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Various improvements related to the new X-ray transform implemementation. #36

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merged 9 commits into from
Nov 2, 2023
Merged

Various improvements related to the new X-ray transform implemementation. #36

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c99da97
Update notebooks from scripts
bwohlberg Aug 8, 2023
0b9c483
Merge branch 'main' into brendt/rename
bwohlberg Sep 28, 2023
e99dee9
Update notebooks
bwohlberg Sep 29, 2023
f226702
Update overview figure
bwohlberg Oct 26, 2023
2fa5340
Update notebooks
Michael-T-McCann Oct 26, 2023
f4e28eb
Remove error message
bwohlberg Oct 26, 2023
605cd76
Merge branch 'main' into brendt/rename
bwohlberg Nov 2, 2023
7dff80e
Fix merge error
bwohlberg Nov 2, 2023
23b76fd
Update notebooks
Nov 2, 2023
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4 changes: 2 additions & 2 deletions notebooks/ct_abel_tv_admm.ipynb
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Expand Up @@ -40,7 +40,7 @@
"import scico.numpy as snp\n",
"from scico import functional, linop, loss, metric, plot\n",
"from scico.examples import create_circular_phantom\n",
"from scico.linop.abel import AbelProjector\n",
"from scico.linop.abel import AbelTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.util import device_info\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -96,7 +96,7 @@
},
"outputs": [],
"source": [
"A = AbelProjector(x_gt.shape)\n",
"A = AbelTransform(x_gt.shape)\n",
"y = A @ x_gt\n",
"np.random.seed(12345)\n",
"y = y + np.random.normal(size=y.shape).astype(np.float32)"
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6 changes: 3 additions & 3 deletions notebooks/ct_abel_tv_admm_tune.ipynb
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Expand Up @@ -53,7 +53,7 @@
"import scico.numpy as snp\n",
"from scico import functional, linop, loss, metric, plot\n",
"from scico.examples import create_circular_phantom\n",
"from scico.linop.abel import AbelProjector\n",
"from scico.linop.abel import AbelTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.ray import tune\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -109,7 +109,7 @@
},
"outputs": [],
"source": [
"A = AbelProjector(x_gt.shape)\n",
"A = AbelTransform(x_gt.shape)\n",
"y = A @ x_gt\n",
"np.random.seed(12345)\n",
"y = y + np.random.normal(size=y.shape).astype(np.float32)"
Expand Down Expand Up @@ -179,7 +179,7 @@
" # Get arrays passed by tune call.\n",
" self.x_gt, self.x0, self.y = snp.array(x_gt), snp.array(x0), snp.array(y)\n",
" # Set up problem to be solved.\n",
" self.A = AbelProjector(self.x_gt.shape)\n",
" self.A = AbelTransform(self.x_gt.shape)\n",
" self.f = loss.SquaredL2Loss(y=self.y, A=self.A)\n",
" self.C = linop.FiniteDifference(input_shape=self.x_gt.shape)\n",
" self.reset_config(config)\n",
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12 changes: 5 additions & 7 deletions notebooks/ct_astra_3d_tv_admm.ipynb
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Expand Up @@ -15,9 +15,9 @@
" $$\\mathrm{argmin}_{\\mathbf{x}} \\; (1/2) \\| \\mathbf{y} - A \\mathbf{x}\n",
" \\|_2^2 + \\lambda \\| C \\mathbf{x} \\|_{2,1} \\;,$$\n",
"\n",
"where $A$ is the Radon transform, $\\mathbf{y}$ is the sinogram, $C$ is\n",
"a 3D finite difference operator, and $\\mathbf{x}$ is the desired\n",
"image."
"where $A$ is the X-ray transform (the CT forward projection operator),\n",
"$\\mathbf{y}$ is the sinogram, $C$ is a 3D finite difference operator,\n",
"and $\\mathbf{x}$ is the desired image."
]
},
{
Expand All @@ -42,7 +42,7 @@
"import scico.numpy as snp\n",
"from scico import functional, linop, loss, metric, plot\n",
"from scico.examples import create_tangle_phantom\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.util import device_info\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -79,9 +79,7 @@
"\n",
"n_projection = 10 # number of projections\n",
"angles = np.linspace(0, np.pi, n_projection) # evenly spaced projection angles\n",
"A = TomographicProjector(\n",
" tangle.shape, [1.0, 1.0], [Nz, max(Nx, Ny)], angles\n",
") # Radon transform operator\n",
"A = XRayTransform(tangle.shape, [1.0, 1.0], [Nz, max(Nx, Ny)], angles) # CT projection operator\n",
"y = A @ tangle # sinogram"
]
},
Expand Down
6 changes: 3 additions & 3 deletions notebooks/ct_astra_modl_train_foam2.ipynb
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Expand Up @@ -68,7 +68,7 @@
"from scico import metric, plot\n",
"from scico.flax.examples import load_ct_data\n",
"from scico.flax.train.traversals import clip_positive, construct_traversal\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"plot.config_notebook_plotting()"
]
},
Expand Down Expand Up @@ -175,12 +175,12 @@
"outputs": [],
"source": [
"angles = np.linspace(0, np.pi, n_projection) # evenly spaced projection angles\n",
"A = TomographicProjector(\n",
"A = XRayTransform(\n",
" input_shape=(N, N),\n",
" detector_spacing=1,\n",
" det_count=N,\n",
" angles=angles,\n",
") # Radon transform operator\n",
") # CT projection operator\n",
"A = (1.0 / N) * A # normalized"
]
},
Expand Down
8 changes: 4 additions & 4 deletions notebooks/ct_astra_noreg_pcg.ipynb
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Expand Up @@ -15,8 +15,8 @@
" $$\\mathrm{argmin}_{\\mathbf{x}} \\; (1/2) \\| \\mathbf{y} - A \\mathbf{x}\n",
" \\|_2^2 \\;,$$\n",
"\n",
"where $A$ is the Radon transform, $\\mathbf{y}$ is the sinogram, and\n",
"$\\mathbf{x}$ is the reconstructed image."
"where $A$ is the X-ray transform (the CT forward projection operator),\n",
"$\\mathbf{y}$ is the sinogram, and $\\mathbf{x}$ is the reconstructed image."
]
},
{
Expand Down Expand Up @@ -44,7 +44,7 @@
"\n",
"from scico import loss, plot\n",
"from scico.linop import CircularConvolve\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"from scico.solver import cg\n",
"plot.config_notebook_plotting()"
]
Expand Down Expand Up @@ -102,7 +102,7 @@
"source": [
"n_projection = N # matches the phantom size so this is not few-view CT\n",
"angles = np.linspace(0, np.pi, n_projection) # evenly spaced projection angles\n",
"A = 1 / N * TomographicProjector(x_gt.shape, 1, N, angles) # Radon transform operator\n",
"A = 1 / N * XRayTransform(x_gt.shape, 1, N, angles) # CT projection operator\n",
"y = A @ x_gt # sinogram"
]
},
Expand Down
6 changes: 3 additions & 3 deletions notebooks/ct_astra_odp_train_foam2.ipynb
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Expand Up @@ -72,7 +72,7 @@
"from scico import metric, plot\n",
"from scico.flax.examples import load_ct_data\n",
"from scico.flax.train.traversals import clip_positive, construct_traversal\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"plot.config_notebook_plotting()"
]
},
Expand Down Expand Up @@ -179,12 +179,12 @@
"outputs": [],
"source": [
"angles = np.linspace(0, np.pi, n_projection) # evenly spaced projection angles\n",
"A = TomographicProjector(\n",
"A = XRayTransform(\n",
" input_shape=(N, N),\n",
" detector_spacing=1,\n",
" det_count=N,\n",
" angles=angles,\n",
") # Radon transform operator\n",
") # CT projection operator\n",
"A = (1.0 / N) * A # normalized"
]
},
Expand Down
10 changes: 5 additions & 5 deletions notebooks/ct_astra_tv_admm.ipynb
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Expand Up @@ -14,9 +14,9 @@
" $$\\mathrm{argmin}_{\\mathbf{x}} \\; (1/2) \\| \\mathbf{y} - A \\mathbf{x}\n",
" \\|_2^2 + \\lambda \\| C \\mathbf{x} \\|_{2,1} \\;,$$\n",
"\n",
"where $A$ is the Radon transform, $\\mathbf{y}$ is the sinogram, $C$ is\n",
"a 2D finite difference operator, and $\\mathbf{x}$ is the desired\n",
"image."
"where $A$ is the X-ray transform (the CT forward projection operator),\n",
"$\\mathbf{y}$ is the sinogram, $C$ is a 2D finite difference operator, and\n",
"$\\mathbf{x}$ is the desired image."
]
},
{
Expand All @@ -41,7 +41,7 @@
"\n",
"import scico.numpy as snp\n",
"from scico import functional, linop, loss, metric, plot\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.util import device_info\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -101,7 +101,7 @@
"source": [
"n_projection = 45 # number of projections\n",
"angles = np.linspace(0, np.pi, n_projection) # evenly spaced projection angles\n",
"A = TomographicProjector(x_gt.shape, 1, N, angles) # Radon transform operator\n",
"A = XRayTransform(x_gt.shape, 1, N, angles) # CT projection operator\n",
"y = A @ x_gt # sinogram"
]
},
Expand Down
14 changes: 7 additions & 7 deletions notebooks/ct_astra_weighted_tv_admm.ipynb
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Expand Up @@ -14,11 +14,11 @@
" $$\\mathrm{argmin}_{\\mathbf{x}} \\; (1/2) \\| \\mathbf{y} - A \\mathbf{x}\n",
" \\|_W^2 + \\lambda \\| C \\mathbf{x} \\|_{2,1} \\;,$$\n",
"\n",
"where $A$ is the Radon transform, $\\mathbf{y}$ is the sinogram, the norm\n",
"weighting $W$ is chosen so that the weighted norm is an approximation to\n",
"the Poisson negative log likelihood <cite data-cite=\"sauer-1993-local\"/>, $C$ is\n",
"a 2D finite difference operator, and $\\mathbf{x}$ is the desired\n",
"image."
"where $A$ is the X-ray transform (the CT forward projection),\n",
"$\\mathbf{y}$ is the sinogram, the norm weighting $W$ is chosen so that\n",
"the weighted norm is an approximation to the Poisson negative log\n",
"likelihood <cite data-cite=\"sauer-1993-local\"/>, $C$ is a 2D finite difference\n",
"operator, and $\\mathbf{x}$ is the desired image."
]
},
{
Expand All @@ -42,7 +42,7 @@
"\n",
"import scico.numpy as snp\n",
"from scico import functional, linop, loss, metric, plot\n",
"from scico.linop.radon_astra import TomographicProjector\n",
"from scico.linop.xray.astra import XRayTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.util import device_info\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -108,7 +108,7 @@
"𝛼 = 1e-2 # attenuation coefficient\n",
"\n",
"angles = np.linspace(0, 2 * np.pi, n_projection) # evenly spaced projection angles\n",
"A = TomographicProjector(x_gt.shape, 1.0, N, angles) # Radon transform operator\n",
"A = XRayTransform(x_gt.shape, 1.0, N, angles) # CT projection operator\n",
"y_c = A @ x_gt # sinogram"
]
},
Expand Down
6 changes: 3 additions & 3 deletions notebooks/ct_fan_svmbir_ppp_bm3d_admm_prox.ipynb
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Expand Up @@ -50,7 +50,7 @@
"from scico import metric, plot\n",
"from scico.functional import BM3D\n",
"from scico.linop import Diagonal, Identity\n",
"from scico.linop.radon_svmbir import SVMBIRExtendedLoss, TomographicProjector\n",
"from scico.linop.xray.svmbir import SVMBIRExtendedLoss, XRayTransform\n",
"from scico.optimize.admm import ADMM, LinearSubproblemSolver\n",
"from scico.util import device_info\n",
"plot.config_notebook_plotting()"
Expand Down Expand Up @@ -122,15 +122,15 @@
"\n",
"dist_source_detector = 1500.0\n",
"magnification = 1.2\n",
"A_fan = TomographicProjector(\n",
"A_fan = XRayTransform(\n",
" x_gt.shape,\n",
" angles,\n",
" num_channels,\n",
" geometry=\"fan-curved\",\n",
" dist_source_detector=dist_source_detector,\n",
" magnification=magnification,\n",
")\n",
"A_parallel = TomographicProjector(\n",
"A_parallel = XRayTransform(\n",
" x_gt.shape,\n",
" angles,\n",
" num_channels,\n",
Expand Down
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