[Neuroimaging] ANN: NiBabel 3.2

[Christopher Markiewicz]

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.

Best,
Chris

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)

Enhancements
------------
* 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)

Maintenance
-----------
* 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 Jarecka)
* 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

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