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NBLAST score matrix builder v2 #69

Merged
merged 21 commits into from
Apr 12, 2022
Merged

NBLAST score matrix builder v2 #69

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c4b123d
conftest: minor fixture changes
clbarnes Nov 25, 2021
30abb72
Dotprops.__len__
clbarnes Nov 25, 2021
3528104
Initial implementation of smat builder
clbarnes Nov 25, 2021
989c648
Fix smat tests
clbarnes Nov 25, 2021
f7d0ae1
Significant refactor of smat.py
clbarnes Nov 25, 2021
7ad5732
smat: calculate digitizers from data
clbarnes Nov 26, 2021
902ed74
Fix tests, finish docs
clbarnes Nov 26, 2021
fa87ae3
smat: cache match results
clbarnes Nov 26, 2021
56d780c
Switch Blaster.append to return numerical indices
clbarnes Nov 29, 2021
f84d02b
Dotprops.dist_dots type annotation fix
clbarnes Nov 29, 2021
c2c79ac
small fixes
clbarnes Nov 29, 2021
57c557f
smat: write out unclipped bounds
clbarnes Nov 29, 2021
8fbee15
incorporate smat.lookup2d into blasting functions
clbarnes Nov 29, 2021
a7f5349
Lookup2d docs
clbarnes Nov 30, 2021
bf00b55
Smat building tutorial
clbarnes Nov 30, 2021
60c26dd
fix lru cache
clbarnes Nov 30, 2021
9246cfb
Remove ScoreFunction references
clbarnes Nov 30, 2021
62a1daa
fix limit_dist test
clbarnes Nov 30, 2021
e3ccc4d
Add SimpleLookup for non-float cases
clbarnes Dec 7, 2021
62b8094
WIP units
clbarnes Feb 9, 2022
dfc6b4b
Revert "WIP units"
clbarnes Apr 11, 2022
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -130,3 +130,5 @@ ENV/
#*.swc
#*.json
MANIFEST

tmp/
9 changes: 9 additions & 0 deletions docs/source/api.rst
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Expand Up @@ -364,6 +364,15 @@ Functions to compare morphology.
navis.synblast
navis.persistence_distances

Utilities for creating your own score matrices for NBLAST can be found in

.. autosummary::
:toctree: generated/

navis.nbl.smat.Lookup2d
navis.nbl.smat.Digitizer
navis.nbl.smat.LookupDistDotBuilder

Polarity metrics
----------------
.. autosummary::
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1 change: 1 addition & 0 deletions docs/source/gallery.rst
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Expand Up @@ -72,6 +72,7 @@ function. There you will also find more examples.
tutorials/nblast
tutorials/nblast_flycircuit
tutorials/nblast_hemibrain
tutorials/smat

.. raw:: html

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