Text of sources not shown

[zhengliuer]

I ran the code in http://visbrain.org/auto_examples/gui_brain/03_sources.html#sphx-glr-auto-examples-gui-brain-03-sources-py, and no text shown.

When I used SourceObj and set the parameter text, also no text.

[EtienneCmb]

I encountered the same issue in the past and it was coming from the TextVisual object of vispy. Can you try this example and see if it works?

[zhengliuer]

It works

[EtienneCmb]

Can you try the following code :

import numpy as np
from visbrain.objects import SourceObj

xyz = np.random.rand(100, 3)
text = [f"s{k}" for k in range(100)]
s_obj = SourceObj('test', xyz, text=text, text_size=20, text_translate=(0., .2, 0.))
s_obj.preview()

[zhengliuer]

Interesting, this works.

[EtienneCmb]

Ok, so I guess it comes from the font size. By default, the font size in the example is really small (kwargs['text_size'] = 1.5 ) you can try to set it to 20?

[zhengliuer]

Sadly, still the same, no text.

[EtienneCmb]

Ok, final test, can you try to increase it drastically to kwargs['text_size'] = 1000?

[zhengliuer]

If I use s_obj.preview(), it shows the text,

But vb.show() shows me nothing.

And if I don't use s_object.preview(), still no text

[zhengliuer]

And font size do is one of the problems, for if I set it to 100, s_object.preview() still no text. Does it have sth to do with the operating system? Mine is win10

[zhengliuer]

OK, font size is the key problem. It seems that the Brain needs much bigger size. I set it to 10000, it shows a little text.
And when using my own data, I need to set it to 100000.

[zhengliuer]

By the way, how do we calculate the connectivity of electrodes? I used mne, are there any other packages?

[EtienneCmb]

I don't think it comes from your system, because I've the same issue. I guess vispy changed the way the TextVisual is handle, in particular the proportion with the displayed scene. In general, I would say that the GUI of visbrain are not as stable as the object level. If you want to "reproduce" the figure, you can try the following code :

import numpy as np

from visbrain.gui import Brain
from visbrain.objects import SourceObj, BrainObj, SceneObj
from visbrain.io import download_file

kwargs = {}

mat = np.load(download_file('xyz_sample.npz', astype='example_data'))
xyz, subjects = mat['xyz'], mat['subjects']

"""The "subjects" list is composed of 6 diffrents subjects and here we set one
unique color (u_color) per subject.
"""
u_color = ["#9b59b6", "#3498db", "white", "#e74c3c", "#34495e", "#2ecc71"]
kwargs['color'] = [u_color[int(k[1])] for k in subjects]
kwargs['alpha'] = 0.7

"""
Now we attach data to each source.
"""
kwargs['data'] = np.arange(len(subjects))

"""The source's radius is proportional to the data attached. But this
proportion can be controlled using a minimum and maximum radius
(s_radiusmin, s_radiusmax)
"""
kwargs['radius_min'] = 2               # Minimum radius
kwargs['radius_max'] = 15              # Maximum radius
kwargs['edge_color'] = (1, 1, 1, 0.5)  # Color of the edges
kwargs['edge_width'] = .5              # Width of the edges
kwargs['symbol'] = 'square'            # Source's symbol

"""
Next, we mask source's data that are comprised between [-20, 20] and color
each source to orange
"""
mask = np.logical_and(xyz[:, 0] >= -20., xyz[:, 0] <= 20)
kwargs['mask'] = mask
kwargs['mask_color'] = 'orange'

"""It's also possible to add text to each source. Here, we show the name of the
subject in yellow.
To avoid a superposition between the text and sources sphere, we introduce an
offset to the text using the s_textshift input
"""
kwargs['text'] = subjects              # Name of the subject
kwargs['text_color'] = "#f39c12"       # Set to yellow the text color
kwargs['text_size'] = 200000              # Size of the text
kwargs['text_translate'] = (1.5, 1.5, 0)
kwargs['text_bold'] = True

"""Create the source object. If you want to previsualize the result without
opening Brain, use s_obj.preview()
"""
s_obj = SourceObj('SourceExample', xyz, **kwargs)

"""Color sources according to the data
"""
# s_obj.color_sources(data=kwargs['data'], cmap='viridis')

"""Colorbar properties
"""
cb_kw = dict(cblabel="Project source activity", cbtxtsz=3., border=False, )

"""Define a brain object with the B3 template and project source's activity
onto the surface
"""
b_obj = BrainObj('B3', **cb_kw)
b_obj.project_sources(s_obj, cmap='viridis', vmin=50., under='orange',
                      vmax=550., over='darkred')

sc = SceneObj()
sc.add_to_subplot(s_obj)
sc.add_to_subplot(b_obj, use_this_cam=True)
sc.preview()

[EtienneCmb]

About the connectivity, yes, MNE provides several ways to do it. I can also recommend IDTxl and a package that I'm currently developing, Frites

[zhengliuer]

Thanks a lot

[zhengliuer]

Hi, I noticed that the repo of Brainets, and I found seegpy. I am doing some analysis based on sEEG, so I am interested in this package. I found that the data format in this package is TRC? What kind of data format is this? And if I've got .edf data, how do I used this package. Some modules, like contacts, may be useful regardless of the format.

[EtienneCmb]

If you want to talk about seegpy, or in general sEEG data analysis, I propose to move to emails

[zhengliuer]

If you want to talk about seegpy, or in general sEEG data analysis, I propose to move to emails

Excellent! And I just found your e-mail.

[zhengliuer]

Hi, is there a way that I can set the default size of brains?

[EtienneCmb]

The brain included in visbrain are usually in the MNI system. That being said, if you have your own template, you can provide the vertices and faces to the BrainObj

[zhengliuer]

Sorry, I should be more clear.

In this pic, the brain is a little small, I am thinking to make it bigger using code if there is a method supporting this. I don't find some method related to this.

[zhengliuer]

And did you get my e-mail which is a Gmail address? I am afraid I didn't send it successfully for I did encounter this situation.

[EtienneCmb]

Ah ok, try with BrainObj('B1'), or B2, it should be better.

Yes I received your email and I answered four hours ago, you didn't get my reply?

[zhengliuer]

Oh, I get it! My phone didn't remind me of that. I shouldn't have believed it, reminding me of Junk emails always, not important ones.