def VTEM_Gabor_IAF(videofile,
output_filename,
Wt,
Wx=2 * np.pi * 4,
Wy=2 * np.pi * 4,
start_frame=0,
end_frame=None,
dx=1.0 / 16,
dy=1.0 / 16,
fps=100,
domain=None,
h5input=True):
"""
Encode a video with IAF neurons and Gabor receptive field
with default parameters
Parameters
-----------
videofile : string
::
Either
1. Filename of a file containing the input video
must be stored using write_memory_to_file in simpleio.py
or using h5write in matlab
Video array with shape (a,b,c)
a: total number of frames
b: number of pixels in y direction
c: number of pixels in x direction
c is the leading dimension
in matlab should be (c,b,a)
2. Or filename of a video file if h5input is set to False.
Will throw an error if OpenCV and the required codec are
not installed
output_filename : string
output filename that will contain the spike info
Wt : float
bandwidth in t variable
if not specified, will use the info in spikefile
Wx : float, optional
bandwidth in x variable
if not specified, will use the info in spikefile
Wy : float, optional
bandwidth in y variable
if not specified, will use the info in spikefile
start_frame : integer, optional
starting frame to be encoded in the video
end_frame : integer, optional
ending frame to be encoded
if not specified, will encoding to the end of the video
dx : integer, optional
spatial resolution in x direction, distance between two pixels
dy: integer, optional
spatial resolution in y direction, distance between two pixels
fps : integer, optional
frames per second of the video
domain : list, optional
list of 2, [a,b], specifying the domain to encode
a in x direction, b in y direction
will only encode the center of the video with size [a,b]
if not specified, the whole video screen will be encoded.
h5input : bool, optional
True if the file specified is an h5 file.
False if the file specified is a video file.
If not specified, is set to True
Notes
-----
The coordinate system is given by the following
::
Row (width / X) major
-----------------------------------------> width
| Y
| ^-------------------->
| |-------------------->
| |-------------------->
| |--------------------> X
|
|
v
height
To specify receptive field parameters, create an object using
vrf.vrf_gabor() with desired parameters and use function
VTEM_IAF
Examples
--------
>>> import atexit
>>> import pycuda.driver as cuda
>>> import numpy as np
>>> from vtem import vtem,vtdm
>>> cuda.init()
>>> context1 = cuda.Device(0).make_context()
>>> atexit.register(cuda.Context.pop)
>>> vtem.VTEM_Gabor_IAF('video.h5', 'spikes.h5', 2*np.pi*10)
"""
if h5input:
h5file = tables.openFile(videofile, 'r')
videoarray = h5file.root.real
else:
videoarray = vio.read_video(videofile)
_, Py, Px = videoarray.shape
gb = vrf.vrf_gabor((Py, Px), domain=domain, dx=dx, dy=dy)
gb.load_parameters()
VTEM_IAF(videoarray,
output_filename,
Wt,
gb,
Wx,
Wy,
start_frame,
end_frame,
dx,
dy,
fps,
domain,
h5input,
npinput=True)
if h5input:
h5file.close()
def VTDM_prepb(spikefile, Dsfilename, dirichfilename, Mx, My = None,
domain=None, Wx = None, Wy = None, dtype = np.complex128):
"""
Prepare decoding with two files Dswfilename and dirichfilename
must be called before VTDM a new spikefile
parameters:
spikefile: the file generated by VTEM containing spike info
Dsfilename: name of the resulting file, containing the spatial
dirichlet coefficients for all RFs
dirichfilename: the name of the resulting file, containing the
spatial reconstruction function for all RFs
Mx: order of dirichlet space in x variable
My: order of dirichlet space in y variable
if not specified, My = Mx
domain: 4-list or 4-tuple, [xstart, xend, ystart, yend]
the spatial domain to recover
Wx: bandwidth in x variable
if not specified, will use the info in spikefile
Wy: bandwidth in y variable
if not specified, will use the info in spikefile
dtype: np.complex128 or np.complex64, accurancy of computing
dirichlet coefficients and the output files will
be in the real format derived from dtype
The coordinate system is given by the following:
row (width / X) major
-----------------------------------------> width
| Y
| ^-------------------->
| |-------------------->
| |-------------------->
| |--------------------> X
|
|
v
height
VTDM_prep computes inner product between two RFs and store in Dswfilename.
VTDM_prepb computes only the dirichlet coefficient of each RF and stores it in
Dsfilename. The inner product is computed in VTDMb.
"""
if dtype not in [np.complex128, np.complex64]:
raise TypeError("dtype must be complex128 or complex64")
spfile = ss.vtem_storage_read(spikefile)
spfile.read_vrf_type()
num_neurons = spfile.read_num_neurons()
print "total neurons: %d" % (num_neurons)
Wt,Wx1,Wy1,Px,Py,dx,dy = spfile.read_video_attributes()
if Wx is None:
Wx = Wx1
else:
Wx = float(Wx)
if Wy is None:
Wy = Wy1
else:
Wy = float(Wy)
Mx = int(Mx)
if My is None:
My = Mx
else:
My = int(My)
rfSx = (2*np.pi) * (Mx/Wx)
rfSy = (2*np.pi) * (My/Wy)
rfPx = int(np.ceil(rfSx/dx/16) * 16)
rfPy = int(np.ceil(rfSy/dy/16) * 16)
oriSx = Px*dx
oriSy = Py*dy
if domain is None:
domain = [-oriSx/2,oriSx/2,-oriSy/2,oriSy/2]
else:
domain = [max(float(domain[0]),-oriSx/2),
min(float(domain[1]), oriSx/2),
max(float(domain[2]),-oriSy/2),
min(float(domain[3]),oriSy/2)]
spfile.select_neurons(domain)
print "select neurons: %d" % (spfile.decode_neurons)
decSx = domain[1]-domain[0]
decSy = domain[3]-domain[2]
decPx = int(np.round(decSx / dx))
decPy = int(np.round(decSy / dy))
if spfile.filter_type == "gabor":
gb = vrf.vrf_gabor((rfPy, rfPx), dx=rfSx/rfPx, dy=rfSy/rfPy,
scale=4, dtype=dtype)
gb.load_parameters(num_neurons=spfile.decode_neurons,
h_alpha=spfile.alpha, h_l=spfile.l, h_x0=spfile.x0,
h_y0=spfile.y0, h_ab=spfile.ab, KAPPA=spfile.KAPPA)
else:
gb = vrf.vrf_cs((rfPy, rfPx), dx=rfSx/rfPx, dy=rfSy/rfPy,
scale=4, dtype=dtype)
gb.load_parameters(num_neurons=spfile.decode_neurons,
h_alpha=spfile.alpha, h_x0=spfile.x0, h_y0=spfile.y0,
sigma_center=spfile.sigma_center,
sigma_surround=spfile.sigma_surround)
d_Ds = gb.compute_Ds(Mx, My)
write_memory_to_file(d_Ds, Dsfilename)
d_dirich = gb.compute_dirich_space_fft(d_Ds, Mx, My, decPx,
decPy, decSx, decSy, Wx, Wy)
write_memory_to_file(d_dirich, dirichfilename)
del d_dirich
spfile.close()
def VTEM_Gabor_IAF(videofile, output_filename, Wt, Wx=2*np.pi*4, Wy=2*np.pi*4,
start_frame=0, end_frame=None, dx=1.0/16, dy=1.0/16,
fps=100, domain=None, h5input=True):
"""
Encode a video with IAF neurons and Gabor receptive field
with default parameters
Parameters
-----------
videofile : string
::
Either
1. Filename of a file containing the input video
must be stored using write_memory_to_file in simpleio.py
or using h5write in matlab
Video array with shape (a,b,c)
a: total number of frames
b: number of pixels in y direction
c: number of pixels in x direction
c is the leading dimension
in matlab should be (c,b,a)
2. Or filename of a video file if h5input is set to False.
Will throw an error if OpenCV and the required codec are
not installed
output_filename : string
output filename that will contain the spike info
Wt : float
bandwidth in t variable
if not specified, will use the info in spikefile
Wx : float, optional
bandwidth in x variable
if not specified, will use the info in spikefile
Wy : float, optional
bandwidth in y variable
if not specified, will use the info in spikefile
start_frame : integer, optional
starting frame to be encoded in the video
end_frame : integer, optional
ending frame to be encoded
if not specified, will encoding to the end of the video
dx : integer, optional
spatial resolution in x direction, distance between two pixels
dy: integer, optional
spatial resolution in y direction, distance between two pixels
fps : integer, optional
frames per second of the video
domain : list, optional
list of 2, [a,b], specifying the domain to encode
a in x direction, b in y direction
will only encode the center of the video with size [a,b]
if not specified, the whole video screen will be encoded.
h5input : bool, optional
True if the file specified is an h5 file.
False if the file specified is a video file.
If not specified, is set to True
Notes
-----
The coordinate system is given by the following
::
Row (width / X) major
-----------------------------------------> width
| Y
| ^-------------------->
| |-------------------->
| |-------------------->
| |--------------------> X
|
|
v
height
To specify receptive field parameters, create an object using
vrf.vrf_gabor() with desired parameters and use function
VTEM_IAF
Examples
--------
>>> import atexit
>>> import pycuda.driver as cuda
>>> import numpy as np
>>> from vtem import vtem,vtdm
>>> cuda.init()
>>> context1 = cuda.Device(0).make_context()
>>> atexit.register(cuda.Context.pop)
>>> vtem.VTEM_Gabor_IAF('video.h5', 'spikes.h5', 2*np.pi*10)
"""
if h5input:
h5file = tables.openFile(videofile, 'r')
videoarray = h5file.root.real
else:
videoarray = vio.read_video(videofile)
_ , Py, Px = videoarray.shape
gb = vrf.vrf_gabor((Py,Px), domain=domain, dx=dx, dy=dy)
gb.load_parameters()
VTEM_IAF(videoarray, output_filename, Wt, gb, Wx, Wy,start_frame,
end_frame, dx, dy, fps, domain, h5input, npinput=True)
if h5input:
h5file.close()
