def run_ssyrk(N, l):
A = randn(N, N).astype('float32', order='F')
C = zeros((N, N), dtype='float32', order='F')
start = time.time()
for i in range(0, l):
blas.ssyrk(1.0, A, c=C, overwrite_c=True)
end = time.time()
timediff = (end - start)
mflops = (N * N * N) * l / timediff
mflops *= 1e-6
size = "%dx%d" % (N, N)
print("%14s :\t%20f MFlops\t%20f sec" % (size, mflops, timediff))
def _XXT(XT):
"""
[Added 30/9/2018]
Computes X @ XT much faster than naive X @ XT.
Notice X @ XT is symmetric, hence instead of doing the
full matrix multiplication X @ XT which takes O(pn^2) time,
compute only the upper triangular which takes slightly
less time and memory.
"""
if XT.dtype == float64:
return dsyrk(1, XT, trans=1).T
return ssyrk(1, XT, trans=1).T
def forward(self, X, mode=''):
if self.l is None: self.__init__(n=self.n, l=X.shape[1])
Y = np.dot(X, self.W)
if 'G' in mode:
self.X = X
#self.Y = Y
if self.SII is None:
self.SII = np.zeros((self.X.shape[1], ) * 2,
dtype='float32',
order='F')
ssyrk(alpha=1.0,
a=self.X,
trans=1,
beta=1.0,
c=self.SII,
overwrite_c=1)
return np.argmax(Y, 1)
print("Calculating shape modes...")
Es = scipy.diag(scipy.sqrt(S) * 3.0).dot(E)
# add Model_Eigenmode
for i,PC in enumerate(Es):
modelSurfaceDSA.PointData.append( PC.reshape((-1,3)) , "Model_Eigenmode_" + str(i+1).rjust(int(scipy.log10(nrOfSurfaces)+1),"0") )
if i>25: break
# add mean distance
meanDistance = scipy.sqrt(scipy.square(scipy.array(allPoints) - meanPoints).sum(axis=2)).mean(axis=0)
modelSurfaceDSA.PointData.append( meanDistance , "Mean_DistanceToMean")
# add tensor
apa = scipy.array(allPoints) - meanPoints
covarianceTensors = scipy.array([ blas.ssyrk( alpha = 1.0 / float(nrOfSurfaces-1) , a = apa[:,i,:].T ) for i in range( apa.shape[1] ) ])
modelSurfaceDSA.PointData.append( covarianceTensors , "CovarianceTensor")
#modelSurfaceDSA.PointData.append( covarianceTensors / scipy.array([scipy.linalg.norm(c) for c in covarianceTensors ]) , "CovarianceTensor_normalized")
print("Writing model...")
# save first and second PC
#scipy.savetxt(args.outputFilename.replace(".vtk","_PC1and2.txt") , Btruncated, delimiter="\t")
# save model
writer = vtk.vtkPolyDataWriter()
writer.SetInputData( modelSurface )
writer.SetFileName( args.outputFilename )
# writer.SetFileTypeToBinary()
writer.Update()
def ssyrk(a, alpha=1):
"""Returns alpha * a @ a.T for float alpha and float32 C-contiguous matrix a.
The result is the lower triangular part of a symmetric matrix."""
return blas.ssyrk(alpha, a.T, trans=1).T