diff --git a/README.md b/README.md index 142773b..e7acc91 100644 --- a/README.md +++ b/README.md @@ -96,7 +96,7 @@ There are a few methods that are specific to simulating parallel MRI (multiple receive coils) based on the -[2012 paper by Guerquin-Kern et al.](http://doi.org/10.1109/TMI.2011.2174158). +[2012 paper by Guerquin-Kern et al.](https://doi.org/10.1109/TMI.2011.2174158). See the [documentation][docs-stable-url] for details. @@ -152,5 +152,5 @@ Tested with Julia ≥ 1.7. [docs-stable-url]: https://JuliaImageRecon.github.io/ImagePhantoms.jl/stable [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg [docs-dev-url]: https://JuliaImageRecon.github.io/ImagePhantoms.jl/dev -[license-img]: http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat +[license-img]: https://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat [license-url]: LICENSE diff --git a/docs/lit/examples/01-overview.jl b/docs/lit/examples/01-overview.jl index 1f59f58..528fa55 100644 --- a/docs/lit/examples/01-overview.jl +++ b/docs/lit/examples/01-overview.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`01-overview.ipynb`](@__NBVIEWER_ROOT_URL__/01-overview.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`01-overview.ipynb`](@__BINDER_ROOT_URL__/01-overview.ipynb). diff --git a/docs/lit/examples/02-ellipse.jl b/docs/lit/examples/02-ellipse.jl index c5c91d0..bfe8cbc 100644 --- a/docs/lit/examples/02-ellipse.jl +++ b/docs/lit/examples/02-ellipse.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`02-ellipse.ipynb`](@__NBVIEWER_ROOT_URL__/02-ellipse.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`02-ellipse.ipynb`](@__BINDER_ROOT_URL__/02-ellipse.ipynb). diff --git a/docs/lit/examples/03-rect.jl b/docs/lit/examples/03-rect.jl index 5d0c446..1461706 100644 --- a/docs/lit/examples/03-rect.jl +++ b/docs/lit/examples/03-rect.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`03-rect.ipynb`](@__NBVIEWER_ROOT_URL__/03-rect.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`03-rect.ipynb`](@__BINDER_ROOT_URL__/03-rect.ipynb). diff --git a/docs/lit/examples/04-gauss.jl b/docs/lit/examples/04-gauss.jl index a51fd6e..bde2236 100644 --- a/docs/lit/examples/04-gauss.jl +++ b/docs/lit/examples/04-gauss.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`04-gauss.ipynb`](@__NBVIEWER_ROOT_URL__/04-gauss.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`04-gauss.ipynb`](@__BINDER_ROOT_URL__/04-gauss.ipynb). diff --git a/docs/lit/examples/05-triangle.jl b/docs/lit/examples/05-triangle.jl index 1a6f591..505da82 100644 --- a/docs/lit/examples/05-triangle.jl +++ b/docs/lit/examples/05-triangle.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`05-triangle.ipynb`](@__NBVIEWER_ROOT_URL__/05-triangle.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`05-triangle.ipynb`](@__BINDER_ROOT_URL__/05-triangle.ipynb). diff --git a/docs/lit/examples/07-shepp.jl b/docs/lit/examples/07-shepp.jl index 3535661..cb65561 100644 --- a/docs/lit/examples/07-shepp.jl +++ b/docs/lit/examples/07-shepp.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`07-shepp.ipynb`](@__NBVIEWER_ROOT_URL__/07-shepp.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`07-shepp.ipynb`](@__BINDER_ROOT_URL__/07-shepp.ipynb). @@ -50,7 +50,7 @@ Original version from: Larry A Shepp, Benjamin F Logan, "The Fourier reconstruction of a head section," IEEE Transactions on Nuclear Science, 21(3):21-42, June 1974. -[doi](http://doi.org/10.1109/TNS.1974.6499235) +[doi](https://doi.org/10.1109/TNS.1974.6499235) This (default) version has low soft tissue contrast, so it usually should be displayed diff --git a/docs/lit/examples/08-focus.jl b/docs/lit/examples/08-focus.jl index 50920ff..b9da843 100644 --- a/docs/lit/examples/08-focus.jl +++ b/docs/lit/examples/08-focus.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`08-focus.ipynb`](@__NBVIEWER_ROOT_URL__/08-focus.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`08-focus.ipynb`](@__BINDER_ROOT_URL__/08-focus.ipynb). diff --git a/docs/lit/examples/09-disk.jl b/docs/lit/examples/09-disk.jl index b046f64..4974ee6 100644 --- a/docs/lit/examples/09-disk.jl +++ b/docs/lit/examples/09-disk.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`09-disk.ipynb`](@__NBVIEWER_ROOT_URL__/09-disk.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`09-disk.ipynb`](@__BINDER_ROOT_URL__/09-disk.ipynb). diff --git a/docs/lit/examples/10-mri-sense.jl b/docs/lit/examples/10-mri-sense.jl index 1044d69..f9a6060 100644 --- a/docs/lit/examples/10-mri-sense.jl +++ b/docs/lit/examples/10-mri-sense.jl @@ -17,7 +17,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`10-mri-sense.ipynb`](@__NBVIEWER_ROOT_URL__/10-mri-sense.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`10-mri-sense.ipynb`](@__BINDER_ROOT_URL__/10-mri-sense.ipynb). @@ -52,7 +52,7 @@ sensitivity maps analytically, rather than committing the "inverse crime" of using rasterized phantoms and maps. See the 2012 paper -[Guerquin-Kern et al.](http://doi.org/10.1109/TMI.2011.2174158) +[Guerquin-Kern et al.](https://doi.org/10.1109/TMI.2011.2174158) that combines analytical k-space values of the phantom with an analytical model for the sensitivity maps. This package follows the recommended approach from that paper. diff --git a/docs/lit/examples/30-3d.jl b/docs/lit/examples/30-3d.jl index aee4c1a..2333cb3 100644 --- a/docs/lit/examples/30-3d.jl +++ b/docs/lit/examples/30-3d.jl @@ -16,7 +16,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`30-3d.ipynb`](@__NBVIEWER_ROOT_URL__/30-3d.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`30-3d.ipynb`](@__BINDER_ROOT_URL__/30-3d.ipynb). @@ -68,7 +68,7 @@ whereas the [X-ray transform](https://en.wikipedia.org/wiki/X-ray_transform) is a collection of (1D) line integrals. See -[Section II.1, Natterer 2001](http://doi.org/10.1137/1.9780898719284). +[Section II.1, Natterer 2001](https://doi.org/10.1137/1.9780898719284). So strictly speaking the `radon` function is a misnomer in 3D, whereas for 2D functions the Radon transform and the X-ray transform coincide. diff --git a/docs/lit/examples/32-ellipsoid.jl b/docs/lit/examples/32-ellipsoid.jl index b7f516e..8c31fea 100644 --- a/docs/lit/examples/32-ellipsoid.jl +++ b/docs/lit/examples/32-ellipsoid.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`32-ellipsoid.ipynb`](@__NBVIEWER_ROOT_URL__/32-ellipsoid.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`32-ellipsoid.ipynb`](@__BINDER_ROOT_URL__/32-ellipsoid.ipynb). diff --git a/docs/lit/examples/33-cuboid.jl b/docs/lit/examples/33-cuboid.jl index 1ff3107..b954fbb 100644 --- a/docs/lit/examples/33-cuboid.jl +++ b/docs/lit/examples/33-cuboid.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`33-cuboid.ipynb`](@__NBVIEWER_ROOT_URL__/33-cuboid.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`33-cuboid.ipynb`](@__BINDER_ROOT_URL__/33-cuboid.ipynb). diff --git a/docs/lit/examples/34-gauss3.jl b/docs/lit/examples/34-gauss3.jl index 415d589..0af513c 100644 --- a/docs/lit/examples/34-gauss3.jl +++ b/docs/lit/examples/34-gauss3.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`34-gauss3.ipynb`](@__NBVIEWER_ROOT_URL__/34-gauss3.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`34-gauss3.ipynb`](@__BINDER_ROOT_URL__/34-gauss3.ipynb). diff --git a/docs/lit/examples/35-cylinder.jl b/docs/lit/examples/35-cylinder.jl index 1a804a1..4a88e18 100644 --- a/docs/lit/examples/35-cylinder.jl +++ b/docs/lit/examples/35-cylinder.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`35-cylinder.ipynb`](@__NBVIEWER_ROOT_URL__/35-cylinder.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`35-cylinder.ipynb`](@__BINDER_ROOT_URL__/35-cylinder.ipynb). diff --git a/docs/lit/examples/36-cone.jl b/docs/lit/examples/36-cone.jl index f0fd83a..9530d8c 100644 --- a/docs/lit/examples/36-cone.jl +++ b/docs/lit/examples/36-cone.jl @@ -15,7 +15,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`36-cone.ipynb`](@__NBVIEWER_ROOT_URL__/36-cone.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`36-cone.ipynb`](@__BINDER_ROOT_URL__/36-cone.ipynb). diff --git a/docs/lit/examples/37-shepp3.jl b/docs/lit/examples/37-shepp3.jl index 1275e02..e85873e 100644 --- a/docs/lit/examples/37-shepp3.jl +++ b/docs/lit/examples/37-shepp3.jl @@ -16,7 +16,7 @@ This page was generated from a single Julia file: #md # using the "Edit on GitHub" link in the top right. #md # The corresponding notebook can be viewed in -#md # [nbviewer](http://nbviewer.jupyter.org/) here: +#md # [nbviewer](https://nbviewer.org/) here: #md # [`37-shepp3.ipynb`](@__NBVIEWER_ROOT_URL__/37-shepp3.ipynb), #md # and opened in [binder](https://mybinder.org/) here: #md # [`37-shepp3.ipynb`](@__BINDER_ROOT_URL__/37-shepp3.ipynb). diff --git a/docs/src/assets/logo.svg b/docs/src/assets/logo.svg index 5c95210..44164cb 100644 --- a/docs/src/assets/logo.svg +++ b/docs/src/assets/logo.svg @@ -1,5 +1,5 @@ - + diff --git a/docs/src/index.md b/docs/src/index.md index c26e735..fc77521 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -14,7 +14,7 @@ used for testing image reconstruction algorithms. The most famous such phantom is the "Shepp Logan" phantom from this -[1974 paper](http://doi.org/10.1109/TNS.1974.6499235). +[1974 paper](https://doi.org/10.1109/TNS.1974.6499235). (A variant of that phantom serves as the logo for the @@ -26,7 +26,7 @@ A phantom is a collection (iterable) of shapes One purpose of this package is to avoid the -[inverse crime](http://doi.org/10.1016/j.cam.2005.09.027) +[inverse crime](https://doi.org/10.1016/j.cam.2005.09.027) of using a discretized or sampled image to generate sinograms or spectra. diff --git a/src/ellipsoid.jl b/src/ellipsoid.jl index 68c71dd..d302606 100644 --- a/src/ellipsoid.jl +++ b/src/ellipsoid.jl @@ -76,7 +76,7 @@ end Fourier transform of unit-radius sphere. The argument `f` is the radial coordinate in k-space and is unitless. See p253 of Bracewell 1978, The Fourier transform and its applications, -or http://doi.org/10.1002/mrm.21292. +or https://doi.org/10.1002/mrm.21292. Formula: `4/3 π` for `f ≈ 0`, otherwise `(sin(2πf) - 2πf cos(2πf)) / (2 * π^2 * f^3)`. diff --git a/src/mri-sense.jl b/src/mri-sense.jl index 07353f6..e49347f 100644 --- a/src/mri-sense.jl +++ b/src/mri-sense.jl @@ -1,7 +1,7 @@ #= mri-sense.jl Methods for generating phantom spectra based on the 2012 paper -[Guerquin-Kern et al.](http://doi.org/10.1109/TMI.2011.2174158) +[Guerquin-Kern et al.](https://doi.org/10.1109/TMI.2011.2174158) that combines analytical k-space values of the phantom with an analytical model for MRI sensitivity maps. =# diff --git a/src/shepplogan.jl b/src/shepplogan.jl index 9aaf8b1..755f47a 100644 --- a/src/shepplogan.jl +++ b/src/shepplogan.jl @@ -28,10 +28,10 @@ Original version from : Larry A Shepp, Benjamin F Logan, "The Fourier reconstruction of a head section," IEEE Transactions on Nuclear Science, 21(3):21-42, June 1974. -[doi](http://doi.org/10.1109/TNS.1974.6499235) +[doi](https://doi.org/10.1109/TNS.1974.6499235) Also in Kak and Slaney 1988 text, p. 255. -[doi](http://doi.org/10.1137/1.9780898719277) +[doi](https://doi.org/10.1137/1.9780898719277) """ struct SheppLogan <: EllipsePhantomVersion end