def c_normalize_bg(tomo, air):
dt, dy, dx = tomo.shape
LIB_TOMOPY.normalize_bg.restype = dtype.as_c_void_p()
LIB_TOMOPY.normalize_bg(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dt),
dtype.as_c_int(dy),
dtype.as_c_int(dx),
dtype.as_c_int(air))
def c_vector3(tomo1, tomo2, tomo3, center1, center2, center3, recon1, recon2, recon3, theta1, theta2, theta3, axis1, axis2, axis3, **kwargs):
if len(tomo1.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo1.shape
else:
dy, dt, dx = tomo1.shape
LIB_TOMOPY.vector3.restype = dtype.as_c_void_p()
return LIB_TOMOPY.vector3(
dtype.as_c_float_p(tomo1),
dtype.as_c_float_p(tomo2),
dtype.as_c_float_p(tomo3),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center1),
dtype.as_c_float_p(center2),
dtype.as_c_float_p(center3),
dtype.as_c_float_p(theta1),
dtype.as_c_float_p(theta2),
dtype.as_c_float_p(theta3),
dtype.as_c_float_p(recon1),
dtype.as_c_float_p(recon2),
dtype.as_c_float_p(recon3),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(axis1),
dtype.as_c_int(axis2),
dtype.as_c_int(axis3))
def c_sirt(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
use_accel = 1 if kwargs['accelerated'] else 0
LIB_TOMOPY.sirt.restype = dtype.as_c_void_p()
return LIB_TOMOPY.sirt(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(use_accel),
dtype.as_c_int(kwargs['pool_size']),
dtype.as_c_char_p(kwargs['interpolation']),
dtype.as_c_char_p(kwargs['device']),
dtype.as_c_int_p(kwargs['grid_size']),
dtype.as_c_int_p(kwargs['block_size']))
def c_project3(objx, objy, objz, center, tomo, theta, axis):
# TODO: we should fix this elsewhere...
# TOMO object must be contiguous for c function to work
contiguous_tomo = np.require(tomo, requirements="AC")
if len(objx.shape) == 2:
# no y-axis (only one slice)
oy = 1
ox, oz = objx.shape
else:
oy, ox, oz = objx.shape
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.project3.restype = dtype.as_c_void_p()
LIB_TOMOPY.project3(
dtype.as_c_float_p(objx),
dtype.as_c_float_p(objy),
dtype.as_c_float_p(objz),
dtype.as_c_int(oy),
dtype.as_c_int(ox),
dtype.as_c_int(oz),
dtype.as_c_float_p(contiguous_tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_int(axis))
tomo[:] = contiguous_tomo[:]
def c_gridrec(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.gridrec.restype = dtype.as_c_void_p()
return LIB_TOMOPY.gridrec(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_char_p(kwargs['filter_name']),
dtype.as_c_float_p(kwargs['filter_par']))
def c_project(obj, center, tomo, theta):
if len(obj.shape) == 2:
# no y-axis (only one slice)
oy = 1
ox, oz = obj.shape
else:
oy, ox, oz = obj.shape
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.project.restype = dtype.as_c_void_p()
LIB_TOMOPY.project(
dtype.as_c_float_p(obj),
dtype.as_c_int(oy),
dtype.as_c_int(ox),
dtype.as_c_int(oz),
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta))
def c_osem(*args):
tomo = mproc.SHARED_TOMO
recon = mproc.SHARED_ARRAY
LIB_TOMOPY.osem.restype = dtype.as_c_void_p()
LIB_TOMOPY.osem(
dtype.as_c_float_p(tomo),
dtype.as_c_int(args[0]), # dx
dtype.as_c_int(args[1]), # dy
dtype.as_c_int(args[2]), # dz
dtype.as_c_float_p(args[3]), # center
dtype.as_c_float_p(args[4]), # theta
dtype.as_c_float_p(recon),
dtype.as_c_int(args[5]['num_gridx']),
dtype.as_c_int(args[5]['num_gridy']),
dtype.as_c_int(args[5]['num_iter']),
dtype.as_c_int(args[5]['num_block']),
dtype.as_c_float_p(args[5]['ind_block']),
dtype.as_c_int(args[6]), # istart
dtype.as_c_int(args[7])) # iend
def c_bart(*args):
tomo = mproc.SHARED_TOMO
recon = mproc.SHARED_ARRAY
LIB_TOMOPY.bart.restype = dtype.as_c_void_p()
LIB_TOMOPY.bart(
dtype.as_c_float_p(tomo),
dtype.as_c_int(args[0]), # dx
dtype.as_c_int(args[1]), # dy
dtype.as_c_int(args[2]), # dz
dtype.as_c_float_p(args[3]), # center
dtype.as_c_float_p(args[4]), # theta
dtype.as_c_float_p(recon),
dtype.as_c_int(args[5]["num_gridx"]),
dtype.as_c_int(args[5]["num_gridy"]),
dtype.as_c_int(args[5]["num_iter"]),
dtype.as_c_int(args[5]["num_block"]),
dtype.as_c_float_p(args[5]["ind_block"]),
dtype.as_c_int(args[6]), # istart
dtype.as_c_int(args[7]),
) # iend
def c_project(ox, oy, oz, theta, center, dx, dy, dz, istart, iend):
obj = mproc.SHARED_OBJ
tomo = mproc.SHARED_ARRAY
LIB_TOMOPY.project.restype = dtype.as_c_void_p()
LIB_TOMOPY.project(
dtype.as_c_float_p(obj),
dtype.as_c_int(ox),
dtype.as_c_int(oy),
dtype.as_c_int(oz),
dtype.as_c_float_p(tomo),
dtype.as_c_int(dx),
dtype.as_c_int(dy),
dtype.as_c_int(dz),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_int(istart),
dtype.as_c_int(iend))
def c_remove_stripe_sf(dx, dy, dz, size, istart, iend):
tomo = mproc.SHARED_ARRAY
LIB_TOMOPY.remove_stripe_sf.restype = dtype.as_c_void_p()
LIB_TOMOPY.remove_stripe_sf(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dx),
dtype.as_c_int(dy),
dtype.as_c_int(dz),
dtype.as_c_int(size),
dtype.as_c_int(istart),
dtype.as_c_int(iend))
def c_sample(mode, arr, dx, dy, dz, level, axis, out):
LIB_TOMOPY.sample.restype = dtype.as_c_void_p()
LIB_TOMOPY.sample(
dtype.as_c_int(mode),
dtype.as_c_float_p(arr),
dtype.as_c_int(dx),
dtype.as_c_int(dy),
dtype.as_c_int(dz),
dtype.as_c_int(level),
dtype.as_c_int(axis),
dtype.as_c_float_p(out))
return out
def c_normalize_bg(dx, dy, dz, air, istart, iend):
tomo = mproc.SHARED_ARRAY
LIB_TOMOPY.normalize_bg.restype = dtype.as_c_void_p()
LIB_TOMOPY.normalize_bg(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dx),
dtype.as_c_int(dy),
dtype.as_c_int(dz),
dtype.as_c_int(air),
dtype.as_c_int(istart),
dtype.as_c_int(iend))
def c_remove_ring(rec, *args):
istart = 0
iend = rec.shape[0]
LIB_TOMOPY.remove_ring.restype = dtype.as_c_void_p()
return LIB_TOMOPY.remove_ring(
dtype.as_c_float_p(rec),
dtype.as_c_float(args[0]), # center_x
dtype.as_c_float(args[1]), # center_y
dtype.as_c_int(args[2]), # dx
dtype.as_c_int(args[3]), # dy
dtype.as_c_int(args[4]), # dz
dtype.as_c_float(args[5]), # thresh_max
dtype.as_c_float(args[6]), # thresh_min
dtype.as_c_float(args[7]), # thresh
dtype.as_c_int(args[8]), # theta_min
dtype.as_c_int(args[9]), # rwidth
dtype.as_c_int(args[10]), # int_mode
dtype.as_c_int(istart), # istart
dtype.as_c_int(iend)) # iend
def c_remove_ring(*args):
data = mproc.SHARED_ARRAY
LIB_TOMOPY.remove_ring.restype = dtype.as_c_void_p()
LIB_TOMOPY.remove_ring(
dtype.as_c_float_p(data),
dtype.as_c_float(args[0]), # center_x
dtype.as_c_float(args[1]), # center_y
dtype.as_c_int(args[2]), # dx
dtype.as_c_int(args[3]), # dy
dtype.as_c_int(args[4]), # dz
dtype.as_c_float(args[5]), # thresh_max
dtype.as_c_float(args[6]), # thresh_min
dtype.as_c_float(args[7]), # thresh
dtype.as_c_int(args[8]), # theta_min
dtype.as_c_int(args[9]), # rwidth
dtype.as_c_int(args[10]), # istart
dtype.as_c_int(args[11])) # iend
def c_gridrec(*args):
tomo = mproc.SHARED_TOMO
recon = mproc.SHARED_ARRAY
LIB_TOMOPY.gridrec.restype = dtype.as_c_void_p()
LIB_TOMOPY.gridrec(
dtype.as_c_float_p(tomo),
dtype.as_c_int(args[0]), # dx
dtype.as_c_int(args[1]), # dy
dtype.as_c_int(args[2]), # dz
dtype.as_c_float_p(args[3]), # center
dtype.as_c_float_p(args[4]), # theta
dtype.as_c_float_p(recon),
dtype.as_c_int(args[5]['num_gridx']),
dtype.as_c_int(args[5]['num_gridy']),
dtype.as_c_char_p(args[5]['filter_name']),
dtype.as_c_int(args[6]), # istart
dtype.as_c_int(args[7])) # iend
def c_ospml_quad(args):
data=args[0]
recon=args[6]
# Call C function.
c_float_p = ctypes.POINTER(ctypes.c_float)
librecon_phi.ospml_quad.restype = ctypes.POINTER(ctypes.c_void_p)
librecon_phi.ospml_quad(data.ctypes.data_as(c_float_p),
dtype.as_c_int(args[1]), # dx
dtype.as_c_int(args[2]), # dy
dtype.as_c_int(args[3]), # dz
dtype.as_c_float_p(args[4]), # center
dtype.as_c_float_p(args[5]), # theta
recon.ctypes.data_as(c_float_p),
dtype.as_c_int(args[7]['num_gridx']),
dtype.as_c_int(args[7]['num_gridy']),
dtype.as_c_int(args[7]['num_iter']),
dtype.as_c_float_p(args[7]['reg_par']),
dtype.as_c_int(args[7]['num_block']),
dtype.as_c_float_p(args[7]['ind_block']))
return recon
def c_fbp(*args):
tomo = mproc.SHARED_TOMO
recon = mproc.SHARED_ARRAY
LIB_TOMOPY.fbp.restype = dtype.as_c_void_p()
LIB_TOMOPY.fbp(
dtype.as_c_float_p(tomo),
dtype.as_c_int(args[0]), # dx
dtype.as_c_int(args[1]), # dy
dtype.as_c_int(args[2]), # dz
dtype.as_c_float_p(args[3]), # center
dtype.as_c_float_p(args[4]), # theta
dtype.as_c_float_p(recon),
dtype.as_c_int(args[5]["num_gridx"]),
dtype.as_c_int(args[5]["num_gridy"]),
dtype.as_c_char_p(args[5]["filter_name"]),
dtype.as_c_float_p(args[5]["filter_par"]), # filter_par
dtype.as_c_int(args[6]), # istart
dtype.as_c_int(args[7]),
) # iend
def c_sirt(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.sirt.restype = dtype.as_c_void_p()
return LIB_TOMOPY.sirt(dtype.as_c_float_p(tomo), dtype.as_c_int(dy),
dtype.as_c_int(dt), dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']))
def c_vector2(tomo1, tomo2, center1, center2, recon1, recon2, recon3, theta1,
theta2, axis1, axis2, **kwargs):
if len(tomo1.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo1.shape
else:
dy, dt, dx = tomo1.shape
LIB_TOMOPY.vector2.restype = dtype.as_c_void_p()
return LIB_TOMOPY.vector2(dtype.as_c_float_p(tomo1),
dtype.as_c_float_p(tomo2), dtype.as_c_int(dy),
dtype.as_c_int(dt), dtype.as_c_int(dx),
dtype.as_c_float_p(center1),
dtype.as_c_float_p(center2),
dtype.as_c_float_p(theta1),
dtype.as_c_float_p(theta2),
dtype.as_c_float_p(recon1),
dtype.as_c_float_p(recon2),
dtype.as_c_float_p(recon3),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(axis1), dtype.as_c_int(axis2))
def c_ospml_quad(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY_RECON.ospml_quad.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.ospml_quad(dtype.as_c_float_p(tomo),
dtype.as_c_int(dy), dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_float_p(kwargs['reg_par']),
dtype.as_c_int(kwargs['num_block']),
dtype.as_c_int_p(kwargs['ind_block']))
def c_ospml_quad(args):
data = args[0]
recon = args[6]
# Call C function.
c_float_p = ctypes.POINTER(ctypes.c_float)
librecon_phi.ospml_quad.restype = ctypes.POINTER(ctypes.c_void_p)
librecon_phi.ospml_quad(
data.ctypes.data_as(c_float_p),
dtype.as_c_int(args[1]), # dx
dtype.as_c_int(args[2]), # dy
dtype.as_c_int(args[3]), # dz
dtype.as_c_float_p(args[4]), # center
dtype.as_c_float_p(args[5]), # theta
recon.ctypes.data_as(c_float_p),
dtype.as_c_int(args[7]['num_gridx']),
dtype.as_c_int(args[7]['num_gridy']),
dtype.as_c_int(args[7]['num_iter']),
dtype.as_c_float_p(args[7]['reg_par']),
dtype.as_c_int(args[7]['num_block']),
dtype.as_c_float_p(args[7]['ind_block']))
return recon
def c_remove_stripe_sf(tomo, size):
# TODO: we should fix this elsewhere...
# TOMO object must be contiguous for c function to work
contiguous_tomo = np.require(tomo, requirements="AC")
dx, dy, dz = tomo.shape
istart = 0
iend = dy
LIB_TOMOPY.remove_stripe_sf.restype = dtype.as_c_void_p()
LIB_TOMOPY.remove_stripe_sf(
dtype.as_c_float_p(contiguous_tomo),
dtype.as_c_int(dx),
dtype.as_c_int(dy),
dtype.as_c_int(dz),
dtype.as_c_int(size),
dtype.as_c_int(istart),
dtype.as_c_int(iend))
tomo[:] = contiguous_tomo[:]
def c_bart(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY_RECON.bart.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.bart(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(kwargs['num_block']),
dtype.as_c_float_p(kwargs['ind_block'])) # TODO: I think this should be int_p
def c_osem(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.osem.restype = dtype.as_c_void_p()
return LIB_TOMOPY.osem(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(kwargs['num_block']),
dtype.as_c_float_p(kwargs['ind_block'])) # TODO: should be int?
def c_sirt(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.sirt.restype = dtype.as_c_void_p()
LIB_TOMOPY.sirt(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']))
def c_project(obj, center, tomo, theta):
if len(obj.shape) == 2:
# no y-axis (only one slice)
oy = 1
ox, oz = obj.shape
else:
oy, ox, oz = obj.shape
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
LIB_TOMOPY.project.restype = dtype.as_c_void_p()
LIB_TOMOPY.project(dtype.as_c_float_p(obj), dtype.as_c_int(oy),
dtype.as_c_int(ox), dtype.as_c_int(oz),
dtype.as_c_float_p(tomo), dtype.as_c_int(dy),
dtype.as_c_int(dt), dtype.as_c_int(dx),
dtype.as_c_float_p(center), dtype.as_c_float_p(theta))
def c_sirt(tomo, center, recon, theta, **kwargs):
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
use_accel = 1 if kwargs['accelerated'] else 0
if use_accel:
return LIB_TOMOPY_ACCEL.cxx_sirt(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']),
dtype.as_c_int(kwargs['pool_size']),
dtype.as_c_char_p(kwargs['interpolation']),
dtype.as_c_char_p(kwargs['device']),
dtype.as_c_int_p(kwargs['grid_size']),
dtype.as_c_int_p(kwargs['block_size']))
else:
LIB_TOMOPY_RECON.sirt.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.sirt(
dtype.as_c_float_p(tomo),
dtype.as_c_int(dy),
dtype.as_c_int(dt),
dtype.as_c_int(dx),
dtype.as_c_float_p(center),
dtype.as_c_float_p(theta),
dtype.as_c_float_p(recon),
dtype.as_c_int(kwargs['num_gridx']),
dtype.as_c_int(kwargs['num_gridy']),
dtype.as_c_int(kwargs['num_iter']))
