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Clean up some example scripts and rerun some notebooks #464

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Nov 9, 2023
Merged

Clean up some example scripts and rerun some notebooks #464

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c106b58
Clean up example script
bwohlberg Nov 7, 2023
1d5fc8b
Revert unintentional changes
bwohlberg Nov 7, 2023
a8cb2ff
Update submodule
bwohlberg Nov 7, 2023
000a2f7
Bump max jaxlib/jax version
bwohlberg Nov 7, 2023
b80e069
Remove device_put from new example scripts
bwohlberg Nov 7, 2023
5cb88d5
Update examples index
bwohlberg Nov 8, 2023
ebd9157
Update submodule
bwohlberg Nov 8, 2023
6882ddf
Update submodule
Nov 8, 2023
3a66ad2
Update submodule
bwohlberg Nov 9, 2023
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2 changes: 1 addition & 1 deletion data
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Submodule data updated 5 files
+6 −3 notebooks/ct_astra_tv_admm.ipynb
+126 −129 notebooks/ct_multi_cs_tv_admm.ipynb
+118 −121 notebooks/ct_multi_tv_admm.ipynb
+371 −0 notebooks/ct_tv_admm.ipynb
+13 −7 notebooks/index.ipynb
3 changes: 3 additions & 0 deletions docs/source/examples.rst
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Expand Up @@ -27,6 +27,7 @@ Computed Tomography
examples/ct_astra_noreg_pcg
examples/ct_astra_3d_tv_admm
examples/ct_astra_tv_admm
examples/ct_tv_admm
examples/ct_astra_weighted_tv_admm
examples/ct_svmbir_tv_multi
examples/ct_svmbir_ppp_bm3d_admm_cg
Expand Down Expand Up @@ -129,6 +130,7 @@ Total Variation
examples/ct_abel_tv_admm
examples/ct_abel_tv_admm_tune
examples/ct_astra_tv_admm
examples/ct_tv_admm
examples/ct_astra_3d_tv_admm
examples/ct_astra_weighted_tv_admm
examples/ct_svmbir_tv_multi
Expand Down Expand Up @@ -197,6 +199,7 @@ ADMM
examples/ct_abel_tv_admm
examples/ct_abel_tv_admm_tune
examples/ct_astra_tv_admm
examples/ct_tv_admm
examples/ct_astra_3d_tv_admm
examples/ct_astra_weighted_tv_admm
examples/ct_svmbir_tv_multi
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12 changes: 9 additions & 3 deletions examples/scripts/README.rst
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Expand Up @@ -18,7 +18,9 @@ Computed Tomography
`ct_astra_3d_tv_admm.py <ct_astra_3d_tv_admm.py>`_
3D TV-Regularized Sparse-View CT Reconstruction
`ct_astra_tv_admm.py <ct_astra_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction
TV-Regularized Sparse-View CT Reconstruction (ASTRA Projector)
`ct_tv_admm.py <ct_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction (Integrated Projector)
`ct_astra_weighted_tv_admm.py <ct_astra_weighted_tv_admm.py>`_
TV-Regularized Low-Dose CT Reconstruction
`ct_svmbir_tv_multi.py <ct_svmbir_tv_multi.py>`_
Expand Down Expand Up @@ -159,7 +161,9 @@ Total Variation
`ct_abel_tv_admm_tune.py <ct_abel_tv_admm_tune.py>`_
Parameter Tuning for TV-Regularized Abel Inversion
`ct_astra_tv_admm.py <ct_astra_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction
TV-Regularized Sparse-View CT Reconstruction (ASTRA Projector)
`ct_tv_admm.py <ct_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction (Integrated Projector)
`ct_astra_3d_tv_admm.py <ct_astra_3d_tv_admm.py>`_
3D TV-Regularized Sparse-View CT Reconstruction
`ct_astra_weighted_tv_admm.py <ct_astra_weighted_tv_admm.py>`_
Expand Down Expand Up @@ -252,7 +256,9 @@ ADMM
`ct_abel_tv_admm_tune.py <ct_abel_tv_admm_tune.py>`_
Parameter Tuning for TV-Regularized Abel Inversion
`ct_astra_tv_admm.py <ct_astra_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction
TV-Regularized Sparse-View CT Reconstruction (ASTRA Projector)
`ct_tv_admm.py <ct_tv_admm.py>`_
TV-Regularized Sparse-View CT Reconstruction (Integrated Projector)
`ct_astra_3d_tv_admm.py <ct_astra_3d_tv_admm.py>`_
3D TV-Regularized Sparse-View CT Reconstruction
`ct_astra_weighted_tv_admm.py <ct_astra_weighted_tv_admm.py>`_
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9 changes: 6 additions & 3 deletions examples/scripts/ct_astra_tv_admm.py
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Expand Up @@ -5,8 +5,8 @@
# with the package.

r"""
TV-Regularized Sparse-View CT Reconstruction
============================================
TV-Regularized Sparse-View CT Reconstruction (ASTRA Projector)
==============================================================

This example demonstrates solution of a sparse-view CT reconstruction
problem with isotropic total variation (TV) regularization
Expand All @@ -16,7 +16,10 @@

where $A$ is the X-ray transform (the CT forward projection operator),
$\mathbf{y}$ is the sinogram, $C$ is a 2D finite difference operator, and
$\mathbf{x}$ is the desired image.
$\mathbf{x}$ is the desired image. This example uses the CT projector
provided by the astra package, while the companion
[example script](ct_tv_admm.rst) uses the projector integrated into
scico.
"""

import numpy as np
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5 changes: 1 addition & 4 deletions examples/scripts/ct_multi_cs_tv_admm.py
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Expand Up @@ -23,8 +23,6 @@

import numpy as np

import jax

from xdesign import Foam, discrete_phantom

import scico.numpy as snp
Expand All @@ -38,8 +36,7 @@
"""
N = 512 # phantom size
np.random.seed(1234)
x_gt = discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N)
x_gt = jax.device_put(x_gt)
x_gt = snp.array(discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N))


"""
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5 changes: 1 addition & 4 deletions examples/scripts/ct_multi_tv_admm.py
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Expand Up @@ -22,8 +22,6 @@

import numpy as np

import jax

from xdesign import Foam, discrete_phantom

import scico.numpy as snp
Expand All @@ -37,8 +35,7 @@
"""
N = 512 # phantom size
np.random.seed(1234)
x_gt = discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N)
x_gt = jax.device_put(x_gt)
x_gt = snp.array(discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N))


"""
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5 changes: 1 addition & 4 deletions examples/scripts/ct_tv_admm.py
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Expand Up @@ -24,8 +24,6 @@

import numpy as np

import jax

from mpl_toolkits.axes_grid1 import make_axes_locatable
from xdesign import Foam, discrete_phantom

Expand All @@ -40,8 +38,7 @@
"""
N = 512 # phantom size
np.random.seed(1234)
x_gt = discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N)
x_gt = jax.device_put(x_gt) # convert to jax type, push to GPU
x_gt = snp.array(discrete_phantom(Foam(size_range=[0.075, 0.0025], gap=1e-3, porosity=1), size=N))


"""
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3 changes: 3 additions & 0 deletions examples/scripts/index.rst
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Expand Up @@ -14,6 +14,7 @@ Computed Tomography
- ct_astra_noreg_pcg.py
- ct_astra_3d_tv_admm.py
- ct_astra_tv_admm.py
- ct_tv_admm.py
- ct_astra_weighted_tv_admm.py
- ct_svmbir_tv_multi.py
- ct_svmbir_ppp_bm3d_admm_cg.py
Expand Down Expand Up @@ -98,6 +99,7 @@ Total Variation
- ct_abel_tv_admm.py
- ct_abel_tv_admm_tune.py
- ct_astra_tv_admm.py
- ct_tv_admm.py
- ct_astra_3d_tv_admm.py
- ct_astra_weighted_tv_admm.py
- ct_svmbir_tv_multi.py
Expand Down Expand Up @@ -154,6 +156,7 @@ ADMM
- ct_abel_tv_admm.py
- ct_abel_tv_admm_tune.py
- ct_astra_tv_admm.py
- ct_tv_admm.py
- ct_astra_3d_tv_admm.py
- ct_astra_weighted_tv_admm.py
- ct_svmbir_tv_multi.py
Expand Down
4 changes: 2 additions & 2 deletions requirements.txt
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Expand Up @@ -3,8 +3,8 @@ scipy>=1.6.0
tifffile
imageio>=2.17
matplotlib
jaxlib>=0.4.3,<=0.4.19
jax>=0.4.3,<=0.4.19
jaxlib>=0.4.3,<=0.4.20
jax>=0.4.3,<=0.4.20
flax>=0.6.1,<=0.6.9
svmbir>=0.3.3
pyabel>=0.9.0
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