Documentation updates.

Dockerfile

@@ -1,7 +1,8 @@
 FROM archlinux
 MAINTAINER J.A. de Jong - j.a.dejong@ascee.nl
 RUN pacman --noconfirm -Sy
-RUN pacman --noconfirm -S git doxygen graphviz lighttpd
+RUN pacman --noconfirm -S git doxygen graphviz lighttpd python-pip
+RUN pip install doxypypy
 WORKDIR /root
 RUN git clone https://code.ascee.nl/ascee/lasp
 WORKDIR /root/lasp

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.17
+# Doxyfile 1.9.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -51,7 +51,7 @@ PROJECT_BRIEF          = "Library for Acoustic Signal Processing"
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           = /home/anne/wip/mycode/lasp/img/LASP_200px.png
+PROJECT_LOGO           = img/LASP_200px.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -93,6 +93,14 @@ ALLOW_UNICODE_NAMES    = NO
 
 OUTPUT_LANGUAGE        = English
 
+# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all generated output in the proper direction.
+# Possible values are: None, LTR, RTL and Context.
+# The default value is: None.
+
+OUTPUT_TEXT_DIRECTION  = None
+
 # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
 # descriptions after the members that are listed in the file and class
 # documentation (similar to Javadoc). Set to NO to disable this.
@@ -225,7 +233,7 @@ MULTILINE_CPP_IS_BRIEF = NO
 # documentation blocks is shown as doxygen documentation.
 # The default value is: YES.
 
-PYTHON_DOCSTRING       = YES
+PYTHON_DOCSTRING       = NO
 
 # If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
 # documentation from any documented member that it re-implements.
@@ -250,16 +258,16 @@ TAB_SIZE               = 4
 # the documentation. An alias has the form:
 # name=value
 # For example adding
-# "sideeffect=@par Side Effects:^^"
+# "sideeffect=@par Side Effects:\n"
 # will allow you to put the command \sideeffect (or @sideeffect) in the
 # documentation, which will result in a user-defined paragraph with heading
-# "Side Effects:". Note that you cannot put \n's in the value part of an alias
+# "Side Effects:". You can put \n's in the value part of an alias to insert
-# to insert newlines (in the resulting output). You can put ^^ in the value part
+# newlines (in the resulting output). You can put ^^ in the value part of an
-# of an alias to insert a newline as if a physical newline was in the original
+# alias to insert a newline as if a physical newline was in the original file.
-# file. When you need a literal { or } or , in the value part of an alias you
+# When you need a literal { or } or , in the value part of an alias you have to
-# have to escape them by means of a backslash (\), this can lead to conflicts
+# escape them by means of a backslash (\), this can lead to conflicts with the
-# with the commands \{ and \} for these it is advised to use the version @{ and
+# commands \{ and \} for these it is advised to use the version @{ and @} or use
-# @} or use a double escape (\\{ and \\})
+# a double escape (\\{ and \\})
 
 ALIASES                =
 
@@ -304,8 +312,8 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 # extension. Doxygen has a built-in mapping, but you can override or extend it
 # using this tag. The format is ext=language, where ext is a file extension, and
 # language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
-# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
+# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
-# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
+# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
 # FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
 # tries to guess whether the code is fixed or free formatted code, this is the
 # default for Fortran type files). For instance to make doxygen treat .inc files
@@ -458,7 +466,7 @@ LOOKUP_CACHE_SIZE      = 0
 # than 0 to get more control over the balance between CPU load and processing
 # speed. At this moment only the input processing can be done using multiple
 # threads. Since this is still an experimental feature the default is set to 1,
-# which effectively disables parallel processing. Please report any issues you
+# which efficively disables parallel processing. Please report any issues you
 # encounter. Generating dot graphs in parallel is controlled by the
 # DOT_NUM_THREADS setting.
 # Minimum value: 0, maximum value: 32, default value: 1.
@@ -602,12 +610,6 @@ HIDE_SCOPE_NAMES       = NO
 
 HIDE_COMPOUND_REFERENCE= NO
 
-# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
-# will show which file needs to be included to use the class.
-# The default value is: YES.
-
-SHOW_HEADERFILE        = YES
-
 # If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
 # the files that are included by a file in the documentation of that file.
 # The default value is: YES.
@@ -765,8 +767,7 @@ FILE_VERSION_FILTER    =
 # output files in an output format independent way. To create the layout file
 # that represents doxygen's defaults, run doxygen with the -l option. You can
 # optionally specify a file name after the option, if omitted DoxygenLayout.xml
-# will be used as the name of the layout file. See also section "Changing the
+# will be used as the name of the layout file.
-# layout of pages" for information.
 #
 # Note that if you run doxygen from a directory containing a file called
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
@@ -812,26 +813,18 @@ WARNINGS               = YES
 WARN_IF_UNDOCUMENTED   = YES
 
 # If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as documenting some parameters in
+# potential errors in the documentation, such as not documenting some parameters
-# a documented function twice, or documenting parameters that don't exist or
+# in a documented function, or documenting parameters that don't exist or using
-# using markup commands wrongly.
+# markup commands wrongly.
 # The default value is: YES.
 
 WARN_IF_DOC_ERROR      = YES
 
-# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
-# function parameter documentation. If set to NO, doxygen will accept that some
-# parameters have no documentation without warning.
-# The default value is: YES.
-
-WARN_IF_INCOMPLETE_DOC = YES
-
 # This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
 # are documented, but have no documentation for their parameters or return
-# value. If set to NO, doxygen will only warn about wrong parameter
+# value. If set to NO, doxygen will only warn about wrong or incomplete
-# documentation, but not about the absence of documentation. If EXTRACT_ALL is
+# parameter documentation, but not about the absence of documentation. If
-# set to YES then this flag will automatically be disabled. See also
+# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
-# WARN_IF_INCOMPLETE_DOC
 # The default value is: NO.
 
 WARN_NO_PARAMDOC       = NO
@@ -857,10 +850,7 @@ WARN_FORMAT            = "$file:$line: $text"
 
 # The WARN_LOGFILE tag can be used to specify a file to which warning and error
 # messages should be written. If left blank the output is written to standard
-# error (stderr). In case the file specified cannot be opened for writing the
+# error (stderr).
-# warning and error messages are written to standard error. When as file - is
-# specified the warning and error messages are written to standard output
-# (stdout).
 
 WARN_LOGFILE           =
 
@@ -898,55 +888,16 @@ INPUT_ENCODING         = UTF-8
 #
 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
 # *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
-# *.hh, *.hxx, *.hpp, *.h++, *.l, *.cs, *.d, *.php, *.php4, *.php5, *.phtml,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C
+# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment),
-# comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
+# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl,
-# *.vhdl, *.ucf, *.qsf and *.ice.
+# *.ucf, *.qsf and *.ice.
 
 FILE_PATTERNS          = *.c \
-                         *.cc \
-                         *.cxx \
                          *.cpp \
-                         *.c++ \
-                         *.java \
-                         *.ii \
-                         *.ixx \
-                         *.ipp \
-                         *.i++ \
-                         *.inl \
-                         *.idl \
-                         *.ddl \
-                         *.odl \
                          *.h \
-                         *.hh \
-                         *.hxx \
-                         *.hpp \
-                         *.h++ \
-                         *.cs \
-                         *.d \
-                         *.php \
-                         *.php4 \
-                         *.php5 \
-                         *.phtml \
-                         *.inc \
-                         *.m \
-                         *.markdown \
                          *.md \
-                         *.mm \
+                         *.py=scripts/py_filter
-                         *.dox \
-                         *.py \
-                         *.pyw \
-                         *.f90 \
-                         *.f95 \
-                         *.f03 \
-                         *.f08 \
-                         *.f \
-                         *.for \
-                         *.tcl \
-                         *.vhd \
-                         *.vhdl \
-                         *.ucf \
-                         *.qsf
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -983,7 +934,7 @@ EXCLUDE_PATTERNS       =
 # (namespaces, classes, functions, etc.) that should be excluded from the
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
-# ANamespace::AClass, ANamespace::*Test
+# AClass::ANamespace, ANamespace::*Test
 #
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
@@ -1158,6 +1109,44 @@ USE_HTAGS              = NO
 
 VERBATIM_HEADERS       = YES
 
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see:
+# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
+# performance. This can be particularly helpful with template rich C++ code for
+# which doxygen's built-in parser lacks the necessary type information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled and the CLANG_ADD_INC_PATHS tag is set to
+# YES then doxygen will add the directory of each input to the include path.
+# The default value is: YES.
+
+CLANG_ADD_INC_PATHS    = YES
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          =
+
+# If clang assisted parsing is enabled you can provide the clang parser with the
+# path to the directory containing a file called compile_commands.json. This
+# file is the compilation database (see:
+# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
+# options used when the source files were built. This is equivalent to
+# specifying the -p option to a clang tool, such as clang-check. These options
+# will then be passed to the parser. Any options specified with CLANG_OPTIONS
+# will be added as well.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse_libclang=ON option for CMake.
+
+CLANG_DATABASE_PATH    =
+
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1268,7 +1257,7 @@ HTML_EXTRA_FILES       =
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
-# this color. Hue is specified as an angle on a color-wheel, see
+# this color. Hue is specified as an angle on a colorwheel, see
 # https://en.wikipedia.org/wiki/Hue for more information. For instance the value
 # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
 # purple, and 360 is red again.
@@ -1278,7 +1267,7 @@ HTML_EXTRA_FILES       =
 HTML_COLORSTYLE_HUE    = 220
 
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
-# in the HTML output. For a value of 0 the output will use gray-scales only. A
+# in the HTML output. For a value of 0 the output will use grayscales only. A
 # value of 255 will produce the most vivid colors.
 # Minimum value: 0, maximum value: 255, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
@@ -1360,13 +1349,6 @@ GENERATE_DOCSET        = NO
 
 DOCSET_FEEDNAME        = "Doxygen generated docs"
 
-# This tag determines the URL of the docset feed. A documentation feed provides
-# an umbrella under which multiple documentation sets from a single provider
-# (such as a company or product suite) can be grouped.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_FEEDURL         =
-
 # This tag specifies a string that should uniquely identify the documentation
 # set bundle. This should be a reverse domain-name style string, e.g.
 # com.mycompany.MyDocSet. Doxygen will append .docset to the name.
@@ -1392,12 +1374,8 @@ DOCSET_PUBLISHER_NAME  = Publisher
 # If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
 # additional HTML index files: index.hhp, index.hhc, and index.hhk. The
 # index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
-# on Windows. In the beginning of 2021 Microsoft took the original page, with
+# (see:
-# a.o. the download links, offline the HTML help workshop was already many years
+# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows.
-# in maintenance mode). You can download the HTML help workshop from the web
-# archives at Installation executable (see:
-# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
-# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
 #
 # The HTML Help Workshop contains a compiler that can convert all HTML output
 # generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
@@ -1556,28 +1534,16 @@ DISABLE_INDEX          = NO
 # to work a browser that supports JavaScript, DHTML, CSS and frames is required
 # (i.e. any modern browser). Windows users are probably better off using the
 # HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
-# further fine tune the look of the index (see "Fine-tuning the output"). As an
+# further fine-tune the look of the index. As an example, the default style
-# example, the default style sheet generated by doxygen has an example that
+# sheet generated by doxygen has an example that shows how to put an image at
-# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
-# Since the tree basically has the same information as the tab index, you could
+# the same information as the tab index, you could consider setting
-# consider setting DISABLE_INDEX to YES when enabling this option.
+# DISABLE_INDEX to YES when enabling this option.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_TREEVIEW      = YES
 
-# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
-# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
-# area (value NO) or if it should extend to the full height of the window (value
-# YES). Setting this to YES gives a layout similar to
-# https://docs.readthedocs.io with more room for contents, but less room for the
-# project logo, title, and description. If either GENERATE_TREEVIEW or
-# DISABLE_INDEX is set to NO, this option has no effect.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FULL_SIDEBAR           = NO
-
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
 #
@@ -1602,13 +1568,6 @@ TREEVIEW_WIDTH         = 250
 
 EXT_LINKS_IN_WINDOW    = NO
 
-# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
-# addresses.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-OBFUSCATE_EMAILS       = YES
-
 # If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
 # tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
 # https://inkscape.org) to generate formulas as SVG images instead of PNGs for
@@ -1657,29 +1616,11 @@ FORMULA_MACROFILE      =
 
 USE_MATHJAX            = NO
 
-# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
-# Note that the different versions of MathJax have different requirements with
-# regards to the different settings, so it is possible that also other MathJax
-# settings have to be changed when switching between the different MathJax
-# versions.
-# Possible values are: MathJax_2 and MathJax_3.
-# The default value is: MathJax_2.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_VERSION        = MathJax_2
-
 # When MathJax is enabled you can set the default output format to be used for
-# the MathJax output. For more details about the output format see MathJax
+# the MathJax output. See the MathJax site (see:
-# version 2 (see:
+# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details.
-# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
-# (see:
-# http://docs.mathjax.org/en/latest/web/components/output.html).
 # Possible values are: HTML-CSS (which is slower, but has the best
-# compatibility. This is the name for Mathjax version 2, for MathJax version 3
+# compatibility), NativeMML (i.e. MathML) and SVG.
-# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
-# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
-# is the name for Mathjax version 3, for MathJax version 2 this will be
-# translated into HTML-CSS) and SVG.
 # The default value is: HTML-CSS.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
@@ -1692,21 +1633,15 @@ MATHJAX_FORMAT         = HTML-CSS
 # MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
 # Content Delivery Network so you can quickly see the result without installing
 # MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from https://www.mathjax.org before deployment. The default value is:
+# MathJax from https://www.mathjax.org before deployment.
-# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
+# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
-# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
-# for MathJax version 2 (see
-# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
-# For example for MathJax version 3 (see
-# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
-# MATHJAX_EXTENSIONS = ams
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_EXTENSIONS     =
@@ -1886,31 +1821,29 @@ PAPER_TYPE             = a4
 
 EXTRA_PACKAGES         =
 
-# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
-# the generated LaTeX document. The header should contain everything until the
+# generated LaTeX document. The header should contain everything until the first
-# first chapter. If it is left blank doxygen will generate a standard header. It
+# chapter. If it is left blank doxygen will generate a standard header. See
-# is highly recommended to start with a default header using
+# section "Doxygen usage" for information on how to let doxygen write the
-# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
+# default header to a separate file.
-# and then modify the file new_header.tex. See also section "Doxygen usage" for
-# information on how to generate the default header that doxygen normally uses.
 #
-# Note: Only use a user-defined header if you know what you are doing!
+# Note: Only use a user-defined header if you know what you are doing! The
-# Note: The header is subject to change so you typically have to regenerate the
+# following commands have a special meaning inside the header: $title,
-# default header when upgrading to a newer version of doxygen. The following
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
-# commands have a special meaning inside the header (and footer): For a
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
-# description of the possible markers and block names see the documentation.
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HEADER           =
 
-# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
-# the generated LaTeX document. The footer should contain everything after the
+# generated LaTeX document. The footer should contain everything after the last
-# last chapter. If it is left blank doxygen will generate a standard footer. See
+# chapter. If it is left blank doxygen will generate a standard footer. See
 # LATEX_HEADER for more information on how to generate a default footer and what
-# special commands can be used inside the footer. See also section "Doxygen
+# special commands can be used inside the footer.
-# usage" for information on how to generate the default footer that doxygen
+#
-# normally uses. Note: Only use a user-defined footer if you know what you are
+# Note: Only use a user-defined footer if you know what you are doing!
-# doing!
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_FOOTER           =
@@ -1955,7 +1888,8 @@ USE_PDFLATEX           = YES
 
 # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
 # command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help.
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -1968,6 +1902,16 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
 # https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
@@ -2048,6 +1992,16 @@ RTF_STYLESHEET_FILE    =
 
 RTF_EXTENSIONS_FILE    =
 
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
 #---------------------------------------------------------------------------
 # Configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -2144,6 +2098,15 @@ GENERATE_DOCBOOK       = NO
 
 DOCBOOK_OUTPUT         = docbook
 
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -2156,6 +2119,10 @@ DOCBOOK_OUTPUT         = docbook
 
 GENERATE_AUTOGEN_DEF   = NO
 
+#---------------------------------------------------------------------------
+# Configuration options related to Sqlite3 output
+#---------------------------------------------------------------------------
+
 #---------------------------------------------------------------------------
 # Configuration options related to the Perl module output
 #---------------------------------------------------------------------------
@@ -2322,6 +2289,15 @@ EXTERNAL_PAGES         = YES
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = YES
+
 # You can include diagrams made with dia in doxygen documentation. Doxygen will
 # then run dia to produce the diagram and insert it in the documentation. The
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.
@@ -2340,7 +2316,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
 # Bell Labs. The other options in this section have no effect if this option is
 # set to NO
-# The default value is: NO.
+# The default value is: YES.
 
 HAVE_DOT               = YES
 
@@ -2378,14 +2354,11 @@ DOT_FONTSIZE           = 10
 
 DOT_FONTPATH           =
 
-# If the CLASS_GRAPH tag is set to YES (or GRAPH) then doxygen will generate a
+# If the CLASS_GRAPH tag is set to YES then doxygen will generate a graph for
-# graph for each documented class showing the direct and indirect inheritance
+# each documented class showing the direct and indirect inheritance relations.
-# relations. In case HAVE_DOT is set as well dot will be used to draw the graph,
+# Setting this tag to YES will force the CLASS_DIAGRAMS tag to NO.
-# otherwise the built-in generator will be used. If the CLASS_GRAPH tag is set
-# to TEXT the direct and indirect inheritance relations will be shown as texts /
-# links.
-# Possible values are: NO, YES, TEXT and GRAPH.
 # The default value is: YES.
+# This tag requires that the tag HAVE_DOT is set to YES.
 
 CLASS_GRAPH            = YES
 
@@ -2514,13 +2487,6 @@ GRAPHICAL_HIERARCHY    = YES
 
 DIRECTORY_GRAPH        = YES
 
-# The DIR_GRAPH_MAX_DEPTH tag can be used to limit the maximum number of levels
-# of child directories generated in directory dependency graphs by dot.
-# Minimum value: 1, maximum value: 25, default value: 1.
-# This tag requires that the tag DIRECTORY_GRAPH is set to YES.
-
-DIR_GRAPH_MAX_DEPTH    = 1
-
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
 # generated by dot. For an explanation of the image formats see the section
 # output formats in the documentation of the dot tool (Graphviz (see:
@@ -2528,7 +2494,9 @@ DIR_GRAPH_MAX_DEPTH    = 1
 # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
 # to make the SVG files visible in IE 9+ (other browsers do not have this
 # requirement).
-# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo,
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo,
 # png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and
 # png:gdiplus:gdiplus.
 # The default value is: png.
@@ -2574,10 +2542,10 @@ MSCFILE_DIRS           =
 DIAFILE_DIRS           =
 
 # When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
-# path where java can find the plantuml.jar file or to the filename of jar file
+# path where java can find the plantuml.jar file. If left blank, it is assumed
-# to be used. If left blank, it is assumed PlantUML is not used or called during
+# PlantUML is not used or called during a preprocessing step. Doxygen will
-# a preprocessing step. Doxygen will generate a warning when it encounters a
+# generate a warning when it encounters a \startuml command in this case and
-# \startuml command in this case and will not generate output for the diagram.
+# will not generate output for the diagram.
 
 PLANTUML_JAR_PATH      =
 
@@ -2639,8 +2607,6 @@ DOT_MULTI_TARGETS      = NO
 # If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
 # explaining the meaning of the various boxes and arrows in the dot generated
 # graphs.
-# Note: This tag requires that UML_LOOK isn't set, i.e. the doxygen internal
-# graphical representation for inheritance and collaboration diagrams is used.
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
@@ -2649,8 +2615,8 @@ GENERATE_LEGEND        = YES
 # If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate
 # files that are used to generate the various graphs.
 #
-# Note: This setting is not only used for dot files but also for msc temporary
+# Note: This setting is not only used for dot files but also for msc and
-# files.
+# plantuml temporary files.
 # The default value is: YES.
 
 DOT_CLEANUP            = YES

README.md

@@ -8,27 +8,39 @@ Welcome to LASP: Library for Acoustic Signal Processing. LASP is a C++ library
 with a Python interface which is supposed to acquire and process (multi) sensor data in real time on a PC and output results.
 
 Current features that are implemented:
-- Compile-time determination of the floating-point accuracy (32/64 bit)
+
-- Fast convolution FIR filter implementation
+- Communication with data acquisition (DAQ) devices, of which:
-- Sample rate decimation by an integer factor of 4.
+    - Internal sound cards via the [RtAudio](http://www.music.mcgill.ca/~gary/rtaudio) backend. Many thanks to Gary P. Scavone et al.
-- Octave filterbank FIR filters designed to comply with IEC 61260
+    - [Measurement Computing](https://www.mccdaq.com) [DT9838A](https://www.mccdaq.com/Products/Sound-Vibration-DAQ/DT9837) signal analyzer.
-  (1995).
+- Configuration of DAQ devices: AC coupling, IEPE, sensitivity physical
+  quantities.
+- Recording of signals from these DAQ devices, and storing in a HDF5 file.
+- Filter designers to create A/C sound pressure weighting
+- Biquad filter designers for low pass, high pass, peaking and notch filters
+- A Peak Programme Meter (PPM) to monitor signal levels from DAQ and to watch
+  for signal clipping.
+- A signal generator to create sine waves, sweeps and noise (white / pink).
+- Equalizers to equalize the output prior to sending.
 - Averaged power spectra and power spectral density determination
   using Welch' method. Taper functions of Hann, Hamming, Bartlett and
   Blackman are provided.
-- A thread-safe job queue including routines to create worker threads.
+- (One third) octave filter bank filters designed to comply with IEC 61260
-- Several linear algebra routines (wrappers around BLAS and LAPACK).
-- A nice debug tracer implementation
-- Third octave filter bank FIR filters designed to comply with IEC 61260
   (1995).
 - Slow and fast time updates of (A/C/Z) weighted sound pressure levels
+- Full Sound Level Meter implementation
+- Real time Sound Level meter, Power / Transfer function estimator
+- Spectra data smoothing algorithms
+- Sensor calibration for microphones
 
 Future features (wish-list)
-- Conventional and delay-and-sum beam-forming algorithms
 
-For now, the source code is well-documented but it requires some
+- Conventional and delay-and-sum beam-forming algorithms
-additional documentation (the math behind it). This will be published
+- Impedance tube measurement processing
-in a sister repository (https://code.ascee.nl/ascee/lasp-doc).
+
+For now, the source code is well-documented on [lasp.ascee.nl](https://lasp.ascee.nl) but it requires some
+additional documentation (the math behind it). This is maintained
+in a sister repository [lasp-doc](https://code.ascee.nl/ascee/lasp-doc). The
+most recent
 
 If you have any question(s), please feel free to contact us: info@ascee.nl.
 
@@ -67,7 +79,10 @@ Configure and run:
 
 ### Build documentation
 
-`$ sudo apt install doxygen`
+In directory:
+
+`$ sudo apt install doxygen graphviz`
+`$ pip install doxypypy`
 
 While still in lasp dir:
 
@@ -77,6 +92,10 @@ This will build the documentation. It can be read by:
 
 `$ <YOUR-BROWSER> doc/html/index.html`
 
+Or via docker:
+
+`$ docker build -t lasp_ascee_nl:latest .`
+
 ## Install
 
 For an editable install (while developing):

src/lasp/__init__.py

@@ -1,4 +1,3 @@
-# Comments are what is imported, state of 6-8-2021
 """
 LASP: Library for Acoustic Signal Processing
 

src/lasp/lasp_cpp.cpp

@@ -8,14 +8,23 @@
  * Welcome to the LASP (Library for Acoustic Signal Processing) code
  * documentation. The code comprises a part which is written in C++, a part
  * that is written in Python, and a part that functions as glue, which is
- * Pybind11 C++ glue code. An example of such a file is the current one.
+ * Pybind11 C++ glue code. An example of such a file is lasp_cpp.cpp.
+ * This is the internal documentation of LASP. It serves as background
+ * information for programmers.
  *
  * \section Installation
  *
- * For the installation manual, please refer to the README.md of the Git
+ * For the installation manual, please refer to the <a
- * repository. It is recommended to install the software from source.
+ * href="https://code.ascee.nl/ASCEE/lasp/src/branch/master/README.md">README</a>
+ * of the Git repository.
  *
  *
+ * \section Usage
+ *
+ * Some usage examples are given in the <a href=
+ * "https://code.ascee.nl/ASCEE/lasp/src/branch/master/examples">examples</a>
+ * directory of the repository.
+ *
  * */
 
 /**
@@ -48,7 +57,6 @@ PYBIND11_MODULE(lasp_cpp, m) {
   m.attr("__version__") = std::to_string(LASP_VERSION_MAJOR) + "." +
                           std::to_string(LASP_VERSION_MINOR);
 
-
   m.attr("LASP_VERSION_MAJOR") = LASP_VERSION_MAJOR;
   m.attr("LASP_VERSION_MINOR") = LASP_VERSION_MINOR;
 }