def test_comparisons():
a = afnumpy.arange(10, dtype="float32") - 5.
b = afnumpy.ones((10), dtype="float32")
a.eval()
a_mask = a < 0.
a_sum = a_mask.sum()
a -= b
assert(a_sum == a_mask.sum())
a_mask = a > 0.
a_sum = a_mask.sum()
a -= b
assert(a_sum == a_mask.sum())
a_mask = a >= 0.
a_sum = a_mask.sum()
a -= b
assert(a_sum == a_mask.sum())
a_mask = a <= 0.
a_sum = a_mask.sum()
a -= b
assert(a_sum == a_mask.sum())
a_mask = a == 0.
a_sum = a_mask.sum()
a *= 0
assert(a_sum == a_mask.sum())
a = afnumpy.arange(10, dtype="float32") - 5.
a.eval()
a_mask = a != 0.
a_sum = a_mask.sum()
a *= 0
assert(a_sum == a_mask.sum())
def test_comparisons():
a = afnumpy.arange(10, dtype="float32") - 5.
b = afnumpy.ones((10), dtype="float32")
a.eval()
a_mask = a < 0.
a_sum = a_mask.sum()
a -= b
assert (a_sum == a_mask.sum())
a_mask = a > 0.
a_sum = a_mask.sum()
a -= b
assert (a_sum == a_mask.sum())
a_mask = a >= 0.
a_sum = a_mask.sum()
a -= b
assert (a_sum == a_mask.sum())
a_mask = a <= 0.
a_sum = a_mask.sum()
a -= b
assert (a_sum == a_mask.sum())
a_mask = a == 0.
a_sum = a_mask.sum()
a *= 0
assert (a_sum == a_mask.sum())
a = afnumpy.arange(10, dtype="float32") - 5.
a.eval()
a_mask = a != 0.
a_sum = a_mask.sum()
a *= 0
assert (a_sum == a_mask.sum())
def test_binary_arithmetic():
a = afnumpy.random.rand(3)
b = numpy.array(a)
fassert(a+a, b+b)
fassert(a+3, b+3)
fassert(3+a, 3+b)
fassert(a-a, b-b)
fassert(a-3, b-3)
fassert(3-a, 3-b)
fassert(a*a, b*b)
fassert(a*3, b*3)
fassert(3*a, 3*b)
fassert(a/a, b/b)
fassert(a/3, b/3)
fassert(3/a, 3/b)
fassert(a**a, b**b)
fassert(a**3, b**3)
fassert(3**a, 3**b)
fassert(a%a, b%b)
fassert(a%3, b%3)
fassert(3%a, 3%b)
# Check for arguments of diffeernt types
a = afnumpy.ones(3,dtype=numpy.uint32)
b = numpy.array(a)
fassert(a+3.0, b+3.0)
# This is a tricky case we won't support for now
# fassert(a+numpy.float32(3.0), b+numpy.float32(3.0))
fassert(3.0+a, 3.0+b)
fassert(a-3.0, b-3.0)
fassert(3.0-a, 3.0-b)
fassert(a*3.0, b*3.0)
fassert(3.0*a, 3.0*b)
fassert(a/3.0, b/3.0)
fassert(3.0/a, 3.0/b)
fassert(3/a, 3/b)
fassert(a**3.0, b**3.0)
fassert(3.0**a, 3.0**b)
fassert(a%3.0, b%3.0)
fassert(3.0%a, 3.0%b)
assert(type(numpy.float32(3)+a) == afnumpy.ndarray)
def test_binary_arithmetic():
a = afnumpy.random.rand(3)
b = numpy.array(a)
fassert(a + a, b + b)
fassert(a + 3, b + 3)
fassert(3 + a, 3 + b)
fassert(a - a, b - b)
fassert(a - 3, b - 3)
fassert(3 - a, 3 - b)
fassert(a * a, b * b)
fassert(a * 3, b * 3)
fassert(3 * a, 3 * b)
fassert(a / a, b / b)
fassert(a / 3, b / 3)
fassert(3 / a, 3 / b)
fassert(a**a, b**b)
fassert(a**3, b**3)
fassert(3**a, 3**b)
fassert(a % a, b % b)
fassert(a % 3, b % 3)
fassert(3 % a, 3 % b)
# Check for arguments of diffeernt types
a = afnumpy.ones(3, dtype=numpy.uint32)
b = numpy.array(a)
fassert(a + 3.0, b + 3.0)
# This is a tricky case we won't support for now
# fassert(a+numpy.float32(3.0), b+numpy.float32(3.0))
fassert(3.0 + a, 3.0 + b)
fassert(a - 3.0, b - 3.0)
fassert(3.0 - a, 3.0 - b)
fassert(a * 3.0, b * 3.0)
fassert(3.0 * a, 3.0 * b)
fassert(a / 3.0, b / 3.0)
fassert(3.0 / a, 3.0 / b)
fassert(3 / a, 3 / b)
fassert(a**3.0, b**3.0)
fassert(3.0**a, 3.0**b)
fassert(a % 3.0, b % 3.0)
fassert(3.0 % a, 3.0 % b)
assert (type(numpy.float32(3) + a) == afnumpy.ndarray)
def meshgrid(*xi, **kwargs):
ndim = len(xi)
copy_ = kwargs.pop('copy', True)
sparse = kwargs.pop('sparse', False)
indexing = kwargs.pop('indexing', 'xy')
if kwargs:
raise TypeError("meshgrid() got an unexpected keyword argument '%s'" %
(list(kwargs)[0], ))
if indexing not in ['xy', 'ij']:
raise ValueError("Valid values for `indexing` are 'xy' and 'ij'.")
s0 = (1, ) * ndim
output = [
afnumpy.asanyarray(x).reshape(s0[:i] + (-1, ) + s0[i + 1::])
for i, x in enumerate(xi)
]
shape = [x.size for x in output]
if indexing == 'xy' and ndim > 1:
# switch first and second axis
output[0].shape = (1, -1) + (1, ) * (ndim - 2)
output[1].shape = (-1, 1) + (1, ) * (ndim - 2)
shape[0], shape[1] = shape[1], shape[0]
if sparse:
if copy_:
return [x.copy() for x in output]
else:
return output
else:
# Return the full N-D matrix (not only the 1-D vector)
if copy_:
# Numpy uses dtype=int but Arrayfire does not support int64 in all functions
mult_fact = afnumpy.ones(shape, dtype=numpy.int32)
return [x * mult_fact for x in output]
else:
return afnumpy.broadcast_arrays(*output)
def meshgrid(*xi, **kwargs):
ndim = len(xi)
copy_ = kwargs.pop('copy', True)
sparse = kwargs.pop('sparse', False)
indexing = kwargs.pop('indexing', 'xy')
if kwargs:
raise TypeError("meshgrid() got an unexpected keyword argument '%s'"
% (list(kwargs)[0],))
if indexing not in ['xy', 'ij']:
raise ValueError(
"Valid values for `indexing` are 'xy' and 'ij'.")
s0 = (1,) * ndim
output = [afnumpy.asanyarray(x).reshape(s0[:i] + (-1,) + s0[i + 1::])
for i, x in enumerate(xi)]
shape = [x.size for x in output]
if indexing == 'xy' and ndim > 1:
# switch first and second axis
output[0].shape = (1, -1) + (1,)*(ndim - 2)
output[1].shape = (-1, 1) + (1,)*(ndim - 2)
shape[0], shape[1] = shape[1], shape[0]
if sparse:
if copy_:
return [x.copy() for x in output]
else:
return output
else:
# Return the full N-D matrix (not only the 1-D vector)
if copy_:
# Numpy uses dtype=int but Arrayfire does not support int64 in all functions
mult_fact = afnumpy.ones(shape, dtype=numpy.int32)
return [x * mult_fact for x in output]
else:
return afnumpy.broadcast_arrays(*output)
def test_add(benchmark):
a = afnumpy.ones((2048, 2048), dtype=numpy.complex64)
b = afnumpy.ones((2048, 2048), dtype=numpy.complex64)
benchmark(afnumpy.add, a, b)
def test_array_copy(benchmark):
a = afnumpy.ones((2048, 2048), dtype=numpy.complex64)
benchmark(afnumpy.array, a, copy=True)
def test_ifftshift(benchmark):
a = afnumpy.ones((256, 256), dtype=numpy.complex64)
benchmark(afnumpy.fft.ifftshift, a)
def test_ones():
a = afnumpy.ones(3)
b = numpy.ones(3)
iassert(a, b)
def test_array_copy(benchmark):
a = afnumpy.ones((2048,2048),dtype=numpy.complex64)
benchmark(afnumpy.array, a, copy=True)
def test_fftshift(benchmark):
a = afnumpy.ones((256,256),dtype=numpy.complex64)
benchmark(afnumpy.fft.fftshift, a)
def gpuMBIR(tomo,angles,center,input_params):
"""
MBIR reconstruction using GPU based gridding operators
Inputs: tomo : 3D numpy sinogram array with dimensions same as tomopy
angles : Array of angles in radians
center : Floating point center of rotation
input_params : A dictionary with the keys
'gpu_device' : Device id of the gpu (For a 4 GPU cluster ; 0-3)
'oversamp_factor': A factor by which to pad the image/data for FFT
'num_iter' : Max number of MBIR iterations
'smoothness' : Regularization constant
'p': MRF shape param
"""
print('Starting GPU MBIR recon')
#allocate space for final answer
af.set_device(input_params['gpu_device']) #Set the device number for gpu based code
#Change tomopy format
new_tomo=np.transpose(tomo,(1,2,0)) #slice, columns, angles
im_size = new_tomo.shape[1]
num_slice = new_tomo.shape[0]
num_angles=new_tomo.shape[2]
pad_size=np.int16(im_size*input_params['oversamp_factor'])
# nufft_scaling = (np.pi/pad_size)**2
num_iter = input_params['num_iter']
mrf_sigma = input_params['smoothness']
mrf_p = input_params['p']
print('MRF params p=%f sigma=%f' %(mrf_p,mrf_sigma))
#Initialize structures for NUFFT
sino={}
geom={}
sino['Ns'] = pad_size#Sinogram size after padding
sino['Ns_orig'] = im_size #size of original sinogram
sino['center'] = center + (sino['Ns']/2 - sino['Ns_orig']/2) #for padded sinogram
sino['angles'] = angles
#Initialize NUFFT parameters
print('Initialize NUFFT params')
nufft_params = init_nufft_params(sino,geom)
temp_y = afnp.zeros((sino['Ns'],num_angles),dtype=afnp.complex64)
temp_x = afnp.zeros((sino['Ns'],sino['Ns']),dtype=afnp.complex64)
x_recon = afnp.zeros((num_slice/2,sino['Ns_orig'],sino['Ns_orig']),dtype=afnp.complex64)
pad_idx = slice(sino['Ns']/2-sino['Ns_orig']/2,sino['Ns']/2+sino['Ns_orig']/2)
#allocate output array
rec_mbir_final=np.zeros((num_slice,sino['Ns_orig'],sino['Ns_orig']),dtype=np.float32)
#Move all data to GPU
print('Moving data to GPU')
slice_1=slice(0,num_slice,2)
slice_2=slice(1,num_slice,2)
gdata=afnp.array(new_tomo[slice_1]+1j*new_tomo[slice_2],dtype=afnp.complex64)
gradient = afnp.zeros((num_slice/2,sino['Ns_orig'],sino['Ns_orig']), dtype=afnp.complex64)#temp array to store the derivative of cost func
z_recon = afnp.zeros((num_slice/2,sino['Ns_orig'],sino['Ns_orig']),dtype=afnp.complex64)#Nesterov method variables
t_nes = 1
#Compute Lipschitz of gradient
print('Computing Lipschitz of gradient')
x_ones= afnp.ones((1,sino['Ns_orig'],sino['Ns_orig']),dtype=afnp.complex64)
temp_x[pad_idx,pad_idx]=x_ones[0]
temp_proj=forward_project(temp_x,nufft_params)
temp_backproj=(back_project(temp_proj,nufft_params))[pad_idx,pad_idx]
print('Adding Hessian of regularizer')
temp_backproj2=afnp.zeros((1,sino['Ns_orig'],sino['Ns_orig']),dtype=afnp.complex64)
temp_backproj2[0]=temp_backproj
add_hessian(mrf_sigma,x_ones, temp_backproj2)
L = np.max([temp_backproj2.real.max(),temp_backproj2.imag.max()])
print('Lipschitz constant = %f' %(L))
del x_ones,temp_proj,temp_backproj,temp_backproj2
#loop over all slices
for iter_num in range(num_iter):
print('Iteration %d of %d'%(iter_num,num_iter))
#Derivative of the data fitting term
for i in range(num_slice/2):
temp_x[pad_idx,pad_idx]=x_recon[i]
Ax = forward_project(temp_x,nufft_params)
temp_y[pad_idx]=gdata[i]
gradient[i] =(back_project((Ax-temp_y),nufft_params))[pad_idx,pad_idx] #nufft_scaling
#Derivative of regularization term
tvd_update(mrf_p,mrf_sigma,x_recon, gradient)
#x_recon-=gradient/L
x_recon,z_recon,t_nes=nesterovOGM2update(x_recon,z_recon,t_nes,gradient,L)
#Move to CPU
#Rescale result to match tomopy
rec_mbir=np.array(x_recon,dtype=np.complex64)
rec_mbir_final[slice_1]=np.array(rec_mbir.real,dtype=np.float32)
rec_mbir_final[slice_2]=np.array(rec_mbir.imag,dtype=np.float32)
return rec_mbir_final
def test_ones():
a = afnumpy.ones(3)
b = numpy.ones(3)
iassert(a, b)
def test_fft2(benchmark):
a = afnumpy.ones((256, 256), dtype=numpy.complex64)
benchmark(afnumpy.fft.fftn, a)
def gpuSIRT(tomo, angles, center, input_params):
print('Starting GPU SIRT recon')
#allocate space for final answer
af.set_device(
input_params['gpu_device']) #Set the device number for gpu based code
#Change tomopy format
new_tomo = np.transpose(tomo, (1, 2, 0)) #slice, columns, angles
im_size = new_tomo.shape[1]
num_slice = new_tomo.shape[0]
num_angles = new_tomo.shape[2]
pad_size = np.int16(im_size * input_params['oversamp_factor'])
nufft_scaling = (np.pi / pad_size)**2
num_iter = input_params['num_iter']
#Initialize structures for NUFFT
sino = {}
geom = {}
sino['Ns'] = pad_size #Sinogram size after padding
sino['Ns_orig'] = im_size #size of original sinogram
sino['center'] = center + (sino['Ns'] / 2 - sino['Ns_orig'] / 2
) #for padded sinogram
sino['angles'] = angles
#Initialize NUFFT parameters
nufft_params = init_nufft_params(sino, geom)
temp_y = afnp.zeros((sino['Ns'], num_angles), dtype=afnp.complex64)
temp_x = afnp.zeros((sino['Ns'], sino['Ns']), dtype=afnp.complex64)
x_recon = afnp.zeros((num_slice / 2, sino['Ns_orig'], sino['Ns_orig']),
dtype=afnp.complex64)
pad_idx = slice(sino['Ns'] / 2 - sino['Ns_orig'] / 2,
sino['Ns'] / 2 + sino['Ns_orig'] / 2)
#allocate output array
rec_sirt_final = np.zeros((num_slice, sino['Ns_orig'], sino['Ns_orig']),
dtype=np.float32)
#Pre-compute diagonal scaling matrices ; one the same size as the image and the other the same as data
#initialize an image of all ones
x_ones = afnp.ones((sino['Ns_orig'], sino['Ns_orig']),
dtype=afnp.complex64)
temp_x[pad_idx, pad_idx] = x_ones
temp_proj = forward_project(temp_x,
nufft_params) * (sino['Ns'] * afnp.pi / 2)
R = 1 / afnp.abs(temp_proj)
R[afnp.isnan(R)] = 0
R[afnp.isinf(R)] = 0
R = afnp.array(R, dtype=afnp.complex64)
#Initialize a sinogram of all ones
y_ones = afnp.ones((sino['Ns_orig'], num_angles), dtype=afnp.complex64)
temp_y[pad_idx] = y_ones
temp_backproj = back_project(temp_y, nufft_params) * nufft_scaling / 2
C = 1 / (afnp.abs(temp_backproj))
C[afnp.isnan(C)] = 0
C[afnp.isinf(C)] = 0
C = afnp.array(C, dtype=afnp.complex64)
#Move all data to GPU
slice_1 = slice(0, num_slice, 2)
slice_2 = slice(1, num_slice, 2)
gdata = afnp.array(new_tomo[slice_1] + 1j * new_tomo[slice_2],
dtype=afnp.complex64)
#loop over all slices
for i in range(num_slice / 2):
for iter_num in range(num_iter):
#filtered back-projection
temp_x[pad_idx, pad_idx] = x_recon[i]
Ax = (np.pi / 2) * sino['Ns'] * forward_project(
temp_x, nufft_params)
temp_y[pad_idx] = gdata[i]
x_recon[i] = x_recon[i] + (
C * back_project(R * (temp_y - Ax), nufft_params) *
nufft_scaling / 2)[pad_idx, pad_idx]
#Move to CPU
#Rescale result to match tomopy
rec_sirt = np.array(x_recon, dtype=np.complex64)
rec_sirt_final[slice_1] = np.array(rec_sirt.real, dtype=np.float32)
rec_sirt_final[slice_2] = np.array(rec_sirt.imag, dtype=np.float32)
return rec_sirt_final
def test_add(benchmark):
a = afnumpy.ones((2048,2048),dtype=numpy.complex64)
b = afnumpy.ones((2048,2048),dtype=numpy.complex64)
benchmark(afnumpy.add, a, b)
def test_ifft2(benchmark):
a = afnumpy.ones((256,256),dtype=numpy.complex64)
benchmark(afnumpy.fft.ifftn, a)
#! /usr/bin/env python import gnufft import afnumpy as afnp vol = afnp.ones((25,256,256), dtype='f') vol = vol + 1j * vol fcn = afnp.zeros((25,256,256), dtype='complex64') mrf_sigma = afnp.ones(1, dtype='f') gnufft.add_hessian(mrf_sigma[0], vol, fcn) print fcn[0,:10,:10] print fcn[0,:10,:10]