Adding more than 1024 points causes the 3D viewer to crash.

[cudmore]

🐛 Bug

Napari crashes if I add more than 1024 3D points and switch to the 3D view. It also crashes with more than 1024 points if I explicit start up Napari with the 3D view.

To Reproduce

import numpy as np
import napari

with napari.gui_qt():
	myViewer = napari.Viewer()

	# works up to 1024 points but crashes if >1024 points
	s = (1025,3)
	# (1025,3) random integers in the range [10, 100)
	myPoints = np.random.randint(10,100,s)
	pointLayer = myViewer.add_points(myPoints)

1. Run the code above
2. Click the 3D view button/icon
3. Napari crashes

Environment

MacOS 10.14.3
Python 3.7.2
Napari 0.2.11

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

napari: 0.2.11
Platform: Darwin-18.2.0-x86_64-i386-64bit
Python: 3.7.2 (v3.7.2:9a3ffc0492, Dec 24 2018, 02:44:43) [Clang 6.0 (clang-600.0.57)]
Qt: 5.13.0
PyQt5: 5.13.0
VisPy: 0.6.4
NumPy: 1.16.4
SciPy: 1.2.1
scikit-image: 0.15.0
Dask: 2.7.0

GL version: 2.1 INTEL-12.4.7
MAX_TEXTURE_SIZE: 16384

[sofroniewn]

This looks like a relatively straight forward bug with our thumbnail generation

Traceback (most recent call last):
  File "/Users/nsofroniew/GitHub/napari/napari/_qt/qt_viewer_buttons.py", line 154, in change_ndisplay
    self.viewer.dims.ndisplay = 3
  File "/Users/nsofroniew/GitHub/napari/napari/components/dims.py", line 296, in ndisplay
    self.events.ndisplay()
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/Users/nsofroniew/GitHub/napari/napari/components/viewer_model.py", line 400, in _update_layers
    layer.dims.ndisplay = self.dims.ndisplay
  File "/Users/nsofroniew/GitHub/napari/napari/components/dims.py", line 296, in ndisplay
    self.events.ndisplay()
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 508, in __call__
    self._invoke_callback(cb, event)
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 529, in _invoke_callback
    cb_event=(cb, event),
  File "/Users/nsofroniew/GitHub/napari/napari/utils/event.py", line 523, in _invoke_callback
    cb(event)
  File "/Users/nsofroniew/GitHub/napari/napari/layers/base/base.py", line 383, in _update_dims
    self.refresh()
  File "/Users/nsofroniew/GitHub/napari/napari/layers/base/base.py", line 602, in refresh
    self._update_thumbnail()
  File "/Users/nsofroniew/GitHub/napari/napari/layers/points/points.py", line 1322, in _update_thumbnail
    colormapped[coords[:, 0], coords[:, 1]] = colors
ValueError: shape mismatch: value array of shape (1025,4) could not be broadcast to indexing result of shape (1024,4)

determined by our usage of a max number of points to use for thumbnail generation - https://github.com/napari/napari/blob/master/napari/layers/points/points.py#L205

@kevinyamauchi can you take on fixing this?

[cudmore]

Thanks for the follow-up and link to the code. Next time I run into a bug like this I will try and take the time to fix it before posting.

[kevinyamauchi]

Thanks for the follow-up and link to the code. Next time I run into a bug like this I will try and take the time to fix it before posting.

No worries! I really appreciate you flagging the bug. I am happy to make a fix today!

[sofroniewn]

Next time I run into a bug like this I will try and take the time to fix it before posting.

@cudmore you're also more than welcome to post bugs right away, ask for pointers, and then try and fix them yourself - no need to struggle alone first!!

[kevinyamauchi]

@cudmore , I just merged a fix into master (#934). Please feel free to let me know if you continue to have issues. Thank you again for bringing this to our attention!