Add segment_ends and Update morphology tips outputs
#1644
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avoid saving to outputs in the helper function but produce the same relevant outputs, update instances of find_tips getting used throughout morphology
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img input not just for plotting debug
add optimal assignment input
since no outputs in sorting, skip the label storage. wasn't used downstream but also don't need to store anymore since _find_tips also doesn't store to outputs
rearrage ome imports and change where things are getting called from
decided to go with returning a list of sorted objects instead of a list of re-sorting IDs
missing branch points, in the case of disconnected leaves, will not be sortable so remove them from returned resorted segments
k034b363
approved these changes
May 9, 2025
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Looks good to me, it works the way I would expect it to and reorders branches to something biologically meaningful on both well behaved and less clean maize pictures. The movement of some functions to helpers makes the previously complex morphology functions quite a bit easier to read as well.
nfahlgren
reviewed
May 16, 2025
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Describe your changes
_iterative_pruneinto the_helper.pyfile to avoid circular imports (this unfortunately touches most of the functions in this package)find_tips(adds a helper function_find_tipsthat is used internally by many functions and doesn't store outputs so they do not accidentally get overwritten)pcv.morphology.segment_endswhich returns: Re-ordered leaf segments, debug image, list of branch point coordinates, list of leaf tip coordinatespcv.morphology.analyze_stemwhere thelabel=Nonewas causing no data to get saved to Outputs. Resolved by updating with appropriate labels.Type of update
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Associated issues
plantcv.morphologysub-package #1643Additional context
tipscoordinates toOutputswas easily overwritten by other morphology functions that utilize thepcv.morphology.find_tipsfunction.For the reviewer
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plantcv/mkdocs.ymlupdating.md