diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 29b0ea2c7218b81db7e3bfce6cc7c473bc03cbf7..804ea4d681206cf5712db304de05980d4c3757ea 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -148,18 +148,6 @@ variables:
- bash ./.ci/test_template.sh
-test:2.7:
- stage: test
- image: pauldmccarthy/fsleyes-py27-wxpy4-gtk2
- <<: *test_template
-
-
-test:3.4:
- stage: test
- image: pauldmccarthy/fsleyes-py34-wxpy4-gtk2
- <<: *test_template
-
-
test:3.5:
stage: test
image: pauldmccarthy/fsleyes-py35-wxpy4-gtk2
@@ -172,6 +160,12 @@ test:3.6:
<<: *test_template
+test:3.7:
+ stage: test
+ image: pauldmccarthy/fsleyes-py37-wxpy4-gtk2
+ <<: *test_template
+
+
#############
# Style stage
#############
@@ -197,7 +191,7 @@ build-doc:
- docker
stage: doc
- image: python:3.5
+ image: python:3.6
script:
- bash ./.ci/build_doc.sh
@@ -218,7 +212,7 @@ build-pypi-dist:
<<: *patch_version
stage: build
- image: python:3.5
+ image: python:3.6
tags:
- docker
@@ -242,7 +236,7 @@ deploy-doc:
<<: *setup_ssh
stage: deploy
when: manual
- image: python:3.5
+ image: python:3.6
tags:
- docker
@@ -259,7 +253,7 @@ deploy-pypi:
<<: *setup_ssh
stage: deploy
when: manual
- image: python:3.5
+ image: python:3.6
tags:
- docker
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1eee76621c908e57090146d99b9f96a00d72dd72..3d6b6527a88a63dd5eb408202c72f153f2eacb83 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,33 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+2.0.0 (Under development)
+-------------------------
+
+
+Added
+^^^^^
+
+* Simple built-in `.deprecated` decorator.
+
+
+Changed
+^^^^^^^
+
+* Removed support for Python 2.7 and 3.4.
+* Minimum required version of ``nibabel`` is now 2.3.
+* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
+ file handles.
+* Increased the minimum required version of ``dcm2niix``.
+
+
+Removed
+^^^^^^^
+
+
+* Many deprecated items removed.
+
+
1.12.0 (Sunday October 21st 2018)
---------------------------------
diff --git a/README.rst b/README.rst
index eadd675aa467956f9cf4d310ac8d5691112ab32c..bdd032b0c4ae2a65ad1ba6c91d6bf317e4a491d0 100644
--- a/README.rst
+++ b/README.rst
@@ -20,6 +20,9 @@ programming library written in Python. It is used by `FSLeyes
<https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
+``fslpy`` is tested against Python versions 3.5, 3.6 and 3.7.
+
+
Installation
------------
@@ -56,8 +59,8 @@ Some extra dependencies are listed in `requirements.txt
on the mesh.
-If you are using Linux, need to install wxPython first, as binaries are not
-available on PyPI. Change the URL for your specific platform::
+If you are using Linux, you need to install wxPython first, as binaries are
+not available on PyPI. Change the URL for your specific platform::
pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
@@ -76,6 +79,14 @@ Dependencies for testing and documentation are listed in the
`requirements-dev.txt <requirements-dev.txt>`_ file.
+Non-Python dependencies
+^^^^^^^^^^^^^^^^^^^^^^^
+
+
+The ``fsl.data.dicom`` module requires the presence of Chris Rorden's
+`dcm2niix <https://github.com/rordenlab/dcm2niix>`_ program.
+
+
Documentation
-------------
diff --git a/doc/fsl.utils.deprecated.rst b/doc/fsl.utils.deprecated.rst
new file mode 100644
index 0000000000000000000000000000000000000000..913da66ccc4e7bbeefa475a6bf738b96479997c2
--- /dev/null
+++ b/doc/fsl.utils.deprecated.rst
@@ -0,0 +1,7 @@
+``fsl.utils.deprecated``
+========================
+
+.. automodule:: fsl.utils.deprecated
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.rst b/doc/fsl.utils.rst
index 574c5296a19c8858702680f0ff14f220f85ef89d..d7bf157ed3154a6c3abe9fefe100da7548ea4087 100644
--- a/doc/fsl.utils.rst
+++ b/doc/fsl.utils.rst
@@ -6,6 +6,7 @@
fsl.utils.assertions
fsl.utils.cache
+ fsl.utils.deprecated
fsl.utils.ensure
fsl.utils.fslsub
fsl.utils.idle
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..b0b018c20e5c1955597fb75f6c740fc796ba861e 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
@@ -35,13 +34,15 @@ import fsl.data.constants as constants
import fsl.data.mesh as fslmesh
-ALLOWED_EXTENSIONS = ['.surf.gii']
+# We include '.gii' here because not all surface
+# GIFTIs follow the file suffix convention.
+ALLOWED_EXTENSIONS = ['.surf.gii', '.gii']
"""List of file extensions that a file containing Gifti surface data
is expected to have.
"""
-EXTENSION_DESCRIPTIONS = ['GIFTI surface file']
+EXTENSION_DESCRIPTIONS = ['GIFTI surface file', 'GIFTI file']
"""A description for each of the :data:`ALLOWED_EXTENSIONS`. """
@@ -306,48 +307,3 @@ 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..1b407a3f7c773066c13e75b5bb207de03986f9c3 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -29,19 +29,17 @@ and file names:
getExt
removeExt
defaultExt
- loadIndexedImageFile
"""
import os
import os.path as op
-import shutil
import string
import logging
import tempfile
+import warnings
import six
-import deprecation
import numpy as np
import scipy.ndimage as ndimage
@@ -53,6 +51,7 @@ import fsl.utils.transform as transform
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.data.constants as constants
import fsl.data.imagewrapper as imagewrapper
@@ -469,10 +468,10 @@ class Nifti(notifier.Notifier, meta.Meta):
self.__worldToVoxMat = transform.invert(self.__voxToWorldMat)
log.debug('Affine changed:\npixdims: '
- '{}\nsform: {}\nqform: {}'.format(
- header.get_zooms(),
- header.get_sform(),
- header.get_qform()))
+ '%s\nsform: %s\nqform: %s',
+ header.get_zooms(),
+ header.get_sform(),
+ header.get_qform())
self.notify(topic='transform')
@@ -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
@@ -821,10 +794,8 @@ class Image(Nifti):
incrementally updated as more data is read from memory
or disk.
- :arg indexed: If ``True``, and the file is gzipped, it is opened
- using the :mod:`indexed_gzip` package. Otherwise the
- file is opened by ``nibabel``. Ignored if ``loadData``
- is ``True``.
+ :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
@@ -839,10 +810,14 @@ class Image(Nifti):
"""
nibImage = None
- fileobj = None
+
+ if indexed is not False:
+ warnings.warn('The indexed argument is deprecated '
+ 'and has no effect',
+ category=DeprecationWarning,
+ stacklevel=2)
if loadData:
- indexed = False
threaded = False
# Take a copy of the header if one has
@@ -868,24 +843,8 @@ class Image(Nifti):
# The image parameter may be the name of an image file
if isinstance(image, six.string_types):
- image = op.abspath(addExt(image))
-
- # Use indexed_gzip to open gzip files
- # if requested - this provides fast
- # on-disk access to the compressed
- # data.
- #
- # If using indexed_gzip, we store a
- # ref to the file object - we'll close
- # it when we are destroyed.
- if indexed and image.endswith('.gz'):
- nibImage, fileobj = loadIndexedImageFile(image)
-
- # Otherwise we let nibabel
- # manage the file reference(s)
- else:
- nibImage = nib.load(image, **kwargs)
-
+ image = op.abspath(addExt(image))
+ nibImage = nib.load(image, **kwargs)
dataSource = image
# Or a numpy array - we wrap it in a nibabel image,
@@ -943,17 +902,16 @@ class Image(Nifti):
Nifti.__init__(self, nibImage.header)
- self.name = name
- self.__lName = '{}_{}'.format(id(self), self.name)
- self.__dataSource = dataSource
- self.__fileobj = fileobj
- self.__threaded = threaded
- self.__nibImage = nibImage
- self.__saveState = dataSource is not None
- self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
- self.name,
- loadData=loadData,
- threaded=threaded)
+ self.name = name
+ self.__lName = '{}_{}'.format(id(self), self.name)
+ self.__dataSource = dataSource
+ self.__threaded = threaded
+ self.__nibImage = nibImage
+ self.__saveState = dataSource is not None
+ self.__imageWrapper = imagewrapper.ImageWrapper(self.nibImage,
+ self.name,
+ loadData=loadData,
+ threaded=threaded)
# Listen to ourself for changes
# to the voxToWorldMat, so we
@@ -992,10 +950,6 @@ class Image(Nifti):
self.__nibImage = None
self.__imageWrapper = None
- if getattr(self, '__fileobj', None) is not None:
- self.__fileobj.close()
- self.__fileobj = None
-
def getImageWrapper(self):
"""Returns the :class:`.ImageWrapper` instance used to manage
@@ -1126,13 +1080,13 @@ class Image(Nifti):
# If an image size threshold has not been specified,
# then we'll calculate the full data range right now.
if sizethres is None or nbytes < sizethres:
- log.debug('{}: Forcing calculation of full '
- 'data range'.format(self.name))
+ log.debug('%s: Forcing calculation of full '
+ 'data range', self.name)
self.__imageWrapper[:]
else:
- log.debug('{}: Calculating data range '
- 'from sample'.format(self.name))
+ log.debug('%s: Calculating data range '
+ 'from sample', self.name)
# Otherwise if the number of values in the
# image is bigger than the size threshold,
@@ -1152,6 +1106,8 @@ class Image(Nifti):
if ``filename`` is ``None``.
"""
+ import fsl.utils.imcp as imcp
+
if self.__dataSource is None and filename is None:
raise ValueError('A file name must be specified')
@@ -1164,87 +1120,45 @@ class Image(Nifti):
if not looksLikeImage(filename):
filename = addExt(filename, mustExist=False)
- log.debug('Saving {} to {}'.format(self.name, filename))
+ log.debug('Saving %s to %s', self.name, filename)
- # If this Image is not managing its
- # own file object, and the image is not
- # memory-mapped, nibabel does all of
- # the hard work.
- newnibimage = False
- sample = self[(slice(0, 5),) + (0,) * (len(self.shape) - 1)]
- ismmap = isinstance(sample, np.memmap)
+ # We save the image out to a temp file,
+ # then close the old image, move the
+ # temp file to the real destination,
+ # then re-open the file.
+ tmphd, tmpfname = tempfile.mkstemp(suffix=getExt(filename))
+ os.close(tmphd)
- if self.__fileobj is None and (not ismmap):
- nib.save(self.__nibImage, filename)
-
- # If the image is memory-mapped, we need
- # to close and re-open the image
- elif self.__fileobj is None:
-
- # We save the image out to a temp file,
- # then close the old image, move the
- # temp file to the real destination,
- # then re-open the file.
- newnibimage = True
- tmphd, tmpfname = tempfile.mkstemp(suffix=op.splitext(filename)[1])
- os.close(tmphd)
-
- try:
- nib.save(self.__nibImage, tmpfname)
+ try:
+ nib.save(self.__nibImage, tmpfname)
- self.__nibImage = None
- self.header = None
+ # nibabel should close any old
+ # file handles when the image/
+ # header refs are deleted
+ self.__nibImage = None
+ self.header = None
- shutil.copy(tmpfname, filename)
+ imcp.imcp(tmpfname, filename, overwrite=True)
- self.__nibImage = nib.load(filename)
- self.header = self.__nibImage.header
+ self.__nibImage = nib.load(filename)
+ self.header = self.__nibImage.header
- except Exception:
- os.remove(tmpfname)
- raise
+ finally:
+ os.remove(tmpfname)
- # Otherwise we've got our own file
- # handle to an IndexedGzipFile
- else:
- # Currently indexed_gzip does not support
- # writing. So we're going to use nibabel
- # to save the image, then close and re-open
- # the file.
- #
- # Unfortunately this means that we'll
- # lose the file index (and fast random
- # access) - I'll fix this when I get a
- # chance to work on indexed_gzip a bit
- # more.
- #
- # Hopefully I should be able to add write
- # support to indexed_gzip, such that it
- # re-builds the index while writing the
- # compressed data. And then be able to
- # transfer the index generated from the
- # write to a new read-only file handle.
- newnibimage = True
- nib.save(self.__nibImage, filename)
- self.__fileobj.close()
- self.__nibImage, self.__fileobj = loadIndexedImageFile(filename)
- self.header = self.__nibImage.header
-
- # If we've created a new nibabel image,
+ # Because we've created a new nibabel image,
# we have to create a new ImageWrapper
# instance too, as we have just destroyed
# the nibabel image we gave to the last
# one.
- if newnibimage:
-
- self.__imageWrapper.deregister(self.__lName)
- self.__imageWrapper = imagewrapper.ImageWrapper(
- self.nibImage,
- self.name,
- loadData=False,
- dataRange=self.dataRange,
- threaded=self.__threaded)
- self.__imageWrapper.register(self.__lName, self.__dataRangeChanged)
+ self.__imageWrapper.deregister(self.__lName)
+ self.__imageWrapper = imagewrapper.ImageWrapper(
+ self.nibImage,
+ self.name,
+ loadData=False,
+ dataRange=self.dataRange,
+ threaded=self.__threaded)
+ self.__imageWrapper.register(self.__lName, self.__dataRangeChanged)
self.__dataSource = filename
self.__saveState = True
@@ -1349,7 +1263,7 @@ class Image(Nifti):
:arg sliceobj: Something which can slice the image data.
"""
- log.debug('{}: __getitem__ [{}]'.format(self.name, sliceobj))
+ log.debug('%s: __getitem__ [%s]', self.name, sliceobj)
return self.__imageWrapper.__getitem__(sliceobj)
@@ -1365,9 +1279,8 @@ class Image(Nifti):
"""
values = np.array(values)
- log.debug('{}: __setitem__ [{} = {}]'.format(self.name,
- sliceobj,
- values.shape))
+ log.debug('%s: __setitem__ [%s = %s]',
+ self.name, sliceobj, values.shape)
with self.__imageWrapper.skip(self.__lName):
@@ -1482,115 +1395,7 @@ def defaultExt():
return options.get(outputType, '.nii.gz')
+@deprecated.deprecated('2.0.0', '3.0.0', 'Use nibabel.load instead.')
def loadIndexedImageFile(filename):
- """Loads the given image file using ``nibabel`` and ``indexed_gzip``.
-
- Returns a tuple containing the ``nibabel`` NIFTI image, and the open
- ``IndexedGzipFile`` handle.
-
- If ``indexed_gzip`` is not present, the image is loaded normally via
- ``nibabel.load``.
- """
-
- import threading
-
- try:
- import indexed_gzip as igzip
- except ImportError:
- return nib.load(filename), None
-
- log.debug('Loading {} using indexed gzip'.format(filename))
-
- # guessed_image_type returns a
- # ref to one of the Nifti1Image
- # or Nifti2Image classes.
- ftype = nib.loadsave.guessed_image_type(filename)
- fobj = igzip.SafeIndexedGzipFile(
- filename=filename,
- spacing=4194304,
- readbuf_size=1048576)
-
- # See the read_segments
- # function below
- fobj._arrayproxy_lock = threading.Lock()
-
- fmap = ftype.make_file_map()
- fmap['image'].fileobj = fobj
- 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
+ """Deprecated - this call is equivalent to calling ``nibabel.load``. """
+ return nib.load(filename)
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 559c0d974f5563edbafef459870cbbb5b504ddac..b73cb879aaf88ffa1e742477b3625fd7da91a590 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -37,11 +37,10 @@ get their definitions straight:
"""
-import logging
-import collections
-import itertools as it
-
-import deprecation
+import logging
+import collections
+import collections.abc as abc
+import itertools as it
import numpy as np
import nibabel as nib
@@ -691,7 +690,7 @@ class ImageWrapper(notifier.Notifier):
# If we are slicing a scalar, the
# assigned value has to be scalar.
- if expNdims == 0 and isinstance(values, collections.Sequence):
+ if expNdims == 0 and isinstance(values, abc.Sequence):
if len(values) > 1:
raise IndexError('Invalid assignment: [{}] = {}'.format(
@@ -717,16 +716,6 @@ 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 +757,6 @@ 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
@@ -849,7 +829,7 @@ def sliceObjToSliceTuple(sliceobj, shape):
# The sliceobj could be a single sliceobj
# or integer, instead of a tuple
- if not isinstance(sliceobj, collections.Sequence):
+ if not isinstance(sliceobj, abc.Sequence):
sliceobj = [sliceobj]
# Turn e.g. array[6] into array[6, :, :]
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/deprecated.py b/fsl/utils/deprecated.py
new file mode 100644
index 0000000000000000000000000000000000000000..c79dddfeb9073420c4d5449edd42ed50d9783b40
--- /dev/null
+++ b/fsl/utils/deprecated.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+#
+# deprecated.py - Decorator for deprecating things.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module provides the :func:`deprecated` function, a simple decorator
+for deprecating functions and methods.
+"""
+
+
+
+import functools as ft
+import inspect
+import warnings
+
+
+_warned_cache = set()
+"""Used by the :func:`deprecated` function to keep track of whether a warning
+has already been emitted for the use of a deprecated item.
+"""
+
+
+def deprecated(vin=None, rin=None, msg=None):
+ """Decorator to mark a function or method as deprecated. A
+ ``DeprecationWarning`` is raised via the standard ``warnings`` module.
+
+ :arg vin: Optional version - the warning message will mention that the
+ function is deprecated from this version.
+
+ :arg rin: Optional version - the warning message will mention that the
+ function will be removed in this version.
+
+ :arg msg: Optional message to use in the warning.
+ """
+
+
+ if vin is not None and rin is not None:
+ msgfmt = '{{name}} is deprecated from version {vin} and will be ' \
+ 'removed in {rin}.'.format(vin=vin, rin=rin)
+ elif vin is not None:
+ msgfmt = '{{name}} is deprecated from version {vin}.'.format(vin=vin)
+ elif rin is not None:
+ msgfmt = '{{name}} is deprecated and will be removed in ' \
+ '{rin}.'.format(rin=rin)
+ else:
+ msgfmt = '{{name}} is deprecated.'
+
+ if msg is not None:
+ msgfmt = msgfmt + ' ' + msg
+
+ def wrapper(thing):
+ name = thing.__name__
+
+ def decorator(*args, **kwargs):
+
+ frame = inspect.stack()[1]
+ ident = '{}:{}'.format(frame.filename, frame.lineno)
+
+ if ident not in _warned_cache:
+ warnings.warn(msgfmt.format(name=name),
+ category=DeprecationWarning,
+ stacklevel=2)
+ _warned_cache.add(ident)
+
+ return thing(*args, **kwargs)
+ return ft.update_wrapper(decorator, thing)
+
+ return wrapper
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)
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index 2a5610dd89c172bec7b349d6e3400ad3b3cf21f6..f574eaa764a8e337cb7616f7eaef254e0dfd3a9d 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -34,9 +34,9 @@ And a few more functions are provided for working with vectors:
normalise
"""
-import numpy as np
-import numpy.linalg as linalg
-import collections
+import numpy as np
+import numpy.linalg as linalg
+import collections.abc as abc
def invert(x):
@@ -94,7 +94,7 @@ def scaleOffsetXform(scales, offsets):
:returns: A ``numpy.float32`` array of size :math:`4 \\times 4`.
"""
- oktypes = (collections.Sequence, np.ndarray)
+ oktypes = (abc.Sequence, np.ndarray)
if not isinstance(scales, oktypes): scales = [scales]
if not isinstance(offsets, oktypes): offsets = [offsets]
@@ -398,7 +398,7 @@ def axisBounds(shape,
if axes is None:
axes = [0, 1, 2]
- elif not isinstance(axes, collections.Iterable):
+ elif not isinstance(axes, abc.Iterable):
scalar = True
axes = [axes]
@@ -507,13 +507,13 @@ def _fillPoints(p, axes):
or an ``N*2`` or ``N*3`` array.
"""
- if not isinstance(p, collections.Iterable): p = [p]
+ if not isinstance(p, abc.Iterable): p = [p]
p = np.array(p)
if axes is None: return p
- if not isinstance(axes, collections.Iterable): axes = [axes]
+ if not isinstance(axes, abc.Iterable): axes = [axes]
if p.ndim == 1:
p = p.reshape((len(p), 1))
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 6728a23272696f295227291d723101cd366e7be5..d3fc2db2379224aa1f3582a1c8e6a96afc8ac164 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -85,21 +85,22 @@ and returned::
"""
-import itertools as it
-import os.path as op
-import os
-import re
-import sys
-import glob
-import random
-import string
-import fnmatch
-import inspect
-import logging
-import tempfile
-import warnings
-import functools
-import collections
+import itertools as it
+import os.path as op
+import collections.abc as abc
+import os
+import re
+import sys
+import glob
+import random
+import string
+import fnmatch
+import inspect
+import logging
+import tempfile
+import warnings
+import functools
+
import six
import nibabel as nib
@@ -282,7 +283,7 @@ def applyArgStyle(style, valsep=None, argmap=None, valmap=None, **kwargs):
# always returns a sequence
def fmtval(val):
- if isinstance(val, collections.Sequence) and \
+ if isinstance(val, abc.Sequence) and \
not isinstance(val, six.string_types):
val = [str(v) for v in val]
diff --git a/requirements-extra.txt b/requirements-extra.txt
index fa62f9919dfc96bbca30c655db0cb1ae8308641c..6d8a4c4b960fb3d8447940c410b486765be4fc41 100644
--- a/requirements-extra.txt
+++ b/requirements-extra.txt
@@ -1,4 +1,4 @@
-indexed_gzip>=0.7.0,<1
-wxpython>=3.0.2.0,<4.1
-trimesh>=2.22.28,<3
+indexed_gzip>=0.7.0
+wxpython==4.*
+trimesh>=2.22.28
rtree==0.8.3
diff --git a/requirements.txt b/requirements.txt
index 51e205639f8e3e8cc298b82ee5116106b036e907..ef041ad9cd02c2d53af3875cb4cecf7d2d077d5f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,4 @@
six==1.*
-deprecation>=1.*,<=2.*
numpy==1.*
-scipy>=0.18,<2
-nibabel==2.*
+scipy>=0.18
+nibabel>=2.3.1
diff --git a/setup.py b/setup.py
index d1212cc37dd875176bbbb267cdb5135787c0f00d..63a6da5b801304ac8f3867c7ab3832eb198aac5e 100644
--- a/setup.py
+++ b/setup.py
@@ -102,10 +102,9 @@ setup(
'Development Status :: 3 - Alpha',
'Intended Audience :: Developers',
'License :: OSI Approved :: Apache Software License',
- 'Programming Language :: Python :: 2.7',
- 'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
+ 'Programming Language :: Python :: 3.7',
'Topic :: Software Development :: Libraries :: Python Modules'],
packages=packages,
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index 9853c5a73a2b6d73cede0606638906f9f817a40d..80be87c74736f39cfa4134a3efa4e804d2ce0db3 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -225,7 +225,7 @@ def test_load_atlas():
reg.rescanAtlases()
probatlas = reg.loadAtlas('harvardoxford-cortical',
- indexed=True, calcRange=False, loadData=False)
+ calcRange=False, loadData=False)
probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
lblatlas = reg.loadAtlas('talairach')
@@ -240,7 +240,7 @@ def test_find():
reg.rescanAtlases()
probatlas = reg.loadAtlas('harvardoxford-cortical',
- indexed=True, calcRange=False, loadData=False)
+ calcRange=False, loadData=False)
probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
lblatlas = reg.loadAtlas('talairach')
@@ -273,7 +273,7 @@ def test_prepareMask():
reg.rescanAtlases()
probatlas = reg.loadAtlas('harvardoxford-cortical',
- indexed=True, loadData=False, calcRange=False)
+ loadData=False, calcRange=False)
probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
lblatlas = reg.loadAtlas('talairach')
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index 29676a09bb81fc0fb280bb602a80e34c8eb72825..f90c8d40618b78ea7f33e0c8168623fcdac31d7c 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -45,8 +45,7 @@ def _get_atlas(atlasID, res, summary=False):
kwargs = {}
else:
kwargs = {'loadData' : False,
- 'calcRange' : False,
- 'indexed' : True}
+ 'calcRange' : False}
atlas = fslatlases.loadAtlas(atlasID,
loadSummary=summary,
diff --git a/tests/test_atlasq_ohi.py b/tests/test_atlasq_ohi.py
index 36279ce693ec0cbeb7c783bf3ece588f6c32431d..2c0e4e7aadbeea076278f215b56a5e851458f43d 100644
--- a/tests/test_atlasq_ohi.py
+++ b/tests/test_atlasq_ohi.py
@@ -98,7 +98,6 @@ def test_coords(seed):
atlas = fslatlases.loadAtlas(
ad.atlasID,
resolution=2,
- indexed=True,
calcRange=False,
loadData=False)
diff --git a/tests/test_atlasq_query.py b/tests/test_atlasq_query.py
index 5ba48f9190fa9d23ec13d7fd231ec16fa283b66c..987cd01141211a28b26739bdb524d8bee3d9f039 100644
--- a/tests/test_atlasq_query.py
+++ b/tests/test_atlasq_query.py
@@ -241,7 +241,7 @@ def _eval_coord_voxel_query(
else:
exp = [q_type, squery, 'No label']
- _stdout = re.sub('\s+', ' ', stdout).strip()
+ _stdout = re.sub(r'\s+', ' ', stdout).strip()
assert _stdout.strip() == ' '.join(exp).strip()
def evalProbNormalOutput(expprops):
@@ -442,7 +442,6 @@ def test_bad_mask(seed):
atlas = fslatlases.loadAtlas(
atlasID,
loadSummary=use_label,
- indexed=True,
loadData=False,
calcRange=False)
ashape = list(atlas.shape[:3])
diff --git a/tests/test_callfsl.py b/tests/test_callfsl.py
deleted file mode 100644
index 25c972e386a2708a46f5fbcfeb139a995f63868b..0000000000000000000000000000000000000000
--- a/tests/test_callfsl.py
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-#
-# test_callfsl.py -
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-
-import os
-import os.path as op
-import subprocess as sp
-
-import numpy as np
-import nibabel as nib
-
-import mock
-import pytest
-
-import fsl.utils.callfsl as callfsl
-from fsl.utils.platform import platform as fslplatform
-
-import tests
-
-
-pytestmark = pytest.mark.fsltest
-
-
-def setup_module():
- fsldir = os.environ.get('FSLDIR', None)
- if fsldir is None or not op.exists(fsldir):
- raise Exception('FSLDIR is not set - callfsl tests cannot be run')
-
-
-# mock subprocess.check_output command
-# which expects 'fslstats -m filename'
-# or 'fslinfo ...'
-def mock_check_output(args):
- if args[0].endswith('fslinfo'):
- return 'info'.encode('utf-8')
-
- img = nib.load(args[-2])
- return str(img.get_data().mean()).encode('utf-8')
-
-
-def test_callfsl():
-
- with tests.testdir() as testdir:
-
- fname = op.join(testdir, 'myimage.nii.gz')
-
- img = tests.make_random_image(fname)
- img = img.get_data()
-
- # Pass a single string
- cmd = 'fslstats {} -m'.format(fname)
-
- with mock.patch('fsl.utils.callfsl.sp.check_output',
- mock_check_output):
- result = callfsl.callFSL(cmd)
-
- assert np.isclose(float(result), img.mean())
-
- # Or pass a list of args
- result = callfsl.callFSL(*cmd.split())
- assert np.isclose(float(result), img.mean())
-
- # Bad commands
- badcmds = ['fslblob', 'fslstats notafile']
-
- for cmd in badcmds:
- with pytest.raises((OSError, sp.CalledProcessError)):
- callfsl.callFSL(cmd)
-
- # No FSL - should crash
- cmd = 'fslinfo {}'.format(fname)
- with mock.patch('fsl.utils.callfsl.sp.check_output',
- mock_check_output):
- callfsl.callFSL(cmd)
-
- try:
- oldval = fslplatform.fsldir
- fslplatform.fsldir = None
- with pytest.raises(Exception):
- callfsl.callFSL(cmd)
- finally:
- fslplatform.fsldir = oldval
diff --git a/tests/test_idle.py b/tests/test_idle.py
index afa45b5ad3e1236b2d4fee4644b7f8f4659c1a03..13a8e3c98d679fb1fe5dcb10044fe163fe6f852b 100644
--- a/tests/test_idle.py
+++ b/tests/test_idle.py
@@ -89,7 +89,7 @@ def _wait_for_idle_loop_to_clear():
idle.idle(busywait)
while not idleDone[0]:
- wx.Yield()
+ wx.GetApp().Yield()
@pytest.mark.wxtest
diff --git a/tests/test_image.py b/tests/test_image.py
index 84a3d244542163e7c164a26a0408c336447af250..d468b4b76a2216b8045b7f2b15b947d4136c6510 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -307,7 +307,6 @@ def _test_Image_atts(imgtype):
assert tuple(i.nibImage.header.get_zooms()) == tuple(pixdims)
assert i.ndim == expndims
- assert i.ndims == expndims
assert i.dtype == dtype
assert i.name == op.basename(path)
assert i.dataSource == fslpath.addExt(path,
@@ -1048,9 +1047,9 @@ def test_image_resample(seed):
fname = op.join(td, 'test.nii')
# Random base image shapes
- for i in range(50):
+ for i in range(25):
- shape = np.random.randint(5, 100, 3)
+ shape = np.random.randint(5, 50, 3)
make_random_image(fname, shape)
img = fslimage.Image(fname, mmap=False)
@@ -1062,7 +1061,7 @@ def test_image_resample(seed):
# Random resampled image shapes
for j in range(10):
- rshape = np.random.randint(5, 100, 3)
+ rshape = np.random.randint(5, 50, 3)
resampled, xf = img.resample(rshape, order=0)
img.save('base.nii.gz')
diff --git a/tests/test_image_advanced.py b/tests/test_image_advanced.py
index 69756278781902081f2b8c3250d7eb6d40319a96..2be8678b603a9d716dc461f770ae65acd89c9173 100644
--- a/tests/test_image_advanced.py
+++ b/tests/test_image_advanced.py
@@ -57,7 +57,6 @@ def _test_image_indexed(threaded):
filename,
loadData=False,
calcRange=False,
- indexed=True,
threaded=threaded)
# First iteration through the image
@@ -72,6 +71,17 @@ def _test_image_indexed(threaded):
assert img.dataRange == (0, vol)
end1 = time.time()
+ # Double check that indexed_gzip is
+ # being used (the internal _opener
+ # attribute is not created until
+ # after the first data access)
+ try:
+ import indexed_gzip as igzip
+ assert isinstance(img.nibImage.dataobj._opener.fobj,
+ igzip.IndexedGzipFile)
+ except ImportError:
+ pass
+
# Second iteration through
start2 = time.time()
for vol in range(data.shape[-1]):
@@ -108,7 +118,6 @@ def _test_image_indexed_read4D(threaded):
filename,
loadData=False,
calcRange=False,
- indexed=True,
threaded=threaded)
# Test reading slice through
@@ -126,6 +135,14 @@ def _test_image_indexed_read4D(threaded):
assert np.all(data == np.arange(nvols))
+ # double check we're indexing as expected
+ try:
+ import indexed_gzip as igzip
+ assert isinstance(img.nibImage.dataobj._opener.fobj,
+ igzip.IndexedGzipFile)
+ except ImportError:
+ pass
+
@pytest.mark.igziptest
@pytest.mark.longtest
@@ -150,13 +167,20 @@ def _test_image_indexed_save(threaded):
filename,
loadData=False,
calcRange=False,
- indexed=True,
threaded=threaded)
# access some data
img[..., 0]
img[..., 40]
+ # double check that igzip is being used
+ try:
+ import indexed_gzip as igzip
+ assert isinstance(img.nibImage.dataobj._opener.fobj,
+ igzip.IndexedGzipFile)
+ except ImportError:
+ pass
+
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
@@ -203,10 +227,8 @@ def _test_image_indexed_save(threaded):
@pytest.mark.longtest
-@pytest.mark.igziptest
def test_image_no_calcRange_threaded(): _test_image_no_calcRange(True)
@pytest.mark.longtest
-@pytest.mark.igziptest
def test_image_no_calcRange_unthreaded(): _test_image_no_calcRange(False)
def _test_image_no_calcRange(threaded):
@@ -228,7 +250,6 @@ def _test_image_no_calcRange(threaded):
# cal_min/max if it is unknown
assert img.dataRange == (95, 643)
-
for i in [0, 7, 40]:
img[..., i]
if threaded:
@@ -238,10 +259,8 @@ def _test_image_no_calcRange(threaded):
@pytest.mark.longtest
-@pytest.mark.igziptest
def test_image_calcRange_threaded(): _test_image_calcRange(True)
@pytest.mark.longtest
-@pytest.mark.igziptest
def test_image_calcRange_unthreaded(): _test_image_calcRange(False)
def _test_image_calcRange(threaded):
diff --git a/tests/test_imagewrapper.py b/tests/test_imagewrapper.py
index 1237cd55d02966fc5596c32825dcec071f9c8b2e..61ed5c21bbdbccef14f769b4547f9fdb8c6fd8a4 100644
--- a/tests/test_imagewrapper.py
+++ b/tests/test_imagewrapper.py
@@ -465,7 +465,10 @@ def _test_expansion(coverage, slices, volumes, expansions):
# coverage, or in one of the expansions.
dimranges = []
for d in range(ndims):
- dimranges.append(np.linspace(nc[0, d], nc[1, d], nc[1, d] / 5, dtype=np.uint32))
+ dimranges.append(np.linspace(nc[0, d],
+ nc[1, d],
+ int(nc[1, d] / 5),
+ dtype=np.uint32))
points = it.product(*dimranges)
diff --git a/tests/test_platform.py b/tests/test_platform.py
index 4531f7534a0950ddf86753c88d8a02e09606f02d..67aefe094bedd91c19772c3d842841134faa07f8 100644
--- a/tests/test_platform.py
+++ b/tests/test_platform.py
@@ -208,33 +208,3 @@ def test_detect_ssh():
p = fslplatform.Platform()
assert not p.inSSHSession
assert not p.inVNCSession
-
-
-@pytest.mark.wxtest
-def test_IsWidgetAlive():
-
- import wx
-
- passed = [False]
- app = wx.App()
- frame = wx.Frame(None)
- btn = wx.Button(frame)
- frame.Show()
-
- def runtest():
-
- try:
-
- passed[0] = fslplatform.isWidgetAlive(btn)
-
- btn.Destroy()
-
- passed[0] = passed[0] and (not fslplatform.isWidgetAlive(btn))
- finally:
- frame.Destroy()
- app.ExitMainLoop()
-
- wx.CallLater(500, runtest)
- app.MainLoop()
-
- assert passed[0]
diff --git a/tests/test_vest.py b/tests/test_vest.py
index 84638a3ce0227fb00b9dbec438cc112cee05e47e..df74b5b8cf656f3a630d7cd29c2da988ab2b5321 100644
--- a/tests/test_vest.py
+++ b/tests/test_vest.py
@@ -9,6 +9,7 @@
import os.path as op
import shutil
import tempfile
+import warnings
import numpy as np
import pytest
@@ -166,9 +167,12 @@ def test_loadVestLutFile():
for i in range(4):
f = testfiles[i]
d = testdata[ i]
- dnorm = (d - d.min()) / (d.max() - d.min())
- lutnorm = vest.loadVestLutFile(f)
- lut = vest.loadVestLutFile(f, normalise=False)
+
+ with warnings.catch_warnings():
+ warnings.simplefilter('ignore')
+ dnorm = (d - d.min()) / (d.max() - d.min())
+ lutnorm = vest.loadVestLutFile(f)
+ lut = vest.loadVestLutFile(f, normalise=False)
assert lut.shape == d.shape
assert lutnorm.shape == dnorm.shape