Mac OS

Obstacles Encountered During downloading_brains Tutorial (macOS)

(contact jduva4@jhu.edu or akodba1@jhu.edu for related questions)

  1. Issues with using a jupyter notebook

  2. If using virtualenv to create the environment rather than conda, make sure that you have Python 3 installed outside of Anaconda (call python --version) because many systems will not. Make sure that pip references Python 3 (the pip --version command should show 3.xx in the path), otherwise pip installs could be updating Python 2 exclusively.

  1. May run into a schema-related error when importing napari in Step 1: “This is specifically a suppressible warning because if you’re using a schema other than the ones in SUPPORTED_VERSIONS, it’s possible that not all functionality will be supported properly. If you don’t want to see these messages, add a warningfilter to your code.” (Source: https://github.com/cwacek/python-jsonschema-objects/issues/184)

  2. Not exclusive to macOS but make sure aws .json file has no dollar signs in the strings and is being edited/saved within the terminal using a program like Nano or Vim. Do not use external editors like Sublime.

  3. AWS Credendials Issues * See below

  4. Section (2) of downloading_brains notebook, Create a Neuroglancer instance and download the volume: make sure variables are correct and functions have correct inputs
    • For Example:

      • Wrong: img, bbox, vox = ngl_sess.pull_voxel(2, v_id, radius, radius, radius)

      • Right: img, bbox, vox = ngl_sess.pull_voxel(2, v_id, radius)

  5. Section (4) of downloading_brains notebook, View the volume: the iPyNb kernel may consistently die when running, not allowing napari to be viewed

    • In terminal, type pip install opencv-contrib-python-headless

    • Or try including %gui qt just above the import napari line.

  6. When installing brainlit on Mac OS BigSur, make sure you are using python==3.9.0 and not python==3.9.1. This is a known issue <https://github.com/napari/napari/issues/1393#issuecomment-745615931>. Please report any other Mac OS BigSur compatibility issues.

Linux

Sometimes there can be issues installing posix-ipc on Linux. In the past, we avoided this by installing version 1.0.5 pip install posix-ipc==1.0.5.

Windows

Importing Brotli and Curses

When installing from source pip install -e . on Windows 10 with Python 3.9.0, sometimes brainlit would appear to install but upon importing, there was an issue with import _brotli.

It was fixed according to this thread where the Visual C++ Redistributable was updated by downloading the x64 version from here.

Also, an import error would occur for _curses. This was fixed by pip install windows-curses like from this thread.

Napari Display Problem

This document reports an issue that is encountered when running the tutorial downloading_brains.ipynb.

The document includes two sections: 1. a brief description of Issue#127 2. a detailed code history

1. Brief Description of Issue#127:

If your drivers/operating system are out of the date: - Windows 7 - python3.7.9

You may get the following error message:

RuntimeError: Using glBindFramebuffer with no OpenGL context.

In the napari window, the images can be seen loaded but cannot be displayed at the screen as shown in the screenshot below: Napari screenshot

2. Detailed Code History

Input 1:

from brainlit.utils.session import NeuroglancerSession
from brainlit.utils.swc import graph_to_paths
import napari

dir = "s3://mouse-light-viz/precomputed_volumes/brain1"
dir_segments = "s3://mouse-light-viz/precomputed_volumes/brain1_segments"
mip = 0
v_id = 0
radius = 75

# get image and center point
ngl_sess = NeuroglancerSession(mip = mip, url = dir, url_segments=dir_segments)
img, bbox, vox = ngl_sess.pull_voxel(2, v_id, radius)
print(f"\n\nDownloaded volume is of shape {img.shape}, with total intensity {sum(sum(sum(img)))}.")

Output 1:

Downloading: 100%|██████████| 1/1 [00:00<00:00, 13.70it/s]
Downloading: 46it [00:38,  1.19it/s]

Downloaded volume is of shape (151, 151, 151), with total intensity 4946609.

Input 2:

G_sub = ngl_sess.get_segments(2, bbox)
paths = graph_to_paths(G_sub)
print(f"Selected volume contains {G_sub.number_of_nodes()} nodes and {len(paths)} paths")

Output 2:

Downloading: 100%|██████████| 1/1 [00:00<00:00,  3.47it/s]
Selected volume contains 6 nodes and 2 paths

Input 3:

with napari.gui_qt():
    viewer = napari.Viewer(ndisplay=3)
    viewer.add_image(img)
    viewer.add_shapes(data=paths, shape_type='path', edge_width=0.1, edge_color='blue', opacity=0.1)
    viewer.add_points(vox, size=1, opacity=0.5)

Output 3:

ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 743, in _parse
    self._gl_initialize()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 851, in _gl_initialize
    if this_version < '2.1':
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\distutils\version.py", line 52, in __lt__
    c = self._cmp(other)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\distutils\version.py", line 335, in _cmp
    if self.version == other.version:
AttributeError: 'LooseVersion' object has no attribute 'version'

ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 53, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native
AttributeError: 'function' object has no attribute '_native'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 72, in _get_gl_func
    func = getattr(_lib, name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'glBindFramebuffer' not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 745, in _parse
    gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, args[0])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 55, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native = _get_gl_func("glBindFramebuffer", None, (ctypes.c_uint, ctypes.c_uint,))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 87, in _get_gl_func
    raise RuntimeError('Using %s with no OpenGL context.' % name)
RuntimeError: Using glBindFramebuffer with no OpenGL context.

WARNING: Error drawing visual <Volume at 0x21be1648>
WARNING:vispy:Error drawing visual <Volume at 0x21be1648>
ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 53, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native
AttributeError: 'function' object has no attribute '_native'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 72, in _get_gl_func
    func = getattr(_lib, name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'glBindFramebuffer' not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw
    self._draw_scene()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 745, in _parse
    gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, args[0])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 55, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native = _get_gl_func("glBindFramebuffer", None, (ctypes.c_uint, ctypes.c_uint,))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 87, in _get_gl_func
    raise RuntimeError('Using %s with no OpenGL context.' % name)
RuntimeError: Using glBindFramebuffer with no OpenGL context.

WARNING: Error drawing visual <Volume at 0x21be1648>
WARNING:vispy:Error drawing visual <Volume at 0x21be1648>
ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 53, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native
AttributeError: 'function' object has no attribute '_native'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 72, in _get_gl_func
    func = getattr(_lib, name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'glBindFramebuffer' not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw
    self._draw_scene()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 745, in _parse
    gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, args[0])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 55, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native = _get_gl_func("glBindFramebuffer", None, (ctypes.c_uint, ctypes.c_uint,))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 87, in _get_gl_func
    raise RuntimeError('Using %s with no OpenGL context.' % name)
RuntimeError: Using glBindFramebuffer with no OpenGL context.

WARNING: Error drawing visual <Volume at 0x21be1648>
WARNING:vispy:Error drawing visual <Volume at 0x21be1648>
ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 53, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native
AttributeError: 'function' object has no attribute '_native'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 72, in _get_gl_func
    func = getattr(_lib, name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'glBindFramebuffer' not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw
    self._draw_scene()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 745, in _parse
    gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, args[0])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 55, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native = _get_gl_func("glBindFramebuffer", None, (ctypes.c_uint, ctypes.c_uint,))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 87, in _get_gl_func
    raise RuntimeError('Using %s with no OpenGL context.' % name)
RuntimeError: Using glBindFramebuffer with no OpenGL context.

WARNING: Error drawing visual <Volume at 0x21be1648>
WARNING:vispy:Error drawing visual <Volume at 0x21be1648>
ERROR:root:Unhandled exception:
Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 53, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native
AttributeError: 'function' object has no attribute '_native'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 72, in _get_gl_func
    func = getattr(_lib, name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\ctypes\__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'glBindFramebuffer' not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\app\backends\_qt.py", line 825, in paintGL
    self._vispy_canvas.events.draw(region=None)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 455, in __call__
    self._invoke_callback(cb, event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 475, in _invoke_callback
    self, cb_event=(cb, event))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    cb(event)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 217, in on_draw
    self._draw_scene()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 266, in _draw_scene
    self.draw_visual(self.scene)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\canvas.py", line 304, in draw_visual
    node.draw()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\scene\visuals.py", line 99, in draw
    self._visual_superclass.draw(self)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\visual.py", line 443, in draw
    self._vshare.index_buffer)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\visuals\shaders\program.py", line 101, in draw
    Program.draw(self, *args, **kwargs)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\program.py", line 533, in draw
    canvas.context.flush_commands()
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\context.py", line 175, in flush_commands
    self.shared.parser.parse([('CURRENT', 0, fbo)])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 819, in parse
    self._parse(command)
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\glir.py", line 745, in _parse
    gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, args[0])
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\_gl2.py", line 55, in glBindFramebuffer
    nativefunc = glBindFramebuffer._native = _get_gl_func("glBindFramebuffer", None, (ctypes.c_uint, ctypes.c_uint,))
File "C:\ProgramData\Miniconda3\envs\brainlit\lib\site-packages\vispy\gloo\gl\gl2.py", line 87, in _get_gl_func
    raise RuntimeError('Using %s with no OpenGL context.' % name)
RuntimeError: Using glBindFramebuffer with no OpenGL context.

WSL 2

WSL2 Installation Instructions

For Windows 10 users that prefer Linux functionality without the speed sacrifice of a Virtual Machine, Brainlit can be installed and run on WSL2. WSL2 is a fully functional Linux kernel that can run ELF64 binaries on a Windows Host. - OS Specifications: Version 1903, Build 18362 or higher - Installation Instructions - Any Linux distribution can be installed. Ubuntu16.04.3 was used for this tutorial.

Install python required libraries and build tools.

Run the below commands to configure the WSL2 environment. See here for more information.

$ sudo apt update && sudo apt install -y build-essential git libexpat1-dev libssl-dev zlib1g-dev
$ libncurses5-dev libbz2-dev liblzma-dev
$ libsqlite3-dev libffi-dev tcl-dev linux-headers-generic libgdbm-dev
$ libreadline-dev tk tk-dev

Install a python version management tool, and create/activate a virtual environment

Install brainlit

Create and save AWS Secrets file

  • See AWS Secrets file section below

Configure jupyter notebook

Install jupyter notebook: $ python -m pip install jupyter notebook and add the following line to your ~/.bashrc script:

export DISPLAY=`grep -oP "(?<=nameserver ).+" /etc/resolv.conf`:0.0

To launch jupyter notebook, you need to type $ jupyter notebook --allow-root, not just $ jupyter notebook Then copy and paste one of the URLs outputted into your web browser. If your browser is unable to connect, try unblocking the default jupyter port via this command: ``$ sudo ufw allow 8888 ``

Configure X11 Port Forwarding

  • Install VcXsrv Windows X Server on your Windows host machine

  • Let VcXsrv through your Public & Private windows firewall. (Control Panel -> System and Security -> Windows Defender Firewall -> Allowed Apps -> Change Settings)

  • Run XLaunch on your Windows Host Machine with default settings AND select the "Disable Access Control" option

  • To confim X11 Port Forwarding is configured, run xclock on the subsystem. This should launch on your windows machine.

Exceptions

AWS Credentials Issues

warning

SECURITY DISCLAIMER :warning:

Do NOT push any official AWS credentials to any repository. These posts are a good reference to get a sense of what pushing AWS credentials implies:

  1. I Published My AWS Secret Key to GitHub by Danny Guo here

  2. Exposing your AWS access keys on Github can be extremely costly. A personal experience. by Guru here

  3. Dev put AWS keys on Github. Then BAD THINGS happened by Darren Pauli here

Brainlit can access data volumes stored in AWS S3 through the CloudVolume package. As specified in the docs, AWS credentials have to be stored in a file called aws-secret.json inside the ~.cloudvolume/secrets/ folder.

Prerequisites to successfully troubleshoot errors related to AWS credentials:

  • The data volume is hosted on S3 (i.e. the link looks like s3://your-bucket-name/some-path/some-folder).

  • Familiarity with IAM Roles and how to create them.

  • An AWS_ACCESS_KEY_ID and an AWS_SECRET_ACCESS_KEY with adequate permissions, provided by an AWS account administrator. Brainlit does not require the IAM user associated with the credentials to have access to the AWS console (i.e. it can be a service account).

Here is a collection of known issues, along with their troubleshoot guide:

Missing AWS_ACCESS_KEY_ID

Error message:

python
~/opt/miniconda3/envs/brainlit/lib/python3.8/site-packages/cloudvolume/connectionpools.py in _create_connection(self)
    99       return boto3.client(
    100         's3',
--> 101         aws_access_key_id=self.credentials['AWS_ACCESS_KEY_ID'],
    102         aws_secret_access_key=self.credentials['AWS_SECRET_ACCESS_KEY'],
    103         region_name='us-east-1',

KeyError: 'AWS_ACCESS_KEY_ID'

This error is thrown when the credentials object has an empty AWS_ACCESS_KEY_ID` entry. This probably indicates that ``aws-secret.json is not stored in the right folder and it cannot be found by CloudVolume. Make sure your credential file is named correctly and stored in ~.cloudvolume/secrets/. If you are a Windows user, the output of this Python snippet is the expansion of ~ for your system:

python
import os
HOME = os.path.expanduser('~')
print(HOME)

example output:

bash
Python 3.8.3 (v3.8.3:6f8c8320e9)
>>> import os
>>> HOME = os.path.expanduser('~')
>>> print(HOME)
C:\Users\user

Empty AKID (Access Key ID)

Error message:

python
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/botocore/client.py in _make_api_call(self, operation_name, api_params)
    654             error_code = parsed_response.get("Error", {}).get("Code")
    655             error_class = self.exceptions.from_code(error_code)
--> 656             raise error_class(parsed_response, operation_name)
    657         else:
    658             return parsed_response
ClientError: An error occurred (AuthorizationHeaderMalformed) when calling the GetObject operation: The authorization header is malformed; a non-empty Access Key (AKID) must be provided in the credential.

This error is thrown when your aws-secret.json file is stored and loaded correctly, and it looks like this:

json
{
"AWS_ACCESS_KEY_ID": "",
"AWS_SECRET_ACCESS_KEY": ""
}

Even though the bucket itself may be public, boto3 requires some non-empty AWS credentials to instantiante the S3 API client.

Access denied

python
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/botocore/client.py in _make_api_call(self, operation_name, api_params)
    654             error_code = parsed_response.get("Error", {}).get("Code")
    655             error_class = self.exceptions.from_code(error_code)
--> 656             raise error_class(parsed_response, operation_name)
    657         else:
    658             return parsed_response
ClientError: An error occurred (AccessDenied) when calling the GetObject operation: Access Denied

This error is thrown when:

  1. The AWS credentials are stored and loaded correctly but are not allowed to access the data volume. A check with an AWS account administrator is required.

  2. There is a typo in your credentials. The content of aws-secret.json should look like this:

json
{
"AWS_ACCESS_KEY_ID": "$YOUR_AWS_ACCESS_KEY_ID",
"AWS_SECRET_ACCESS_KEY": "$AWS_SECRET_ACCESS_KEY"
}

where the $ are placeholder characters and should be replaced along with the rest of the string with the official AWS credentials.