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[WIP] Numba accelerated alpha filtrations #23

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[WIP] Numba accelerated alpha filtrations #23

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da9b064
First njit attempt
ulupo Nov 3, 2020
62e8671
Fix errors, use nopython=False
ulupo Nov 3, 2020
2f60589
Some code cleanup
ulupo Nov 4, 2020
3a8ef5f
Fix np.min to min
ulupo Nov 4, 2020
c43f8ea
Use contiguous arrays and @ operator
ulupo Nov 4, 2020
62bc3ff
Simplify if-else
ulupo Nov 4, 2020
3ff757d
Improve comments, use more idiomatic slicing
ulupo Nov 4, 2020
dc632f4
Remove else as it always needs to be executed, offer alternative in c…
ulupo Nov 4, 2020
a8afbeb
Merge branch 'master' into numba_accelerated_alpha
ulupo Jan 25, 2021
a49a7df
First stab using Miroslav Fiedler's method for determining the circum…
ulupo Jan 25, 2021
c0ef706
Fix function name
ulupo Jan 25, 2021
0929857
Remove numba decorator
ulupo Jan 25, 2021
3caac00
Fix indexing error
ulupo Jan 25, 2021
7e8c7c6
Use dict comprehension
ulupo Jan 25, 2021
a1da7f4
Make special loop for 1d simplices
ulupo Jan 25, 2021
47bee44
Change to a dimension-by-dimension approach to enumerate simplices mi…
ulupo Jan 26, 2021
dcd5c5e
Use cdist instead of pdist for performance
ulupo Jan 26, 2021
2faf22b
Use numba for pairwise distances
ulupo Jan 26, 2021
bfa68d3
Optimize numba function
ulupo Jan 26, 2021
f9e44ba
Fix error
ulupo Jan 26, 2021
ae8e1aa
Add convert to float step
ulupo Jan 26, 2021
334652e
Remove unused MIN_DET variable
ulupo Jan 26, 2021
14c4335
Remove itertools import
ulupo Jan 26, 2021
03bd604
Add numba requirement in setup.py
ulupo Jan 27, 2021
0173191
Minor improvements
ulupo Jan 27, 2021
26caa7f
Add idea folder to gitignore
ulupo Jan 27, 2021
e75b26a
Fully njitted version
ulupo Jan 28, 2021
765f724
Remove unused imports
ulupo Jan 28, 2021
0e34aa8
Avoid populating TypedDicts in python code by using "unsafe" numba fe…
ulupo Feb 1, 2021
b5801b4
Fix small mistake in populating simplices_
ulupo Feb 3, 2021
ca3f88d
Attempt to numerically control using condition numbers
ulupo Apr 22, 2021
3d8b9ef
Linting
ulupo Apr 22, 2021
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4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -5,4 +5,6 @@ cechmate.egg-info
.ipynb_checkpoints
.DS_Store

stubs
stubs

*.idea
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