CHANGELOG.rst 39 KB
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This document contains the ``fslpy`` release history in reverse chronological
order.
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3.6.0 (Under development)
-------------------------


Changed
^^^^^^^


* The :class:`.TaskThread` now allows an error handler function to be
  specified, which is run on the :mod:`.idle` loop.


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3.5.3 (Tuesday 9th February 2021)
---------------------------------


Fixed
^^^^^


* Fixed a bug in :func:`.featanalysis.loadClusterResults` (!281).


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3.5.2 (Friday 29th January 2021)
---------------------------------


Fixed
^^^^^


* Adjusted the :func:`.dicom.scanDir` function so that it will set a
  default value for ``SeriesDescription`` if it is not present in the
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  ``dcm2niix`` ``json`` output (!279).
* Fixed some issues with API documentation generation (!279).
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3.5.1 (Thursday 21st January 2021)
----------------------------------


Added
^^^^^


* New :func:`.featanalysis.loadFsf` function, for loading arbitrary ``.fsf``
  files (!276).


Fixed
^^^^^


* Adjustments to :mod:`.dicom` tests to work with different versions of
  ``dcm2niix`` (!277).


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3.5.0 (Wednesday 20th January 2021)
-----------------------------------
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Added
^^^^^


* New ``fsl_anat.tree``, for use with the :mod:`.filetree` package (!264).
* New :func:`.fsl_prepare_fieldmap` wrapper function (!265).
* The :class:`.fslmaths` wrapper now supports the ``fslmaths -s`` option
  via the :meth:`.fslmaths.smooth` method (!271).


Fixed
^^^^^


* Windows/WSL-specific workaround to the :func:`fsl.utils.run.run` function to
  avoid console windows from popping up, when used from a graphical program
  (!272).


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3.4.0 (Tuesday 20th October 2020)
---------------------------------


Added
^^^^^


* New :mod:`.tbss` wrapper functions for `TBSS
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS>`_ commands.


Changed
^^^^^^^


* Calls to functions in the :mod:`.assertions` module are disabled when a
  wrapper function is called with ``cmdonly=True``.


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3.3.3 (Wednesday 13th October 2020)
-----------------------------------


Changed
^^^^^^^


* The :func:`.fileOrImage` (and related) decorators will not manipulate the
  return value of a decorated function if an argument ``cmdonly=True`` is
  passed. This is so that wrapper functions will directly return the command
  that would be executed when ``cmdonly=True``.


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3.3.2 (Tuesday 12th October 2020)
---------------------------------


Changed
^^^^^^^


* Most :func:`.wrapper` functions now accept an argument called ``cmdonly``
  which, if ``True``, will cause the generated command-line call to be
  returned, instead of executed.


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3.3.1 (Thursday 8th October 2020)
---------------------------------


Changed
^^^^^^^


* The :func:`.affine.decompose` and :func:`.affine.compose` functions now
  have the ability to return/accept shear components.


Fixed
^^^^^


* Fixed a bug in the :func:`.affine.decompose` function which was corrupting
  the scale estimates when given an affine containing shears.

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3.3.0 (Tuesday 22nd September 2020)
-----------------------------------
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Added
^^^^^

* New ported versions of various core FSL tools, including ``imrm``, ``imln``,
  ``imtest``, ``fsl_abspath``, ``remove_ext``, ``Text2Vest``, and
  ``Vest2Text``.
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* New :func:`.gps` function, wrapping the FSL ``gps`` command.
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* New :func:`.vest.loadVestFile` and :func:`.vest.generateVest` functions.
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Changed
^^^^^^^


* Updates to the BIDS filetree specification.
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Fixed
^^^^^
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* The :class:`.CoefficientField` class now works with alternate reference
  images (i.e. a reference image with different dimensions to that which
  was originally used when the non-linear transformation was calculated).
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3.2.2 (Thursday 9th July 2020)
------------------------------


Changed
^^^^^^^


* The :func:`.fslsub.func_to_cmd` function allows more fine-grained control
  over whether the script file is removed after the job has finished running.

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3.2.1 (Tuesday 23rd June 2020)
------------------------------


Changed
^^^^^^^


* Minor updates to documentation.


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3.2.0 (Thursday 11th June 2020)
-------------------------------


Added
^^^^^


* A new :func:`.fslsub.hold` function to wait on previously submitted jobs, to
  be used in place of the ``wait`` function.
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Removed
^^^^^^^


* The :func:`.fslsub.wait` (and :func:`.run.wait`) function has been removed, as
  repeated calls to ``qstat`` can adversely affect the cluster job submission
  system.


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3.1.0 (Thursday 21st May 2020)
------------------------------
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Added
^^^^^


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* New :mod:`.cifti` module, providing classes and functions for working with
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  `CIFTI <https://www.nitrc.org/projects/cifti/>`_ data.
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* New :func:`.winpath` and :func:`wslpath` functions for working with paths
  when using FSL in a Windows Subsystem for Linux (WSL) environment.
* New :func:`.wslcmd` function for generating a path to a FSL command installed
  in a WSL environment.
* New :meth:`.Platform.fslwsl` attribute for detecting whether FSL is installed
  in a WSL environment.
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* New :meth:`.Image.niftiDataType` property.
* The :class:`.FileTree` class has been updated to allow creation of
  deep copies via the new :meth:`.FileTree.copy` method.


Changed
^^^^^^^


* :func:`.Image` objects created from ``numpy`` arrays will be NIFTI1 or
  NIFTI2, depending on the value of the ``$FSLOUTPUTTYPE`` environment
  variable.
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Fixed
^^^^^


* Updated the :func:`.fast` wrapper to support some single-character
  command-line flags.


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3.0.1 (Wednesday 15th April 2020)
---------------------------------


Changed
^^^^^^^


* The :func:`.isMelodicDir` function now accepts directories that do not end
  with ``.ica``, as long as all required files are present.
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* Added the ``dataclasses`` backport, so ``fslpy`` is now compatible with
  Python 3.6 again.
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3.0.0 (Sunday 29th March 2020)
------------------------------
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Added
^^^^^


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* New wrapper functions for the FSL :class:`.fslstats`, :func:`.prelude` and
  :func:`applyxfm4D` commands.
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* New ``firstDot`` option to the :func:`.path.getExt`,
  :func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
  rudimentary support for double-barrelled filenames.
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* The :func:`.nonlinear.applyDeformation` function now accepts a ``premat``
  affine, which is applied to the input image before the deformation field.
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* New :class:`.SubmitParams` class, providing a higer level interface for
  cluster submission.
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* New :meth:`.FileTree.load_json` and  :meth:`.FileTree.save_json` methods.
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Changed
^^^^^^^


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* ``fslpy`` now requires a minimum Python version of 3.7.
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* The default value for the ``partial_fill`` option to :meth:`.FileTree.read`
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  has been changed to ``False``. Accordingly, the :class:`.FileTreeQuery`
  calls the :meth:`.FileTree.partial_fill` method on the ``FileTree`` it is
  given.
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* The :func:`.gifti.relatedFiles` function now supports files with
  BIDS-style naming conventions.
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* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through any
  additional keyword arguments to ``subprocess.Popen`` or, if ``submit=True``,
  to :func:`fslsub.submit`.
* The :func:`.fslsub.submit` function now accepts an ``env`` option, allowing
  environment variables to be specified.
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* The :func:`.run.runfsl` function now raises an error on attempts to
  run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
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* The :mod:`.bids` module has been updated to support files with any
  extension, not just those in the core BIDS specification (``.nii``,
  ``.nii.gz``, ``.json``, ``.tsv``).
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* The return value of a function decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute
  called ``stdout``, instead of ``output``.
* Output files of functions decorated with :func:`.fileOrImage`,
  :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the
  :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
  results object, in addition to being accessed as dict items.
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* Wrapper functions decorated with the :func:`.fileOrImage`,
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  :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
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  arguments and return values through unchanged if an argument called ``submit``
  is passed in, and is set to ``True`` (or any non-``False``
  value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if
  any in-memory objects or ``LOAD`` symbols are passed.
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* The :func:`.fileOrText` decorator has been updated to work with input
  values - file paths must be passed in as ``pathlib.Path`` objects, so they
  can be differentiated from input values.
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* Loaded :class:`.Image` objects returned by :mod:`fsl.wrappers` functions
  are now named according to the wrapper function argument name.
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Fixed
^^^^^


* Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
  preparing shell command arguments, instead of performing a naive whitespace
  split.
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* Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
  functions.
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* Fixed the :func:`.DeformationField.transform` method so it works with
  a single set of coordinates.
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* :class:`.Image` creation does not fail if ``loadMeta`` is set, and a
  sidecar file containing invalid JSON is present.
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Removed
^^^^^^^


* Removed the deprecated ``.StatisticAtlas.proportions``,
  ``.StatisticAtlas.coordProportions``, and
  ``.StatisticAtlas.maskProportions`` methods.
* Removed the deprecated ``indexed`` option to :meth:`.Image.__init__`.
* Removed the deprecated ``.Image.resample`` method.
* Removed the deprecated ``.image.loadIndexedImageFile`` function.
* Removed the deprecatd ``.FileTreeQuery.short_names`` and
  ``.Match.short_name`` properties.
* Removed the deprecated ``.idle.inIdle``, ``.idle.cancelIdle``,
  ``.idle.idleReset``, ``.idle.getIdleTimeout``, and
  ``.idle.setIdleTimeout`` functions.
* Removed the deprecated ``resample.calculateMatrix`` function.


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2.8.4 (Monday 2nd March 2020)
-----------------------------


Added
^^^^^


* Added a new ``partial_fill`` option to :meth:`.FileTree.read`, which
  effectively eliminates any variables which only have one value. This was
  added to accommodate some behavioural changes that were introduced in 2.8.2.



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2.8.3 (Friday 28th February 2020)
---------------------------------


Fixed
^^^^^


* Fixed a bug in the :meth:`.Image.save` method.

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2.8.2 (Thursday 27th February 2020)
-----------------------------------


Fixed
^^^^^


* Fixed some subtle bugs in the :func:`.filetree.utils.get_all` function.


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2.8.1 (Thursday 20th February 2020)
-----------------------------------
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Fixed
^^^^^


* Fixed a bug where an error would be raised on attempts to load an image file
  without a BIDS-compatible name from a BIDS-like directory.

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2.8.0 (Wednesday 29th January 2020)
-----------------------------------
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Added
^^^^^


* New :meth:`.Nifti.adjust` method, for creating a copy of a :class:`.Nifti`
  header with adjusted shape, pixdims, and affine. This can be useful for
  creating a resampling reference.
* New :func:`.affine.rescale` function, for adjusting a scaling matrix.
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* New :func:`.mghimage.voxToSurfMat` function, for creating a
  voxel-to-freesurfer affine transform from any image.
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Changed
^^^^^^^


* The :class:`.ImageWrapper` now maintains its own image data cache, rather
  than depending on ``nibabel``.
* Internal changes to avoid using the deprecated
  ``nibabel.dataobj_images.DataobjImage.get_data`` method.


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Fixed
^^^^^


* Improved the algorithm used by the :func:`.mesh.needsFixing` function.
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* The :meth:`.fslmaths.run` method now accepts :attr:`.wrappers.LOAD` as an
  output specification.
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* Fixed a bug in the :class:`.Mesh` class to prevent indices from being loaded
  as floating point type.
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* Fixed a bug in the :func:`.resample` function.
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* Fixed a bug in the :class:`.MGHImage` class, which was causing pixdims to
  be overridden by scales derived from the affine.
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Deprecated
^^^^^^^^^^


* :func:`.calculateMatrix` - its functionality has been moved to the
  :func:`.affine.rescale` function.


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2.7.0 (Wednesday 6th November 2019)
-----------------------------------
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Added
^^^^^


* New ``until`` option to the :func:`.idle.block` function.
* New :meth:`.Idle.neverQueue` setting, which can be used to force all
  tasks passed to :func:`.idle.idle` to be executed synchronously.
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* New :meth:`.IdleLoop.synchronous` context manager, to temporarily change the
  value of :meth:`.IdleLoop.neverQueue`.
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* New :mod:`.bids` module, containing a few simple functions for working with
  `BIDS <https://bids.neuroimaging.io>`_ datasets.
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* New :func:`.image.loadMetadata` function, and ``loadMeta`` option to the
  :class:`.Image` class, to automatically find and load any sidecar JSON files
  associated with an image file.
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Changed
^^^^^^^


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* Internal reorganisation in the :mod:`.idle` module.
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Fixed
^^^^^


* Fixed incorrect usage of ``setuptools.find_packages``, which was causing
  unit tests to be installed.


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Deprecated
^^^^^^^^^^


* :func:`.idle.inIdle` - replaced by :meth:`.IdleLoop.inIdle`.
* :func:`.idle.cancelIdle` - replaced by :meth:`.IdleLoop.cancelIdle`.
* :func:`.idle.idleReser` - replaced by :meth:`.IdleLoop.idleReset`.
* :func:`.idle.getIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.
* :func:`.idle.setIdleTimeout` - replaced by :meth:`.IdleLoop.callRate`.


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2.6.2 (Monday 7th October 2019)
-------------------------------


Changed
^^^^^^^


* Added a debugging hook in the :mod:`.idle` module.
* The :func:`.fslsub.submit` function is now more flexible in the way it
  accepts the command and input arguments.
* The :func:`.run.prepareArgs` function has been renamed (from
  ``_prepareArgs``).


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2.6.1 (Thursday 19th September 2019)
------------------------------------


Changed
^^^^^^^


* ``fslpy`` is no longer tested against Python 3.5, and is now tested against
  Python 3.6, 3.7, and 3.8.


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2.6.0 (Tuesday 10th September 2019)
-----------------------------------
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Added
^^^^^


* New :meth:`.Image.iscomplex` attribute.
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* Support for a new ``Statistic`` atlas type.
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Changed
^^^^^^^


* The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
  as a least-recently-used cache.
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* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
  for the :mod:`.query` module to work with file tree hierarchies.
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* The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
  either a binary mask, or a mask with the original label value, to be
  returned.
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* The :mod:`.dicom` module has been updated to work with the latest version of
  ``dcm2niix``.
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Deprecated
^^^^^^^^^^


* :meth:`.ProbabilisticAtlas.proportions`,
  :meth:`.ProbabilisticAtlas.maskProportions`, and
  :meth:`.ProbabilisticAtlas.labelProportions` have been deprecated in favour
  of :meth:`.StatisticAtlas.values`, :meth:`.StatisticAtlas.maskValues`, and
  :meth:`.StatisticAtlas.labelValues`
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2.5.0 (Tuesday 6th August 2019)
-------------------------------
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Added
^^^^^


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* New :meth:`.Image.getAffine` method, for retrieving an affine between any of
  the voxel, FSL, or world coordinate systems.
* New :mod:`fsl.transforms` package, which contains classes and functions for
  working with linear and non-linear FLIRT and FNIRT transformations.
* New static methods :meth:`.Nifti.determineShape`,
  :meth:`.Nifti.determineAffine`, :meth:`.Nifti.generateAffines`, and
  :meth:`.Nifti.identifyAffine`.
* New prototype :mod:`fsl.transforms.x5`  module, for reading/writing linear
  and non-linear X5 files (*preliminary release, subject to change*).
* New prototype :mod:`.fsl_convert_x5` :mod:`.fsl_apply_x5` programs, for
  working with X5 transformations (*preliminary release, subject to change*).

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Changed
^^^^^^^


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* The :mod:`.vest.looksLikeVestLutFile` function has been made slightly more
  lenient.
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* `h5py <https://www.h5py.org/>`_ has been added to the ``fslpy`` dependencies.


Deprecated
^^^^^^^^^^


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* The :mod:`fsl.utils.transform` module has been deprecated; its functions can
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  now be found in the :mod:`fsl.transforms.affine` and
  :mod:`fsl.transform.flirt` modules.
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2.4.0 (Wednesday July 24th 2019)
--------------------------------


Added
^^^^^


* New :mod:`.image.roi` module, for extracting an ROI of an image, or expanding
  its field-of-view.


Changed
^^^^^^^


* The :mod:`.resample_image` script has been updated to support resampling of
  images with more than 3 dimensions.


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2.3.1 (Friday July 5th 2019)
----------------------------


Fixed
^^^^^


* The :class:`.Bitmap` class now supports greyscale images and palette images.


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2.3.0 (Tuesday June 25th 2019)
------------------------------
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Added
^^^^^


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* New :class:`.Bitmap` class, for loading bitmap images. The
  :meth:`.Bitmap.asImage` method can be used to convert a ``Bitmap`` into
  an :class:`.Image`.
* The :class:`.Image` class now has support for the ``RGB24`` and ``RGBA32``
  NIfTI data types.
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* New :attr:`.Image.nvals` property, for use with ``RGB24``/``RGBA32``
  images.
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* New :meth:`.LabelAtlas.get` and :meth:`ProbabilisticAtlas.get` methods,
  which return an :class:`.Image` for a specific region.
* The :meth:`.AtlasDescription.find` method also now a ``name`` parameter,
  allowing labels to be looked up by name.
* New :meth:`.FileTree.defines` and :meth:`.FileTree.on_disk` methods, to
  replace the :func:`.FileTree.exists` method.


Fixed
^^^^^


* The :func:`.makeWriteable` function will always create a copy of an
  ``array`` if its base is a ``bytes`` object.
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* Fixed a bug in the :meth:`.GitfitMesh.loadVertices` method.
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* Fixed a bug in the :meth:`.Mesh.addVertices` method where the wrong face
  normals could be used for newly added vertex sets.
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2.2.0 (Wednesday May 8th 2019)
------------------------------
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Added
^^^^^


* New :mod:`.resample_image` script.
* New :mod:`.resample` module (replacing the :func:`.Image.resample` method),
  containing functions to resample an :class:`.Image`.
* New :func:`.resample.resampleToPixdim` and
  :func:`.resample.resampleToReference` functions, convenience wrappers around
  :func:`.resample.resample`.
* New :func:`.idle.block` function.


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Changed
^^^^^^^


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* The :func:`.resample` function (formerly :meth:`.Image.resample`) now
  accepts ``origin`` and ``matrix`` parameters, which can be used to adjust
  the alignment of the voxel grids of the input and output images.
* The :func:`.transform.decompose` function now accepts both ``(3, 3)``
  and ``(4, 4)`` matrices.


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Fixed
^^^^^


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* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
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Deprecated
^^^^^^^^^^


* The :meth:`.Image.resample` method has been deprecated in favour of the
  :func:`.resample.resample` function.
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2.1.0 (Saturday April 13th 2019)
--------------------------------
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Added
^^^^^


* New tensor conversion routines in the :mod:`.dtifit` module (Michiel
  Cottaar).
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* New :func:`.makeWriteable` function which ensures that a ``numpy.array`` is
  writeable, and creates a copy if necessary
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Changed
^^^^^^^


* The :class:`.GiftiMesh` class no longer creates copies of the mesh
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  vertex/index arrays. This means that, these arrays will be flagged as
  read-only.
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* The :class:`.Mesh` class handles vertex data sets requiring different
  triangle unwinding orders, at the cost of potentially having to store
  two copies of the mesh indices.
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Fixed
^^^^^


* The :class:`.FeatDesign` class now handles "compressed" voxelwise EV files,
  such as those generated by `PNM
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_.


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2.0.1 (Monday April 1st 2019)
-----------------------------


Fixed
^^^^^


* Fixed a bug with the :func:`.gifti.relatedFiles` function returning
  duplicate files.


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2.0.0 (Friday March 20th 2019)
------------------------------
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Added
^^^^^

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* New :mod:`fsl.utils.filetree` package for defining and working with
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  file/directory templates (Michiel Cottaar).
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* Simple built-in :mod:`.deprecated` decorator.
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* New :mod:`fsl.data.utils` module, which currently contains one function
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  file/directory paths.
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Changed
^^^^^^^

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* Removed support for Python 2.7 and 3.4.
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* Minimum required version of ``nibabel`` is now 2.3.
* The :class:`.Image` class now fully delegates to ``nibabel`` for managing
  file handles.
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* The :class:`.GiftiMesh` class can now load surface files which contain
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  vertex data, and will accept surface files which end in ``.gii``, rather
  than requiring files which end in ``.surf.gii``.
* The ``name`` property of :class:`.Mesh` instances can now be updated.
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Removed
^^^^^^^

* Many deprecated items removed.


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Deprecated
^^^^^^^^^^


* Deprecated the :func:`.loadIndexedImageFile`  function, and the ``indexed``
  flag to the :class:`.Image` constructor.


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1.13.3 (Friday February 8th 2019)
---------------------------------


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Fixed
^^^^^

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* Fixed an issue with the :func:`.dicom.loadSeries` using memory-mapping for
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  image files that would subsequently be deleted.
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* Fixed an issue in the :class:`.GiftiMesh` class, where
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  ``numpy``/``nibabel`` was returning read-only index arrays.


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1.13.2 (Friday November 30th 2018)
----------------------------------


Changed
^^^^^^^


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* The :meth:`.Image.resample` method now supports images with more than three
  dimensions.
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* The :func:`fsl.utils.fslsub.submit` now returns the job-id as a string
  rather than a one-element tuple. It now also accepts a nested sequence
  of job ids rather than just a flat sequence. This will also changes the
  output from the function wrappers in :mod:`fsl.wrappers` if submitted.
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Fixed
^^^^^
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* Fix to the :class:`.ImageWrapper` regarding complex data types.


1.13.1 (Friday November 23rd 2018)
----------------------------------
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Fixed
^^^^^


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* Added a missing ``image`` attribute in the :class:`.VoxelwiseConfoundEV`
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  class.
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* Make sure that FEAT ``Cluster`` objects (created by the
  :func:`.loadClusterResults` function) contain ``p`` and ``logp`` attributes,
  even when cluster thresholding was not used.
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1.13.0 (Thursday 22nd November 2018)
------------------------------------
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Added
^^^^^

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* New wrapper functions for :func:`.fsl_anat`, :func:`.applytopup` (Martin
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  Craig).
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* New :func:`.fileOrText` decorator for use in wrapper functions (Martin
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  Craig).


Changed
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^^^^^^^

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* Various minor changes and enhancements to the FSL function :mod:`.wrappers`
  interfaces (Martin Craig).
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Fixed
^^^^^

* The ``immv`` and ``imcp`` scripts now accept incorrect file extensions on
  input arguments.
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1.12.0 (Sunday October 21st 2018)
---------------------------------
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Changed
^^^^^^^


* The ``extract_noise`` script has been renamed to :mod:`.fsl_ents`.
* Increased the minimum required version of ``dcm2niix`` in the
  :mod:`fsl.data.dicom` module.


Deprecated
^^^^^^^^^^


* The ``extract_noise`` script.


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1.11.1 (Friday September 14th 2018
----------------------------------


Fixed
^^^^^


* Fixed a Python 2 incompatibility in the :mod:`.settings` module.


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1.11.0 (Thursday September 13th 2018)
-------------------------------------


Added
^^^^^


* A couple of new convenience functions to the :mod:`.settings` module.


Changed
^^^^^^^


* Development (test and documentation dependencies) are no longer listed
  in ``setup.py`` - they now need to be installed manually.
* Removed conda build infrastructure.


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1.10.3 (Sunday September 9th 2018)
----------------------------------


Added
^^^^^


* The :func:`.parseVersionString` function accepts (and ignores) `local
  version identifer
  <https://www.python.org/dev/peps/pep-0440/#local-version-identifiers>`_
  strings.


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1.10.2 (Friday September 7th 2018)
----------------------------------


Fixed
^^^^^


* The :meth:`.Image.save` method was not handling memory-mapped images
  correctly.


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1.10.1 (Friday August 3rd 2018)
-------------------------------


Changed
^^^^^^^


* Minor adjustmenets to improve Windows compatibility.


Fixed
^^^^^

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* The :mod:`.FEATImage.getCOPE` method was returning PE images.
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1.10.0 (Wednesday July 18th 2018)
---------------------------------
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Added
^^^^^


* A new script, :mod:`.extract_noise`, which can be used to extract ICA
  component time courses from a MELODIC ICA analysis.
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