From 47180e632befbfbdf4638aa3e479e88c746d72e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Tue, 31 May 2022 21:33:56 -0400 Subject: [PATCH] ENH: Use https instead of http when https works https is more tamper-resistant and more private so we use it instead of http when it is available. Following https://github.com/InsightSoftwareConsortium/ITK/pull/3428/commits/9cd0f2053f0cf181ec4412bf896301faf0cc2092t pus --- .hooks-config.bash | 2 +- CMake/CTestCustom.cmake.in | 10 +++---- CMake/ExternalData.cmake | 2 +- CMake/ITKSetStandardCompilerFlags.cmake | 2 +- ...rMacroCheckExternalProjectDependency.cmake | 2 +- CMake/SlicerMacroEmptyExternalProject.cmake | 4 +-- CONTRIBUTING.md | 2 +- Latex/Insight.bib | 24 ++++++++--------- Latex/gitdags.sty | 4 +-- README.md | 6 ++--- .../Latex/01-PrintedPreamble-Common.tex | 2 +- SoftwareGuide/Latex/02-Cover-Book1.tex | 2 +- SoftwareGuide/Latex/03-Abstract-Common.tex | 4 +-- .../Latex/Appendices/CodingStyleGuide.tex | 26 +++++++++---------- .../Latex/Appendices/GitWorkflow.tex | 4 +-- SoftwareGuide/Latex/Appendices/Licenses.tex | 2 +- .../Latex/Architecture/DataRepresentation.tex | 2 +- .../Latex/Architecture/SystemOverview.tex | 8 +++--- .../ConfidenceConnectedOnBrainWeb.tex | 2 +- .../Latex/DesignAndFunctionality/IO.tex | 10 +++---- .../DesignAndFunctionality/Registration.tex | 4 +-- ...ualizingDeformationFieldsUsingParaview.tex | 2 +- .../DevelopmentGuidelines/CreateAModule.tex | 2 +- .../DevelopmentGuidelines/SoftwareProcess.tex | 6 ++--- .../Latex/Introduction/Installation.tex | 4 +-- .../Latex/Introduction/Introduction.tex | 6 ++--- Utilities/GitSetup/LICENSE | 4 +-- Utilities/GitSetup/NOTICE | 2 +- Utilities/GitSetup/config.sample | 4 +-- Utilities/GitSetup/git-review-push | 2 +- Utilities/GitSetup/github-tips | 2 +- Utilities/GitSetup/setup-github | 2 +- Utilities/GitSetup/setup-hooks | 2 +- Utilities/GitSetup/setup-ssh | 2 +- Utilities/GitSetup/setup-stage | 2 +- Utilities/GitSetup/setup-upstream | 2 +- Utilities/GitSetup/setup-user | 2 +- Utilities/GitSetup/tips | 2 +- Utilities/Hooks/commit-msg | 2 +- Utilities/Hooks/pre-commit | 2 +- Utilities/Hooks/prepare-commit-msg | 2 +- Utilities/SetupForDevelopment.sh | 2 +- 42 files changed, 90 insertions(+), 90 deletions(-) diff --git a/.hooks-config.bash b/.hooks-config.bash index 5de6f437..e83854aa 100644 --- a/.hooks-config.bash +++ b/.hooks-config.bash @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0.txt +# https://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/CMake/CTestCustom.cmake.in b/CMake/CTestCustom.cmake.in index 8c103b1a..b9100972 100644 --- a/CMake/CTestCustom.cmake.in +++ b/CMake/CTestCustom.cmake.in @@ -11,10 +11,10 @@ # # For further details regarding this file, -# see http://www.cmake.org/Wiki/CMake_Testing_With_CTest#Customizing_CTest +# see https://www.cmake.org/Wiki/CMake_Testing_With_CTest#Customizing_CTest # # and -# http://www.kitware.com/blog/home/post/27 +# https://www.kitware.com/blog/home/post/27 # #---------------------------------------------------------------------- @@ -159,9 +159,9 @@ set(CTEST_CUSTOM_WARNING_EXCEPTION # Suppressing warnings about GL_GLEXT_LEGACY, the link reported below # report a similar problem with GL_GLEXT_PROTOTYPE. - # http://lists.apple.com/archives/mac-opengl/2009/Dec/msg00081.html + # https://lists.apple.com/archives/mac-opengl/2009/Dec/msg00081.html # That problem could be solved installing a newer version of X11 SDK - # See http://xquartz.macosforge.org/trac/changeset/343 + # See https://xquartz.macosforge.org/trac/changeset/343 ".*warning.*GL_GLEXT_LEGACY.*redefined" # ITK suppressions @@ -315,7 +315,7 @@ set(CTEST_CUSTOM_WARNING_EXCEPTION # Suppressing warnings about duplicate libraries in Darwin # At some point this may be addressed by CMake feature request: - # http://public.kitware.com/Bug/view.php?id=10179 + # https://public.kitware.com/Bug/view.php?id=10179 "ld.*warning.*duplicate dylib.*" ) endif() diff --git a/CMake/ExternalData.cmake b/CMake/ExternalData.cmake index efcc5636..ad29770b 100644 --- a/CMake/ExternalData.cmake +++ b/CMake/ExternalData.cmake @@ -55,7 +55,7 @@ # Example usage: # include(ExternalData) # set(ExternalData_URL_TEMPLATES "file:///local/%(algo)/%(hash)" -# "http://data.org/%(algo)/%(hash)") +# "https://data.org/%(algo)/%(hash)") # ExternalData_Add_Test(MyData # NAME MyTest # COMMAND MyExe DATA{MyInput.png} diff --git a/CMake/ITKSetStandardCompilerFlags.cmake b/CMake/ITKSetStandardCompilerFlags.cmake index 4f0bf6f6..053c1437 100644 --- a/CMake/ITKSetStandardCompilerFlags.cmake +++ b/CMake/ITKSetStandardCompilerFlags.cmake @@ -155,7 +155,7 @@ macro(check_compiler_platform_flags) # With MS compilers on Win64, we need the /bigobj switch, else generated # code results in objects with number of sections exceeding object file # format. - # see http://msdn.microsoft.com/en-us/library/ms173499.aspx + # see https://msdn.microsoft.com/en-us/library/ms173499.aspx if(MSVC_VERSION GREATER 1310) set(ITK_REQUIRED_CXX_FLAGS "${ITK_REQUIRED_CXX_FLAGS} /bigobj") endif() diff --git a/CMake/SlicerMacroCheckExternalProjectDependency.cmake b/CMake/SlicerMacroCheckExternalProjectDependency.cmake index 173b8ee2..6712bb55 100644 --- a/CMake/SlicerMacroCheckExternalProjectDependency.cmake +++ b/CMake/SlicerMacroCheckExternalProjectDependency.cmake @@ -5,7 +5,7 @@ # Copyright (c) Kitware Inc. # # See COPYRIGHT.txt -# or http://www.slicer.org/copyright/copyright.txt for details. +# or https://www.slicer.org/copyright/copyright.txt for details. # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/CMake/SlicerMacroEmptyExternalProject.cmake b/CMake/SlicerMacroEmptyExternalProject.cmake index 957cc5b6..226fbe95 100644 --- a/CMake/SlicerMacroEmptyExternalProject.cmake +++ b/CMake/SlicerMacroEmptyExternalProject.cmake @@ -8,7 +8,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.commontk.org/LICENSE +# https://www.commontk.org/LICENSE # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, @@ -18,7 +18,7 @@ # ########################################################################### -# See https://github.com/commontk/CTK/blob/master/CMake/ctkMacroEmptyExternalProject.cmake +# See https://github.com/commontk/CTK/blob/master/CMake/ctkMacroEmptyExternalProject.cmake # # Convenient macro allowing to define a "empty" project in case an external one is provided diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 86332fcf..89334385 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -98,6 +98,6 @@ Some Helpful Git Commands [Git]: https://git-scm.com/ -[VIM]: http://www.vim.org/ +[VIM]: https://www.vim.org/ [GitHub]: https://github.com/ [Pull Request]: https://help.github.com/articles/about-pull-requests/ diff --git a/Latex/Insight.bib b/Latex/Insight.bib index 7dd29a06..ee3df521 100644 --- a/Latex/Insight.bib +++ b/Latex/Insight.bib @@ -35,7 +35,7 @@ @InProceedings{Whitaker1994c @Manual{POVRay, Title = "Persistence of Vision, Ray-Tracer", - Address = "http://www.povray.org", + Address = "https://www.povray.org", } @Book{Romeny1994, @@ -55,7 +55,7 @@ @Book{ToErrIsHuman2001 @TechReport{Aisemberg, Author = "G.O. Aisemberg", Title = "Vertebrate embryology", - Address = "http://lcw.lehman.edu/lehman/depts/biology/aisemberg/Bio268.html", + Address = "https://lcw.lehman.edu/lehman/depts/biology/aisemberg/Bio268.html", Institution = "Department of Biological Sciences. Lehman College, City University of New York", year = 1998, @@ -758,7 +758,7 @@ @TechReport{Culver1999 Title = "Intrinsic scale for boundary representation of two-dimensional objects", Institution = "MIDAG, University of North Carolina at Chapel Hill", - annote = "http://www.cs.unc.edu/~culver", + annote = "https://www.cs.unc.edu/~culver", year = 1999, } @@ -824,7 +824,7 @@ @TechReport{Deriche1993 Institution = "Unite de recherche INRIA Sophia-Antipolis", Number = "1893", Note = "Research Repport", - annote = "http://www.inria.fr", + annote = "https://www.inria.fr", year = 1993, month = "avril", } @@ -832,7 +832,7 @@ @TechReport{Deriche1993 @Book{Darwin1999, Author = "C. Darwin", Title = "On the Origin of Species", - Publisher = "http://www.gutenberg.org", + Publisher = "https://www.gutenberg.org", Edition = "sixth", year = 1999, } @@ -2753,7 +2753,7 @@ @TechReport{Monga1990 Title = "From Voxel to Curvature", Institution = "INRIA", Number = "1356", - Note = "http://www.inria.fr", + Note = "https://www.inria.fr", year = 1990, month = "decembre", } @@ -2763,7 +2763,7 @@ @TechReport{Monga1992 Title = "Using Partial Derivatives of 3D Images to Extract Typical Surface Features ", Institution = "INRIA", - Note = "http://www.inria.fr", + Note = "https://www.inria.fr", year = 1992, } @@ -3490,7 +3490,7 @@ @Manual{OpenGLSpecification Title = "The OpenGL Graphics System: A Specification (Version 1.2)", Author = "M. Segal and K. Akeley", - Address = "http://www.opengl.org", + Address = "https://www.opengl.org", month = "march", year = 1998, } @@ -3908,7 +3908,7 @@ @TechReport{Udupa1998 Author = "J. K. Udupa and S. Samarasekera", Title = "Extraction of fuzzy object information in multidimensional images for quantifying MS lesions of the brain", year = 1998, - Institution = "United States Patent Office http://www.uspto.gov", + Institution = "United States Patent Office https://www.uspto.gov", Number = "5,812,691" } @@ -4803,7 +4803,7 @@ @Manual{CreatisINSA-Lyon Title = "The GDCM Library", Institution = "CREATIS (France)", Organization = "CNRS, INSERM, INSA Lyon, UCB Lyon", - Address = "http://www.creatis.insa-lyon.fr/Public/Gdcm/" + Address = "https://www.creatis.insa-lyon.fr/Public/Gdcm/" } @InProceedings{Chung2002, @@ -4854,7 +4854,7 @@ @Manual{OpenJPEG Title = "OpenJPEG", Institution = "Communications and Remote Sensing Laboratory (TELE)", Organization = "Universit\'{e} Catholique de Louvain (UCL), Belgium", - Address = "http://www.openjpeg.org" + Address = "https://www.openjpeg.org" } @TechReport{JPEG2000KeyAdvantages, @@ -4863,7 +4863,7 @@ @TechReport{JPEG2000KeyAdvantages Institution = "Aware Inc.", Year = 2002, Month = "February", - Address = "http://medical.nema.org/Dicom/minutes/WG-04/2002/2002-02-27/Weisfeiler.doc" + Address = "https://medical.nema.org/Dicom/minutes/WG-04/2002/2002-02-27/Weisfeiler.doc" } @inproceedings{ marcellin00overview, diff --git a/Latex/gitdags.sty b/Latex/gitdags.sty index d2470524..805a25f6 100644 --- a/Latex/gitdags.sty +++ b/Latex/gitdags.sty @@ -6,7 +6,7 @@ %% of this license or (at your option) any later version. %% The latest version of this license is in %% -%% http://www.latex-project.org/lppl.txt +%% https://www.latex-project.org/lppl.txt %% %% and version 1.3 or later is part of all distributions of LaTeX %% version 2005/12/01 or later. @@ -64,7 +64,7 @@ } } -% To cancel a shadow (see http://tex.stackexchange.com/a/198298/21891) +% To cancel a shadow (see https://tex.stackexchange.com/a/198298/21891) \tikzset{reset preaction/.code={\def\tikz@preactions{}}} % --- repository history graphs --- diff --git a/README.md b/README.md index 20a28272..d5bcac38 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ All the dependencies described belowe are available pre-installed in a [Docker] image. This is the easiest way to build and contribute to The Software Guide. - 1. Download and [install Docker](http://docs.docker.com/installation/). + 1. Download and [install Docker](https://docs.docker.com/installation/). 2. From a shell, run ```sh docker run --name software-guide -p 8888:8888 insighttoolkit/itksoftwareguide-edit:latest @@ -175,12 +175,12 @@ Troubleshooting [BibTeX]: http://www.bibtex.org/ [Docker]: https://www.docker.com/ -[dvips]: http://tug.org/texinfohtml/dvips.html +[dvips]: https://tug.org/texinfohtml/dvips.html [Git]: https://git-scm.com/ [ImageMagick]: https://www.imagemagick.org [LaTeX]: https://www.latex-project.org// [Minted]: https://ctan.org/pkg/minted?lang=en [MikTex]: https://miktex.org/ [ps2pdf]: https://www.ps2pdf.com/ -[Pygments]: http://pygments.org/ +[Pygments]: https://pygments.org/ [Python]: https://www.python.org/ diff --git a/SoftwareGuide/Latex/01-PrintedPreamble-Common.tex b/SoftwareGuide/Latex/01-PrintedPreamble-Common.tex index 76a01526..7cc87d08 100644 --- a/SoftwareGuide/Latex/01-PrintedPreamble-Common.tex +++ b/SoftwareGuide/Latex/01-PrintedPreamble-Common.tex @@ -26,7 +26,7 @@ \copyright \the\year \; Kitware, Inc. \emph{(cover, preface, postface)}\\ \copyright \the\year \; Insight Software Consortium \emph{(main text body)}\\ -Published by Kitware, Inc. \texttt{http://www.kitware.com} +Published by Kitware, Inc. \texttt{https://www.kitware.com} \normalsize \end{center} \end{minipage} diff --git a/SoftwareGuide/Latex/02-Cover-Book1.tex b/SoftwareGuide/Latex/02-Cover-Book1.tex index 305ed5bb..0123c163 100644 --- a/SoftwareGuide/Latex/02-Cover-Book1.tex +++ b/SoftwareGuide/Latex/02-Cover-Book1.tex @@ -21,7 +21,7 @@ \chapter*{About the Cover} image was visualized in VolView.\footnote{VolView is a commercial product from Kitware. It supports ITK plug-ins and is available as a free viewer or may be licensed with advanced functionality. See -http://www.kitware.com/products/volview.html for information.} The cluster +https://www.kitware.com/products/volview.html for information.} The cluster corresponding to the statistical distribution of blue values was identified visually, and a separating plane was manually defined in RGB space. The equation of this plane was subsequently used to discriminate pixels in the diff --git a/SoftwareGuide/Latex/03-Abstract-Common.tex b/SoftwareGuide/Latex/03-Abstract-Common.tex index 723c3dfe..fd146a39 100644 --- a/SoftwareGuide/Latex/03-Abstract-Common.tex +++ b/SoftwareGuide/Latex/03-Abstract-Common.tex @@ -24,7 +24,7 @@ \chapter*{Abstract} algorithms can be applied to arbitrary spatial dimensions and pixel types. An automated wrapping system integrated with ITK generates an interface between -C++ and a high-level programming language \href{http://www.python.org}{Python}. +C++ and a high-level programming language \href{https://www.python.org}{Python}. This enables rapid prototyping and faster exploration of ideas by shortening the edit-compile-execute cycle. In addition to automated wrapping, the \href{https://www.itk.org/Wiki/SimpleITK}{SimpleITK} project @@ -41,7 +41,7 @@ \chapter*{Abstract} ITK community is what helps manage the rapid evolution of the software. Testing is what keeps the software stable. An extensive testing process supported by the system known as -\href{http://open.cdash.org/index.php?project=Insight}{CDash} +\href{https://open.cdash.org/index.php?project=Insight}{CDash} measures the quality of ITK code on a daily basis. The ITK Testing Dashboard is updated continuously, reflecting the quality of the code at any moment. diff --git a/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex b/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex index 06078d92..30c9ff84 100644 --- a/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex +++ b/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex @@ -85,7 +85,7 @@ \section{Overview} Please discuss with the ITK community members if you wish to add, modify, or delete the rules described in these guidelines. -See \href{http://www.itk.org/ITK/help/mailing.html}{http://www.itk.org/ITK/help/mailing.html} +See \href{https://www.itk.org/ITK/help/mailing.html}{https://www.itk.org/ITK/help/mailing.html} for more information about joining the ITK community members discussion. This forum is one of the best venues in which to propose changes to these style guidelines. @@ -154,7 +154,7 @@ \subsection{Implementation Language} wrappers on the C++ counterparts. ITK's Python wrappers can be easily installed. See Section~\ref{sec:ModuleWrapping} on page~\pageref{sec:ModuleWrapping} for further details. Users requiring a Python interface for ITK classes may refer to -SimpleITK (\href{http://www.simpleitk.org/}{http://www.simpleitk.org/}). +SimpleITK (\href{https://www.simpleitk.org/}{https://www.simpleitk.org/}). Additionally, SimpleITK offers interpreted language bindings for Java, C\#, R, Tcl, and Ruby. @@ -270,7 +270,7 @@ \subsection{CMake Build Environment} cross-platform build system that enables community members to write simple makefiles (named \code{CMakeLists.txt}) that are processed to generated native build tools for a particular operating system/compiler combination. See the -CMake web pages at \href{http://www.cmake.org}{http://www.cmake.org} for more +CMake web pages at \href{https://www.cmake.org}{https://www.cmake.org} for more information. See Section~\ref{sec:UsingCMakeForConfiguringAndBuildingITK} on page @@ -346,7 +346,7 @@ \section{Copyright} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -1097,8 +1097,8 @@ \subsection{Naming Template Parameters} and \code{class} was purposed for declaring template parameters. It was later discovered that this lead to ambiguity in some valid code constructs, and the \code{typename} key word was added. It is often agreed -(\href{http://blogs.msdn.com/b/slippman/archive/2004/08/11/212768.aspx} -{http://blogs.msdn.com/b/slippman/archive/2004/08/11/212768.aspx}) that +(\href{https://blogs.msdn.com/b/slippman/archive/2004/08/11/212768.aspx} +{https://blogs.msdn.com/b/slippman/archive/2004/08/11/212768.aspx}) that \code{typename} is marginally more expressive in its intent and ITK should consistently use \code{typename} instead of \code{class}. @@ -1793,7 +1793,7 @@ \subsection{Class Layout} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -1877,7 +1877,7 @@ \subsection{Class Layout} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -2428,7 +2428,7 @@ \subsection{Alignment} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -2710,7 +2710,7 @@ \subsection{Empty Lines} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -2804,7 +2804,7 @@ \subsection{Empty Lines} * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * - * http://www.apache.org/licenses/LICENSE-2.0.txt + * https://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, @@ -4032,8 +4032,8 @@ \section{Doxygen Documentation System} ITK community members are required at a minimum to insert Doxygen commands listed in this section. -See more at \href{http://www.stack.nl/~dimitri/doxygen/} -{http://www.stack.nl/~dimitri/doxygen/} +See more at \href{https://www.stack.nl/~dimitri/doxygen/} +{https://www.stack.nl/~dimitri/doxygen/} \subsection{General Principles} diff --git a/SoftwareGuide/Latex/Appendices/GitWorkflow.tex b/SoftwareGuide/Latex/Appendices/GitWorkflow.tex index 76b01818..465942e6 100644 --- a/SoftwareGuide/Latex/Appendices/GitWorkflow.tex +++ b/SoftwareGuide/Latex/Appendices/GitWorkflow.tex @@ -9,7 +9,7 @@ \chapter{ITK Git Workflow} \section{Git Setup} \label{sec:Git Setup} -Visit the main \href{http://www.git-scm.com/download}{Git download site}, and +Visit the main \href{https://www.git-scm.com/download}{Git download site}, and depending on your operating system, follow the guidelines. @@ -121,7 +121,7 @@ \subsection{A Primer} few years of using Git. It is worth trying to explain some high-level Git concepts. A -\href{http://carthik.net/blog/vault/2007/08/21/its-a-feature-not-a-bug/}{feature} +\href{https://carthik.net/blog/vault/2007/08/21/its-a-feature-not-a-bug/}{feature} (or a \href{https://blog.codinghorror.com/thats-not-a-bug-its-a-feature-request/}{bug}) that sets Git apart from Subversion is its distributed nature. In practice, diff --git a/SoftwareGuide/Latex/Appendices/Licenses.tex b/SoftwareGuide/Latex/Appendices/Licenses.tex index 47f2d910..6b40bfe3 100644 --- a/SoftwareGuide/Latex/Appendices/Licenses.tex +++ b/SoftwareGuide/Latex/Appendices/Licenses.tex @@ -102,7 +102,7 @@ \subsection{MetaIO} \subsection{Netlib's SLATEC} This code is in the public domain. From -\url{http://www.netlib.org/slatec/guide}: +\url{https://www.netlib.org/slatec/guide}: \begin{verbatim} SECTION 4. OBTAINING THE LIBRARY diff --git a/SoftwareGuide/Latex/Architecture/DataRepresentation.tex b/SoftwareGuide/Latex/Architecture/DataRepresentation.tex index e4724d0b..c829eaf7 100644 --- a/SoftwareGuide/Latex/Architecture/DataRepresentation.tex +++ b/SoftwareGuide/Latex/Architecture/DataRepresentation.tex @@ -10,7 +10,7 @@ \section{Image} \label{sec:ImageSection} The \doxygen{Image} class follows the spirit of -\href{http://www.boost.org/more/generic_programming.html}{Generic Programming}, +\href{https://www.boost.org/more/generic_programming.html}{Generic Programming}, where types are separated from the algorithmic behavior of the class. ITK supports images with any pixel type and any spatial dimension. diff --git a/SoftwareGuide/Latex/Architecture/SystemOverview.tex b/SoftwareGuide/Latex/Architecture/SystemOverview.tex index a3c8a6da..141c680f 100644 --- a/SoftwareGuide/Latex/Architecture/SystemOverview.tex +++ b/SoftwareGuide/Latex/Architecture/SystemOverview.tex @@ -22,7 +22,7 @@ \section{System Organization} \item[Numerics.] ITK uses VXL's VNL numerics libraries. These are easy-to-use C++ wrappers around the Netlib Fortran numerical - analysis routines \footnote{\url{http://www.netlib.org}}. + analysis routines \footnote{\url{https://www.netlib.org}}. \item[Data Representation and Access.] Two principal classes are used to represent data: the \doxygen{Image} and \doxygen{Mesh} @@ -81,7 +81,7 @@ \section{System Organization} tool is used to produce an XML description of arbitrarily complex C++ code. An interface generator script is then used to transform the XML description into wrappers using the - SWIG\footnote{\url{http://www.swig.org/}} package. + SWIG\footnote{\url{https://www.swig.org/}} package. \end{description} @@ -545,10 +545,10 @@ \section{Numerics} Most VNL routines are implemented as wrappers around the high-quality Fortran routines that have been developed by the numerical analysis community over the last forty years and placed in the public domain. The central repository -for these programs is the ``netlib'' server.\footnote{\url{http://www.netlib.org/}} The +for these programs is the ``netlib'' server.\footnote{\url{https://www.netlib.org/}} The National Institute of Standards and Technology (NIST) provides an excellent search interface to this repository in its \emph{Guide to Available Mathematical -Software (GAMS)},\footnote{\url{http://gams.nist.gov}} both as a decision tree and a +Software (GAMS)},\footnote{\url{https://gams.nist.gov}} both as a decision tree and a text search. ITK also provides additional numerics functionality. A suite of optimizers, that diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex b/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex index b5dda24b..25eba60d 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex @@ -1,6 +1,6 @@ \subsubsection{Application of the Confidence Connected filter on the Brain Web Data} This section shows some results obtained by applying the Confidence Connected filter on the BrainWeb database. The filter was applied on a 181 $\times$ 217 $\times$ 181 crosssection of the {\it brainweb165a10f17} dataset. The data is a MR T1 acquisition, with an intensity non-uniformity of 20\% and a slice thickness 1mm. The dataset may be obtained from -\code{http://www.bic.mni.mcgill.ca/brainweb/} or +\code{https://www.bic.mni.mcgill.ca/brainweb/} or \code{https://data.kitware.com/\#folder/5882712d8d777f4f3f3072df} The previous code was used in this example replacing the image dimension by 3. diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/IO.tex b/SoftwareGuide/Latex/DesignAndFunctionality/IO.tex index ce413244..653eaef0 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/IO.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/IO.tex @@ -196,8 +196,8 @@ \subsection{Foreword} With the introduction of computed tomography (CT) followed by other digital diagnostic imaging modalities such as MRI in the 1970's, and the increasing use of computers in clinical applications, the American College of Radiology -(ACR)\footnote{\url{http://www.acr.org}} and the National Electrical -Manufacturers Association (NEMA)\footnote{\url{http://www.nema.org}} recognized +(ACR)\footnote{\url{https://www.acr.org}} and the National Electrical +Manufacturers Association (NEMA)\footnote{\url{https://www.nema.org}} recognized the need for a standard method for transferring images as well as associated information between devices manufactured from various vendors. @@ -240,13 +240,13 @@ \subsection{Foreword} DICOM functionalities in ITK are provided by the GDCM library. This open source library was developed by the CREATIS -Team~\footnote{\url{http://www.creatis.insa-lyon.fr}} at +Team~\footnote{\url{https://www.creatis.insa-lyon.fr}} at INSA-Lyon~\cite{CreatisINSA-Lyon}. Although originally this library was distributed under a LGPL -License\footnote{\url{http://www.gnu.org/copyleft/lesser.html}}, the CREATIS Team was +License\footnote{\url{https://www.gnu.org/copyleft/lesser.html}}, the CREATIS Team was lucid enough to understand the limitations of that license and agreed to adopt the more open BSD-like -License\footnote{\url{http://www.opensource.org/licenses/bsd-license.php}}. +License\footnote{\url{https://www.opensource.org/licenses/bsd-license.php}}. This change in their licensing made possible to distribute GDCM along with ITK. diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex b/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex index 6bba186d..d768d5b7 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex @@ -520,7 +520,7 @@ \section{Registration Troubleshooting} \subsection{Too many samples outside moving image buffer} -http://public.kitware.com/pipermail/insight-users/2007-March/021442.html +https://public.kitware.com/pipermail/insight-users/2007-March/021442.html This is a common error message in image registration. @@ -568,7 +568,7 @@ \subsection{General heuristics for parameter fine-tunning} -http://public.kitware.com/pipermail/insight-users/2007-March/021435.html +https://public.kitware.com/pipermail/insight-users/2007-March/021435.html Here is some advice on how to fine tune the parameters of the registration process. diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex b/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex index d752940f..4b7a59e1 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex @@ -9,7 +9,7 @@ % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Vector deformation fields may be visualized using ParaView. -ParaView \cite{ParaviewBook} is an open-source, multi-platform visualization application and uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using a unique blend of Tcl/Tk and C++. You may download it from http://paraview.org. +ParaView \cite{ParaviewBook} is an open-source, multi-platform visualization application and uses the Visualization Toolkit as the data processing and rendering engine and has a user interface written using a unique blend of Tcl/Tk and C++. You may download it from https://paraview.org. \subsection{Visualizing 2D deformation fields} Let us visualize the deformation field obtained from Demons Registration algorithm generated from ITK/Examples/RegistrationITKv4/DeformableRegistration2.cxx. diff --git a/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex b/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex index fe6aafe4..28f525c4 100644 --- a/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex +++ b/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex @@ -1326,7 +1326,7 @@ \section{Contributing with a Remote Module} made available in the ITK repository as a Remote Module. The Remote Module infrastructure enables fast dissemination of research code through ITK without increasing the size of the main repository. The Insight Journal -(\url{http://www.insight-journal.org/}) adds support for ITK module submissions +(\url{https://www.insight-journal.org/}) adds support for ITK module submissions with automatic dashboard testing (see Section~\ref{sec:CDash} on page~\pageref{sec:CDash} for further details). diff --git a/SoftwareGuide/Latex/DevelopmentGuidelines/SoftwareProcess.tex b/SoftwareGuide/Latex/DevelopmentGuidelines/SoftwareProcess.tex index 1dbf031f..a0d8032f 100644 --- a/SoftwareGuide/Latex/DevelopmentGuidelines/SoftwareProcess.tex +++ b/SoftwareGuide/Latex/DevelopmentGuidelines/SoftwareProcess.tex @@ -68,7 +68,7 @@ \section{CDash Regression Testing System} \index{CDash} One of the unique features of the ITK software process is its use of the CDash -regression testing system (\url{http://www.cdash.org}). In a +regression testing system (\url{https://www.cdash.org}). In a nutshell, what CDash does is to provide quantifiable feedback to developers as they check in new code and make changes. The feedback consists of the results of a variety of tests, and the results are posted on a publicly-accessible @@ -94,7 +94,7 @@ \section{CDash Regression Testing System} be obtained from \begin{center} -\url{http://www.cdash.org} +\url{https://www.cdash.org} \end{center} CDash supports a variety of test types. These include the following. @@ -234,5 +234,5 @@ \section{The Effectiveness of the Process} or changes to external subsystems such as the VXL/VNL numerics library. All of these tools that make up the process (CMake, Git, and CDash) are open-source. Many large and small systems such as VTK (The Visualization -Toolkit \url{http://www.vtk.org}) use the same process with similar +Toolkit \url{https://www.vtk.org}) use the same process with similar results. We encourage the adoption of the process in your environment. diff --git a/SoftwareGuide/Latex/Introduction/Installation.tex b/SoftwareGuide/Latex/Introduction/Installation.tex index 6d79805d..a5fbf026 100644 --- a/SoftwareGuide/Latex/Introduction/Installation.tex +++ b/SoftwareGuide/Latex/Introduction/Installation.tex @@ -69,7 +69,7 @@ \section{Obtaining the Software} \ref{sec:DownloadingFromGit}). When working from the repository, please be aware of the ITK quality testing dashboard. The Insight Toolkit is heavily tested using the open-source CDash regression testing -system\footnote{\url{http://open.cdash.org/index.php?project=Insight}}. Before +system\footnote{\url{https://open.cdash.org/index.php?project=Insight}}. Before updating the repository, make sure that the dashboard is \emph{green}, indicating stable code. (Learn more about the ITK dashboard and quality assurance process in Section \ref{sec:CDash} on page \pageref{sec:CDash}.) @@ -127,7 +127,7 @@ \subsection{Data} The Insight Toolkit was designed to support the Visible Human Project and its associated data. This data is available from the National Library of -Medicine at \url{http://www.nlm.nih.gov/research/visible/visible_human.html}. +Medicine at \url{https://www.nlm.nih.gov/research/visible/visible_human.html}. Another source of data can be obtained from the ITK Web site at either of the following: diff --git a/SoftwareGuide/Latex/Introduction/Introduction.tex b/SoftwareGuide/Latex/Introduction/Introduction.tex index 1eb1cc19..3a9a3b2a 100644 --- a/SoftwareGuide/Latex/Introduction/Introduction.tex +++ b/SoftwareGuide/Latex/Introduction/Introduction.tex @@ -139,8 +139,8 @@ \section{Software Organization} \begin{itemize} \item \code{ITK/Modules/Bridge} --- classes used to connect with the other analysis libraries or visualization libraries, such as - OpenCV\footnote{\url{http://opencv.org}} and - VTK\footnote{\url{http://www.vtk.org}}. + OpenCV\footnote{\url{https://opencv.org}} and + VTK\footnote{\url{https://www.vtk.org}}. \item \code{ITK/Modules/Compatibility} --- collects together classes for backwards compatibility with ITK Version 3, and classes that are deprecated -- i.e. scheduled for removal from future versions of ITK. @@ -233,7 +233,7 @@ \section{The Insight Community and Support} ITK in proposed work. \item For those developing commercial applications with ITK, support - and consulting are available from Kitware \footnote{\url{http://www.kitware.com}}. + and consulting are available from Kitware \footnote{\url{https://www.kitware.com}}. Kitware also offers short ITK courses either at a site of your choice or periodically at Kitware offices. diff --git a/Utilities/GitSetup/LICENSE b/Utilities/GitSetup/LICENSE index d6456956..62589edd 100644 --- a/Utilities/GitSetup/LICENSE +++ b/Utilities/GitSetup/LICENSE @@ -1,7 +1,7 @@ Apache License Version 2.0, January 2004 - http://www.apache.org/licenses/ + https://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION @@ -193,7 +193,7 @@ you may not use this file except in compliance with the License. You may obtain a copy of the License at - http://www.apache.org/licenses/LICENSE-2.0 + https://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/NOTICE b/Utilities/GitSetup/NOTICE index 0d32c02e..5287545f 100644 --- a/Utilities/GitSetup/NOTICE +++ b/Utilities/GitSetup/NOTICE @@ -2,4 +2,4 @@ Kitware Local Git Setup Scripts Copyright 2010-2012 Kitware, Inc. This product includes software developed at Kitware, Inc. -(http://www.kitware.com/). +(https://www.kitware.com/). diff --git a/Utilities/GitSetup/config.sample b/Utilities/GitSetup/config.sample index bba2382c..f9295de8 100644 --- a/Utilities/GitSetup/config.sample +++ b/Utilities/GitSetup/config.sample @@ -3,7 +3,7 @@ # Copy to "config" and edit as necessary. [hooks] - url = http://public.kitware.com/GitSetup.git + url = https://public.kitware.com/GitSetup.git #branch = hooks [ssh] @@ -17,6 +17,6 @@ [gerrit] #project = Project - site = http://review.source.kitware.com + site = https://review.source.kitware.com # pushurl placeholder "$username" is literal pushurl = $username@review.source.kitware.com:Project diff --git a/Utilities/GitSetup/git-review-push b/Utilities/GitSetup/git-review-push index 9891a1e2..3530c69f 100755 --- a/Utilities/GitSetup/git-review-push +++ b/Utilities/GitSetup/git-review-push @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/github-tips b/Utilities/GitSetup/github-tips index 4c976fcc..5a94aa75 100755 --- a/Utilities/GitSetup/github-tips +++ b/Utilities/GitSetup/github-tips @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-github b/Utilities/GitSetup/setup-github index 0cc7e448..cbb4a9d4 100755 --- a/Utilities/GitSetup/setup-github +++ b/Utilities/GitSetup/setup-github @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-hooks b/Utilities/GitSetup/setup-hooks index c07985ae..b84a6dd6 100755 --- a/Utilities/GitSetup/setup-hooks +++ b/Utilities/GitSetup/setup-hooks @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-ssh b/Utilities/GitSetup/setup-ssh index 8920a5bd..1e53d322 100755 --- a/Utilities/GitSetup/setup-ssh +++ b/Utilities/GitSetup/setup-ssh @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-stage b/Utilities/GitSetup/setup-stage index ce6ec457..9ee5aa80 100755 --- a/Utilities/GitSetup/setup-stage +++ b/Utilities/GitSetup/setup-stage @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-upstream b/Utilities/GitSetup/setup-upstream index 92ce1dae..b5c999af 100755 --- a/Utilities/GitSetup/setup-upstream +++ b/Utilities/GitSetup/setup-upstream @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/setup-user b/Utilities/GitSetup/setup-user index 1af439c4..81b8e48f 100755 --- a/Utilities/GitSetup/setup-user +++ b/Utilities/GitSetup/setup-user @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/GitSetup/tips b/Utilities/GitSetup/tips index 784e1ed8..f7471e03 100755 --- a/Utilities/GitSetup/tips +++ b/Utilities/GitSetup/tips @@ -6,7 +6,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/Hooks/commit-msg b/Utilities/Hooks/commit-msg index 0cd23ac2..a215bf87 100755 --- a/Utilities/Hooks/commit-msg +++ b/Utilities/Hooks/commit-msg @@ -7,7 +7,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0.txt +# https://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/Hooks/pre-commit b/Utilities/Hooks/pre-commit index dced3ecb..c724cb27 100755 --- a/Utilities/Hooks/pre-commit +++ b/Utilities/Hooks/pre-commit @@ -7,7 +7,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0.txt +# https://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/Hooks/prepare-commit-msg b/Utilities/Hooks/prepare-commit-msg index 9ff9ca23..dca9eb65 100755 --- a/Utilities/Hooks/prepare-commit-msg +++ b/Utilities/Hooks/prepare-commit-msg @@ -7,7 +7,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0.txt +# https://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, diff --git a/Utilities/SetupForDevelopment.sh b/Utilities/SetupForDevelopment.sh index 05ccfe8f..9262ca75 100755 --- a/Utilities/SetupForDevelopment.sh +++ b/Utilities/SetupForDevelopment.sh @@ -7,7 +7,7 @@ # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0.txt +# https://www.apache.org/licenses/LICENSE-2.0.txt # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS,