Visualization problem using visbrain

[aya-almasri]

Hi, I have a problem with the vizualisation using Visbrain. I am just installing the ‘Slam’ environment, on my Windows 10 system, as indicated in the GitHub https://brain-slam.github.io/slam/, by relying on an anaconda virtual environment. conda create -q -n slam python=3.6 conda activate slam

pip install brain-slam

I started by trying to run the examples provided https://brain-slam.github.io/slam/auto_examples/index.html

For example, the one entitled ‘Example of curvature estimation in slam’, and I obtained the following error: “No module named Visbrain”. So I installed Visbrain as indicated the following website : https://github.com/EtienneCmb/visbrain First, I installed the Visbrain requires, before installed Visbrain. • NumPy >= 1.13 • SciPy • VisPy >= 0.5.3 • Matplotlib >= 1.5.5 • PyQt5 • Pillow • PyOpenGL I tried again to run the example ‘Example of curvature estimation in slam’, and I obtain the following error: runfile('C:/Users/Ayama/stage/slam-master/examples/example_curvature.py', wdir='C:/Users/Ayama/stage/slam-master/examples') Calculating vertex normals .... Please wait Finished calculating vertex normals Calculating curvature tensors ... Please wait Finished Calculating curvature tensors Calculating Principal Components ... Please wait Finished Calculating principal components C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\line\line.py:395: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. ('color', np.float32, 4)]) C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\line\arrow.py:57: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. ('linewidth', np.float32, 1) C:\Users\Ayama\anaconda3\envs\slam\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='gui') created C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\gloo\buffer.py:454: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. data = data.view(dtype=[('f0', data.dtype.base, c)]) Creation of a scene BrainObj(name='gui') added to the scene WARNING | Data defined on a dense grid; ignore smoothing. Add data to specific vertices. Data scaled between (-0.419, 0.595) Get colorbar properties from BrainObj(name='gui') object ColorbarObj(name='guiCbar') created ColorbarObj(name='guiCbar') added to the scene WARNING | dpi parameter is not active if print_size is None. Use for example print_size=(5, 5) Traceback (most recent call last):

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 1349, in do_open encode_chunked=req.has_header('Transfer-encoding'))

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 1287, in request self._send_request(method, url, body, headers, encode_chunked)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 1333, in _send_request self.endheaders(body, encode_chunked=encode_chunked)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 1282, in endheaders self._send_output(message_body, encode_chunked=encode_chunked)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 1042, in _send_output self.send(msg)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 980, in send self.connect()

File "C:\Users\Ayama\anaconda3\envs\slam\lib\http\client.py", line 952, in connect (self.host,self.port), self.timeout, self.source_address)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\socket.py", line 704, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM):

File "C:\Users\Ayama\anaconda3\envs\slam\lib\socket.py", line 745, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags):

gaierror: [Errno 11001] getaddrinfo failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fetching.py", line 239, in _fetch_file data = urllib.request.urlopen(url, timeout=15.)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 223, in urlopen return opener.open(url, data, timeout)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 526, in open response = self._open(req, data)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 544, in _open '_open', req)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 504, in _call_chain result = func(*args)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 1377, in http_open return self.do_open(http.client.HTTPConnection, req)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\urllib\request.py", line 1351, in do_open raise URLError(err)

URLError: <urlopen error [Errno 11001] getaddrinfo failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "C:\Users\Ayama\AppData\Roaming\Python\Python36\site-packages\visbrain\io\write_image.py", line 393, in write_fig_canvas img = canvas.render(region=region)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\scene\canvas.py", line 244, in render self._draw_scene(bgcolor=bgcolor)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\scene\canvas.py", line 253, in _draw_scene self.draw_visual(self.scene)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\scene\canvas.py", line 291, in draw_visual node.draw()

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\scene\visuals.py", line 98, in draw self._visual_superclass.draw(self)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\visual.py", line 588, in draw v.draw()

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\scene\visuals.py", line 98, in draw self._visual_superclass.draw(self)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\visual.py", line 432, in draw if self._prepare_draw(view=self) is False:

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\text\text.py", line 446, in _prepare_draw self._font._lowres_size) for t in text])

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\text\text.py", line 446, in self._font._lowres_size) for t in text])

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\text\text.py", line 157, in _text_to_vbo glyph = font[char]

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\text\text.py", line 69, in getitem self._load_char(char)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\text\text.py", line 83, in _load_char _load_glyph(self._font, char, self._glyphs)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fonts_freetype.py", line 50, in _load_glyph face = _load_font(f['face'], f['bold'], f['italic'])

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fonts_freetype.py", line 34, in _load_font fname = _get_vispy_font_filename(face, bold, italic)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fonts_vispy_fonts.py", line 20, in _get_vispy_font_filename return load_data_file('fonts/%s' % name)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fetching.py", line 68, in load_data_file _fetch_file(url, fname)

File "C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\util\fetching.py", line 243, in _fetch_file 'Dataset fetching aborted (%s)' % (url, e))

RuntimeError: Error while fetching file http://github.com/vispy/demo-data/raw/master/fonts/OpenSans-Bold.ttf. Dataset fetching aborted (<urlopen error [Errno 11001] getaddrinfo failed>)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "C:\Users\Ayama\stage\slam-master\examples\example_curvature.py", line 48, in visb_sc.preview()

File "C:\Users\Ayama\AppData\Roaming\Python\Python36\site-packages\visbrain\objects\scene_obj.py", line 684, in preview mpl_preview(self.canvas, widget=self.canvas.central_widget)

File "C:\Users\Ayama\AppData\Roaming\Python\Python36\site-packages\visbrain\io\write_image.py", line 454, in mpl_preview img = write_fig_canvas(None, canvas, **kw)[..., 0:-1]

File "C:\Users\Ayama\AppData\Roaming\Python\Python36\site-packages\visbrain\io\write_image.py", line 395, in write_fig_canvas raise ValueError("Can not render the canvas. Try to decrease the "

ValueError: Can not render the canvas. Try to decrease the resolution

[EtienneCmb]

Hi @a-almasri ,

There are many different errors in your outputs. I propose to first create a simple test.py with the following code inside :

from visbrain.objects import BrainObj

BrainObj('B1').preview()

And then run your script. Do you have errors?

[aya-almasri]

Hi @EtienneCmb ,

Thank you for your response. After running the script, I correctly obtained the result of the visualization :

The following is shown in the Python console:

C:\Users\Ayama\anaconda3\envs\slam\python.exe C:/Users/Ayama/PycharmProjects/my_work_slam/visbrain_functioning_test.py C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\line\line.py:395: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. ('color', np.float32, 4)]) C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\visuals\line\arrow.py:57: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. ('linewidth', np.float32, 1) C:\Users\Ayama\anaconda3\envs\slam\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='B1') created Downloading C:\Users\Ayama\visbrain_data\templates\B1.npz STATUS : 100.0% 2375680 / 2372325 C:\Users\Ayama\anaconda3\envs\slam\lib\site-packages\vispy\gloo\buffer.py:454: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. data = data.view(dtype=[('f0', data.dtype.base, c)])

Kindly,

[ZhengL97]

Hi, it seems that you should upgrade your version of matplotlib.