From 3058d704b4aa9612ab51f9d54d791050dffa4bbc Mon Sep 17 00:00:00 2001 From: Nicola VIGANO Date: Mon, 31 Oct 2022 16:17:01 +0100 Subject: [PATCH] Updated documentation Signed-off-by: Nicola VIGANO --- docs/_sources/changelog.md.txt | 13 +- docs/changelog.html | 239 +++++++++++++++++-------------- docs/doctrees/changelog.doctree | Bin 73383 -> 77529 bytes docs/doctrees/environment.pickle | Bin 449315 -> 450539 bytes docs/index.html | 33 ++--- docs/searchindex.js | 2 +- 6 files changed, 162 insertions(+), 125 deletions(-) diff --git a/docs/_sources/changelog.md.txt b/docs/_sources/changelog.md.txt index a669a11..7456b1a 100644 --- a/docs/_sources/changelog.md.txt +++ b/docs/_sources/changelog.md.txt @@ -4,7 +4,18 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -[Unreleased]: https://www.github.com/cicwi/corrct/compare/v0.7.0...develop +[Unreleased]: https://www.github.com/cicwi/corrct/compare/v0.7.1...develop + +## 0.7.1 - 2022-10-31 +### Added +- More documentation / tutorial content. +- Energy conversion functions (keV to m, and viceversa). +- Tapering for truncated volumes in FSC computation. +### Fixed +- Typo that preventing using `ProjectionGeometry` from `models`. +- Shape dimensions (XYZ vs ZXY) interpretation in `VolumeGeometry` and other functions. +- Cross-validation data term initialization in solvers. +- Tapering to circular masks. ## 0.7.0 - 2022-10-11 ### Added diff --git a/docs/changelog.html b/docs/changelog.html index 0dfa236..8ad12fc 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -41,83 +41,88 @@
  • Tutorial
  • corrct
  • Changelog
      -
    • 0.7.0 - 2022-10-11
        +
      • 0.7.1 - 2022-10-31
        • -
      • 0.6.0 - 2022-09-08
          +
        • 0.7.0 - 2022-10-11
          • -
        • 0.5.1 - 2022-06-23
            +
          • 0.6.0 - 2022-09-08
            • -
          • 0.5.0 - 2022-04-14
              +
            • 0.5.1 - 2022-06-23
              • -
            • 0.4.2 - 2022-01-14
                +
              • 0.5.0 - 2022-04-14
                • -
              • 0.4.1 - 2021-12-06
                  +
                • 0.4.2 - 2022-01-14
                  • -
                • 0.4.0 - 2021-11-29
                    +
                  • 0.4.1 - 2021-12-06
                    • -
                  • 0.3.2 - 2021-04-15
                      +
                    • 0.4.0 - 2021-11-29
                      • -
                    • 0.3.1 - 2020-10-20
                        +
                      • 0.3.2 - 2021-04-15
                        • -
                      • 0.3.0 - 2020-09-23
                          +
                        • 0.3.1 - 2020-10-20
                          • -
                        • 0.2.4 - 2020-06-01
                            +
                          • 0.3.0 - 2020-09-23
                            • -
                          • 0.2.3 - 2020-05-05
                              +
                            • 0.2.4 - 2020-06-01
                              • -
                            • 0.2.2 - 2020-03-30
                                +
                              • 0.2.3 - 2020-05-05
                                • -
                              • 0.2.1 - 2020-02-25
                                  +
                                • 0.2.2 - 2020-03-30
                                  • -
                                • 0.2.0 - 2019-11-05
                                    +
                                  • 0.2.1 - 2020-02-25
                                    • -
                                  • 0.1.0 - 2019-10-29 @@ -154,10 +159,30 @@

                                    ChangelogKeep a Changelog, and this project adheres to Semantic Versioning.

                                    -

                                    0.7.0 - 2022-10-11

                                    +

                                    0.7.1 - 2022-10-31

                                    Added

                                      +

                                    • More documentation / tutorial content.

                                      • +

                                    • Energy conversion functions (keV to m, and viceversa).

                                      • +

                                    • Tapering for truncated volumes in FSC computation.

                                      • +
                                    +
                                    +
                                    +

                                    Fixed

                                    +
                                      +

                                    • Typo that preventing using ProjectionGeometry from models.

                                      • +

                                    • Shape dimensions (XYZ vs ZXY) interpretation in VolumeGeometry and other functions.

                                      • +

                                    • Cross-validation data term initialization in solvers.

                                      • +

                                    • Tapering to circular masks.

                                      • +
                                    +
                                    +
                                    +
                                    +

                                    0.7.0 - 2022-10-11

                                    +
                                    +

                                    Added

                                    +

                                    • Wide API refactoring: renamed various modules, and moved processing routines to sub-package.

                                    • Initial draft of tutorial. More documentation on the way.

                                    • Line intersection computation.

                                      • @@ -165,8 +190,8 @@

                                      Added

                                    • Tests: initial support for projectors.

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Typo in function name.

                                    • Simplified examples 01 and 02.

                                      • @@ -174,10 +199,10 @@

                                      Fixed

                                    -
                                    -

                                    0.6.0 - 2022-09-08

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.6.0 - 2022-09-08

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Potential memory leak in astra-toolbox projector backend.

                                    • Gradient and laplacian implementations for arbitrary directions.

                                      • @@ -198,10 +223,10 @@

                                      Fixed

                                    -
                                    -

                                    0.5.1 - 2022-06-23

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.5.1 - 2022-06-23

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Border behavior in convolution operator.

                                    • Sanitized projector’s angle input.

                                      • @@ -226,10 +251,10 @@

                                      Fixed

                                    -
                                    -

                                    0.5.0 - 2022-04-14

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.5.0 - 2022-04-14

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Pixel weights, when having small outliers.

                                    • Volume mask generation

                                      • @@ -256,18 +281,18 @@

                                      Fixed

                                    -
                                    -

                                    0.4.2 - 2022-01-14

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.4.2 - 2022-01-14

                                    +
                                    +

                                    Added

                                    • Support for XRF line handling (Siegbahn).

                                    • Support for log-scaling of data weigths.

                                    • More type hinting and docstrings.

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • 3D volume support (especially in astra-toolbox backend).

                                    • Attenuation correction in 3D volumes.

                                      • @@ -280,17 +305,17 @@

                                      Fixed

                                    -
                                    -

                                    0.4.1 - 2021-12-06

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.4.1 - 2021-12-06

                                    +
                                    +

                                    Added

                                    • Uncertainty propagation functions, for weighted minimizations.

                                    • Unpreconditioned l1-minimization (standard behavior).

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Double application of weights in SIRT weighted least squares.

                                    • Use PDHG preconditioning by default.

                                      • @@ -298,10 +323,10 @@

                                      Fixed

                                    -
                                    -

                                    0.4.0 - 2021-11-29

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.4.0 - 2021-11-29

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Size of transformed volumes in dwt.

                                    • Deprecation warnings from recent numpy versions.

                                      • @@ -327,10 +352,10 @@

                                      Fixed

                                    -
                                    -

                                    0.3.2 - 2021-04-15

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.3.2 - 2021-04-15

                                    +
                                    +

                                    Added

                                    • scikit-image backend, as preferred in 2D non-GPU reconstructions.

                                    • Renamed AttenuationProjector into ProjectorAttenuationXRF.

                                      • @@ -339,8 +364,8 @@

                                      Added

                                    • Projection matrix based projector.

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • PyWavelets interface change.

                                    • Background usage in the data terms.

                                      • @@ -349,18 +374,18 @@

                                      Fixed

                                    -
                                    -

                                    0.3.1 - 2020-10-20

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.3.1 - 2020-10-20

                                    +
                                    +

                                    Added

                                    • FFT operator, and FFT regularizer.

                                    • l2-gradient (smooth) regularizer.

                                    • Support for multiple regularizers.

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Norm l2b (deadzone) is also weighted now.

                                    • Weighted least-squares implementation.

                                      • @@ -369,10 +394,10 @@

                                      Fixed

                                    -
                                    -

                                    0.3.0 - 2020-09-23

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.3.0 - 2020-09-23

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Python hard crash when CUDA not available.

                                    • Examples to comply with recent changes.

                                      • @@ -410,10 +435,10 @@

                                      Fixed

                                    -
                                    -

                                    0.2.4 - 2020-06-01

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.2.4 - 2020-06-01

                                    +
                                    +

                                    Added

                                    • Operator form (based on scipy.linalg.LinearOperator) for regularizers and projectors

                                    • Data fidelity function classes, including weighted least-squares

                                      • @@ -422,8 +447,8 @@

                                      Added

                                    • Multi-dimensional volume mask creation

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • SIRT regularization

                                    • Windows conda package build, and Python 3.8 target

                                      • @@ -432,10 +457,10 @@

                                      Fixed

                                    -
                                    -

                                    0.2.3 - 2020-05-05

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.2.3 - 2020-05-05

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Copy-paste error, and detector data axis order in SART algorithm implementation

                                    • Weights for masks in SART algorithm

                                      • @@ -458,10 +483,10 @@

                                      Fixed

                                    -
                                    -

                                    0.2.2 - 2020-03-30

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.2.2 - 2020-03-30

                                    +
                                    +

                                    Added

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • Wavelet decomposition along one dimension

                                    • TV regularizer for dimensions larger than ndims

                                      • @@ -479,33 +504,33 @@

                                      Fixed

                                    -
                                    -

                                    0.2.1 - 2020-02-25

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.2.1 - 2020-02-25

                                    +
                                    +

                                    Added

                                    • New regularizers: non-decimated wavelets and laplacian

                                    • Solvers: added projection masks, relaxation parameters, sirt regularizers

                                    • Uncorrected projector for 2D and 3D data

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • sub-pixel attenuation correction

                                    -
                                    -

                                    0.2.0 - 2019-11-05

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.2.0 - 2019-11-05

                                    +
                                    +

                                    Added

                                    • Multi-detector reconstruction

                                    -
                                    -

                                    Fixed

                                    +
                                    +

                                    Fixed

                                    • TV-min sign

                                    • Solvers’ name visualization

                                      • @@ -513,10 +538,10 @@

                                      Fixed

                                    -
                                    -

                                    0.1.0 - 2019-10-29

                                    -
                                    -

                                    Added

                                    +
                                    +

                                    0.1.0 - 2019-10-29

                                    +
                                    +

                                    Added

                                    • Initial release, with corrected forward and back-projections.

                                    • SIRT, SART, and Chambolle-Pock solvers.

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zF+JWw!T+gm$M(1Nd0~$b&%n$ywzvxsU6LK2e6XxLHKi`)T`(w4#~D_oRrS zz@wi^i~~E6*MFT+T>A_9z@9{)cjgqN>ne80%1bKhY6{CLXPT%_%bbIa?!d;;qHNj) reP}FE{Wm;SJMjWelcome to the documentation of PyCorrectedEmissionCT!
                                    • Changelog
                                    diff --git a/docs/searchindex.js b/docs/searchindex.js index 40133b4..bbff632 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["LICENSE", "changelog", "corrct", "corrct.processing", "index", "modules", "readme", "tutorial"], "filenames": ["LICENSE.md", "changelog.md", "corrct.rst", "corrct.processing.rst", "index.rst", "modules.rst", "readme.md", "tutorial.md"], "titles": ["<no title>", "Changelog", "corrct package", "corrct.processing package", "Welcome to the documentation of PyCorrectedEmissionCT!", "corrct", "PyCorrectedEmissionCT (corrct)", "Tutorial"], "terms": {"bsd": [0, 6], "3": [0, 2, 3, 4, 6], "claus": [0, 6], "licens": [0, 4], "copyright": 0, "c": [0, 6], "2019": [0, 4], "nicola": [0, 2, 3, 6], "vigan\u00f2": [0, 2, 3, 6, 7], "all": [0, 1, 2, 3, 7], "right": [0, 2, 6], "reserv": 0, "redistribut": 0, "us": [0, 1, 2, 3, 6, 7], "sourc": [0, 2, 3], "binari": 0, "form": [0, 1], "without": 0, 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