[ismrmrd] 01/16: initial commit of Sphinx documentation
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Wed Jan 14 20:02:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to annotated tag v1.2.0
in repository ismrmrd.
commit 8602a8c7a4b229c64a8adcbc1bbac5ffecfca454
Author: Joseph Naegele <joseph.naegele at gmail.com>
Date: Thu Nov 13 12:13:17 2014 -0500
initial commit of Sphinx documentation
---
doc/CMakeLists.txt | 23 +-
doc/Doxyfile.in | 8 +-
doc/Makefile.sphinx.in | 177 +++++++++
doc/source/api.rst | 6 +
doc/source/conf.py | 273 ++++++++++++++
doc/source/index.rst | 546 +++++++++++++++++++++++++++
utilities/generate_cartesian_shepp_logan.cpp | 1 +
utilities/recon_cartesian_2d.cpp | 2 +-
8 files changed, 1026 insertions(+), 10 deletions(-)
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index 1c884c8..008d24d 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -1,10 +1,23 @@
find_package(Doxygen)
if(DOXYGEN_FOUND)
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
- add_custom_target(doc ${DOXYGEN_EXECUTABLE}
- ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating API documentation with Doxygen" VERBATIM)
- add_custom_target(apidoc DEPENDS doc)
+ set(API_DOC_DIR ${CMAKE_CURRENT_BINARY_DIR}/html/api)
+ set(DOXYFILE ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${DOXYFILE} @ONLY)
+
+ add_custom_target(apidoc
+ COMMAND ${CMAKE_COMMAND} -E make_directory ${API_DOC_DIR}
+ COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYFILE}
+ COMMENT "Generating API documentation using Doxygen" VERBATIM)
else(DOXYGEN_FOUND)
MESSAGE("Doxygen not found. Will not be able to build documentation")
endif(DOXYGEN_FOUND)
+
+set(SPHINX_MAKEFILE ${CMAKE_CURRENT_BINARY_DIR}/Makefile.sphinx)
+configure_file(Makefile.sphinx.in ${SPHINX_MAKEFILE} @ONLY)
+add_custom_target(htmldoc
+ COMMAND make -f ${SPHINX_MAKEFILE} html
+ COMMENT "Generating HTML docs using Sphinx" VERBATIM)
+
+add_custom_target(doc)
+add_dependencies(doc apidoc htmldoc)
diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
index c7c93c4..29a0a53 100644
--- a/doc/Doxyfile.in
+++ b/doc/Doxyfile.in
@@ -58,7 +58,7 @@ PROJECT_LOGO =
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
-OUTPUT_DIRECTORY =
+OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
# directories (in 2 levels) under the output directory of each output format and
@@ -1020,7 +1020,7 @@ GENERATE_HTML = YES
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_OUTPUT = html
+HTML_OUTPUT = @API_DOC_DIR@
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
@@ -1555,7 +1555,7 @@ EXTRA_SEARCH_MAPPINGS =
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
-GENERATE_LATEX = YES
+GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -1803,7 +1803,7 @@ MAN_LINKS = NO
# captures the structure of the code including all documentation.
# The default value is: NO.
-GENERATE_XML = NO
+GENERATE_XML = YES
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/doc/Makefile.sphinx.in b/doc/Makefile.sphinx.in
new file mode 100644
index 0000000..f43540a
--- /dev/null
+++ b/doc/Makefile.sphinx.in
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = @CMAKE_CURRENT_BINARY_DIR@
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) @CMAKE_CURRENT_SOURCE_DIR@/source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) @CMAKE_CURRENT_SOURCE_DIR@/source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " xml to make Docutils-native XML files"
+ @echo " pseudoxml to make pseudoxml-XML files for display purposes"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ISMRMRD.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ISMRMRD.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/ISMRMRD"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ISMRMRD"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through platex and dvipdfmx..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+ @echo
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+ @echo
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/doc/source/api.rst b/doc/source/api.rst
new file mode 100644
index 0000000..5b95e6c
--- /dev/null
+++ b/doc/source/api.rst
@@ -0,0 +1,6 @@
+ISMRMRD C/C++ API
+=================
+
+.. contents::
+
+.. doxygenindex::
diff --git a/doc/source/conf.py b/doc/source/conf.py
new file mode 100644
index 0000000..a62a228
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,273 @@
+# -*- coding: utf-8 -*-
+#
+# ISMRMRD documentation build configuration file, created by
+# sphinx-quickstart on Thu Nov 13 10:11:39 2014.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+#import breathe
+import sphinx_bootstrap_theme
+
+# 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.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# 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.doctest',
+ 'sphinx.ext.todo',
+ 'sphinx.ext.mathjax',
+ #'breathe'
+]
+
+#breathe_projects = { 'ISMRMRD': '/Users/naegelejd/src/github.com/ismrmrd/ismrmrd/build/doc/api/xml' }
+#breathe_default_project = 'ISMRMRD'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'ISMRMRD'
+copyright = u'2014, ISMRMRD Developers'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.1'
+# The full version, including alpha/beta/rc tags.
+release = '1.1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- 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 = 'bootstrap'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+ 'navbar_links': [
+ ('API Reference', "api/index.html", True)
+ ]
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ISMRMRDdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ ('index', 'ISMRMRD.tex', u'ISMRMRD Documentation',
+ u'ISMRMRD Developers', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'ismrmrd', u'ISMRMRD Documentation',
+ [u'ISMRMRD Developers'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'ISMRMRD', u'ISMRMRD Documentation',
+ u'ISMRMRD Developers', 'ISMRMRD', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
diff --git a/doc/source/index.rst b/doc/source/index.rst
new file mode 100644
index 0000000..56bd326
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,546 @@
+.. ISMRMRD documentation master file, created by
+ sphinx-quickstart on Thu Nov 13 10:11:39 2014.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+ISMRM Raw Data Format (ISMRMRD)
+===================================
+
+Contents:
+
+.. toctree::
+ :maxdepth: 2
+
+.. contents::
+
+Preamble
+---------
+
+A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This document describes such a common raw data format and attempts to capture the data fields that are require to describe enough details about the magnetic resonance experiment to reconstruct images from the data.
+This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop. Comments and requests for additions/modifications can be sent to:
+
+* Michael S. Hansen (michael DOT hansen AT nih DOT gov)
+* Wally Block (wblock AT cae DOT wisc DOT edu)
+* Mark Griswold (mag46 AT case DOT edu)
+* Brian Hargreaves (bah AT stanford DOT edu)
+* Peter Boernert (peter DOT boernert AT philips DOT com)
+* Sebastian Kozerke (kozerke AT biomed DOT ee DOT ethz DOT ch)
+* Craig Meyer (cmeyer AT virginia DOT edu)
+* Doug Noll (dnoll AT umich DOT edu)
+* Jim Pipe (Jim.Pipe AT DignityHealth DOT org)
+
+Developers/Contributors
+------------------------
+
+* Michael S. Hansen, National Institutes of Health, USA
+* Nick Zwart, Barrow Neurological Institute, Phoenix, Arizona
+* Souheil Inati, National Institutes of Health, USA
+* Joe Naegele, National Institutes of Health, USA
+* Kaveh Vahedipour, Juelich Research Centre, Juelich, Germany
+
+Obtaining and Installing
+-------------------------
+
+The source code, examples, and example datasets can be found on the ISMRM Raw Data Sourceforge website_.
+
+.. _website: http://sourceforge.net/projects/ismrmrd
+
+To download the source code, clone the git archive::
+
+ git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
+
+Alternatively download the zip file with the source code::
+
+ wget https://sourceforge.net/projects/ismrmrd/files/src/ismrmrd_latest.zip
+
+API Documentation can be found at http://ismrmrd.sourceforge.net/api.
+
+
+Dependencies
+.............
+
+The ISMRM Raw Data format is described by an XML schema_ and some C-style structs with fixed memory layout and as such does not have dependencies. However, it uses HDF5 files for storage and a C++ library for reading and writing the ISMRMRD files is included in this distribution. Furthermore, since the XML header is defined with an XML schema_, we encourage using XML data binding when writing software using the format. In the ISMRMRD distribution we use the CodeSynthesis XSD (http://www. [...]
+
+
+* HDF5 (version 1.8 or higher) libraries. Available from http://www.hdfgroup.org/downloads/index.html.
+* Boost (http://www.boost.org/)
+* CodeSynthesis XSD (http://www.codesynthesis.com/products/xsd/)
+* Xerces-C XML parser library (http://xerces.apache.org/xerces-c/)
+* Cmake build tool (http://www.cmake.org/)
+* Doxygen if you would like to generate API documentation (http://www.doxygen.org)
+* Git if you would like to use the source code archive (http://git-scm.com/)
+* FFTW if you would like to compile some of the example applications
+ (http://www.fftw.org)
+
+.. note:: It is only necessary to install the dependencies if you wish to develop compiled C/C++ software, which uses the ISMRMRD format. The format can be read in Matlab without installing any additional software.
+
+
+Linux installation
+...................
+
+The dependencies mentioned above should be included in most linux distributions. On Ubuntu you can install all required dependencies with::
+
+ sudo apt-get install libhdf5-serial-dev h5utils cmake cmake-curses-gui libboost-all-dev libxerces-c-dev xsdcxx doxygen git
+
+After installation of dependencies, the library can be installed with::
+
+ git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
+ cd ismrmrd-code/
+ mkdir build
+ cd build
+ cmake ../
+ make
+ sudo make install
+
+Last command will install the library in ``/usr/local/ismrmrd``.
+
+Mac OSX Installation
+.....................
+
+There are numerous different package management systems for Mac. In this example, we have used MacPorts (http://www.macports.org/). First install the dependencies available in MacPorts::
+
+ sudo port install wget hdf5-18 h5utils boost xercesc3 git-core git-extras cmake doxygen
+
+Next install CodeSynthesis XSD (http://www.codesynthesis.com/products/xsd/)::
+
+ wget http://www.codesynthesis.com/download/xsd/3.3/macosx/i686/xsd-3.3.0-i686-macosx.tar.bz2
+ tar -xzf xsd-3.3.0-i686-macosx.tar.bz2
+ cd xsd-3.3.0-i686-macosx
+ sudo cp bin/xsd /usr/local/bin/
+ sudo cp -r libxsd/xsd /usr/local/include/
+
+See faq_ for details on problems on some Mac OSX Lion systems.
+
+Last step is to download and compile::
+
+ git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
+ cd ismrmrd-code/
+ mkdir build
+ cd build/
+ cmake ../
+ make
+ sudo make install
+
+Last command will install the library in ``/usr/local/ismrmrd``.
+
+
+Windows Installation
+.....................
+
+Setting up a Windows development environment is usually a bit more challenging than working on Unix platforms where most library dependencies are easily installed with package management systems (see above). The general Windows installation instructions (you may have to make adjustments for your setup) is as follows:
+
+* Starting with a Windows 7 (64-bit) machine with Visual Studio 2010 installed.
+
+* Install CMake (http://www.cmake.org/files/v2.8/cmake-2.8.9-win32-x86.exe)
+
+* Install Git (http://msysgit.googlecode.com/files/Git-1.7.11-preview20120710.exe)
+
+* Install HDF5 (http://www.hdfgroup.org/ftp/HDF5/current/bin/windows/HDF5189-win64-vs10-shared.zip)
+
+* Install HDFView (http://www.hdfgroup.org/ftp/HDF5/hdf-java/hdfview/hdfview_install_win64.exe)
+
+* Install CodeSynthesis XSD (http://www.codesynthesis.com/download/xsd/3.3/windows/i686/xsd-3.3.msi)
+
+* Install Boost (http://boostpro.com/download/x64/boost_1_51_setup.exe)
+
+ - Just install everything for VS2010 and worry about which versions you need later.
+
+* Install FFTW (ftp://ftp.fftw.org/pub/fftw/fftw-3.3.2-dll64.zip)
+
+ - You need to create ``.lib`` files manually after installing. See instructions at http://www.fftw.org/install/windows.html
+
+* Make sure the paths to your new libraries are in your PATH environment variable:
+
+ - Boost libraries (typically ``C:\Program Files\boost\boost_1_51\lib``)
+ - Code Synthesis XSD (typically ``C:\Program Files (x86)\CodeSynthesis XSD 3.3\bin\;C:\Program Files (x86)\CodeSynthesis XSD 3.3\bin64\``)
+ - FFTW libraries (typically ``C:\MRILibraries\fftw3``)
+ - HDF5 libraries (typically ``C:\Program Files\HDF Group\HDF5\1.8.9\bin``)
+ - ISMRMRD (typically ``C:\Program Files\ismrmrd\bin;C:\Program Files\ismrmrd\bin``)
+
+This can seem a bit daunting, we have included a Windows powershell_ script, which you can use to guide you through the installation process.
+
+.. _powershell: ../WindowsISMRMRDInstallDependencies.ps1
+
+After installing all dependencies, download the code, e.g. from a git bash shell::
+
+ git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
+ cd ismrmrd-code/
+ mkdir build
+ cd build/
+ cmake-gui.exe
+
+Last command will open CMake's graphical user interface. Hit the configure button and deal with the dependencies that CMake is unable to find. Hit configure again and repeat the process until CMake has enough information to configure. Once the configuration is complete, you can hit generate to generate a Visual Studio project, which you can open and use to build ISMRMRD. There are step-by-step commands included in the powershell_ script below to guide you through the CMake configuration [...]
+
+ cmake -G"Visual Studio 10 Win64" -DBOOST_ROOT=C:/Program Files/boost/boost_1_51 \
+ -DXERCESC_INCLUDE_DIR=C:/Program Files (x86)/CodeSynthesis XSD 3.3/include/xercesc \
+ -DXERCESC_LIBRARIES=C:/Program Files (x86)/CodeSynthesis XSD 3.3/lib64/vc-10.0/xerces-c_3.lib \
+ -DXSD_DIR=C:/Program Files (x86)/CodeSynthesis XSD 3.3 \
+ -DFFTW3_INCLUDE_DIR=C:/MRILibraries/fftw3 \
+ -DFFTW3F_LIBRARY=C:/MRILibraries/fftw3/libfftw3f-3.lib ../
+
+Again, you may have to adjust for your specific installation paths. After generating the Visual Studio project, you can build from a Visual Studio Command Prompt with::
+
+ msbuild .\ISMRMRD.sln /p:Configuration=Release
+
+
+Overview
+---------
+
+The raw data format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs). A raw data set consist mainly of 2 sections:
+
+1. A flexible XML format document that can contain an arbitrary number of fields and accommodate everything from simple values (b-values, etc.) to entire vendor protocols, etc. This purpose of this XML document is to provide parameters that may be meaningful for some experiments but not for others. This XML format is defined by an XML Schema Definition file (ismrmrd.xsd).
+2. Raw data section. This section contains all the acquired data in the experiment. Each data item is preceded by a C-struct with encoding numbers, etc. Following this data header is a channel header and data for each acquired channel. The raw data headers are defined in a C/C++ header file (ismrmrd.h)
+
+In addition to these sections, the ISMRMRD format also specifies an image header for storing reconstructed images and the accompanying C++ library provides a convenient way of writing such images into HDF5 files along with generic arrays for storing less well defined data structures, e.g. coil sensitivity maps or other calibration data.
+
+Flexible Data Header
+.....................
+
+The flexible data structure is defined by the xml schema definition in ``schema/ismrmrd.xsd`` (schema_ is included in appendix below).
+
+An example of an XML file for a Cartesian 3D acquisition could look like:
+
+.. include:: ../../schema/ismrmrd_example.xml
+ :literal:
+
+The most critical elements for image reconstruction are contained in the ``<encoding>`` section of the document, which describes the encoded spaced and also the target reconstructed space. Along with the ``<encodingLimits>`` this section allows the reconstruction program to determine matrix sizes, oversampling factors, partial Fourier, etc. In the example above, data is acquired with two-fold oversampling in the read-out (``x``) direction, which is reflected in the larger matrix size in [...]
+
+::
+
+ 0 70 139
+ |-------------------------------------|-------------------------------------------|
+ ****************************************************
+ ^ ^ ^
+ 0 28 83
+
+After FFT, only the central 116 lines are kept, i.e. there is a reduced field of view in the phase encoding direction. Center and encoding limits for the readout dimension is not given in the XML header. This is to accommodate sequences where the center of the readout may change from readout to readout (alternating directions of readout). There is a field on the individual data headers (see below) to indicate the center of the readout.
+
+An experiment can have multiple encoding spaces and it is possible to indicate on each acquired data readout, which encoding space the data belongs to (see below).
+
+In addition to the defined field in the xml header, it is possible to add an arbitrary number of user defined parameters to accommodate special sequence parameters. Please consult the xml schema_ to see how user parameters are defined. Briefly, the XML header can have a section at the end which looks like:
+
+::
+
+ <userParameters>
+ <userParameterLong>
+ <name>MyVar1</name><value>1003</value>
+ </userParameterLong>
+ <userParameterLong>
+ <name>MyVar2</name><value>1999</value>
+ </userParameterLong>
+ <userParameterDouble>
+ <name>MyDoubleVar</name><value>87.6676</value>
+ </userParameterDouble>
+ </userParameters>
+
+
+Fixed Data structures
+......................
+
+Each raw data acquisition is preceded by the following fixed layout structure:
+
+.. include:: ../../include/ismrmrd/ismrmrd.h
+ :literal:
+ :start-after: typedef struct ISMRMRD_AcquisitionHeader {
+ :end-before: } ISMRMRD_AcquisitionHeader;
+
+Where EncodingCounters are defined as:
+
+.. include:: ../../include/ismrmrd/ismrmrd.h
+ :literal:
+ :start-after: typedef struct ISMRMRD_EncodingCounters {
+ :end-before: } ISMRMRD_EncodingCounters;
+
+The interpretation of some of these fields may vary from sequence to sequence, i.e. for a Cartesian sequence, ``kspace_encode_step_1`` would be the phase encoding step, for a spiral sequence where phase encoding direction does not make sense, it would be the spiral interleave number. The ``encoding_space_ref`` enables the user to tie an acquisition to a specific encoding space (see above) in case there are multiple, e.g. in situations where a calibration scan may be integrated in the acq [...]
+
+The flags field is a bit mask, which in principle can be used freely by the user, but suggested flag values are given in ``ismrmrd.h``, it is recommended not to use already designated flag bits for custom purposes. There are a set of bits reserved for prototyping (bits 57-64), please see ``ismrmrd.h`` for details.
+
+The header contains a ``trajectory_dimensions`` field. If the value of this field is larger than 0, it means that trajectories are stored with each individual acquisition. For a 2D acquisition, the ``trajectory_dimensions`` would typically be 2 and the convention (for memory layout) is that the header is followed immediately by the trajectory before the complex data. There is an example of how this memory layout could be implemented with a C++ class in the ``ismrmrd.h`` file:
+
+::
+
+ class Acquisition
+ {
+
+ //....
+
+ AcquisitionHeader head_; //Header, see above
+
+ float* traj_; //Trajectory, elements = head_.trajectory_dimensions*head_.number_of_samples
+ // [kx,ky,kx,ky.....] (for head_.trajectory_dimensions = 2)
+ // [kx,ky,kz,kx,ky,kz,.....] (for head_.trajectory_dimensions = 3)
+
+ float* data_; //Actual data, elements = head_.number_of_samples*head_.active_channels*2
+ // [re,im,re,im,.....,re,im,re,im,.....,re,im,re,im,.....]
+ // ---channel 1-------channel 2---------channel 3-----
+
+ };
+
+This suggested memory layout is only a suggestion. The HDF5 interface (see below) can be used to read the data into many different data structures. In fact, the user can choose to read only part of the header or not read the data, etc.
+
+As mentioned above, the ISMRMRD format also suggests a way to store reconstructed images (or maybe image data used for calibration). An ``ImageHeader`` structure is defined in ``ismrmrd.h``:
+
+.. include:: ../../include/ismrmrd/ismrmrd.h
+ :literal:
+ :start-after: typedef struct ISMRMRD_ImageHeader {
+ :end-before: } ISMRMRD_ImageHeader;
+
+In a similar fashion to the raw data acquisition data, the intention is to store a header followed by the image data. Since image data can be in several different format (e.g. float, complex, etc.), the memory layout is less well defined but can be described as::
+
+ template <typename T> class Image {
+
+ ImageHeader head_; //ImageHeader as defined above
+ T* data_; //Data, array of size (matrix_size[0]*matrix_size[1]*matrix_size[2]*channels),
+ //first spatial dimension is fastest changing array index, channels outer most (slowest changing).
+ };
+
+
+
+File Storage
+-------------
+
+The ISMRM Raw Data format is stored in HDF5 format. Details on this format can be found at the HDF5_ website. Briefly it is a hierarchical data format (much like a file system), which can contain multiple variable organized in groups (like folders in a file system). The variables can contain arrays of data values, custom defined structs, or simple text fields. It is the convention (but not a requirement) that the ISMRMRD datasets are stored in a group called ``/dataset``. The XML configu [...]
+
+::
+
+ >> data = h5read('simple_gre.h5', '/dataset/data');
+ >> data
+
+ data =
+
+ head: [1x1 struct]
+ traj: {1x1281 cell}
+ data: {1x1281 cell}
+
+ >> data.head
+
+ ans =
+
+ version: [1x1281 uint16]
+ flags: [1x1281 uint64]
+ measurement_uid: [1x1281 uint32]
+ scan_counter: [1x1281 uint32]
+ acquisition_time_stamp: [1x1281 uint32]
+ physiology_time_stamp: [3x1281 uint32]
+ number_of_samples: [1x1281 uint16]
+ available_channels: [1x1281 uint16]
+ active_channels: [1x1281 uint16]
+ channel_mask: [16x1281 uint64]
+ discard_pre: [1x1281 uint16]
+ discard_post: [1x1281 uint16]
+ center_sample: [1x1281 uint16]
+ encoding_space_ref: [1x1281 uint16]
+ trajectory_dimensions: [1x1281 uint16]
+ sample_time_us: [1x1281 single]
+ position: [3x1281 single]
+ read_dir: [3x1281 single]
+ phase_dir: [3x1281 single]
+ slice_dir: [3x1281 single]
+ patient_table_position: [3x1281 single]
+ idx: [1x1 struct]
+ user_int: [8x1281 int32]
+ user_float: [8x1281 single]
+
+ >>
+
+The HDF5 file format can be access from C, C++, and java using the libraries provided on the HDF5 website. The ISMRMRD distribution also comes with some C++ wrappers that can be used for easy access (read and write) from C++ programs. See below.
+
+In addition to storing acquisition data and images as defined by the headers above, the HDF5 format also enables storage of generic multi-dimensional arrays. The ISMRMRD format does not explicitly define how such data should be stored, but leaves it open for the user to add variables and data as dictated by a given application.
+
+.. _HDF5: http://www.hdfgroup.org/HDF5/
+
+C++ Support Library
+--------------------
+
+To enable easy prototyping of C++ software using the ISMRMRD data format, a simple C++ wrapper class is provided (defined in ``ismrmrd_hdf5.h``):
+
+::
+
+ class EXPORTISMRMRD IsmrmrdDataset
+ {
+ public:
+
+ IsmrmrdDataset(const char* filename, const char* groupname, bool create_file_if_needed = true)
+ : filename_(filename)
+ , groupname_(groupname)
+ , file_open_(false)
+ , dataset_open_(false)
+ , create_file_if_needed_(create_file_if_needed)
+ {
+ std::ifstream ifile(filename_.c_str());
+ file_exists_ = ifile;
+
+ if (openHDF5File() < 0) {
+ std::cerr << "IsmrmrdDataset: Error opening HDF file." << std::endl;
+ }
+
+ if (!linkExists(groupname_.c_str())) {
+ if (createGroupForDataset(groupname_.c_str()) < 0) {
+ std::cerr << "IsmrmrdDataset: Error create HDF5 group." << std::endl;
+ }
+ }
+
+ xml_header_path_ = groupname_ + std::string("/xml");
+ data_path_ = groupname_ + std::string("/data");
+ }
+
+ int appendAcquisition(Acquisition* a);
+ boost::shared_ptr<Acquisition> readAcquisition(unsigned long index = 0);
+ unsigned long getNumberOfAcquisitions();
+
+ int writeHeader(std::string& xml);
+ boost::shared_ptr<std::string> readHeader();
+
+ template <typename T> int appendImage(Image<T>& m, const char* varname);
+ template <typename T> boost::shared_ptr< Image<T> > readImage(const char* varname, unsigned long index = 0);
+
+ int appendImageHeader(ImageHeader& h, const char* varname);
+ boost::shared_ptr< ImageHeader > readImageHeader(const char* varname, unsigned long index = 0);
+
+ template <typename T> int appendArray(NDArrayContainer<T>& a, const char* varname);
+ template <typename T> int appendArray(std::vector<unsigned int>& dimensions, T* data, const char* varname);
+ template <typename T> boost::shared_ptr< NDArrayContainer<T> > readArray(const char* varname, unsigned long index = 0);
+ };
+
+
+Using this wrapper, C++ applications can be programmed as:
+
+::
+
+ boost::shared_ptr<ISMRMRD::IsmrmrdDataset> ismrmrd_dataset(new ISMRMRD::IsmrmrdDataset(hdf5_in_data_file,hdf5_in_group));
+ boost::shared_ptr<std::string> xml_config = ismrmrd_dataset->readHeader();
+
+ //Do something with the header
+
+ unsigned long acquisitions = ismrmrd_dataset->getNumberOfAcquisitions();
+
+ for (unsigned long int i = 0; i < acquisitions; i++) {
+ boost::shared_ptr<ISMRMRD::Acquisition> acq_tmp = ismrmrd_dataset->readAcquisition(i);
+ //Do something with the data
+ }
+
+Since the XML part of the header is defined in the ``schema/ismrmrd.xsd`` file, it is possible to use XML data binding tools such as CodeSynthesys XSD to generate a C++ class representation of the header for easy access to the fields. The ``cmake`` build files that accompany the ISMRMRD distribution automatically tries to find CodeSynthesis XSD and generate such a binding. With the C++ representation of the header it can be parsed with something like:
+
+::
+
+ xml_schema::properties props;
+ props.schema_location ("http://www.ismrm.org/ISMRMRD",std::string("/full/path/to/ismrmrd.xsd"));
+ std::istringstream str_stream(xml, std::stringstream::in);
+ boost::shared_ptr<ISMRMRD::ismrmrdHeader> cfg;
+
+ try {
+ cfg = boost::shared_ptr<ISMRMRD::ismrmrdHeader>(ISMRMRD::ismrmrdHeader_ (str_stream,0,props));
+ } catch (const xml_schema::exception& e) {
+ std::cout << "Failed to parse XML Parameters: " << e.what() << std::endl;
+ }
+
+ //Use the configuration, e.g.:
+ std::cout << "Number of encoding spaces: " << cfg->encoding().size() << std::endl;
+
+Again, this is not a requirement for using the ISMRMRD format, the XML can be parsed with numerous other xml parsing libraries. The schema file ``schema/ismrmrd.xsd`` gives the user the option of validating the XML header before parsing, which is recommended to reduce the chance of hard to detect errors in your code due to missing or malformed parameters.
+
+C++ Example Applications
+..........................
+
+The distribution includes two example applications, one that creates a simple 2D single-channel dataset from scratch and one that reconstructs this dataset (you need FFTW installed to compile these test applications). The data generation application looks like this (``generate_cartesian_shepp_logan.cpp``):
+
+.. include:: ../../utilities/generate_cartesian_shepp_logan.cpp
+ :literal:
+ :start-after: // MAIN APPLICATION
+
+To reconstruct this synthetic dataset, you can use the test reconstruction application (``recon_cartesian_2d.cpp``):
+
+.. include:: ../../utilities/recon_cartesian_2d.cpp
+ :literal:
+ :start-after: // MAIN APPLICATION
+
+
+Matlab Example Code and Datasets
+--------------------------------
+
+The ``examples`` folder contains some matlab code to illustrate simple interaction with the ISMRMRD data format. The examples use test data sets, wich can be downloaded from the Sourceforge website_. Go to the ``examples/data`` folder and type the following to download the data::
+
+ wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5
+ wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5
+ wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5
+
+
+For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the ``examples/matlab`` folder):
+
+::
+
+ >> images = simple_cartesian_recon('../data/simple_gre.h5');
+ Reconstructing image 1....done
+ Reconstructing image 2....done
+ Reconstructing image 3....done
+ Reconstructing image 4....done
+ Reconstructing image 5....done
+ Reconstructing image 6....done
+ Reconstructing image 7....done
+ Reconstructing image 8....done
+ Reconstructing image 9....done
+ Reconstructing image 10....done
+ >>
+
+You should see one of the reconstructed images display. An example is also given of a 3D acquisition with partial Fourier, phase and slice oversampling, etc. Reconstruct this dataset with:
+
+::
+
+ >> images = simple_cartesian_recon('../data/3D_partial_fourier.h5');
+ Reconstructing image 1....done
+
+The center slice of the volume should be displayed at the end of the reconstruction.
+
+Finally, there is also a spiral dataset. This dataset illustrates how the flexible section of the ``<trajectoryDescription>`` can be used to add user defined parameters and an identifier to describe the trajectory. This dataset is also an example of storing the trajectory with the data for direct reconstruction. Reconstruct this dataset with:
+
+::
+
+ >> images = simple_spiral_recon('../data/simple_spiral.h5');
+ Reconstructing image 1....done
+ Reconstructing image 2....done
+ Reconstructing image 3....done
+ Reconstructing image 4....done
+ Reconstructing image 5....done
+ Reconstructing image 6....done
+ Reconstructing image 7....done
+ Reconstructing image 8....done
+ Reconstructing image 9....done
+ Reconstructing image 10....done
+ >>
+
+Appendix
+---------
+
+Frequently Asked Questions
+...........................
+.. _faq:
+
+* I am trying to compile on Mac OSX Lion and I am getting strange errors.
+
+ in version 3.3.0 of CodeSynthesis XSD there is a problem with the clang compiler. It can build with clang on os x 10.7 (Lion) by editing
+ `/usr/local/include/xsd/cxx/zc-istream.txx`. Change line 35 from::
+
+ setg (b, b, e);
+
+ to::
+
+ std::streambuf::setg (b, b, e);
+
+ See also:
+ http://codesynthesis.com/pipermail/xsd-users/2011-May/003283.html
+
+XML Schema Definition
+......................
+.. _schema:
+
+.. include:: ../../schema/ismrmrd.xsd
+ :literal:
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/utilities/generate_cartesian_shepp_logan.cpp b/utilities/generate_cartesian_shepp_logan.cpp
index 7564626..0199e0e 100644
--- a/utilities/generate_cartesian_shepp_logan.cpp
+++ b/utilities/generate_cartesian_shepp_logan.cpp
@@ -20,6 +20,7 @@
using namespace ISMRMRD;
namespace po = boost::program_options;
+// MAIN APPLICATION
int main(int argc, char** argv)
{
/** TODO
diff --git a/utilities/recon_cartesian_2d.cpp b/utilities/recon_cartesian_2d.cpp
index aa658f6..3c09b0b 100644
--- a/utilities/recon_cartesian_2d.cpp
+++ b/utilities/recon_cartesian_2d.cpp
@@ -32,7 +32,7 @@ void print_usage(const char* application)
std::cout << " - " << application << " <HDF5_FILENAME> " << std::endl;
}
-/* MAIN APPLICATION */
+// MAIN APPLICATION
int main(int argc, char** argv)
{
if (argc < 2) {
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