Update examples (#540)

* Minor comment edits * Fix missing typing import * Docs fixes * Improve docs * Docs fixes * Add missing dependency (due to recent changes in other packages) for building notebooks * Update submodule * Fix script to notebook conversion bug * Update submodule * Update submodule * Update submodule * Update submodule * Add missing dependency for building notebooks * Update submodule * Improve example script docstring * Update submodule * Avoid ray complaints * Remove second ray.init call * Update submodule * Update submodule * Update submodule * Replace deprecated matplotlib method * Update submodule * Update submodule * Remove largely redundant example * Update example index * Rename example script * Edit script title and fix docs * Update example index * Update submodule * Update submodule * void doctest errors resulting from unimportable astra or svmbir * Avoid doctest errors resulting from unimportable astra or svmbir --------- Co-authored-by: Brendt Wohlberg <[email protected]>
lanl · Jul 19, 2024 · 4450fac · 4450fac
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Showing 19 changed files with 138 additions and 258 deletions.
diff --git a/.github/workflows/pytest_ubuntu.yml b/.github/workflows/pytest_ubuntu.yml
@@ -89,7 +89,7 @@ jobs:
       - name: Run doc tests
         if: matrix.group == 1
         run: |
-          pytest --ignore-glob="*test_*.py" --doctest-modules scico
+          pytest --ignore-glob="*test_*.py" --ignore=scico/linop/xray --doctest-modules scico
           pytest --doctest-glob="*.rst" docs
 
   coverage:

diff --git a/data b/data
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -38,7 +38,6 @@ Computed Tomography
    examples/ct_astra_odp_train_foam2
    examples/ct_astra_unet_train_foam2
    examples/ct_projector_comparison
-   examples/ct_multi_cs_tv_admm
    examples/ct_multi_tv_admm
 
 Deconvolution
@@ -137,6 +136,7 @@ Total Variation
    examples/ct_astra_3d_tv_admm
    examples/ct_astra_3d_tv_padmm
    examples/ct_astra_weighted_tv_admm
+   examples/ct_multi_tv_admm
    examples/ct_svmbir_tv_multi
    examples/deconv_circ_tv_admm
    examples/deconv_tv_admm
@@ -208,6 +208,7 @@ ADMM
    examples/ct_tv_admm
    examples/ct_astra_3d_tv_admm
    examples/ct_astra_weighted_tv_admm
+   examples/ct_multi_tv_admm
    examples/ct_svmbir_tv_multi
    examples/ct_svmbir_ppp_bm3d_admm_cg
    examples/ct_svmbir_ppp_bm3d_admm_prox

diff --git a/docs/source/style.rst b/docs/source/style.rst
@@ -439,7 +439,7 @@ classes, or method definitions.
 
        Comment explaining example 1.
 
-       >>> np.add(1, 2)
+       >>> int(np.add(1, 2))
        3
 
        Comment explaining a new example.

diff --git a/examples/jnb.py b/examples/jnb.py
@@ -33,11 +33,12 @@ def py_file_to_string(src):
             if import_seen:
                 # Once an import statement has been seen, break on encountering a line that
                 # is neither an import statement nor a newline, nor a component of an import
-                # statement extended over multiple lines, nor an os.environ statement, nor
-                # components of a try/except construction (note that handling of these final
-                # two cases is probably not very robust).
+                # statement extended over multiple lines, nor an os.environ statement, nor a
+                # ray.init statement, nor components of a try/except construction (note that
+                # handling of these final two cases is probably not very robust).
                 if not re.match(
-                    r"(^import|^from|^\n$|^\W+[^\W]|^\)$|^os.environ|^try:$|^except)", line
+                    r"(^import|^from|^\n$|^\W+[^\W]|^\)$|^os.environ|^ray.init|^try:$|^except)",
+                    line,
                 ):
                     lines.append(line)
                     break

diff --git a/examples/notebooks_requirements.txt b/examples/notebooks_requirements.txt
@@ -1,4 +1,6 @@
 -r examples-requirements.txt
+ipykernel
+ipywidgets
 nbformat
 nbconvert
 nb_conda_kernels

diff --git a/examples/scripts/README.rst b/examples/scripts/README.rst
@@ -41,8 +41,6 @@ Computed Tomography
       CT Training and Reconstructions with UNet
    `ct_projector_comparison.py <ct_projector_comparison.py>`_
       X-ray Transform Comparison
-   `ct_multi_cs_tv_admm.py <ct_multi_cs_tv_admm.py>`_
-      TV-Regularized Sparse-View CT Reconstruction (Multiple Projectors, Common Sinogram)
    `ct_multi_tv_admm.py <ct_multi_tv_admm.py>`_
       TV-Regularized Sparse-View CT Reconstruction (Multiple Projectors)
 
@@ -176,6 +174,8 @@ Total Variation
       3D TV-Regularized Sparse-View CT Reconstruction (Proximal ADMM Solver)
    `ct_astra_weighted_tv_admm.py <ct_astra_weighted_tv_admm.py>`_
       TV-Regularized Low-Dose CT Reconstruction
+   `ct_multi_tv_admm.py <ct_multi_tv_admm.py>`_
+      TV-Regularized Sparse-View CT Reconstruction (Multiple Projectors)
    `ct_svmbir_tv_multi.py <ct_svmbir_tv_multi.py>`_
       TV-Regularized CT Reconstruction (Multiple Algorithms)
    `deconv_circ_tv_admm.py <deconv_circ_tv_admm.py>`_
@@ -275,6 +275,8 @@ ADMM
       3D TV-Regularized Sparse-View CT Reconstruction (ADMM Solver)
    `ct_astra_weighted_tv_admm.py <ct_astra_weighted_tv_admm.py>`_
       TV-Regularized Low-Dose CT Reconstruction
+   `ct_multi_tv_admm.py <ct_multi_tv_admm.py>`_
+      TV-Regularized Sparse-View CT Reconstruction (Multiple Projectors)
    `ct_svmbir_tv_multi.py <ct_svmbir_tv_multi.py>`_
       TV-Regularized CT Reconstruction (Multiple Algorithms)
    `ct_svmbir_ppp_bm3d_admm_cg.py <ct_svmbir_ppp_bm3d_admm_cg.py>`_

diff --git a/examples/scripts/ct_multi_cs_tv_admm.py b/examples/scripts/ct_multi_cs_tv_admm.py
+2,213 −451		notebooks/ct_abel_tv_admm_tune.ipynb
+54 −54		notebooks/ct_astra_3d_tv_admm.ipynb
+5 −5		notebooks/ct_astra_3d_tv_padmm.ipynb
+108 −375		notebooks/ct_astra_modl_train_foam2.ipynb
+60 −56		notebooks/ct_astra_noreg_pcg.ipynb
+345 −541		notebooks/ct_astra_odp_train_foam2.ipynb
+110 −78		notebooks/ct_astra_tv_admm.ipynb
+158 −189		notebooks/ct_astra_unet_train_foam2.ipynb
+558 −260		notebooks/ct_astra_weighted_tv_admm.ipynb
+0 −755		notebooks/ct_multi_cs_tv_admm.ipynb
+1,492 −155		notebooks/ct_multi_tv_admm.ipynb
+72 −72		notebooks/ct_projector_comparison.ipynb
+70 −76		notebooks/ct_tv_admm.ipynb
+106 −104		notebooks/deconv_circ_tv_admm.ipynb
+42 −34		notebooks/deconv_datagen_bsds.ipynb
+79 −80		notebooks/deconv_microscopy_allchn_tv_admm.ipynb
+4 −4		notebooks/deconv_microscopy_tv_admm.ipynb
+101 −277		notebooks/deconv_modl_train_foam1.ipynb
+117 −235		notebooks/deconv_odp_train_foam1.ipynb
+102 −102		notebooks/deconv_tv_admm.ipynb
+5,127 −401		notebooks/deconv_tv_admm_tune.ipynb
+105 −105		notebooks/deconv_tv_padmm.ipynb
+95 −178		notebooks/denoise_dncnn_train_bsds.ipynb
+245 −251		notebooks/denoise_tv_admm.ipynb
+5 −3		notebooks/index.ipynb
+326 −284		notebooks/sparsecode_conv_admm.ipynb
+350 −290		notebooks/sparsecode_conv_md_admm.ipynb
+567 −338		notebooks/sparsecode_poisson_apgm.ipynb
+118 −116		notebooks/video_rpca_admm.ipynb