nids2001 · nids2001 · Apr 23, 2021 · Apr 30, 2021 · Apr 30, 2021 · Apr 30, 2021
diff --git a/.gitignore b/.gitignore
@@ -18,3 +18,6 @@ install_manifest.txt
 CTestTestfile.cmake
 DartConfiguration.tcl
 xCode_bin*
+
+# Sphinx builds
+docs/_build/
diff --git a/docs/_static/css/main.css b/docs/_static/css/main.css
@@ -0,0 +1,11 @@
+@import url('https://fonts.googleapis.com/css2?family=Fira+Sans:ital,wght@0,400;0,600;1,400&family=Staatliches&display=swap');
+@import url('https://fonts.googleapis.com/css2?family=Patua+One&display=swap');
+
+body {
+  font-family: 'Fira Sans', sans-serif !important;
+}
+
+h1, h2, h3, h4, h5, h6 {
+  font-family: 'Patua One', cursive;
+  /* font-size: 2.2rem; */
+}
diff --git a/docs/_static/seg3d.png b/docs/_static/seg3d.png
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
@@ -0,0 +1,5 @@
+{% extends "!layout.html" %}
+{% block rootrellink %}
+    <li><a href="https://project.invalid/">Project Homepage</a> &raquo;</li>
+    {{ super() }}
+{% endblock %}
diff --git a/docs/bib.rst b/docs/bib.rst
@@ -0,0 +1,3 @@
+Bibliography
+============
+.. bibliography::
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,139 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
+
+# from recommonmark.transform import AutoStructify
+
+# -- Project information -----------------------------------------------------
+
+project = 'Seg3D'
+copyright = '2021, The Scientific Computing and Imaging Institute at the University of Utah'
+author = 'To be Added'
+
+# The full version, including alpha/beta/rc tags
+release = '0.01'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+#extensions = [
+#        'sphinx.ext.autodoc',
+#        'sphinx.ext.napoleon',
+#        'recommonmark',
+#        'sphinxcontrib.bibtex',
+#        'sphinx_markdown_tables'
+#]
+
+extensions = [
+        'sphinx.ext.autodoc',
+        'sphinx.ext.napoleon',
+        'myst_parser',
+        'sphinx_markdown_tables',
+        'sphinxcontrib.bibtex',
+        'notfound.extension'
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # Allow code fence using ::: (see https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html#syntax-colon-fence)
+    "linkify",  # Allow automatic creation of links from URLs (it is sufficient to write https://google.com instead of <https://google.com>)
+    "substitution"
+]
+
+# Auto-generate header anchors up to level 6, so that it can be referenced like [](file.md#header-anchor).
+# (see https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html#auto-generated-header-anchors)
+myst_heading_anchors = 6
+
+# auto number figures
+numfig = True
+
+# Path for bibtex files
+bibtex_bibfiles = ['references.bib']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+
+notfound_context = {
+    'title': 'Page Not Found',
+    'body': '''
+<h1>Page Not Found</h1>
+<p>Sorry, we couldn't find that page.</p>
+<p>Try using the search box or go to the homepage.</p>
+''',
+}
+
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# the master toctree doc
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'python'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_book_theme'
+
+#html_theme = 'groundwork'
+
+# html_style = '/css/main.css'
+
+#on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+#if not on_rtd:  # only import and set the theme if we're building docs locally
+#    import sphinx_rtd_theme
+#    html_theme = 'sphinx_book_theme'
+#    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+
+
+html_static_path = ['_static']
+
+html_css_files = ['css/main.css']
+
+html_title = project
+
+html_logo = '_static/seg3d.png'
+
+html_theme_options = {
+    'logo_only': True
+}
+
+autosectionlabel_prefix_document = True
diff --git a/docs/dev_docs/build.md b/docs/dev_docs/build.md
@@ -0,0 +1,209 @@
+Build Seg3D
+=================
+
+<!-- * [Installing Seg3D from source](#installing-seg3d-from-source)
+  * [Compiler Requirements](#compiler-requirements)
+    * [Windows](#windows)
+    * [Mac OS X](#mac-os-x)
+    * [Linux](#linux)
+  * [Dependencies](#dependencies)
+    * [Qt](#qt)
+      * [Seg3D 2.4 And Newer](#seg3d-24-and-newer)
+        * [Mac OS X](#mac-os-x-2)
+        * [Linux](#linux-2)
+      * [Seg3D 2.0 to 2.3](#seg3d-20-to-23)
+        * [Windows](#windows)
+        * [Mac OS X](#mac-os-x-1)
+        * [Linux](#linux-1)
+  * [Compiling Seg3D](#compiling-seg3d)
+    * [Seg3D 2.4 And Newer](#seg3d-24-and-newer-1)
+    * [Optional Image Registration Tools](#optional-image-registration-tools)
+  * [Seg3D Packages](#seg3d-packages)
+* [Seg3D Data](#seg3d-data)
+* [Seg3D Support](#seg3d-support) -->
+
+<!-- Created by [gh-md-toc](https://github.com/ekalinin/github-markdown-toc) -->
+
+## Installing Seg3D from source
+
+### Compiler Requirements
+
+**At least C++11 64-bit compiler support is required.**
+
+#### Windows
+
+The current source code must be compiled with the 64-bit version of Visual Studio 2013.
+Visual Studio 2015 support is coming soon.
+If building the installer using CPack, NSIS is required.
+The code has not been tested under Cygwin or MinGW compilers.
+
+#### Mac OS X
+
+The source code base was built with Xcode 5-7 as well as GNU Make and Ninja and works for both environments on OS X 10.8+.
+If building the installer using CPack, PackageMaker is required.
+
+#### Linux
+
+The code base has been tested for use with GCC, and this is the recommended compiler for
+linux. GNU Make and Ninja build systems can be used. **Compiler must support C++11.**
+
+### Dependencies
+
+#### Qt
+
+##### Seg3D 2.4 And Newer
+
+Before building Seg3D, please make sure that **Qt 5.9** has been installed on your system.
+
+###### Windows
+
+A typical Qt 5.9 build is as follows:
+
++ Qt will need to be built from the command line using [Visual C++ command line tools](https://msdn.microsoft.com/en-us/library/f35ctcxw(v=vs.120).aspx). Troubleshooting tips can be found [here](http://stackoverflow.com/questions/21476588/where-is-developer-command-prompt-for-vs2013).
++ Perl and Python are required before building Qt from source. The link below includes download links for both dependencies.
++ Refer to the [Qt docs](http://doc.qt.io/qt-5/windows-requirements.html#building-from-source) for requirements for building from source.
++ Run ```configure``` from this new directory with the following parameters (using the ***-fast*** flag to speed up build process can be helpful too):
+
+```
+configure -platform win32-msvc2013 -no-gif -qt-libpng -qt-zlib -qt-libjpeg -no-openssl -skip qtwebengine -skip qtwebkit -D _BIND_TO_CURRENT_VCLIBS_VERSION=1 -debug-and-release -opensource -opengl desktop
+```
+
++ You will be asked a few questions on license before configuring.
++ Now run nmake and compile all of Qt (this is a long build).
+
+###### Mac OS X
+
+Qt binaries are available on the Qt website or can be built from source code.
+
+###### Linux
+
+Qt 5 static libraries are **NOT** supported. If building from source, ensure that the shared library build is enabled.
+
+If building from source, use the following:
+
+```
+./configure -qt-xcb -qt-zlib -nomake examples -nomake tests -skip qtwayland -skip qtwebengine -skip qtwebkit -opengl desktop
+```
+
+##### Seg3D 2.0 to 2.3
+
+Before building Seg3D, please make sure that **Qt 4.7-4.8** has been installed on your system.
+
+###### Windows
+
+A Visual Studio binary build is available.
+To our knowledge the Windows Visual Studio development libraries are only available in a 32-bit version.
+A 64-bit version can be built from the source code download, configuring it as described on the Qt webpage.
+A typical Qt build is as follows:
+
++ Download the open source version of Seg3D2. [Qt 4.8](http://download.qt.io/archive/qt/4.8/) is recommended.
++ Qt will need to be built from the command line using [Visual C++ command line tools](https://msdn.microsoft.com/en-us/library/f35ctcxw(v=vs.120).aspx). Troubleshooting tips can be found [here](http://stackoverflow.com/questions/21476588/where-is-developer-command-prompt-for-vs2013).
++ Create a new directory called ***C:\Qt\4.8-64bit*** (or name of your choice), change into that directory and copy all the source files into it.
++ Now, run ```configure.exe``` from this new directory with the following parameters (using the ***-fast*** flag to speed up build process can be helpful too):
+
+```
+configure.exe -platform win32-msvc2013 -no-gif -qt-libpng -qt-zlib -no-libmng -qt-libtiff -qt-libjpeg -no-openssl
+-no-phonon -no-phonon-backend -no-qt3support -D _BIND_TO_CURRENT_VCLIBS_VERSION=1
+-debug-and-release -opensource
+```
+
++ You will be asked a few questions on license before configuring.
++ Now run nmake and compile all of Qt (this is a long build).
+
+###### Mac OS X
+
+Qt binaries are available on the Qt website or can be built from source code.
+
+###### Linux
+
+Qt is available from most package managers. Look for Qt 4.7-4.8.
+
+#### CMake
+
+[CMake](https://cmake.org/) versions 2.8 - 3.4 are supported.
+
+
+### Compiling Seg3D
+
+Once you have obtained a compatible compiler and installed Qt on your system, you need to
+download and install CMake (<http://www.cmake.org>) to actually build the software.
+CMake is a platform independent configuring system that is used for generating Makefiles,
+Visual Studio project files, or Xcode project files.
+
+Once CMake has been installed, run CMake from your build (***bin***) directory and give a path to the CMake ***Superbuild*** directory containing the master CMakeLists.txt file.
+
+You may build Seg3D with [Ninja](https://ninja-build.org) by adding the tag "`-G Ninja`" to your cmake command. Note: Mac users will have to install Ninja with [Homebrew](https://brew.sh).
+
+#### Seg3D 2.4 And Newer
+
+CMake requires a path to the Qt 5 install directory. Typically, this directory will contain ***bin*** and ***lib*** directories.
+For example, for Qt installed on Mac OS X from the Qt 5 binaries on the Qt site:
+
+```
+cd bin
+```
+
+```
+cmake -DQt5_PATH:PATH=/Users/test/Qt5.5.1/5.5/clang_64 ../Superbuild
+```
+
+If building on Linux, the path may be under /usr/lib or /usr/lib64.
+
+The console version ``ccmake``, or GUI version can also be used.
+Set the **Qt5_PATH** variable to the location of the Qt 5 installation.
+
+After configuration is done, generate the make files or project files for your favorite
+development environment and build.
+
+The build script can also be used:
+
+```
+./build.sh --qt5=/Users/test/Qt5.5.1/5.5/clang_64
+```
+
+The Seg3D application will be built in bin/Seg3D.
+
+#### Seg3D 2.0 to 2.3
+
+Running cmake on the command line:
+
+```
+cd bin
+```
+
+```
+cmake ../Superbuild
+```
+
+Following the previous example, the Seg3D application will be built in bin/Seg3D.
+
+The console version ``ccmake``, or GUI version can also be used.
+You may be prompted to specify your location of the Qt installation.
+If you installed Qt in the default location, it should find Qt automatically.
+
+After configuration is done, generate the make files or project files for your favorite
+development environment and build.
+
+A bash build script (build.sh) is also available for Linux and Mac OS X to simplify the process.
+Usage information is available using the ***--help*** flag:
+
+```
+./build.sh --help
+```
+
+#### Optional Image Registration Tools
+
+To build the optional [python-based image registrations tools](ir-tools), the CMake option **BUILD_MOSAIC_TOOLS** must be turned on, either on the command line with the flag **-DBUILD_MOSAIC_TOOLS:BOOL=ON**, or in the console or GUI interfaces.
+
+### Seg3D Packages
+
+Build the ***package*** target in Visual Studio or Xcode, or ``make package`` using GNU make on Mac OS X.
+
+## Seg3D Data
+
+Seg3D sample data (also used in the tutorial) is available [here](https://github.com/CIBC-Internal/Seg3DData/releases).
+
+## Seg3D Support
+
+For questions and issues regarding building the software from source,
+please email our support list: [seg3d@sci.utah.edu](mailto:seg3d@sci.utah.edu)