CHANGELOG.rst 49.4 KB
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.. |right_arrow|  unicode:: U+21D2
.. |command_key|  unicode:: U+2318
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.. |shift_key|    unicode:: U+21E7
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.. |control_key|  unicode:: U+2303
.. |eye_icon|     image::   images/eye_icon.png
.. |spanner_icon| image::   images/spanner_icon.png
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This document contains the ``fsleyes`` release history in reverse
chronological order.
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1.4.0 (Monday 2nd May 2022)
---------------------------
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Added
^^^^^


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* FSLeyes is now able to visualise TrackVis ``.trk`` and Mrtrix3 ``.tck``
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  tractogram files, containing tractography streamlines (!307, !312).
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* New *Invert modulata alpha* display setting (available via the
  ``--inverModulateAlpha`` command-line option), which can be used to
  make regions with high intensity more transparent (!311).
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* New ``--index`` command-line option for ``volume`` overlays, allowing
  the indices for all non-spatial dimensions to be specified (!304).
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* New option to display the coordinates for the current location on the
  canvases of an ortho view (available on the command-line via
  ``--showLocation``) (!314).
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* New option to control the location cursor width on ortho/lightbox views
  (available on the command-line via ``--cursorWidth``) (!314).
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Changed
^^^^^^^


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* Improvements to overlay blending, and default volume quality settings, in
  the 3D view (!309).
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Fixed
^^^^^


* Fixed an issue with loading FIRST subcortical segmentation VTK meshes (!306).
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* Fixed an issue with the ``--updatecheck`` commmand line argument (!306).
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* Fixed some bugs in the *File tree panel* (!315).
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Removed
^^^^^^^


* The ``--occlusion`` command-line option has been rendered obsolete by the
  improved 3D overlay blending, and so has been removed (along with the
  corresponding option in the 3D view settings panel).

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1.3.3 (Thursday 23rd December 2021)
-----------------------------------
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Fixed
^^^^^


* Fixed an issue with black screenshot images in some environments (e.g.
  SSH sessions in mobaxterm) (!301).
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* Removed ``pyobj-core`` and ``pyobjc-framework-cocoa`` from the list
  of dependencies (!302).
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1.3.2 (Thursday 9th December 2021)
----------------------------------


Fixed
^^^^^

* Fixed an issue with line vector display when running FSLeyes in an
  environment which doesn't support floating point textures (!299).


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1.3.1  (Thursday 2nd December 2021)
-----------------------------------


Fixed
^^^^^

* Updated Jupyter notebook integration to work with newer versions of
  ``ipykernel`` (!297).
* Various small tweaks for Python 3.10 compatibility (!297).


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1.3.0 (Monday 18th October 2021)
--------------------------------
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Added
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* The 3D view now allows the display location to be set to the corresponding
  location under the mouse on a volume overlay, by shift+clicking (!290).
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* The display range for a ``volume`` overlay can now be adjusted interactively
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  by |command_key| + |shift_key| + right clicking (|control_key| + |shift_key|
  on Linux) and dragging to select a region - the display range will be set to
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  the minimum/maximum voxel intensities within that region (!293).
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Changed
^^^^^^^


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* The *Sample along line* tool now supports 2D and multi-channel (e.g. RGB)
  images (currently plotting the mean intensity across channels for the
  latter).
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* Small improvementsto the *File* |right_arrow| *Add from XNAT* dialog (!291).
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Fixed
^^^^^

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* The **Display space** |right_arrow| *Scaled voxel coordinates* setting no
  longer applies a L/R flip for images with neurological data storage order
  (!289).
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* The high clipping range is no longer set when loading a Melodic image
  with the ``--autoDisplay`` / ``-ad`` option.(!293).
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1.2.0 (Monday 13th September 2021)
----------------------------------
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Added
^^^^^


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* The **Display space** setting can now be set to *Scaled voxel coordinates*
  on ortho and lightbox views. This causes all images to be displayed in
  scaled voxels, with the origin for each image set to the centre of voxel
  ``(0, 0, 0)`` (!286).


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Changed
^^^^^^^


* The *scale vectors to unit length* option for line vector overlays now
  scales the vector colouring, in addition to lengths (!285).


Fixed
^^^^^


* Fixed an issue on macOS / Big Sur whereby an image specified on the
  command-line could be loaded twice (!285).
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* Fixed some rendering issues for images stored as type ``NIFTI_TYPE_RGB24``
  (!285).
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1.1.0 (Friday 6th August 2021)
------------------------------
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Added
^^^^^


* New ``--interpolation`` option for ``mesh`` overlays, which allows
  nearest-neighbour or linear interpolation to be selected when colouring
  meshes with vertex data. This replaces the ``--flatShading`` option (!278).


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Changed
^^^^^^^


* The Location panel now displays the region label associated with the current
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  vertex for mesh overlays which are being coloured with a lookup table (!278).
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Fixed
^^^^^


* Fixed a bug which was preventing the same colour map or lookup table file to
  be specified more than once on the command line (!278).
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* Fixed the *Check for updates* menu item - it now queries ``conda-forge`` for
  the latest available FSLeyes version (!279).
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* Fixed a bug which had broken volume navigation in the time series view
  (!283).
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Deprecated
^^^^^^^^^^


* The ``--flatShading`` option for ``mesh`` overlays is equivalent to using
  ``--interpolation nearest`` (!278).


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1.0.15 (Thursday 22nd July 2021)
--------------------------------


Fixed
^^^^^


* Fixed a subtle bug affecting ``fsleyes render``, where taking a screenshot
  of a large 4D image could result in an infinite loop or segmentation fault
  (!275).


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1.0.14 (Friday 16th July 2021)
------------------------------


Fixed
^^^^^


* Fixed an issue with image copying, which could cause pixdims to be changed
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  slightly (!270).
* The x-axis of the power spectrum view can can now show frequencies of ICA
  power spectra for for MELODIC overlays (!271).
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1.0.13 (Tuesday 6th July 2021)
------------------------------


Fixed
^^^^^


* Fixed a circular import issue, affecting programmatic use of FSLeyes (!268).


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1.0.12 (Monday 28th June 2021)
------------------------------


Fixed
^^^^^


* Fixed an issue with Jupyter Notebook integration on macOS (!266).


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1.0.11 (Monday 14th June 2021)
------------------------------


Fixed
^^^^^


* Fixed a compatibility issue with NoMachine/x2go-like remote environments
  (!264).


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1.0.10 (Wednesday 2nd June 2021)
--------------------------------


Fixed
^^^^^


* Fixed an issue with removing data series from plot views (!262).


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1.0.9 (Wednesday 2nd June 2021)
-------------------------------


Fixed
^^^^^


* Fixed an issue with opening the overlay display panel in 3D views (!260).


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1.0.8 (Wednesday 26th May 2021)
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Changed
^^^^^^^


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* Gamma correction is no longer disabled when log scaling is active (!256).
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Fixed
^^^^^


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* Fixed a problem with API documentation generation (!256, !258).
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1.0.7 (Monday 24th May 2021)
----------------------------


Added
^^^^^


* New *logarithmic scaling* option (``--logScale`` on the command-line) for
  volume overlays, which causes voxel intensities to be mapped to the colour
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  map logarithmically, rather than linearly (!254).
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1.0.6 (Monday 24th May 2021)
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Changed
^^^^^^^


* Overlay display options which refer to other overlays (e.g. *Clip by*) now
  use the display name of the other overlay, rather than their file base name
  (!251).
* Restored compatibiilty with wxPython 4.0.* (!250).


Fixed
^^^^^


* Fixed a bug related to positioning of line vectors, tensors and FODs for
  images with non-isotropic voxels (!250).

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1.0.5 (Thursday 6th May 2021)
-----------------------------


Fixed
^^^^^

* Fixed some issues with shutting down cleanly (!248).
* Fixed a bug when saving a layout with plugin-provided view panels (!248).


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1.0.4 (Tuesday 4th May 2021)
----------------------------
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Changed
^^^^^^^


* Improved ortho edit mode performance on large images (!246).
* Suppressed some warning messages (!246).


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Fixed
^^^^^


* Fixed an issue with the :attr:`.PlotCanvas.limits` becoming out of sync with
  the ``matplotlib.Axes`` limits (!246).
* The ``file-tree`` library is now optional (!246).


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1.0.3 (Friday 23rd April 2021)
------------------------------


Fixed
^^^^^


* Fixed an issue with the management of built-in asset files (e.g. icons,
  colour maps, etc). Asset files are now located inside the ``fsleyes``
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  package directory (!244).
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1.0.2 (Thursday 22nd April 2021)
--------------------------------
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Fixed
^^^^^


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* Fixed some issues with FSLeyes plugin management (!242).
* Fixed some issues with GL initialisations on GTK2 versions of ``wxpython``
  (!242).
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* New ``--annotations`` command-line option, allowing annotations to be
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  loaded from a file into an ortho view (!242).
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1.0.1 (Tuesday 20th April 2021)
-------------------------------


Fixed
^^^^^


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* Fixed compatibility issues with recent versions of matplotlib (!240).
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1.0.0 (Monday 19th April 2021)
------------------------------
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Added
^^^^^


* The lighting effect in the 3D view is now applied to ``volume`` overlays
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  (OpenGL 2.1 or newer only) (!222).
* New ``--lightDistance`` option (for 3D view), allowing the distance of the
  light source from the centre of the display bounding box to be set (!222).
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* New ``--noBlendByIntensity`` option, for ``volume`` overlays in the 3D view,
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  allowing the modulation of samples by voxel intensity to be disabled (!222).
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* New ``-ixh``, ``-ixv``, ``-iyh``, ``-iyv``, ``-izh``, and ``-izv`` options,
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  allowing ortho canvases to be inverted vertically or horizontally (!225).
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* New ``--modulateMode`` option for ``rgbvector``, ``linevector``, ``tensor``
  and ``sh`` overlays, allowing modulation to be applied to either brightness
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  or transparency (!231).
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* New option to copy/paste 2D selections between slices when editing a NIFTI
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  image (!232).
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* New *annotation* panel, allowing simple shapes and text to be overlaid on
  the canvases of an ortho view. Annotations can be saved to/loaded from file,
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  via new options in the *Tools* menu (!233).
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* New *Sample along line* tool, allowing data from an image to be sampled
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  along a line and plotted (!235).
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Changed
^^^^^^^


* Text labels drawn on GL canvases are now created using ``matplotilb`` rather
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  than [Free]GLUT (!221).
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* Removed dependence on [Free]GLUT - this means that ``fsleyes render`` can
  now be used on headless systems without using ``xvfb-run``, as long as
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  `OSMesa <https://docs.mesa3d.org/osmesa.html>`_ is installed (!221).
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* The ``--lightPos`` command-line option (for the 3D view) has been changed to
  expect three rotation values (in degrees), which specify the position of the
  light source with respect to the centre of the display bounding box. This
  can be combined with the new ``--lightDistance`` option to specify the
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  position of the light source (!222).
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* FSLeyes no longer ignores the ``LIBGL_ALWAYS_INDIRECT`` environment
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  variable (!222).
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* FSLeyes attempts to determine a suitable value for ``PYOPENGL_PLATFORM``
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  if it is not already set (!222).
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* FSLeyes should now work with both Wayland/EGL and X11/GLX builds of wxPython
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  on Linux (!222).
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* The normalisation method used in the power spectrum panel has been adjusted
  so that, instead of the data being normalised to unit variance before the
  fourier transform, the fourier-transformed data itself is normalised to the
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  range [-1, 1] (!224).
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* The *Show command line for scene* option will display a warning if any
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  overlays are not saved (!226).
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* The :class:`.FileTreePanel` has been updated to work with the
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  new `file-tree <https://pypi.org/project/file-tree/>`_ library (!230).
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* Change to the interface for copying/pasting data between images - there is
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  now a single button for copying, pasting, and clearing the clipboard (!232).
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* :class:`.annotations.TextAnnotation` objects can now be positioned in the
  display coordinate system, in addition to being positioned at pixel locations
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  on a canvas (!232).
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* Changes to the FSLeyes plugin system to ease the development of FSLeyes
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  controls that use custom interaction profiles, and to improve switching
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  between different interaction proflies (!234).
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* The FSLeyes plugin system now supports tools which are bound to a specific
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  view panel (!234).
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* Many built-in FSLeyes control panels and tools have been migrated into the
  FSLeyes plugin system so that they are dynamically loaded as plugins, rather
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  than being hard-coded (!234).
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* It is now possible to save and re-load view/control panel layouts with
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  plugin-provided views and control panels (!234).
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Fixed
^^^^^

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* Various fixes and improvements to the lighting effect on ``mesh`` overlays
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  in the 3D view (!222).
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* When opening a ``melodic_IC.nii.gz`` file with the
  ``--autoDisplay'`/``-ad``, option, the ``melodic_IC`` file is now selected
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  by default, instead of the ``mean`` underlay (!219).
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* Fixed a bug in image texture preparation for complex data types, when
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  running in a limited GL environment (e.g. VNC) (!220).
* Compatibility fixes for newer versions of Jupyter `notebook` (!227).
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* Fixed a problem with macOS desktop integration - it should now be possible
  to open a file with FSLeyes as the default application, and to drag a file
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  onto the FSLeyes.app icon (!228).
* Improved stability when running under macOS+XQuartz (!229).
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* Fixed an issue with screenshots generated by ``fsleyes render`` containing
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  transparent pixels (!233).
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* Fixed a collision between the ``-mc`` and ``-a`` command-line options for
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  mesh overlays (!233).
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0.34.2 (Tuesday 14th July 2020)
-------------------------------


Fixed
^^^^^


* Added support for high-DPI scaling under macOS with wxPython >= 4.1.0 (!217).


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0.34.1 (Monday 13th July 2020)
------------------------------


Fixed
^^^^^


* Fixed an issue with Jupyter Notebook integration on conda+macOS installations
  (!215).
* Fixed an issue with the high-DPI option not appearing in the view settings panel
  under macOS (!215).


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0.34.0 (Wednesday 8th July 2020)
--------------------------------


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Added
^^^^^


* New option under the *Tools* menu which allows data from an image overlay to
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  be projected onto a surface overlay (!213).
* New *Flat shading* display option when viewing surfaces in 3D (!213).
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Changed
^^^^^^^


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* Tweaked GL initialisation to avoid errors when running via XQuartz (!211).
* Minor adjustment to Jupyter Notebook integration (!213).
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* NaN values in mesh overlay vertex data are now handled in the same manner as
  clipped values - previously they would be displayed in the low colour from the
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  selected colour map (!213).
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0.33.2 (Tuesday 23rd June 2020)
-------------------------------


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Added
^^^^^


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* Added some more line styles to the plotting panels (!206).
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* Added a new "accessible" lookup table, courtesy of Paul Tol
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  (https://personal.sron.nl/~pault/) (!206).
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Changed
^^^^^^^


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* Increased the default plotting line width (!206).
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* The default plot colours are now from a pre-generated accessible palette,
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  rather than being randomly generated (!206).
* The default plot line style is also rotated, in addition the plot colour
  (!206).
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* Adjusted the histogram panel so that, when plotting a probability histogram,
  the values are normalised by bin-width (!203).
* A minor adjustment to the default font, to improve readability on some
  platforms (!202).


Fixed
^^^^^


* Fixed an issue with FSLeyes not shutting down cleanly (!204).


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0.33.1 (Monday 8th June 2020)
-----------------------------


Changed
^^^^^^^

* Changed the :func:`.embed` function so that a parent ``wx`` object is
  not required.


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0.33.0 (Tuesday 26th May 2020)
------------------------------
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Added
^^^^^


* New *modulate alpha* option for volume and mesh overlays, which causes
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  opacity to be modulated by voxel/vertex intensity (!193).
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Changed
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* The minimum supported Python version is now 3.7, due to reliance upon
  a recent version of `fslpy` (!190).
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* The :func:`.embed` function accepts a ``mkFrame`` argument, allowing
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  it to be called without creating a :class:`.FSLeyesFrame` (!195).
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* A warning is now displayed in the location panel when images with different
  orientations, resolutions and/or fields-of-view are being displayed (!198).
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Fixed
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* Fixed a bug in the *Export data series* action, which was causing
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  a crash on macOS (!190).
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* Importing modules from the current directory in the Notebook/shell
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  environments is now possible within standalone versions of FSLeyes (!189).
* Fixed a small bug in the :func:`.embed` function (!189).
* Fixed a bug in the *Add from XNAT* action (!192).
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* Adjusted the Jupyter Notebook integration so it does not rely on the
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  existence of a command called ``jupyter-notebook`` (!191).
* Fixed a couple of bugs in the RGB vector overlay code (!194).
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* Fixed a bug in ortho edit mode (!196).
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0.32.3 (Monday 2nd March 2020)
------------------------------
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Fixed
^^^^^


* Fixed a bug which occurred when using 3D mode on platforms with
  limited OpenGL capabilities.
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* Fixed some minor issues in the file tree panel.
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0.32.2 (Friday 21st February 2020)
----------------------------------


Fixed
^^^^^


* The animated GIF changes in 0.32.1 broke movie mode.


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0.32.1 (Thursday 20th February 2020)
------------------------------------
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Changed
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* Any mesh overlay can now be displayed in the Freesurfer mesh coordinate
  system - not just Freesurfer meshes.
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* Internal changes to avoid using the deprecated
  ``nibabel.dataobj_images.DataobjImage.get_data`` method.


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Fixed
^^^^^


* Fixed a bug which caused mesh display to be corrupted when changing rows in
  the file tree panel.
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* Added support for high-DPI displays on platforms other than macOS.
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* Fixed a bug in animated GIF generation.
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* Fixed a bug which occurred when editing 4D images.
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0.32.0 (Thursday 7th November 2019)
-----------------------------------
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Added
^^^^^


* New ``--notebookFile`` command-line option, which starts the Jupyter notebook
  server, and opens a specified notebook file.
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* New option to change the location of the *Notes* column in the file treee
  panel.
* New ``--unitLength`` option for the *RGB vector* overlay type, which scales
  the vector data to unit length.
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* Metadata from JSON sidecar files (e.g. in BIDS data sets) is now displayed
  in the overlay information panel.
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Changed
^^^^^^^


* The :func:`.main.embed` function has been changed so that it now works in a
  synchronous manner, rather than using an asynchronous callback function.
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* The Jupyter notebook server is now configured so that its root directory
  is the current working directory.
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* Small valued regions are no longer shown in the atlas information panel.
  They are thresholded according to the ``lower`` threshold in the
  :class:`.AtlasDescription`.
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Fixed
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* Fixed a bug in :class:`.MeshOpts` bounds calculation.
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* Fixed a bug in Jupyter notebook integration, where an error in the notebook
  would stop the kernel from executing any more commands.
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* The *Robust FOV* and load/export affine transformation options now work
  with in-memory images.
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0.31.2 (Tuesday October 22nd 2019)
----------------------------------
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Changed
^^^^^^^


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* FSLeyes is now more lenient towards NIfTI images with extreme qform affines.
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* Various changes to improve GTK3 compatibility.
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* Various changes to reduce warnings and unnecessary output messages.
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Fixed
^^^^^


* Image texture data is now prepared off the main thread; this was the
  behaviour before version 0.30.0, but was accidentally disabled for that
  release.


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0.31.1 (Tuesday October 8th 2019)
---------------------------------


Fixed
^^^^^


* Fixed a bug in edit mode where the image texture would not get updated
  correctly in restricted environments (e.g. VNC) with certain image data
  types.


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0.31.0 (Thursday September 10th 2019)
-------------------------------------
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Added
^^^^^


* New *File tree* control panel, for viewing data contained in structured
  directories.
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* New ``complex`` overlay type, for displaying images with a complex data type.
* Support in plot panels for complex images - data from the real, imaginary,
  magnitude, and/or phase components can be plotted.
* New plot panel options to invert axes, and to apply scale/offsets.
* New power spectrum panel options to apply phase correction to complex image
  data.
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* The atlas panel has basic support for more general "Statistic" atlas types.
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* New *File* |right_arrow| *New image* menu option, a shortcut to create a
  new empty image.
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Changed
^^^^^^^


* Images with a complex data type are no longer split into separate real and
  imaginary ``volume`` overlays - they are loaded as a single image, and
  displayed as ``complex`` overlays.
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* The *Overlay* |right_arrow| *Copy* menu option now supports complex and
  RGB(A) images.
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* The plugin interface for tools has changed slightly - tools provided by
  FSLeyes plugins are now passed references to the :class:`.OverlayList`, the
  :class:`.DisplayContext`, and to the main :class:`.FSLeyesFrame`, to their
  ``__init__`` method.
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Fixed
^^^^^


* Fixed a bug in the :class:`.OverlayGroup` where old display settings were
  mistakenly being applied to newly added overlays.
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* Fixed a number of minor bugs in the plot panel logic.
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0.30.1 (Wednesday 7th August 2019)
----------------------------------
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* The *Crop* tool can now be used to expand the field-of-view of an image,
  in addition to cropping an image.
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* The label overlay ``--lut`` command-line option will accepts colour map
  files.
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Fixed
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* Added support for editing 2D images.
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* Fixed a bug in the mesh vertex picking logic which would occur when multiple
  views were open.
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0.30.0 (Thursday 27th June 2019)
--------------------------------
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Added
^^^^^


* The volume overlay type now has support for NIfTI images of type ``RGB24``
  and ``RGBA32``, via a new *Channel* setting.
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* New *RGB(A)* overlay type, for displaying the above image types.
* FSLeyes can now load bitmap images (e.g. ``.jpg``, ``.png``, etc.).  When a
  bitmap file is loaded it is internally converted into a 2D NIfTI image.
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* New alternative main function :func:`fsleyes.filtermain.main`, which filters
  out useless warnings that originate from underlying libraries (e.g. ``wx``,
  GTK, Cocoa, etc).
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* New ``--cliserver`` option, allowing command-line arguments to be passed
  to a single FSLeyes instance.
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Changed
^^^^^^^


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* The :mod:`fsleyes.gl.textures` package has been cleaned up and refactored
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  without any attempt to preserve backwards compatibility. Much of the texture
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  data handling code is now shared by the :class:`.Texture2D` and
  :class:`.Texture3D` classes.
* The :class:`.NiftiOpts` class has been moved into a separate module.
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* 2D NIfTI images are now displayed with a 2D texture - this means that
  the maximum dimension size for 2D images is now 16384 on typical
  hardware.
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* The *Freesurfer coordinates* coordinate space option is no longer available
  on non-freesurfer mesh overlays.
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0.29.0 (Sunday May 12th 2019)
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Added
^^^^^


* The *Tools* |right_arrow| *Resample image* option now allows an
  image to be resampled to the space of another image.
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* New ``-stdb`` and ``-std1mmb``  command-line options for loading
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  brain-extracted versions of the MNI152 templtes.


Fixed
^^^^^


* Fixed an issue where images with unconventional voxel storage orders were
  being transformed into the display coordinate system in a slightly
  inaccurate manner.
* FIxed an issue with orthographic edit mode being incorrectly disabled when
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  the selected overlay is changed.
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0.28.3 (Sunday April 14th 2019)
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-------------------------------


Fixed
^^^^^


* More PyOpenGL / read-only ``numpy`` array workarounds.


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0.28.2 (Sunday April 14th 2019)
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-------------------------------
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Changed
^^^^^^^

* The update check option does not verify SSL certificates when downloading
  the latest version string.


Fixed
^^^^^


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* Fixed an issue with the MIP overlay on macOS.
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* Workarounds for the inability of PyOpenGL to accept read-only ``numpy``
  arrays.
* Minimum required ``fslpy`` version is now 2.1, so that "compressed"
  voxelwise EVs (suh as those generated by `PNM
  <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_) are supported.


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0.28.1 (Monday April 8th 2019)
------------------------------


Fixed
^^^^^


* Fixed a bug in drag-and-drop functionality.


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0.28.0 (Friday April 5th 2019)
------------------------------
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Added
^^^^^


* Added metadata to allow better integration with Linux desktop environments.
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* Added ability to drag-and-drop files onto the FSLeyes window to open them.
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* The ``--vertexSet`` and ``--vertexData`` command-line options now cause the
  last vertex set/data to be selected, and also support GIFTI surface files
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  which contain multiple vertex sets and vertex data.
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* New :meth:`.ControlMixin.defaultLayout` method, which can be overridden by
  control panels (including plugins) to customise the default panel
  positioning/layout.
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Changed
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* FSLeyes no longer depends on the ``deprecation`` library.


Fixed
^^^^^


* Jupyter Notebook integration has been updated to work with newer versions
  of the ``ipykernel`` library.
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* Fixed bug with initial directory shown in open file dialogs.
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* Fixed a bug which would sometimes cause 4D image data display to be
  corrupted on macOS.
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* Fixed a bug which was preventing image textures from being updated when
  non-3D data regions were changed.
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Deprecated
^^^^^^^^^^


* The :func:`fsleyes.overlay.guessDataSourceType` function has been deprecated,
  as it has been replaced by the :func:`fsl.data.utils.guessType` function.


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


Fixed
^^^^^


* Fixed initialisation bug on platforms with a non-English language.


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