NF: Add zstd compression support

[vanandrew]

Some stuff I was playing around with... This PR adds zstd compression/decompression support for the Opener class.

zstd (Zstandard) is a relatively new compression library that boasts significant improvements in compression/decompression speeds over zlib with minimal differences in compression ratios.

Results from bench_fileslice.py with zst added:

*************************
Bytes slice - raw (ratio)
*************************

+-----------------+--------------+--------------+--------------+--------------+
|                 |   mid int    |    step 1    | half step 1  | step mid int |
+=================+==============+==============+==============+==============+
| axis 0, len 64  | 0.73 (4.40)  | 0.23 (1.38)  | 0.21 (1.25)  | 0.19 (1.15)  |
| axis 1, len 64  | 0.02 (0.12)  | 0.17 (1.01)  | 0.13 (0.81)  | 0.02 (0.14)  |
| axis 2, len 32  | 0.01 (0.04)  | 0.12 (0.73)  | 0.13 (0.77)  | 0.02 (0.14)  |
| axis 3, len 100 | 0.00 (0.00)  | 0.15 (0.90)  | 0.09 (0.56)  | 0.00 (0.03)  |
+-----------------+--------------+--------------+--------------+--------------+
Base time: 0.17

************************
File slice - raw (ratio)
************************

+-----------------+--------------+--------------+--------------+--------------+
|                 |   mid int    |    step 1    | half step 1  | step mid int |
+=================+==============+==============+==============+==============+
| axis 0, len 64  | 1.19 (10.13) | 0.16 (1.40)  | 0.16 (1.36)  | 0.11 (0.96)  |
| axis 1, len 64  | 0.03 (0.24)  | 0.12 (1.04)  | 0.17 (1.44)  | 0.07 (0.59)  |
| axis 2, len 32  | 0.01 (0.07)  | 0.17 (1.42)  | 0.15 (1.28)  | 0.02 (0.15)  |
| axis 3, len 100 | 0.00 (0.01)  | 0.15 (1.31)  | 0.07 (0.60)  | 0.01 (0.04)  |
+-----------------+--------------+--------------+--------------+--------------+
Base time: 0.12

**********************
gz slice - raw (ratio)
**********************

+-----------------+--------------+--------------+--------------+--------------+
|                 |   mid int    |    step 1    | half step 1  | step mid int |
+=================+==============+==============+==============+==============+
| axis 0, len 64  | 3.21 (2.41)  | 1.32 (0.99)  | 1.15 (0.86)  | 1.15 (0.86)  |
| axis 1, len 64  | 1.23 (0.92)  | 1.19 (0.89)  | 1.29 (0.96)  | 1.64 (1.23)  |
| axis 2, len 32  | 1.36 (1.02)  | 1.19 (0.89)  | 1.27 (0.95)  | 1.31 (0.98)  |
| axis 3, len 100 | 0.58 (0.43)  | 1.21 (0.91)  | 0.58 (0.43)  | 0.60 (0.45)  |
+-----------------+--------------+--------------+--------------+--------------+
Base time: 1.34

***********************
zst slice - raw (ratio)
***********************

+-----------------+--------------+--------------+--------------+--------------+
|                 |   mid int    |    step 1    | half step 1  | step mid int |
+=================+==============+==============+==============+==============+
| axis 0, len 64  | 2.09 (4.08)  | 0.65 (1.27)  | 0.51 (0.99)  | 0.48 (0.94)  |
| axis 1, len 64  | 0.80 (1.56)  | 0.50 (0.98)  | 0.57 (1.11)  | 0.46 (0.91)  |
| axis 2, len 32  | 0.36 (0.71)  | 0.52 (1.01)  | 0.45 (0.89)  | 0.37 (0.72)  |
| axis 3, len 100 | 0.17 (0.34)  | 0.46 (0.89)  | 0.19 (0.37)  | 0.18 (0.36)  |
+-----------------+--------------+--------------+--------------+--------------+
Base time: 0.51

[pep8speaks]

Hello @vanandrew, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 nibabel.

Comment last updated at 2021-06-04 17:54:08 UTC

[codecov]

Codecov Report

Merging #1005 (258d0cd) into master (62aea04) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1005      +/-   ##
==========================================
- Coverage   92.26%   92.26%   -0.01%     
==========================================
  Files         100      100              
  Lines       12164    12201      +37     
  Branches     2128     2134       +6     
==========================================
+ Hits        11223    11257      +34     
- Misses        615      616       +1     
- Partials      326      328       +2     

Impacted Files	Coverage Δ
nibabel/analyze.py	98.52% <100.00%> (ø)
nibabel/brikhead.py	97.50% <100.00%> (ø)
nibabel/loadsave.py	93.84% <100.00%> (+1.25%)	⬆️
nibabel/minc1.py	90.24% <100.00%> (ø)
nibabel/openers.py	95.57% <100.00%> (+0.47%)	⬆️
nibabel/volumeutils.py	93.52% <100.00%> (-0.38%)	⬇️
nibabel/nifti1.py	92.10% <0.00%> (-0.46%)	⬇️
nibabel/filebasedimages.py	88.65% <0.00%> (+1.41%)	⬆️

---

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[effigies]

Thanks for this! Been a little burnt out, so trying to take it easy this week. If nobody does a proper review by next Monday, please feel free to @ me.

[effigies]

@vanandrew Thanks for your patience. Overall this looks good, and I wanted to try my suggestions before sending you down the rabbit hole, so I ended up just submitting vanandrew#1.

[vanandrew]

Almost forgot about this PR myself,,, Going on vacation starting next week, so I'll try to take a look at/merge vanandrew#1 this week before I leave.

[vanandrew]

Your changes seem fine to me. I merged in vanandrew#1.

[effigies]

Looks good. Thanks for the PR!