def sum_t(self, a, axis, out):
if len(a.shape) < 3 and (axis == 0 or axis == 1):
cumisc.sum(a, axis=axis, out=out)
elif axis is None:
cumisc.sum(a.reshape((a.size, 1)), axis=0, out=out)
else:
raise NotImplementedError
def _correlate_fft(self, frames_flat, cufft_plan):
npix = frames_flat.shape[1]
d_in = cufft_plan.data_in
d_in.fill(0)
f_out1 = cufft_plan.data_out
f_out2 = garray.zeros_like(cufft_plan.data_out)
# fft(pad(frames_flat), axis=1)
d_in[:, :self.nframes] = frames_flat.T.astype("f")
f_out1 = cufft_plan.fft(d_in, output=f_out1)
# frames_flat.sum(axis=1)
# skmisc.sum() only works on base data, not gpuarray views,
# so we sum on the whole array and then extract the right subset.
skmisc.sum(d_in, axis=0, out=self.d_sums_denom_tmp)
# fft(pad(frames_flat[::-1]), axis=1)
d_in.fill(0)
d_in[:, :self.nframes] = frames_flat.T[:, ::-1].astype("f")
f_out2 = cufft_plan.fft(d_in, output=f_out2)
# product, ifft
f_out1 *= f_out2
num = cufft_plan.ifft(f_out1, output=d_in)
# numerator of g_2
skmisc.sum(num, axis=0, out=self.d_sums)
# denominator of g_2: correlate(d_sums_denom)
self._correlate_denom(npix)
self.d_numerator /= self.d_denom
res = self.d_numerator.get()
return res
def _rbf_kernel_vectorized_cublas(data1,
data2,
sigma=10): # pragma: no cover
"""kernel for edge similarity computed with the vectorized method
Args:
data1 (TYPE): pssm data 1
data2 (TYPE): pssm dta 2
sigma (int, optional): exponent of the exponetial
Returns:
np.array: value of the rbk kernel for all the pairs
"""
beta = 2 * sigma**2
d1_ = gpuarray.to_gpu(data1.astype(np.float32))
d2_ = gpuarray.to_gpu(data2.astype(np.float32))
mgpu = -2 * culinalg.dot(d1_, d2_, transa='N', transb='T')
vgpu = cumisc.sum(d1_**2, axis=1)[:, None]
cumisc.add_matvec(mgpu, vgpu, out=mgpu)
vgpu = cumisc.sum(d2_**2, axis=1)
cumisc.add_matvec(mgpu, vgpu, out=mgpu)
mcpu = mgpu.get()
return np.exp(-mcpu / beta).reshape(-1)
def sum_t(self, a, axis, out):
if len(a.shape) < 3 and (axis == 0 or axis == 1):
cumisc.sum(a, axis=axis, out=out)
elif axis is None:
cumisc.sum(a.reshape((a.size, 1)), axis=0, out=out)
else:
raise NotImplementedError
def sum_t(self, a, axis, out):
if len(a.shape) < 3 and (axis == 0 or axis == 1):
cumisc.sum(a, axis, out)
elif axis is None:
self.copy_to(cumisc.sum(a), out)
else:
raise NotImplementedError
def meanUnderMask(volume, mask=None, p=1, gpu=False):
"""
meanValueUnderMask: Determines the mean value under a mask
@param volume: The volume
@type volume: L{pytom_volume.vol}
@param mask: The mask
@type mask: L{pytom_volume.vol}
@param p: precomputed number of voxels in mask
@type p: float
@return: A value (scalar)
@rtype: single
@change: support None as mask, FF 08.07.2014
"""
return sum((volume * mask)) / sum(mask)
def __init__(self, volume, template, mask, wedge, stdV, gpu=True):
self.volume = gu.to_gpu(volume)
self.template = Volume(template)
self.templatePadded = gu.zeros_like(self.volume, dtype=np.float32)
self.mask = Volume(mask)
self.maskPadded = gu.zeros_like(self.volume, dtype=np.float32)
self.sOrg = mask.shape
self.sPad = volume.shape
print(self.sPad, self.sOrg)
rotate(self.mask, [0, 0, 0], self.maskPadded, self.sPad, self.sOrg)
#paste_in_center_gpu(self.template.d_data, self.templatePadded, np.int32(self.sPad), np.int32(self.maskSize), block=(10, 10, 10), grid=(8,1,1))
#rotate(self.template, [0, 0, 0], self.templatePadded, self.sPad, self.maskSize)
print(volume.shape, stdV.shape, wedge.shape)
self.wedge = gu.to_gpu(wedge)
self.stdV = gu.to_gpu(stdV)
self.fwd_plan = Plan(volume.shape, volume.dtype, np.complex64)
self.inv_plan = Plan(volume.shape, np.complex64, volume.dtype)
self.volume_fft = gu.zeros_like(self.volume, dtype=np.complex64)
self.template_fft = gu.zeros_like(self.volume, dtype=np.complex64)
self.ccc_map = gu.zeros_like(self.volume, dtype=np.float32)
self.norm_volume = np.prod(volume.shape)
self.scores = gu.ones_like(self.volume, dtype=np.float32) * -1000
self.angles = gu.ones_like(self.volume, dtype=np.float32) * -1000
self.p = sum(self.mask.d_data)
def fast_matmul(x, y, x_type, y_type):
'''
use pycuda to compute c = a * b
'''
linalg.init()
a_gpu = gpuarray.to_gpu(x.astype(x_type))
a_t_gpu = gpuarray.to_gpu(x.T.copy().astype(x_type))
b_gpu = gpuarray.to_gpu(y.astype(y_type))
# row_sum = gpuarray.zeros(shape = x[0].shape, dtype = x_type)
row_sum = 0
# a = np.asarray(x, x_type)
# b = np.asarray(y, y_type)
# a_gpu = gpuarray.to_gpu(a)
# b_gpu = gpuarray.to_gpu(b)
t1_inside = time.time()
c_gpu = linalg.dot(a_gpu, b_gpu)
for a_i in a_gpu:
# row_sum = misc.add(row_sum, a_i)
row_sum += a_i
gg = linalg.dot(a_gpu, b_gpu)
gg = linalg.dot(a_i, a_i)
gg = reduce(linalg.dot, (a_gpu, b_gpu, b_gpu, b_gpu))
# tmp1, tmp2 = linalg.dot(a_gpu, b_gpu), linalg.dot(b_gpu, b_gpu)
z_gpu = a_gpu.copy()
tmp = a_t_gpu
# print('x.T\n', x.T)
# print('tmp\n', tmp)
# print('x = a_gpu: ', np.allclose(x, a_gpu.get()))
# print('x.T = tmp: ', np.allclose(x.T, tmp.get()))
a_prod = linalg.dot(a_gpu, tmp)
t2_inside = time.time()
print('inside cost {:.4f}s'.format(t2_inside - t1_inside))
a = np.random.randint(-5, 5, (3, 4)).astype(np.float32)
a_gpu = gpuarray.to_gpu(a)
norm_gpu = linalg.norm(a_gpu)
print('is norm right?', np.linalg.norm(a) == norm_gpu)
a_gpu = abs(a_gpu)
column_sum = misc.sum(a_gpu, axis=0)
column_sum = column_sum.reshape((1, -1))
all_one_gpu = gpuarray.to_gpu(np.ones((3, 1), np.float32))
div_mat_gpu = linalg.dot(all_one_gpu, column_sum)
norm_1 = a_gpu / (div_mat_gpu + 1e-3)
print(a_gpu)
print(column_sum)
print(column_sum.shape)
print(norm_1)
# abs_a = a_gpu.__abs__()
# print(a)
# print(abs_a)
# c = abs_a + a_gpu
# print(repr(c))
# print(type(c))
# c = 1/2 * c
# print(a_gpu, c)
return c_gpu.get(), a_prod.get(), row_sum.get()
def log_loss(y_true, y_prob):
"""Compute Logistic loss for classification.
Parameters
----------
y_true : array-like or label indicator matrix
Ground truth (correct) labels.
y_prob : array-like of float, shape = (n_samples, n_classes)
Predicted probabilities, as returned by a classifier's
predict_proba method.
Returns
-------
loss : float
The degree to which the samples are correctly predicted.
"""
if y_prob.dtype == np.float64:
cuClip(y_prob.gpudata,
np.float64(1e-10),
np.float64(1 - 1e-10),
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
else:
cuClipf(y_prob.gpudata,
np.float32(1e-10),
np.float32(1 - 1e-10),
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
if y_prob.shape[1] == 1:
y_prob = gpuarray.to_gpu(
np.append(1 - y_prob.get(), y_prob.get(), axis=1))
if y_true.shape[1] == 1:
y_true = gpuarray.to_gpu(
np.append(1 - y_true.get(), y_true.get(), axis=1))
tmp_gpu = gpuarray.GPUArray(y_prob.shape, y_prob.dtype)
if y_prob.dtype == np.float64:
cuLogLoss(y_true.gpudata,
y_prob.gpudata,
tmp_gpu.gpudata,
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
else:
cuLogLossf(y_true.gpudata,
y_prob.gpudata,
tmp_gpu.gpudata,
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
#total = float(misc.sum(y_true * tmp_gpu).get())
total = float(cumisc.sum(tmp_gpu).get())
return (-total) / y_prob.shape[0]
def softmax_gpu2d(x: gpuarray.GPUArray, dim):
assert len(x.shape) == 2, 'expected 2-dimension array'
assert 0 <= dim <= 1, "expected 0 <= dim <=1"
exp_ker = exp_float_ker if x.dtype == np.float32 else exp_double_ker
x_exp = gpuarray.empty_like(x)
exp_ker(x, x_exp)
x_exp_sum = misc.sum(x_gpu=x_exp, axis=dim)
x_exp = misc.div_matvec(x_gpu=x_exp, a_gpu=x_exp_sum, axis=1 - dim)
return x_exp
def binary_log_loss(y_true, y_prob):
"""Compute binary logistic loss for classification.
This is identical to log_loss in binary classification case,
but is kept for its use in multilabel case.
Parameters
----------
y_true : array-like or label indicator matrix
Ground truth (correct) labels.
y_prob : array-like of float, shape = (n_samples, n_classes)
Predicted probabilities, as returned by a classifier's
predict_proba method.
Returns
-------
loss : float
The degree to which the samples are correctly predicted.
"""
if y_prob.dtype == np.float64:
cuClip(y_prob.gpudata,
np.float64(1e-10),
np.float64(1 - 1e-10),
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
else:
cuClipf(y_prob.gpudata,
np.float32(1e-10),
np.float32(1 - 1e-10),
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
tmp_gpu = gpuarray.GPUArray(y_prob.shape, y_prob.dtype)
if y_prob.dtype == np.float64:
cuBinaryLogLoss(y_true.gpudata,
y_prob.gpudata,
tmp_gpu.gpudata,
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
else:
cuBinaryLogLossf(y_true.gpudata,
y_prob.gpudata,
tmp_gpu.gpudata,
np.int32(y_prob.size),
block=(blockSize, 1, 1),
grid=(int((y_prob.size - 1) / blockSize + 1), 1, 1))
total = float(cumisc.sum(tmp_gpu).get())
return (-total) / y_prob.shape[0]
def _impl_test_sum(self, dtype):
x = np.random.normal(scale=5.0, size=(3, 5))
x = x.astype(dtype=dtype, order='C')
x_gpu = gpuarray.to_gpu(x)
assert_allclose(misc.sum(x_gpu).get(),
x.sum(),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=0).get(),
x.sum(axis=0),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=1).get(),
x.sum(axis=1),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
x = x.astype(dtype=dtype, order='F')
x_gpu = gpuarray.to_gpu(x)
assert_allclose(misc.sum(x_gpu).get(),
x.sum(),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=0).get(),
x.sum(axis=0),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=1).get(),
x.sum(axis=1),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
def marginilize_rots_scales(self, posteriors, phases, shift_x, shift_y):
shift_ind = self.ravel_shift_index(shift_x, shift_y)
W = np.zeros((self.n_images, self.converter.get_num_prolates()), np.complex64)
if config.is_use_gpu:
W_gpu = gpuarray.zeros(W.shape, dtype='complex64')
for i in np.arange(self.n_images):
Wi = misc.sum(linalg.dot(posteriors[i, shift_ind], phases), axis=0).reshape((1,-1))
slice_assign_kernel.slice_assign_1d(W_gpu, Wi, i)
W = W_gpu.get()
else:
for i in np.arange(self.n_images):
W[i] = np.sum(np.dot(posteriors[i, shift_ind], phases), axis=0)
return W
def _cuda_norm(self, X):
"""Caluclate L2-norm on gpu.
Parameters
----------
X: array
Array to normalize
Returns
-------
normX: array
Normalized array
"""
return misc.divide(X, misc.sum(X**2, axis=1, keepdims=True)**0.5)
def impl_test_sum(self, dtype):
x = np.random.normal(scale=5.0, size=(3, 5))
x = x.astype(dtype=dtype, order='C')
x_gpu = gpuarray.to_gpu(x)
assert np.allclose(misc.sum(x_gpu).get(), x.sum())
assert np.allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0))
assert np.allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1))
x = x.astype(dtype=dtype, order='F')
x_gpu = gpuarray.to_gpu(x)
assert np.allclose(misc.sum(x_gpu).get(), x.sum())
assert np.allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0))
assert np.allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1))
def impl_test_sum(self, dtype):
x = np.random.normal(scale=5.0, size=(3, 5))
x = x.astype(dtype=dtype, order='C')
x_gpu = gpuarray.to_gpu(x)
assert np.allclose(misc.sum(x_gpu).get(), x.sum())
assert np.allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0))
assert np.allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1))
x = x.astype(dtype=dtype, order='F')
x_gpu = gpuarray.to_gpu(x)
assert np.allclose(misc.sum(x_gpu).get(), x.sum())
assert np.allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0))
assert np.allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1))
def get_distances_to_centers(self, data):
# make sure the array is c order
data = np.asarray(data, dtype=np.float32, order='C')
# ship to gpu
data_gpu = gpuarray.to_gpu(data)
# alloc space on gpu for distances
dists_shape = (data.shape[0], self.centers.shape[0])
dists_gpu = gpuarray.zeros(dists_shape, np.float32)
# calc data norms on gpu
data_norms = cumisc.sum(data_gpu**2, axis=1)
# calc distance on gpu
cumisc.add_matvec(dists_gpu, self.center_norms, 1, dists_gpu)
cumisc.add_matvec(dists_gpu, data_norms, 0, dists_gpu)
culinalg.add_dot(data_gpu, self.centers_gpu,
dists_gpu, transb='T', alpha=-2.0)
return dists_gpu
def run_gpu(self):
"""
Solves the MFTIE on GPU. The result is stored on an attribute
"self.phase" containing a GPU array.
"""
# Extract pre-allocated GPU arrays
# extract inputs
iIo = self.iIo
nm2 = self.inverse_laplacian
dzI = self.dzI
ky, kx = self.k
Nz, Ny, Nx = self.shape
# create outputs
ft_dzI = gpuarray.empty((Nz, Ny, Nx), np.complex64)
gradx = gpuarray.empty((Nz, Ny, Nx), np.complex64)
grady = gpuarray.empty((Nz, Ny, Nx), np.complex64)
# extract plans
ft3dcc = self.pft3dcc
ft2dcc = self.pft2dcc
# Do the math!
# FT(dzI)
cu_fft.fft(dzI, ft_dzI, ft3dcc)
# IFT(k*nm2*...)
cu_fft.ifft((ft_dzI * nm2) * kx, gradx, ft3dcc, True)
cu_fft.ifft((ft_dzI * nm2) * ky, grady, ft3dcc, True)
# FT(... / Io)
cu_fft.fft(gradx * iIo, gradx, ft3dcc)
cu_fft.fft(grady * iIo, grady, ft3dcc)
# Sum_z(nm2*(k*...))
Slapl = misc.sum(
(nm2 * (kx * gradx + ky * grady)).reshape(Nz, Ny * Nx),
0).reshape(Ny, Nx)
# IFT(...)
cu_fft.ifft(Slapl, self.phdata, ft2dcc, True)
def thunk():
alpha = gpuarray.to_gpu(np.squeeze(np.asarray(inputs[0]))[:, None])
x_t = gpuarray.to_gpu(np.asarray(inputs[1])[0, :, :])
x_f = gpuarray.to_gpu(np.asarray(inputs[2])[0, :, :])
Xt = cumath.exp(misc.add(linalg.dot(x_t, A), b))
Xf = cumath.exp(misc.add(linalg.dot(x_f, A), b))
Xtn = misc.sum(Xt, axis=1, keepdims=True)
Xfn = misc.sum(Xf, axis=1, keepdims=True)
Xt = misc.divide(Xt, Xtn)
Xf = misc.divide(Xf, Xfn)
w = misc.multiply(Xt, alpha) + misc.multiply(Xf, 1 - alpha)
wp = cumath.log(w)
wpn = misc.sum(wp, axis=1, keepdims=True) / self.n
wp = misc.subtract(wp, wpn)
t1 = misc.sum(x * wp, axis=1)
t2 = (self.n + depth) * cumath.log(misc.sum(w, axis=1))
t3 = depth * wpn
outputs[0][0] = misc.sum(t1 - t2 + t3).get()
for v in node.outputs:
compute_map[v][0] = True
def _impl_test_sum(self, dtype):
x = np.random.normal(scale=5.0, size=(3, 5))
x = x.astype(dtype=dtype, order='C')
x_gpu = gpuarray.to_gpu(x)
assert_allclose(misc.sum(x_gpu).get(), x.sum(),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
x = x.astype(dtype=dtype, order='F')
x_gpu = gpuarray.to_gpu(x)
assert_allclose(misc.sum(x_gpu).get(), x.sum(),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=0).get(), x.sum(axis=0),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
assert_allclose(misc.sum(x_gpu, axis=1).get(), x.sum(axis=1),
rtol=dtype_to_rtol[dtype],
atol=dtype_to_atol[dtype])
def thunk():
alpha = gpuarray.to_gpu(np.squeeze(np.asarray(inputs[0]))[:, None])
x_t = gpuarray.to_gpu(np.asarray(inputs[1])[0, :, :])
x_f = gpuarray.to_gpu(np.asarray(inputs[2])[0, :, :])
Xt = cumath.exp(misc.add(linalg.dot(x_t, A), b))
Xf = cumath.exp(misc.add(linalg.dot(x_f, A), b))
Xtn = misc.sum(Xt, axis=1, keepdims=True)
Xfn = misc.sum(Xf, axis=1, keepdims=True)
Xt = misc.divide(Xt, Xtn)
Xf = misc.divide(Xf, Xfn)
w = misc.multiply(Xt, alpha) + misc.multiply(Xf, 1 - alpha)
dq = Xt - Xf
qdw = dq / w
t1 = misc.sum(x * qdw, axis=1)
f = 2 * depth + self.base.n
t2 = f * misc.sum(dq, axis=1) / misc.sum(w, axis=1)
t3 = misc.sum(x, axis=1) * misc.sum(qdw, axis=1)
dalpha = t1 - t2 + t3
del dq, t1, f, t2, t3
iw = 1 / w
S1 = misc.multiply(
depth[:, None] * (self.base.n - 1) / self.base.n, iw)
S2 = (self.base.n + depth[:, None]) / cumath.log(
misc.sum(w, axis=1, keepdims=True))
F = misc.multiply(misc.subtract((x * iw) - S1, S2), alpha)
del w, iw, S1, S2
cast = gpuarray.zeros((x_t.shape[1], Xt.shape[1]),
dtype=theano.config.floatX)
dLq_t = gpuarray.zeros(x_t.shape, dtype=theano.config.floatX)
dLq_f = gpuarray.zeros(x_f.shape, dtype=theano.config.floatX)
for i in range(Xt.shape[0]):
S1 = misc.multiply(Xt[None, i, :], A)
S2 = misc.sum(S1, axis=1, keepdims=True)
S2 = misc.multiply(S2, misc.add(Xt[None, i, :], cast))
dLq_t[i, :] = misc.sum(misc.multiply(F[None, i, :], S1 - S2),
axis=1)
S1 = misc.multiply(Xf[None, i, :], A)
S2 = misc.sum(S1, axis=1, keepdims=True)
S2 = misc.multiply(S2, misc.add(Xf[None, i, :], cast))
dLq_f[i, :] = misc.sum(misc.multiply(F[None, i, :], S1 - S2),
axis=1)
outputs[0][0] = dalpha.get()
outputs[1][0] = dLq_t.get()
outputs[2][0] = dLq_f.get()
for v in node.outputs:
compute_map[v][0] = True
def almLasso_mat_fun(self):
'''
This function represents the Augumented Lagrangian Multipliers method for Lasso problem.
The lagrangian form of the Lasso can be expressed as following:
MIN{ 1/2||Y-XBHETA||_2^2 + lambda||THETA||_1} s.t B-T=0
When applied to this problem, the ADMM updates take the form
BHETA^t+1 = (XtX + rhoI)^-1(Xty + rho^t - mu^t)
THETA^t+1 = Shrinkage_lambda/rho(BHETA(t+1) + mu(t)/rho)
mu(t+1) = mu(t) + rho(BHETA(t+1) - BHETA(t+1))
The algorithm involves a 'ridge regression' update for BHETA, a soft-thresholding (shrinkage) step for THETA and
then a simple linear update for mu
NB: Actually, this ADMM version contains several variations such as the using of two penalty parameters instead
of just one of them (mu1, mu2)
'''
print('\tADMM processing...')
alpha1 = alpha2 = 0
if (len(self.reg_params) == 1):
alpha1 = self.reg_params[0]
alpha2 = self.reg_params[0]
elif (len(self.reg_params) == 2):
alpha1 = self.reg_params[0]
alpha2 = self.reg_params[1]
#thresholds parameters for stopping criteria
if (len(self.thr) == 1):
thr1 = self.thr[0]
thr2 = self.thr[0]
elif (len(self.thr) == 2):
thr1 = self.thr[0]
thr2 = self.thr[1]
# entry condition
err1 = 10 * thr1
err2 = 10 * thr2
start_time = time.time()
# setting penalty parameters for the ALM
mu1p = alpha1 * 1 / self.computeLambda()
print("\t\t-Compute Lambda- Time = %s seconds" %
(time.time() - start_time))
mu2p = alpha2 * 1
mu1 = mu1p
mu2 = mu2p
i = 1
start_time = time.time()
if self.GPU == True:
# defining penalty parameters e constraint to minimize, lambda and C matrix respectively
THETA = misc.zeros((self.num_columns, self.num_columns),
dtype='float64')
lambda2 = misc.zeros((self.num_columns, self.num_columns),
dtype='float64')
gpu_data = gpuarray.to_gpu(self.data)
P_GPU = linalg.dot(gpu_data, gpu_data, transa='T')
OP1 = P_GPU
linalg.scale(np.float32(mu1), OP1)
OP2 = linalg.eye(self.num_columns)
linalg.scale(mu2, OP2)
if self.affine == True:
print('\t\tGPU affine...')
OP3 = misc.ones((self.num_columns, self.num_columns),
dtype='float64')
linalg.scale(mu2, OP3)
lambda3 = misc.zeros((1, self.num_columns), dtype='float64')
# TODO: Because of some problem with linalg.inv version of scikit-cuda we fix it using np.linalg.inv of numpy
A = np.linalg.inv(
misc.add(misc.add(OP1.get(), OP2.get()), OP3.get()))
A_GPU = gpuarray.to_gpu(A)
while ((err1 > thr1 or err2 > thr1) and i < self.max_iter):
_lambda2 = gpuarray.to_gpu(lambda2)
_lambda3 = gpuarray.to_gpu(lambda3)
linalg.scale(1 / mu2, _lambda2)
term_OP2 = gpuarray.to_gpu(_lambda2.get())
OP2 = gpuarray.to_gpu(misc.subtract(THETA, term_OP2))
linalg.scale(mu2, OP2)
OP4 = gpuarray.to_gpu(
np.matlib.repmat(_lambda3.get(), self.num_columns, 1))
# updating Z
BHETA = linalg.dot(
A_GPU, misc.add(misc.add(misc.add(OP1, OP2), OP3),
OP4))
# deallocating unnecessary GPU variables
OP2.gpudata.free()
OP4.gpudata.free()
_lambda2.gpudata.free()
_lambda3.gpudata.free()
# updating C
THETA = misc.add(BHETA, term_OP2)
THETA = self.shrinkL1Lq(THETA.get(), 1 / mu2)
THETA = THETA.astype('float64')
# updating Lagrange multipliers
term_lambda2 = misc.subtract(BHETA, gpuarray.to_gpu(THETA))
linalg.scale(mu2, term_lambda2)
term_lambda2 = gpuarray.to_gpu(term_lambda2.get())
lambda2 = misc.add(lambda2, term_lambda2) # on GPU
term_lambda3 = misc.subtract(
misc.ones((1, self.num_columns), dtype='float64'),
misc.sum(BHETA, axis=0))
linalg.scale(mu2, term_lambda3)
term_lambda3 = gpuarray.to_gpu(term_lambda3.get())
lambda3 = misc.add(lambda3, term_lambda3) # on GPU
# deallocating unnecessary GPU variables
term_OP2.gpudata.free()
term_lambda2.gpudata.free()
term_lambda3.gpudata.free()
err1 = self.errorCoef(BHETA.get(), THETA)
err2 = self.errorCoef(np.sum(BHETA.get(), axis=0),
np.ones([1, self.num_columns]))
# deallocating unnecessary GPU variables
BHETA.gpudata.free()
THETA = gpuarray.to_gpu((THETA))
# reporting errors
if (self.verbose and (i % self.step == 0)):
print(
'\t\tIteration = %d, ||Z - C|| = %2.5e, ||1 - C^T 1|| = %2.5e'
% (i, err1, err2))
i += 1
THETA = THETA.get()
Err = [err1, err2]
if (self.verbose):
print(
'\t\tTerminating ADMM at iteration %5.0f, \n ||Z - C|| = %2.5e, ||1 - C^T 1|| = %2.5e. \n'
% (i, err1, err2))
else:
print '\t\tGPU not affine'
# TODO: Because of some problem with linalg.inv version of scikit-cuda we fix it using np.linalg.inv of numpy
A = np.linalg.inv(misc.add(OP1.get(), OP2.get()))
A_GPU = gpuarray.to_gpu(A)
while (err1 > thr1 and i < self.max_iter):
_lambda2 = gpuarray.to_gpu(lambda2)
term_OP2 = THETA
linalg.scale(mu2, term_OP2)
term_OP2 = misc.subtract(term_OP2, _lambda2)
OP2 = gpuarray.to_gpu(term_OP2.get())
BHETA = linalg.dot(A_GPU, misc.add(OP1, OP2))
linalg.scale(1 / mu2, _lambda2)
term_THETA = gpuarray.to_gpu(_lambda2.get())
THETA = misc.add(BHETA, term_THETA)
THETA = self.shrinkL1Lq(THETA.get(), 1 / mu2)
THETA = THETA.astype('float32')
# updating Lagrange multipliers
term_lambda2 = misc.subtract(BHETA, gpuarray.to_gpu(THETA))
linalg.scale(mu2, term_lambda2)
term_lambda2 = gpuarray.to_gpu(term_lambda2.get())
lambda2 = misc.add(lambda2, term_lambda2) # on GPU
err1 = self.errorCoef(BHETA.get(), THETA)
THETA = gpuarray.to_gpu((THETA))
# reporting errors
if (self.verbose and (i % self.step == 0)):
print('\t\tIteration %5.0f, ||Z - C|| = %2.5e' %
(i, err1))
i += 1
THETA = THETA.get()
Err = [err1, err2]
if (self.verbose):
print(
'\t\tTerminating ADMM at iteration %5.0f, \n ||Z - C|| = %2.5e'
% (i, err1))
else: #CPU version
# defining penalty parameters e constraint to minimize, lambda and C matrix respectively
THETA = np.zeros([self.num_columns, self.num_columns])
lambda2 = np.zeros([self.num_columns, self.num_columns])
P = self.data.T.dot(self.data)
OP1 = np.multiply(P, mu1)
if self.affine == True:
# INITIALIZATION
lambda3 = np.zeros(self.num_columns).T
A = np.linalg.inv(
np.multiply(mu1, P) +
np.multiply(mu2, np.eye(self.num_columns, dtype=int)) +
np.multiply(mu2,
np.ones([self.num_columns, self.num_columns])))
OP3 = np.multiply(
mu2, np.ones([self.num_columns, self.num_columns]))
while ((err1 > thr1 or err2 > thr1) and i < self.max_iter):
# updating Bheta
OP2 = np.multiply(THETA - np.divide(lambda2, mu2), mu2)
OP4 = np.matlib.repmat(lambda3, self.num_columns, 1)
BHETA = A.dot(OP1 + OP2 + OP3 + OP4)
# updating C
THETA = BHETA + np.divide(lambda2, mu2)
THETA = self.shrinkL1Lq(THETA, 1 / mu2)
# updating Lagrange multipliers
lambda2 = lambda2 + np.multiply(mu2, BHETA - THETA)
lambda3 = lambda3 + np.multiply(
mu2,
np.ones([1, self.num_columns]) - np.sum(BHETA, axis=0))
err1 = self.errorCoef(BHETA, THETA)
err2 = self.errorCoef(np.sum(BHETA, axis=0),
np.ones([1, self.num_columns]))
# mu1 = min(mu1 * (1 + 10 ^ -5), 10 ^ 2 * mu1p);
# mu2 = min(mu2 * (1 + 10 ^ -5), 10 ^ 2 * mu2p);
# reporting errors
if (self.verbose and (i % self.step == 0)):
print(
'\t\tIteration = %d, ||Z - C|| = %2.5e, ||1 - C^T 1|| = %2.5e'
% (i, err1, err2))
i += 1
Err = [err1, err2]
if (self.verbose):
print(
'\t\tTerminating ADMM at iteration %5.0f, \n ||Z - C|| = %2.5e, ||1 - C^T 1|| = %2.5e. \n'
% (i, err1, err2))
else:
print '\t\tCPU not affine'
A = np.linalg.inv(
OP1 +
np.multiply(mu2, np.eye(self.num_columns, dtype=int)))
while (err1 > thr1 and i < self.max_iter):
# updating Z
OP2 = np.multiply(mu2, THETA) - lambda2
BHETA = A.dot(OP1 + OP2)
# updating C
THETA = BHETA + np.divide(lambda2, mu2)
THETA = self.shrinkL1Lq(THETA, 1 / mu2)
# updating Lagrange multipliers
lambda2 = lambda2 + np.multiply(mu2, BHETA - THETA)
# computing errors
err1 = self.errorCoef(BHETA, THETA)
# reporting errors
if (self.verbose and (i % self.step == 0)):
print('\t\tIteration %5.0f, ||Z - C|| = %2.5e' %
(i, err1))
i += 1
Err = [err1, err2]
if (self.verbose):
print(
'\t\tTerminating ADMM at iteration %5.0f, \n ||Z - C|| = %2.5e'
% (i, err1))
print("\t\t-ADMM- Time = %s seconds" % (time.time() - start_time))
return THETA, Err
import pycuda.gpuarray as gpuarray
import pycuda.autoinit
import numpy as np
from skcuda import misc
def rolling_window(a, window):
shape = a.shape[:-1] + (a.shape[-1] - window + 1, window)
strides = a.strides + (a.strides[-1],)
return np.lib.stride_tricks.as_strided(a, shape=shape, strides=strides)
a = np.arange(100000,dtype=np.float32)
b = np.array(rolling_window(a,5))
misc.init()
dest_gpu = gpuarray.to_gpu(b)
c = misc.sum(dest_gpu,axis=1)
def sum_diagonals(self, d_arr, d_out):
self.d_diags.fill(0)
self._kern_args[0] = d_arr.gpudata
self.extract_diags_kernel(*self._kern_args, grid=self._grid, block=self._blocks)
skmisc.sum(self.d_diags, axis=1, out=d_out)
def __init__(self, centers):
culinalg.init()
self.centers = centers.astype(np.float32)
self.centers_gpu = gpuarray.to_gpu(self.centers)
self.center_norms = cumisc.sum(self.centers_gpu**2, axis=1)
def demosaick_gpu(img):
img = gp.to_gpu(img)
p2x = im2col(img, _i2c2)
cm.log(img + _eps, out=img)
p1x = im2col(img, _i2c1)
wA = p1x.shape[0]
wB = p2x.shape[0]
hA = p1x.shape[1]
hB = p2x.shape[1]
# Path 1
p1x = p1x.reshape([wA * hA, 576])
p1y = lg.dot(p1x, _wts.int1)
cm.exp(p1y, out=p1y)
p1y = p1y.reshape([wA * hA * 64, 3 * _ofac])
p1x = lg.dot(p1y, _wts.int2)
msc.add_matvec(p1x, _wts.int2b, out=p1x)
p1x = p1x.reshape([wA * hA * 64 * 3, _ofac])
# Path 2
# conv1
p2x = p2x.reshape([wB * hB, 64])
p2y = lg.dot(p2x, _wts.c1)
msc.add_matvec(p2y, _wts.c1b, out=p2y)
gp.maximum(p2y, 0., p2y)
p2y = p2y.reshape([wB, hB, _numsel])
# conv2
shI = [wB - 1, hB - 1, _numsel]
shM = [(wB - 1) * (hB - 1), _numsel]
p2x = gp.empty(shM, dtype=np.float32)
pTT = gp.empty(shI, dtype=np.float32)
pTT = pTT.reshape(shI)
pTT[...] = p2y[0:-1, 0:-1, :]
pTT = pTT.reshape(shM)
p2x = lg.dot(pTT, _wts.c200)
pTT = pTT.reshape(shI)
pTT[...] = p2y[0:-1, 1:, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c201, p2x)
pTT = pTT.reshape(shI)
pTT[...] = p2y[1:, 0:-1, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c210, p2x)
pTT = pTT.reshape(shI)
pTT[...] = p2y[1:, 1:, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c211, p2x)
msc.add_matvec(p2x, _wts.c2b, out=p2x)
gp.maximum(p2x, 0., p2x)
p2x = p2x.reshape(shI)
# conv 3
shI = [wB - 2, hB - 2, _numsel]
shM = [(wB - 2) * (hB - 2), _numsel]
p2y = gp.empty(shM, dtype=np.float32)
pTT = gp.empty(shI, dtype=np.float32)
pTT = pTT.reshape(shI)
pTT[...] = p2x[0:-1, 0:-1, :]
pTT = pTT.reshape(shM)
p2y = lg.dot(pTT, _wts.c300)
pTT = pTT.reshape(shI)
pTT[...] = p2x[0:-1, 1:, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c301, p2y)
pTT = pTT.reshape(shI)
pTT[...] = p2x[1:, 0:-1, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c310, p2y)
pTT = pTT.reshape(shI)
pTT[...] = p2x[1:, 1:, :]
pTT = pTT.reshape(shM)
lg.add_dot(pTT, _wts.c311, p2y)
msc.add_matvec(p2y, _wts.c3b, out=p2y)
gp.maximum(p2y, 0., p2y)
p2x = lg.dot(p2y, _wts.sout)
msc.add_matvec(p2x, _wts.soutb, out=p2x)
gp.maximum(p2x, 0., p2x)
p2x = p2x.reshape(p1x.shape)
# Combine
p1x *= p2x
p1 = msc.sum(p1x, axis=1)
gp.maximum(p1, 0., p1)
gp.minimum(p1, 1., p1)
p1 = p1.reshape([wA, hA, 64 * 3])
im = p2im(p1.get())
return im