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FilFinder3d #57

Merged
merged 75 commits into from
Aug 26, 2024
Merged

FilFinder3d #57

merged 75 commits into from
Aug 26, 2024

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samdf96
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@samdf96 samdf96 commented Apr 3, 2020

Beginning work on 3D filaments.

  • FilFinder3D.py
    • Houses the FilFinder3D class object with functions.
  • test_graph.py
    • Houses a Networkx.Graph() object to be used for test cases. Also runs the test case with included FITS data.
  • project_test.py
    • deprecated, initial build functions -> converted into FilFinder3D class.
  • notes.txt
    • General notes and TODO list.

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coveralls commented Apr 3, 2020 •
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Coverage Status

Coverage decreased (-2.08%) to 70.042% when pulling ff08607 on samdf96:FilFinder3D into c2ee9f8 on e-koch:master.

@e-koch e-koch mentioned this pull request Jun 22, 2020
Merged
@e-koch e-koch force-pushed the FilFinder3D branch 2 times, most recently from 1bdce25 to 80e09b1 Compare May 12, 2021 20:20
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codecov bot commented May 12, 2021 •
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samdf96 and others added 25 commits April 19, 2024 09:53
@e-koch
Initial Work, see notes.txt
4a5b7a6
@e-koch
Updates to FilFinder3D class
33e598a
@e-koch
New Functions in FilFinder3D class
42210aa
@e-koch
Fixed errors in class. Added test case.
54b8b68
@e-koch
Test case FITS data added.
ee6775f
@e-koch
Updates to filament/branches
886a84e
@e-koch
filament_trimmer added
4016124
@e-koch
Move 3D code into main package; split out Filament classes
18fb94a
@e-koch
One more rename to prep for the PPP vs. PPV split
d2cce33
@e-koch
Start the PPV vs. PPP split; and split out functions common to both
2d02912
@e-koch
Add skan to required packages
539b2a0
@e-koch
skan needs pandas, but doesn't install it automatically I guess
26093a6
@e-koch
skan needs numba, so it's going to be an optional dependence
241f28e
@e-koch
Clean-up other skan imports
e3a66c9
@e-koch
Add testing with a dev version of skan
15b7a90
@e-koch
Add in using Skeleton from skan. Need to implement longest path fro…
5ec92ae 
…m there
@e-koch
Minimal longest path working
179f7dd
@e-koch
Basic pruning added for PPP filaments; trying to get a faster longest…
76907b6 
… path calculation working
@e-koch
Up max_npath
dd45b44
@e-koch
Pass arguments; fixes for the skeleton pruning
7fdfb43
@e-koch
Add 3D scatter plotting for skeletons
ed8ba46
@e-koch
Also need to skip branches that don't have an end point, where deleti…
27743c5 
…ng would split the overall connectivity
@e-koch
Remove useless node that comes in the conversion
86fc18b
@e-koch
Pixel coords need to be int
f0c8b7b
@e-koch
Add in creating the final pruned skeleton array
e708379
e-koch added 25 commits April 29, 2024 12:05
@e-koch
Add 3D to top level imports
e0c31ab
@e-koch
Fix for updated versions of Skan
20ed56b
@e-koch
Fix graph call for networkx >3
d6f3e46
@e-koch
Updates to fix skeleton graph creation
b2c1e10
@e-koch
Added returning list of label, y, x for each pixel in a labeled skeleton
93f9234
@e-koch
First attempt at handling perfect loops (note: only implemented for F…
a2f1ee5 
…ilFinderPPV for now)
@e-koch
Generate a docstring
1b3b90d
@e-koch
Optionally raise an error if the longest path calc fails
ae30d4f
@e-koch
Force min pixel number and dtype bool for skeletons
6330b15
@e-koch
Implement basic arctan flattening for images; WIP updates for 3D plot…
b0ff62c 
…ting
@e-koch
Prototype for 3D visualization of the skeleton with plotly
cb48ae6
@e-koch
Move single filament plotter to the filament object class
f562881
@e-koch
Update conftest
b786e2c
@e-koch
Fix -1 in coords relative to skan skeleton
8d10ec8
@e-koch
Remove one more instance of the -1 offset no longer needed
45e2894
@e-koch
Implement longest path spatial and spectral lengths; fix diff abs for…
63d3f2f 
… ppv spectral length
@e-koch
More -1 offsets...
4793c3a
@e-koch
Initial ppv simple tests; basic use w/o pruning passes
7004bcb
@e-koch
continued fun with +1 offsets; fixes for 3d pruning coord matches
80b7740
@e-koch
Passing 1 branch test for ppv
2979903
@e-koch
Comment out pickling test for FilamentPPV until implementation is com…
01978f3 
…plete
@e-koch
Add initial unit tests for spatial and spectral pruning
4b65a36
@e-koch
Implement spatial and spectral only pruning options for FilamentPPV
3837feb
@e-koch
Add warnings on use of 3D filaments in prep for initial merge to master
d17287c
@e-koch
Merge branch 'master' into FilFinder3D
a2eb672
@e-koch e-koch merged commit a2b5bbb into e-koch:master Aug 26, 2024
1 of 9 checks passed
@e-koch
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e-koch commented Aug 26, 2024

Merged in current versions here as they're partially tested and feature complete.

FilFinderPPV and FilFinderPPP both raise warnings when initializing to use with caution while still in development.

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3 participants
@samdf96 @coveralls @e-koch