Implement Younger Monocot Pipeline #64
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WalkthroughThe changes primarily focus on enhancing the functionality of the Changes
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Review Status
Actionable comments generated: 4
Files selected for processing (4)
- sleap_roots/lengths.py (2 hunks)
- sleap_roots/trait_pipelines.py (1 hunks)
- tests/test_lengths.py (2 hunks)
- tests/test_trait_pipelines.py (2 hunks)
Additional comments (Suppressed): 11
tests/test_trait_pipelines.py (1)
- 1-5: The import of
YoungerMonocotPipelineandfind_all_seriesis new. Ensure that these classes/functions are correctly implemented and tested.tests/test_lengths.py (6)
165-166: This test case for scalar inputs in the
get_grav_indexfunction is well written and covers an important scenario.169-174: This test case for array inputs in the
get_grav_indexfunction is well written and covers an important scenario.177-183: This test case correctly checks for a ValueError when there is a shape mismatch between the input arrays to the
get_grav_indexfunction.186-191: This test case correctly checks the handling of NaN values in the
get_grav_indexfunction.194-199: This test case correctly checks the handling of zero lengths in the
get_grav_indexfunction.202-206: These test cases correctly check the handling of invalid scalar values in the
get_grav_indexfunction.sleap_roots/trait_pipelines.py (3)
904-905: The new
YoungerMonocotPipelineclass is a subclass of thePipelineclass and is designed to compute traits for younger monocot plants. This is a good addition as it allows for more specific trait computation for different types of plants.920-1343: The
define_traitsmethod has been overridden in theYoungerMonocotPipelineclass to define the trait computation pipeline specific to younger monocot plants. The method returns a list ofTraitDefobjects representing the traits to be computed. EachTraitDefobject includes a name, a function (fn) that computes the trait, a list of input traits required for computing the trait, flags indicating whether the trait is scalar or should be included in downstream CSV files, additional keyword arguments for the computation function, and a description of the trait. This is a comprehensive set of traits for younger monocot plants and covers various aspects such as root lengths, angles, intersections, network length, etc.1345-1373: The
get_initial_frame_traitsmethod has been updated to return initial traits for a plant frame. It takes aplantSeries object and aframe_idxas inputs and returns a dictionary of initial traits with keys: "primary_pts" and "main_pts". The method handles cases where there are no instances for primary and main roots by returning arrays with NaN values. This is a good practice as it ensures that the output shape is consistent regardless of the input.sleap_roots/lengths.py (1)
- 1-6: The import statement for
get_base_tip_disthas been removed. Ensure that this function is no longer used in the codebase or has been replaced with an equivalent functionality.
Codecov Report
@@ Coverage Diff @@
## main #64 +/- ##
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+ Coverage 77.05% 78.30% +1.24%
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Files 13 13
Lines 789 802 +13
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+ Hits 608 628 +20
+ Misses 181 174 -7
... and 1 file with indirect coverage changes 📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
There was a problem hiding this comment.
Review Status
Actionable comments generated: 2
Files selected for processing (4)
- sleap_roots/lengths.py (2 hunks)
- sleap_roots/trait_pipelines.py (1 hunks)
- tests/test_lengths.py (2 hunks)
- tests/test_trait_pipelines.py (2 hunks)
Files skipped from review due to trivial changes (2)
- sleap_roots/trait_pipelines.py
- tests/test_lengths.py
Additional comments (Suppressed): 2
tests/test_trait_pipelines.py (1)
- 1-5: The import of
YoungerMonocotPipelineandfind_all_seriesis new in this hunk. Ensure that these classes/functions are correctly implemented and tested elsewhere in the codebase.sleap_roots/lengths.py (1)
- 1-6: The import of
get_base_tip_distfromsleap_roots.baseshas been removed. Ensure that this function is not used elsewhere in the code or if it's used, it's imported correctly.
There was a problem hiding this comment.
Review Status
Actionable comments generated: 2
Files selected for processing (1)
- tests/test_trait_pipelines.py (2 hunks)
Additional comments (Suppressed): 1
tests/test_trait_pipelines.py (1)
- 1-5: The import of
YoungerMonocotPipelineandfind_all_seriesis new in this hunk. Ensure that these classes/functions are correctly implemented and tested elsewhere in the codebase.
There was a problem hiding this comment.
Review Status
Actionable comments generated: 1
Files selected for processing (2)
- sleap_roots/lengths.py (2 hunks)
- tests/test_lengths.py (2 hunks)
Files skipped from review due to trivial changes (1)
- tests/test_lengths.py
Additional comments (Suppressed): 1
sleap_roots/lengths.py (1)
- 1-6: The import of
get_base_tip_distfromsleap_roots.baseshas been removed. Ensure that this function is no longer used in the codebase or has been replaced appropriately.
* Start `YoungerMonocotPipeline` * Add `main_grav_indices` * Add younger monocot data * Edit `YoungMonocotPipeline` * Test `YoungerMonocotPipeline` * Fix trait definitions * Fix description of `main_grav_indices` * Test gravitropism index * Fixed test for `grav_index` for NaN values * Add tests for `get_grav_index` for expected output shape
YoungerMonocotPipelineas subclass ofPipelineYoungerMonocotPipelineSummary by CodeRabbit
YoungerMonocotPipelineclass for trait computation of younger monocot plants, including root lengths, angles, intersections, and network length.get_grav_indexfunction insleap_roots/lengths.pyto handle both scalar and array inputs uniformly, improving code flexibility and robustness.get_grav_indexfunction covering various scenarios such as scalar inputs, array inputs, shape mismatch, NaN values, and zero lengths.test_younger_monocot_pipelineto validate the functionality of the newly introducedYoungerMonocotPipelineclass.