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Pass COR and tilt to CIL reconstruction #1051

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merged 4 commits into from
Jul 21, 2021
Merged

Pass COR and tilt to CIL reconstruction #1051

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eca5bc3
Pass COR and tilt to CIL reconstruction
samtygier-stfc Jul 13, 2021
04524dc
Merge branch 'master' into 1042_cil_cor
DolicaAkelloEgwel Jul 15, 2021
ed2d0ca
Merge branch 'master' into 1042_cil_cor
DolicaAkelloEgwel Jul 16, 2021
1cbbb6b
Merge branch 'master' into 1042_cil_cor
DolicaAkelloEgwel Jul 21, 2021
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39 changes: 18 additions & 21 deletions mantidimaging/core/reconstruct/cil_recon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,25 +29,6 @@


class CILRecon(BaseRecon):
@staticmethod
def get_IMAT_AcquisitionGeometry(angles, shape):
pixel_size = (1., 1.)
if len(shape) == 3:
# shape of full data [angles, v_pixels, h_pixels]
ag = AcquisitionGeometry.create_Parallel3D()
pixel_num_h, pixel_num_v = shape[2], shape[1]
ag.set_panel([pixel_num_h, pixel_num_v], pixel_size=pixel_size)
elif len(shape) == 2:
# shape of sinogram is [angles, h_pixels]
ag = AcquisitionGeometry.create_Parallel2D()
pixel_num_h = shape[1]
ag.set_panel(pixel_num_h, pixel_size=pixel_size)
else:
raise ValueError("Shape should have 2 or 3 dimensions")

ag.set_angles(angles=angles, angle_unit='radian')
return ag

@staticmethod
def set_up_TV_regularisation(image_geometry, acquisition_data):
# Forward operator
Expand Down Expand Up @@ -87,9 +68,15 @@ def single_sino(sino: np.ndarray, cor: ScalarCoR, proj_angles: ProjectionAngles,
Should return a numpy array,
"""
sino = BaseRecon.negative_log(sino)
pixel_num_h = sino.shape[1]
pixel_size = 1.
rot_pos_x = (cor.value - pixel_num_h / 2) * pixel_size
ag = AcquisitionGeometry.create_Parallel2D(rotation_axis_position=[rot_pos_x, 0])

ag = CILRecon.get_IMAT_AcquisitionGeometry(proj_angles.value, sino.shape)
ag.set_panel(pixel_num_h, pixel_size=pixel_size)
ag.set_labels(DataOrder.ASTRA_AG_LABELS)
ag.set_angles(angles=proj_angles.value, angle_unit='radian')

# stick it into an AcquisitionData
data = ag.allocate(None)
data.fill(sino)
Expand Down Expand Up @@ -129,7 +116,17 @@ def full(images: Images, cors: List[ScalarCoR], recon_params: ReconstructionPara

angles = images.projection_angles(recon_params.max_projection_angle).value
shape = images.data.shape
ag = CILRecon.get_IMAT_AcquisitionGeometry(angles, shape)
pixel_num_h, pixel_num_v = shape[2], shape[1]
pixel_size = 1.
if recon_params.tilt is None:
raise ValueError("recon_params.tilt is not set")
rot_pos = [(cors[pixel_num_v // 2].value - pixel_num_h / 2) * pixel_size, 0, 0]
slope = -np.tan(np.deg2rad(recon_params.tilt.value))
rot_angle = [slope, 0, 1]

ag = AcquisitionGeometry.create_Parallel3D(rotation_axis_position=rot_pos, rotation_axis_direction=rot_angle)
ag.set_panel([pixel_num_h, pixel_num_v], pixel_size=(pixel_size, pixel_size))
ag.set_angles(angles=angles, angle_unit='radian')
ag.set_labels(DataOrder.TIGRE_AG_LABELS)

# stick it into an AcquisitionData
Expand Down