napari: napari 3D view mode, vispy shader errors
🐛 Bug
To Reproduce
Steps to reproduce the behavior:
- Create clean napari environment
conda create -n napari-clean python=3.10 napari -c conda-forge
conda activate napari-clean
- Launch napari and load some example data
import napari
import numpy as np
arr = np.random.random((10,10,10))
viewer = napari.view_image(arr)
- Switch napari to 3D view mode, and observe error message
WARNING: Unsubstituted placeholders in code: ['$sample', '$sample', '$sample', '$sample', '$sample', '$sample', '$sample']
replacements made: ['viewtransformf', 'raycasting_setup', 'before_loop', 'in_loop', 'after_loop', 'sampler_type', 'post', 'pre', 'clip_with_planes', 'cmap', 'get_data']
WARNING: Error drawing visual <Volume at 0x7f441cdfa8f0>
WARNING: Error drawing visual <Volume at 0x7f441cdfa8f0>
Traceback (most recent call last):
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/app/backends/_qt.py", line 903, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 453, in __call__
self._invoke_callback(cb, event)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 471, in _invoke_callback
_handle_exception(self.ignore_callback_errors,
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 469, in _invoke_callback
cb(event)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 218, in on_draw
self._draw_scene()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 277, in _draw_scene
self.draw_visual(self.scene)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 315, in draw_visual
node.draw()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/visuals.py", line 103, in draw
self._visual_superclass.draw(self)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/visuals/visual.py", line 451, in draw
self._program.draw(self._vshare.draw_mode,
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/visuals/shaders/program.py", line 102, in draw
Program.draw(self, *args, **kwargs)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/program.py", line 526, in draw
canvas.context.flush_commands()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/context.py", line 172, in flush_commands
self.glir.flush(self.shared.parser)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 582, in flush
self._shared.flush(parser)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 504, in flush
parser.parse(self._filter(self.clear(), parser))
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 822, in parse
self._parse(command)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 792, in _parse
ob.set_data(*args)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 931, in set_data
raise RuntimeError("Shader compilation error in %s:\n%s" %
RuntimeError: Shader compilation error in GL_FRAGMENT_SHADER:
on line 329: error: syntax error, unexpected $undefined
vec4 color0 = $sample(u_volumetex, loc);
If you suspect this is an IPython 8.5.0 bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@python.org
You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.
Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
%config Application.verbose_crash=True
Traceback (most recent call last):
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/app/backends/_qt.py", line 903, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 453, in __call__
self._invoke_callback(cb, event)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 471, in _invoke_callback
_handle_exception(self.ignore_callback_errors,
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/util/event.py", line 469, in _invoke_callback
cb(event)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 218, in on_draw
self._draw_scene()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 277, in _draw_scene
self.draw_visual(self.scene)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/canvas.py", line 315, in draw_visual
node.draw()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/scene/visuals.py", line 103, in draw
self._visual_superclass.draw(self)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/visuals/visual.py", line 451, in draw
self._program.draw(self._vshare.draw_mode,
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/visuals/shaders/program.py", line 102, in draw
Program.draw(self, *args, **kwargs)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/program.py", line 526, in draw
canvas.context.flush_commands()
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/context.py", line 172, in flush_commands
self.glir.flush(self.shared.parser)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 582, in flush
self._shared.flush(parser)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 504, in flush
parser.parse(self._filter(self.clear(), parser))
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 822, in parse
self._parse(command)
File "/home/genevieb/em95/miniconda/conda/envs/napari-clean-py310/lib/python3.10/site-packages/vispy/gloo/glir.py", line 778, in _parse
raise RuntimeError('Cannot %s object %i because it '
RuntimeError: Cannot SIZE object 72 because it does not exist
If you suspect this is an IPython 8.5.0 bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@python.org
You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.
Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
%config Application.verbose_crash=True
Expected behavior
I expected napari to switch into the 3d view mode without errors. I also expected that a clean conda installation would not allow an incompatible/broken vispy version to be installed with napari.
Environment
- Please copy and paste the information at napari info option in help menubar here:
napari: 0.4.14
Platform: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-glibc2.17
Python: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:35:26) [GCC 10.4.0]
Qt: 5.15.4
PyQt5: 5.15.7
NumPy: 1.23.3
SciPy: 1.9.1
Dask: 2022.9.2
VisPy: 0.11.0
OpenGL:
- GL version: 2.1 Mesa 18.3.4
- MAX_TEXTURE_SIZE: 8192
Screens:
- screen 1: resolution 3440x1336, scale 1.0
Plugins:
- console: 0.0.6
- scikit-image: 0.4.14
- svg: 0.1.6
- Any other relevant information:
print(vispy.sys_info())
Platform: Linux-3.10.0-1160.71.1.el7.x86_64-x86_64-with-glibc2.17
Python: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:35:26) [GCC 10.4.0]
NumPy: 1.23.3
Backend: PyQt5
pyqt4: None
pyqt5: ('PyQt5', '5.15.7', '5.15.4')
pyqt6: None
pyside: None
pyside2: None
pyside6: None
pyglet: None
glfw: None
sdl2: None
wx: None
egl: EGL 1.5 NVIDIA: OpenGL_ES OpenGL
osmesa: None
tkinter: None
jupyter_rfb: None
_test: None
GL version: '2.1 Mesa 18.3.4'
MAX_TEXTURE_SIZE: 8192
Extensions: 'GL_ARB_multisample GL_EXT_abgr GL_EXT_bgra GL_EXT_blend_color GL_EXT_blend_minmax GL_EXT_blend_subtract GL_EXT_copy_texture GL_EXT_subtexture GL_EXT_texture_object GL_EXT_vertex_array GL_EXT_compiled_vertex_array GL_EXT_texture GL_EXT_texture3D GL_IBM_rasterpos_clip GL_ARB_point_parameters GL_EXT_draw_range_elements GL_EXT_packed_pixels GL_EXT_point_parameters GL_EXT_rescale_normal GL_EXT_separate_specular_color GL_EXT_texture_edge_clamp GL_SGIS_generate_mipmap GL_SGIS_texture_border_clamp GL_SGIS_texture_edge_clamp GL_SGIS_texture_lod GL_ARB_framebuffer_sRGB GL_ARB_multitexture GL_EXT_framebuffer_sRGB GL_IBM_multimode_draw_arrays GL_IBM_texture_mirrored_repeat GL_ARB_texture_cube_map GL_ARB_texture_env_add GL_ARB_transpose_matrix GL_EXT_blend_func_separate GL_EXT_fog_coord GL_EXT_multi_draw_arrays GL_EXT_secondary_color GL_EXT_texture_env_add GL_EXT_texture_lod_bias GL_INGR_blend_func_separate GL_NV_blend_square GL_NV_light_max_exponent GL_NV_texgen_reflection GL_NV_texture_env_combine4 GL_S3_s3tc GL_SUN_multi_draw_arrays GL_ARB_texture_border_clamp GL_ARB_texture_compression GL_EXT_framebuffer_object GL_EXT_texture_compression_s3tc GL_EXT_texture_env_combine GL_EXT_texture_env_dot3 GL_MESA_window_pos GL_NV_packed_depth_stencil GL_NV_texture_rectangle GL_ARB_depth_texture GL_ARB_occlusion_query GL_ARB_shadow GL_ARB_texture_env_combine GL_ARB_texture_env_crossbar GL_ARB_texture_env_dot3 GL_ARB_texture_mirrored_repeat GL_ARB_window_pos GL_ATI_fragment_shader GL_EXT_stencil_two_side GL_EXT_texture_cube_map GL_NV_depth_clamp GL_NV_fog_distance GL_APPLE_packed_pixels GL_ARB_draw_buffers GL_ARB_fragment_program GL_ARB_fragment_shader GL_ARB_shader_objects GL_ARB_vertex_program GL_ARB_vertex_shader GL_ATI_draw_buffers GL_ATI_texture_env_combine3 GL_EXT_shadow_funcs GL_EXT_stencil_wrap GL_MESA_pack_invert GL_MESA_ycbcr_texture GL_NV_primitive_restart GL_ARB_depth_clamp GL_ARB_fragment_program_shadow GL_ARB_half_float_pixel GL_ARB_occlusion_query2 GL_ARB_point_sprite GL_ARB_shading_language_100 GL_ARB_sync GL_ARB_texture_non_power_of_two GL_ARB_vertex_buffer_object GL_ATI_blend_equation_separate GL_EXT_blend_equation_separate GL_OES_read_format GL_ARB_color_buffer_float GL_ARB_pixel_buffer_object GL_ARB_texture_compression_rgtc GL_ARB_texture_rectangle GL_ATI_texture_compression_3dc GL_EXT_packed_float GL_EXT_pixel_buffer_object GL_EXT_texture_compression_dxt1 GL_EXT_texture_compression_rgtc GL_EXT_texture_mirror_clamp GL_EXT_texture_rectangle GL_EXT_texture_sRGB GL_EXT_texture_shared_exponent GL_ARB_framebuffer_object GL_EXT_framebuffer_blit GL_EXT_framebuffer_multisample GL_EXT_packed_depth_stencil GL_ARB_vertex_array_object GL_ATI_separate_stencil GL_ATI_texture_mirror_once GL_EXT_draw_buffers2 GL_EXT_draw_instanced GL_EXT_gpu_program_parameters GL_EXT_texture_array GL_EXT_texture_compression_latc GL_EXT_texture_integer GL_EXT_texture_sRGB_decode GL_EXT_timer_query GL_OES_EGL_image GL_ARB_copy_buffer GL_ARB_depth_buffer_float GL_ARB_draw_instanced GL_ARB_half_float_vertex GL_ARB_instanced_arrays GL_ARB_map_buffer_range GL_ARB_texture_buffer_object GL_ARB_texture_rg GL_ARB_texture_swizzle GL_ARB_vertex_array_bgra GL_EXT_texture_swizzle GL_EXT_vertex_array_bgra GL_NV_conditional_render GL_AMD_conservative_depth GL_AMD_draw_buffers_blend GL_AMD_seamless_cubemap_per_texture GL_AMD_shader_stencil_export GL_ARB_ES2_compatibility GL_ARB_blend_func_extended GL_ARB_debug_output GL_ARB_draw_buffers_blend GL_ARB_draw_elements_base_vertex GL_ARB_explicit_attrib_location GL_ARB_fragment_coord_conventions GL_ARB_provoking_vertex GL_ARB_sampler_objects GL_ARB_seamless_cube_map GL_ARB_shader_stencil_export GL_ARB_shader_texture_lod GL_ARB_texture_buffer_object_rgb32 GL_ARB_texture_cube_map_array GL_ARB_texture_gather GL_ARB_texture_multisample GL_ARB_texture_query_lod GL_ARB_texture_rgb10_a2ui GL_ARB_uniform_buffer_object GL_ARB_vertex_type_2_10_10_10_rev GL_EXT_provoking_vertex GL_EXT_texture_snorm GL_MESA_texture_signed_rgba GL_ARB_draw_indirect GL_ARB_get_program_binary GL_ARB_robustness GL_ARB_separate_shader_objects GL_ARB_shader_bit_encoding GL_ARB_texture_compression_bptc GL_ARB_timer_query GL_ARB_transform_feedback2 GL_ARB_transform_feedback3 GL_ARB_viewport_array GL_AMD_multi_draw_indirect GL_ANGLE_texture_compression_dxt3 GL_ANGLE_texture_compression_dxt5 GL_ARB_base_instance GL_ARB_compressed_texture_pixel_storage GL_ARB_conservative_depth GL_ARB_internalformat_query GL_ARB_map_buffer_alignment GL_ARB_shading_language_420pack GL_ARB_shading_language_packing GL_ARB_texture_storage GL_ARB_transform_feedback_instanced GL_EXT_framebuffer_multisample_blit_scaled GL_EXT_transform_feedback GL_AMD_shader_trinary_minmax GL_ARB_ES3_compatibility GL_ARB_arrays_of_arrays GL_ARB_clear_buffer_object GL_ARB_copy_image GL_ARB_explicit_uniform_location GL_ARB_fragment_layer_viewport GL_ARB_invalidate_subdata GL_ARB_multi_draw_indirect GL_ARB_program_interface_query GL_ARB_stencil_texturing GL_ARB_texture_buffer_range GL_ARB_texture_query_levels GL_ARB_texture_storage_multisample GL_ARB_texture_view GL_ARB_vertex_attrib_binding GL_KHR_debug GL_KHR_texture_compression_astc_ldr GL_ARB_buffer_storage GL_ARB_clear_texture GL_ARB_enhanced_layouts GL_ARB_internalformat_query2 GL_ARB_multi_bind GL_ARB_seamless_cubemap_per_texture GL_ARB_texture_mirror_clamp_to_edge GL_ARB_texture_stencil8 GL_ARB_vertex_type_10f_11f_11f_rev GL_EXT_shader_integer_mix GL_ARB_clip_control GL_ARB_conditional_render_inverted GL_ARB_cull_distance GL_ARB_get_texture_sub_image GL_ARB_pipeline_statistics_query GL_ARB_transform_feedback_overflow_query GL_EXT_polygon_offset_clamp GL_KHR_context_flush_control GL_KHR_no_error GL_KHR_texture_compression_astc_sliced_3d GL_MESA_shader_integer_functions GL_ARB_polygon_offset_clamp '
Additional context
I’ve seen similar-ish issues, and there seems to be some confusion about whether it’s a vispy or a napari problem. For example: https://github.com/napari/napari/issues/4570 (although that example seems different, because I think it was determined that the 3d image size was too large, and the minimal bug reproduction above uses only a (10,10,10) array)
About this issue
- Original URL
- State: closed
- Created 2 years ago
- Comments: 18 (15 by maintainers)
@GenevieveBuckley you are using mixed conda-forge defaults channel. This will lead, almost surely to segfaults, you should when debugging, try the following command:
mamba list
vispy.sys_info
Again, conda/mamba will have a hard time picking between:
the solution is just to update napari to use the newest vispy, or to specify the version in the install
"napari>=X.Y.Z"I hope this all helps.Mark
Please see testing in the original issue: https://github.com/napari/napari/issues/4891#issuecomment-1283985799 Using vanilla conda solver now properly installs 0.4.16 from conda-forge with proper vispy. If 0.4.15 is specified, the vispy also matches.
Eep! Situation is worse right now with conda install not working at all. (mamba does work, at some point maybe should just change the docs to suggest mamba?) I think I have a fix in PR: https://github.com/conda-forge/conda-forge-repodata-patches-feedstock/pull/333