def create_dn_buffer(size,
units,
points,
dn_inner=.0,
rad_inner=0,
dn_outer=.1,
rad_outer=.4):
Nx, Ny, Nz = size
dx, dy, dz = units
program = OCLProgram(absPath("kernels/bpm_3d_spheres.cl"))
dn_g = OCLArray.empty((Nz, Ny, Nx), dtype=np.float32)
# sort by z
ps = np.array(points)
ps = ps[np.argsort(ps[:, 2]), :]
Np = ps.shape[0]
pointsBuf = OCLArray.from_array(ps.flatten().astype(np.float32))
program.run_kernel("fill_dn", (Nx, Ny, Nz), None, dn_g.data,
pointsBuf.data, np.int32(Np), np.float32(dx),
np.float32(dy), np.float32(dz), np.float32(dn_inner),
np.float32(rad_inner), np.float32(dn_outer),
np.float32(rad_outer))
return dn_g
def setup(self, size, units, lam=0.5, n0=1.0, use_fresnel_approx=False):
"""
sets up the internal variables e.g. propagators etc...
:param size: the size of the geometry in pixels (Nx,Ny,Nz)
:param units: the phyiscal units of each voxel in microns (dx,dy,dz)
:param lam: the wavelength of light in microns
:param n0: the refractive index of the surrounding media
:param use_fresnel_approx: if True, uses fresnel approximation for propagator
"""
Bpm3d_Base.setup(self, size, units, lam=lam, n0=n0, use_fresnel_approx=use_fresnel_approx)
# setting up the gpu buffers and kernels
self.program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
Nx, Ny = self.size[:2]
plan = fft_plan(())
self._H_g = OCLArray.from_array(self._H.astype(np.complex64))
self.scatter_weights_g = OCLArray.from_array(self.scatter_weights.astype(np.float32))
self.gfactor_weights_g = OCLArray.from_array(self.gfactor_weights.astype(np.float32))
self.scatter_cross_sec_g = OCLArray.zeros(Nz, "float32")
self.gfactor_g = OCLArray.zeros(Nz, "float32")
self.reduce_kernel = OCLReductionKernel(
np.float32,
neutral="0",
reduce_expr="a+b",
map_expr="weights[i]*cfloat_abs(field[i]-(i==0)*plain)*cfloat_abs(field[i]-(i==0)*plain)",
arguments="__global cfloat_t *field, __global float * weights,cfloat_t plain",
)
def create_dn_buffer(size, units,points,
dn_inner = .0, rad_inner = 0,
dn_outer = .1, rad_outer = .4):
Nx, Ny, Nz = size
dx, dy, dz = units
program = OCLProgram(absPath("kernels/bpm_3d_spheres.cl"))
dn_g = OCLArray.empty((Nz,Ny,Nx),dtype=np.float32)
# sort by z
ps = np.array(points)
ps = ps[np.argsort(ps[:,2]),:]
Np = ps.shape[0]
pointsBuf = OCLArray.from_array(ps.flatten().astype(np.float32))
program.run_kernel("fill_dn",(Nx,Ny,Nz),None,dn_g.data,
pointsBuf.data,np.int32(Np),
np.float32(dx),np.float32(dy),np.float32(dz),
np.float32(dn_inner),np.float32(rad_inner),
np.float32(dn_outer),np.float32(rad_outer))
return dn_g
def _setup_impl(self):
"""setting up the gpu buffers and kernels
"""
self.bpm_program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
Nx, Ny, Nz = self.size
self._plan = fft_plan((Ny, Nx))
self._H_g = OCLArray.from_array(self._H.astype(np.complex64))
if not self.dn is None and self.n_volumes == 1:
self.dn_g = OCLArray.from_array(self.dn)
self.scatter_weights_g = OCLArray.from_array(
self.scatter_weights.astype(np.float32))
self.gfactor_weights_g = OCLArray.from_array(
self.gfactor_weights.astype(np.float32))
self.scatter_cross_sec_g = OCLArray.zeros(Nz, "float32")
self.gfactor_g = OCLArray.zeros(Nz, "float32")
def _setup_impl(self):
"""setting up the gpu buffers and kernels
"""
self.bpm_program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
Nx, Ny, Nz = self.size
self._plan = fft_plan((Ny,Nx))
self._H_g = OCLArray.from_array(self._H.astype(np.complex64))
if not self.dn is None and self.n_volumes==1:
self.dn_g = OCLArray.from_array(self.dn)
self.scatter_weights_g = OCLArray.from_array(self.scatter_weights.astype(np.float32))
self.gfactor_weights_g = OCLArray.from_array(self.gfactor_weights.astype(np.float32))
self.scatter_cross_sec_g = OCLArray.zeros(Nz,"float32")
self.gfactor_g = OCLArray.zeros(Nz,"float32")
def setup(self, size, units, lam = .5, n0 = 1.,
use_fresnel_approx = False):
"""
sets up the internal variables e.g. propagators etc...
:param size: the size of the geometry in pixels (Nx,Ny,Nz)
:param units: the phyiscal units of each voxel in microns (dx,dy,dz)
:param lam: the wavelength of light in microns
:param n0: the refractive index of the surrounding media
:param use_fresnel_approx: if True, uses fresnel approximation for propagator
"""
Bpm3d_Base.setup(self,size, units, lam = lam, n0 = n0,
use_fresnel_approx = use_fresnel_approx)
#setting up the gpu buffers and kernels
self.program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
Nx, Ny = self.size[:2]
plan = fft_plan(())
self._H_g = OCLArray.from_array(self._H.astype(np.complex64))
self.scatter_weights_g = OCLArray.from_array(self.scatter_weights.astype(np.float32))
self.gfactor_weights_g = OCLArray.from_array(self.gfactor_weights.astype(np.float32))
self.scatter_cross_sec_g = OCLArray.zeros(Nz,"float32")
self.gfactor_g = OCLArray.zeros(Nz,"float32")
self.reduce_kernel = OCLReductionKernel(
np.float32, neutral="0",
reduce_expr="a+b",
map_expr="weights[i]*cfloat_abs(field[i]-(i==0)*plain)*cfloat_abs(field[i]-(i==0)*plain)",
arguments="__global cfloat_t *field, __global float * weights,cfloat_t plain")
def bpm_3d_inverse(u, units, lam=.5, use_fresnel_approx=False):
"""
size - the dimension of the image to be calulcated in pixels (Nx,Ny,Nz)
units - the unit lengths of each dimensions in microns
lam - the wavelength
u - the complex field distribution
returns
dn - the refractive index of the medium (can be complex)
"""
clock = StopWatch()
clock.tic("setup")
Nz, Ny, Nx = u.shape
dx, dy, dz = units
#setting up the propagator
k0 = 2. * np.pi / lam
kxs = np.arange(-Nx / 2., Nx / 2.) / Nx
kys = np.arange(-Ny / 2., Ny / 2.) / Ny
KY, KX = np.meshgrid(kxs, kys, indexing="ij")
H0 = np.sqrt(0.j + (1. / lam)**2 - KX**2 / dx**2 - KY**2 / dy**2)
if use_fresnel_approx:
H0 = 1. / lam * (0.j + 1. - .5 * lam**2 *
(KX**2 / dx**2 + KY**2 / dy**2))
outsideInds = np.isnan(H0)
H = np.exp(2.j * np.pi * dz * H0)
H[outsideInds] = 0.
H0[outsideInds] = 0.
H = np.fft.fftshift(H).astype(np.complex64)
"""
setting up the gpu buffers and kernels
"""
program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
# program = OCLProgram(src_str = kernel_str)
kernel_divide = OCLElementwiseKernel(
"cfloat_t *a_g, cfloat_t *b_g,float kz, cfloat_t *res_g",
"res_g[i] = (cfloat_t)(i,0.)", "divide")
plan = ocl_fft_plan((Ny, Nx))
plane_g = OCLArray.empty((Ny, Nx), np.complex64)
plane0_g = OCLArray.empty((Ny, Nx), np.complex64)
h_g = OCLArray.from_array(H.astype(np.complex64))
u_g = OCLArray.from_array(u.astype(np.complex64))
dn_g = OCLArray.empty((Nz, Ny, Nx), dtype=np.complex64)
clock.toc("setup")
clock.tic("run")
for i in range(Nz - 1):
program.run_kernel("copy_complex", (Nx * Ny, ), None, u_g.data,
plane_g.data, np.int32(i * Nx * Ny))
#calculate the propagated plane
ocl_fft(plane_g, inplace=True, plan=plan)
program.run_kernel("mult", (Nx * Ny, ), None, plane_g.data, h_g.data)
ocl_fft(plane_g, inplace=True, inverse=True, plan=plan)
dn_g[i + 1, ...] = plane_g
# program.run_kernel("copy_complex",(Nx*Ny,),None,
# u_g.data,plane0_g.data,np.int32((i+1)*Nx*Ny))
# program.run_kernel("divide_dn_complex",(Nx*Ny,),None,
# plane0_g.data,plane_g.data,dn_g.data,
# np.float32(k0*dz),
# np.int32((i+1)*Nx*Ny))
clock.toc("run")
print clock
return dn_g.get()
def bpm_3d_inverse(u,units, lam = .5,
use_fresnel_approx = False):
"""
size - the dimension of the image to be calulcated in pixels (Nx,Ny,Nz)
units - the unit lengths of each dimensions in microns
lam - the wavelength
u - the complex field distribution
returns
dn - the refractive index of the medium (can be complex)
"""
clock = StopWatch()
clock.tic("setup")
Nz, Ny, Nx = u.shape
dx, dy, dz = units
#setting up the propagator
k0 = 2.*np.pi/lam
kxs = np.arange(-Nx/2.,Nx/2.)/Nx
kys = np.arange(-Ny/2.,Ny/2.)/Ny
KY, KX = np.meshgrid(kxs,kys, indexing= "ij")
H0 = np.sqrt(0.j+(1./lam)**2-KX**2/dx**2-KY**2/dy**2)
if use_fresnel_approx:
H0 = 1./lam*(0.j+1.-.5*lam**2*(KX**2/dx**2+KY**2/dy**2))
outsideInds = np.isnan(H0)
H = np.exp(2.j*np.pi*dz*H0)
H[outsideInds] = 0.
H0[outsideInds] = 0.
H = np.fft.fftshift(H).astype(np.complex64)
"""
setting up the gpu buffers and kernels
"""
program = OCLProgram(absPath("kernels/bpm_3d_kernels.cl"))
# program = OCLProgram(src_str = kernel_str)
kernel_divide = OCLElementwiseKernel(
"cfloat_t *a_g, cfloat_t *b_g,float kz, cfloat_t *res_g",
"res_g[i] = (cfloat_t)(i,0.)",
"divide")
plan = ocl_fft_plan((Ny,Nx))
plane_g = OCLArray.empty((Ny,Nx),np.complex64)
plane0_g = OCLArray.empty((Ny,Nx),np.complex64)
h_g = OCLArray.from_array(H.astype(np.complex64))
u_g = OCLArray.from_array(u.astype(np.complex64))
dn_g = OCLArray.empty((Nz,Ny,Nx),dtype=np.complex64)
clock.toc("setup")
clock.tic("run")
for i in range(Nz-1):
program.run_kernel("copy_complex",(Nx*Ny,),None,
u_g.data,plane_g.data,np.int32(i*Nx*Ny))
#calculate the propagated plane
ocl_fft(plane_g,inplace = True, plan = plan)
program.run_kernel("mult",(Nx*Ny,),None,
plane_g.data,h_g.data)
ocl_fft(plane_g,inplace = True, inverse = True, plan = plan)
dn_g[i+1,...] = plane_g
# program.run_kernel("copy_complex",(Nx*Ny,),None,
# u_g.data,plane0_g.data,np.int32((i+1)*Nx*Ny))
# program.run_kernel("divide_dn_complex",(Nx*Ny,),None,
# plane0_g.data,plane_g.data,dn_g.data,
# np.float32(k0*dz),
# np.int32((i+1)*Nx*Ny))
clock.toc("run")
print clock
return dn_g.get()