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Add editing and refactor entire code base #86

Merged
merged 137 commits into from
Oct 18, 2024
Merged

Add editing and refactor entire code base #86

merged 137 commits into from
Oct 18, 2024

Commits on Sep 17, 2024

  1. Reorganize everything

    @cmalinmayor
    cmalinmayor committed Sep 17, 2024
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  2. More reorganization! Old functionality runs now

    @cmalinmayor
    cmalinmayor committed Sep 17, 2024
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  3. Implement tracks controller functions, kind of

    @cmalinmayor
    cmalinmayor committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. update yaml commands

    @AnniekStok
    AnniekStok committed Sep 18, 2024
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  2. add ClassVar to refresh signal definition

    @AnniekStok
    AnniekStok committed Sep 18, 2024
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  3. remove the __future__ annotations as this breaks in the injection whe… 

    …n starting widgets from the plugins menu
    @AnniekStok
    AnniekStok committed Sep 18, 2024
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  4. basic implementation of adding/deleting nodes in the points layer and… 

    … tree widget
    @AnniekStok
    AnniekStok committed Sep 18, 2024
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  5. call the assign_tracklet_id function from motile_toolbox after removi… 

    …ng a node, to reassign the tracklet_ids
    @AnniekStok
    AnniekStok committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. relabel segmentation when deleting a node

    @AnniekStok
    AnniekStok committed Sep 19, 2024
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  2. implement menu functions for adding and deleting nodes and edges

    @AnniekStok
    AnniekStok committed Sep 19, 2024
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  3. Use NodeAttr.TRACK_ID and keep track of track ids in Tracks object

    @cmalinmayor
    cmalinmayor committed Sep 19, 2024
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  4. Only reassign track and segmentation ids for cahnged lineages

    @cmalinmayor
    cmalinmayor committed Sep 19, 2024
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  5. delete segmentation when node is deleted

    @AnniekStok
    AnniekStok committed Sep 19, 2024
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  6. recolor the tracks layer after node/edge update

    @AnniekStok
    AnniekStok committed Sep 19, 2024
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  7. handle refresh in the tracks_viewer, restore selection and maintain z… 

    …oom in treewidget
    @AnniekStok
    AnniekStok committed Sep 19, 2024
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Commits on Sep 23, 2024

  1. implement editing from the segmentation, including adding new nodes, … 

    …removing nodes, and updating their size
    @AnniekStok
    AnniekStok committed Sep 23, 2024
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  2. allow creation of edges more than one time point apart - still have t… 

    …o implement a separate validation function
    @AnniekStok
    AnniekStok committed Sep 23, 2024
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  3. update the autorange logic, refreshing when switching between all/lin… 

    …eage and tree/area but not when viewing the tree
    @AnniekStok
    AnniekStok committed Sep 23, 2024
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  4. implement function for validating proposed edges

    @AnniekStok
    AnniekStok committed Sep 23, 2024
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  5. First attempt at implementing undo

    @cmalinmayor
    cmalinmayor committed Sep 23, 2024
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  6. fix bugs in handling updates coming from the labels layer

    @AnniekStok
    AnniekStok committed Sep 23, 2024
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  7. add redo button to editing menu

    @AnniekStok
    AnniekStok committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. implement undo/redo for the labels layer

    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  2. undo accidental removal of signal

    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  3. undo accidental removal of signal

    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  4. induce autorange if the tracks_updated signal comes from a new run

    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  5. display a messagebox when attempting to merge tracks, optionally disc… 

    …arding the existing edge. How to combine this delete edge action with the add action in an Actiongroup?
    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  6. Make TracksList independent of MotileRuns

    @cmalinmayor
    cmalinmayor committed Sep 24, 2024
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  7. do not allow moving points if there is a seg layer, but update attrib… 

    …utes if points were the source for tracking
    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  8. automatically set the brush color in the labels layer to the track id… 

    …: this way it is also easier to add a segmentation for a new point
    @AnniekStok
    AnniekStok committed Sep 24, 2024
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  9. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. make sure that the dict mapping node_id to track_id is created when a… 

    … run solve is complete (if it was not already done at init)
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  2. restructure and simplify colormap logic for the labels layer

    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  3. centralize the colormap in the tracks_viewer, and update across all v… 

    …iewers (in the case the user shuffles the colors in the labels layer)
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  4. fix bug in the tracks layer: track_ids were out of sync with the grap… 

    …h because they were regenerated. Hence the apparent colormap issue. Implemented an adapted version of the to_napari_tracks_layer function that does not reassign track_ids, but takes them from the provided graph
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  5. force refresh the colormap in the trackslayer by reapplying the turbo… 

    … colormap, otherwise colors do not update correctly when the user shuffles the label colors
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  6. remove the build-in properties on the labels layer as this was showin… 

    …g incorrect results because we cannot assign different properties to the same label at a different time point. Instead use a new attribute node_properties to store this information to keep it accessible when clicking on a label
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  7. override the default _type_string in trackpoints and tracklabels laye… 

    …rs to return normal points and labels for saving purposes
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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  8. combine widgets in a multi widget but also allow to open them separat… 

    …ely. There appears to be a bug when opening the TracksListWidget after the MultiWidget was already called
    @AnniekStok
    AnniekStok committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. implement keybindings for editing

    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  2. first check if an edge exists before deleting - otherwise we recolor … 

    …when we should not
    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  3. set blending to translucent_no_depth for points to make them better v… 

    …isible in 3D view
    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  4. use the same keybinding (Q) for toggling all/lineage in tree and in v… 

    …iewer
    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  5. convert tracks.scale to list when saving because array is not json se… 

    …rializable
    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  6. fix directory path when loading tracks

    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  7. fix issue in the labels colormap that resulted in incorrect visibilit… 

    …y/invisibility and highlighting due to use of the cycliclabelcolormap, we do need the directmap because there are typically more track_ids than colors
    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  8. put the combined widget at the top of the list in the napari.yaml

    @AnniekStok
    AnniekStok committed Sep 26, 2024
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  9. Bugfix: Motile Runs not saved and loaded properly from Tracks list

    @cmalinmayor
    cmalinmayor committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. refactor action handling to use new ActionHistory class, taking care … 

    …of the entire undo/redo logic including segmentation updates
    @AnniekStok
    AnniekStok committed Sep 27, 2024
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  2. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Sep 27, 2024
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  3. emit a selection update event after refresh, even if there are no nod… 

    …es selected (for setting the opacity in the labels layer)
    @AnniekStok
    AnniekStok committed Sep 27, 2024
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  4. bugfix: make sure that the None and 0 (if provided) keys in the color… 

    …map dict always have opacity of 0, otherwise we end up with the weird case of nontransparent blackness
    @AnniekStok
    AnniekStok committed Sep 27, 2024
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Commits on Oct 1, 2024

  1. Move napari layer functions from TracksViewer into TracksLayerGroup

    @cmalinmayor
    cmalinmayor committed Oct 1, 2024
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  2. Update tests for new motile run

    @cmalinmayor
    cmalinmayor committed Oct 1, 2024
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  3. Add test and better docstrings for action history

    @cmalinmayor
    cmalinmayor committed Oct 1, 2024
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  4. Incorporate pixel updates into all node actions

    @cmalinmayor
    cmalinmayor committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. first check if the labels layer is present and not in edit mode befor… 

    …e centering the view, as centering while editing is annoying especially in 3D
    @AnniekStok
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  2. disable selecting nodes in the seg_layer when in 3D lineage mode. Oth… 

    …erwise, check whether the selected label is visible (non zero in the colormap opacity)
    @AnniekStok
    AnniekStok committed Oct 2, 2024
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  3. Merge branch 'refactor_for_editing' of github.com:funkelab/motile_nap… 

    …ari_plugin into refactor_for_editing
    @cmalinmayor
    cmalinmayor committed Oct 2, 2024
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  4. Add tests for edge actions

    @cmalinmayor
    cmalinmayor committed Oct 2, 2024
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Commits on Oct 4, 2024

  1. Bugfix for MotileRun ave/load

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  2. Remove Timer from thread warning

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  3. Add comment from Kyle about 3D view centering

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  4. Use type aliases to define Node and Edge types

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  5. Fix type annotations in tracks controller

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  6. Use multi widget in run hela script

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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  7. Fix type annotations in action history

    @cmalinmayor
    cmalinmayor committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. Remove node_id_to_track_id, add track_time_to_node mapping

    @cmalinmayor
    cmalinmayor committed Oct 7, 2024
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  2. Refactored labels update (working but slow)

    @cmalinmayor
    cmalinmayor committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. Call other functions in update_segmentation

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Commits on Oct 9, 2024

  1. use rectangular selection in treeview to append a list of nodes to th… 

    …e selection, rescaling the view range if necessary
    @AnniekStok
    AnniekStok committed Oct 9, 2024
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  2. Pass pixels to delete from paint event and combine actions for adding… 

    … valid edges
    @cmalinmayor
    cmalinmayor committed Oct 9, 2024
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  3. Make pixels optional when deleting nodes

    @cmalinmayor
    cmalinmayor committed Oct 9, 2024
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  4. Fix keyerror in set_seg_id

    @cmalinmayor
    cmalinmayor committed Oct 9, 2024
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  5. Second fix for key error in set_seg_id

    @cmalinmayor
    cmalinmayor committed Oct 9, 2024
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Commits on Oct 11, 2024

  1. bug fixing: update the tracks.seg_time_to_node and max_track_id in up… 

    …date_tracks, otherwise they are empty. Also call the update signal before updating the node selecting (if a node is new, it is otherwise not yet in the tree dataframe)
    @AnniekStok
    AnniekStok committed Oct 11, 2024
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  2. make pixels optional in add_nodes

    @AnniekStok
    AnniekStok committed Oct 11, 2024
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  3. finish merge

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    AnniekStok committed Oct 11, 2024
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Commits on Oct 12, 2024

  1. add new sample data: mouse embryo membrane data

    @AnniekStok
    AnniekStok committed Oct 12, 2024
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Commits on Oct 14, 2024

  1. Refactor Tracks with getters and setters and tests

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  2. Merge branch 'refactor_for_editing' of github.com:funkelab/motile_nap… 

    …ari_plugin into refactor_for_editing
    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  3. update docs

    @AnniekStok
    AnniekStok committed Oct 14, 2024
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  4. Merge branch 'refactor_for_editing' of github.com:funkelab/motile_nap… 

    …ari_plugin into refactor_for_editing
    @cmalinmayor
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  5. Test tracks_controller._add_nodes

    @cmalinmayor
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  6. Change MotileRun to SolutionGraph

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  7. Test tracks_controller._delete_nodes

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  8. Make more complex test graph

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  9. Remove unused tracks controller functionality

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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  10. Set invalid layers to None in TracksLayerGroup

    @cmalinmayor
    cmalinmayor committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. rename combined motile widgets to Motile Main Widgets in plugin dropdown

    @AnniekStok
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  2. fix usage of _add_nodes, since a tuple of two elements is returned an… 

    …d not a single action
    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  3. fix adding nodes from points without seg

    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  4. fix create_edge: only edges are expected as inputs, no attributes

    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  5. fix typo

    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  6. Remove apply function from Action API

    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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  7. Merge branch 'refactor_for_editing' of github.com:funkelab/motile_nap… 

    …ari_plugin into refactor_for_editing
    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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  8. Update action history to keep everything and use new Action API

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    cmalinmayor committed Oct 15, 2024
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  9. update _delete_nodes, combining all to be deleted edges in a single D… 

    …eleteEdges action, and all to be created skip edges in a single AddEdges action
    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  10. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  11. add all the actions in _delete_nodes at the end

    @AnniekStok
    AnniekStok committed Oct 15, 2024
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  12. Refactor _add_nodes to first delete edges, then add nodes, then add e… 

    …dges
    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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  13. Get all tests to pass for tracks controller

    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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  14. Minor bugfixes

    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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  15. Fix moving points in points-only tracks

    @cmalinmayor
    cmalinmayor committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. fix colormap refresh issue by calling update_selection, which fixes t… 

    …he highlighting of selected nodes
    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  2. fix treeview rescaling issue by removing padding in set_range

    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  3. fix treeview display in lineage mode: when deleting a node, keep show… 

    …ing the previous lineages instead of a black tree view. Also make sure to complete reset the view when there is a new run
    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  4. make sure that arrays are converted to lists when saving

    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  5. store the previously visible nodes and reuse them for the napari view… 

    …s in case mode == lineage and self.selected_nodes is empty
    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  6. check which nodes were previously visible and are still present in th… 

    …e graph in a more efficient manner
    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  7. Add cropped hela to sample data

    @cmalinmayor
    cmalinmayor committed Oct 16, 2024
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  8. Catch pyqtgraph error about different X and Y lengths

    @cmalinmayor
    cmalinmayor committed Oct 16, 2024
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  9. Don't remove layers when going back to editing in motile menu

    @cmalinmayor
    cmalinmayor committed Oct 16, 2024
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  10. comment out sections for non-implemented editing buttons

    @AnniekStok
    AnniekStok committed Oct 16, 2024
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  11. put tree view controls in collapsible and squeeze everything to be mo… 

    …re compact
    @AnniekStok
    AnniekStok committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. check the previous track_df sorting (if available) to keep the lineag… 

    …e tree as consistently ordered as possible when editing
    @AnniekStok
    AnniekStok committed Oct 17, 2024
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  2. bugfix: do not connect tracks_viewer to the refresh signal multiple t… 

    …imes
    @AnniekStok
    AnniekStok committed Oct 17, 2024
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  3. Fix csv export and move to SolutionTracks

    @cmalinmayor
    cmalinmayor committed Oct 17, 2024
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  4. disconnect TracksViewer from any previous Tracks before reassigning s… 

    …elf.tracks and connecting self.tracks.refresh again, to prevent emitting multiple signals
    @AnniekStok
    AnniekStok committed Oct 17, 2024
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  5. Make MenusWidget and remove individual menu widgets

    @cmalinmayor
    cmalinmayor committed Oct 17, 2024
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  6. Update hela script to use new main widget

    @cmalinmayor
    cmalinmayor committed Oct 17, 2024
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  7. Merge branch 'refactor_for_editing' of github.com:funkelab/motile_nap… 

    …ari_plugin into refactor_for_editing
    @cmalinmayor
    cmalinmayor committed Oct 17, 2024
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  8. update docs

    @AnniekStok
    AnniekStok committed Oct 17, 2024
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  9. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. reset view at init of lineage view

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  2. rename tracks list to Results list

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  3. Check type of input layer at initializaiton of motile run editor

    @cmalinmayor
    cmalinmayor committed Oct 18, 2024
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  4. adding points to sample data

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  5. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  6. move scrollarea from motile_widget to menu_widget

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  7. update yaml with points sample data

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  8. Update documentation to include new features in getting started

    @cmalinmayor
    cmalinmayor committed Oct 18, 2024
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  9. include points in the hela sample data, returning all three layers to… 

    …gether
    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  10. Merge branch 'refactor_for_editing' of https://github.com/funkelab/mo… 

    …tile_napari_plugin into refactor_for_editing
    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  11. also hide input points layer after run is complete

    @AnniekStok
    AnniekStok committed Oct 18, 2024
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  12. Merge branch 'main' into refactor_for_editing

    @cmalinmayor
    cmalinmayor committed Oct 18, 2024
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  13. Fix external tracks and update toolbox version

    @cmalinmayor
    cmalinmayor committed Oct 18, 2024
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