Merge branch 'main' into mike/3d_xray

.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:

CHANGES.rst

@@ -11,6 +11,8 @@ Version 0.0.6   (unreleased)
   ``linop.Parallel3dProjector``.
 • New functional ``functional.IsotropicTVNorm`` and faster implementation
   of ``functional.AnisotropicTVNorm``.
+• New linear operators ``linop.ProjectedGradient``, ``linop.PolarGradient``,
+  ``linop.CylindricalGradient``, and ``linop.SphericalGradient``.
 • Rename ``scico.numpy.util.parse_axes`` to
   ``scico.numpy.util.normalize_axes``.
 • Rename ``scico.flax.save_weights`` and ``scico.flax.load_weights`` to

docs/docs_requirements.txt

@@ -3,13 +3,13 @@ sphinx>=5.0.0
 sphinxcontrib-napoleon
 sphinxcontrib-bibtex
 sphinx-autodoc-typehints
-furo
+furo>=2024.5.6
 jinja2<3.1.0  # temporary fix for jinja2/nbconvert bug
 traitlets!=5.2.2  # temporary fix for ipython/traitlets#741
 nbsphinx
 ipython
 ipython_genutils
 py2jn
-pygraphviz>=1.7
+pygraphviz>=1.9
 pandoc
 docutils>=0.18

docs/source/conf/15-theme.py

@@ -6,7 +6,7 @@
 html_theme = "furo"
 
 html_theme_options = {
-    "top_of_page_button": None,
+    "top_of_page_buttons": [],
     # "sidebar_hide_name": True,
 }
 

docs/source/examples.rst

@@ -86,6 +86,7 @@ Miscellaneous
    examples/demosaic_ppp_bm3d_admm
    examples/superres_ppp_dncnn_admm
    examples/denoise_l1tv_admm
+   examples/denoise_ptv_pdhg
    examples/denoise_tv_admm
    examples/denoise_tv_apgm
    examples/denoise_tv_multi
@@ -138,6 +139,7 @@ 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
@@ -146,6 +148,7 @@ Total Variation
    examples/deconv_microscopy_tv_admm
    examples/deconv_microscopy_allchn_tv_admm
    examples/denoise_l1tv_admm
+   examples/denoise_ptv_pdhg
    examples/denoise_tv_admm
    examples/denoise_tv_apgm
    examples/denoise_tv_multi
@@ -209,6 +212,7 @@ 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
@@ -272,6 +276,7 @@ PDHG
    :maxdepth: 1
 
    examples/ct_svmbir_tv_multi
+   examples/denoise_ptv_pdhg
    examples/denoise_tv_multi
    examples/denoise_cplx_tv_pdhg
 

docs/source/references.bib

@@ -362,6 +362,15 @@ @Book {goodman-2005-fourier
   edition =	 3
 }
 
+@Misc {hossein-2024-total,
+  title =	 {Total Variation Regularization for Tomographic
+                  Reconstruction of Cylindrically Symmetric Objects},
+  author =	 {Maliha Hossain and Charles A. Bouman and Brendt
+                  Wohlberg},
+  year =	 2024,
+  eprint =	 {2406.17928}
+}
+
 @Article {huber-1964-robust,
   doi =		 {10.1214/aoms/1177703732},
   year =	 1964,
@@ -776,6 +785,7 @@ @Article {zhang-2021-plug
   pages =	 {6360--6376}
 }
 
+
 @Article {zhou-2006-adaptive,
   author =	 {Bin Zhou and Li Gao and Yu-Hong Dai},
   title =	 {Gradient Methods with Adaptive Step-Sizes},

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.

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

examples/notebooks_requirements.txt

@@ -1,4 +1,6 @@
 -r examples-requirements.txt
+ipykernel
+ipywidgets
 nbformat
 nbconvert
 nb_conda_kernels

examples/scripts/README.rst

@@ -43,8 +43,6 @@ Computed Tomography
       2D X-ray Transform Comparison
    `ct_projector_comparison_3d.py <ct_projector_comparison_3d.py>`_
       3D 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)
 
@@ -105,6 +103,8 @@ Miscellaneous
       PPP (with DnCNN) Image Superresolution
    `denoise_l1tv_admm.py <denoise_l1tv_admm.py>`_
       ℓ1 Total Variation Denoising
+   `denoise_ptv_pdhg.py <denoise_ptv_pdhg.py>`_
+      Polar Total Variation Denoising (PDHG)
    `denoise_tv_admm.py <denoise_tv_admm.py>`_
       Total Variation Denoising (ADMM)
    `denoise_tv_apgm.py <denoise_tv_apgm.py>`_
@@ -178,6 +178,8 @@ 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>`_
@@ -194,6 +196,8 @@ Total Variation
       Deconvolution Microscopy (All Channels)
    `denoise_l1tv_admm.py <denoise_l1tv_admm.py>`_
       ℓ1 Total Variation Denoising
+   `denoise_ptv_pdhg.py <denoise_ptv_pdhg.py>`_
+      Polar Total Variation Denoising (PDHG)
    `denoise_tv_admm.py <denoise_tv_admm.py>`_
       Total Variation Denoising (ADMM)
    `denoise_tv_apgm.py <denoise_tv_apgm.py>`_
@@ -277,6 +281,8 @@ 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>`_
@@ -359,6 +365,8 @@ PDHG
 
     `ct_svmbir_tv_multi.py <ct_svmbir_tv_multi.py>`_
        TV-Regularized CT Reconstruction (Multiple Algorithms)
+    `denoise_ptv_pdhg.py <denoise_ptv_pdhg.py>`_
+       Polar Total Variation Denoising (PDHG)
     `denoise_tv_multi.py <denoise_tv_multi.py>`_
        Comparison of Optimization Algorithms for Total Variation Denoising
     `denoise_cplx_tv_pdhg.py <denoise_cplx_tv_pdhg.py>`_