[Points, vispy] Traceback when toggling Points layer to 3D

[psobolewskiPhD]

🐛 Bug Report

First reported here:
https://napari.zulipchat.com/#narrow/stream/212875-general/topic/vispy.20.22Last.20dimension.20should.20be.202.20not.203.22.20error

Creating a points layer and toggling to 3D results in a traceback:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/Dev/vispy/vispy/app/backends/_qt.py:928, in CanvasBackendDesktop.paintGL(self=<vispy.app.backends._qt.CanvasBackendDesktop object>)
    926 # (0, 0, self.width(), self.height()))
    927 self._vispy_canvas.set_current()
--> 928 self._vispy_canvas.events.draw(region=None)
        self._vispy_canvas = <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>
        self._vispy_canvas.events.draw = <vispy.util.event.EventEmitter object at 0x28a227770>
        self = <vispy.app.backends._qt.CanvasBackendDesktop object at 0x28a296c10>
        self._vispy_canvas.events = <vispy.util.event.EmitterGroup object at 0x28a2278c0>
    930 # Clear the alpha channel with QOpenGLWidget (Qt >= 5.4), otherwise the
    931 # window is translucent behind non-opaque objects.
    932 # Reference:  MRtrix3/mrtrix3#266
    933 if QT5_NEW_API or PYSIDE6_API or PYQT6_API:

File ~/Dev/vispy/vispy/util/event.py:453, in EventEmitter.__call__(self=<vispy.util.event.EventEmitter object>, *args=(), **kwargs={'region': None})
    450 if self._emitting > 1:
    451     raise RuntimeError('EventEmitter loop detected!')
--> 453 self._invoke_callback(cb, event)
        event = <DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>
        self = <vispy.util.event.EventEmitter object at 0x28a227770>
        cb = <bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>>
    454 if event.blocked:
    455     break

File ~/Dev/vispy/vispy/util/event.py:471, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6)>>, event=<DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>)
    469     cb(event)
    470 except Exception:
--> 471     _handle_exception(self.ignore_callback_errors,
        self = <vispy.util.event.EventEmitter object at 0x28a227770>
        cb = <bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>>
        event = <DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>
        (cb, event) = (<bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>>, <DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>)
    472                       self.print_callback_errors,
    473                       self, cb_event=(cb, event))

File ~/Dev/vispy/vispy/util/event.py:469, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6)>>, event=<DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>)
    467 def _invoke_callback(self, cb, event):
    468     try:
--> 469         cb(event)
        cb = <bound method SceneCanvas.on_draw of <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>>
        event = <DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>
    470     except Exception:
    471         _handle_exception(self.ignore_callback_errors,
    472                           self.print_callback_errors,
    473                           self, cb_event=(cb, event))

File ~/Dev/vispy/vispy/scene/canvas.py:219, in SceneCanvas.on_draw(self=<NapariSceneCanvas (PyQt6)>, event=<DrawEvent blocked=False handled=False native=None region=None source=None sources=[] type=draw>)
    216 # Now that a draw event is going to be handled, open up the
    217 # scheduling of further updates
    218 self._update_pending = False
--> 219 self._draw_scene()
        self = <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>

File ~/Dev/vispy/vispy/scene/canvas.py:278, in SceneCanvas._draw_scene(self=<NapariSceneCanvas (PyQt6)>, bgcolor=<class 'numpy.ndarray'> (4,) float32)
    276     bgcolor = self._bgcolor
    277 self.context.clear(color=bgcolor, depth=True)
--> 278 self.draw_visual(self.scene)
        self = <NapariSceneCanvas (PyQt6) at 0x16e6ffbf0>

File ~/Dev/vispy/vispy/scene/canvas.py:316, in SceneCanvas.draw_visual(self=<NapariSceneCanvas (PyQt6)>, visual=<SubScene>, event=None)
    314         else:
    315             if hasattr(node, 'draw'):
--> 316                 node.draw()
        node = <PointsVisual at 0x29327d460>
    317                 prof.mark(str(node))
    318 else:

File ~/Dev/vispy/vispy/scene/visuals.py:106, in VisualNode.draw(self=<PointsVisual>)
    104 if self.picking and not self.interactive:
    105     return
--> 106 self._visual_superclass.draw(self)
        self = <PointsVisual at 0x29327d460>
        self._visual_superclass = <class 'vispy.visuals.visual.CompoundVisual'>

File ~/Dev/vispy/vispy/visuals/visual.py:668, in CompoundVisual.draw(self=<PointsVisual>)
    666 for v in self._subvisuals:
    667     if v.visible:
--> 668         v.draw()
        v = <Line at 0x293050da0>

File ~/Dev/vispy/vispy/scene/visuals.py:106, in VisualNode.draw(self=<Line>)
    104 if self.picking and not self.interactive:
    105     return
--> 106 self._visual_superclass.draw(self)
        self = <Line at 0x293050da0>
        self._visual_superclass = <class 'vispy.visuals.line.line.LineVisual'>

File ~/Dev/vispy/vispy/visuals/visual.py:668, in CompoundVisual.draw(self=<Line>)
    666 for v in self._subvisuals:
    667     if v.visible:
--> 668         v.draw()
        v = <vispy.visuals.line.line._GLLineVisual object at 0x2932e5f40>

File ~/Dev/vispy/vispy/visuals/visual.py:505, in Visual.draw(self=<vispy.visuals.line.line._GLLineVisual object>)
    503 if not self.visible:
    504     return
--> 505 if self._prepare_draw(view=self) is False:
        self = <vispy.visuals.line.line._GLLineVisual object at 0x2932e5f40>
    506     return
    508 if self._vshare.draw_mode is None:

File ~/Dev/vispy/vispy/visuals/line/line.py:331, in _GLLineVisual._prepare_draw(self=<vispy.visuals.line.line._GLLineVisual object>, view=<vispy.visuals.line.line._GLLineVisual object>)
    329     return False
    330 pos = np.ascontiguousarray(self._parent._pos, dtype=np.float32)
--> 331 self._pos_vbo.set_data(pos)
        pos = <class 'numpy.ndarray'> (1, 3) float32
        self._pos_vbo = <VertexBuffer size=1 last_dim=2>
        self = <vispy.visuals.line.line._GLLineVisual object at 0x2932e5f40>
    332 self._program.vert['position'] = self._pos_vbo
    333 self._program.vert['to_vec4'] = self._ensure_vec4_func(pos.shape[-1])

File ~/Dev/vispy/vispy/gloo/buffer.py:189, in DataBuffer.set_data(self=<VertexBuffer size=1 last_dim=2>, data=<class 'numpy.ndarray'> (1, 3) float32, copy=False, **kwargs={})
    175 def set_data(self, data, copy=False, **kwargs):
    176     """Set data (deferred operation)
    177
    178     Parameters
   (...)
    187         Additional arguments.
    188     """
--> 189     data = self._prepare_data(data, **kwargs)
        data = <class 'numpy.ndarray'> (1, 3) float32
        self = <VertexBuffer size=1 last_dim=2>
        kwargs = {}
    190     self._dtype = data.dtype
    191     # This works around some strange NumPy bug where a float32 array
    192     # of shape (155407, 1) was said to have strides
    193     # (4, 9223372036854775807), which is crazy

File ~/Dev/vispy/vispy/gloo/buffer.py:446, in VertexBuffer._prepare_data(self=<VertexBuffer size=1 last_dim=2>, data=<class 'numpy.ndarray'> (1, 3) float32, convert=False)
    444     c = 1
    445 if self._last_dim and c != self._last_dim:
--> 446     raise ValueError('Last dimension should be %s not %s'
        'Last dimension should be %s not %s'
                                 % (self._last_dim, c) = 'Last dimension should be 2 not 3'
        c = 3
        self._last_dim = 2
        self = <VertexBuffer size=1 last_dim=2>
        (self._last_dim, c) = (2, 3)
    447                      % (self._last_dim, c))
    448 dtype_def = ('f0', data.dtype.base)
    449 if c != 1:
    450     # numpy dtypes with size 1 are ambiguous, only add size if it is greater than 1

ValueError: Last dimension should be 2 not 3

The error is spammed, even upon return to 2D, and results in significant performance degradation.

💡 Steps to Reproduce

The following script will reproduce:

import numpy as np
import napari

data =  np.random.rand(3, 2)
viewer = napari.Viewer()

viewer.add_points(data)
viewer.dims.ndisplay = 3

napari.run()

Alternately just launch napari, add points layer, and toggle to 3D.

💡 Expected Behavior

No error.

🌎 Environment

napari: 0.5.0a2.dev649+g2d2cac676
Platform: macOS-13.3.1-arm64-arm-64bit
System: MacOS 13.3.1
Python: 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:54:21) [Clang 16.0.6 ]
Qt: 6.6.1
PyQt6:
NumPy: 1.26.4
SciPy: 1.12.0
Dask: 2024.3.1
VisPy: 0.14.3.dev3
magicgui: 0.8.2
superqt: 0.6.2
in-n-out: 0.2.0
app-model: 0.2.5
npe2: 0.7.4

OpenGL:

• GL version: 2.1 Metal - 83.1
• MAX_TEXTURE_SIZE: 16384
• GL_MAX_3D_TEXTURE_SIZE: 2048

Screens:

• screen 1: resolution 1680x1050, scale 2.0

Optional:

• numba: 0.59.0
• triangle not installed

Settings path:

• /Users/piotrsobolewski/Library/Application Support/napari/napari-dev_a1eb8b76ba95fa16ad06e26097b46b8455dfbf0b/settings.yaml
  Plugins:
• napari: 0.5.0a2.dev604+gfe4740ef3.d20240319 (81 contributions)
• napari-console: 0.0.9 (0 contributions)
• napari-svg: 0.1.10 (2 contributions)
• napari-threedee: 0.0.20.dev1+g65d1b01 (22 contributions)
• zarpaint: 0.3.1 (14 contributions)

💡 Additional Context

The root cause is here:
https://github.com/napari/napari/pull/6896/files#r1602264036

But the question is how are all tests passing and what can we do about it.

[andy-sweet]

I keep running into this, so assigned myself to spend a little time thinking about how to write a test that fails on main.

[andy-sweet]

Quickly unassigning because I failed to write any test that fails on main ...

I started with some that don't require the whole viewer, but they all pass.

def test_2d_to_3d_vispy_layer():
    """See https://github.com/napari/napari/issues/6925"""
    layer = Points(np.zeros((4, 2)))
    visual = VispyPointsLayer(layer)
    dims = Dims(ndim=3, ndisplay=2)
    layer._slice_dims(dims)

    dims.ndisplay = 3
    layer._slice_dims(dims)


def test_2d_to_3d_viewer_model():
    """See https://github.com/napari/napari/issues/6925"""
    viewer = ViewerModel()
    layer = viewer.add_points(np.zeros((4, 2)))
    visual = VispyPointsLayer(layer)

    viewer.dims.ndisplay = 3


def test_2d_to_3d_vispy_canvas():
    """See https://github.com/napari/napari/issues/6925"""
    viewer = ViewerModel()
    layer = viewer.add_points(np.zeros((4, 2)))
    canvas = VispyCanvas(viewer, KeymapHandler())
    visual = VispyPointsLayer(layer)
    canvas.add_layer_visual_mapping(layer, visual)

    viewer.dims.ndisplay = 3

There may be some state that could be inspected/asserted to cause a failure (e.g. looking at the width of the line visual), but that may assume too much about the implementation details.

Then I tried the higher level test suggested on Zulip and even that passes:

def test_points_2d_to_3d(make_napari_viewer):
    """See https://github.com/napari/napari/issues/6925"""
    viewer = make_napari_viewer(ndisplay=2, show=True)
    layer = viewer.add_points()
    viewer.dims.ndisplay = 3

I then tried run the reproducer above as a script and even that was fine!

But I can manually reproduce by clicking the 2/3D display button.

[andy-sweet]

Ah, maybe this needs QApplication::processEvents?

Adding that does make this reproducible for me:

def test_points_2d_to_3d(make_napari_viewer):
    """See https://github.com/napari/napari/issues/6925"""
    viewer = make_napari_viewer(ndisplay=2, show=True)
    viewer.add_points()
    QApplication.processEvents()
    viewer.dims.ndisplay = 3
    QApplication.processEvents()

[andy-sweet]

Also note that while using a Points layer with no data is enough to create the issue for me (as above), the test we add should have some data.

[psobolewskiPhD]

Interesting, the script from the OP does reproduce with no additional input for me -- fresh pull from main: eab7661

Thanks for investigating!

[brisvag]

I bumped into this again... I put together the suggestions from above in a PR: #7004.