diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py
index 53b7edefe067583d0ea94aaddcc4024b5faa663e..1457c54eed7f4e017500de67d033f5b4b5626052 100644
--- a/fsl/data/dicom.py
+++ b/fsl/data/dicom.py
@@ -32,7 +32,6 @@ import re
import glob
import json
import logging
-import deprecation
import nibabel as nib
@@ -80,38 +79,6 @@ class DicomImage(fslimage.Image):
return self.__dicomDir
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use metaKeys instead')
- def keys(self):
- """Deprecated - use :meth:`.Image.metaKeys`. """
- return self.metaKeys()
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use metaValues instead')
- def values(self):
- """Deprecated - use :meth:`.Image.metaValues`. """
- return self.metaValues()
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use metaItems instead')
- def items(self):
- """Deprecated - use :meth:`.Image.metaItems`. """
- return self.metaItems()
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use getMeta instead')
- def get(self, *args, **kwargs):
- """Deprecated - use :meth:`.Image.getMeta`. """
- return self.getMeta(*args, **kwargs)
-
-
@memoize.memoize
def enabled():
"""Returns ``True`` if ``dcm2niix`` is present, and recent enough,
diff --git a/fsl/data/gifti.py b/fsl/data/gifti.py
index cd5185183d1770db9080f512d6df7b99a61dad51..d957d75c18e2898693fd95161c16c10c2bfc484e 100644
--- a/fsl/data/gifti.py
+++ b/fsl/data/gifti.py
@@ -25,7 +25,6 @@ are available:
import glob
import os.path as op
-import deprecation
import numpy as np
import nibabel as nib
@@ -306,48 +305,3 @@ def relatedFiles(fname, ftypes=None):
glob.glob(op.join(dirname, '{}*{}'.format(prefix, ftype))))
return [r for r in related if r != path]
-
-
-class GiftiSurface(fslmesh.TriangleMesh):
- """Deprecated - use GiftiMesh instead. """
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use GiftiMesh instead')
- def __init__(self, infile, fixWinding=False):
- """Deprecated - use GiftiMesh instead. """
- surfimg, vertices, indices = loadGiftiSurface(infile)
-
- fslmesh.TriangleMesh.__init__(self, vertices, indices, fixWinding)
-
- name = fslpath.removeExt(op.basename(infile), ALLOWED_EXTENSIONS)
- infile = op.abspath(infile)
-
- self._Mesh__name = name
- self._Mesh__dataSource = infile
- self.surfImg = surfimg
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use GiftiMesh instead')
- def loadVertexData(self, dataSource, vertexData=None):
- """Deprecated - use GiftiMesh instead. """
-
- if vertexData is None:
- if dataSource.endswith('.gii'):
- vertexData = loadGiftiVertexData(dataSource)[1]
- else:
- vertexData = None
-
- return fslmesh.TriangleMesh.loadVertexData(
- self, dataSource, vertexData)
-
-
-@deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use loadGiftiMesh instead')
-def loadGiftiSurface(filename):
- """Deprecated - use loadGiftiMesh instead."""
- return loadGiftiMesh(filename)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 6d1a7e4a831b7539805adb6c8068d22d677b7db2..c607cf47dbeac31e50bdcd21be87aa2d1ef9f975 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -41,7 +41,6 @@ import logging
import tempfile
import six
-import deprecation
import numpy as np
import scipy.ndimage as ndimage
@@ -502,23 +501,6 @@ class Nifti(notifier.Notifier, meta.Meta):
return len(self.__shape)
- @property
- @deprecation.deprecated(deprecated_in='1.9.0',
- removed_in='2.0.0',
- details='Use ndim instead')
- def ndims(self):
- """Deprecated - use :mod::meth:``ndim`` instead. """
- return self.ndim
-
-
- @deprecation.deprecated(deprecated_in='1.1.0',
- removed_in='2.0.0',
- details='Use ndims instead')
- def is4DImage(self):
- """Returns ``True`` if this image is 4D, ``False`` otherwise. """
- return len(self.__shape) > 3 and self.__shape[3] > 1
-
-
def getXFormCode(self, code=None):
"""This method returns the code contained in the NIFTI header,
indicating the space to which the (transformed) image is oriented.
@@ -605,15 +587,6 @@ class Nifti(notifier.Notifier, meta.Meta):
return npla.det(self.__voxToWorldMat) > 0
- @memoize.Instanceify(memoize.memoize)
- @deprecation.deprecated(deprecated_in='1.2.0',
- removed_in='2.0.0',
- details='Use voxToScaledVoxMat instead')
- def voxelsToScaledVoxels(self):
- """See :meth:`voxToScaledVoxMat`."""
- return self.voxToScaledVoxMat
-
-
@property
def voxToScaledVoxMat(self):
"""Returns a transformation matrix which transforms from voxel
@@ -1519,78 +1492,3 @@ def loadIndexedImageFile(filename):
image = ftype.from_file_map(fmap)
return image, fobj
-
-
-@deprecation.deprecated(deprecated_in='1.3.0',
- removed_in='2.0.0',
- details='Upgrade to nibabel 2.2.0')
-def read_segments(fileobj, segments, n_bytes):
- """This function is used in place of the
- ``nibabel.fileslice.read_segments`` function to ensure thread-safe read
- access to image data via the ``nibabel.arrayproxy.ArrayProxy`` (the
- ``dataobj`` attribute of a ``nibabel`` image).
-
- The ``nibabel`` implementation uses multiple calls to ``seek`` and
- ``read`` to read segments of data from the file. When accessed by multiple
- threads, these seeks and reads can become intertwined, which causes a read
- from one thread to read data from the seek location requested by the other
- thread.
-
- This implementation protects the seek/read pairs with a
- ``threading.Lock``, which is added to ``IndexedGzipFile`` instances that
- are created in the :func:`loadIndexedImageFile` function.
-
- .. note:: This patch is not required in nibabel 2.2.0 and newer. It will
- be removed from ``fslpy`` in version 2.0.0.
- """
-
- from mmap import mmap
-
- try:
- # fileobj is a nibabel.openers.ImageOpener - the
- # actual file is available via the fobj attribute
- lock = getattr(fileobj.fobj, '_arrayproxy_lock')
-
- except AttributeError:
- return fileslice.orig_read_segments(fileobj, segments, n_bytes)
-
- if len(segments) == 0:
- if n_bytes != 0:
- raise ValueError("No segments, but non-zero n_bytes")
- return b''
- if len(segments) == 1:
- offset, length = segments[0]
-
- lock.acquire()
- try:
- fileobj.seek(offset)
- bytes = fileobj.read(length)
- finally:
- lock.release()
-
- if len(bytes) != n_bytes:
- raise ValueError("Whoops, not enough data in file")
- return bytes
-
- # More than one segment
- bytes = mmap(-1, n_bytes)
- for offset, length in segments:
-
- lock.acquire()
- try:
- fileobj.seek(offset)
- bytes.write(fileobj.read(length))
- finally:
- lock.release()
-
- if bytes.tell() != n_bytes:
- raise ValueError("Oh dear, n_bytes does not look right")
- return bytes
-
-
-# Monkey-patch the above implementation into
-# nibabel. FSLeyes requires at least 2.1.0 -
-# newer versions do not need to be patched.
-if nib.__version__ == '2.1.0':
- fileslice.orig_read_segments = fileslice.read_segments
- fileslice.read_segments = read_segments
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 559c0d974f5563edbafef459870cbbb5b504ddac..eccf8518485bdbb921f4c010db1bf197962f21e2 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -41,8 +41,6 @@ import logging
import collections
import itertools as it
-import deprecation
-
import numpy as np
import nibabel as nib
@@ -717,16 +715,6 @@ class ImageWrapper(notifier.Notifier):
self.__updateDataRangeOnWrite(slices, values)
-@deprecation.deprecated(deprecated_in='1.7.0',
- removed_in='2.0.0',
- details='Moved to fsl.utils.naninfrange')
-def naninfrange(data):
- """Deprecated - moved to :mod:`fsl.utils.naninfrange`. """
-
- from fsl.utils.naninfrange import naninfrange
- return naninfrange(data)
-
-
def isValidFancySliceObj(sliceobj, shape):
"""Returns ``True`` if the given ``sliceobj`` is a valid and fancy slice
object.
@@ -768,15 +756,6 @@ def canonicalSliceObj(sliceobj, shape):
return nib.fileslice.canonical_slicers(sliceobj, shape)
-@deprecation.deprecated(deprecated_in='1.7.0',
- removed_in='2.0.0',
- details='moved to the fsl.data.image module')
-def canonicalShape(shape):
- """Deprecated - moved to the :mod:`fsl.data.image` module. """
- from fsl.data.image import canonicalShape
- return canonicalShape(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
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index 59fc266c702e3b82427be74fc764ab41d0797c70..55b996069dfcb54b616bcc616b8b70eff90e02a7 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -30,9 +30,6 @@ various things with meshes:
import logging
import collections
-import six
-import deprecation
-
import os.path as op
import numpy as np
@@ -763,109 +760,3 @@ def needsFixing(vertices, indices, fnormals, loBounds, hiBounds):
# If it isn't, we need to flip the
# triangle winding order.
return np.dot(n, transform.normalise(camera - vert)) < 0
-
-
-class TriangleMesh(Mesh):
- """Deprecated - use :class:`fsl.data.mesh.Mesh`, or one of its sub-classes
- instead.
- """
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use fsl.data.mesh.Mesh, or one '
- 'of its sub-classes instead')
- def __init__(self, data, indices=None, fixWinding=False):
-
- import fsl.data.vtk as fslvtk
-
- if isinstance(data, six.string_types):
- name = op.basename(data)
- dataSource = data
- mesh = fslvtk.VTKMesh(data, fixWinding=False)
- vertices = mesh.vertices
- indices = mesh.indices
-
- else:
- name = 'TriangleMesh'
- dataSource = None
- vertices = data
-
- Mesh.__init__(self, indices, name=name, dataSource=dataSource)
- self.addVertices(vertices, 'default', fixWinding=fixWinding)
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use the Mesh class instead')
- def loadVertexData(self, dataSource, vertexData=None):
-
- nvertices = self.vertices.shape[0]
-
- # Currently only white-space delimited
- # text files are supported
- if vertexData is None:
- vertexData = np.loadtxt(dataSource)
- vertexData.reshape(nvertices, -1)
-
- if vertexData.shape[0] != nvertices:
- raise ValueError('Incompatible size: {}'.format(dataSource))
-
- self.addVertexData(dataSource, vertexData)
-
- return vertexData
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use bounds instead')
- def getBounds(self):
- """Deprecated - use :meth:`bounds` instead. """
- return self.bounds
-
-
- @deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use the Mesh class instead')
- def getVertexData(self, dataSource):
- try:
- return Mesh.getVertexData(self, dataSource)
- except KeyError:
- return self.loadVertexData(dataSource)
-
-
-@deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use fsl.data.vtk.loadVTKPolydataFile instead')
-def loadVTKPolydataFile(*args, **kwargs):
- """Deprecated - use :func:`fsl.data.vtk.loadVTKPolydataFile` instead. """
- import fsl.data.vtk as fslvtk
- return fslvtk.loadVTKPolydataFile(*args, **kwargs)
-
-
-@deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use fsl.data.vtk.getFIRSTPrefix instead')
-def getFIRSTPrefix(*args, **kwargs):
- """Deprecated - use :func:`fsl.data.vtk.getFIRSTPrefix` instead. """
- import fsl.data.vtk as fslvtk
- return fslvtk.getFIRSTPrefix(*args, **kwargs)
-
-
-@deprecation.deprecated(deprecated_in='1.6.0',
- removed_in='2.0.0',
- details='Use fsl.data.vtk.findReferenceImage instead')
-def findReferenceImage(*args, **kwargs):
- """Deprecated - use :func:`fsl.data.vtk.findReferenceImage` instead. """
- import fsl.data.vtk as fslvtk
- return fslvtk.findReferenceImage(*args, **kwargs)
-
-
-ALLOWED_EXTENSIONS = ['.vtk']
-"""Deprecated, will be removed in fslpy 2.0.0. Use
-:attr:`fsl.data.vtk.ALLOWED_EXTENSIONS` instead."""
-
-
-EXTENSION_DESCRIPTIONS = ['VTK polygon model file']
-"""Deprecated, will be removed in fslpy 2.0.0. Use
-:attr:`fsl.data.vtk.EXTENSION_DESCRIPTIONS` instead."""
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
deleted file mode 100644
index 520f77ce62c2c5bd4586571469c305369eb00934..0000000000000000000000000000000000000000
--- a/fsl/utils/async.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-#
-# async.py - Deprecaed - use the idle module instead.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""This module is deprecated - use the :mod:`.idle` module instead. """
-
-
-import logging
-import warnings
-
-from .idle import (run, # noqa
- idleReset,
- getIdleTimeout,
- setIdleTimeout,
- inIdle,
- cancelIdle,
- idle,
- idleWhen,
- wait,
- TaskThreadVeto,
- TaskThread,
- mutex)
-
-
-log = logging.getLogger(__name__)
-
-
-warnings.warn('fsl.utils.async is deprecated and will be removed '
- 'in fslpy 2.0.0 - use fsl.utils.idle instead',
- DeprecationWarning)
-log.warning('fsl.utils.async is deprecated and will be removed '
- 'in fslpy 2.0.0 - use fsl.utils.idle instead')
diff --git a/fsl/utils/callfsl.py b/fsl/utils/callfsl.py
deleted file mode 100644
index 598df885bc0d595dda214aff7d1670e0336df85e..0000000000000000000000000000000000000000
--- a/fsl/utils/callfsl.py
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-#
-# callfsl.py - The callFSL function.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""Deprecated - use :mod:`fsl.utils.run` instead.
-
-This module provides the :func:`callFSL` function, which can be
-used to call a FSL command, and retrieve the result.
-"""
-
-
-import logging
-import subprocess as sp
-import os.path as op
-
-import deprecation
-
-from fsl.utils.platform import platform as fslplatform
-
-
-log = logging.getLogger(__name__)
-
-
-@deprecation.deprecated(deprecated_in='1.8.0',
- removed_in='2.0.0',
- details='Use fsl.utils.run.runfsl instead')
-def callFSL(*args):
- """Call a FSL command and return the result.
-
- You can pass the command and arguments as a single string, or as a
- list/tuple.
- """
-
- if fslplatform.fsldir is None:
- raise RuntimeError('FSL cannot be found!')
-
- # If we've been given a single argument,
- # assume it is a string containing the
- # command and its arguments. Otherwise,
- # assume it is a sequence containing
- # separate command and arguments.
- if len(args) == 1:
- args = args[0].split()
-
- args = list(args)
- args[0] = op.join(fslplatform.fsldir, 'bin', args[0])
-
- log.debug('callfsl: {}'.format(' '.join(args)))
-
- result = sp.check_output(args).decode('utf-8')
-
- log.debug('result: {}'.format(result))
-
- return result
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index cd2764ef9a9accc9a9f0f1a9d4f7e7837a687a8f..26706f31814ba805062fc04fdbc49abd205bda6f 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -17,7 +17,6 @@ import os
import os.path as op
import sys
import importlib
-import deprecation
import fsl.utils.notifier as notifier
@@ -73,34 +72,6 @@ are running the Linux/GTK wx build.
"""
-@deprecation.deprecated(deprecated_in='1.2.2',
- removed_in='2.0.0',
- details='Use fsleyes_widgets.isalive instead')
-def isWidgetAlive(widget):
- """Returns ``True`` if the given ``wx.Window`` object is "alive" (i.e.
- has not been destroyed), ``False`` otherwise. Works in both wxPython
- and wxPython/Phoenix.
-
- .. warning:: Don't try to test whether a ``wx.MenuItem`` has been
- destroyed, as it will probably result in segmentation
- faults. Check the parent ``wx.Menu`` instead.
- """
-
- import wx
-
- if platform.wxFlavour == platform.WX_PHOENIX:
- excType = RuntimeError
- elif platform.wxFlavour == platform.WX_PYTHON:
- excType = wx.PyDeadObjectError
-
- try:
- widget.GetParent()
- return True
-
- except excType:
- return False
-
-
class Platform(notifier.Notifier):
"""The ``Platform`` class contains a handful of properties which contain
information about the platform we are running on.
@@ -138,7 +109,6 @@ class Platform(notifier.Notifier):
self.WX_MAC_COCOA = WX_MAC_COCOA
self.WX_MAC_CARBON = WX_MAC_CARBON
self.WX_GTK = WX_GTK
- self.isWidgetAlive = isWidgetAlive
self.__inSSHSession = False
self.__inVNCSession = False
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index a5b9df816f9605edf62b8daa62d082142a898057..e4a4c51961c74c23554fca53cb3fd0394000467b 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -144,10 +144,6 @@ def run(*args, **kwargs):
exception is not raised. Ignored if ``submit`` is
specified.
- :arg err: Deprecated - use ``stderr`` instead.
-
- :arg ret: Deprecated - use ``exitcode`` instead.
-
:arg submit: Must be passed as a keyword argument. Defaults to ``None``.
If ``True``, the command is submitted as a cluster job via
the :func:`.fslsub.submit` function. May also be a
@@ -175,17 +171,6 @@ def run(*args, **kwargs):
``stderr``, and ``exitcode`` arguments.
"""
- if 'err' in kwargs:
- warnings.warn('err is deprecated and will be removed '
- 'in fslpy 2.0.0 - use stderr instead',
- DeprecationWarning)
- kwargs['stderr'] = kwargs.get('stderr', kwargs['err'])
- if 'ret' in kwargs:
- warnings.warn('ret is deprecated and will be removed '
- 'in fslpy 2.0.0 - use exitcode instead',
- DeprecationWarning)
- kwargs['exitcode'] = kwargs.get('exitcode', kwargs['ret'])
-
returnStdout = kwargs.get('stdout', True)
returnStderr = kwargs.get('stderr', False)
returnExitcode = kwargs.get('exitcode', False)