def profileNCSC(n_reps):
"""
The C reference version for comparison.
"""
numpy.random.seed(1)
data = numpy.random.uniform(low=10.0,
high=20.0,
size=(n_reps, n_pts,
n_pts)).astype(dtype=numpy.float32)
gamma = numpy.random.uniform(low=2.0, high=4.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask = numpy.fft.fftshift(pyRef.createOTFMask().reshape(16, 16))
ref_u = numpy.zeros_like(data)
ncs_sr = ncsC.NCSCSubRegion(r_size=n_pts)
start_time = time.time()
for i in range(n_reps):
ncs_sr.newRegion(data[i, :, :], gamma)
ncs_sr.setOTFMask(otf_mask)
ref_u[i, :, :] = ncs_sr.cSolve(alpha, verbose=False)
e_time = time.time() - start_time
ncs_sr.cleanup()
print("CNSC {0:.6f} seconds".format(e_time))
def test_ncs_noise_reduction_2():
# Setup
numpy.random.seed(1)
n_reps = 10
data = numpy.random.uniform(low = 10.0, high = 20.0, size = (n_reps, n_pts, n_pts)).astype(dtype = numpy.float32)
gamma = numpy.random.uniform(low = 2.0, high = 4.0, size = (n_reps, n_pts, n_pts)).astype(dtype = numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
# OpenCL Setup.
u = numpy.zeros((n_reps, n_pts, n_pts), dtype = numpy.float32)
iters = numpy.zeros(n_reps, dtype = numpy.int32)
status = numpy.zeros(n_reps, dtype = numpy.int32)
data_buffer = cl.Buffer(context, cl.mem_flags.READ_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = data)
gamma_buffer = cl.Buffer(context, cl.mem_flags.READ_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = gamma)
otf_mask_buffer = cl.Buffer(context, cl.mem_flags.READ_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = otf_mask_shift)
u_buffer = cl.Buffer(context, cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = u)
iters_buffer = cl.Buffer(context, cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = iters)
status_buffer = cl.Buffer(context, cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf = status)
# OpenCL noise reduction.
program.ncsReduceNoise(queue, (n_reps*16,), (16,),
data_buffer,
gamma_buffer,
otf_mask_buffer,
u_buffer,
iters_buffer,
status_buffer,
numpy.float32(alpha))
cl.enqueue_copy(queue, u, u_buffer).wait()
cl.enqueue_copy(queue, iters, iters_buffer).wait()
cl.enqueue_copy(queue, status, status_buffer).wait()
queue.finish()
# NCSC noise reduction.
otf_mask = numpy.fft.fftshift(otf_mask_shift.reshape(16, 16))
ref_u = numpy.zeros_like(data)
ncs_sr = ncsC.NCSCSubRegion(r_size = n_pts)
for i in range(n_reps):
ncs_sr.newRegion(data[i,:,:], gamma[i,:,:])
ncs_sr.setOTFMask(otf_mask)
ref_u[i,:,:] = ncs_sr.cSolve(alpha, verbose = False)
ncs_sr.cleanup()
for i in range(n_reps):
norm_diff = numpy.max(numpy.abs(u[i,:,:] - ref_u[i,:,:]))/numpy.max(ref_u[i,:,:])
assert(norm_diff < 1.0e-2), "failed {0:d} {1:.3f}".format(i, norm_diff)
def profile(n_reps):
"""
Report how long it takes to reduce the noise in X sub-regions.
"""
# Setup
numpy.random.seed(1)
data = numpy.random.uniform(low=10.0,
high=20.0,
size=(n_reps, n_pts,
n_pts)).astype(dtype=numpy.float32)
gamma = numpy.random.uniform(low=2.0, high=4.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
# OpenCL Setup.
u = numpy.zeros((n_reps, n_pts, n_pts), dtype=numpy.float32)
iters = numpy.zeros(n_reps, dtype=numpy.int32)
status = numpy.zeros(n_reps, dtype=numpy.int32)
data_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=data)
gamma_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=gamma)
otf_mask_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=otf_mask_shift)
u_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf=u)
iters_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=iters)
status_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=status)
ev1 = program.ncsReduceNoise(queue, (n_reps, ), (1, ), data_buffer,
gamma_buffer, otf_mask_buffer, u_buffer,
iters_buffer, status_buffer,
numpy.float32(alpha))
cl.enqueue_copy(queue, u, u_buffer).wait()
cl.enqueue_copy(queue, iters, iters_buffer).wait()
cl.enqueue_copy(queue, status, status_buffer).wait()
queue.finish()
e_time = 1.0e-9 * (ev1.profile.end - ev1.profile.start)
print("OpenCL {0:.6f} seconds".format(e_time))
def test_calc_nc():
n_pts = 16
for i in range(100):
# OpenCL
u = numpy.random.uniform(low=1.0, high=10.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
nc = numpy.zeros(1, dtype=numpy.float32)
u_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=u)
otf_mask_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=otf_mask_shift)
nc_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=nc)
program.calc_nc_test(queue, (1, ), (1, ), u_buffer, otf_mask_buffer,
nc_buffer)
cl.enqueue_copy(queue, nc, nc_buffer).wait()
queue.finish()
# Reference 1
otf_mask = numpy.fft.fftshift(otf_mask_shift.reshape(16, 16))
ncs_sr = ncsC.NCSCSubRegion(r_size=n_pts)
ncs_sr.setOTFMask(otf_mask)
ncs_sr.setU(u)
ref1_nc = ncs_sr.calcNoiseContribution()
ncs_sr.cleanup()
norm_diff = abs(nc[0] - ref1_nc) / abs(ref1_nc)
assert (norm_diff <
1.0e-3), "Difference in results! {0:.6f}".format(norm_diff)
# Reference 2
u_r = numpy.copy(u).flatten()
u_c = numpy.zeros_like(u_r)
u_fft_r = numpy.zeros_like(u_r)
u_fft_c = numpy.zeros_like(u_c)
otf_mask_sqr = (otf_mask_shift * otf_mask_shift).flatten()
pyRef.fft_16x16(u_r, u_c, u_fft_r, u_fft_c)
ref2_nc = pyRef.calcNoiseContribution(u_fft_r, u_fft_c, otf_mask_sqr)
norm_diff = abs(nc[0] - ref2_nc) / abs(ref2_nc)
assert (norm_diff <
1.0e-3), "Difference in results! {0:.6f}".format(norm_diff)
def test_calc_nc_grad_1():
n_pts = 16
for i in range(10):
# OpenCL gradient calculation.
u = numpy.random.uniform(low = 1.0, high = 10.0, size = (n_pts, n_pts)).astype(dtype = numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
grad = numpy.zeros((n_pts, n_pts)).astype(numpy.float32)
u_buffer = cl.Buffer(context, cl.mem_flags.READ_ONLY | cl.mem_flags.COPY_HOST_PTR, hostbuf = u)
otf_mask_buffer = cl.Buffer(context, cl.mem_flags.READ_ONLY | cl.mem_flags.COPY_HOST_PTR, hostbuf = otf_mask_shift)
grad_buffer = cl.Buffer(context, cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR, hostbuf = grad)
program.calc_nc_grad_test(queue, (16,), (16,),
u_buffer,
otf_mask_buffer,
grad_buffer)
cl.enqueue_copy(queue, grad, grad_buffer).wait()
queue.finish()
# Reference 1
otf_mask = numpy.fft.fftshift(otf_mask_shift.reshape(16, 16))
ncs_sr = ncsC.NCSCSubRegion(r_size = n_pts)
ncs_sr.setOTFMask(otf_mask)
ncs_sr.setU(u)
ncs_sr.calcNoiseContribution()
ref1_grad = ncs_sr.calcNCGradient().reshape(grad.shape)
ncs_sr.cleanup()
ref_norm = numpy.abs(ref1_grad)
ref_norm[(ref_norm<1.0)] = 1.0
max_diff = numpy.max(numpy.abs(grad - ref1_grad)/ref_norm)
assert (max_diff < 1.0e-5), "Difference in results! {0:.8f}".format(max_diff)
# Reference 2
u_r = numpy.copy(u).flatten()
u_c = numpy.zeros_like(u_r)
u_fft_r = numpy.zeros_like(u_r)
u_fft_c = numpy.zeros_like(u_r)
ref2_grad = numpy.zeros_like(u_r)
otf_mask_sqr = otf_mask_shift * otf_mask_shift
pyRef.fft_16x16(u_r, u_c, u_fft_r, u_fft_c)
pyRef.calcNCGradientIFFT(u_fft_r, u_fft_c, otf_mask_sqr, ref2_grad)
ref_norm = numpy.abs(ref2_grad)
ref_norm[(ref_norm<1.0)] = 1.0
max_diff = numpy.max(numpy.abs(grad.flatten() - ref2_grad)/ref_norm)
assert (max_diff < 1.0e-5), "Difference in results! {0:.8f}".format(max_diff)
def test_ncs_noise_reduction_2():
# Setup
numpy.random.seed(1)
n_reps = 10
data = numpy.random.uniform(low=10.0,
high=20.0,
size=(n_reps, n_pts,
n_pts)).astype(dtype=numpy.float32)
gamma = numpy.random.uniform(low=2.0,
high=4.0,
size=(n_reps, n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
# CUDA Setup.
u = numpy.zeros((n_reps, n_pts, n_pts), dtype=numpy.float32)
iters = numpy.zeros(n_reps, dtype=numpy.int32)
status = numpy.zeros(n_reps, dtype=numpy.int32)
# CUDA noise reduction.
ncsReduceNoise(drv.In(data),
drv.In(gamma),
drv.In(otf_mask_shift),
drv.Out(u),
drv.Out(iters),
drv.Out(status),
numpy.float32(alpha),
block=(16, 1, 1),
grid=(n_reps, 1))
# NCSC noise reduction.
otf_mask = numpy.fft.fftshift(otf_mask_shift.reshape(16, 16))
ref_u = numpy.zeros_like(data)
ncs_sr = ncsC.NCSCSubRegion(r_size=n_pts)
for i in range(n_reps):
ncs_sr.newRegion(data[i, :, :], gamma[i, :, :])
ncs_sr.setOTFMask(otf_mask)
ref_u[i, :, :] = ncs_sr.cSolve(alpha, verbose=False)
ncs_sr.cleanup()
for i in range(n_reps):
norm_diff = numpy.max(
numpy.abs(u[i, :, :] - ref_u[i, :, :])) / numpy.max(ref_u[i, :, :])
assert (norm_diff < 1.0e-2), "failed {0:d} {1:.3f}".format(
i, norm_diff)
def test_ncs_noise_reduction_1():
# Setup
numpy.random.seed(1)
data = numpy.random.uniform(low=10.0, high=20.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
gamma = numpy.random.uniform(low=2.0, high=4.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
# CUDA Setup.
u = numpy.zeros((n_pts, n_pts), dtype=numpy.float32)
iters = numpy.zeros(1, dtype=numpy.int32)
status = numpy.zeros(1, dtype=numpy.int32)
# CUDA noise reduction.
ncsReduceNoise(drv.In(data),
drv.In(gamma),
drv.In(otf_mask_shift),
drv.Out(u),
drv.Out(iters),
drv.Out(status),
numpy.float32(alpha),
block=(16, 1, 1),
grid=(1, 1))
# Python reference version.
ref_u = numpy.zeros(data.size)
ref_iters = numpy.zeros_like(iters)
ref_status = numpy.zeros_like(status)
[py_u_fft_grad_r, py_u_fft_grad_c] = pyRef.createUFFTGrad()
pyRef.ncsReduceNoise(py_u_fft_grad_r, py_u_fft_grad_c, data, gamma,
otf_mask_shift, ref_u, ref_iters, ref_status,
numpy.float32(alpha))
ref_u = numpy.reshape(ref_u, data.shape)
norm_diff = numpy.max(numpy.abs(u[:, :] - ref_u[:, :])) / numpy.max(
ref_u[:, :])
assert (norm_diff < 1.0e-2), str(norm_diff)
def test_ncs_noise_reduction_1():
# Setup
numpy.random.seed(1)
data = numpy.random.uniform(low=10.0, high=20.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
gamma = numpy.random.uniform(low=2.0, high=4.0,
size=(n_pts,
n_pts)).astype(dtype=numpy.float32)
otf_mask_shift = pyRef.createOTFMask()
# OpenCL Setup.
u = numpy.zeros((n_pts, n_pts), dtype=numpy.float32)
iters = numpy.zeros(1, dtype=numpy.int32)
status = numpy.zeros(1, dtype=numpy.int32)
data_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=data)
gamma_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=gamma)
otf_mask_buffer = cl.Buffer(context,
cl.mem_flags.READ_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=otf_mask_shift)
u_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY | cl.mem_flags.COPY_HOST_PTR,
hostbuf=u)
iters_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=iters)
status_buffer = cl.Buffer(context,
cl.mem_flags.WRITE_ONLY
| cl.mem_flags.COPY_HOST_PTR,
hostbuf=status)
# OpenCL noise reduction.
program.ncsReduceNoise(queue, (1, ), (1, ), data_buffer, gamma_buffer,
otf_mask_buffer, u_buffer, iters_buffer,
status_buffer, numpy.float32(alpha))
cl.enqueue_copy(queue, u, u_buffer).wait()
cl.enqueue_copy(queue, iters, iters_buffer).wait()
cl.enqueue_copy(queue, status, status_buffer).wait()
queue.finish()
# Python reference version.
ref_u = numpy.zeros(data.size)
ref_iters = numpy.zeros_like(iters)
ref_status = numpy.zeros_like(status)
[py_u_fft_grad_r, py_u_fft_grad_c] = pyRef.createUFFTGrad()
pyRef.ncsReduceNoise(py_u_fft_grad_r, py_u_fft_grad_c, data, gamma,
otf_mask_shift, ref_u, ref_iters, ref_status,
numpy.float32(alpha))
ref_u = numpy.reshape(ref_u, data.shape)
norm_diff = numpy.max(numpy.abs(u[:, :] - ref_u[:, :])) / numpy.max(
ref_u[:, :])
assert (norm_diff < 1.0e-2), str(norm_diff)
