==> Installing dependencies for pyside: llvm, gdbm, openssl, readline, sqlite, xz, python, python@2, qt
==> Installing pyside dependency: llvm
==> Downloading https://homebrew.bintray.com/bottles/llvm-6.0.1.el_capitan.bottle.tar.gz
==> Installing pyside dependency: llvm
==> Downloading https://homebrew.bintray.com/bottles/llvm-6.0.1.el_capitan.bottle.tar.gz
ImportError: dlopen(/Users/RMASISO/anaconda/lib/python3.5/site-packages/PyQt5/QtCore.so, 2): Symbol not found: _PySlice_AdjustIndices
Referenced from: /Users/RMASISO/anaconda/lib/python3.5/site-packages/PyQt5/QtCore.so
Expected in: flat namespace
in /Users/RMASISO/anaconda/lib/python3.5/site-packages/PyQt5/QtCore.so
Referenced from: /Users/RMASISO/anaconda/lib/python3.5/site-packages/PyQt5/QtCore.so
Expected in: flat namespace
in /Users/RMASISO/anaconda/lib/python3.5/site-packages/PyQt5/QtCore.so
May be Homebrew/homebrew-core#24972?
so i already did the 3.6 environment :/
Hi @tanermetin ! I don't have any experience with emotiv or muse. However, it seems that they give the possibility to export the data in european data format (.edf) or EEGLab format, which are both accepted by Visbrain. If you are interest in BCI, I would suggest you take a look at https://openbci.com/ . Thanks, Raphael
thank you @raphaelvallat , yes saw them and actually impressed the story of openBCI. products are a bit pricey compared to others but beauty is in opensource. also there is an active community(compared to emotiv's support). I hope to have more questions when i got my hands dirty with visbrain. bonjour,
Hello visbrain community, I'm trying to use the example scripts of visbrain to better understand how it works but I keep running into the same issue in the examples. It seems to occur when it tries to download a file. Here's what my terminal output looks like:
/anaconda3/envs/visbrainEnv/lib/python3.6/site-packages/vispy/visuals/isocurve.py:22: UserWarning: VisPy is not yet compatible with matplotlib 2.2+
warnings.warn("VisPy is not yet compatible with matplotlib 2.2+")
Data successfully loaded (/Users/sportsnoah14/visbrain_data/example_data/sleep_edf/excerpt2.edf):
- Sampling-frequency : 200.00Hz
- Number of time points (before down-sampling): 360000
- Down-sampling frequency : 100.00Hz
- Number of time points (after down-sampling): 180000
- Number of channels : 23
Hypnogram successfully loaded (/Users/sportsnoah14/visbrain_data/example_data/sleep_edf/Hypnogram_excerpt2.txt)
/Applications/visbrain/visbrain/io/read_sleep.py:208: UserWarning: Wrong channel data amplitude.
warn("Wrong channel data amplitude. ")
Traceback (most recent call last):
File "/Users/sportsnoah14/Documents/Research_knowledge/Coding_Learn/Python/visbrain/python_scripts/gui_sleep/load_edf_local.py", line 29, in <module>
Sleep(data=dfile, hypno=hfile, config_file=cfile).show()
File "/Applications/visbrain/visbrain/gui/sleep/sleep.py", line 157, in __init__
Visuals.__init__(self)
File "/Applications/visbrain/visbrain/gui/sleep/visuals/visuals.py", line 1103, in __init__
parent=self._topoCanvas.wc.scene)
File "/Applications/visbrain/visbrain/gui/sleep/visuals/visuals.py", line 752, in __init__
TopoMesh.__init__(self, **kwargs)
File "/Applications/visbrain/visbrain/visuals/topo_visual.py", line 196, in __init__
auto = self._get_channel_coordinates(xyz, channels, system, unit)
File "/Applications/visbrain/visbrain/visuals/topo_visual.py", line 382, in _get_channel_coordinates
xyz, keeponly = self._get_coordinates_from_name(channels)
File "/Applications/visbrain/visbrain/visuals/topo_visual.py", line 437, in _get_coordinates_from_name
path = download_file('eegref.npz', astype='topo')
File "/Applications/visbrain/visbrain/io/download.py", line 99, in download_file
filename, url = name, get_data_url(name, astype)
File "/Applications/visbrain/visbrain/io/download.py", line 35, in get_data_url
urls = load_config_json(get_data_url_path())[astype]
File "/Applications/visbrain/visbrain/io/rw_config.py", line 47, in load_config_json
with open(filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Applicat/data_url.json'
Any help would be greatly appreciated. Thank you
Hello @sportnoah14 ,
I've never seen this error.
1) Is it this example that you're trying to run?
2) I suspect a path error to the config file. Can you try to run Sleep but without the config input? Sleep(data=dfile, hypno=hfile).show()
Hi, I get the following error trying to start the
00_brain_control.py:runfile('C:/Users/reppling/Documents/GitHub/visbrain/examples/gui_brain/00_brain_control.py', wdir='C:/Users/reppling/Documents/GitHub/visbrain/examples/gui_brain')
C:\Continuum\anaconda3\lib\site-packages\vispy\visuals\isocurve.py:22: UserWarning: VisPy is not yet compatible with matplotlib 2.2+
warnings.warn("VisPy is not yet compatible with matplotlib 2.2+")
BrainObj(name='B3') created
VolumeObj(name='brodmann') created
Traceback (most recent call last):
File "<ipython-input-1-eb725fac0ef4>", line 1, in <module>
runfile('C:/Users/reppling/Documents/GitHub/visbrain/examples/gui_brain/00_brain_control.py', wdir='C:/Users/reppling/Documents/GitHub/visbrain/examples/gui_brain')
File "C:\Continuum\anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 827, in runfile
execfile(filename, namespace)
File "C:\Continuum\anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/reppling/Documents/GitHub/visbrain/examples/gui_brain/00_brain_control.py", line 59, in <module>
vb = Brain(brain_obj=b_obj, bgcolor='slateblue')
File "c:\users\reppling\documents\github\visbrain\visbrain\gui\brain\brain.py", line 106, in __init__
Visuals.__init__(self, self.view.wc, **kwargs)
File "c:\users\reppling\documents\github\visbrain\visbrain\gui\brain\visuals.py", line 75, in __init__
self.volume = VolumeObj('brodmann')
File "c:\users\reppling\documents\github\visbrain\visbrain\objects\volume_obj.py", line 262, in __init__
self(name, vol, hdr, threshold, cmap, method, select)
File "c:\users\reppling\documents\github\visbrain\visbrain\objects\volume_obj.py", line 267, in __call__
_Volume.__call__(self, name, vol=vol, hdr=hdr)
File "c:\users\reppling\documents\github\visbrain\visbrain\objects\volume_obj.py", line 104, in __call__
labels, index = arch['labels'], arch['index']
File "C:\Continuum\anaconda3\lib\site-packages\numpy\lib\npyio.py", line 262, in __getitem__
pickle_kwargs=self.pickle_kwargs)
File "C:\Continuum\anaconda3\lib\site-packages\numpy\lib\format.py", line 692, in read_array
raise ValueError("Object arrays cannot be loaded when "
ValueError: Object arrays cannot be loaded when allow_pickle=False
WARNING: QSocketNotifier: Multiple socket notifiers for same socket 1936 and type Read
WARNING: QSocketNotifier: Multiple socket notifiers for same socket 1936 and type Read
Hi every one, why the sc.preview gets no output when every line of http://visbrain.org/auto_examples/objects/plot_roi_object.html#sphx-glr-auto-examples-objects-plot-roi-object-py runs without error?
also when I change the mpl argument of preview(). I get an error: got an unexpected keyword argument 'mpl'. But 'mpl' is a changeable argument as shown in the documents.
I am trying to create an animation showing connectivity changes over time in the brain. So far I haven't found a way to iteratively update the values of connectivity objects and have it be displayed. How can I achieve this?
Hi @granul_jabes_twitter , actually, I just realized that there's no easy way to do it. But here's an example of how to create a gif with a changing connectivity object :
import numpy as np
import imageio
from visbrain.objects import SceneObj, BrainObj, ConnectObj
n_sources = 10
n_pic = 10
xyz = np.random.uniform(-50, 50, (n_sources, 3))
writer = imageio.get_writer('animate_conn.gif')
for k in range(n_pic):
# random connectivity strentgh
conn = np.random.rand(n_sources, n_sources)
# create the scene
sc = SceneObj()
b_obj = BrainObj('white')
c_obj = ConnectObj('anim_conn', xyz, conn)
sc.add_to_subplot(b_obj)
sc.add_to_subplot(c_obj)
# render the scene
im = sc.render()
writer.append_data(im)
writer.close()
Hi there! I'm trying to open the Brain module of visbrain using 'from visbrain.gui import Brain' followed by 'Brain().show()'. However, I keep getting the following error: ImportError: cannot import name 'imresize' from 'scipy.misc'. How might I be able to troubleshoot this?
Hi,
I’m using Visbrain for visualization of cortical surface plots, and generating images using the screenshot function in BrainObj (no GUI is needed). Everything is working fine when I run it on my local computer. However, I want to be able to run my scripts on a remote server, but when I try this, I get an error when trying to import BrainObj. I think this is related to PyQt and I get the error message:
"qt.qpa.xcb: could not connect to display :23.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb."
I there a way to run Visbrain in a headless mode?
Hi @lassemadsen ,
For headless mode, you can get inspiration from the travis file used to run visbrain on a server especially this line
I'm not sure if this is the right place to ask, but are there any plans to add support for either .ndf or .h5 file formats to the Sleep module?
The data is stored in the ndf format with just time and voltage information and then converted to h5 for loading in python with custom modules
@SteffanAJones about HDF5 support, it depends on what you mean. If it's adding to Sleep the ability to stream HDF5 segments without loading everything into the memory the answer is no, mainly because everything has been coded to have all of the data in the RAM. If your question is to load HDF5 files within Sleep the problem is that this kind of formats are hierarchical which means that the software doesn't know the entry name (like .mat or .npz). But Sleep is also compatible without NumPy arrays, which means that you can load your data using h5py and then send the array to Sleep.
(but I agree that HDF5 should be widely adopted :D )