[Neuroimaging] ANN: NiBabel 3.2
bertrand.thirion at inria.fr
Tue Oct 20 12:29:43 EDT 2020
Thx Chris !
On 20/10/2020 15:55, Christopher Markiewicz wrote:
> Hi all,
> NiBabel 3.2 is released today. Python 3.6+ and Numpy 1.14+ are
> supported in this version. Please cite this version with
> doi:10.5281/zenodo.4109791 (https://doi.org/10.5281/zenodo.4109791).
> This release includes two new commandline utilities: nib-roi and
> nib-stats. nib-roi allows cropping and flipping images using Python
> slicing syntax. nib-stats, and the Python API nibabel.imagestats, is
> inspired by fslstats, and is intended to provide common calculations
> on images.
> Much thanks to new contributors Jonathan Daniel, Markéta Calábková,
> Carl Gauthier and Julian Klug, as well as familiar faces who have
> reported bugs, submitted PRs and especially reviewed contributions.
> The next planned minor release series will be 4.0, which will see some
> deprecations and removals, so please pay attention to any warnings
> that may be popping up. Judging from this last round, we can probably
> expect a release candidate around February or March.
> The full changelog follows.
> Most work on NiBabel so far has been by Matthew Brett (MB), Chris
> Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben
> Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav
> Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian
> Wassermann, Stephan Gerhard and Ross Markello (RM).
> References like "pr/298" refer to github pull request numbers.
> 3.2.0 (Tuesday 20 October 2020)
> New feature release in the 3.2.x series.
> New features
> * ``nib-stats`` CLI tool to expose new ``nibabel.imagestats`` API.
> Initial implementation of volume calculations, a la ``fslstats -V``.
> (pr/952) (Julian Klug, reviewed by CM and GitHub user 0rC0)
> * ``nib-roi`` CLI tool to crop images and/or flip axes (pr/947) (CM,
> reviewed by Chris Cheng and Mathias Goncalves)
> * Parser for Siemens "ASCCONV" text format (pr/896) (Brendan Moloney
> and MB, reviewed by CM)
> * Drop confusing mention of ``img.to_filename()`` in getting started
> guide (pr/946) (Fernando Pérez-Garcia, reviewed by MB, CM)
> * Implement ``to_bytes()``/``from_bytes()`` methods for
> ``Cifti2Image`` (pr/938) (CM, reviewed by Mathias Goncalves)
> * Clean up of DICOM documentation (pr/910) (Jonathan Daniel, reviewed
> by MB)
> Bug fixes
> * Use canvas manager API to set title in ``OrthoSlicer3D`` (pr/958)
> (EL, reviewed by CM)
> * Record units as seconds parrec2nii; previously set TR to seconds but
> retained msec units (pr/931) (CM, reviewed by MB)
> * Reflect on-disk dimensions in NIfTI-2 view of CIFTI-2 images
> (pr/930) (Mathias Goncalves and CM)
> * Fix outdated Python 2 and Sympy code in DICOM derivations (pr/911)
> (MB, reviewed by CM)
> * Change string with invalid escape to raw string (pr/909) (EL,
> reviewed by MB)
> * Fix typo in docs (pr/955) (Carl Gauthier, reviewed by CM)
> * Purge nose from nisext tests (pr/934) (Markéta Calábková, reviewed
> by CM)
> * Suppress expected warnings in tests (pr/949) (CM, reviewed by Dorota
> * Various cleanups and modernizations (pr/916, pr/917, pr/918, pr/919)
> (Jonathan Daniel, reviewed by CM)
> * SVG logo for improved appearance in with zooming (pr/914) (Jonathan
> Daniel, reviewed by CM)
> API changes and deprecations
> * Drop support for Numpy < 1.13 (pr/922) (CM)
> * Warn on use of ``onetime.setattr_on_read``, which has been a
> deprecated alias of ``auto_attr`` (pr/948) (CM, reviewed by Ariel Rokem)
> Chris Markiewicz
> Center for Reproducible Neuroscience
> Stanford University
> Neuroimaging mailing list
> Neuroimaging at python.org
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