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PAF Grouping #33

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merged 36 commits into from
Jan 20, 2024
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c387584
init commit
alckasoc Dec 19, 2023
85539d2
init commit
alckasoc Dec 19, 2023
e4afd94
storage classes
alckasoc Dec 19, 2023
6d4a770
added get_connection_candidates
alckasoc Dec 21, 2023
ae241fe
added make_line_subs
alckasoc Dec 21, 2023
244426e
added get_paf_lines
alckasoc Dec 21, 2023
0226828
added compute_distance_penalty
alckasoc Dec 21, 2023
9018b1e
added score_paf_lines
alckasoc Dec 21, 2023
5f7bb19
added score_paf_lines batch
alckasoc Jan 3, 2024
7e014bd
added docstring
alckasoc Jan 3, 2024
542dc7c
added match_candidates_sample
alckasoc Jan 3, 2024
83396f3
added test case for match_candidates_sample
alckasoc Jan 3, 2024
eafdad5
added match_candidates_batch
alckasoc Jan 4, 2024
e44999f
added test case for match_candidates_batch
alckasoc Jan 4, 2024
9a79951
added make_predict_instances, assign_connections_to_instance; added u…
alckasoc Jan 4, 2024
400630a
added unit test make_predicted_instances"
alckasoc Jan 4, 2024
0412b47
black formatted and pydocstyle
alckasoc Jan 4, 2024
08f7d14
added group_instances_sample
alckasoc Jan 5, 2024
93ac8e0
added test_group_instances_sample
alckasoc Jan 5, 2024
3416772
removed converting tuple to numpy -> error
alckasoc Jan 9, 2024
6237699
added group_instance_batch
alckasoc Jan 9, 2024
f8dfd91
added test case
alckasoc Jan 9, 2024
56aad04
black formatted
alckasoc Jan 9, 2024
448569b
added pafscorer; needs to update type hints
alckasoc Jan 9, 2024
1fdf490
fixed sneaky typing issue with sorted_edge_inds
alckasoc Jan 9, 2024
5f1e974
fixed type hints + docs in PAFScorer
alckasoc Jan 9, 2024
a18640f
black formatted
alckasoc Jan 9, 2024
addac8a
test commit; only thing left is config
alckasoc Jan 9, 2024
f5b784c
added omegaconf
alckasoc Jan 10, 2024
16ffb15
removed duplicates
alckasoc Jan 11, 2024
c67b9b7
added score_paf_lines unit test"
alckasoc Jan 11, 2024
f0c1556
added test cases
alckasoc Jan 11, 2024
835638e
added codecov; needs to be updated; not sure how to configure this th…
alckasoc Jan 11, 2024
7fda982
added attrs and codecov.yml
alckasoc Jan 13, 2024
aba60bd
added more tests
alckasoc Jan 13, 2024
0a55f57
black formatted
alckasoc Jan 13, 2024
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17 changes: 17 additions & 0 deletions codecov.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
coverage:
ignore:
- "tests"
status:
project: # Measures overall project coverage.
default: false
package:
target: auto
threshold: 2% # Less leeway with backend code.
paths:
- "sleap_nn/"
patch: # Only measures lines adjusted in the pull request.
default: false
package:
target: 95% # All backend code should be tested...
paths:
- "sleap_nn/"
1 change: 1 addition & 0 deletions sleap_nn/data/edge_maps.py
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
"""Transformers for generating edge confidence maps and part affinity fields."""
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