System error with Qtcore

[JulienLefevreMars]

Hello !

I am working on vector fields defined on meshes - I develop my own class for that - and I want to display it with visbrain :-)

I have tried the following code adapting one of the example you provided

`def visbrain_plot_vector_field(vector_field):

# Mesh
mesh = vector_field.mesh
b_obj = BrainObj('Mesh', vertices=np.array(mesh.vertices),
                     faces=np.array(mesh.faces),
                     translucent=False)
# Vector field
dtype = [('vertices', float, 3), ('normals', float, 3)]  # Arrows dtype
arrows = np.zeros(mesh.vertices.shape[0], dtype=dtype)  # Empty arrows array
arrows['vertices'] = mesh.vertices  # Set the vertices
arrows['normals'] = 0.1*vector_field.coordinates_3d  # Set the normals
v_obj = VectorObj('VectorField', arrows)
visb_sc = Brain(brain_obj=b_obj, vector_obj=v_obj)
visb_sc.show()
return visb_sc`

but I have the following error

File "/home/julienlefevre/Documents/Softs/anaconda3/lib/python3.7/site-packages/visbrain/gui/brain/interface/gui/brain_gui.py", line 1881, in setupUi QtCore.QMetaObject.connectSlotsByName(MainWindow) SystemError: <built-in function connectSlotsByName> returned a result with an error set

visbrain is working with my configuration (through the slam module) and I have also tried another way to add vector fields by using ScenObj + add_suplot applied to BrainObj and VectorObj which displays something but not expected. Last, but not least, when using visbrain through slam I obtain figures that I cannot rotate. I don't know if all those things are related...

The version of visbrain is 0.4.5 (I have done an update with pip but it did not change the version, whereas it is said 0.4.6 on the website) Thanks in advance for the help !

Julien

PS: sorry for the code insertion, I did not manage to do it properly

[EtienneCmb]

Hi Julien,

The Brain class is a GUI that merges visbrain objects and also contains buttons for interaction. I would first strongly suggest to use the SceneObj as it is way more flexible and stable. In addition, the scenes can be returned by other functions, I'm not so sure for the GUI.

BrainObj and VectorObj which displays something but not expected

• Are you able to display the scene with the mesh and the vectors?
• Do you have interactions? (rotation / translation)
• When you say that it's not expected, you mean the orientation of the vectors?

[JulienLefevreMars]

Hi Etienne and thank you for the super fast answer !

• So I am able now to display a scene with mesh and vectors, following the approach with SceneObj. I had just a problem with the color of the arrows (black as the background :-) ).
• I have no interactions

I added my new visualization funcion if it can help.

`def visbrain_plot_vector_field(vector_field): visb_sc = SceneObj(bgcolor='black', size=(1000, 1000))

# Mesh
mesh = vector_field.mesh
b_obj = BrainObj('Mesh', vertices=np.array(mesh.vertices),
                     faces=np.array(mesh.faces),
                     translucent=False)
visb_sc.add_to_subplot(b_obj,row=0,col=0)

# Vector field

dtype = [('vertices', float, 3), ('normals', float, 3)]  # Arrows dtype
arrows = np.zeros(mesh.vertices.shape[0], dtype=dtype)  # Empty arrows array
arrows['vertices'] = mesh.vertices  # Set the vertices
arrows['normals'] = 0.01*vector_field.coordinates_3d  # Set the normals

v_obj = VectorObj('VectorField', arrows,color='white')
visb_sc.add_to_subplot(v_obj)
return visb_sc

`

[EtienneCmb]

So I am able now to display a scene with mesh and vectors, following the approach with SceneObj. I had just a problem with the color of the arrows (black as the background :-) ).

I suggest two small tests :

1. Can you try to set a white background to the SceneObj with SceneObj(bgcolor='white') and check that indeed you've black arrows
2. You can try to give random data to have colormaped arrows :

   data = np.random.rand(mesh.vertices.shape[0])
   v_obj = VectorObj('VectorField', arrows, color='white', data=data)

3. Did you try to run this example?

I have no interactions

This is more problematic to me. First thing first, Visbrain is (unfortunately) not compatible with ipython or Jupyter, therefore you've to launch python scripts... The most basic example that cames to my mind to check this interaction issue is :

from visbrain.objects import BrainObj

BrainObj('B1').preview()

Does it works?

[EtienneCmb]

You could also try to run your python script, from a terminal, outside of your IDE (spyder, pycharm etc.).

[EtienneCmb]

And probably outside of Frioul :\

[JulienLefevreMars]

Thanks again !

1. Can you try to set a white background to the [SceneObj](http://visbrain.org/generated/visbrain.objects.SceneObj.html#visbrain.objects.SceneObj) with `SceneObj(bgcolor='white')` and check that indeed you've black arrows

It works perfectly well. So one the previous issue, linked to same color for background and arrows is fixed

I have no interactions

This is more problematic to me. First thing first, Visbrain is (unfortunately) not compatible with ipython or Jupyter, therefore you've to launch python scripts... The most basic example that cames to my mind to check this interaction issue is :

from visbrain.objects import BrainObj

BrainObj('B1').preview()

Does it works?

It works fine in a python shell, I can interact with the figure but with pycharm, on my laptop (not frioul), the figure is static and there are no interactions. So probaly it is linked to pycharm configuration.

Well, in any case, I thank you a lot for all those precious hints. I am now able to visualize nice vector fields !

[EtienneCmb]

Cool Julien ! If I remember correctly, Guillaume is using Pycharm, maybe you could ask whether there's a config to change to have interactive figures...

See u ;)

[JulienLefevreMars]

Good point. I will ask him. See u (in another issue to follow :-) )