Support visualizing multiple SpatialData objects #112

Activity

1. kevinyamauchi commented on Jun 9, 2023

   

   kevinyamauchi

   on Jun 9, 2023

   Collaborator

   More actions

   @melonora , would you be able to take this one? @LucaMarconato has some demo code already on the spatialdata branch. @LucaMarconato , can please link the code?
2. kevinyamauchi

   assigned

   melonora

   on Jun 9, 2023
3. LucaMarconato commented on Jun 9, 2023

   

   LucaMarconato

   on Jun 9, 2023

   Last edited by LucaMarconato

   MemberAuthor

   More actions

   Yes, for instance the commented line here is an example (the paths above needs to be adjusted): https://github.com/scverse/napari-spatialdata/blob/2590e1e8191091820478b470ef7aee8bfd322be8/src/napari_spatialdata/interactive.py#LL687C1-L687C42
4. melonora commented on Jun 9, 2023

   

   melonora

   on Jun 9, 2023

   Collaborator

   More actions

   I have this also in follow up PRs which I did not open yet. I keep track of the spatialdata object in the layer metadata, similar to what Luca did on the spatialdata branch.
5. melonora commented on Jun 9, 2023

   

   melonora

   on Jun 9, 2023

   Collaborator

   More actions

   I can open them, but they are branched from the layer_visibility branch so that was why I was waiting a bit.
6. melonora commented on Jul 4, 2023

   

   melonora

   on Jul 4, 2023

   Last edited by melonora

   Collaborator

   More actions

   @kevinyamauchi @LucaMarconato After #120, I will add the possibility of having multiple spatialdata objects being visualized in one napari-spatialdata instance. This requires a few changes overall. This serves as an initial proposal.

   Proposal

   There are several ways by which a user could load multiple SpatialData objects.

   1. Interactive(sdatas: list[SpatialData])
   2. SpatialDataViewer.add_sdata(sdata: SpatialData)
   3. Drag and drop interaction.

   I believe the SpatialData objects ultimately can live as an EventedSet in SdataWidget. This allows us to create callbacks upon add, remove and discard
   events among others. Currently other emitted events wouldn't be important I think.

   Populating CoordinateSystemWidget and ElementWidget

   In the SdataWidget initialization, the CoordinateSystemWidget and ElementWidget are both created. The widgets do not hold a reference to the SdataWidget, but callbacks can be created in the respective widgets and connected to the event in the SdataWidget. The respective callbacks would take care of populating the items of the widgets also when later adding or removing new data.

   class SdataWidget(...):
       self._sdatas = EventedSet(sdatas)
       self.coordinate_system_widget = CoordinateSystemWidget(self._sdatas)
       self.elements_widget = ElementWidget(self._sdatas)
       
       self._sdatas.events.add.connect(self.coordinate_system_widget._add_items)
       ...
       
   class CoordinateSystemWidget(QListWidget):
       def __init__(self, sdatas: EventedSet(SpatialData)):
           super().__init__()
   
           self._sdatas = sdatas
           self._init_items(self._sdatas)
   
       def _init_items(sdatas: EventedSet):
           """initial populating of widget items"""
   
      def _add_items(event):
          ...
   
   class ElementWidget(QListWidget)
          ...

   Of note is that elements of multiple spatialdata objects can have the same name. We would have to choose to either disallow it, be ok with napari showing "copied" names (integer between parentheses) or come up with an appropriate suffix. Dependent on choice there would be additional functionality of the callbacks in this section. Personally, I think the latter would have preference.

   What do you think?
7. LucaMarconato commented on Jul 4, 2023

   

   LucaMarconato

   on Jul 4, 2023

   MemberAuthor

   More actions

   Thanks Wouter, I prefer 1. since it was what we used so far, but we could also allow the user to use add_sdata() later (this is actually what happens in the spatialdata branch: there is an equivalent private function that allows for that).

   Drag and drops interactions would be also nice, but we can add it later.

   Re the multiple names I would prefer having napari automatically handle it so that we don't have to add extra suffix logic.
8. melonora commented on Jul 5, 2023

   

   melonora

   on Jul 5, 2023

   Collaborator

   More actions

   I would say both option 1 and 2 are very doable, as initially the only thing that happens when adding a SpatialData object should be populating the CoordinateSystemWidget and the ElementWidget. This can be done by just adding items.

   Regarding the names I think it would be nice to modify the copy names of the layer in such a way that it at least indicates which layers share the SpatialData object, but I would have to find out first what would be the best way to achieve that.

   👍React with 👍1Reacted by LucaMarconato
9. melonora commented on Sep 1, 2023

   

   melonora

   on Sep 1, 2023

   Collaborator

   More actions

   closed by #136
10. melonora

    closed this as completedon Sep 1, 2023