Shift-E on point elements doesn't retain annotations (i.e. additional DataFrame columns)

[m-albert]

Thanks for this awesome package!

I just wanted to quickly leave the following report here:

After viewing a points element in napari and saving it back to the SpatialData object using "Shift-E", annotations are not retained.

Reproducer:

from spatialdata import SpatialData
from spatialdata.models import PointsModel
import pandas as pd

sdata = SpatialData()

sdata['points'] = PointsModel.parse(
        pd.DataFrame({
            'x': [1, 2],
            'y': [3, 4],
            'category': ['A', 'B'],
        }),
    )

sdata['points'].columns # Index(['x', 'y', 'category'], dtype='object')

from napari_spatialdata import Interactive

interactive = Interactive(sdata)
interactive.add_element("points", "global")

# press Shift-E

sdata['points'].columns # sdata['points'].columns # no longer contains column 'category' (no longer contains column 'category')

Versions used:

napari_spatialdata.__version__: 0.5.4.post0
spatialdata.__version__: 0.4.0

[melonora]

Thanks for reporting, I am looking into it

[melonora]

will take a bit longer to do something about this. Main thing is that for points we never took into account the additional columns and then when exporting it overwrites.

[m-albert]

Thank you for checking, I was assuming so. There's no rush for me, just wanted to report what I observed.

I currently use a very hacky way of saving my additional column manually:

    # modify Shift-E binding to save points layer together with dragged mask
    orig_shift_e_func = [v for k, v in viewer.keymap.items() if 'Shift+E' in str(k)][0]

    def f(viewer):
        selected_layers = list(viewer.layers.selection)
        # apply the modified Shift-E function to point layers
        # to other layers, use the original Shift-E function
        for sl in selected_layers:
            if type(sl) == napari.layers.Points:
                print("Modified Shift-E")
                save_points_layer(sl)
            else:
                viewer.layers.selection = set([sl])
                orig_shift_e_func(viewer)
        viewer.layers.selection = set(selected_layers)

    def save_points_layer(l):
        df = create_points_element_from_df(
            pd.DataFrame({
                "x": l.data[:, 1],
                "y": l.data[:, 0],
                "dragged": dragged_mask,
            }))
        sdata[f"ablation_marks_pos_maldi_region_{maldi_region_index}"] = df
        print(f"Saved points layer '{l.name}' to sdata")

    viewer.bind_key("Shift-E", f, overwrite=True)