napari: Napari 0.3.4 release crashes when switching to volume rendering

🐛 Bug

Napari 0.3.4 (release version) crashes when trying to render volume in 3D.

To Reproduce

Steps to reproduce the behavior:

Load a volume
Display and navigate through slices in 2D
Switch to 3D -> Crash

napari_vol_crash

(stardist) λ napari
WARNING: Error drawing visual <Volume at 0x1b6364c0d48>
10:17:55 WARNING Error drawing visual <Volume at 0x1b6364c0d48>
WARNING: Traceback (most recent call last):
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\latebind.py", line 43, in __call__
    return self._finalCall( *args, **named )
TypeError: 'NoneType' object is not callable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw

    self._draw_scene()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\context.py", line 176, in flush_commands
    self.glir.flush(self.shared.parser)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 572, in flush
    self._shared.flush(parser)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 494, in flush
    parser.parse(self._filter(self.clear(), parser))
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 789, in _parse
    ob.set_size(*args)  # Texture[1D, 2D, 3D], RenderBuffer
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 1624, in set_size
    gl.GL_BYTE, shape[:3])
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 1573, in glTexImage3D
    width, height, depth, border, format, type, None)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\latebind.py", line 47, in __call__
    return self._finalCall( *args, **named )
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\wrapper.py", line 882, in wrapperCall

    result = wrappedOperation( *cArguments )
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\platform\baseplatform.py", line 425, in __call__
    self.__name__, self.__name__,
OpenGL.error.NullFunctionError: Attempt to call an undefined function glTexImage3D, check for bool(glTexImage3D) before calling
10:17:56 WARNING Traceback (most recent call last):
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\latebind.py", line 43, in __call__
    return self._finalCall( *args, **named )
TypeError: 'NoneType' object is not callable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw

    self._draw_scene()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\context.py", line 176, in flush_commands
    self.glir.flush(self.shared.parser)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 572, in flush
    self._shared.flush(parser)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 494, in flush
    parser.parse(self._filter(self.clear(), parser))
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 789, in _parse
    ob.set_size(*args)  # Texture[1D, 2D, 3D], RenderBuffer
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 1624, in set_size
    gl.GL_BYTE, shape[:3])
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\vispy\gloo\glir.py", line 1573, in glTexImage3D
    width, height, depth, border, format, type, None)
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\latebind.py", line 47, in __call__
    return self._finalCall( *args, **named )
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\wrapper.py", line 882, in wrapperCall

    result = wrappedOperation( *cArguments )
  File "c:\users\volker\anaconda3\envs\stardist\lib\site-packages\OpenGL\platform\baseplatform.py", line 425, in __call__
    self.__name__, self.__name__,
OpenGL.error.NullFunctionError: Attempt to call an undefined function glTexImage3D, check for bool(glTexImage3D) before calling

Expected behavior

The same volume renders fine in an earlier version of napari.

Environment

Please copy and paste the information at napari info option in help menubar here:

napari: 0.3.4
Platform: Windows-10-10.0.18362-SP0
Python: 3.7.7 (default, Apr 15 2020, 05:09:04) [MSC v.1916 64 bit (AMD64)]
Qt: 5.14.2
PyQt5: 5.14.2
NumPy: 1.18.1
SciPy: 1.3.1
Dask: 2.18.0
VisPy: 0.6.4

GL version: 4.6.0 - Build 26.20.100.7812
MAX_TEXTURE_SIZE: 16384

Plugins:
- napari-plugin-engine: 0.1.6
- svg: 0.1.3

This was pip installed into an existing conda environment from the PyPI release.

Additional context

In the same environment, when I open an IPython console before switching to volume rendering (same volume), napari does not crash !

napari_vol_no_crash

Also, the volume renders fine in one of my older napari installations/environments that has the same version of vispy, which rules out my initial thought that this would be a vispy issue. My current guess is that this may be PyQt-related. The environment below works. Note a few things are different, notably PySide instead of PyQt.

napari: 0.3.1+12.g0cd943c
Platform: Windows-10-10.0.18362-SP0
Python: 3.7.7 (default, May 6 2020, 11:45:54) [MSC v.1916 64 bit (AMD64)]
Qt: 5.14.2
PySide2: 5.14.2.1
NumPy: 1.18.4
SciPy: 1.4.1
Dask: 2.16.0
VisPy: 0.6.4

GL version: 4.6.0 - Build 26.20.100.7812
MAX_TEXTURE_SIZE: 16384

Plugins:
- napari-plugin-engine: 0.1.5
- svg: 0.1.2

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 51 (45 by maintainers)

Commits related to this issue

Revert "remove scipy.stats import (#1250)" This reverts commit 96e9722419a5b0adddbc14fe12c69a7d769f8758. Fixes #1347 See https://github.com/napari/napari/issues/1347 for more details. — committed to jni/napari by jni 4 years ago
Revert "remove scipy.stats import (#1250)" This reverts commit 96e9722419a5b0adddbc14fe12c69a7d769f8758. Fixes #1347 See https://github.com/napari/napari/issues/1347 for more details. — committed to jni/napari by jni 4 years ago
Add reference to issue #1347 — committed to jni/napari by jni 4 years ago
Revert "remove scipy.stats import (#1250)" (#1371) * Revert "remove scipy.stats import (#1250)" This reverts commit 96e9722419a5b0adddbc14fe12c69a7d769f8758. Fixes #1347 See https://github.c... — committed to napari/napari by jni 4 years ago

Most upvoted comments

I found the nd_labels.py consistently produce the problem: run the python file -> merge dimension -> drag and crashed

liu-ziyang on Jun 30, 2020

Yes, after adding the import as suggested it no longer crashes for that volume.

VolkerH on Jun 18, 2020

This has been closed by #1445

sofroniewn on Jul 15, 2020

fwiw, the reproduce of the problem only works for me on windows. On macbook everything worked out fine. If we can reproduce on other platform and see the same issue, maybe it is certain graphical driver being incompatible with opengl/vispy?

liu-ziyang on Jun 30, 2020

my investigation leads me to a few related threads, fwiw: https://github.com/vispy/vispy/pull/1394 https://github.com/vispy/vispy/issues/1540

and my stack traced to a suspecious call to <WinDLL ‘opengl32’, handle 7ffdf3570000 at 0x1aae1d22880> from vispy 0.6.4: venv\Lib\site-packages\vispy\gloo\gl_gl2.py line 415

liu-ziyang on Jun 29, 2020

The IndexError in size = [size[i] for i in self.dims.displayed] seems to be a direct result of the error in _calc_bbox as the bbox calculation (or seomthing upstream) drops a dimension. So if the _calc_bbox has been dropped/replaced in #1360 there is a good chance it is gone (will try and confirm).

VolkerH on Jun 19, 2020

to clarify, are you saying napari.view_image(data) is not fixed by scipy.stats, though?

On my system, import scipy.stats ... napari.view_image(data) and v=napari.view_image(data) (without import scipy.stats) both work, but not simply napari.view_image(data).

cgohlke on Jun 18, 2020