source/tomopy/util/extern/recon.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
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"""
Module for recon library wrappers.
"""
import numpy as np
import tomopy.util.dtype as dtype
from . import c_shared_lib
from .accel import c_accel_mlem
from .accel import c_accel_sirt
__author__ = "Doga Gursoy"
__copyright__ = "Copyright (c) 2015, UChicago Argonne, LLC."
__docformat__ = 'restructuredtext en'
__all__ = ['c_project',
'c_project2',
'c_project3',
'c_art',
'c_bart',
'c_fbp',
'c_mlem',
'c_osem',
'c_ospml_hybrid',
'c_ospml_quad',
'c_pml_hybrid',
'c_pml_quad',
'c_sirt',
'c_tv',
'c_grad',
'c_tikh',
'c_vector',
'c_vector2',
'c_vector3']
LIB_TOMOPY_RECON = c_shared_lib("tomo-recon")
def c_project(obj, center, tomo, theta):
# 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(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_RECON.project.restype = dtype.as_c_void_p()
LIB_TOMOPY_RECON.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(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))
tomo[:] = contiguous_tomo[:]
def c_project2(objx, objy, center, tomo, theta):
# 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_RECON.project2.restype = dtype.as_c_void_p()
LIB_TOMOPY_RECON.project2(
dtype.as_c_float_p(objx),
dtype.as_c_float_p(objy),
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))
tomo[:] = contiguous_tomo[:]
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_RECON.project3.restype = dtype.as_c_void_p()
LIB_TOMOPY_RECON.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_art(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.art.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.art(
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_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_int_p(kwargs['ind_block']))
def c_fbp(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.fbp.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.fbp(
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'])) # filter_par
def c_mlem(tomo, center, recon, theta, **kwargs):
if kwargs['accelerated']:
return c_accel_mlem(tomo, center, recon, theta, **kwargs)
else:
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
kwargs['ind_block'] = np.arange(1, dtype='int32')
kwargs['num_block'] = 1
LIB_TOMOPY_RECON.osem.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.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_int_p(kwargs['ind_block']),
)
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_RECON.osem.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.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_int_p(kwargs['ind_block']))
def c_ospml_hybrid(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_hybrid.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.ospml_hybrid(
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(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_pml_hybrid(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
kwargs['ind_block'] = np.arange(1, dtype='int32')
kwargs['num_block'] = 1
LIB_TOMOPY_RECON.ospml_hybrid.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.ospml_hybrid(
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_pml_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
kwargs['ind_block'] = np.arange(1, dtype='int32')
kwargs['num_block'] = 1
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_sirt(tomo, center, recon, theta, **kwargs):
if kwargs['accelerated']:
return c_accel_sirt(tomo, center, recon, theta, **kwargs)
else:
if len(tomo.shape) == 2:
# no y-axis (only one slice)
dy = 1
dt, dx = tomo.shape
else:
dy, dt, dx = tomo.shape
kwargs['ind_block'] = np.arange(1, dtype='int32')
kwargs['num_block'] = 1
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_int_p(kwargs['ind_block']))
def c_tv(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.tv.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.tv(
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']))
def c_grad(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.grad.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.grad(
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']))
def c_tikh(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.tikh.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.tikh(
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_data']),
dtype.as_c_float_p(kwargs['reg_par']))
def c_vector(tomo, center, recon1, recon2, 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.vector.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.vector(
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(recon1),
dtype.as_c_float_p(recon2),
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_RECON.vector2.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.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_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_RECON.vector3.restype = dtype.as_c_void_p()
return LIB_TOMOPY_RECON.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))