diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 28ca1825a5b3804ca4e6e5cbabad9084a1470fb4..fa30529fb12cba90cd8d97bb5f8cc27de900331f 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -58,7 +58,6 @@ import fsl.utils.image.resample as resample
import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.settings as fslsettings
-import fsl.utils.deprecated as deprecated
log = logging.getLogger(__name__)
@@ -1085,24 +1084,6 @@ class StatisticAtlas(Atlas):
return avgvals
- @deprecated.deprecated('2.6.0', '3.0.0', 'Use values instead')
- def proportions(self, *args, **kwargs):
- """Deprecated - use :meth:`values` instead. """
- return self.values(*args, **kwargs)
-
-
- @deprecated.deprecated('2.6.0', '3.0.0', 'Use coordValues instead')
- def coordProportions(self, *args, **kwargs):
- """Deprecated - use :meth:`coordValues` instead. """
- return self.coordValues(*args, **kwargs)
-
-
- @deprecated.deprecated('2.6.0', '3.0.0', 'Use maskValues instead')
- def maskProportions(self, *args, **kwargs):
- """Deprecated - use :meth:`maskValues` instead. """
- return self.maskValues(*args, **kwargs)
-
-
class ProbabilisticAtlas(StatisticAtlas):
"""A 4D atlas which contains one volume for each region. Each volume
contains probabiliy values for one region, between 0 and 100.
diff --git a/fsl/data/image.py b/fsl/data/image.py
index d54c75b045ac70d24950ec33990bc1588e8cc694..8cc5c62087b25ebe9f463dcc7e95b1f57f3fe484 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -52,7 +52,6 @@ import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.memoize as memoize
import fsl.utils.path as fslpath
-import fsl.utils.deprecated as deprecated
import fsl.utils.bids as fslbids
import fsl.data.constants as constants
import fsl.data.imagewrapper as imagewrapper
@@ -993,7 +992,6 @@ class Image(Nifti):
xform=None,
loadData=True,
calcRange=True,
- indexed=False,
threaded=False,
dataSource=None,
loadMeta=False,
@@ -1035,9 +1033,6 @@ class Image(Nifti):
incrementally updated as more data is read from memory
or disk.
- :arg indexed: Deprecated. Has no effect, and will be removed in
- ``fslpy`` 3.0.
-
:arg threaded: If ``True``, the :class:`.ImageWrapper` will use a
separate thread for data range calculation. Defaults
to ``False``. Ignored if ``loadData`` is ``True``.
@@ -1059,12 +1054,6 @@ class Image(Nifti):
nibImage = None
saved = False
- if indexed is not False:
- warnings.warn('The indexed argument is deprecated '
- 'and has no effect',
- category=DeprecationWarning,
- stacklevel=2)
-
if loadData:
threaded = False
@@ -1463,14 +1452,6 @@ class Image(Nifti):
self.notify(topic='saveState')
- @deprecated.deprecated('2.2.0', '3.0.0',
- 'Use fsl.utils.image.resample instead.')
- def resample(self, *args, **kwargs):
- """Deprecated - use :func:`.image.resample` instead. """
- from fsl.utils.image.resample import resample
- return resample(self, *args, **kwargs)
-
-
def __getitem__(self, sliceobj):
"""Access the image data with the specified ``sliceobj``.
@@ -1661,9 +1642,3 @@ def defaultExt():
outputType = os.environ.get('FSLOUTPUTTYPE', 'NIFTI_GZ')
return options.get(outputType, '.nii.gz')
-
-
-@deprecated.deprecated('2.0.0', '3.0.0', 'Use nibabel.load instead.')
-def loadIndexedImageFile(filename):
- """Deprecated - this call is equivalent to calling ``nibabel.load``. """
- return nib.load(filename)
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index d371bcdf37a7d31d7ed333e602ba50f992477ade..a83982083515261bb7cefd063fe697e03d5ed698 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -31,8 +31,7 @@ from typing import Dict, List, Tuple
import numpy as np
-from fsl.utils.deprecated import deprecated
-from . import FileTree
+from . import FileTree
log = logging.getLogger(__name__)
@@ -207,15 +206,6 @@ class FileTreeQuery(object):
return list(self.__templatevars.keys())
- @property
- @deprecated('2.6.0', '3.0.0', 'Use templates instead')
- def short_names(self) -> List[str]:
- """Returns a list containing all templates of the ``FileTree`` that
- are present in the directory.
- """
- return self.templates
-
-
def query(self, template, asarray=False, **variables):
"""Search for files of the given ``template``, which match
the specified ``variables``. All hits are returned for variables
@@ -292,12 +282,6 @@ class Match(object):
return self.__filename
- @property
- @deprecated('2.6.0', '3.0.0', 'Use template instead')
- def short_name(self):
- return self.template
-
-
@property
def template(self):
return self.__template
diff --git a/fsl/utils/idle.py b/fsl/utils/idle.py
index d2c93aeb08e0928df4e0dcceb84adf32dc98550f..bef726633b40f8977a3a77a429d77917f7c398b0 100644
--- a/fsl/utils/idle.py
+++ b/fsl/utils/idle.py
@@ -85,8 +85,6 @@ from collections import abc
try: import queue
except ImportError: import Queue as queue
-from fsl.utils.deprecated import deprecated
-
log = logging.getLogger(__name__)
@@ -597,36 +595,6 @@ def idleWhen(*args, **kwargs):
idleLoop.idleWhen(*args, **kwargs)
-@deprecated('2.7.0', '3.0.0', 'Use idleLoop.inIdle instead')
-def inIdle(taskName):
- """Deprecated - use ``idleLoop.inIdle`` instead. """
- return idleLoop.inIdle(taskName)
-
-
-@deprecated('2.7.0', '3.0.0', 'Use idleLoop.cancelIdle instead')
-def cancelIdle(taskName):
- """Deprecated - use ``idleLoop.cancelIdle`` instead. """
- return idleLoop.cancelIdle(taskName)
-
-
-@deprecated('2.7.0', '3.0.0', 'Use idleLoop.reset instead')
-def idleReset():
- """Deprecated - use ``idleLoop.reset`` instead. """
- return idleLoop.reset()
-
-
-@deprecated('2.7.0', '3.0.0', 'Use idleLoop.callRate instead')
-def getIdleTimeout():
- """Deprecated - use ``idleLoop.callRate`` instead. """
- return idleLoop.callRate
-
-
-@deprecated('2.7.0', '3.0.0', 'Use idleLoop.callRate instead')
-def setIdleTimeout(timeout=None):
- """Deprecated - use ``idleLoop.callRate`` instead. """
- idleLoop.callRate = timeout
-
-
def block(secs, delta=0.01, until=None):
"""Blocks for the specified number of seconds, yielding to the main ``wx``
loop.
diff --git a/fsl/utils/image/resample.py b/fsl/utils/image/resample.py
index 371e87b602c60b777bc6e8587aec32b185f08e1d..f5918fad29f18ff0912968c56293ed67ac44c0ae 100644
--- a/fsl/utils/image/resample.py
+++ b/fsl/utils/image/resample.py
@@ -18,7 +18,6 @@ import numpy as np
import scipy.ndimage as ndimage
import fsl.transform.affine as affine
-import fsl.utils.deprecated as deprecated
def resampleToPixdims(image, newPixdims, **kwargs):
@@ -282,13 +281,3 @@ def applySmoothing(data, matrix, newShape):
sigma[ratio >= 1.1] *= 0.425
return ndimage.gaussian_filter(data, sigma)
-
-
-@deprecated.deprecated('2.8.0', '3.0.0',
- 'Use fsl.transform.affine.rescale instead')
-def calculateMatrix(oldShape, newShape, origin):
- """Deprecated - use :func:`.affine.rescale` instead. """
- xform = affine.rescale(oldShape, newShape, origin)
- if np.all(np.isclose(xform, np.eye(len(oldShape) + 1))):
- return None
- return xform[:-1, :]
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
deleted file mode 100644
index b3d51afb21f0e5a5a861458d4fde9e2e62daebc2..0000000000000000000000000000000000000000
--- a/fsl/utils/transform.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-#
-# transforms.py - Deprecated
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""The ``fsl.utils.transform`` module is deprecated - use the
-:mod:`fsl.transform` module instead.
-"""
-
-
-import fsl.utils.deprecated as deprecated
-from fsl.transform.affine import * # noqa
-from fsl.transform.flirt import (flirtMatrixToSform, # noqa
- sformToFlirtMatrix)
-
-
-deprecated.warn('fsl.utils.transform',
- vin='2.4.0',
- rin='3.0.0',
- msg='Use the fsl.transform module instead')