example notebook #2
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KrisThielemans
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Jun 27, 2024
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| #%% | |||
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This is a CBCT example. It could be useful to some, but more than likely it is confusing to most. Please remove.
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| ## Requirements | ||
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| - CIL with callbacks https://github.com/TomographicImaging/CIL/pull/1659 |
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this has long been merged.
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| ### Installation | ||
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| Currently building from this SuperBuild branch https://github.com/SyneRBI/SIRF-SuperBuild/pull/718 |
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should be master as well.
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| docker/compose.sh -dgb -- --build-arg EXTRA_BUILD_FLAGS='-DGadgetron_TAG=6202fb7352a14fb82817b57a97d928c988eb0f4b -DISMRMRD_TAG=v1.13.7 -Dsiemens_to_ismrmrd_TAG=v1.2.11 -DDEVEL_BUILD=ON -DBUILD_CIL=ON -DCCPi-Regularisation-Toolkit_TAG=origin/master' --build-arg RUN_CTEST=0 | ||
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| ``` |
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most of this should no longer be there.
| docker/compose.sh -dgb -- --build-arg EXTRA_BUILD_FLAGS='-DGadgetron_TAG=6202fb7352a14fb82817b57a97d928c988eb0f4b -DISMRMRD_TAG=v1.13.7 -Dsiemens_to_ismrmrd_TAG=v1.2.11 -DDEVEL_BUILD=ON -DBUILD_CIL=ON -DCCPi-Regularisation-Toolkit_TAG=origin/master' --build-arg RUN_CTEST=0 | ||
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| ``` | ||
| where `-dgb` tells to `b`uild the `g`pu and `d`evelopment branches. The whole lot of flags can be checked [here](https://github.com/SyneRBI/SIRF-SuperBuild/blob/c21a2a45591550a6e257fc6f3dc343294b2c3127/docker/compose.sh#L24-L31) |
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| "# add RDP prior to the objective functions\n", | ||
| "step_size = 1e-7\n", | ||
| "add_regulariser = True\n", | ||
| "if add_regulariser:\n", | ||
| " alpha = 500\n", | ||
| " prior = construct_RDP(alpha, initial_image, kappa)\n", | ||
| " # epsilon = initial_image.max()*1e-4\n", | ||
| " # prior = add_RDP(alpha, epsilon, obj_funs)\n", | ||
| " add_prior(prior, obj_funs)\n", | ||
| " step_size = 1e-10" | ||
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will have to be replaced after merging #20
| "# ISTA default step_size is 0.99*2.0/F.L\n", | ||
| "step_size_rule = ConstantStepSize(step_size)\n", | ||
| "\n", | ||
| "alg = GD(initial=initial_image, objective_function=F, step_size=step_size_rule)" |
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Not using ISTA here, but GD. Please change and add positivity constraint
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this file is out-of-date. Don't merge.
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@KrisThielemans this PR is definitely old and not intended for merging (yet). Marked as draft. |
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An example is currently available. |
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part of #1