Commit 630b9e1a authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

MNT: Aah. Remove all the deprecated things.

parent 7c0b28e2
......@@ -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.
......@@ -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 as constants
import as imagewrapper
......@@ -993,7 +992,6 @@ class Image(Nifti):
......@@ -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',
if loadData:
threaded = False
......@@ -1463,14 +1452,6 @@ class Image(Nifti):
@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)
......@@ -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())
@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
@deprecated('2.6.0', '3.0.0', 'Use template instead')
def short_name(self):
return self.template
def template(self):
return self.__template
......@@ -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``
......@@ -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, :]
#!/usr/bin/env python
# - Deprecated
# Author: Paul McCarthy <>
"""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
msg='Use the fsl.transform module instead')
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