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Adding periodic boundary condition support to tobac #127

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merged 94 commits into from
Feb 8, 2023
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7470e4c
Update feature_detection.py
galexsky Sep 14, 2021
d6fc85d
Updated documentation
freemansw1 Nov 11, 2021
7ac7bb2
Update analysis.rst
galexsky Nov 11, 2021
41da11e
Update installation.rst
galexsky Nov 11, 2021
250b69d
Updated documentation (#2)
freemansw1 Nov 11, 2021
df6b6b0
Updated the tracking function to the new, faster option (#4)
freemansw1 Nov 11, 2021
d158a9f
Merge branch 'master' into updated_docs
freemansw1 Nov 12, 2021
7685da1
Added conf.py for sphinx to the doc folder.
freemansw1 Nov 12, 2021
68d6d99
Added API docs
freemansw1 Nov 12, 2021
c79d80a
Switched centerofgravity documentation to numpy style
freemansw1 Nov 12, 2021
a1f6e16
Continued updates to the docstrings to match numpy formatting
freemansw1 Nov 12, 2021
7547471
Merge branch 'master' into dev
freemansw1 Nov 16, 2021
83f2281
Updated most docstrings on the remainder of the functions
freemansw1 Nov 16, 2021
d285d89
Merge pull request #8 from freemansw1/updated_docs
freemansw1 Nov 16, 2021
64290af
Merge branch 'master' into dev
freemansw1 Nov 16, 2021
4e4a8bd
Speeding up 2D feature detection using what we learned from 3D (#10)
freemansw1 Nov 22, 2021
7ed73a1
Updated to remove reference to depreciated function (#11)
freemansw1 Nov 30, 2021
f4297ce
Merge branch 'master' into dev
freemansw1 Jan 4, 2022
50c339f
added pip to the docker file because it is not automatically installe…
freemansw1 Jan 4, 2022
18d5a3e
Combining 2D and 3D code and speedups to both (#19)
freemansw1 Feb 21, 2022
32b1131
Added new 3D and PBC segmentation
galexsky Feb 23, 2022
bc53463
Fixed a bug with the n_erosion_threshold in 3D
freemansw1 Feb 23, 2022
b1c70e0
Moved some common functions to the utils module
freemansw1 Mar 10, 2022
9183193
Removed deprecaded code, updated args
galexsky Mar 11, 2022
f880ebd
Added missing seed_3D_flag
galexsky Mar 11, 2022
c42f401
Starting to clean up
freemansw1 Mar 14, 2022
57c9fb8
continuing to clean up code, started process of adding tests
freemansw1 Mar 18, 2022
9000ae1
More cleanup of segmentation, adding more tests to segmentation and f…
freemansw1 Mar 18, 2022
a83ef75
Cleaning up of segmentation code, updating tests, cleaning up other code
freemansw1 Mar 20, 2022
b9309c9
More cleaning up of segmentation
freemansw1 Mar 20, 2022
9b7ec69
Added compatibility of new PBC segmentation with 2D data
freemansw1 Mar 20, 2022
c25c247
fixed more bugs in segmentation with 2D inputs
freemansw1 Mar 21, 2022
f7b945a
Adding more tests to PBC segmentation
freemansw1 Mar 22, 2022
897bcab
Added corner test case where it fails
freemansw1 Mar 24, 2022
46de448
Potential fix to corner point bug
freemansw1 Mar 24, 2022
0d52522
Moved get_pbc_coordinates to utilities so that we can use it for segm…
freemansw1 Mar 24, 2022
0141005
Updated docs, added start to test function for 3D box
freemansw1 Mar 24, 2022
f9b18b3
Added notes to myself
freemansw1 Mar 24, 2022
e581250
Added comments and todos
freemansw1 Mar 24, 2022
22e22c2
Update segmentation.py
galexsky Mar 24, 2022
e0c75fb
Revert "Update segmentation.py"
freemansw1 Mar 24, 2022
77a80a7
Added new comments explaining PBC seg approach
galexsky Mar 24, 2022
f21b05a
Updated non PBC seed box code
freemansw1 Mar 24, 2022
7aa0b37
Added code coverage files to gitignore
freemansw1 Mar 25, 2022
b4cbe35
Segmentation now transposes to improve code readability
freemansw1 Mar 27, 2022
3a0d777
Added new test to theoretically check buddy box
freemansw1 Mar 27, 2022
e096d88
Got buddy boxes working for more cases
freemansw1 Mar 28, 2022
55c2f9f
Added new test that tests buddy box better.
freemansw1 Mar 28, 2022
c72bc66
Fixed wall_label overwrite procedure
galexsky Apr 4, 2022
e2c9d5f
Fixed buddy box segmentation bug.
freemansw1 Apr 6, 2022
ab42d31
fixed github actions dockerfile location
freemansw1 Apr 6, 2022
e24e2f9
Added 3D segmentation with PBCs. (#21)
freemansw1 Apr 8, 2022
e5fbd31
Updated some comments
galexsky Apr 8, 2022
3ec7eee
updated docs writing
freemansw1 Apr 15, 2022
5c6430a
fixed erosion not working
freemansw1 Apr 15, 2022
ff99d71
Merge branch 'dev' into 3D_PBC_segmentation_new
freemansw1 Apr 15, 2022
68f2730
Merge pull request #25 from freemansw1/3D_PBC_segmentation_new
freemansw1 Apr 15, 2022
0b8e373
Cleaning up of unnecessary code
freemansw1 Apr 16, 2022
9894e1c
Cut out a lot more unnecessary code.
freemansw1 Apr 16, 2022
c24c820
Resolves #29 and clarifies the documentation
freemansw1 Apr 16, 2022
282a439
Resolves #26
freemansw1 Apr 16, 2022
fbcd069
Added a new function in testing to test grid coordinates
freemansw1 Apr 17, 2022
d46334b
Added test for add_coordinate
freemansw1 Apr 17, 2022
a9aca6d
Added new test for add_coordinates
freemansw1 Apr 17, 2022
1efb5e2
Revert "Cut out a lot more unnecessary code."
freemansw1 Apr 19, 2022
3b33008
Several improvements to `dev` (#36)
freemansw1 Apr 25, 2022
acd21fa
Bugfix on vertical coordinate implementation
galexsky Apr 28, 2022
19b75f8
Added a lot of new logic around vertical axes in feature detection
freemansw1 May 1, 2022
34129e7
Allowed z coordinates to be in any axis
freemansw1 May 1, 2022
ff6f56f
Cleaning up of feature detection code
freemansw1 May 1, 2022
f7e9367
Resolves #33
freemansw1 May 1, 2022
af778fd
Tweak to vertical coord function and ncells fix
galexsky May 1, 2022
7017915
Revert "Tweak to vertical coord function and ncells fix"
galexsky May 1, 2022
be4c109
Fix to ncells
galexsky May 1, 2022
acee974
Revert "Fix to ncells"
galexsky May 1, 2022
133e7c4
Update to find_vertical_axis_from_coord
galexsky May 1, 2022
ea506e7
Added in framework for subsetting
freemansw1 May 2, 2022
1d715c9
Black formatting
freemansw1 May 2, 2022
b40d740
Merge remote-tracking branch 'csu-tobac-csu/dev' into dev-3D-PBC-support
freemansw1 May 2, 2022
2dedc58
Reformatted files
freemansw1 May 3, 2022
f77d6fe
Rename test_util.py to test_utils.py
JuliaKukulies Jun 8, 2022
254ae0e
Reverting changes not relevant to 3D/PBC
freemansw1 Jul 1, 2022
da4b06a
Updates from changes requested by @JuliaKukulies
freemansw1 Jul 1, 2022
b4a4f74
fixed black formatting
freemansw1 Jul 1, 2022
132804e
Merge branch 'dev' into dev-3D-PBC-support
freemansw1 Jul 11, 2022
9a4b0f5
Black formatting
freemansw1 Jul 11, 2022
fe19487
Black formatting (again)
freemansw1 Jul 11, 2022
4f81fe6
Merge branch 'RC_v1.5.0' into dev-3D-PBC-support
freemansw1 Oct 24, 2022
ea9922f
Updated code for RC_V1.5.0 changes. Switched 3D tracking to random only.
freemansw1 Nov 9, 2022
dd8c78c
updates from comments
freemansw1 Nov 30, 2022
f9df0b6
Merge branch 'RC_v1.5.0' into dev-3D-PBC-support
freemansw1 Nov 30, 2022
9f95c53
Merge branch 'dev-3D-PBC-support' of https://github.com/galexsky/toba…
freemansw1 Nov 30, 2022
3b3855d
black formatting
freemansw1 Nov 30, 2022
23ceda3
code cleanup
freemansw1 Nov 30, 2022
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1 change: 1 addition & 0 deletions conda-requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
numpy
scipy
scikit-image
scikit-learn
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pandas
pytables
matplotlib
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7 changes: 7 additions & 0 deletions doc/feature_detection_output.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,3 +9,10 @@ Variables that are common to all feature detection files:
:file: ./feature_detection_base_out_vars.csv
:widths: 3, 35, 3, 3
:header-rows: 1

Variables that are included when using 3D feature detection in addition to those above:

.. csv-table:: tobac 3D Feature Detection Output Variables
:file: ./feature_detection_3D_out_vars.csv
:widths: 3, 35, 3, 3
:header-rows: 1
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