def skimage_radon_forward_projector(volume, geometry, proj_space, out=None):
"""Calculate forward projection using skimage.
Parameters
----------
volume : `DiscretizedSpaceElement`
The volume to project.
geometry : `Geometry`
The projection geometry to use.
proj_space : `DiscretizedSpace`
Space in which the projections (sinograms) live.
out : ``proj_space`` element, optional
Element to which the result should be written.
Returns
-------
sinogram : ``proj_space`` element
Result of the forward projection. If ``out`` was given, the returned
object is a reference to it.
"""
# Lazy import due to significant import time
from skimage.transform import radon
# Check basic requirements. Fully checking should be in wrapper
assert volume.shape[0] == volume.shape[1]
theta = np.degrees(geometry.angles)
skimage_range = skimage_proj_space(geometry, volume.space, proj_space)
# Rotate volume from (x, y) to (rows, cols), then project
sino_arr = radon(
np.rot90(volume.asarray(), 1), theta=theta, circle=False
)
sinogram = skimage_range.element(sino_arr.T)
if out is None:
out = proj_space.element()
with writable_array(out) as out_arr:
point_collocation(
clamped_interpolation(skimage_range, sinogram),
proj_space.grid.meshgrid,
out=out_arr,
)
scale = volume.space.cell_sides[0]
out *= scale
return out
def astra_cuda_forward_projector(vol_data, geometry, proj_space, out=None):
"""Run an ASTRA forward projection on the given data using the GPU.
Parameters
----------
vol_data : `DiscreteLpElement`
Volume data to which the projector is applied
geometry : `Geometry`
Geometry defining the tomographic setup
proj_space : `DiscreteLp`
Space to which the calling operator maps
out : ``proj_space`` element, optional
Element of the projection space to which the result is written. If
``None``, an element in ``proj_space`` is created.
Returns
-------
out : ``proj_space`` element
Projection data resulting from the application of the projector.
If ``out`` was provided, the returned object is a reference to it.
"""
if not isinstance(vol_data, DiscreteLpElement):
raise TypeError('volume data {!r} is not a DiscreteLpElement '
'instance'.format(vol_data))
if not isinstance(geometry, Geometry):
raise TypeError('geometry {!r} is not a Geometry instance'
''.format(geometry))
if vol_data.ndim != geometry.ndim:
raise ValueError('dimensions {} of volume data and {} of geometry '
'do not match'
''.format(vol_data.ndim, geometry.ndim))
if not isinstance(proj_space, DiscreteLp):
raise TypeError('projection space {!r} is not a DiscreteLp '
'instance'.format(proj_space))
if out is not None:
if not isinstance(out, DiscreteLpElement):
raise TypeError('`out` {} is neither None nor a '
'DiscreteLpElement instance'.format(out))
ndim = vol_data.ndim
# Create astra geometries
vol_geom = astra_volume_geometry(vol_data.space)
proj_geom = astra_projection_geometry(geometry)
# Create ASTRA data structures
# In the case dim == 3, we need to swap axes, so can't perform the FP
# in-place
vol_id = astra_data(vol_geom, datatype='volume', data=vol_data,
allow_copy=True)
# Create projector
proj_id = astra_projector('nearest', vol_geom, proj_geom, ndim,
impl='cuda')
if ndim == 2:
if out is None:
out = proj_space.element()
# Wrap the array in correct dtype etc if needed
with writable_array(out, dtype='float32', order='C') as arr:
sino_id = astra_data(proj_geom, datatype='projection', data=arr)
# Create algorithm
algo_id = astra_algorithm('forward', ndim, vol_id, sino_id,
proj_id=proj_id, impl='cuda')
# Run algorithm
astra.algorithm.run(algo_id)
elif ndim == 3:
sino_id = astra_data(proj_geom, datatype='projection',
ndim=proj_space.ndim)
# Create algorithm
algo_id = astra_algorithm('forward', ndim, vol_id, sino_id,
proj_id=proj_id, impl='cuda')
# Run algorithm
astra.algorithm.run(algo_id)
if out is None:
out = proj_space.element(np.rollaxis(astra.data3d.get(sino_id),
0, 3))
else:
out[:] = np.rollaxis(astra.data3d.get(sino_id), 0, 3)
else:
raise RuntimeError('unknown ndim')
# Fix inconsistent scaling
if isinstance(geometry, Parallel2dGeometry):
# parallel2d scales with pixel stride
out *= 1 / float(geometry.det_partition.cell_sides[0])
# Delete ASTRA objects
astra.algorithm.delete(algo_id)
if ndim == 2:
astra.data2d.delete((vol_id, sino_id))
astra.projector.delete(proj_id)
else:
astra.data3d.delete((vol_id, sino_id))
astra.projector3d.delete(proj_id)
return out
def skimage_radon_back_projector(sinogram, geometry, vol_space, out=None):
"""Calculate forward projection using skimage.
Parameters
----------
sinogram : `DiscretizedSpaceElement`
Sinogram (projections) to backproject.
geometry : `Geometry`
The projection geometry to use.
vol_space : `DiscretizedSpace`
Space in which reconstructed volumes live.
out : ``vol_space`` element, optional
An element to which the result should be written.
Returns
-------
volume : ``vol_space`` element
Result of the back-projection. If ``out`` was given, the returned
object is a reference to it.
"""
# Lazy import due to significant import time
from skimage.transform import iradon
theta = np.degrees(geometry.angles)
skimage_range = skimage_proj_space(geometry, vol_space, sinogram.space)
skimage_sinogram = skimage_range.element()
with writable_array(skimage_sinogram) as sino_arr:
point_collocation(
clamped_interpolation(sinogram.space, sinogram),
skimage_range.grid.meshgrid,
out=sino_arr,
)
if out is None:
out = vol_space.element()
else:
# Only do asserts here since these are backend functions
assert out in vol_space
# Rotate back from (rows, cols) to (x, y), then back-project (no filter)
backproj = iradon(
skimage_sinogram.asarray().T,
theta,
output_size=vol_space.shape[0],
filter=None,
circle=False,
)
out[:] = np.rot90(backproj, -1)
# Empirically determined value, gives correct scaling
scaling_factor = 4 * geometry.motion_params.length / (2 * np.pi)
# Correct in case of non-weighted spaces
proj_volume = np.prod(sinogram.space.partition.extent)
proj_size = sinogram.space.partition.size
proj_weighting = proj_volume / proj_size
scaling_factor *= sinogram.space.weighting.const / proj_weighting
scaling_factor /= vol_space.weighting.const / vol_space.cell_volume
# Correctly scale the output
out *= scaling_factor
return out
def astra_cuda_back_projector(proj_data, geometry, reco_space, out=None):
"""Run an ASTRA backward projection on the given data using the GPU.
Parameters
----------
proj_data : `DiscreteLp` element
Projection data to which the backward projector is applied
geometry : `Geometry`
Geometry defining the tomographic setup
reco_space : `DiscreteLp`
Space to which the calling operator maps
out : ``reco_space`` element, optional
Element of the reconstruction space to which the result is written.
If ``None``, an element in ``reco_space`` is created.
Returns
-------
out : ``reco_space`` element
Reconstruction data resulting from the application of the backward
projector. If ``out`` was provided, the returned object is a
reference to it.
"""
if not isinstance(proj_data, DiscreteLpElement):
raise TypeError('projection data {!r} is not a DiscreteLpElement '
'instance'.format(proj_data))
if not isinstance(geometry, Geometry):
raise TypeError('geometry {!r} is not a Geometry instance'
''.format(geometry))
if not isinstance(reco_space, DiscreteLp):
raise TypeError('reconstruction space {!r} is not a DiscreteLp '
'instance'.format(reco_space))
if reco_space.ndim != geometry.ndim:
raise ValueError('dimensions {} of reconstruction space and {} of '
'geometry do not match'.format(reco_space.ndim,
geometry.ndim))
if out is not None:
if not isinstance(out, DiscreteLpElement):
raise TypeError('`out` {} is neither None nor a '
'DiscreteLpElement instance'.format(out))
ndim = proj_data.ndim
# Create geometries
vol_geom = astra_volume_geometry(reco_space)
proj_geom = astra_projection_geometry(geometry)
if ndim == 2:
swapped_proj_data = proj_data
else:
swapped_proj_data = np.ascontiguousarray(
np.rollaxis(proj_data.asarray(), 2, 0))
sino_id = astra_data(proj_geom, datatype='projection',
data=swapped_proj_data, allow_copy=True)
# Create projector
proj_id = astra_projector('nearest', vol_geom, proj_geom, ndim,
impl='cuda')
# Reconstruction volume
if out is None:
out = reco_space.element()
# Wrap the array in correct dtype etc if needed
with writable_array(out, dtype='float32', order='C') as arr:
vol_id = astra_data(vol_geom, datatype='volume', data=arr,
ndim=reco_space.ndim)
# Create algorithm
algo_id = astra_algorithm('backward', ndim, vol_id, sino_id,
proj_id=proj_id, impl='cuda')
# Run algorithm
astra.algorithm.run(algo_id)
out *= astra_cuda_bp_scaling_factor(reco_space, geometry)
# Delete ASTRA objects
astra.algorithm.delete(algo_id)
if ndim == 2:
astra.data2d.delete((vol_id, sino_id))
astra.projector.delete(proj_id)
else:
astra.data3d.delete((vol_id, sino_id))
astra.projector3d.delete(proj_id)
return out