuple(sliceobj)
+def adjustCoverage(oldCoverage, slices):
+ """Adjusts/expands the given ``oldCoverage`` so that it covers the
+ given set of ``slices``.
+
+ :arg oldCoverage: A sequence of (low, high) index pairs
+ :arg slices: A sequence of (low, high) index pairs. If ``slices``
+ contains more dimensions than are specified in
+ ``oldCoverage``, the trailing dimensions are ignored.
+
+ :return: A list of (low, high) tuples containing the adjusted coverage.
+ """
+
+ newCoverage = []
+
+ for dim in range(len(oldCoverage)):
+
+ low, high = slices[ dim]
+ lowCover, highCover = oldCoverage[dim]
+
+ if lowCover is None or low < lowCover: lowCover = low
+ if highCover is None or high > highCover: highCover = high
+
+ newCoverage.append((lowCover, highCover))
+
+ return newCoverage
+
-def sliceCovered(slices, sliceCoverage, shape, realDims):
+def sliceCovered(slices, coverage, shape, realDims):
"""Returns ``True`` if the portion of the image data calculated by
the given ``slices` has already been calculated, ``False`` otherwise.
+
+ :arg slices:
+ :arg coverage:
+ :arg shape:
+ :arg volDim:
"""
lowVol, highVol = slices[realDims - 1]
@@ -289,11 +348,11 @@ def sliceCovered(slices, sliceCoverage, shape, realDims):
for vol in range(lowVol, highVol):
- coverage = sliceCoverage[vol]
+ volCoverage = coverage[vol]
for dim, size in enumerate(shape):
- lowCover, highCover = coverage[dim]
+ lowCover, highCover = volCoverage[dim]
if lowCover is None or highCover is None:
return False
@@ -309,7 +368,7 @@ def sliceCovered(slices, sliceCoverage, shape, realDims):
return True
-def calcSliceExpansion(slices, sliceCoverage, realDims, padDims):
+def calcSliceExpansion(slices, coverage, realDims, padDims):
"""
"""
@@ -324,13 +383,13 @@ def calcSliceExpansion(slices, sliceCoverage, realDims, padDims):
for vol in volumes:
- coverage = sliceCoverage[vol]
- expansion = []
+ volCoverage = coverage[vol]
+ expansion = []
for dim in range(realDims - 1):
- lowCover, highCover = coverage[dim]
- lowSlice, highSlice = slices[ dim]
+ lowCover, highCover = volCoverage[dim]
+ lowSlice, highSlice = slices[ dim]
if lowCover is None: lowCover = lowSlice
if highCover is None: highCover = highSlice
@@ -345,22 +404,3 @@ def calcSliceExpansion(slices, sliceCoverage, realDims, padDims):
expansions.append(expansion)
return volumes, expansions
-
-
-def adjustSliceCoverage(oldCoverage, slices, realDims):
- """
- """
-
- newCoverage = []
-
- for dim in range(realDims - 1):
-
- low, high = slices[ dim]
- lowCover, highCover = oldCoverage[dim]
-
- if lowCover is None or low < lowCover: lowCover = low
- if highCover is None or high < highCover: highCover = high
-
- newCoverage.append((lowCover, highCover))
-
- return newCoverage