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Refactoring trait pipeline (2/2) #48

Merged
merged 42 commits into from
Aug 2, 2023
Merged

Refactoring trait pipeline (2/2) #48

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98ce00c
Map convex hull traits
eberrigan Jul 25, 2023
d6bd4bb
Change primary to lateral when monocots is True
eberrigan Jul 25, 2023
4d7bc4d
Get tips x and y coordinates uses network map
eberrigan Jul 25, 2023
51d60ab
Change "stem" to "root"
eberrigan Jul 25, 2023
a73ebcd
Fix tip y map
eberrigan Jul 25, 2023
fc155f8
Change root width back to take lateral_pts
eberrigan Jul 25, 2023
ff9530d
Changing the order of positional arguments to match others (primary i…
eberrigan Jul 25, 2023
c6e58a3
Fix plotting for using sleap-io API
eberrigan Jul 26, 2023
1bd4ddd
Merge branch 'elizabeth/fix_plotting' into elizabeth/pipeline_cache
eberrigan Jul 26, 2023
25e1047
Make positional arguments consistent
eberrigan Jul 26, 2023
eb973bd
Refactor `get_base_xs` to use graph
eberrigan Jul 26, 2023
fd30b78
Map `scanline_intersection_counts` and use keyword arguments
eberrigan Jul 26, 2023
4b529ae
Refactor `get_base_ys`, `get_base_length`, and `base_ct_density` to u…
eberrigan Jul 27, 2023
296fcc7
Clean up dependencies. Fix tip_ys.
eberrigan Jul 27, 2023
8f8a39a
Refactor `get_root_lengths_max` for use with graph
eberrigan Jul 27, 2023
a25e8b9
Refactor `get_base_tip_dist` to make base and tip pts or all points o…
eberrigan Jul 27, 2023
01ea8bc
Delete `primary_depth`
eberrigan Jul 27, 2023
617f379
Delete traitsgraph
eberrigan Jul 27, 2023
383d454
Delete traitsgraph dependencies
eberrigan Jul 27, 2023
132ac7e
Refactor base-related traits to use graph optionally
eberrigan Jul 27, 2023
3f3967f
Delete traits graph dependency
eberrigan Jul 27, 2023
2f9465f
Use `get_primary_pts` from series class
eberrigan Jul 27, 2023
7cf6817
Delete `get_primary_depth` tests
eberrigan Jul 27, 2023
2f64aaf
Fix trait map for base traits
eberrigan Jul 28, 2023
a88dafc
Delete test for traitsgraph.py
eberrigan Jul 28, 2023
2294d14
Standardize trait definition in trait map
eberrigan Jul 31, 2023
7d4c612
Change "graph" to "trait"
eberrigan Jul 31, 2023
393ee9a
Fix docstrings in `get_bases`
eberrigan Aug 1, 2023
519ec93
Use `TraitDef` class
eberrigan Aug 1, 2023
2b54f73
Fix docstrings
eberrigan Aug 1, 2023
b3430da
Add argument to class `TraitDef` whether to include in csv or if scalar
eberrigan Aug 1, 2023
3b67c58
Change `attr` to `attrs`
eberrigan Aug 1, 2023
d352e86
Add `lengths.py` for length-related traits.
eberrigan Aug 1, 2023
676d055
Add `primary_max_length_pts` to trait definitions
eberrigan Aug 1, 2023
2d437fd
Add `pts_all_array` and `convex_hull` trait definitions
eberrigan Aug 2, 2023
1412c8a
Fix docstring
eberrigan Aug 2, 2023
0979969
Import base-related trait to `lengths.py`
eberrigan Aug 2, 2023
c00fa12
Make sure arrays of points are 2-dimensional
eberrigan Aug 2, 2023
2033e08
Streamline point-related functions
eberrigan Aug 2, 2023
f37a40c
Vectorize `get_node_ind`
eberrigan Aug 2, 2023
a603943
Add trait definitions until `lateral_lengths`
eberrigan Aug 2, 2023
716b670
Delete unnecessary code
eberrigan Aug 2, 2023
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1 change: 0 additions & 1 deletion sleap_roots/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
import sleap_roots.scanline
import sleap_roots.series
import sleap_roots.summary
import sleap_roots.traitsgraph
import sleap_roots.graphpipeline
from sleap_roots.graphpipeline import get_all_plants_traits
from sleap_roots.series import Series
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