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Computer Graphics Project 2013

License: GNU General Public License v3.0

C 1.25% Python 39.12% TeX 4.96% MATLAB 54.66%

brainactivity3d's People

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the-neuro kingjuli nagyistoce hugo-w annitrolla

brainactivity3d's Issues

Glowish source location spheres

Glow
Motion blur effect

Display location of the source in the model

Try ICA (Independent component analysis) to localize the source in 3d

Have source location positions change smoothly rather than by jumping

I.e. let us say the old sources are at positions {p_1, p_2, p_3}.
The new sources are located at {q_1, q_2, q_3}.

Match up p_i with q_i-s.
Set the relevant destination for each source.
At each animation frame move each source closer towards its current destination until it reaches it.

Estimate number of sources based on data

PCA?

Realistic lighting

equal from all directions
valleys are darker
details are visilble

Bad file descriptor errors on Mac OS X

The pre-compiled binary for Mac OS X doesn't work correctly.
Invoking brainactivity displays the following messages:

Looking for device
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [1]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [2]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [3]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [4]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [5]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [6]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [7]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [8]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [9]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [10]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [11]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [12]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [13]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [14]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Restarting gevent.core.dispatch() after an error [15]: [Errno 9] Bad file descriptor
[warn] kevent: Bad file descriptor
Process Process-2:
Traceback (most recent call last):
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/multiprocessing.process", line 258, in _bootstrap
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/multiprocessing.process", line 114, in run
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/lib.epoc", line 20, in epoc_reader
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/gevent.hub", line 79, in sleep
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/gevent.hub", line 164, in switch
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/gevent.hub", line 179, in run
  File "core.pyx", line 398, in gevent.core.dispatch (gevent/core.c:6132)
IOError: [Errno 9] Bad file descriptor
Could not connect to the device. Running with dummy data.
/Users/hiroki-tamakoshi/Downloads/brainactivity/sklearn/decomposition/fastica_.py:107: UserWarning: FastICA did not converge. You might want to increase the number of iterations.
Traceback (most recent call last):
  File "_ctypes/callbacks.c", line 314, in 'calling callback function'
  File "<string>", line 251, in display
  File "<string>", line 279, in brain_scene
  File "<string>", line 508, in draw_electrodes
  File "<string>", line 546, in draw_electrode
  File "<string>", line 557, in draw_label
  File "/Users/kuz/Development/BrainActivity3D/binaries/MacOSX/build/onedir/out00-PYZ.pyz/OpenGL.platform.baseplatform", line 384, in __call__
OpenGL.error.NullFunctionError: Attempt to call an undefined function glutBitmapString, check for bool(glutBitmapString) before calling
Traceback (most recent call last):
  File "_ctypes/callbacks.c", line 314, in 'calling callback function'
  File "<string>", line 305, in idle
  File "<string>", line 248, in display
  File "<string>", line 630, in draw_background
  File "latebind.pyx", line 32, in OpenGL_accelerate.latebind.LateBind.__call__ (src/latebind.c:667)
  File "errorchecker.pyx", line 50, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError (src/errorchecker.c:854)
OpenGL.error.GLError: GLError(
    err = 1282,
    description = 'invalid operation',
    baseOperation = glUniform1i,
    cArguments = (0, 0)
)

EPOC Control Panel provided officially works as expected.

My environment is as follows:

Mac OS X Mavericks
SDK is the Research Edition 1.0.0.5
EPOC Control Panel 2.0.0.20

Paint brain according to lobes

Using MeshLab paint mesh faces in differenrt colors for dirrefent lobes: https://github.com/kuz/BrainActivity3D/blob/master/doc/Images/Brain%20lobes.jpg

Make brain simpler by reducing the number of vertices

By replacing each ten vertices with estimated coordinate-wise average

Fix ESC button functionality

I think it doesn't work now (yeah, it was working before) because now there are several threads which probably stay running while the rest of the program tries to stop.

Convert .srf and glue hemispheres together

Scroll zoom in/out current mouse position

Source localization makes everything very slow

Check if will be good enough if just replace it with data chunks of reasonable size (up to 1 sec). Current solution takes in 240 seconds of data, has every right to be slow. But still need to check this out (separate threads for graphics and data computations?)

Old models
lib/eegica.py
lib/optimize.py

Draw activity location using dummy signal and dummy source localization

Add dummy function read_sample()
Add dummy function get_source_location()
Visualize their output as if they were real

Window reshape

update projection ratio
translate & scale the brain (? maybe scale is enough)

PyInstaller

.mtl and textures

Traceback (most recent call last):
  File "brainactivity.py", line 111, in <module>
    main()
  File "brainactivity.py", line 107, in main
    init()
  File "brainactivity.py", line 44, in init
    init_model()
  File "brainactivity.py", line 101, in init_model
    brain = objloader.OBJ('al.obj', 'model', swapyz=False)
  File "/Users/kuz/Development/BrainActivity3D/lib/objloader.py", line 61, in __init__
    self.mtl = MTL(values[1], path)
  File "/Users/kuz/Development/BrainActivity3D/lib/objloader.py", line 18, in MTL
    surf = pygame.image.load(mtl['map_Kd'])
pygame.error: Couldn't open textures/fabric1.rgb

Aligning colors

It would be nice to align color of the message about the source with its color.

Make source localization meaningful

Problems with current one:

source can appear outside the brain (yeey!)
constant K does not stay same
after each computation it jumps to new location, should make it stable somehow

Use fragment shader for lighting

Бикоз итс веей мор бьютифул!

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