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WIP: add coords arg to geom->vec converters
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@kohr-h
kohr-h committed Sep 10, 2018
1 parent 7f560e8 commit 8d211d6
Showing 1 changed file with 58 additions and 12 deletions.
70 changes: 58 additions & 12 deletions odl/tomo/backends/astra_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,7 @@ def astra_projection_geometry(geometry):
geometry.ndim == 2):
det_count = geometry.detector.size
if astra_supports('par2d_vec_geometry'):
vecs = parallel_2d_geom_to_astra_vecs(geometry)
vecs = parallel_2d_geom_to_astra_vecs(geometry, coords='ASTRA')
proj_geom = astra.create_proj_geom('parallel_vec', det_count, vecs)
else:
det_width = geometry.det_partition.cell_sides[0]
Expand All @@ -288,7 +288,7 @@ def astra_projection_geometry(geometry):
isinstance(geometry.detector, (Flat1dDetector, Flat2dDetector)) and
geometry.ndim == 2):
det_count = geometry.detector.size
vecs = cone_2d_geom_to_astra_vecs(geometry)
vecs = cone_2d_geom_to_astra_vecs(geometry, coords='ASTRA')
proj_geom = astra.create_proj_geom('fanflat_vec', det_count, vecs)

# Cone 2D vec
Expand All @@ -304,7 +304,7 @@ def astra_projection_geometry(geometry):
# Swap detector axes (see `parallel_3d_geom_to_astra_vecs`)
det_row_count = geometry.det_partition.shape[0]
det_col_count = geometry.det_partition.shape[1]
vecs = parallel_3d_geom_to_astra_vecs(geometry)
vecs = parallel_3d_geom_to_astra_vecs(geometry, coords='ASTRA')
proj_geom = astra.create_proj_geom(
'parallel3d_vec', det_row_count, det_col_count, vecs)

Expand All @@ -323,7 +323,7 @@ def astra_projection_geometry(geometry):
# Swap detector axes (see `conebeam_3d_geom_to_astra_vecs`)
det_row_count = geometry.det_partition.shape[0]
det_col_count = geometry.det_partition.shape[1]
vecs = cone_3d_geom_to_astra_vecs(geometry)
vecs = cone_3d_geom_to_astra_vecs(geometry, coords='ASTRA')
proj_geom = astra.create_proj_geom(
'cone_vec', det_row_count, det_col_count, vecs)

Expand Down Expand Up @@ -466,7 +466,7 @@ def vecs_astra_to_odl_coords(vecs):
'array with shape {}'.format(vecs.shape))


def parallel_2d_geom_to_astra_vecs(geometry):
def parallel_2d_geom_to_astra_vecs(geometry, coords='ODL'):
"""Create vectors for ASTRA projection geometries from an ODL geometry.
The 2D vectors are used to create an ASTRA projection geometry for
Expand All @@ -491,18 +491,29 @@ def parallel_2d_geom_to_astra_vecs(geometry):
Parameters
----------
geometry : `Geometry`
ODL projection geometry from which to create the ASTRA geometry.
ODL projection geometry from which to create the ASTRA vectors.
coords : {'ODL', 'ASTRA'}, optional
Coordinate system in which the resulting vectors should be
represented.
Returns
-------
vectors : `numpy.ndarray`
Array of shape ``(num_angles, 6)`` containing the vectors.
See Also
--------
vecs_odl_to_astra_coords : Conversion to ASTRA coordinates
References
----------
.. _ASTRA projection geometry documentation:
http://www.astra-toolbox.com/docs/geom2d.html#projection-geometries
"""
coords, coords_in = str(coords).upper(), coords
if coords not in ('ODL', 'ASTRA'):
raise ValueError('`coords` {!r} not understood'.format(coords_in))

angles = geometry.angles
mid_pt = geometry.det_params.mid_pt
vectors = np.zeros((angles.size, 6))
Expand All @@ -519,10 +530,13 @@ def parallel_2d_geom_to_astra_vecs(geometry):
px_size = geometry.det_partition.cell_sides[0]
vectors[:, 4:6] = det_axis * px_size

return vecs_odl_to_astra_coords(vectors)
if coords == 'ASTRA':
vectors = vecs_odl_to_astra_coords(vectors)

return vectors


def parallel_3d_geom_to_astra_vecs(geometry):
def parallel_3d_geom_to_astra_vecs(geometry, coords='ODL'):
"""Create vectors for ASTRA projection geometries from an ODL geometry.
The 3D vectors are used to create an ASTRA projection geometry for
Expand All @@ -548,7 +562,10 @@ def parallel_3d_geom_to_astra_vecs(geometry):
Parameters
----------
geometry : `Geometry`
ODL projection geometry from which to create the ASTRA geometry.
ODL projection geometry from which to create the ASTRA vectors.
coords : {'ODL', 'ASTRA'}, optional
Coordinate system in which the resulting vectors should be
represented.
Returns
-------
Expand All @@ -560,6 +577,12 @@ def parallel_3d_geom_to_astra_vecs(geometry):
.. _ASTRA projection geometry documentation:
http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
"""
coords, coords_in = str(coords).upper(), coords
if coords not in ('ODL', 'ASTRA'):
raise ValueError('`coords` {!r} not understood'.format(coords_in))

# TODO: use `coords`

angles = geometry.angles
mid_pt = geometry.det_params.mid_pt

Expand All @@ -582,13 +605,15 @@ def parallel_3d_geom_to_astra_vecs(geometry):
# Instead we swap `u` and `v`, resulting in the effective ASTRA result
# `(u, theta, v)`. Here we only need to swap axes 0 and 1, which
# keeps at least contiguous blocks in `v`.
#
# TODO: this swapping should not happen in this function!
vectors[:, 9:12] = det_axes[0] * px_sizes[0]
vectors[:, 6:9] = det_axes[1] * px_sizes[1]

return vecs_odl_to_astra_coords(vectors)


def cone_2d_geom_to_astra_vecs(geometry):
def cone_2d_geom_to_astra_vecs(geometry, coords='ODL'):
"""Create vectors for ASTRA projection geometries from an ODL geometry.
The 2D vectors are used to create an ASTRA projection geometry for
Expand All @@ -614,6 +639,9 @@ def cone_2d_geom_to_astra_vecs(geometry):
----------
geometry : `Geometry`
ODL projection geometry from which to create the ASTRA vectors.
coords : {'ODL', 'ASTRA'}, optional
Coordinate system in which the resulting vectors should be
represented.
Returns
-------
Expand All @@ -625,6 +653,10 @@ def cone_2d_geom_to_astra_vecs(geometry):
.. _ASTRA projection geometry documentation:
http://www.astra-toolbox.com/docs/geom2d.html#projection-geometries
"""
coords, coords_in = str(coords).upper(), coords
if coords not in ('ODL', 'ASTRA'):
raise ValueError('`coords` {!r} not understood'.format(coords_in))

angles = geometry.angles
mid_pt = geometry.det_params.mid_pt
vectors = np.zeros((angles.size, 6))
Expand All @@ -641,10 +673,13 @@ def cone_2d_geom_to_astra_vecs(geometry):
px_size = geometry.det_partition.cell_sides[0]
vectors[:, 4:6] = det_axis * px_size

return vecs_odl_to_astra_coords(vectors)
if coords == 'ASTRA':
vectors = vecs_odl_to_astra_coords(vectors)

return vectors

def cone_3d_geom_to_astra_vecs(geometry):

def cone_3d_geom_to_astra_vecs(geometry, coords='ODL'):
"""Create vectors for ASTRA projection geometries from an ODL geometry.
The 3D vectors are used to create an ASTRA projection geometry for
Expand All @@ -671,6 +706,9 @@ def cone_3d_geom_to_astra_vecs(geometry):
----------
geometry : `Geometry`
ODL projection geometry from which to create the ASTRA vectors.
coords : {'ODL', 'ASTRA'}, optional
Coordinate system in which the resulting vectors should be
represented.
Returns
-------
Expand All @@ -682,6 +720,12 @@ def cone_3d_geom_to_astra_vecs(geometry):
.. _ASTRA projection geometry documentation:
http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
"""
coords, coords_in = str(coords).upper(), coords
if coords not in ('ODL', 'ASTRA'):
raise ValueError('`coords` {!r} not understood'.format(coords_in))

# TODO: use `coords`

angles = geometry.angles
mid_pt = geometry.det_params.mid_pt
vectors = np.zeros((angles.size, 12))
Expand All @@ -703,6 +747,8 @@ def cone_3d_geom_to_astra_vecs(geometry):
# Instead we swap `u` and `v`, resulting in the effective ASTRA result
# `(u, theta, v)`. Here we only need to swap axes 0 and 1, which
# keeps at least contiguous blocks in `v`.
#
# TODO: this swapping should not happen in this function!
vectors[:, 9:12] = det_axes[0] * px_sizes[0]
vectors[:, 6:9] = det_axes[1] * px_sizes[1]

Expand Down

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