Closed schienstockd closed 1 year ago
Hi @schienstockd ! That's no good, thanks for the report.
I'm travelling at the moment, will get to this soon but as a short term fix could you try commenting out line 34 here?
https://github.com/napari/napari-animation/blob/main/napari_animation/viewer_state.py
Thanks! - I tried that, did not change anything.
Huh, interesting! Could you provide a small example of some tracks data? I think napari is just not serialising this information and it would be good to fix upstream :)
That is just from the napari documentation: https://napari.org/stable/howtos/layers/tracks.html
It always reverts back to time
.
import napari
from skimage import data
import numpy as np
hubble_image = data.hubble_deep_field()
tracks_data = np.asarray([
[1, 0, 236, 0],
[1, 1, 236, 100],
[1, 2, 236, 200],
[1, 3, 236, 500],
[1, 4, 236, 1000],
[2, 0, 436, 0],
[2, 1, 436, 100],
[2, 2, 436, 200],
[2, 3, 436, 500],
[2, 4, 436, 1000],
[3, 0, 636, 0],
[3, 1, 636, 100],
[3, 2, 636, 200],
[3, 3, 636, 500],
[3, 4, 636, 1000]
])
track_confidence = np.array(5*[0.9] + 5*[0.3] + 5 * [0.1])
properties = {
'time': tracks_data[:, 1],
'confidence': track_confidence
}
viewer = napari.view_image(hubble_image)
viewer.add_tracks(tracks_data, properties=properties)
napari.run()
sorry for the delay here - I've found the issue, basically...
ViewerState
I can temporarily fix in napari-animation by not tracking properties which may be sane anyway, that can be a lot of data to drag around. Will also try to fix upstream in napari
@schienstockd fixed in #141 Thanks for the report and providing a runnable example, made things much easier to debug!
https://user-images.githubusercontent.com/7307488/201485516-1189b167-736b-42c7-b510-45784bf12e6f.mp4
should be available in v0.0.5 on PyPI soon
https://github.com/napari/napari-animation/actions/runs/3451750009
Thanks!
Hello,
I am trying to record live cell imaging movies. I am using a
tracks
layer which has differentcolor by
values:I choose
speed
, thencapture
the frames and then create a movie. While creating the movie, it always switches back totrack_id
but I would like to recordspeed
or any of the other measurements.