From 6e51658e35515de91e3b570c2d3390c7139107ff Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 28 Mar 2022 17:46:53 +0100
Subject: [PATCH] MNT: Mark ImageWrapper as deprecated
---
fsl/data/imagewrapper.py | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index c9fec4a47..196110fcf 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -7,6 +7,9 @@
"""This module provides the :class:`ImageWrapper` class, which can be used
to manage data access to ``nibabel`` NIFTI images.
+.. note:: This module is deprecated - it is being moved to the FSLeyes project,
+ and will be removed in a future version of fslpy.
+
Terminology
-----------
@@ -45,6 +48,8 @@ import itertools as it
import numpy as np
import nibabel as nib
+
+import fsl.utils.deprecated as deprecated
import fsl.utils.notifier as notifier
import fsl.utils.naninfrange as nir
import fsl.utils.idle as idle
@@ -148,6 +153,8 @@ class ImageWrapper(notifier.Notifier):
"""
+ @deprecated.deprecated('3.9.0', '4.0.0',
+ 'The ImageWrapper has been migrated to FSLeyes')
def __init__(self,
image,
name=None,
@@ -725,6 +732,8 @@ class ImageWrapper(notifier.Notifier):
self.__updateDataRangeOnWrite(slices, values)
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def isValidFancySliceObj(sliceobj, shape):
"""Returns ``True`` if the given ``sliceobj`` is a valid and fancy slice
object.
@@ -745,6 +754,8 @@ def isValidFancySliceObj(sliceobj, shape):
np.prod(sliceobj.shape) == np.prod(shape))
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def canonicalSliceObj(sliceobj, shape):
"""Returns a canonical version of the given ``sliceobj``. See the
``nibabel.fileslice.canonical_slicers`` function.
@@ -766,6 +777,8 @@ def canonicalSliceObj(sliceobj, shape):
return nib.fileslice.canonical_slicers(sliceobj, shape)
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
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
@@ -821,6 +834,8 @@ def expectedShape(sliceobj, shape):
return len(expShape), expShape
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
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
@@ -861,6 +876,8 @@ def sliceObjToSliceTuple(sliceobj, shape):
return tuple(indices)
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def sliceTupleToSliceObj(slices):
"""Turns a sequence of (low, high) index pairs into a tuple of array
``slice`` objects.
@@ -876,6 +893,8 @@ def sliceTupleToSliceObj(slices):
return tuple(sliceobj)
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def adjustCoverage(oldCoverage, slices):
"""Adjusts/expands the given ``oldCoverage`` so that it covers the
given set of ``slices``.
@@ -924,6 +943,8 @@ return code for the :func:`sliceOverlap` function.
"""
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def sliceOverlap(slices, coverage):
"""Determines whether the given ``slices`` overlap with the given
``coverage``.
@@ -991,6 +1012,8 @@ 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')
def sliceCovered(slices, coverage):
"""Returns ``True`` if the portion of the image data calculated by
the given ``slices` has already been calculated, ``False`` otherwise.
@@ -1023,6 +1046,8 @@ def sliceCovered(slices, coverage):
return True
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def calcExpansion(slices, coverage):
"""Calculates a series of *expansion* slices, which can be used to expand
the given ``coverage`` so that it includes the given ``slices``.
@@ -1193,6 +1218,8 @@ def calcExpansion(slices, coverage):
return volumes, expansions
+@deprecated.deprecated('3.9.0', '4.0.0',
+ 'The imagewrapper module been migrated to FSLeyes')
def collapseExpansions(expansions, numDims):
"""Scans through the given list of expansions (each assumed to pertain
to a single 3D image), and combines any which cover the same
--
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