brainrender-gui KeyError: 'notebookBackend'

Hi, I just made a fresh install of brainrender with pip in a new conda environment (conda create --name brainrender2 python=3.7)( the only additional thing I installed was spyder), on Kubuntu20.04, and brainrender-gui gives following errors:

(brainrender2) kiosk@stitcher:/mnt/data/Friedrich/DRD003240222Malinda$ brainrender-gui ╭─ file: /home/kiosk/anaconda3/envs/brainrender2/bin/brainrender-gui:8 line 8 ──────────────────────────────────────────────╮ │ │ │ Error line: │ │ 8 sys.exit(clilaunch()) │ │ │ │ Local variables │ │ │ │ object value type info │ │ ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── │ │ clilaunch = <Command clilaunch> click.core.Command │ │ │ ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─ file: /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/_jupyter.py:12 line 12 ────────────╮ │ │ │ Error line: │ │ 12 if vedo.settings.notebookBackend == “k3d”: │ │ │ │ Local variables │ │ │ │ object value type info │ │ ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── │ │ self = <repr-error “‘Scene’ object has no attribute brainrender.scene.Scene │ │ ‘actors’”> │ │ │ ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─ file: /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/vedo/utils.py:238 line 238 ────────────────────╮ │ │ │ Error line: │ │ 238 return self[k] │ │ │ │ Local variables │ │ │ │ object value type info │ │ ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── │ │ k = notebookBackend builtins.str Length: 15 │ │ │ │ self = { vedo.utils.dotdict │ │ ‘warn_on_setting’: ‘bool’, │ │ ‘defaultFont’: ‘str’, │ │ ‘screeshotScale’: ‘int’, │ │ ‘screenshotTransparentBackground’: ‘bool’, │ │ ‘screeshotLargeImage’: ‘bool’, │ │ ‘allowInteraction’: ‘bool’, │ │ ‘hackCallScreenSize’: ‘bool’, │ │ ‘enableDefaultMouseCallbacks’: ‘bool’, │ │ ‘enableDefaultKeyboardCallbacks’: ‘bool’, │ │ ‘immediateRendering’: ‘bool’, │ │ ‘rendererFrameColor’: ‘NoneType’, │ │ ‘rendererFrameAlpha’: ‘float’, │ │ ‘rendererFrameWidth’: ‘float’, │ │ ‘rendererFramePadding’: ‘float’, │ │ ‘renderLinesAsTubes’: ‘bool’, │ │ ‘hiddenLineRemoval’: ‘bool’, │ │ ‘pointSmoothing’: ‘bool’, │ │ ‘lineSmoothing’: ‘bool’, │ │ ‘polygonSmoothing’: ‘bool’, │ │ ‘visibleGridEdges’: ‘bool’, │ │ ‘lightFollowsCamera’: ‘bool’, │ │ ‘twoSidedLighting’: ‘bool’, │ │ ‘useDepthPeeling’: ‘bool’, │ │ ‘multiSamples’: ‘int’, │ │ ‘alphaBitPlanes’: ‘int’, │ │ ‘maxNumberOfPeels’: ‘int’, │ │ ‘occlusionRatio’: ‘float’, │ │ ‘useFXAA’: ‘bool’, │ │ ‘preserveDepthBuffer’: ‘bool’, │ │ ‘useSSAO’: ‘bool’, │ │ ‘SSAORadius’: ‘float’, │ │ ‘SSAOBias’: ‘float’, │ │ ‘SSAOKernelSize’: ‘int’, │ │ ‘SSAOBlur’: ‘bool’, │ │ ‘usePolygonOffset’: ‘bool’, │ │ ‘polygonOffsetFactor’: ‘float’, │ │ ‘polygonOffsetUnits’: ‘float’, │ │ ‘interpolateScalarsBeforeMapping’: ‘bool’, │ │ ‘useParallelProjection’: ‘bool’, │ │ ‘windowSplittingPosition’: ‘NoneType’, │ │ ‘tiffOrientationType’: ‘int’, │ │ ‘annotatedCubeColor’: ‘tuple’, │ │ ‘annotatedCubeTextColor’: ‘NoneType’, │ │ ‘annotatedCubeTextScale’: ‘float’, │ │ ‘annotatedCubeTexts’: ‘list’, │ │ ‘enablePrintColor’: ‘bool’, │ │ ‘k3dMenuVisibility’: ‘bool’, │ │ ‘k3dPlotHeight’: ‘int’, │ │ ‘k3dAntialias’: ‘bool’, │ │ ‘k3dLighting’: ‘float’, │ │ ‘k3dCameraAutoFit’: ‘bool’, │ │ ‘k3dGridAutoFit’: ‘bool’, │ │ ‘k3dAxesHelper’: ‘bool’, │ │ ‘k3dPointShader’: ‘str’, │ │ ‘k3dLineShader’: ‘str’, │ │ ‘flagDelay’: ‘int’, │ │ ‘flagFont’: ‘str’, │ │ ‘flagFontSize’: ‘int’, │ │ ‘flagJustification’: ‘int’, │ │ ‘flagAngle’: ‘int’, │ │ ‘flagBold’: ‘bool’, │ │ ‘flagItalic’: ‘bool’, │ │ ‘flagShadow’: ‘bool’, │ │ ‘flagColor’: ‘str’, │ │ ‘flagBackgroundColor’: ‘str’, │ │ ‘font_parameters’: ‘dict’ │ │ } │ │ │ ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/bin/brainrender-gui:8 in <module> │ │ │ │ 5 from brainrender.gui.init import clilaunch │ │ 6 if name == ‘main’: │ │ 7 │ sys.argv[0] = re.sub(r’(-script.pyw|.exe)?$‘, ‘’, sys.argv[0]) │ │ ❱ 8 │ sys.exit(clilaunch()) │ │ 9 │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/click/core.py:1128 in │ │ call │ │ │ │ 1125 │ │ │ 1126 │ def call(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │ │ 1127 │ │ “”“Alias for :meth:main.”“” │ │ ❱ 1128 │ │ return self.main(*args, **kwargs) │ │ 1129 │ │ 1130 │ │ 1131 class Command(BaseCommand): │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/click/core.py:1053 in main │ │ │ │ 1050 │ │ try: │ │ 1051 │ │ │ try: │ │ 1052 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │ │ ❱ 1053 │ │ │ │ │ rv = self.invoke(ctx) │ │ 1054 │ │ │ │ │ if not standalone_mode: │ │ 1055 │ │ │ │ │ │ return rv │ │ 1056 │ │ │ │ │ # it’s not safe to ctx.exit(rv) here! │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/click/core.py:1395 in invoke │ │ │ │ 1392 │ │ │ echo(style(message, fg=“red”), err=True) │ │ 1393 │ │ │ │ 1394 │ │ if self.callback is not None: │ │ ❱ 1395 │ │ │ return ctx.invoke(self.callback, **ctx.params) │ │ 1396 │ │ │ 1397 │ def shell_complete(self, ctx: Context, incomplete: str) -> t.List[“CompletionItem”]: │ │ 1398 │ │ “”"Return a list of completions for the incomplete value. Looks │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/click/core.py:754 in invoke │ │ │ │ 751 │ │ │ │ 752 │ │ with augment_usage_errors(__self): │ │ 753 │ │ │ with ctx: │ │ ❱ 754 │ │ │ │ return __callback(*args, **kwargs) │ │ 755 │ │ │ 756 │ def forward( │ │ 757 │ │ __self, _cmd: “Command”, *args: t.Any, **kwargs: t.Any # noqa: B902 │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/gui/init.py: │ │ 34 in clilaunch │ │ │ │ 31 def clilaunch(atlas=None, axes=False, output=None): │ │ 32 │ app = QApplication(sys.argv) │ │ 33 │ app.setApplicationName(“Brainrender GUIs”) │ │ ❱ 34 │ ex = App(atlas_name=atlas, axes=axes, screenshots_folder=output) │ │ 35 │ app.aboutToQuit.connect(ex.onClose) │ │ 36 │ ex.show() │ │ 37 │ sys.exit(app.exec()) │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/gui/app.py:48 in │ │ init │ │ │ │ 45 │ │ # Get vtkWidget plotter and creates a scene embedded in it │ │ 46 │ │ new_plotter = Plotter(qtWidget=self.vtkWidget) │ │ 47 │ │ self.scene = Scene( │ │ ❱ 48 │ │ │ *args, atlas_name=atlas_name, plotter=new_plotter, **kwargs │ │ 49 │ │ ) │ │ 50 │ │ │ │ 51 │ │ # Initialize parent classes │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/scene.py:50 in │ │ init │ │ │ │ 47 │ │ logger.debug( │ │ 48 │ │ │ f"Creating scene with parameters: root: {root}, atlas_name: ‘{atlas_name}’’, │ │ 49 │ │ ) │ │ ❱ 50 │ │ JupyterMixIn.init(self) │ │ 51 │ │ │ │ 52 │ │ self.actors = [] # stores all actors in the scene │ │ 53 │ │ self.labels = [] # stores all labels actors in scene │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/_jupyter.py:12 │ │ in init │ │ │ │ 9 class JupyterMixIn: # pragma: no cover │ │ 10 │ def init(self): # pragma: no cover │ │ 11 │ │ # keep track if we are in a jupyter notebook │ │ ❱ 12 │ │ if vedo.settings.notebookBackend == “k3d”: │ │ 13 │ │ │ self.backend = “k3d” │ │ 14 │ │ elif vedo.settings.notebookBackend == “itkwidgets”: │ │ 15 │ │ │ self.backend = “itkwidgets” │ │ │ │ /home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/vedo/utils.py:238 in │ │ getattr │ │ │ │ 235 │ │ │ │ self[k] = dotdict(v) │ │ 236 │ │ │ 237 │ def getattr(self, k): │ │ ❱ 238 │ │ return self[k] │ │ 239 │ │ │ 240 │ def setattr(self, k, v): │ │ 241 │ │ if self.warn_on_setting: │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ KeyError: ‘notebookBackend’ Exception ignored in: <function Scene.del at 0x7fab395cb440> Traceback (most recent call last): File “/home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/scene.py”, line 102, in del self.close() File “/home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/render.py”, line 281, in close self.plotter.close() AttributeError: ‘NoneType’ object has no attribute ‘close’ Exception ignored in: <function Scene.del at 0x7fab395cb440> Traceback (most recent call last): File “/home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/scene.py”, line 102, in del self.close() File “/home/kiosk/anaconda3/envs/brainrender2/lib/python3.7/site-packages/brainrender/render.py”, line 281, in close self.plotter.close() AttributeError: ‘NoneType’ object has no attribute ‘close’

Any idea what could be going on? I got a similar notebookBackend error (in a separate conda env) when I ran brainrender from spyder, which could be solved by adding a line vedo.settings[‘notebookBackend’] = ‘False’

cheers, John

[marcomusy]

Have you tried: pip install vedo==2021.0.5

[marcomusy]

I’ve seen it before: https://discourse.vtk.org/t/vtkproppicker-not-working-in-osx-and-qt/8057 but unfortunately i’m not familiar with qt at all and I’m not sure what to do with it 😦