reducing coordinate opacity makes black dots on the image layer

[McHaillet]

Here, a short video of the issue (recorded directly after I opened Blik):

Screencast.from.02-08-23.16.49.56.webm

[brisvag]

Confirm I can't reproduce on my machine. Can you paste the output of napari --info?

[McHaillet]

Voila:

napari: 0.4.18
Platform: Linux-5.14.0-1050-oem-x86_64-with-glibc2.35
System: Ubuntu 22.04.2 LTS
Python: 3.10.12 (main, Jul  5 2023, 18:54:27) [GCC 11.2.0]
Qt: 5.15.2
PyQt5: 5.15.9
NumPy: 1.25.1
SciPy: 1.11.1
Dask: 2023.7.1
VisPy: 0.12.2
magicgui: 0.7.2
superqt: unknown
in-n-out: 0.1.8
app-model: 0.2.0
npe2: 0.7.2

OpenGL:
  - GL version:  4.6.0 NVIDIA 535.86.10
  - MAX_TEXTURE_SIZE: 32768

Screens:
  - screen 1: resolution 1920x1080, scale 1.0
  - screen 2: resolution 1920x1080, scale 1.0

Settings path:
  - /home/marten/.config/napari/blik_env_4f55b458f76e0e18212ea2a8e7f36b42c679bdf4/settings.yaml
Plugins:
  - blik: 0.4.1.dev18+ga13c049 (22 contributions)
  - napari: 0.4.18 (77 contributions)
  - napari-console: 0.0.8 (0 contributions)
  - napari-label-interpolator: 0.1.0 (2 contributions)
  - napari-properties-plotter: 0.2.2 (2 contributions)
  - napari-properties-viewer: 0.0.2 (2 contributions)
  - napari-svg: 0.1.10 (2 contributions)

[brisvag]

This sounds like a napari issue... If you run this in ipython, do you see the same issue instead of a half-transparent point?

import napari
import numpy as np
v = napari.Viewer()
v.add_image(np.random.rand(100, 100))
v.add_points(np.array([50, 50]), opacity=0.4)

I see this, for reference:

[McHaillet]

Seems like here it does work. Would it help to run napari with --debug mode or something? Maybe I could get some additional info there

[brisvag]

For now we just need to find a minimal reproducer; I think it's an openGL issue, so it's unlikely to come out of napari code specifically, I'll probably have to dig into vispy.

Try this:

import napari
import numpy as np
v = napari.Viewer()
v.add_image(np.random.rand(100, 100))
v.add_points(np.array([50, 50]), opacity=0.4, shading='spherical')

and if it's still fine, change the point colors to 'teal'?

[McHaillet]

This also works fine, as well as changing colors to teal.

[brisvag]

Nasty bug :P some other things to try:

• change layer order (image above points) and see if it's affected
• change image blending mode to translucent from translucent no depth

[McHaillet]

will try it tomorrow morning!

[McHaillet]

I tried those things but don't get the issue. Also tried making it 3D and using the out_of_slice_display (as below), but also does not reproduce it.

v.add_image(np.random.rand(10, 100, 100))
v.add_points(np.array([5, 50, 50]), opacity=0.4, shading='spherical', out_of_slice_display=True)

[brisvag]

Ok, I actually got it to reproduce. In my case, it's indeed because of the layer order. Basically, if you have the image above the points and make the points transparent, the thing you see behind the points is the canvas (black). This is actually kind of unsolvable because of how opengl blending works (unless we break other things). Here's a comment mentioning this exact issue (and approrpiately, it was me who said "let's cross that bridge when we get to it" xD).

So for you the solution should be: move the points layer above the images. Does that work?

[McHaillet]

It's a been while, sorry for that.

That indeed solves the problem haha
Maybe you could switch the default order of the layers in Blik to prevent the issue?

[brisvag]

I already have a little trick like that in fact (sorting layers before adding them), the problem is, it doesn'y work xD napari gives the files to readers one by one instead of as a list... Not sure there's a solution to that other than writing my own entry point script.