napari-omero Traceback when attempting to open image after successful connection to omero

I'm able to connect to our Omero server using the master branch pulled from GIT, but when I attempt to pull an image I get a crash. The minimal reproducible step for me is to launch napari_omero from my env, log in using my credentials, and then double click an image to load. I am running this through VScode on an Ubuntu server using a virtual desktop.

(omeroenv) dstabley@ultra94:~/napari-omero$ napari_omero

** (python:83093): WARNING **: 10:31:37.834: AT-SPI: Could not obtain desktop path or name


** (python:83093): WARNING **: 10:31:37.882: AT-SPI: Could not obtain desktop path or name


** (python:83093): WARNING **: 10:31:37.882: atk-bridge: get_device_events_reply: unknown signature

** (python:83093): WARNING **: 10:31:37.882: atk-bridge: get_device_events_reply: unknown signature

** (python:83093): WARNING **: 10:31:37.882: atk-bridge: GetRegisteredEvents returned message with unknown signature

** (python:83093): WARNING **: 10:31:37.929: AT-SPI: Could not obtain desktop path or name


** (python:83093): WARNING **: 10:31:37.929: atk-bridge: get_device_events_reply: unknown signature

** (python:83093): WARNING **: 10:31:37.929: atk-bridge: get_device_events_reply: unknown signature

** (python:83093): WARNING **: 10:31:37.929: atk-bridge: GetRegisteredEvents returned message with unknown signature
/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/dask_utils.py:173: UserWarning: For best performance with Dask arrays in napari, please upgrade Dask to v2.15.0 or later. Current version is 2.13.0
  'For best performance with Dask arrays in napari, please '
WARNING: Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7f2ee3ca5630>
WARNING:vispy:Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7f2ee3ca5630>
Aborted (core dumped)
(omeroenv) dstabley@ultra94:~/napari-omero$ napari_omero

** (python:83978): WARNING **: 10:36:18.327: AT-SPI: Could not obtain desktop path or name


** (python:83978): WARNING **: 10:36:18.361: AT-SPI: Could not obtain desktop path or name


** (python:83978): WARNING **: 10:36:18.361: atk-bridge: get_device_events_reply: unknown signature

** (python:83978): WARNING **: 10:36:18.362: atk-bridge: get_device_events_reply: unknown signature

** (python:83978): WARNING **: 10:36:18.362: atk-bridge: GetRegisteredEvents returned message with unknown signature

** (python:83978): WARNING **: 10:36:18.402: AT-SPI: Could not obtain desktop path or name


** (python:83978): WARNING **: 10:36:18.402: atk-bridge: get_device_events_reply: unknown signature

** (python:83978): WARNING **: 10:36:18.402: atk-bridge: get_device_events_reply: unknown signature

** (python:83978): WARNING **: 10:36:18.402: atk-bridge: GetRegisteredEvents returned message with unknown signature
/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/dask_utils.py:173: UserWarning: For best performance with Dask arrays in napari, please upgrade Dask to v2.15.0 or later. Current version is 2.13.0
  'For best performance with Dask arrays in napari, please '
WARNING: Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7fbe6d562630>
WARNING:vispy:Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7fbe6d562630>
Aborted (core dumped)
(omeroenv) dstabley@ultra94:~/napari-omero$ napari_omero

** (python:84312): WARNING **: 10:36:37.100: AT-SPI: Could not obtain desktop path or name


** (python:84312): WARNING **: 10:36:37.121: AT-SPI: Could not obtain desktop path or name


** (python:84312): WARNING **: 10:36:37.122: atk-bridge: get_device_events_reply: unknown signature

** (python:84312): WARNING **: 10:36:37.122: atk-bridge: get_device_events_reply: unknown signature

** (python:84312): WARNING **: 10:36:37.122: atk-bridge: GetRegisteredEvents returned message with unknown signature

** (python:84312): WARNING **: 10:36:37.136: AT-SPI: Could not obtain desktop path or name


** (python:84312): WARNING **: 10:36:37.136: atk-bridge: get_device_events_reply: unknown signature

** (python:84312): WARNING **: 10:36:37.136: atk-bridge: get_device_events_reply: unknown signature

** (python:84312): WARNING **: 10:36:37.136: atk-bridge: GetRegisteredEvents returned message with unknown signature
/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/dask_utils.py:173: UserWarning: For best performance with Dask arrays in napari, please upgrade Dask to v2.15.0 or later. Current version is 2.13.0
  'For best performance with Dask arrays in napari, please '
WARNING: Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7efec754b630>
WARNING:vispy:Traceback (most recent call last):
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 70, in _on_thumbnail_selected
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg/napari_omero/widgets/main.py", line 84, in load_image
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/components/layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/list/_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/home/solecgrp/dstabley/anaconda3/envs/omeroenv/lib/python3.6/site-packages/napari/_qt/qt_viewer.py", line 264, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x7efec754b630>
Aborted (core dumped)

Jun 26 '20 16:06 dstabley

hi @dstabley, looks like you're in a somewhat old environment (based on that dask version error). I don't yet know what's going on here... but do you still do you get the same error if you work in a fresh environment as described here? (note, you'll need to pip install from github ... so use pip install git+git://github.com/tlambert03/napari-omero.git instead of pip install napari-omero

depending on how you installed napari-omero (for instance, if you didn't use an editable install, but then you recloned), it may also be that your napari_omero command script is stale and that you need to reinstall

Jun 26 '20 16:06 tlambert03

@tlambert03 I had been using my project's dev environment, but I just confirmed this with a brand new environment following your instructions. I cloned the repo to my local drive, made an env from your yml file, then ran the setup.py script. I then launched napari_omero, got the gui, saw that it was connected and could see my images. However, when I double click an image I get the same error as previously.

The only thing I can't test thus far is the direct pip install git+git//URL method as this linux server seems to have that route blocked (keeps timing out).

Jun 26 '20 17:06 dstabley

oh actually... are you always double clicking? I can actually see why that might cause this bug (which is fundamentally a problem with the way I'm clearing the viewer when loading a new image). if you single click and wait does it change anything?

Jun 26 '20 17:06 tlambert03

@tlambert03 just confirmed that single click also does the same thing. I can navigate the entire tree but can't open anything.

Jun 26 '20 18:06 dstabley

ok thanks for checking. one more question: The stack trace indicates this is a bug in napari with removing a layer (and napari-omero attempts to remove all layers before loading one). but I'm still a little confused why it would happen on the first load, and not 2nd+ ... do you happen to have any layers already loaded in napari when you do this? (not that you shouldn't be able to do that... just curious)

Jun 26 '20 18:06 tlambert03

@tlambert03 I don't have any layers loaded. I just ran an interesting test, though. I uploaded a new synthetic data TIFF I had to my server and it loaded fine. I then noticed the images I had been trying to access have a common bug we were having where the metadata Z and T series were swapped. I'm guessing that maybe the plugin can't handle this metadata mismatch. Omero handles it on the server side, but if you're pulling on the assumption of a given number of planes or data shape it may cause a problem. One other detail is that the image that worked is 8 bit and the one that crashed is 16 bit.

Jun 26 '20 18:06 dstabley

definitely interesting. I can certainly see how that might create a problem. but i can't quite see how it would result in the KeyError in this stack track! 😅 i can probably prevent that key error... which may then reveal an additional problem if you have a metadata mismatch.

Jun 26 '20 18:06 tlambert03

Ok great, let me know. I'm happy to run additional tests.

Jun 26 '20 18:06 dstabley

@tlambert03 one more question - what is the most efficient way to grab an image that is loaded into Napari as a numpy stack in the backend? I haven't done this yet but pulling an Omero image and doing an operation on it would be cool.

Jun 26 '20 18:06 dstabley

all of the layers have a data attribute that holds the numpy array. so for example:

import napari
import numpy as np

with napari.gui_qt():
    viewer = napari.Viewer()
    # just as an example to get a layer... it doesn't matter
    # where the layer comes from, could have been loaded from OMERO
    napari.add_image(np.random.rand(16,128,128))

    # once you have a loaded layer, you need to get the layer object, like the "first" layer
    layer = viewer.layers[0]
    # here's the actual numpy (or dask, in the case of napari-omero) array
    layer.data

Jun 26 '20 19:06 tlambert03

@tlambert03 some more interesting behavior. When I load an image through the standalone napari_omero viewer it loads fine, but when I add the napari_omero extension as a dockable widget in the embedded napari viewer in my application as such:

class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
    def __init__(self, *args, obj=None, **kwargs):
          self.viewer = napari.Viewer()
          self.viewer.window.add_dock_widget(OMEROWidget(), area="right")

I get the following when trying the same operation (note that there were no layers in the napari viewer as it had just been initialized and no operations had been performed):

WARNING: Traceback (most recent call last):
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg\napari_omero\widgets\main.py", line 70, in _on_thumbnail_selected
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg\napari_omero\widgets\main.py", line 84, in load_image
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\components\layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\list\_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 523, in _invoke_callback
    cb(event)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\_qt\qt_viewer.py", line 246, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x1c94e8972e8>
WARNING:vispy:Traceback (most recent call last):
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg\napari_omero\widgets\main.py", line 70, in _on_thumbnail_selected
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari_omero-0.1.1.dev5+g6d45d4c-py3.6.egg\napari_omero\widgets\main.py", line 84, in load_image
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\components\layerlist.py", line 139, in remove_selected
    self.pop(i)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\list\_model.py", line 64, in pop
    self.events.removed(item=obj, index=key)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\utils\event.py", line 523, in _invoke_callback
    cb(event)
  File "C:\Users\Daniel\anaconda3\envs\NIML_Lattice_Tools\lib\site-packages\napari\_qt\qt_viewer.py", line 246, in _remove_layer
    vispy_layer = self.layer_to_visual[layer]
KeyError: <Image layer '0' at 0x1c94e8972e8>

Jun 26 '20 19:06 dstabley

@tlambert03 Further development on the previous post - if I pre-load a points layer into my application's embedded Napari viewer before clicking on the Omero image selection it works properly. This is reproducible. I suspect that maybe this comes from https://github.com/tlambert03/napari-omero/blob/master/src/napari_omero/widgets/main.py line 83 and 84:

def load_image(self, wrapper: BlitzObjectWrapper):
        self.viewer.layers.select_all()
        self.viewer.layers.remove_selected()

        type_ = wrapper.__class__.__name__[1:-7]
        id_ = wrapper.getId()
        self.viewer.open(f"{type_}:{id_}", plugin="omero")

Where the function selects all layers - is it possible that because my window initializes with no layers that this is throwing an exception? It's all I can think of as for why creating a null points layer fixes the crash.

Jun 26 '20 20:06 dstabley

It’s definitely related to those two lines, but it should still not be an error to call remove_selected with no layers in the viewer. I need to look closer at the napari events there to see why it might be happening

Jun 26 '20 20:06 tlambert03