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Visualise pose tracks as a napari Tracks layer #4

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Tracked by #50
niksirbi opened this issue Jan 11, 2023 · 4 comments
Open
Tracked by #50

Visualise pose tracks as a napari Tracks layer #4

niksirbi opened this issue Jan 11, 2023 · 4 comments
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enhancement New optional feature GUI Graphical User Interface

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@niksirbi
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Plot body part trajectory. See example implementation here

@niksirbi niksirbi converted this from a draft issue Jan 11, 2023
@niksirbi niksirbi self-assigned this Jan 11, 2023
@niksirbi niksirbi added the enhancement New optional feature label Jan 11, 2023
@niksirbi niksirbi added this to the MVP v0.1.0 milestone Jan 11, 2023
@niksirbi niksirbi added core feature a core functionality that must be implemented and removed enhancement New optional feature labels Mar 14, 2023
@niksirbi
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Could also be part of the napari frontend, coercing the tracks layer (see #31)

@niksirbi niksirbi moved this from 📝 Todo to 🚧 In Progress in movement progress tracker Sep 19, 2023
@niksirbi
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Current plan

We will first try to plot the Trajectory in napari.
The idea is to display individual keypoint tracks via the napari Tracks layer.
The user should be able to:

  • color the tracks by various attributes (individual, keypoint, confidence, time)
  • select a subset of the data to display (individuals, keypoints, time window, confidence threshold)

This will most likely necessitate a custom widget to supplement the native capabilities of the Tracks layer.

Potential blockers

Issues with handling of NaN values in napari tracks and their properties

@niksirbi niksirbi added the GUI Graphical User Interface label Sep 20, 2023
@niksirbi niksirbi modified the milestones: v 0.1 (MVP), v0.1 - alpha release Oct 16, 2023
@niksirbi
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NaN values continue being a problem, see also https://forum.image.sc/t/tracks-layer-with-blank-nan-values-in-properties/81834

We are considering some hacky workarounds until this issue is fixed in napari. For example, we can set NaNs to a placeholder value (99999? out of canvas? zero?) and make them transparent.

@sfmig sfmig removed this from the v0.1 - alpha release milestone Aug 27, 2024
@niksirbi
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niksirbi commented Aug 27, 2024

After discussion with @sfmig today, we decided to make this issue more concrete, the initial name and scope were too broad and ambiguous. From now on, we take this issue to mean the visualisation of movement poses datasets as a napari Tracks layes, enabling us to plot a "tail" of variable length for each keypoint. This is a saparate issue to visualising the keypoints themselves as a napari Points layer.

For "trajectory plots" and the like in matplotlib, see issue #282

@niksirbi niksirbi changed the title Plot trajectory Visualise pose tracks as a napari Tracks layer Aug 27, 2024
@sfmig sfmig moved this from 🚧 In Progress to 🤔 Triage in movement progress tracker Aug 27, 2024
@sfmig sfmig added enhancement New optional feature and removed core feature a core functionality that must be implemented labels Aug 27, 2024
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Labels
enhancement New optional feature GUI Graphical User Interface
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