develop Merge doxygen from 1.12 branch (#2095)

CMakeLists.txt

@@ -12,6 +12,11 @@ if (POLICY CMP0083)
   cmake_policy (SET CMP0083 NEW)
 endif ()
 
+# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+    cmake_policy(SET CMP0135 NEW)
+endif()
+
 #-----------------------------------------------------------------------------
 # Instructions for use : Normal Build
 #

CTestConfig.cmake

@@ -12,7 +12,7 @@
 ## This file should be placed in the root directory of your project.
 ## Then modify the CMakeLists.txt file in the root directory of your
 ## project to incorporate the testing dashboard.
-## # The following are required to use Dart and the CDash dashboard.
+## # The following are required to use Dart and the CDash dashboard
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
 set (CTEST_PROJECT_NAME "HDF5")

config/cmake/UseJava.cmake

@@ -1448,6 +1448,7 @@ function(create_javadoc _target)
 
     add_custom_target(${_target}_javadoc ALL
         COMMAND ${Java_JAVADOC_EXECUTABLE}
+                -Xdoclint:none
                 ${_javadoc_options}
                 ${_javadoc_files}
                 ${_javadoc_packages}

configure.ac

@@ -1213,6 +1213,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
 
   AC_SUBST([DOXYGEN_PACKAGE])
   AC_SUBST([DOXYGEN_VERSION_STRING])
+  AC_SUBST([DOXYGEN_DIR])
   AC_SUBST([DOXYGEN_INCLUDE_ALIASES])
   AC_SUBST([DOXYGEN_PROJECT_LOGO])
   AC_SUBST([DOXYGEN_PROJECT_BRIEF])
@@ -1237,6 +1238,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
 # SRCDIR Environment variables used inside doxygen macro for the source location:
   DOXYGEN_PACKAGE=${PACKAGE_NAME}
   DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
+  DOXYGEN_DIR='$(SRCDIR)/doxygen'
   DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
   DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
   DOXYGEN_PROJECT_BRIEF=''
@@ -1249,14 +1251,14 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
   DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
   DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
-  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/FF-IH_FileGroup.gif $(SRCDIR)/doxygen/img/FF-IH_FileObject.gif $(SRCDIR)/doxygen/img/FileFormatSpecChunkDiagram.jpg $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png $(SRCDIR)/doxygen/img/HDFG-logo.png $(SRCDIR)/doxygen/img/IOFlow2.gif $(SRCDIR)/doxygen/img/IOFlow3.gif $(SRCDIR)/doxygen/img/IOFlow.gif $(SRCDIR)/doxygen/img/PaletteExample1.gif $(SRCDIR)/doxygen/img/Palettes.fm.anc.gif'
+  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js'
   DOXYGEN_TAG_FILE=hdf5.tag
   DOXYGEN_SERVER_BASED_SEARCH=NO
   DOXYGEN_EXTERNAL_SEARCH=NO
   DOXYGEN_SEARCHENGINE_URL=
   DOXYGEN_STRIP_FROM_PATH='$(SRCDIR)'
   DOXYGEN_STRIP_FROM_INC_PATH='$(SRCDIR)'
-  DOXYGEN_PREDEFINED='H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD'
+  DOXYGEN_PREDEFINED='H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN_FORTRAN'
 
   DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
 fi

doxygen/CMakeLists.txt

@@ -7,11 +7,12 @@ project (HDF5_DOXYGEN C)
 if (DOXYGEN_FOUND)
   set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME})
   set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING})
+  set (DOXYGEN_DIR ${HDF5_DOXYGEN_DIR})
   set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
   set (DOXYGEN_INCLUDE_ALIASES aliases)
   set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
   set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
-  set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
+  set (DOXYGEN_PROJECT_BRIEF "API Reference")
   set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SOURCE_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}")
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
@@ -28,7 +29,7 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_SEARCHENGINE_URL)
   set (DOXYGEN_STRIP_FROM_PATH ${HDF5_SOURCE_DIR})
   set (DOXYGEN_STRIP_FROM_INC_PATH ${HDF5_SOURCE_DIR})
-  set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_HAVE_SUBFILING_VFD H5_HAVE_IOC_VFD")
+  set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN_FORTRAN H5_HAVE_SUBFILING_VFD H5_HAVE_IOC_VFD")
 
 # This configure and individual custom targets work together
   # Replace variables inside @@ with the current values

doxygen/Doxyfile.in

@@ -280,13 +280,13 @@ OPTIMIZE_OUTPUT_FOR_C  = YES
 # qualified scopes will look different, etc.
 # The default value is: NO.
 
-OPTIMIZE_OUTPUT_JAVA   = NO
+OPTIMIZE_OUTPUT_JAVA   = YES
 
 # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
 # sources. Doxygen will then generate output that is tailored for Fortran.
 # The default value is: NO.
 
-OPTIMIZE_FOR_FORTRAN   = NO
+OPTIMIZE_FOR_FORTRAN   = YES
 
 # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
 # sources. Doxygen will then generate output that is tailored for VHDL.
@@ -875,7 +875,11 @@ FILE_PATTERNS          = H5*public.h \
                          H5VLconnector.h \
                          H5VLconnector_passthru.h \
                          H5VLnative.h \
+                         H5Zdevelop.h \
                          H5version.h \
+                         H5*.java \
+                         HDF*.java \
+                         *.F90 \
                          *.dox
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
@@ -944,7 +948,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = @HDF5_DOXYGEN_DIR@/img
+IMAGE_PATH             = @DOXYGEN_DIR@/img
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

doxygen/aliases

@@ -379,4 +379,4 @@ ALIASES += obj_info_fields="<table><tr><th>Flag</th><th>Purpose</th></tr><tr><td
 
 ALIASES += fortran_error="Returns 0 if successful and -1 if it fails."
 ALIASES += fortran_approved="The preferred API, Fortran 2003 version."
-ALIASES += fortran_obsolete="Obsolete API, use the Fortran 2003 version instead."
+ALIASES += fortran_obsolete="Obsolete API, use the Fortran 2003 version instead."

doxygen/dox/DDLBNF110.dox

@@ -126,7 +126,7 @@ This section contains a brief explanation of the symbols used in the DDL.
 
 <reference> ::= H5T_REFERENCE { <ref_type> }
 
-<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG | H5T_STD_REF | UNDEFINED
+<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG
 
 <compound_type> ::= H5T_COMPOUND {
                         <member_type_def>+

doxygen/dox/FileFormatSpec.dox

@@ -0,0 +1,23 @@
+/** \page FMT3 HDF5 File Format Specification Version 3.0
+
+\htmlinclude H5.format.html
+
+*/
+
+/** \page FMT2 HDF5 File Format Specification Version 2.0
+
+\htmlinclude H5.format.2.0.html
+
+*/
+
+/** \page FMT11 HDF5 File Format Specification Version 1.1
+
+\htmlinclude H5.format.1.1.html
+
+*/
+
+/** \page FMT1 HDF5 File Format Specification Version 1.0
+
+\htmlinclude H5.format.1.0.html
+
+*/

doxygen/dox/GettingStarted.dox

@@ -1,3 +1,100 @@
-/** \page GettingStarted \Code{Hello, HDF5!}
+/** @page GettingStarted Getting Started with HDF5
 
- */
+Navigate back: \ref index "Main"
+<hr>
+
+\section sec_learn Learning HDF5
+There are several resources for learning about HDF5. The HDF Group provides an on-line HDF5 tutorial,
+documentation, examples, and videos. There are also tutorials provided by other organizations that are very useful for learning about HDF5.
+
+\subsection subsec_learn_intro The HDF Group Resources
+For a quick introduction to HDF5 see the following:
+<table>
+<tr>
+<td style="background-color:#F5F5F5">
+@ref IntroHDF5
+</td>
+<td>
+A very brief introduction to HDF5 and the HDF5 programming model and APIs
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+@ref LearnHDFView
+</td>
+<td>
+A tutorial for learning how to use HDFView. NO programming involved!
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+@ref LearnBasics
+</td>
+<td>
+Step by step instructions for learning HDF5 that include programming examples
+</td>
+</tr>
+</table>
+
+\subsection subsec_learn_tutor The HDF Group Tutorials and Examples
+These tutorials and examples are available for learning about the HDF5 High Level APIs, tools,
+Parallel HDF5, and the HDF5-1.10 VDS and SWMR new features:
+<table>
+<tr>
+<td style="background-color:#F5F5F5">
+<a href="https://portal.hdfgroup.org/display/HDF5/Introduction+to+the+HDF5+High+Level+APIs">Using the High Level APIs</a>
+</td>
+<td>
+\ref H5LT    \ref H5IM    \ref H5TB    \ref H5PT    \ref H5DS
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+<a href="https://portal.hdfgroup.org/display/HDF5/Introduction+to+Parallel+HDF5">Introduction to Parallel HDF5</a>
+</td>
+<td>
+A brief introduction to Parallel HDF5. If you are new to HDF5 please see the @ref LearnBasics topic first. 
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+\ref ViewTools
+</td>
+<td>
+\li @ref LearnHDFView
+\li @ref ViewToolsCommand
+\li @ref ViewToolsJPSS
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+HDF5-1.10 New Features
+</td>
+<td>
+\li <a href="https://portal.hdfgroup.org/display/HDF5/Introduction+to+the+Virtual+Dataset++-+VDS">Introduction to the Virtual Dataset - VDS</a>
+\li <a href="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48812567">Introduction to Single-Writer/Multiple-Reader (SWMR)</a>
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+Example Programs
+</td>
+<td>
+\ref HDF5Examples
+</td>
+</tr>
+<tr>
+<td style="background-color:#F5F5F5">
+Videos
+</td>
+<td>
+\li <a href="https://www.youtube.com/watch?v=BAjsCldRMMc">Introduction to HDF5</a>
+\li <a href="https://www.youtube.com/watch?v=qrI27pI0P1E">Parallel HDF5</a>
+</td>
+</tr>
+</table>
+
+<hr>
+Navigate back: \ref index "Main"
+
+*/

doxygen/dox/IntroHDF5.dox

@@ -0,0 +1,627 @@
+/** @page IntroHDF5 Introduction to HDF5
+
+Navigate back: \ref index "Main" / \ref GettingStarted
+<hr>
+
+\section sec_intro_desc HDF5 Description
+HDF5 consists of a file format for storing HDF5 data, a data model for logically organizing and accessing
+HDF5 data from an application, and the software (libraries, language interfaces, and tools) for working with this format.
+
+\subsection subsec_intro_desc_file File Format
+HDF5 consists of a file format for storing HDF5 data, a data model for logically organizing and accessing HDF5 data from an application,
+and the software (libraries, language interfaces, and tools) for working with this format.
+
+\subsection subsec_intro_desc_dm Data Model
+The HDF5 Data Model, also known as the HDF5 Abstract (or Logical) Data Model consists of
+the building blocks for data organization and specification in HDF5.
+
+An HDF5 file (an object in itself) can be thought of as a container (or group) that holds
+a variety of heterogeneous data objects (or datasets). The datasets can be images, tables,
+graphs, and even documents, such as PDF or Excel:
+
+<table>
+<tr>
+<td>
+\image html fileobj.png
+</td>
+</tr>
+</table>
+
+The two primary objects in the HDF5 Data Model are groups and datasets.
+
+There are also a variety of other objects in the HDF5 Data Model that support groups and datasets,
+including datatypes, dataspaces, properties and attributes.
+
+\subsubsection subsec_intro_desc_dm_group Groups
+HDF5 groups (and links) organize data objects. Every HDF5 file contains a root group that can
+contain other groups or be linked to objects in other files.
+
+<table>
+<caption>There are two groups in the HDF5 file depicted above: Viz and SimOut.
+Under the Viz group are a variety of images and a table that is shared with the SimOut group.
+The SimOut group contains a 3-dimensional array, a 2-dimensional array and a link to a 2-dimensional
+array in another HDF5 file.</caption>
+<tr>
+<td>
+\image html group.png
+</td>
+</tr>
+</table>
+
+Working with groups and group members is similar in many ways to working with directories and files
+in UNIX. As with UNIX directories and files, objects in an HDF5 file are often described by giving
+their full (or absolute) path names.
+\li / signifies the root group.
+\li /foo signifies a member of the root group called foo.
+\li /foo/zoo signifies a member of the group foo, which in turn is a member of the root group.
+
+\subsubsection subsec_intro_desc_dm_dset Datasets
+HDF5 datasets organize and contain the “raw” data values. A dataset consists of metadata
+that describes the data, in addition to the data itself:
+
+<table>
+<caption>In this picture, the data is stored as a three dimensional dataset of size 4 x 5 x 6 with an integer datatype.
+It contains attributes, Time and Pressure, and the dataset is chunked and compressed.</caption>
+<tr>
+<td>
+\image html dataset.png
+</td>
+</tr>
+</table>
+
+Datatypes, dataspaces, properties and (optional) attributes are HDF5 objects that describe a dataset.
+The datatype describes the individual data elements.
+
+\subsection subsec_intro_desc_props Datatypes, Dataspaces, Properties and Attributes
+
+\subsubsection subsec_intro_desc_prop_dtype Datatypes
+The datatype describes the individual data elements in a dataset. It provides complete information for
+data conversion to or from that datatype.
+
+<table>
+<caption>In the dataset depicted, each element of the dataset is a 32-bit integer.</caption>
+<tr>
+<td>
+\image html datatype.png
+</td>
+</tr>
+</table>
+
+Datatypes in HDF5 can be grouped into:
+<ul>
+<li>
+<b>Pre-Defined Datatypes</b>: These are datatypes that are created by HDF5. They are actually opened (and closed)
+by HDF5 and can have different values from one HDF5 session to the next. There are two types of pre-defined datatypes:
+<ul>
+<li>
+Standard datatypes are the same on all platforms and are what you see in an HDF5 file. Their names are of the form
+H5T_ARCH_BASE where ARCH is an architecture name and BASE is a pro­gramming type name. For example, #H5T_IEEE_F32BE
+indicates a standard Big Endian floating point type.
+</li>
+<li>
+Native datatypes are used to simplify memory operations (reading, writing) and are NOT the same on different platforms.
+For example, #H5T_NATIVE_INT indicates an int (C).
+</li>
+</ul>
+</li>
+<li>
+<b>Derived Datatypes</b>: These are datatypes that are created or derived from the pre-defined datatypes.
+An example of a commonly used derived datatype is a string of more than one character. Compound datatypes
+are also derived types.  A compound datatype can be used to create a simple table, and can also be nested,
+in which it includes one more other compound datatypes.
+<table>
+<caption>This is an example of a dataset with a compound datatype. Each element in the dataset consists
+of a 16-bit integer, a character, a 32-bit integer, and a 2x3x2 array of 32-bit floats (the datatype).
+It is a 2-dimensional 5 x 3 array (the dataspace). The datatype should not be confused with the dataspace.
+</caption>
+<tr>
+<td>
+\image html cmpnddtype.png
+</td>
+</tr>
+</table>
+</li>
+</ul>
+
+\subsubsection subsec_intro_desc_prop_dspace Dataspaces
+A dataspace describes the layout of a dataset’s data elements. It can consist of no elements (NULL),
+a single element (scalar), or a simple array.
+
+<table>
+<caption>This image illustrates a dataspace that is an array with dimensions of 5 x 3 and a rank (number of dimensions) of 2.</caption>
+<tr>
+<td>
+\image html dataspace1.png
+</td>
+</tr>
+</table>
+
+A dataspace can have dimensions that are fixed (unchanging) or unlimited, which means they can grow
+in size (i.e. they are extendible).
+
+There are two roles of a dataspace:
+\li It contains the spatial information (logical layout) of a dataset stored in a file. This includes the rank and dimensions of a dataset, which are a permanent part of the dataset definition.
+\li It describes an application’s data buffers and data elements participating in I/O. In other words, it can be used to select a portion or subset of a dataset.
+
+<table>
+<caption>The dataspace is used to describe both the logical layout of a dataset and a subset of a dataset.</caption>
+<tr>
+<td>
+\image html dataspace.png
+</td>
+</tr>
+</table>
+
+\subsubsection subsec_intro_desc_prop_property Properties
+A property is a characteristic or feature of an HDF5 object. There are default properties which
+handle the most common needs. These default properties can be modified using the HDF5 Property
+List API to take advantage of more powerful or unusual features of HDF5 objects.
+
+<table>
+<tr>
+<td>
+\image html properties.png
+</td>
+</tr>
+</table>
+
+For example, the data storage layout property of a dataset is contiguous by default. For better
+performance, the layout can be modified to be chunked or chunked and compressed:
+
+\subsubsection subsec_intro_desc_prop_attr Attributes
+Attributes can optionally be associated with HDF5 objects. They have two parts: a name and a value.
+Attributes are accessed by opening the object that they are attached to so are not independent objects.
+Typically an attribute is small in size and contains user metadata about the object that it is attached to.
+
+Attributes look similar to HDF5 datasets in that they have a datatype and dataspace. However, they
+do not support partial I/O operations, and they cannot be compressed or extended.
+
+\subsection subsec_intro_desc_soft HDF5 Software
+The HDF5 software is written in C and includes optional wrappers for C++, FORTRAN (90 and F2003),
+and Java. The HDF5 binary distribution consists of the HDF5 libraries, include files, command-line
+utilities, scripts for compiling applications, and example programs.
+
+\subsubsection subsec_intro_desc_soft_apis HDF5 APIs and Libraries
+There are APIs for each type of object in HDF5. For example, all C routines in the HDF5 library
+begin with a prefix of the form H5*, where * is one or two uppercase letters indicating the type
+of object on which the function operates:
+\li @ref H5A     <b>A</b>ttribute Interface
+\li @ref H5D     <b>D</b>ataset Interface
+\li @ref H5F     <b>F</b>ile Interface
+
+The HDF5 High Level APIs simplify many of the steps required to create and access objects, as well
+as providing templates for storing objects. Following is a list of the High Level APIs:
+\li @ref H5LT – simplifies steps in creating datasets and attributes
+\li @ref H5IM – defines a standard for storing images in HDF5
+\li @ref H5TB – condenses the steps required to create tables
+\li @ref H5DS – provides a standard for dimension scale storage
+\li @ref H5PT – provides a standard for storing packet data
+
+\subsubsection subsec_intro_desc_soft_tools Tools
+Useful tools for working with HDF5 files include:
+\li h5dump:             A utility to dump or display the contents of an HDF5 File
+\li h5cc, h5c++, h5fc:  Unix scripts for compiling applications
+\li HDFView:            A java browser to view HDF (HDF4 and HDF5) files
+
+<h4>h5dump</h4>
+The h5dump utility displays the contents of an HDF5 file in Data Description Language (\ref DDLBNF110).
+Below is an example of h5dump output for an HDF5 file that contains no objects:
+\code
+$ h5dump file.h5
+   HDF5 "file.h5" {
+   GROUP "/" {
+   }
+   }
+\endcode
+
+With large files and datasets the output from h5dump can be overwhelming.
+There are options that can be used to examine specific parts of an HDF5 file.
+Some useful h5dump options are included below:
+\code
+   -H, --header      Display header information only (no data)
+   -d <name>      Display a dataset with a specified path and name
+   -p                          Display properties
+   -n                          Display the contents of the file
+\endcode
+
+<h4>h5cc, h5fc, h5c++</h4>
+The built HDF5 binaries include the h5cc, h5fc, h5c++ compile scripts for compiling applications.
+When using these scripts there is no need to specify the HDF5 libraries and include files.
+Compiler options can be passed to the scripts.
+
+<h4>HDFView</h4>
+The HDFView tool allows browsing of data in HDF (HDF4 and HDF5) files. 
+
+\section sec_intro_pm Introduction to the HDF5 Programming Model and APIs
+The HDF5 Application Programming Interface is extensive, but a few functions do most of the work.
+
+To introduce the programming model, examples in Python and C are included below. The Python examples
+use the HDF5 Python APIs (h5py). See the Examples from "Learning the Basics" page for complete examples
+that can be downloaded and run for C, FORTRAN, C++, Java and Python.
+
+The general paradigm for working with objects in HDF5 is to:
+\li Open the object.
+\li Access the object.
+\li Close the object.
+
+The library imposes an order on the operations by argument dependencies. For example, a file must be
+opened before a dataset because the dataset open call requires a file handle as an argument. Objects
+can be closed in any order. However, once an object is closed it no longer can be accessed.
+
+Keep the following in mind when looking at the example programs included in this section:
+<ul>
+<li>
+<ul>
+<li>
+C routines begin with the prefix “H5*” where * is a single letter indicating the object on which the
+operation is to be performed.
+</li>
+<li>
+FORTRAN routines are similar; they begin with “h5*” and end with “_f”.
+</li>
+<li>
+Java routines are similar; the routine names begin with “H5*” and are prefixed with “H5.” as the class. Constants are
+in the HDF5Constants class and are prefixed with "HDF5Constants.". The function arguments
+are usually similar, @see @ref HDF5LIB
+</li>
+</ul>
+For example:
+<ul>
+<li>
+File Interface:<ul><li>#H5Fopen (C)</li><li>h5fopen_f (FORTRAN)</li><li>H5.H5Fopen (Java)</li></ul>
+</li>
+<li>
+Dataset Interface:<ul><li>#H5Dopen (C)</li><li>h5dopen_f (FORTRAN)</li><li>H5.H5Dopen (Java)</li></ul>
+</li>
+<li>
+Dataspace interface:<ul><li>#H5Sclose (C)</li><li>h5sclose_f (FORTRAN)</li><li>H5.H5Sclose (Java)</li></ul>
+</li>
+</ul>
+The HDF5 Python APIs use methods associated with specific objects.
+</li>
+<li>
+For portability, the HDF5 library has its own defined types. Some common types that you will see
+in the example code are:
+<ul>
+<li>
+#hid_t is used for object handles
+</li>
+<li>
+hsize_t is used for dimensions
+</li>
+<li>
+#herr_t is used for many return values
+</li>
+</ul>
+</li>
+<li>
+Language specific files must be included in applications:
+<ul>
+<li>
+Python:   Add <code>"import h5py / import numpy"</code>
+</li>
+<li>
+C:        Add <code>"#include hdf5.h"</code>
+</li>
+<li>
+FORTRAN:  Add <code>"USE HDF5"</code> and call h5open_f and h5close_f to initialize and close the HDF5 FORTRAN interface
+</li>
+<li>
+Java:     Add <code>"import hdf.hdf5lib.H5;
+                     import hdf.hdf5lib.HDF5Constants;"</code>
+</li>
+</ul>
+</li>
+</ul>
+
+\subsection subsec_intro_pm_file Steps to create a file
+To create an HDF5 file you must:
+\li Specify property lists (or use the defaults).
+\li Create the file.
+\li Close the file (and property lists if needed).
+
+Example:
+<table>
+<caption>The following Python and C examples create a file, file.h5, and then close it.
+The resulting HDF5 file will only contain a root group:</caption>
+<tr>
+<td>
+\image html crtf-pic.png
+</td>
+</tr>
+</table>
+
+Calling h5py.File with ‘w’ for the file access flag will create a new HDF5 file and overwrite
+an existing file with the same name.  “file” is the file handle returned from opening the file.
+When finished with the file, it must be closed. When not specifying property lists, the default
+property lists are used:
+
+<table>
+<tr>
+<td>
+<em>Python</em>
+\code
+   import h5py
+   file = h5py.File (‘file.h5’, ‘w’)
+   file.close ()
+\endcode
+</td>
+</tr>
+</table>
+
+The H5Fcreate function creates an HDF5 file. #H5F_ACC_TRUNC is the file access flag to create a new
+file and overwrite an existing file with the same name, and #H5P_DEFAULT is the value specified to
+use a default property list.
+
+<table>
+<tr>
+<td>
+<em>C</em>
+\code
+   #include “hdf5.h”
+
+   int main() {
+       hid_t       file_id;
+       herr_t      status;
+
+       file_id = H5Fcreate ("file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);   
+       status = H5Fclose (file_id);
+   }
+\endcode
+</td>
+</tr>
+</table>
+
+\subsection subsec_intro_pm_dataset Steps to create a dataset
+As described previously, an HDF5 dataset consists of the raw data, as well as the metadata that
+describes the data (datatype, spatial information, and properties). To create a dataset you must:
+\li Define the dataset characteristics (datatype, dataspace, properties).
+\li Decide which group to attach the dataset to.
+\li Create the dataset.
+\li Close the dataset handle from step 3.
+
+Example:
+<table>
+<caption>The code excerpts below show the calls that need to be made to create a 4 x 6 integer dataset dset
+in a file dset.h5. The dataset will be located in the root group:</caption>
+<tr>
+<td>
+\image html crtdset.png
+</td>
+</tr>
+</table>
+
+With Python, the creation of the dataspace is included as a parameter in the dataset creation method.
+Just one call will create a 4 x 6 integer dataset dset. A pre-defined Big Endian 32-bit integer datatype
+is specified. The create_dataset method creates the dataset in the root group (the file object).
+The dataset is close by the Python interface.
+
+<table>
+<tr>
+<td>
+<em>Python</em>
+\code
+   dataset = file.create_dataset("dset",(4, 6), h5py.h5t.STD_I32BE)
+\endcode
+</td>
+</tr>
+</table>
+
+To create the same dataset in C, you must specify the dataspace with the #H5Screate_simple function,
+create the dataset by calling #H5Dcreate, and then close the dataspace and dataset with calls to #H5Dclose
+and #H5Sclose. #H5P_DEFAULT is specified to use a default property list. Note that the file identifier
+(file_id) is passed in as the first parameter to #H5Dcreate, which creates the dataset in the root group.
+
+<table>
+<tr>
+<td>
+<em>C</em>
+\code
+   // Create the dataspace for the dataset.
+   dims[0] = 4;
+   dims[1] = 6;
+
+   dataspace_id = H5Screate_simple(2, dims, NULL);
+
+   // Create the dataset.
+   dataset_id = H5Dcreate (file_id, "/dset", H5T_STD_I32BE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+   // Close the dataset and dataspace
+   status = H5Dclose(dataset_id);
+   status = H5Sclose(dataspace_id);
+\endcode
+</td>
+</tr>
+</table>
+
+\subsection subsec_intro_pm_write Writing to or reading from a dataset
+Once you have created or opened a dataset you can write to it:
+
+<table>
+<tr>
+<td>
+<em>Python</em>
+\code
+   data = np.zeros((4,6))
+   for i in range(4):
+      for j in range(6):
+         data[i][j]= i*6+j+1
+
+   dataset[...] = data       <-- Write data to dataset
+   data_read = dataset[...]  <-- Read data from dataset
+\endcode
+</td>
+</tr>
+</table>
+
+#H5S_ALL is passed in for the memory and file dataspace parameters to indicate that the entire dataspace
+of the dataset is specified. These two parameters can be modified to allow subsetting of a dataset.
+The native predefined datatype, #H5T_NATIVE_INT, is used for reading and writing so that HDF5 will do
+any necessary integer conversions:
+
+<table>
+<tr>
+<td>
+<em>C</em>
+\code
+   status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data);
+   status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data);
+\endcode
+</td>
+</tr>
+</table>
+
+\subsection subsec_intro_pm_group Steps to create a group
+An HDF5 group is a structure containing zero or more HDF5 objects. Before you can create a group you must
+obtain the location identifier of where the group is to be created. Following are the steps that are required:
+\li Decide where to put the group – in the “root group” (or file identifier) or in another group. Open the group if it is not already open.
+\li Define properties or use the default.
+\li Create the group.
+\li Close the group.
+
+<table>
+<caption>Creates attributes that are attached to the dataset dset</caption>
+<tr>
+<td>
+\image html crtgrp.png
+</td>
+</tr>
+</table>
+
+The code below opens the dataset dset.h5 with read/write permission and creates a group MyGroup in the root group.
+Properties are not specified so the defaults are used:
+
+<table>
+<tr>
+<td>
+<em>Python</em>
+\code
+   import h5py
+   file = h5py.File('dset.h5', 'r+')  
+   group = file.create_group ('MyGroup')
+   file.close()
+\endcode
+</td>
+</tr>
+</table>
+
+To create the group MyGroup in the root group, you must call #H5Gcreate, passing in the file identifier returned
+from opening or creating the file. The default property lists are specified with #H5P_DEFAULT. The group is then
+closed:
+
+<table>
+<tr>
+<td>
+<em>C</em>
+\code
+   group_id = H5Gcreate (file_id, "MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+   status = H5Gclose (group_id);
+\endcode
+</td>
+</tr>
+</table>
+
+\subsection subsec_intro_pm_attr Steps to create and write to an attribute
+To create an attribute you must open the object that you wish to attach the attribute to. Then you can create,
+access, and close the attribute as needed:
+\li Open the object that you wish to add an attribute to.
+\li Create the attribute
+\li Write to the attribute
+\li Close the attribute and the object it is attached to.
+
+<table>
+<caption>Creates attributes that are attached to the dataset dset</caption>
+<tr>
+<td>
+\image html crtatt.png
+</td>
+</tr>
+</table>
+
+The dataspace, datatype, and data are specified in the call to create an attribute in Python:
+
+<table>
+<tr>
+<td>
+<em>Python</em>
+\code
+   dataset.attrs["Units"] = “Meters per second”  <-- Create string
+   attr_data = np.zeros((2,))
+   attr_data[0] = 100
+   attr_data[1] = 200
+   dataset.attrs.create("Speed", attr_data, (2,), “i”) <-- Create Integer
+\endcode
+</td>
+</tr>
+</table>
+
+To create an integer attribute in C, you must create the dataspace, create the attribute, write
+to it and then close it in separate steps:
+
+<table>
+<tr>
+<td>
+<em>C</em>
+\code
+   hid_t       attribute_id, dataspace_id;  // identifiers
+   hsize_t     dims;
+   int         attr_data[2];
+   herr_t      status;
+
+      ...
+
+   // Initialize the attribute data.
+   attr_data[0] = 100;
+   attr_data[1] = 200;
+
+   // Create the data space for the attribute.
+   dims = 2;
+   dataspace_id = H5Screate_simple(1, &dims, NULL);
+
+   // Create a dataset attribute.
+   attribute_id = H5Acreate2 (dataset_id, "Units", H5T_STD_I32BE,
+                              dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
+
+   // Write the attribute data.
+   status = H5Awrite(attribute_id, H5T_NATIVE_INT, attr_data);
+
+   // Close the attribute.
+   status = H5Aclose(attribute_id);
+
+   // Close the dataspace.
+   status = H5Sclose(dataspace_id);
+\endcode
+</td>
+</tr>
+</table>
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted
+
+
+@page HDF5Examples HDF5 Examples
+Example programs of how to use HDF5 are provided below.
+For HDF-EOS specific examples, see the <a href="http://hdfeos.org/zoo/index.php">examples</a>
+of how to access and visualize NASA HDF-EOS files using IDL, MATLAB, and NCL on the
+<a href="http://hdfeos.org/">HDF-EOS Tools and Information Center</a> page.
+
+\section secHDF5Examples Examples
+\li \ref LBExamples
+\li <a href="https://portal.hdfgroup.org/display/HDF5/Examples+by+API">Examples by API</a>
+\li <a href="https://portal.hdfgroup.org/display/HDF5/Examples+in+the+Source+Code">Examples in the Source Code</a>
+\li <a href="https://portal.hdfgroup.org/display/HDF5/Other+Examples">Other Examples</a>
+
+\section secHDF5ExamplesCompile How To Compile
+For information on compiling in C, C++ and Fortran, see: \ref LBCompiling
+
+\section secHDF5ExamplesOther Other Examples
+<a href="http://hdfeos.org/zoo/index.php">IDL, MATLAB, and NCL Examples for HDF-EOS</a>
+Examples of how to access and visualize NASA HDF-EOS files using IDL, MATLAB, and NCL.
+
+<a href="https://support.hdfgroup.org/ftp/HDF5/examples/misc-examples/">Miscellaneous Examples</a>
+These (very old) examples resulted from working with users, and are not fully tested. Most of them are in C, with a few in Fortran and Java.
+
+<a href="https://support.hdfgroup.org/ftp/HDF5/examples/special_values_HDF5_example.tar">Using Special Values</a>
+These examples show how to create special values in an HDF5 application.
+
+*/

doxygen/dox/LearnBasics.dox

@@ -0,0 +1,183 @@
+/** @page LearnBasics Learning the Basics
+
+Navigate back: \ref index "Main" / \ref GettingStarted
+<hr>
+
+\section secIntro Introduction
+The following topics cover the basic features in HDF5. The topics build on each other and are
+intended to be completed in order. Some sections use files created in earlier sections. The
+examples used can also be found on the \ref LBExamples
+page and in the HDF5 source code (C, C++, Fortran).
+
+\section Topics Topics
+\li @subpage LBFileOrg
+\li @subpage LBAPI
+\li @subpage LBProg
+\li @subpage LBFileCreate
+\li @subpage LBDsetCreate
+\li @subpage LBDsetRW
+\li @subpage LBAttrCreate
+\li @subpage LBGrpCreate
+\li @subpage LBGrpCreateNames
+\li @subpage LBGrpDset
+\li @subpage LBDsetSubRW
+\li @subpage LBDatatypes
+\li @subpage LBPropsList
+\li @subpage LBDsetLayout
+\li @subpage LBExtDset
+\li @subpage LBComDset
+\li @subpage LBContents
+\li @subpage LBQuiz
+\li @subpage LBQuizAnswers
+\li @subpage LBCompiling
+\li @subpage LBTraining
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted
+
+
+@page LBExamples Examples from Learning the Basics
+
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
+<hr>
+
+\section secLBExamples
+These examples are used in the \ref LearnBasics topic. See \ref LBCompiling for details on compiling them.
+PLEASE NOTE that the example programs are listed in the order they are expected to be run. Some example
+programs use files created in earlier examples.
+
+\section secLBExamplesSrc HDF5 Source Code Examples
+These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) binaries.
+<table>
+<tr>
+<th>Feature
+</th>
+<th>Examples
+</th>
+<th>Comments
+</th>
+<tr>
+<td>Create a file
+</td>
+<td>C  Fortran  C++  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateFile.java">Java</a>  Python
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create a dataset
+</td>
+<td><a href="https://raw.githubusercontent.com//HDFGroup/hdf5/hdf5_1_10/examples/h5_crtdat.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_crtdat.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_crtdat.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateDataset.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_crtdat.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Read and write to a dataset
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_rdwt.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_rdwt.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_rdwt.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_ReadWrite.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_rdwt.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create an attribute
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_crtatt.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_crtatt.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_crtatt.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateAttribute.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_crtatt.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create a group
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_crtgrp.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_crtgrp.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_crtgrp.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateGroup.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_crtgrp.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create groups in a file using absolute and relative paths
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_crtgrpar.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_crtgrpar.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_crtgrpar.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateGroupAbsoluteRelative.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_crtgrpar.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create datasets in a group
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_crtgrpd.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_crtgrpd.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_crtgrpd.cpp">C++</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/java/examples/intro/H5_CreateGroupDataset.java">Java</a>  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_crtgrpd.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+<tr>
+<td>Create a file and dataset and select/read a subset from the dataset
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_subset.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_subset.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_subset.cpp">C++</a>  Java  Python
+</td>
+<td>Also see examples to Write by row (and column) below.
+</td>
+</tr>
+<tr>
+<td>Create an extendible (unlimited dimension) dataset
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_extend.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_extend.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_extend.cpp">C++</a>  Java  Python
+</td>
+<td>Also see examples to Extend by row (and column) below
+</td>
+</tr>
+<tr>
+<td>Create a chunked and compressed dataset
+</td>
+<td><a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/examples/h5_cmprss.c">C</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/fortran/examples/h5_cmprss.f90">Fortran</a>  <a href="https://raw.githubusercontent.com/HDFGroup/hdf5/hdf5_1_10/c++/examples/h5tutr_cmprss.cpp">C++</a>  Java  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/Py/h5_cmprss.py">Python</a>
+</td>
+<td>
+</td>
+</tr>
+</table>
+
+*See <a href="https://github.com/scotmartin1234/HDF5Mathematica">HDF5Mathematica</a> for user-contributed
+HDF5 Mathematica Wrappers and Introductory Tutorial Examples. The examples use P/Invoke.
+
+\section secLBExamplesAddl Additional Examples
+These examples make minor changes to the tutorial examples.
+<table>
+<tr>
+<th>Feature
+</th>
+<th>Examples
+</th>
+</tr>
+<tr>
+<td>Write by row
+</td>
+<td><a href="">C</a>  <a href="">Fortran</a>
+</td>
+</tr>
+<tr>
+<td>Write by column
+</td>
+<td><a href="">C</a>  <a href="">Fortran</a>
+</td>
+</tr>
+<tr>
+<td>Extend by row
+</td>
+<td><a href="">C</a>  <a href="">Fortran</a>
+</td>
+</tr>
+<tr>
+<td>Extend by column
+</td>
+<td><a href="">C</a>  <a href="">Fortran</a>
+</td>
+</tr>
+</table>
+
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
+
+*/

doxygen/dox/LearnHDFView.dox

@@ -0,0 +1,472 @@
+/** @page LearnHDFView Learning HDF5 with HDFView
+
+Navigate back: \ref index "Main" / \ref GettingStarted
+<hr>
+
+This tutorial enables you to get a feel for HDF5 by using the HDFView browser. It does NOT require
+any programming experience.
+
+\section sec_learn_hv_install HDFView Installation
+\li Download and install HDFView. It can be downloaded from the <a href="https://portal.hdfgroup.org/display/support/Download+HDFView">Download HDFView</a> page.
+\li Obtain the  <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> text file, used in the tutorial.
+
+\section sec_learn_hv_begin Begin Tutorial
+Once you have HDFView installed, bring it up and you are ready to begin the tutorial.
+
+<table style="background-color:#FAFAD2">
+<caption>
+Unable to complete tutorial because fields are greyed out?
+</caption>
+<tr>
+<td>
+This tutorial requires that the default HDFView File Access Mode be Read / Write. If fields are greyed out so that you cannot select them, then the File Access Mode is Read Only.
+
+To change the File Access Mode follow these steps:
+<ul>
+<li>Bring up HDFView</li>
+<li>Left-mouse click on the Tools pull-down menu and select User Options.</li>
+<li>A Preferences window pops up with the General Settings tab selected.
+About half-way down you will see Default File Access Mode.
+Select Read / Write.</li>
+<li>Click on Apply and Close at the bottom of the window.</li>
+<li>Close down HDFView.</li>
+<li>Bring HDFView back up and try the tutorial again.</li>
+PLEASE BE AWARE that selecting a File Access Mode of Read / Write can result in changes to the timestamp of HDF files that are viewed with HDFView. In general, a File Access Mode
+of Read Only should be used to ensure that this does not occur.
+</ul>
+</td>
+</tr>
+</table>
+
+\subsection subsec_learn_hv_begin_topics Topics Covered
+Following are the topics covered in the tutorial. The first topic creates the file that is used in
+the subsequent topics.
+<ul>
+<li>@ref subsec_learn_hv_topics_file</li>
+<li>@ref subsec_learn_hv_topics_image</li>
+<li>@ref subsec_learn_hv_topics_attr</li>
+<li>@ref subsec_learn_hv_topics_compress</li>
+<li>@ref subsec_learn_hv_topics_subset</li>
+<li>@ref subsec_learn_hv_topics_table</li>
+</ul>
+
+\section sec_learn_hv_topics Topics
+
+\subsection subsec_learn_hv_topics_file Creating a New HDF5 File with a Contiguous Dataset
+The steps below describe how to create a file (storm.h5), group (/Data), and a contiguous dataset
+(/Data/Storm) using HDFView. A group is an HDF5 object that allows objects to be collected together.
+A dataset is an array of data values. A contiguous dataset is one that is stored as a single block
+in the HDF5 file.
+<ul>
+<li>Select the <em>File</em> pull-down menu at the top left, and then select <em>New -> HDF5</em>.</li>
+<li>Specify a location and type in <em>storm.h5</em> for the name of your file, and click on the <em>Save</em> button.
+You will see the <em>storm.h5</em> file in the TableView:
+<table>
+<tr>
+<td>
+\image html storm.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Right click on <em>storm.h5</em>, and select <em>New -> Group</em>.</li>
+<li>Enter <em>Data</em> for the name of the group and then click the <em>Ok</em> button. You will see the group <em>Data</em> in the TableView.
+<table>
+<tr>
+<td>
+\image html DataGroup.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Right click on the group <em>Data</em> and select <em>New -> Dataset</em>.</li>
+<li>A window pops up on the right. Fill in the information as follows, and then click <em>Ok</em> (leave the
+Datatype information as is):
+<table>
+<tr>
+<th>Dataset Name
+</th>
+<td><em>Storm</em>
+</td>
+</tr>
+<tr>
+<th>Under Dataspace, Current size
+</th>
+<td>57x57
+</td>
+</tr>
+<tr>
+<th>Layout
+</th>
+<td><em>Contiguous</em> (default)
+</td>
+</tr>
+</table>
+</li>
+<li>Click to expand the <em>Data</em> group in the tree view to see the <em>Storm</em> dataset:
+<table>
+<tr>
+<td>
+\image html StormDataset.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Double left click on the <em>Storm</em> dataset in the tree view. A window with an empty spreadsheet pops open.</li>
+<li>Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset.
+
+If you downloaded <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a>,
+then click on the <em>Import/Export Data</em> menu and select <em>Import Data from -> Text File</em>.
+Specify a location, select <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a>
+and click on the <em>Open</em> button. Answer <em>Yes</em> in the dialog box that
+pops up (which asks if you wish to paste the selected data).
+
+Alternately, you can copy/paste directly. Select and copy the data in a separate window. Position your
+cursor at (0,0) in your table, and select <em>Paste</em> from the <em>Table</em> menu.
+
+The values will be entered into the spreadsheet.
+<table>
+<tr>
+<td>
+\image html datasetwdata.png 
+</td>
+</tr>
+</table>
+</li>
+<li><em>Table -> Close</em> the dataset, and save the data.</li>
+</ul>
+
+\subsection subsec_learn_hv_topics_image Displaying a Dataset as an Image
+Any dataset can be viewed as an image in HDFView. Below are the steps that demonstrate this.
+<ul>
+<li>Right click on <em>Storm</em> in the tree view, and select <em>Open As</em>.</li>
+<li>Select the <em>Image</em> button under <em>Display As</em> (near the top) in the Dataset Selection window that pops
+up. Then click <em>OK</em> at the bottom of the window to display the image.
+<table>
+<tr>
+<td>
+\image html showasimage.png 
+</td>
+</tr>
+</table>
+</li>
+<li>The rainbow icon brings you to the Image Palette window. Click on that to play with the palette
+(GrayWave probably is the best choice). Close.</li>
+</ul>
+
+\subsection subsec_learn_hv_topics_attr Creating Attributes
+Additional information to describe an object can be stored in attributes. An attribute can be
+added to a group or dataset with HDFView.
+
+The following illustrates how to add an attribute to the group <em>/Data</em>:
+<ul>
+<li>Click on the <em>/Data</em> folder in the tree view. You will see two tabs, <em>Object Attribute Info</em> and
+<em>General Object Info</em>, in the pane on the right site of the HDFView window.
+<table>
+<tr>
+<td>
+\image html noattrs.png 
+</td>
+</tr>
+</table>
+</li>
+<li>With the left mouse button, select the <em>Add Attribute</em> button.</li>
+<li>Select the <em>Add Attribute</em> button to add an attribute with these values:</li>
+<table>
+<tr>
+<th>Name
+</th>
+<td><em>BatchID</em>
+</td>
+</tr>
+<tr>
+<th>Type
+</th>
+<td>INTEGER
+</td>
+</tr>
+<tr>
+<th>Size (bits)
+</th>
+<td>32
+</td>
+</table>
+<li>Select the <em>Ok</em> button. The attribute will show up under the <em>Object Attribute Info</em> tab.</li>
+<li>Double-click the BatchID attribute line to open the data table for BatchID.</li>
+<li>Click in the first cell and enter <em>3343</em> followed by the enter key.</li>
+<li><em>Table -> Close</em>, answer <em>Yes</em> in the dialog box that
+pops up (which asks if you wish to paste the selected data).</li>
+</ul>
+Adding an attribute to a dataset is very similar to adding an attribute to a group. For example,
+the following adds an attribute to the <em>/Storm</em> dataset:
+<ul>
+<li>Left mouse click on the <em>/Storm</em> dataset in the tree view. You will see the <em>Object Attribute
+Info</em> and <em>General Object Info</em> tabs on the right</li>
+<li>In the <em>Object Attribute Info</em> pane select the <em>Add Attribute</em> button and enter an attribute with
+these values. (Be sure to add a <em>String Length</em> or the string will be truncated to one character!):</li>
+<table>
+<tr>
+<th>Name
+</th>
+<td><em>Units</em>
+</td>
+</tr>
+<tr>
+<th>Type
+</th>
+<td>STRING
+</td>
+</tr>
+<tr>
+<th>String Length
+</th>
+<td>3
+</td>
+</table>
+<li>Select the <em>Ok</em> button. The attribute will show up under the <em>Object Attribute Info</em> tab.</li>
+<li>Double-click the Units attribute line to open the data table for Units.</li>
+<li>Click in the first cell and enter <em>m/s</em> followed by the enter key.</li>
+<li><em>Table -> Close</em>, answer <em>Yes</em> in the dialog box that
+pops up (which asks if you wish to paste the selected data).
+<table>
+<tr>
+<td>
+\image html scarletletter.png 
+</td>
+</tr>
+</table>
+</li>
+</ul>
+
+\subsection subsec_learn_hv_topics_compress Creating a Compressed and Chunked Dataset
+A chunked and compressed dataset can be created using HDFView. A compressed dataset is a dataset
+whose size has been compressed to take up less space. In order to compress an HDF5 dataset, the
+dataset must be stored with a chunked dataset layout (as multiple <em>chunks</em> that are stored separately
+in the file).
+
+Please note that the chunk sizes used in this topic are for demonstration purposes only. For
+information on chunking and specifying an appropriate chunk size, see the
+<a href="https://confluence.hdfgroup.org/display/HDF5/Chunking+in+HDF5">Chunking in HDF5</a> documentation.
+
+Also see the HDF5 Tutorial topic on \ref secLBComDsetCreate.
+<ul>
+<li>Right click on storm.h5. Select <em>New -> Group</em>.</li>
+<li>Enter <em>Image</em> for the name of the group, and click the <em>OK</em> button to create the group.
+<table>
+<tr>
+<td>
+\image html newgroupimage.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Right click on the <em>Image</em> group, and select <em>New -> Dataset</em>.</li>
+<li>Enter the following information for the dataset. Leave the <em>Datatype</em> as is (INTEGER):
+<table>
+<tr>
+<th>Dataset name
+</th>
+<td><em>Another Storm</em>
+</td>
+</tr>
+<tr>
+<th>Under Dataspace, Current size
+</th>
+<td>57x57
+</td>
+</tr>
+<tr>
+<th>Storage Layout
+</th>
+<td>Chunked
+</td>
+</tr>
+<tr>
+<th>Chunk Size
+</th>
+<td>20x20
+</td>
+</tr>
+<tr>
+<th>Compression
+</th>
+<td>gzip
+</td>
+</tr>
+<tr>
+<th>Compression Level
+</th>
+<td>9
+</td>
+</table>
+You will see the <em>Another Storm</em> dataset in the <em>Image</em> group:
+<table>
+<tr>
+<td>
+\image html hdfview-anthrstrm.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Double left-mouse click on the <em>Another Storm</em> dataset to display the spreadsheet:
+<table>
+<tr>
+<td>
+\image html hdfview-anthrstrm-sprdsht.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset. (See the previous topic for copying
+<a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> into a dataset.)</li>
+<li><em>Table -> Close</em>, and save the data.</li>
+<li>Right click on <em>Another Storm</em>, and select <em>Open As</em>.</li>
+<li>Select the <em>Image</em> button in the Dataset Selection window that pops up. Click the <em>Ok</em> button at the
+bottom of the window to view the dataset as an image.
+<table>
+<tr>
+<td>
+\image html hdfview-anthrstrm-img.png 
+</td>
+</tr>
+</table>
+</li>
+</ul>
+
+\subsection subsec_learn_hv_topics_subset Creating an Image and a Subset
+A previous topic demonstrated how to view any dataset as an image in HDFView. With HDFView you can also
+create an image to begin with, as is shown below.
+<ul>
+<li>Right click on the <em>Data</em> group and select <em>New -> Image</em>.</li>
+<li>A window pops up on the right. Enter the following and then click <em>Ok</em>:</li>
+<table>
+<tr>
+<th>Image name
+</th>
+<td><em>Storm Image</em>
+</td>
+</tr>
+<tr>
+<th>Height
+</th>
+<td>57
+</td>
+</tr>
+<tr>
+<th>Width
+</th>
+<td>57
+</td>
+</table>
+
+<li>Close the dataset.</li>
+<li>Expand the <em>Data</em> group to see its contents. You will see the <em>Storm Image</em> dataset.
+<table>
+<tr>
+<td>
+\image html hdfview-imgicon.png 
+</td>
+</tr>
+</table>
+</li>
+<li>
+Add data to the <em>Storm Image</em> dataset as was shown previously:
+<ul>
+<li>Right click on <em>Storm Image</em>, and select <em>Open As</em> to open the Dataset Selection window.</li>
+<li>Click on the <em>Spreadsheet</em> button at the top left of the Dataset Selection window to view the image
+as a spreadsheet.</li>
+<li>Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset.</li>
+<li>Close the dataset and save the data.</li>
+</ul>
+</li>
+<li>Left double click on <em>Storm Image</em> to see the image. Close the dataset.</li>
+<li>Right click on <em>Storm Image</em> and select <em>Open As</em> to bring up the Data Selection window.</li>
+<li>Select a subset by clicking the left mouse on the image in the window and dragging the mouse.
+Notice that the Height and Width values change. Select to display it as an image. Click <em>Ok</em>.
+<table>
+<tr>
+<td>
+\image html hdfview-imgsubset.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Position the cursor in the middle of the image. Press Shift+Left Mouse button and hold, and then
+drag the mouse to select another subset.</li>
+<li>Select <em>Image->Write Selection to Image</em>. Enter <em>Subset</em> for the new image name. Click <em>Ok</em>. The <em>Subset</em>
+image will appear in the tree view on the left.</li>
+<li>Left double click on the image <em>Subset</em> to bring it up on the right.
+<table>
+<tr>
+<td>
+\image html hdfview-newimgsubset.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Close the <em>Subset</em> image.</li>
+</ul>
+
+\subsection subsec_learn_hv_topics_table Creating a Table (Compound Dataset)
+A dataset with a compound datatype contains data elements that consist of multiple fields. If the
+dataspace for the compound dataset is one-dimensional, then the dataset can be viewed as a table in
+HDFView, as is shown below.
+<ul>
+<li>Right button click on the group <em>Data</em>. Select <em>New -> Compound DS</em>.</li>
+<li>A window pops up. Only fill in the following fields:
+<table>
+<tr>
+<th>Dataset name
+</th>
+<td>Table
+</td>
+</tr>
+<tr>
+<th>Dataspace (Current size only)
+</th>
+<td>4
+</td>
+</tr>
+<tr>
+<th>Compound Datatype Properties:
+<br />Number of Members
+</th>
+<td>3
+</td>
+</tr>
+<tr>
+<th>Compound Datatype Properties:
+<br /><em>Name</em> / Datatype / Size
+</th>
+<td><em>Description</em> / string / 4
+<br /><em>Temperature</em> / float / 1
+<br /><em>Pressure</em> / double / 1
+</td>
+</tr>
+</table>
+
+<table>
+<tr>
+<td>
+\image html hdfview-newcmpd.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Click Ok at the bottom.</li>
+<li>Open the Data group (if it is not open) and double left click on the Table object.
+<table>
+<tr>
+<td>
+\image html hdfview-table.png 
+</td>
+</tr>
+</table>
+</li>
+<li>Close the dataset.</li>
+</ul>
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted
+
+*/

doxygen/dox/ReferenceManual.dox

@@ -1,53 +1,32 @@
 /** \page RM HDF5 Reference Manual
 
-The functions provided by the HDF5 C-API are grouped into the following
+The functions provided by the HDF5 API are grouped into the following
 \Emph{modules}:
 
 <table>
 <tr><th>Modules</th></tr>
 <tr valign="top">
 <td>
-
 <table>
 <tr valign="top"><td style="border: none;">
-\li \ref H5A "Attributes (H5A)"
+\include{doc} core_menu.md
-\li \ref H5D "Datasets (H5D)"
+</td>
-\li \ref H5S "Dataspaces (H5S)"
+</tr>
-\li \ref H5T "Datatypes (H5T)"
+<tr valign="top"><td style="border: none;">
-\li \ref H5E "Error Handling (H5E)"
+<!--  High-level library -->
-\li \ref H5ES "Event Sets (H5ES)"
+\include{doc} high_level_menu.md
-\li \ref H5F "Files (H5F)"
+</td>
-\li \ref H5Z "Filters (H5Z)"
+</tr>
-\li \ref H5G "Groups (H5G)"
+<tr valign="top"><td style="border: none;">
-</td><td style="border: none;">
+<!--  Fortran library -->
-\li \ref H5I "Identifiers (H5I)"
+\include{doc} fortran_menu.md
-\li \ref H5 "Library General (H5)"
+</td>
-\li \ref H5L "Links (H5L)"
+</tr>
-\li \ref H5M "Maps (H5M)"
+<tr valign="top"><td style="border: none;">
-\li \ref H5O "Objects (H5O)"
+<!--  Java library -->
-\li \ref H5P "Property Lists (H5P)"
+\include{doc} java_menu.md
-\li \ref H5PL "Dynamically-loaded Plugins (H5PL)"
+</td>
-\li \ref H5R "References (H5R)"
+</tr>
-\li \ref H5VL "Virtual Object Layer (H5VL)"
-</td><td style="border: none;">
-\li \ref high_level
-    <ul>
-    <li>\ref H5LT "Lite (H5LT, H5LD)"
-    <li>\ref H5IM "Images (H5IM)"
-    <li>\ref H5TB "Table (H5TB)"
-    <li>\ref H5PT "Packet Table (H5PT)"
-    <li>\ref H5DS "Dimension Scale (H5DS)"
-    <li>\ref H5DO "Optimizations (H5DO)"
-    <li>\ref H5LR "Extensions (H5LR, H5LT)"
-    </ul>
-</td></tr>
-<tr><td colspan="3" style="border: none;">
-\a Core \a library: \ref H5 \ref H5A \ref H5D \ref H5E \ref H5ES \ref H5F \ref H5G \ref H5I \ref H5L
-\ref H5M \ref H5O \ref H5P \ref H5PL \ref H5R \ref H5S \ref H5T \ref H5VL \ref H5Z
-</td></tr>
-<tr><td colspan="3" style="border: none;">
-\a High-level \a library: \ref H5LT \ref H5IM \ref H5TB \ref H5PT \ref H5DS \ref H5DO \ref H5LR
-</td></tr>
 <tr>
 <td><a href="./deprecated.html">Deprecated functions</a></td>
 <td>Functions with \ref ASYNC</td>

doxygen/dox/Specifications.dox

@@ -2,20 +2,20 @@
 
 \section DDL
 
-\li \ref DDLBNF110 "DDL in BNF through HDF5 1.10"
+\li \ref DDLBNF110
-\li \ref DDLBNF112 "DDL in BNF for HDF5 1.12 and above"
+\li \ref DDLBNF112
 
 \section File Format
 
-\li \ref FMT1 "HDF5 File Format Specification Version 1.0"
+\li \ref FMT1
-\li \ref FMT11 "HDF5 File Format Specification Version 1.1"
+\li \ref FMT11
-\li \ref FMT2 "HDF5 File Format Specification Version 2.0"
+\li \ref FMT2
-\li \ref FMT3 "HDF5 File Format Specification Version 3.0"
+\li \ref FMT3
 
 \section Other
 
-\li \ref IMG "HDF5 Image and Palette Specification Version 1.2"
+\li \ref IMG
-\li \ref TBL "HDF5 Table Specification Version 1.0"
+\li \ref TBL
 \li <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
       HDF5 Dimension Scale Specification</a>
 

doxygen/dox/TechnicalNotes.dox

@@ -1,13 +1,13 @@
 /** \page TN Technical Notes
 
-\li \link api-compat-macros API Compatibility Macros \endlink
+\li \ref api-compat-macros
-\li \ref APPDBG "Debugging HDF5 Applications"
+\li \ref APPDBG
-\li \ref FMTDISC "File Format Walkthrough"
+\li \ref FMTDISC
-\li \ref FILTER "Filters"
+\li \ref FILTER
-\li \ref IOFLOW "HDF5 Raw I/O Flow Notes"
+\li \ref IOFLOW
-\li \ref TNMDC "Metadata Caching in HDF5"
+\li \ref TNMDC
-\li \ref MT "Thread Safe library"
+\li \ref MT
-\li \ref VFL "Virtual File Layer"
+\li \ref VFL
 
  */
 

doxygen/dox/UsersGuide.dox

@@ -0,0 +1,403 @@
+/** \page UG HDF5 User Guide
+
+<center>
+HDF5 Release 1.14
+
+\image html HDFG-logo.png "The HDF Group"
+
+</center>
+
+\ref sec_data_model
+\li \ref subsec_data_model_intro
+\li \ref subsec_data_model_abstract
+    <ul>
+        <li> \ref subsubsec_data_model_abstract_file
+        <li> \ref subsubsec_data_model_abstract_group
+        <li> \ref subsubsec_data_model_abstract_dataset
+        <li> \ref subsubsec_data_model_abstract_space
+        <li> \ref subsubsec_data_model_abstract_type
+        <li> \ref subsubsec_data_model_abstract_attr
+        <li> \ref subsubsec_data_model_abstract_plist
+        <li> \ref subsubsec_data_model_abstract_link
+    </ul>
+\li \ref subsec_data_model_storage
+    <ul>
+        <li> \ref subsubsec_data_model_storage_spec
+        <li> \ref subsubsec_data_model_storage_imple
+    </ul>
+\li \ref subsec_data_model_structure
+    <ul>
+        <li> \ref subsubsec_data_model_structure_file
+        <li> \ref subsubsec_data_model_structure_path
+        <li> \ref subsubsec_data_model_structure_example
+    </ul>
+
+\ref sec_program
+\li \ref subsec_program_intro
+\li \ref subsec_program_model
+    <ul>
+        <li> \ref subsubsec_program_model_create
+        <li> \ref subsubsec_program_model_dset
+        <li> \ref subsubsec_program_model_close
+        <li> \ref subsubsec_program_model_data
+        <li> \ref subsubsec_program_model_partial
+        <li> \ref subsubsec_program_model_info
+        <li> \ref subsubsec_program_model_compound
+        <li> \ref subsubsec_program_model_extend
+        <li> \ref subsubsec_program_model_group
+        <li> \ref subsubsec_program_model_attr
+    </ul>
+\li \ref subsec_program_transfer_pipeline
+
+\ref sec_file
+\li \ref subsec_file_intro
+\li \ref subsec_file_access_modes
+\li \ref subsec_file_creation_access
+\li \ref subsec_file_drivers
+\li \ref subsec_file_program_model
+    <ul>
+        <li> \ref subsubsec_file_program_model_create
+        <li> \ref subsubsec_file_program_model_open
+        <li> \ref subsubsec_file_program_model_close
+    </ul>
+\li \ref subsec_file_h5dump
+\li \ref subsec_file_summary
+\li \ref subsec_file_create
+\li \ref subsec_file_closes
+\li \ref subsec_file_property_lists
+    <ul>
+        <li> \ref subsubsec_file_property_lists_create
+        <li> \ref subsubsec_file_property_lists_props
+        <li> \ref subsubsec_file_property_lists_access
+    </ul>
+\li \ref subsec_file_alternate_drivers
+    <ul>
+        <li> \ref subsubsec_file_alternate_drivers_id
+        <li> \ref subsubsec_file_alternate_drivers_sec2
+        <li> \ref subsubsec_file_alternate_drivers_direct
+        <li> \ref subsubsec_file_alternate_drivers_log
+        <li> \ref subsubsec_file_alternate_drivers_win
+        <li> \ref subsubsec_file_alternate_drivers_stdio
+        <li> \ref subsubsec_file_alternate_drivers_mem
+        <li> \ref subsubsec_file_alternate_drivers_family
+        <li> \ref subsubsec_file_alternate_drivers_multi
+        <li> \ref subsubsec_file_alternate_drivers_split
+        <li> \ref subsubsec_file_alternate_drivers_par
+    </ul>
+\li \ref subsec_file_examples
+    <ul>
+        <li> \ref subsubsec_file_examples_trunc
+        <li> \ref subsubsec_file_examples_props
+        <li> \ref subsubsec_file_examples_access
+    </ul>
+\li \ref subsec_file_multiple
+
+\ref sec_group
+\li \ref subsec_group_intro
+\li \ref subsec_group_descr
+    <ul>
+        <li> \ref subsubsec_group_descr_object
+        <li> \ref subsubsec_group_descr_model
+        <li> \ref subsubsec_group_descr_path
+        <li> \ref subsubsec_group_descr_impl
+    </ul>
+\li \ref subsec_group_h5dump
+\li \ref subsec_group_function
+\li \ref subsec_group_program
+    <ul>
+        <li> \ref subsubsec_group_program_create
+        <li> \ref subsubsec_group_program_open
+        <li> \ref subsubsec_group_program_dataset
+        <li> \ref subsubsec_group_program_close
+        <li> \ref subsubsec_group_program_links
+        <li> \ref subsubsec_group_program_info
+        <li> \ref subsubsec_group_program_objs
+        <li> \ref subsubsec_group_program_all
+    </ul>
+\li \ref subsec_group_examples
+
+\ref sec_dataset
+\li \ref subsec_dataset_intro
+\li \ref subsec_dataset_function
+\li \ref subsec_dataset_program
+    <ul>
+        <li> \ref subsubsec_dataset_program_general
+        <li> \ref subsubsec_dataset_program_create
+        <li> \ref subsubsec_dataset_program_transfer
+        <li> \ref subsubsec_dataset_program_read
+    </ul>
+\li \ref subsec_dataset_transfer Data Transfer
+    <ul>
+        <li> \ref subsubsec_dataset_transfer_pipe
+        <li> \ref subsubsec_dataset_transfer_filter
+        <li> \ref subsubsec_dataset_transfer_drive
+        <li> \ref subsubsec_dataset_transfer_props
+        <li> \ref subsubsec_dataset_transfer_store
+        <li> \ref subsubsec_dataset_transfer_partial
+    </ul>
+\li \ref subsec_dataset_allocation
+    <ul>
+        <li> \ref subsubsec_dataset_allocation_store
+        <li> \ref subsubsec_dataset_allocation_delete
+        <li> \ref subsubsec_dataset_allocation_release
+        <li> \ref subsubsec_dataset_allocation_ext
+    </ul>
+\li \ref subsec_dataset_filters
+    <ul>
+        <li> \ref subsubsec_dataset_filters_nbit
+        <li> \ref subsubsec_dataset_filters_scale
+        <li> \ref subsubsec_dataset_filters_szip
+    </ul>
+
+\ref sec_datatype
+\li \ref subsec_datatype_intro
+\li \ref subsec_datatype_model
+    <ul>
+        <li> \ref subsubsec_datatype_model_class
+        <li> \ref subsubsec_datatype_model_predefine
+    </ul>
+\li \ref subsec_datatype_usage
+    <ul>
+        <li> \ref subsubsec_datatype_usage_object
+        <li> \ref subsubsec_datatype_usage_create
+        <li> \ref subsubsec_datatype_usage_transfer
+        <li> \ref subsubsec_datatype_usage_discover
+        <li> \ref subsubsec_datatype_usage_user
+    </ul>
+\li \ref subsec_datatype_function
+\li \ref subsec_datatype_program
+    <ul>
+        <li> \ref subsubsec_datatype_program_discover
+        <li> \ref subsubsec_datatype_program_define
+    </ul>
+\li \ref subsec_datatype_other
+    <ul>
+        <li> \ref subsubsec_datatype_other_strings
+        <li> \ref subsubsec_datatype_other_refs
+        <li> \ref subsubsec_datatype_other_enum
+        <li> \ref subsubsec_datatype_other_opaque
+        <li> \ref subsubsec_datatype_other_bitfield
+    </ul>
+\li \ref subsec_datatype_fill
+\li \ref subsec_datatype_complex
+    <ul>
+        <li> \ref subsubsec_datatype_complex_create
+        <li> \ref subsubsec_datatype_complex_analyze
+    </ul>
+\li \ref subsec_datatype_life
+\li \ref subsec_datatype_transfer
+\li \ref subsec_datatype_text
+
+\ref sec_dataspace
+\li \ref subsec_dataspace_intro
+\li \ref subsec_dataspace_function
+\li \ref subsec_dataspace_program
+    <ul>
+        <li> \ref subsubsec_dataspace_program_object
+        <li> \ref subsubsec_dataspace_program_model
+    </ul>
+\li \ref subsec_dataspace_transfer
+    <ul>
+        <li> \ref subsubsec_dataspace_transfer_select
+        <li> \ref subsubsec_dataspace_transfer_model
+    </ul>
+\li \ref subsec_dataspace_select
+\li \ref subsec_dataspace_refer
+    <ul>
+        <li> \ref subsubsec_dataspace_refer_use
+        <li> \ref subsubsec_dataspace_refer_create
+        <li> \ref subsubsec_dataspace_refer_read
+    </ul>
+\li \ref subsec_dataspace_sample
+
+\ref sec_attribute
+\li \ref subsec_attribute_intro
+\li \ref subsec_attribute_program
+    <ul>
+        <li> <!-- \subsubsection subsubsec_attribute_program_exist --> To Open and Read or Write an Existing Attribute </li>
+    </ul>
+\li \ref subsec_error_H5A
+\li \ref subsec_attribute_work
+    <ul>
+        <li> \ref subsubsec_attribute_work_struct
+        <li> \ref subsubsec_attribute_work_create
+        <li> \ref subsubsec_attribute_work_access
+        <li> \ref subsubsec_attribute_work_info
+        <li> \ref subsubsec_attribute_work_iterate
+        <li> \ref subsubsec_attribute_work_delete
+        <li> \ref subsubsec_attribute_work_close
+    </ul>
+\li \ref subsec_attribute_special
+
+\ref sec_error
+\li \ref subsec_error_intro
+\li \ref subsec_error_program
+\li \ref subsec_error_H5E
+\li \ref subsec_error_ops
+    <ul>
+        <li> \ref subsubsec_error_ops_stack
+        <li> \ref subsubsec_error_ops_print
+        <li> \ref subsubsec_error_ops_mute
+        <li> \ref subsubsec_error_ops_custom_print
+        <li> \ref subsubsec_error_ops_walk
+        <li> \ref subsubsec_error_ops_travers
+    </ul>
+\li \ref subsec_error_adv
+    <ul>
+        <li> \ref subsubsec_error_adv_more
+        <li> \ref subsubsec_error_adv_app
+    </ul>
+
+\ref sec_plist
+\li \ref subsec_plist_intro
+\li \ref subsec_plist_class
+    <ul>
+        <li> \ref subsubsec_plist_class
+        <li> \ref subsubsec_plist_lists
+        <li> \ref subsubsec_plist_props
+    </ul>
+\li \ref subsec_plist_program
+    <ul>
+        <li> \ref subsubsec_plist_default
+        <li> \ref subsubsec_plist_basic
+        <li> \ref subsubsec_plist_additional
+    </ul>
+\li \ref subsec_plist_generic
+\li \ref subsec_plist_H5P
+\li \ref subsec_plist_resources
+\li \ref subsec_plist_notes
+
+\ref sec_vol
+\li \ref subsec_vol_intro
+\li \ref subsec_vol_abstract_layer
+\li \ref subsec_vol_connect
+\li \ref subsec_vol_use
+
+\ref sec_async
+\li \ref subsec_async_intro
+
+\ref sec_map
+
+\ref sec_addition
+
+\page AR_UG Additional Resources
+
+\section sec_addition Additional Resources
+These documents provide additional information for the use and tuning of specific HDF5 features.
+ <table style=" border-spacing:0; padding-left:6.00pt; padding-top:6.00pt; padding-right:6.00pt; padding-bottom:6.00pt; float:aligncenter; width:100%; max-width:432.00pt;" cellspacing="0">
+  <caption x-list-start="1" style="font-size: 12.0pt;">Table of Additional resources</caption>
+  <tr style="height: 23.00pt;">
+  <th style="width: 234.000pt; border-top-style: solid; border-top-width: 1px; border-top-color: #228a22; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align : top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Document</p>
+</th>
+  <th style="width: 198.000pt; border-top-style: solid; border-top-width: 1px; border-top-color: #228a22; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align : top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Comments</p>
+</th>
+</tr>
+  <tr style="height: 23.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span>@ref HDF5Examples</span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Code examples by API. </p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/Chunking/index.html">Chunking in HDF5</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Structuring the use of chunking and tuning it for performance.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span class="FM_LT_LinkText"><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/DirectChunkWrite/UsingDirectChunkWrite.pdf">Using the Direct Chunk Write Function</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes another way that chunks can be written to datasets.</p>
+</td>
+</tr>
+  <tr style="height: 88.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/CommittedDatatypeCopying/CopyingCommittedDatatypesWithH5Ocopy.pdf">Copying Committed Datatypes with H5Ocopy</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to copy to another file a dataset that uses a committed datatype or an object with an attribute that uses a committed datatype so that the committed datatype in the destination file can be used by multiple objects.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/MetadataCache/index.html">Metadata Caching in HDF5</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Managing the HDF5 metadata cache and tuning it for performance.</p>
+</td>
+</tr>
+  <tr style="height: 49.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf">HDF5 Dynamically Loaded Filters</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how an HDF5 application can apply a filter that is not registered with the HDF5 Library.</p>
+</td>
+</tr>
+  <tr style="height: 62.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/FileImageOperations/HDF5FileImageOperations.pdf">HDF5 File Image Operations</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to work with HDF5 files in memory. Disk I/O is not required when file images are opened, created, read from, or written to.</p>
+</td>
+</tr>
+  <tr style="height: 62.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/ModifiedRegionWrites/ModifiedRegionWrites.pdf">Modified Region Writes</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how to set write operations for in-memory files so that only modified regions are written to storage. Available when the Core (Memory) VFD is used.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/UsingIdentifiers/index.html">Using Identifiers</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how identifiers behave and how they should be treated.</p>
+</td>
+</tr>
+  <tr style="height: 36.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/UsingUnicode/index.html">Using UTF-8 Encoding in HDF5 Applications</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes the use of UTF-8 Unicode character encodings in HDF5 applications.</p>
+</td>
+</tr>
+  <tr style="height: 49.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Advanced/FreeingMemory/FreeingMemoryAllocatedByTheHdf5Library.pdf">Freeing Memory Allocated by the HDF5 Library</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>Describes how inconsistent memory management can cause heap corruption or resource leaks and possible solutions.</p>
+</td>
+</tr>
+  <tr style="height: 23.00pt;">
+  <td style="width: 234.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p style="font-style: italic; color: #0000ff;"><span><a href="http://www.hdfgroup.org/HDF5/doc/Glossary.html">HDF5 Glossary</a></span></p>
+</td>
+  <td style="width: 198.000pt; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #228a22; vertical-align: top;padding-left: 6.00pt; padding-top: 3.00pt; padding-right: 6.00pt; padding-bottom: 3.00pt;">
+  <p>A glossary of terms.</p>
+</td>
+</tr>
+ </table>
+
+Previous Chapter \ref sec_plist
+
+\par Don't like what you see? - You can help to improve this User Guide
+     Complete the survey linked near the top of this page!\n
+     We treat documentation like code: Fork the
+     <a href="https://github.com/HDFGroup/hdf5">HDF5 repo</a>, make changes, and create a
+     <a href="https://github.com/HDFGroup/hdf5/pulls">pull request</a> !\n
+
+*/

doxygen/dox/ViewTools2.dox

@@ -0,0 +1,786 @@
+/** @page ViewToolsEdit Command-line Tools For Editing HDF5 Files
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+<hr>
+
+\section secViewToolsEditTOC Contents
+<ul>
+<li>\ref secViewToolsEditRemove</li>
+<li>\ref secViewToolsEditChange</li>
+<li>\ref secViewToolsEditApply</li>
+<li>\ref secViewToolsEditCopy</li>
+<li>\ref secViewToolsEditAdd</li>
+</ul>
+
+\section secViewToolsEditRemove Remove Inaccessible Objects and Unused Space in a File
+HDF5 files may accumulate unused space when they are read and rewritten to or if objects are deleted within
+them. With many edits and deletions this unused space can add up to a sizable amount.
+
+The <code style="background-color:whitesmoke;">h5repack</code> tool can be used to remove unused space in an HDF5
+file. If no options other than the input and output HDF5 files are specified on the
+<code style="background-color:whitesmoke;">h5repack</code> command line, it will write the file to the new
+file, getting rid of the unused space:
+\code
+h5repack <input file> <output file>
+\endcode
+
+\section secViewToolsEditChange Change a Dataset's Storage Layout
+The <code style="background-color:whitesmoke;">h5repack</code> utility can be used to change a dataset's storage
+layout. By default, the storage layout of a dataset is defined at creation time and it cannot be changed.
+However, with h5repack you can write an HDF5 file to a new file and change the layout for objects in the new file.
+
+The <code style="background-color:whitesmoke;">-l</code> option in <code style="background-color:whitesmoke;">h5repack</code>
+is used to change the layout for an object. The string following the <code style="background-color:whitesmoke;">-l</code>
+option defines the layout type and parameters for specified objects (or all objects):
+\code
+h5repack -l [list of objects:]<layout type>=<layout parameters> <input file> <output file>
+\endcode
+
+If no object is specified, then everything in the input file will be written to the output file with the specified
+layout type and parameters. If objects are specified then everything in the input file will be written to the
+output file as is, except for those specified objects. They will be written to the output file with the given
+layout type and parameters.
+
+Following is a description of the dataset layouts and the <code style="background-color:whitesmoke;">h5repack</code>
+options to use to change a dataset:
+<table>
+<tr>
+<th>Storage Layout</th><th>h5repack Option</th><th>Description</th>
+</tr>
+<tr>
+<td>Contiguous  
+</td>
+<td>CONTI
+</td>
+<td>Data is stored physically together
+</td>
+</tr>
+<tr>
+<td>Chunked 
+</td>
+<td>CHUNK=DIM[xDIM...xDIM]
+</td>
+<td>Data is stored in DIM[xDIM...xDIM] chunks
+</td>
+</tr>
+<tr>
+<td>Compact 
+</td>
+<td>COMPA
+</td>
+<td>Data is stored in the header of the object (less I/O)
+</td>
+</tr>
+</table>
+
+If you type <code style="background-color:whitesmoke;">h5repack -h</code> on the command line, you will see
+a detailed usage statement with examples of modifying the layout.
+
+In the following example, the dataset <code style="background-color:whitesmoke;">/dset</code> in the file
+dset.h5 is contiguous, as shown by the <code style="background-color:whitesmoke;">h5dump -pH</code> command.
+The <code style="background-color:whitesmoke;">h5repack</code> utility writes dset.h5 to a new file, dsetrpk.h5,
+where the dataset <code style="background-color:whitesmoke;">dset</code> is chunked. This can be seen by examining
+the resulting dsetrpk.h5 file with <code style="background-color:whitesmoke;">h5dump</code>, as shown:
+\code
+$ h5dump -pH dset.h5
+HDF5 "dset.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+      STORAGE_LAYOUT {
+         CONTIGUOUS
+         SIZE 96
+         OFFSET 1400
+      }
+      FILTERS {
+         NONE
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_LATE
+      }
+   }
+}
+}
+
+$ h5repack -l dset:CHUNK=4x6 dset.h5 dsetrpk.h5
+
+$ h5dump -pH dsetrpk.h5
+HDF5 "dsetrpk.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 4, 6 )
+         SIZE 96
+      }
+      FILTERS {
+         NONE
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+}
+}
+\endcode
+
+There can be many reasons that the storage layout needs to be changed for a dataset. For example,
+there may be a performance issue with a dataset due to a small chunk size.
+
+\section secViewToolsEditApply Apply Compression Filter to a Dataset
+The <code style="background-color:whitesmoke;">h5repack</code> utility can be used to compress or
+remove compression from a dataset in a file. By default, compression cannot be added to or removed
+from a dataset once it has been created. However, with <code style="background-color:whitesmoke;">h5repack</code>
+you can write a file to a new file and specify a compression filter to apply to a dataset or datasets in the new file.
+
+To apply a filter to an object in an HDF5 file, specify the <code style="background-color:whitesmoke;">-f</code> option,
+where the string following the <code style="background-color:whitesmoke;">-f</code> option defines the filter and
+its parameters (if there are any) to apply to a given object or objects:
+\code
+h5repack -f [list of objects:]<name of filter>=<filter parameters> <input file> <output file>
+\endcode
+
+If no objects are specified then everything in the input file will be written to the output file with
+the filter and parameters specified. If objects are specified, then everything in the input file will
+be written to the output file as is, except for the specified objects. They will be written to the
+output file with the filter and parameters specified.
+
+If you type <code style="background-color:whitesmoke;">h5repack --help</code> on the command line,
+you will see a detailed usage statement with examples of modifying a filter. There are actually
+numerous filters that you can apply to a dataset:
+<table>
+<tr>
+<th>Filter<th></th>Options</th>
+</tr>
+<tr>
+<td>GZIP compression (levels 1-9)
+<td>GZIP=&lt;deflation level&gt;
+</td>
+</tr>
+<tr>
+<td>SZIP compression
+<td>SZIP=<pixels per block,coding>
+</td>
+</tr>
+<tr>
+<td>Shuffle filter
+<td>SHUF
+</td>
+</tr>
+<tr>
+<td>Checksum filter
+<td>FLET
+</td>
+</tr>
+<tr>
+<td>NBIT compression
+<td>NBIT
+</td>
+</tr>
+<tr>
+<td>HDF5 Scale/Offset filter
+<td>SOFF=<scale_factor,scale_type>
+</td>
+</tr>
+<tr>
+<td>User defined filter
+<td>UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
+</td>
+</tr>
+<tr>
+<td>Remove ALL filters
+</td>
+<td>NONE
+</td>
+</tr>
+</table>
+
+Be aware that a dataset must be chunked to apply compression to it. If the dataset is not already chunked,
+then <code style="background-color:whitesmoke;">h5repack</code> will apply chunking to it. Both chunking
+and compression cannot be applied to a dataset at the same time with <code style="background-color:whitesmoke;">h5repack</code>.
+
+In the following example,
+\li <em>h5dump</em> lists the properties for the objects in <em>dset.h5</em>. Note that the dataset <em>dset</em> is contiguous.
+\li <em>h5repack</em> writes dset.h5 into a new file <em>dsetrpk.h5</em>, applying GZIP Level 5 compression to the dataset <em>/dset</em> in dsetrpk.h5.
+\li <em>h5dump</em> lists the properties for the new <em>dsetrpk.h5</em> file. Note that <em>/dset</em> is both compressed and chunked.
+
+<em>Example</em>
+\code
+$ h5dump -pH dset.h5
+HDF5 "dset.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 12, 18 ) / ( 12, 18 ) }
+      STORAGE_LAYOUT {
+         CONTIGUOUS
+         SIZE 864
+         OFFSET 1400
+      }
+      FILTERS {
+         NONE
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_LATE
+      }
+   }
+}
+}
+
+$ h5repack -f dset:GZIP=5 dset.h5 dsetrpk.h5
+
+$ h5dump -pH dsetrpk.h5
+HDF5 "dsetrpk.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 12, 18 ) / ( 12, 18 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 12, 18 )
+         SIZE 160 (5.400:1 COMPRESSION)
+      }
+      FILTERS {
+         COMPRESSION DEFLATE { LEVEL 5 }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+}
+}
+\endcode
+
+\section secViewToolsEditCopy Copy Objects to Another File
+The <code style="background-color:whitesmoke;">h5copy</code> utility can be used to copy an object or
+objects from one HDF5 file to another or to a different location in the same file. It uses the
+#H5Ocopy and #H5Lcopy APIs in HDF5.
+
+Following are some of the options that can be used with <code style="background-color:whitesmoke;">h5copy</code>.
+<table>
+<tr>
+<th>h5copy Options</th><th>Description</th>
+</tr>
+<tr>
+<td>-i, --input
+</td>
+<td>Input file name
+</td>
+</tr>
+<tr>
+<td>-o, --output
+</td>
+<td>Output file name
+</td>
+</tr>
+<tr>
+<td>-s, --source
+</td>
+<td>Source object name
+</td>
+</tr>
+<tr>
+<td>-d, --destination
+</td>
+<td>Destination object name
+</td>
+</tr>
+<tr>
+<td>-p, --parents
+</td>
+<td>Make parent groups as needed
+</td>
+</tr>
+<tr>
+<td>-v, --verbose
+</td>
+<td>Verbose mode
+</td>
+</tr>
+<tr>
+<td>-f, --flag
+</td>
+<td>Flag type
+</td>
+</tr>
+</table>
+
+For a complete list of options and information on using <code style="background-color:whitesmoke;">h5copy</code>, type:
+\code
+h5copy --help
+\endcode
+
+In the example below, the dataset <code style="background-color:whitesmoke;">/MyGroup/Group_A/dset2</code>
+in <code style="background-color:whitesmoke;">groups.h5</code> gets copied to the root
+("<code style="background-color:whitesmoke;">/</code>") group of a new file,
+<code style="background-color:whitesmoke;">newgroup.h5</code>, with the name
+<code style="background-color:whitesmoke;">dset3</code>:
+\code
+$h5dump -H groups.h5
+HDF5 "groups.h5" {
+GROUP "/" {
+   GROUP "MyGroup" {
+      GROUP "Group_A" {
+         DATASET "dset2" {
+            DATATYPE  H5T_STD_I32BE
+            DATASPACE  SIMPLE { ( 2, 10 ) / ( 2, 10 ) }
+         }
+      }
+      GROUP "Group_B" {
+      }
+      DATASET "dset1" {
+         DATATYPE  H5T_STD_I32BE
+         DATASPACE  SIMPLE { ( 3, 3 ) / ( 3, 3 ) }
+      }
+   }
+}
+}
+
+$ h5copy -i groups.h5 -o newgroup.h5 -s /MyGroup/Group_A/dset2 -d /dset3
+
+$ h5dump -H newgroup.h5
+HDF5 "newgroup.h5" {
+GROUP "/" {
+   DATASET "dset3" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 2, 10 ) / ( 2, 10 ) }
+   }
+}
+}
+\endcode
+
+There are also <code style="background-color:whitesmoke;">h5copy</code> flags that can be specified
+with the <code style="background-color:whitesmoke;">-f</code> option. In the example below, the
+<code style="background-color:whitesmoke;">-f shallow</code> option specifies to copy only the
+immediate members of the group <code style="background-color:whitesmoke;">/MyGroup</code> from
+the <code style="background-color:whitesmoke;">groups.h5</code> file mentioned above to a new
+file <code style="background-color:whitesmoke;">mygrouponly.h5</code>:
+\code
+h5copy -v -i groups.h5 -o mygrouponly.h5 -s /MyGroup -d /MyGroup -f shallow
+\endcode
+
+The output of the above command is shown below. The verbose option <code style="background-color:whitesmoke;">-v</code>
+describes the action that was taken, as shown in the highlighted text.
+\code
+Copying file <groups.h5> and object </MyGroup> to file <mygrouponly.h5> and object </MyGroup>
+Using shallow flag
+
+$ h5dump -H mygrouponly.h5
+HDF5 "mygrouponly.h5" {
+GROUP "/" {
+   GROUP "MyGroup" {
+      GROUP "Group_A" {
+      }
+      GROUP "Group_B" {
+      }
+      DATASET "dset1" {
+         DATATYPE  H5T_STD_I32BE
+         DATASPACE  SIMPLE { ( 3, 3 ) / ( 3, 3 ) }
+      }
+   }
+}
+}
+\endcode
+
+\section secViewToolsEditAdd Add or Remove User Block from File
+The user block is a space in an HDF5 file that is not interpreted by the HDF5 library. It is a property
+list that can be added when creating a file. See the #H5Pset_userblock API in the \ref RM for more
+information regarding this property.
+
+Once created in a file, the user block cannot be removed. However, you can use the
+<code style="background-color:whitesmoke;">h5jam</code> and <code style="background-color:whitesmoke;">h5unjam</code>
+utilities to add or remove a user block from a file into a new file.
+
+These two utilities work similarly, except that <code style="background-color:whitesmoke;">h5jam</code>
+adds a user block to a file and <code style="background-color:whitesmoke;">h5unjam</code> removes the user
+block. You can also overwrite or delete a user block in a file.
+
+Specify the <code style="background-color:whitesmoke;">-h</code> option to see a complete list of options
+that can be used with <code style="background-color:whitesmoke;">h5jam</code> and
+<code style="background-color:whitesmoke;">h5unjam</code>. For example:
+\code
+   h5jam -h
+   h5unjam -h
+\endcode
+
+Below are the basic options for adding or removing a user block with <code style="background-color:whitesmoke;">h5jam</code>
+and <code style="background-color:whitesmoke;">h5unjam</code>:
+
+<table>
+<tr>
+<th>h5copy Options</th><th>Description</th>
+</tr>
+<tr>
+<td>-i
+</td>
+<td>Input File
+</td>
+</tr>
+<tr>
+<td>-o
+</td>
+<td>Output File
+</td>
+</tr>
+<tr>
+<td>-u
+</td>
+<td>File to add or remove from user block
+</td>
+</tr>
+</table>
+
+Let's say you wanted to add the program that creates an HDF5 file to its user block. As an example, you
+can take the <code style="background-color:whitesmoke;">h5_crtgrpar.c</code> program from the
+\ref LBExamples
+and add it to the file it creates, <code style="background-color:whitesmoke;">groups.h5</code>. This can
+be done with <code style="background-color:whitesmoke;">h5jam</code>, as follows:
+\code
+h5jam -i groups.h5 -u h5_crtgrpar.c -o groupsub.h5
+\endcode
+
+You can actually view the file with more <code style="background-color:whitesmoke;">groupsub.h5</code>
+to see that the <code style="background-color:whitesmoke;">h5_crtgrpar.c</code> file is indeed included.
+
+To remove the user block that was just added, type:
+\code
+h5unjam -i groupsub.h5 -u h5_crtgrparNEW.c -o groups-noub.h5
+\endcode
+
+This writes the user block in the file <code style="background-color:whitesmoke;">groupsub.h5</code>
+into <code style="background-color:whitesmoke;">h5_crtgrparNEW.c</code>. The new HDF5 file,
+<code style="background-color:whitesmoke;">groups-noub.h5</code>, will not contain a user block.
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+
+*/
+
+/** @page ViewToolsConvert Command-line Tools For Converting HDF5 Files
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+<hr>
+
+\section secViewToolsConvertTOC Contents
+<ul>
+<li>\ref secViewToolsConvertASCII</li>
+<li>\ref secViewToolsConvertBinary</li>
+<li>\ref secViewToolsConvertExport</li>
+</ul>
+
+\section secViewToolsConvertASCII Output HDF5 Dataset into an ASCII File (to Import into Excel and Other Applications)
+The <code style="background-color:whitesmoke;">h5dump</code> utility can be used to convert an HDF5 dataset
+into an ASCII file, which can then be imported into Excel and other applications. The following options are used:
+<table>
+<tr>
+<th>Options</th><th>Description</th>
+</tr>
+<tr>
+<td> -d D, --dataset=D
+</td>
+<td>Display dataset D
+</td>
+</tr>
+<tr>
+<td> -o F, --output=F 
+</td>
+<td>Output raw data into file F
+</td>
+</tr>
+<tr>
+<td> -y, --noindex
+</td>
+<td>Suppress printing of array indices with the data
+</td>
+</tr>
+<tr>
+<td> -w N, --width=N
+</td>
+<td>Set N number of columns of output. A value of 0
+sets the number to 65535 (the maximum)
+</td>
+</tr>
+</table>
+
+As an example, <code style="background-color:whitesmoke;">h5_crtdat.c</code> from the \ref LBDsetCreate
+HDF5 Tutorial topic, creates the file <code style="background-color:whitesmoke;">dset.h5</code> with
+a dataset <code style="background-color:whitesmoke;">/dset</code> that is a 4 x 6 integer array. The
+following is displayed when viewing <code style="background-color:whitesmoke;">dset.h5</code> with
+<code style="background-color:whitesmoke;">h5dump</code>:
+\code
+$ h5dump dset.h5
+HDF5 "dset.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+      DATA {
+      (0,0): 1, 2, 3, 4, 5, 6,
+      (1,0): 7, 8, 9, 10, 11, 12,
+      (2,0): 13, 14, 15, 16, 17, 18,
+      (3,0): 19, 20, 21, 22, 23, 24
+      }
+   }
+}
+}
+\endcode
+
+The following command will output the values of the <code style="background-color:whitesmoke;">/dset</code>
+dataset to the ASCII file <code style="background-color:whitesmoke;">dset.asci</code>:
+\code
+h5dump -d /dset -o dset.asci -y -w 50 dset.h5
+\endcode
+
+In particular, note that:
+\li The default behavior of <code style="background-color:whitesmoke;">h5dump</code> is to print indices,
+and the <code style="background-color:whitesmoke;">-y</code> option suppresses this.
+\li The <code style="background-color:whitesmoke;">-w 50</code> option tells
+<code style="background-color:whitesmoke;">h5dump</code> to allow 50 columns for outputting the data. The
+value specified must be large enough to accommodate the dimension size of the dataset multiplied by the
+number of positions and spaces needed to print each value. If the value is not large enough, the output
+will wrap to the next line, and the data will not display as expected in Excel or other applications. To
+ensure that the output does not wrap to the next line, you can also specify 0 (zero) for the
+<code style="background-color:whitesmoke;">-w</code> option.
+
+In addition to creating the ASCII file <code style="background-color:whitesmoke;">dset.asci</code>, the
+above command outputs the metadata of the specified dataset:
+\code
+HDF5 "dset.h5" {
+DATASET "/dset" {
+   DATATYPE  H5T_STD_I32BE
+   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+   DATA {
+   }
+}
+}
+\endcode
+
+The <code style="background-color:whitesmoke;">dset.asci</code> file will contain the values for the dataset:
+\code
+      1, 2, 3, 4, 5, 6,
+      7, 8, 9, 10, 11, 12,
+      13, 14, 15, 16, 17, 18,
+      19, 20, 21, 22, 23, 24
+\endcode
+
+\section secViewToolsConvertBinary Output HDF5 Dataset into Binary File
+The <code style="background-color:whitesmoke;">h5dump</code> utility can be used to convert an
+HDF5 dataset to a binary file with the following options:
+<table>
+<tr>
+<th>Options</th><th>Description</th>
+</tr>
+<tr>
+<td>-d D, --dataset=D
+</td>
+<td>Display dataset D
+</td>
+</tr>
+<tr>
+<td>-o F, --output=F 
+</td>
+<td>Output raw data into file F
+</td>
+</tr>
+<tr>
+<td>-b B, --binary=B
+</td>
+<td>Binary file output of form B.
+Valid values are: LE, BE, NATIVE, FILE
+</td>
+</tr>
+</table>
+
+As an example, <code style="background-color:whitesmoke;">h5_crtdat.c</code> from the
+\ref LBDsetCreate HDF5 Tutorial topic, creates the file dset.h5 with a dataset
+<code style="background-color:whitesmoke;">/dset</code> that is a 4 x 6 integer array. The
+following is displayed when viewing <code style="background-color:whitesmoke;">dset.h5</code>
+with <code style="background-color:whitesmoke;">h5dump</code>:
+\code
+$ h5dump -d /dset/ dset.h5
+HDF5 "dset.h5" {
+DATASET "/dset/" {
+   DATATYPE  H5T_STD_I32BE
+   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+   DATA {
+   (0,0): 1, 2, 3, 4, 5, 6,
+   (1,0): 7, 8, 9, 10, 11, 12,
+   (2,0): 13, 14, 15, 16, 17, 18,
+   (3,0): 19, 20, 21, 22, 23, 24
+   }
+}
+}
+\endcode
+
+As specified by the <code style="background-color:whitesmoke;">-d</code> and
+<code style="background-color:whitesmoke;">-o</code> options, the following
+<code style="background-color:whitesmoke;">h5dump</code> command will output the values of the dataset
+<code style="background-color:whitesmoke;">/dset </code>to a file called
+<code style="background-color:whitesmoke;">dset.bin</code>. The <code style="background-color:whitesmoke;">-b</code>
+option specifies that the output will be binary in Little Endian format (LE).
+
+\code
+h5dump -d /dset -b LE -o dset.bin dset.h5
+\endcode
+
+This command outputs the metadata for the dataset, as well as creating the binary file
+<code style="background-color:whitesmoke;">dset.bin</code>:
+\code
+HDF5 "dset.h5" {
+DATASET "/dset" {
+   DATATYPE  H5T_STD_I32BE
+   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+   DATA {
+   }
+}
+}
+\endcode
+
+If you look at the resulting <code style="background-color:whitesmoke;">dset.bin</code> file with
+a binary editor, you will see that it contains the dataset's values. For example (on Linux) you will see:
+\code
+$ od -t d dset.bin
+0000000           1           2           3           4
+0000020           5           6           7           8
+0000040           9          10          11          12
+0000060          13          14          15          16
+0000100          17          18          19          20
+0000120          21          22          23          24
+0000140
+\endcode
+
+\section secViewToolsConvertExport Export from h5dump and Import into HDF5
+The <code style="background-color:whitesmoke;">h5import</code> utility can use the output of
+<code style="background-color:whitesmoke;">h5dump</code> as input to create a dataset or file.
+
+The <code style="background-color:whitesmoke;">h5dump</code> utility must first create two files:
+\li A DDL file, which will be used as an <code style="background-color:whitesmoke;">h5import</code> configuration file
+\li A raw data file containing the data to be imported
+
+The DDL file must be generated with the <code style="background-color:whitesmoke;">h5dump -p</code> option, to generate properties.
+
+The raw data file that can be imported into HDF5 using this method may contain either numeric or string data with the following restrictions:
+\li Numeric data requires the use of the <code style="background-color:whitesmoke;">h5dump -b</code> option to produce a binary data file.
+\li String data must be written with the <code style="background-color:whitesmoke;">h5dump -y</code> and
+<code style="background-color:whitesmoke;">--width=1</code> options, generating a single column of strings without indices.
+
+Two examples follow: the first imports a dataset with a numeric datatype. Note that numeric data requires
+the use of the <code style="background-color:whitesmoke;">h5dump -b</code> option to produce a binary data
+file. The example program (<code style="background-color:whitesmoke;">h5_crtdat.c</code>) that creates this
+file is included with the \ref IntroHDF5 tutorial and can be obtained from the \ref LBExamples page:
+\code
+h5dump -p -d "/dset" --ddl=dsetbin.dmp -o dset.bin -b dset.h5
+h5import dset.bin -c dsetbin.dmp -o new-dset.h5
+\endcode
+
+The output before and after running these commands is shown below:
+\code
+$  h5dump dset.h5
+HDF5 "dset.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+      DATA {
+      (0,0): 1, 2, 3, 4, 5, 6,
+      (1,0): 7, 8, 9, 10, 11, 12,
+      (2,0): 13, 14, 15, 16, 17, 18,
+      (3,0): 19, 20, 21, 22, 23, 24
+      }
+   }
+}
+}
+$ h5dump -p -d "/dset" --ddl=dsetbin.dmp -o dset.bin -b dset.h5
+
+$ h5import dset.bin -c dsetbin.dmp -o new-dset.h5
+
+$ h5dump new-dset.h5
+HDF5 "new-dset.h5" {
+GROUP "/" {
+   DATASET "dset" {
+      DATATYPE  H5T_STD_I32BE
+      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
+      DATA {
+      (0,0): 1, 2, 3, 4, 5, 6,
+      (1,0): 7, 8, 9, 10, 11, 12,
+      (2,0): 13, 14, 15, 16, 17, 18,
+      (3,0): 19, 20, 21, 22, 23, 24
+      }
+   }
+}
+}
+\endcode
+
+The second example imports string data. The example program that creates this file can be downloaded
+from the <a href="https://portal.hdfgroup.org/display/HDF5/Examples+by+API">Examples by API</a> page.
+
+Note that string data requires use of the <code style="background-color:whitesmoke;">h5dump -y</code>
+option to exclude indexes and the <code style="background-color:whitesmoke;">h5dump --width=1</code>
+option to generate a single column of strings. The <code style="background-color:whitesmoke;">-o</code>
+option outputs the data into an ASCII file.
+\code
+h5dump -p -d "/DS1" -O vlstring.dmp -o vlstring.ascii -y --width=1 h5ex_t_vlstring.h5
+h5import vlstring.ascii -c vlstring.dmp -o new-vlstring.h5
+\endcode
+
+The output before and after running these commands is shown below:
+\code
+$ h5dump h5ex_t_vlstring.h5
+HDF5 "h5ex_t_vlstring.h5" {
+GROUP "/" {
+   DATASET "DS1" {
+      DATATYPE  H5T_STRING {
+         STRSIZE H5T_VARIABLE;
+         STRPAD H5T_STR_SPACEPAD;
+         CSET H5T_CSET_ASCII;
+         CTYPE H5T_C_S1;
+      }
+      DATASPACE  SIMPLE { ( 4 ) / ( 4 ) }
+      DATA {
+      (0): "Parting", "is such", "sweet", "sorrow."
+      }
+   }
+}
+}
+
+$ h5dump -p -d "/DS1" -O vlstring.dmp -o vlstring.ascii -y --width=1 h5ex_t_vlstring.h5
+
+$ h5import vlstring.ascii -c vlstring.dmp -o new-vlstring.h5
+
+$ h5dump new-vlstring.h5
+HDF5 "new-vlstring.h5" {
+GROUP "/" {
+   DATASET "DS1" {
+      DATATYPE  H5T_STRING {
+         STRSIZE H5T_VARIABLE;
+         STRPAD H5T_STR_NULLTERM;
+         CSET H5T_CSET_ASCII;
+         CTYPE H5T_C_S1;
+      }
+      DATASPACE  SIMPLE { ( 4 ) / ( 4 ) }
+      DATA {
+      (0): "Parting", "is such", "sweet", "sorrow."
+      }
+   }
+}
+\endcode
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+
+*/

doxygen/dox/ViewToolsJPSS.dox

@@ -0,0 +1,763 @@
+/** @page ViewToolsJPSS Use Case: Examining a JPSS NPP File With HDF5 Tools
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+<hr>
+
+\section secViewToolsJPSSTOC Contents
+<ul>
+<li>\ref secViewToolsJPSSDeter</li>
+<li>\ref secViewToolsJPSSView</li>
+<li>\ref secViewToolsJPSSExam</li>
+</ul>
+
+This tutorial illustrates how to use the HDF5 tools to examine NPP files from the JPSS project. The following files are discussed:
+\code
+SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 (<a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5.gz">gzipped file</a>)
+SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 (<a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5.gz">gzipped file</a>)
+\endcode
+
+\section secViewToolsJPSSDeter Determining File Contents
+The first thing you may want to do is determine what is in your file. You can use the command-line tools or HDFView to do this:
+\li @ref subsecViewToolsJPSSDeter_h5dump
+\li @ref subsecViewToolsJPSSDeter_h5ls
+\li @ref subsecViewToolsJPSSDeter_HDFView
+
+JPSS NPP files all contain two root level groups:
+<table>
+<tr>
+<th>Group</th><th>Description</th>
+</tr>
+<tr>
+<td>/All_Data
+</td>
+<td>Contains the raw data and optional geo-location information.
+</td>
+</tr>
+<tr>
+<td>/Data_Products
+</td>
+<td>Contains a dataset ending in <code style="background-color:whitesmoke;">Aggr</code> with
+references to objects in the <code style="background-color:whitesmoke;">/All_Data</code> group.
+Contains granules (datasets with a name ending in <code style="background-color:whitesmoke;">Gran_#</code>)
+with references to selected regions in datasets under <code style="background-color:whitesmoke;">/All_Data</code>.
+</td>
+</tr>
+</table>
+
+\subsection subsecViewToolsJPSSDeter_h5dump h5dump
+With <code style="background-color:whitesmoke;">h5dump</code> you can see a list of the objects
+in the file using the <code style="background-color:whitesmoke;">-n</code> option:
+\code
+h5dump -n <file>
+\endcode
+
+For example:
+\code
+$ h5dump -n SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
+HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
+FILE_CONTENTS {
+ group      /
+ group      /All_Data
+ group      /All_Data/VIIRS-M9-SDR_All
+ dataset    /All_Data/VIIRS-M9-SDR_All/ModeGran
+ dataset    /All_Data/VIIRS-M9-SDR_All/ModeScan
+ dataset    /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums
+ dataset    /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts
+ dataset    /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts
+ dataset    /All_Data/VIIRS-M9-SDR_All/NumberOfScans
+ dataset    /All_Data/VIIRS-M9-SDR_All/PadByte1
+ dataset    /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR
+ dataset    /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR
+ dataset    /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR
+ dataset    /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR
+ dataset    /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR
+ dataset    /All_Data/VIIRS-M9-SDR_All/Radiance
+ dataset    /All_Data/VIIRS-M9-SDR_All/RadianceFactors
+ dataset    /All_Data/VIIRS-M9-SDR_All/Reflectance
+ dataset    /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors
+ group      /Data_Products
+ group      /Data_Products/VIIRS-M9-SDR
+ dataset    /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr
+ dataset    /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0
+ dataset    /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1
+ dataset    /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2
+ dataset    /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3
+ }
+}
+\endcode
+
+In the output above you can see that there are four granules (ending in
+<code style="background-color:whitesmoke;">Gran_#</code>) in the
+<code style="background-color:whitesmoke;">/Data_Products/VIIRS-M9-SDR/</code> group.
+
+\subsection subsecViewToolsJPSSDeter_h5ls h5ls
+With <code style="background-color:whitesmoke;">h5ls</code> you can see a list of the objects in the
+file using the <code style="background-color:whitesmoke;">-lr</code>
+options. The <code style="background-color:whitesmoke;">h5ls</code> utility also shows shape and size
+(dataspace) information about datasets.
+\code
+h5ls -lr <file>
+\endcode
+
+For example:
+\code
+$ h5ls -lr SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
+/                        Group
+/All_Data                Group
+/All_Data/VIIRS-M9-SDR_All Group
+/All_Data/VIIRS-M9-SDR_All/ModeGran Dataset {4/Inf}
+/All_Data/VIIRS-M9-SDR_All/ModeScan Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/NumberOfScans Dataset {4/Inf}
+/All_Data/VIIRS-M9-SDR_All/PadByte1 Dataset {12/Inf}
+/All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR Dataset {3072/Inf, 3200/Inf}
+/All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR Dataset {192/Inf}
+/All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR Dataset {3072/Inf}
+/All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR Dataset {64/Inf}
+/All_Data/VIIRS-M9-SDR_All/Radiance Dataset {3072/Inf, 3200/Inf}
+/All_Data/VIIRS-M9-SDR_All/RadianceFactors Dataset {8/Inf}
+/All_Data/VIIRS-M9-SDR_All/Reflectance Dataset {3072/Inf, 3200/Inf}
+/All_Data/VIIRS-M9-SDR_All/ReflectanceFactors Dataset {8/Inf}
+/Data_Products           Group
+/Data_Products/VIIRS-M9-SDR Group
+/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr Dataset {16/Inf}
+/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0 Dataset {16/Inf}
+/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1 Dataset {16/Inf}
+/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2 Dataset {16/Inf}
+/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3 Dataset {16/Inf}
+\endcode
+Note that the <code style="background-color:whitesmoke;">Inf</code> indicates that those datasets are appendable or unlimited in size.
+
+\subsection subsecViewToolsJPSSDeter_HDFView HDFView
+If you open the file in HDFView, it will display the file and the root level groups within
+it in the TreeView on the left. An HDF5 file is a folder with a "5" in the middle, followed
+by the file name. There are two folders (groups) within the JPSS file
+(<code style="background-color:whitesmoke;">All_Data/</code> and <code style="background-color:whitesmoke;">Data Products/</code>),
+which you can select to see their contents:
+<table>
+<tr>
+<td>
+\image html hdfview-tree.png 
+</td>
+</tr>
+</table>
+
+If you click twice with the left-mouse button on a folder or group in the TreeView, the contents
+of the folder will be listed. If you click twice on an object such as a dataset, a window with
+the object's values will be displayed.
+
+Underneath the <code style="background-color:whitesmoke;">VIIRS-M1-SDR</code> folder are what HDF5
+calls datasets. The scarlet letter <code style="background-color:whitesmoke;">"A"</code> attached
+to the group and datasets under <code style="background-color:whitesmoke;">Data_Products/</code>
+indicates that there are attributes associated with them.
+
+\section secViewToolsJPSSView Viewing the User Block
+All JPSS files contain a user block in XML with information about the file. The user block is an
+optional space allocated at the beginning of an HDF5 file that is not interpreted by the HDF5
+library. Its size is a multiple of 512.
+
+Since the user block in JPSS files is stored in ASCII and it is stored at the beginning of an
+HDF5 file, you could use a text editor or viewer to examine it. However, there are HDF5 utilities
+that can help with this:
+<table>
+<tr>
+<th>Utility</th><th>Description</th>
+</tr>
+<tr>
+<td>h5unjam
+</td>
+<td>Extracts a user block from an HDF5 file
+</td>
+</tr>
+<tr>
+<td>h5dump
+</td>
+<td>The -B (--superblock) option displays the size of the user block in an HDF5 file
+</td>
+</tr>
+</table>
+
+\subsection subsecViewToolsJPSSView_h5unjam h5unjam
+The \ref secViewToolsEditAdd tutorial topic discusses the use of the
+<code style="background-color:whitesmoke;">h5jam</code> and <code style="background-color:whitesmoke;">h5unjam</code>
+utilities for adding or removing a user block from a file. An input HDF5 file
+(<code style="background-color:whitesmoke;">-i</code>), output HDF5 file
+(<code style="background-color:whitesmoke;">-o</code>), and user block text file
+(<code style="background-color:whitesmoke;">-u</code>) can be specified with these tools. You can use the
+<code style="background-color:whitesmoke;">h5unjam</code> tool to extract and view the user block in a JPSS file:
+\code
+h5unjam -i <Input HDF5 File> -o <Output HDF5 File> -u <User Block File>
+\endcode
+
+For example this command will extract the user block into the file UB.xml:
+\code
+$ h5unjam -i SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 
+          -o svm09-noUB.h5 -u UB.xml
+\endcode
+
+The input HDF5 file remains unchanged. The output HDF5 file will not contain the user block.
+The <code style="background-color:whitesmoke;">UB.xml</code> file contains the user block
+which can be viewed with a browser.
+
+\subsection subsecViewToolsJPSSView_h5dump h5dump
+The h5dump utility has the <code style="background-color:whitesmoke;">-B (--superblock)</code> option for displaying the superblock in an HDF5 file.
+The superblock contains information about the file such as the file signature, file consistency flags,
+the number of bytes to store addresses and size of an object, as well as the size of the user block:
+\code
+h5dump -B (--superblock)
+\endcode
+
+Below is an example (Unix):
+\code
+$ h5dump -B -H SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 | more
+HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
+SUPER_BLOCK {
+   SUPERBLOCK_VERSION 0
+   FREELIST_VERSION 0
+   SYMBOLTABLE_VERSION 0
+   OBJECTHEADER_VERSION 0
+   OFFSET_SIZE 8
+   LENGTH_SIZE 8
+   BTREE_RANK 16
+   BTREE_LEAF 4
+   ISTORE_K 32
+   USER_BLOCK {
+      USERBLOCK_SIZE 1024
+   }
+}
+\endcode
+
+Once you have the size of the user block, you can extract it from the file using system commands.
+For example, on Unix platforms you can use the head command-line tool:
+\code
+head -c <USERBLOCK_SIZE> <JPSS File> >& USERBLOCK.xml
+\endcode
+
+There are Unix tools for Windows that may work, such as <a href="http://gnuwin32.sourceforge.net/packages/coreutils.htm">CoreUtils for Windows</a>.
+
+\section secViewToolsJPSSExam Examining a Granule
+<ul>
+<li>@ref subsecViewToolsJPSSExam_h5dump<br />
+<ul>
+<li>@ref subsubsecViewToolsJPSSExam_h5dumpRegRef</li>
+<li>@ref subsubsecViewToolsJPSSExam_h5dumpQuality</li>
+<li>@ref subsubsecViewToolsJPSSExam_h5dumpProps</li>
+</ul></li>
+<li>@ref subsecViewToolsJPSSExamr_HDFView</li>
+</ul>
+
+\subsection subsecViewToolsJPSSExam_h5dump h5dump
+There are several options that you may first want to use when examining a granule with h5dump:
+<table>
+<tr>
+<th>Option</th><th>Description</th>
+</tr>
+<tr>
+<td>-H, --header
+</td>
+<td>Prints header (metadata) information only
+</td>
+</tr>
+<tr>
+<td>-d D, --dataset=D
+</td>
+<td>Specifies the granule dataset
+</td>
+</tr>
+<tr>
+<td>-A 0, --onlyattr=0
+</td>
+<td>Suppresses attributes
+</td>
+</tr>
+<tr>
+<td>-p, --properties
+</td>
+<td>Show properties of datasets
+(See Properties)
+</td>
+</tr>
+</table>
+
+You would specify the dataset (<code style="background-color:whitesmoke;">-d D</code>) and the
+<code style="background-color:whitesmoke;">-H</code> options to view the metadata associated with
+a specific granule. There are many attributes associated with a granule and
+<code style="background-color:whitesmoke;">-A 0</code> can be used to suppress those.
+
+For example:
+\code
+h5dump -H -A 0 -d "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" 
+        SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
+\endcode
+
+This command displays:
+\code
+   HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
+   DATASET "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" {
+      DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+      DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+   }
+   }
+\endcode
+
+To see the actual contents of the granule remove the <code style="background-color:whitesmoke;">-H</code> option:
+\code
+h5dump -A 0 -d "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" 
+       SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
+\endcode
+
+The above command displays:
+\code
+HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
+DATASET "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" {
+   DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+   DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+   DATA {
+      DATASET /All_Data/VIIRS-M9-SDR_All/Radiance {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/Reflectance {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/ModeScan {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/ModeGran {(0)-(0)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/PadByte1 {(0)-(2)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfScans {(0)-(0)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR {(0)-(47)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR {(0)-(767)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/RadianceFactors {(0)-(1)},
+      DATASET /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors {(0)-(1)}
+   }
+}
+}
+\endcode
+
+As you can see in the output above, the datatype for this dataset is:
+\code
+DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+\endcode
+
+This indicates that it is a dataset specifically for storing references to regions (or subsets)
+in other datasets. The dataset contains 16 such references, and more can be added to it, as
+indicated by the dataspace (in other words it is unlimited):
+\code
+DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+\endcode
+
+\subsubsection subsubsecViewToolsJPSSExam_h5dumpRegRef Viewing a Region Reference
+What if we wanted to look at the <code style="background-color:whitesmoke;">NumberOfScans</code> data for a specific granule in a file?
+
+First, we may be interested in determining whether the scans were done at night or in the day. If a scan was at night, there will be no data.
+
+The attribute <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> is used to determine when the scan was done. If you don't know where this attribute is located, you can use the <code style="background-color:whitesmoke;">-N</code> option to search for it in the file. If you were to run this command on the <code style="background-color:whitesmoke;">SVM09</code> file used above, you would see that the <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> attribute has a value of <code style="background-color:whitesmoke;">Night</code> for the four granules in the file. Indeed, if you actually examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data, you will see that only fill values are written.
+
+For that reason we will examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data for the <code style="background-color:whitesmoke;">SVMO1</code> file below, as it was obtained during the day:
+\code
+h5dump -N N_Day_Night_Flag SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+\endcode
+
+It displays:
+\code
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+ATTRIBUTE "N_Day_Night_Flag" {
+   DATATYPE  H5T_STRING {
+      STRSIZE 4;
+      STRPAD H5T_STR_NULLTERM;
+      CSET H5T_CSET_ASCII;
+      CTYPE H5T_C_S1;
+   }
+   DATASPACE  SIMPLE { ( 1, 1 ) / ( 1, 1 ) }
+   DATA {
+   (0,0): "Day"
+   }
+}
+}
+\endcode
+
+There is just one granule in this <code style="background-color:whitesmoke;">SVM01</code> file, as shown below:
+\code
+$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+FILE_CONTENTS {
+ group      /
+ group      /All_Data
+ group      /All_Data/VIIRS-M1-SDR_All
+ dataset    /All_Data/VIIRS-M1-SDR_All/ModeGran
+ dataset    /All_Data/VIIRS-M1-SDR_All/ModeScan
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfScans
+ dataset    /All_Data/VIIRS-M1-SDR_All/PadByte1
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR
+ dataset    /All_Data/VIIRS-M1-SDR_All/Radiance
+ dataset    /All_Data/VIIRS-M1-SDR_All/RadianceFactors
+ dataset    /All_Data/VIIRS-M1-SDR_All/Reflectance
+ dataset    /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors
+ group      /Data_Products
+ group      /Data_Products/VIIRS-M1-SDR
+ dataset    /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr
+ dataset    /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0
+ }
+}
+\endcode
+
+Now examine the references in the <code style="background-color:whitesmoke;">VIIRS-M1-SDR_Gran_0</code> granule
+\code
+$ h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" 
+       SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
+   DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+   DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+   DATA {
+      DATASET /All_Data/VIIRS-M1-SDR_All/Radiance {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/Reflectance {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/ModeScan {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/ModeGran {(0)-(0)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/PadByte1 {(0)-(2)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR {(0)-(47)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR {(0)-(767)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/RadianceFactors {(0)-(1)},
+      DATASET /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors {(0)-(1)}
+   }
+}
+}
+\endcode
+
+In the output above, you can see that the <code style="background-color:whitesmoke;">NumberOfScans</code>
+reference is the sixth reference in the granule counting from the top.
+
+The list of references shown above is a 0-based index to the dataset. Therefore, to specify
+<code style="background-color:whitesmoke;">NumberOfScans</code>, enter a start offset of
+<code style="background-color:whitesmoke;">5</code> for the <code style="background-color:whitesmoke;">-s</code>
+option (the sixth reference minus 1). To see the region reference data, use the <code style="background-color:whitesmoke;">-R</code> option.
+
+This command will display the data in the <code style="background-color:whitesmoke;">NumberOfScans</code> region reference:
+\code
+h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" -s 5 -R
+       SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+\endcode
+
+It displays the number of scans (48):
+\code
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
+   DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+   DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+   SUBSET {
+      START ( 5 );
+      STRIDE ( 1 );
+      COUNT ( 1 );
+      BLOCK ( 1 );
+      DATA {
+      (5): DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {
+         (5): REGION_TYPE BLOCK  (0)-(0)
+         (5): DATATYPE  H5T_STD_I32BE
+         (5): DATASPACE  SIMPLE { ( 1 ) / ( H5S_UNLIMITED ) }
+         (5): DATA {
+            (0): 48
+         (5):  }
+      (5): }
+      }
+   }
+}
+}
+\endcode
+
+The <code style="background-color:whitesmoke;">-s</code> option may be familiar as one of the options
+that was described in the \ref secViewToolsViewSub tutorial topic. The other subsetting options are not included,
+indicating that the default values are used.
+
+If you leave off the <code style="background-color:whitesmoke;">-R</code> option, you will see the subset selection, but not the data:
+\code
+$ h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" -s 5 
+   SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
+   DATATYPE  H5T_REFERENCE { H5T_STD_REF_DSETREG }
+   DATASPACE  SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
+   SUBSET {
+      START ( 5 );
+      STRIDE ( 1 );
+      COUNT ( 1 );
+      BLOCK ( 1 );
+      DATA {
+         DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)}
+      }
+   }
+}
+}
+\endcode
+
+\subsubsection subsubsecViewToolsJPSSExam_h5dumpQuality Viewing a Quality Flag
+The quality flags in an NPP file can be viewed with h5dump using the <code style="background-color:whitesmoke;">-M</code>
+option. Quality flags are packed into each integer value in a quality flag dataset. Quality flag datasets in NPP
+files begin with the letters <code style="background-color:whitesmoke;">QF</code>.
+
+In the following NPP file, there are five Quality Flag datasets
+(<code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/QF*</code>):
+\code
+$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+FILE_CONTENTS {
+ group      /
+ group      /All_Data
+ group      /All_Data/VIIRS-M1-SDR_All
+ dataset    /All_Data/VIIRS-M1-SDR_All/ModeGran
+ dataset    /All_Data/VIIRS-M1-SDR_All/ModeScan
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts
+ dataset    /All_Data/VIIRS-M1-SDR_All/NumberOfScans
+ dataset    /All_Data/VIIRS-M1-SDR_All/PadByte1
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR
+ dataset    /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR
+ dataset    /All_Data/VIIRS-M1-SDR_All/Radiance
+ dataset    /All_Data/VIIRS-M1-SDR_All/RadianceFactors
+ dataset    /All_Data/VIIRS-M1-SDR_All/Reflectance
+ dataset    /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors
+ group      /Data_Products
+ group      /Data_Products/VIIRS-M1-SDR
+ dataset    /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr
+ dataset    /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0
+ }
+}
+\endcode
+
+The flags in this particular dataset happen to be stored in every two bits of each quality flag dataset
+element, and the values range from 0 to 2. In other words, to see the quality flag values for this
+dataset, these bits would be examined: 0 and 1, 2 and 3, 4 and 5, or 6 and 7 (This information was
+obtained from the Product Profile XML File.)
+
+For example, bits 0 and 1 in the <code style="background-color:whitesmoke;">VQF1_VIIRSMBANDSDR</code> dataset specify the flag that
+"Indicates calibration quality due to bad space view offsets, OBC view offsets, etc or use of a
+previous calibration view". It has 3 values: Good (0), Poor (1), or No Calibration (2).
+
+The <code style="background-color:whitesmoke;">-M</code> option is used to specify the quality
+flag bit offset (<code style="background-color:whitesmoke;">O</code>) and length (<code style="background-color:whitesmoke;">L</code>):
+\code
+h5dump -d DATASET -M O,L FILE
+\endcode
+
+To view the first quality flag (0-1) in a 5 x 6 subset of the <code style="background-color:whitesmoke;">QF1_VIIRSMBANDSDR</code> dataset, specify:
+\code
+h5dump -d "/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR[0,0;;5,6;]" 
+       -M 0,2 SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+\endcode
+
+This outputs:
+\code
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+DATASET "/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR" {
+   DATATYPE  H5T_STD_U8BE
+   DATASPACE  SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
+   PACKED_BITS OFFSET=0 LENGTH=2
+   SUBSET {
+      START ( 0, 0 );
+      STRIDE ( 1, 1 );
+      COUNT ( 5, 6 );
+      BLOCK ( 1, 1 );
+      DATA {
+      (0,0): 2, 2, 2, 2, 2, 2,
+      (1,0): 2, 2, 2, 2, 2, 2,
+      (2,0): 0, 0, 0, 0, 0, 0,
+      (3,0): 0, 0, 0, 0, 0, 0,
+      (4,0): 0, 0, 0, 0, 0, 0
+      }
+   }
+}
+}
+\endcode
+
+To view more than one quality flag at a time simply add the bit offset and length values to
+<code style="background-color:whitesmoke;">-M</code>, separated by commas. For example, this
+<code style="background-color:whitesmoke;">-M</code> option specifies bits 0-1 and 2-3:
+\code
+h5dump -d DATASET -M 0,2,2,2 FILE
+\endcode
+
+\subsubsection subsubsecViewToolsJPSSExam_h5dumpProps Properties
+To view properties of a specific dataset with <code style="background-color:whitesmoke;">h5dump</code>
+use the <code style="background-color:whitesmoke;">-p</code> option along with the
+<code style="background-color:whitesmoke;">-d</code> option. Depending on the number of attributes
+and the amount of data, the <code style="background-color:whitesmoke;">-A 0</code> and
+<code style="background-color:whitesmoke;">-H</code> options can also be specified to suppress
+printing of attributes and data values:
+\code
+h5dump -p -H -A 0 -d DATASET
+\endcode
+
+The <code style="background-color:whitesmoke;">-p</code> option shows any compression filters
+associated with a dataset, as well as layout and fill value information. This option can be helpful
+in diagnosing performance and other issues.
+
+As an example, examine the <code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/Radiance</code>
+dataset in the <code style="background-color:whitesmoke;">SVM01</code> file:
+\code
+$ h5dump -p -H -A 0 -d "/All_Data/VIIRS-M1-SDR_All/Radiance" 
+   SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
+DATASET "/All_Data/VIIRS-M1-SDR_All/Radiance" {
+   DATATYPE  H5T_STD_U16BE
+   DATASPACE  SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
+   STORAGE_LAYOUT {
+      CHUNKED ( 768, 3200 )
+      SIZE 4915200
+   }
+   FILTERS {
+      NONE
+   }
+   FILLVALUE {
+      FILL_TIME H5D_FILL_TIME_IFSET
+      VALUE  65529
+   }
+   ALLOCATION_TIME {
+      H5D_ALLOC_TIME_INCR
+   }
+}
+}
+\endcode
+
+We can see that the chunk size for this dataset is 768 x 3200, and the storage size is 4915200.
+
+What if the chunk size were smaller?
+
+The dataset was modified to have a chunk size of 1 x 10, using the
+<code style="background-color:whitesmoke;">h5repack</code> utility, as shown below.
+\code
+$ h5repack -l /All_Data/VIIRS-M1-SDR_All/Radiance:CHUNK=1x10 
+   SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 SVM01repack.h5
+
+$ h5dump -p -H -A 0 -d "/All_Data/VIIRS-M1-SDR_All/Radiance" SVM01repack.h5
+HDF5 "SVM01repack.h5" {
+DATASET "/All_Data/VIIRS-M1-SDR_All/Radiance" {
+   DATATYPE  H5T_STD_U16BE
+   DATASPACE  SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
+   STORAGE_LAYOUT {
+      CHUNKED ( 1, 10 )
+      SIZE 4915200
+   }
+   FILTERS {
+      NONE
+   }
+   FILLVALUE {
+      FILL_TIME H5D_FILL_TIME_IFSET
+      VALUE  65529
+   }
+   ALLOCATION_TIME {
+      H5D_ALLOC_TIME_INCR
+   }
+}
+}
+\endcode
+
+In this case, the storage size of the dataset is the same, but the size of the file almost doubled!:
+\code
+$ ls -1sh
+total 35M
+12M SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
+23M SVM01repack.h5
+\endcode
+
+In general, the smaller the chunk size, the more chunks that HDF5 has to keep track of, which increases
+the size of the file and can affect performance.
+
+\subsection subsecViewToolsJPSSExamr_HDFView HDFView
+As mentioned previously, the structure of an HDF5 file is displayed in the TreeView on the left side of the HDFView screen,
+and you can click on objects and have metadata information displayed on the right side.
+
+To discover more about the granule <code style="background-color:whitesmoke;">/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0</code>
+in the <code style="background-color:whitesmoke;">SVM01</code> file shown below in the TreeView, position
+the mouse over the granule and click to select. Properties for the object is displayed on the right side of the HDFView screen.
+You can see Datatype and Dataspace information on the <code style="background-color:whitesmoke;">General Object Info</code>
+tab, any Attributes associated with the granulewill be on the
+<code style="background-color:whitesmoke;">Object Attribute Info</code> tab. In the
+<code style="background-color:whitesmoke;">General Object Info</code>, you can see that the dataset is a
+Region Reference dataset, and that there are sixteen Region References in this dataset:
+<table>
+<tr>
+<td>
+\image html hdfview-prop.png 
+</td>
+</tr>
+</table>
+
+To examine the data in the granule, click twice on it with the left mouse button in the TreeView,
+and it will open in a new window.:
+<table>
+<tr>
+<td>
+\image html hdfview-regref.png 
+</td>
+</tr>
+</table>
+
+If you click twice with the left mouse button on the fifth Region Reference
+<code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/NumberOfScans</code> a window
+will pop up with the value(s) of the reference:
+<table>
+<tr>
+<td>
+\image html hdfview-regref2.png 
+</td>
+</tr>
+</table>
+
+You can also set a user option to automatically show the value(s) in a Region Reference. Under the
+<code style="background-color:whitesmoke;">Tools</code> pull-down menu, select
+<code style="background-color:whitesmoke;">User Options</code> and then select
+<code style="background-color:whitesmoke;">HDF Settings</code> and then select
+<code style="background-color:whitesmoke;">Show RegRef Values</code> in the
+<code style="background-color:whitesmoke;">Data</code> section (see the middle of the image below):
+<table>
+<tr>
+<td>
+\image html hdfview-regrefval.png 
+</td>
+</tr>
+</table>
+
+Then you will automatically see the values of the Region Reference when you open it and select an entry:
+<table>
+<tr>
+<td>
+\image html hdfview-regref1.png 
+</td>
+</tr>
+</table>
+
+You can view and set quality flags by clicking the right mouse button over a quality flags dataset under
+<code style="background-color:whitesmoke;">All_Data</code> and selecting
+<code style="background-color:whitesmoke;">Open As</code> from the pop-up menu. In the middle of
+the window that pops up, you will see where you can specify <code style="background-color:whitesmoke;">Bitmask</code> options.
+<table>
+<tr>
+<td>
+\image html hdfview-qf.png 
+</td>
+</tr>
+</table>
+
+<hr>
+Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
+
+*/

doxygen/dox/high_level/extension.dox

@@ -1,60 +1,51 @@
 /** \defgroup H5LR Extensions
  *
- * <em>Working with region references, hyperslab selections, 
+ * <em>Working with region references, hyperslab selections,
  * and bit-fields (H5LR, H5LT)</em>
  *
- * The following reference manual entries describe high-level HDF5 C and Fortran APIs 
+ * The following reference manual entries describe high-level HDF5 C and Fortran APIs
- * for working with region references, hyperslab selections, and bit-fields. 
+ * for working with region references, hyperslab selections, and bit-fields.
- * These functions were created as part of a project supporting 
+ * These functions were created as part of a project supporting
  * NPP/NPOESS Data Production and Exploitation (
  * <a href="https://support.hdfgroup.org/projects/jpss/documentation">
- * project </a>, 
+ * project</a>, <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
- * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
+ * software </a>).
- * software </a>). 
+ * While they were written to facilitate access to NPP, NPOESS, and JPSS
- * While they were written to facilitate access to NPP, NPOESS, and JPSS 
+ * data in the HDF5 format, these functions may be useful to anyone working
- * data in the HDF5 format, these functions may be useful to anyone working 
  * with region references, hyperslab selections, or bit-fields.
  *
  * Note that these functions are not part of the standard HDF5 distribution; 
- * the 
+ * the <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
- * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
+ * software </a>
- * software </a> 
  * must be separately downloaded and installed.
  *
- * A comprehensive guide to this library, 
+ * A comprehensive guide to this library,
- * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf"> 
+ * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf">
  * <em>User Guide to the HDF5 High-level Library for Handling Region References and Hyperslab Selections</em></a>
- * is available at 
+ * is available at
  * https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf.
  *
  * - \ref H5LRcopy_reference
- *        \n Copies data from the specified dataset to a new location and 
+ *        \n Copies data from the specified dataset to a new location and creates a reference to it.
- *        creates a reference to it.
  * - \ref H5LRcopy_region
- *        \n  Copies data from a referenced region to a region in a 
+ *        \n  Copies data from a referenced region to a region in a destination dataset.
- *        destination dataset.
  * - \ref H5LRcreate_ref_to_all
- *        \n  Creates a dataset with the region references to the data in all 
+ *        \n  Creates a dataset with the region references to the data in all datasets located under a
- *        datasets located under a specified group in a file or creates a 
+ *        specified group in a file or creates a dataset with object references to all objects (groups or datasets)
- *        dataset with object references to all objects (groups or datasets) 
  *        located under a specified group in a file.
  * - \ref H5LRcreate_region_references
- *        \n Creates an array of region references using an array of paths to 
+ *        \n Creates an array of region references using an array of paths to
  *        datasets and an array of corresponding hyperslab descriptions.
  * - \ref H5LRget_region_info
  *        \n Retrieves information about the data a region reference points to.
  * - \ref H5LRmake_dataset
- *        \n Creates and writes a dataset containing a list of 
+ *        \n Creates and writes a dataset containing a list of region references.
- *        region references.
  * - \ref H5LRread_region
- *        \n  Retrieves raw data pointed to by a region reference to 
+ *        \n  Retrieves raw data pointed to by a region reference to an application buffer.
- *        an application buffer.
  * - \ref H5LTcopy_region
- *        \n Copies data from a specified region in a source dataset 
+ *        \n Copies data from a specified region in a source dataset to a specified region in a destination dataset.
- *        to a specified region in a destination dataset.
  * - \ref H5LTread_bitfield_value
- *        \n Retrieves the values of quality flags for each element 
+ *        \n Retrieves the values of quality flags for each element to the application provided buffer.
- *        to the application provided buffer.
  * - \ref H5LTread_region
  *        \n Reads selected data to an application buffer.
  *
@@ -77,24 +68,24 @@
  * \param[in] path          Path to the dataset being created
  * \param[in] type_id       Datatype of the dataset
  * \param[in] buf_size      Size of the \p loc_id_ref and \p buf arrays
- * \param[in] loc_id_ref    Array of object identifiers; each identifier 
+ * \param[in] loc_id_ref    Array of object identifiers; each identifier
- *                          describes to which HDF5 file the corresponding 
+ *                          describes to which HDF5 file the corresponding
  *                          region reference belongs to
  * \param[in] buf           Array of region references
  *
  * \return \herr_t
  *
- * \details Given an array of size \p buf_size of region references \p buf, 
+ * \details Given an array of size \p buf_size of region references \p buf,
- *          the function will create a dataset with path \p path, at location 
+ *          the function will create a dataset with path \p path, at location
- *          specified by \p loc_id and of a datatype specified by \p type_id, 
+ *          specified by \p loc_id and of a datatype specified by \p type_id,
- *          and will write data associated with each region reference in the order 
+ *          and will write data associated with each region reference in the order
- *          corresponding to the order of the region references in the buffer. 
+ *          corresponding to the order of the region references in the buffer.
- *          It is assumed that all referenced hyperslabs have the same dimensionality, 
+ *          It is assumed that all referenced hyperslabs have the same dimensionality,
- *          and only the size of the slowest changing dimension may differ. 
+ *          and only the size of the slowest changing dimension may differ.
- *          Each reference in the \p buf array belongs to the file identified 
+ *          Each reference in the \p buf array belongs to the file identified
  *          by the corresponding object identifiers in the array \p loc_id_ref.
  *
- *          If \p path does not exist in \p loc_id then the function will 
+ *          If \p path does not exist in \p loc_id then the function will
  *          create the path specified by \p path automatically.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -103,10 +94,10 @@
  *
  */
 H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
-				 const char *path, 
+                 const char *path,
-				 hid_t type_id, const size_t buf_size,
+                 hid_t type_id, const size_t buf_size,
-				 const hid_t *loc_id_ref,
+                 const hid_t *loc_id_ref,
-				 const hdset_reg_ref_t *buf);
+                 const hdset_reg_ref_t *buf);
 
 /*-------------------------------------------------------------------------
  *
@@ -119,49 +110,46 @@ H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Creates an array of region references using an array of paths to 
+ * \brief Creates an array of region references using an array of paths to
  *        datasets and an array of corresponding hyperslab descriptions.
  *
  * \param[in] obj_id        File identifier for the HDF5 file containing
  *                          the referenced regions or an object identifier
  *                          for any object in that file
- * \param[in] num_elem      Number of elements in the \p path and 
+ * \param[in] num_elem      Number of elements in the \p path and \p buf arrays
- *                          \p buf arrays
+ * \param[in] path          Array of pointers to strings, which contain
- * \param[in] path          Array of pointers to strings, which contain 
+ *                          the paths to the target datasets for the region references
- *                          the paths to the target datasets for the 
- *                          region references
  * \param[in] block_coord   Array of hyperslab coordinate
- * \param[out] buf          Buffer for returning an array of region 
+ * \param[out] buf          Buffer for returning an array of region references
- *                          references
  *
  * \return \herr_t
  *
  * \note    **Motivation:**
- * \note    H5LRcreate_region_references() is useful when creating 
+ * \note    H5LRcreate_region_references() is useful when creating
  *          large numbers of similar region references.
  *
- * \details H5LRcreate_region_references() creates a list of region references 
+ * \details H5LRcreate_region_references() creates a list of region references
- *          given an array of paths to datasets and another array listing the 
+ *          given an array of paths to datasets and another array listing the
  *          corner coordinates of the corresponding hyperslabs.
  *
  *          \p path parameter is an array of pointers to strings.
  *
- *          \p num_elem specifies the number of region references to be created, 
+ *          \p num_elem specifies the number of region references to be created,
  *          thus specifying the size of the \p path and \p _buf arrays.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates of the 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of the
- *          starting point following by the coordinates of the ending point of 
+ *          starting point following by the coordinates of the ending point of
- *          the hyperslab, repeated \p num_elem times for each hyperslab. 
+ *          the hyperslab, repeated \p num_elem times for each hyperslab.
- *          For example, creating two region references to two hyperslabs, 
+ *          For example, creating two region references to two hyperslabs,
- *          one with a rectangular hyperslab region starting at element (2,2) 
+ *          one with a rectangular hyperslab region starting at element (2,2)
- *          to element (5,4) and the second rectangular region starting at 
+ *          to element (5,4) and the second rectangular region starting at
- *          element (7,7) to element (9,10), results in \p block_coord 
+ *          element (7,7) to element (9,10), results in \p block_coord
  *          being {2,2,5,4, 7,7,9,10}.
  *
- *          The rank of the hyperslab will be the same as the rank of the 
+ *          The rank of the hyperslab will be the same as the rank of the
- *          target dataset. H5LRcreate_region_references() will retrieve 
+ *          target dataset. H5LRcreate_region_references() will retrieve
- *          the rank for each dataset and will use those values to interpret 
+ *          the rank for each dataset and will use those values to interpret
- *          the values in the buffer. Please note that rank may vary from one 
+ *          the values in the buffer. Please note that rank may vary from one
  *          dataset to another.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -170,43 +158,39 @@ H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
  *
  */
 H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
-					     size_t num_elem,
+                      size_t num_elem,
-					     const char **path,
+                      const char **path,
-					     const hsize_t *block_coord,
+                      const hsize_t *block_coord,
-					     hdset_reg_ref_t *buf);
+                      hdset_reg_ref_t *buf);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from the specified dataset to a new location and 
+ * \brief Copies data from the specified dataset to a new location and creates a reference to it.
- *        creates a reference to it.
  *
- * \param[in] obj_id        Identifier of any object in a file an 
+ * \param[in] obj_id        Identifier of any object in a file an HDF5 reference belongs to
- *                          HDF5 reference belongs to
  * \param[in] ref           Reference to the datasets region
- * \param[in] file          Name of the destination file 
+ * \param[in] file          Name of the destination file
  * \param[in] path          Full path to the destination dataset
- * \param[in] block_coord   Hyperslab coordinates in the destination 
+ * \param[in] block_coord   Hyperslab coordinates in the destination dataset
- *                          dataset
+ * \param[out] ref_new      Region reference to the new location of data
- * \param[out] ref_new      Region reference to the new location of 
- *                          data
  *
  * \return \herr_t
  *
- * \details Given a data set pointed to by a region reference, the function 
+ * \details Given a data set pointed to by a region reference, the function
- *          H5LRcopy_reference() will copy the hyperslab data referenced by 
+ *          H5LRcopy_reference() will copy the hyperslab data referenced by
- *          a datasets region reference into existing dataset specified by 
+ *          a datasets region reference into existing dataset specified by
- *          its path \p path in the file with the name \p file, and to location 
+ *          its path \p path in the file with the name \p file, and to location
- *          specified by the hyperslab coordinates \p block_coord. It will 
+ *          specified by the hyperslab coordinates \p block_coord. It will
- *          create the region reference \p ref_new to point to the new location. 
+ *          create the region reference \p ref_new to point to the new location.
- *          The number of elements in the old and newly specified regions has 
+ *          The number of elements in the old and newly specified regions has
  *          to be the same.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates of 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates of
- *          the starting point following by the coordinates of the ending 
+ *          the starting point following by the coordinates of the ending
- *          point of the hyperslab. For example, to extract a rectangular 
+ *          point of the hyperslab. For example, to extract a rectangular
- *          hyperslab region starting at element (2,2) to element (5,4) 
+ *          hyperslab region starting at element (2,2) to element (5,4)
  *          then \p block_coord would be {2, 2, 5, 4}.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -215,41 +199,39 @@ H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const char *file,
-				    const char *path, const hsize_t *block_coord, 
+                     const char *path, const hsize_t *block_coord,
-				    hdset_reg_ref_t *ref_new);
+                     hdset_reg_ref_t *ref_new);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from a referenced region to a region in a 
+ * \brief Copies data from a referenced region to a region in a destination dataset.
- *        destination dataset.
  *
- * \param[in] obj_id        Identifier of any object in a file 
+ * \param[in] obj_id        Identifier of any object in a file
  *                          dataset region reference belongs to
  * \param[in] ref           Dataset region reference
- * \param[in] file          Name of the destination file 
+ * \param[in] file          Name of the destination file
  * \param[in] path          Full path to the destination dataset
- * \param[in] block_coord   Hyperslab coordinates in the destination 
+ * \param[in] block_coord   Hyperslab coordinates in the destination dataset
- *                          dataset
  *
  * \return \herr_t
  *
- * \details Given a dataset region reference \p ref in a source file 
+ * \details Given a dataset region reference \p ref in a source file
- *          specified by an identifier of any object in that file 
+ *          specified by an identifier of any object in that file
- *          \p obj_id, the function will write data to the existing 
+ *          \p obj_id, the function will write data to the existing
- *          dataset \p path in file \p file to the simple hyperslab 
+ *          dataset \p path in file \p file to the simple hyperslab
  *          specified by \p block_coord.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates
- *          of the starting point following by the coordinates of the 
+ *          of the starting point following by the coordinates of the
- *          ending point of the hyperslab. For example, to specify a 
+ *          ending point of the hyperslab. For example, to specify a
- *          rectangular hyperslab destination region starting at element 
+ *          rectangular hyperslab destination region starting at element
  *          (2,2) to element (5,4) then \p block_coord would be {2, 2, 5, 4}.
  *
- *          If \p path does not exist in the destination file (as may be 
+ *          If \p path does not exist in the destination file (as may be
- *          the case when writing to a new file) then the dataset will be 
+ *          the case when writing to a new file) then the dataset will be
- *          copied directly to the \p path and \p block_coord will be 
+ *          copied directly to the \p path and \p block_coord will be
  *          disregarded.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -258,71 +240,66 @@ H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const ch
  *
  */
 H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
-				hdset_reg_ref_t *ref,
+                 hdset_reg_ref_t *ref,
-				const char *file,
+                 const char *file,
-				const char *path,
+                 const char *path,
-				const hsize_t *block_coord);
+                 const hsize_t *block_coord);
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Creates a dataset with the region references to the data 
+ * \brief Creates a dataset with the region references to the data
- *        in all datasets located under a specified group in a file 
+ *        in all datasets located under a specified group in a file
- *        or creates a dataset with object references to all objects 
+ *        or creates a dataset with object references to all objects
  *        (groups or datasets) located under a specified group in a file.
  *
  * \fg_loc_id
- * \param[in] group_path    Absolute or relative path to the group 
+ * \param[in] group_path    Absolute or relative path to the group at which traversal starts
- *                          at which traversal starts
+ * \param[in] ds_path       Absolute or relative path to the dataset with region references to be created
- * \param[in] ds_path       Absolute or relative path to the dataset 
+ * \param[in] index_type    Index_type; see valid values below in description
- *                          with region references to be created
+ * \param[in] order         Order in which index is traversed; see valid values below in description
- * \param[in] index_type    Index_type; 
+ * \param[in] ref_type      Reference type; see valid values below in description
- *                          see valid values below in description
- * \param[in] order         Order in which index is traversed; 
- *                          see valid values below in description
- * \param[in] ref_type      Reference type;
- *                          see valid values below in description
  *
  * \return \herr_t
  *
- * \details H5LRcreate_ref_to_all() creates a dataset with the 
+ * \details H5LRcreate_ref_to_all() creates a dataset with the
- *          region references to the data in all datasets located 
+ *          region references to the data in all datasets located
- *          under a specified group in a file or creates a dataset with 
+ *          under a specified group in a file or creates a dataset with
- *          object references to all objects (groups or datasets) located 
+ *          object references to all objects (groups or datasets) located
  *          under a specified group in a file.
  *
- *          Given a dataset path \p ds_path in a file specified by the 
+ *          Given a dataset path \p ds_path in a file specified by the
- *          \p loc_id identifier, the function H5LRcreate_ref_to_all() 
+ *          \p loc_id identifier, the function H5LRcreate_ref_to_all()
- *          will create a contiguous one-dimensional dataset with the 
+ *          will create a contiguous one-dimensional dataset with the
- *          region references or object references depending on the value 
+ *          region references or object references depending on the value
- *          of the \p ref_type parameter. When \p ref_type is 
+ *          of the \p ref_type parameter. When \p ref_type is
- *          #H5R_DATASET_REGION, each region reference points to all data 
+ *          #H5R_DATASET_REGION, each region reference points to all data
- *          in a dataset encountered by an internally called H5Lvisit() 
+ *          in a dataset encountered by an internally called H5Lvisit()
- *          routine, which starts at the group specified by the \p loc_id 
+ *          routine, which starts at the group specified by the \p loc_id
  *          and \p group_path parameters. In a like manner, when
- *          \p ref_type is #H5R_OBJECT, each object reference points to 
+ *          \p ref_type is #H5R_OBJECT, each object reference points to
  *          an object (a group or a dataset) encountered by H5Lvisit().
  *
- *          If \p ds_path does not exist in \p loc_id then the function 
+ *          If \p ds_path does not exist in \p loc_id then the function
  *          will create the path specified by \p ds_path automatically.
  *
- *          \p index_type specifies the index to be used. 
+ *          \p index_type specifies the index to be used.
  *          Valid values include the following:
  *          - #H5_INDEX_NAME        Alphanumeric index on name
  *          - #H5_INDEX_CRT_ORDER   Index on creation order
  *
- *          \p order specifies the order in which objects are to be 
+ *          \p order specifies the order in which objects are to be
- *          inspected along the index specified in \p index_type. 
+ *          inspected along the index specified in \p index_type.
  *          Valid values include the following:
  *          - #H5_ITER_INC      Increasing order
  *          - #H5_ITER_DEC      Decreasing order
  *          - #H5_ITER_NATIVE   Fastest available order
  *
- *          For more detailed information on these two parameters, 
+ *          For more detailed information on these two parameters,
- *          see H5Lvisit().
+ *          @see H5Lvisit().
  *
- *          \p ref_type specifies the type of the reference to be used. 
+ *          \p ref_type specifies the type of the reference to be used.
  *          Valid values include the following:
  *          - #H5R_DATASET_REGION   Dataset region reference
  *          - #H5R_OBJECT           Object reference
@@ -333,7 +310,7 @@ H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
-					 const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
+                  const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
 
 /*-------------------------------------------------------------------------
  *
@@ -352,30 +329,27 @@ H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
  * \param[in] obj_id        File identifier for the HDF5 file containing
  *                          the dataset with the referenced region or an
  *                          object identifier for any object in that file
- * \param[in] ref           Region reference specifying data to be read
+ * \param[in] ref           Region reference specifying data to be read in
- *                          in
+ * \param[in] mem_type      Memory datatype of data read from referenced
- * \param[in] mem_type      Memory datatype of data read from referenced 
  *                          region into the application buffer
- * \param[in,out] numelem   Number of elements to be read into buffer 
+ * \param[in,out] numelem   Number of elements to be read into buffer \p buf
- *                          \p buf
+ * \param[out] buf          Buffer in which data is returned to the application
- * \param[out] buf          Buffer in which data is returned to the 
- *                          application
  *
  * \return \herr_t
  *
- * \details H5LRread_region() reads data pointed to by the region 
+ * \details H5LRread_region() reads data pointed to by the region
  *          reference \p ref into the buffer \p buf.
  *
- *          \p numelem specifies the number of elements to be read 
+ *          \p numelem specifies the number of elements to be read
- *          into \p buf. When the size of the reference region is unknown, 
+ *          into \p buf. When the size of the reference region is unknown,
- *          H5LRread_region() can be called with \p buf set to NULL; 
+ *          H5LRread_region() can be called with \p buf set to NULL;
- *          the number of elements in the referenced region will be returned 
+ *          the number of elements in the referenced region will be returned
  *          in \p numelem.
  *
- *          The buffer buf must be big enough to hold \p numelem elements 
+ *          The buffer buf must be big enough to hold \p numelem elements
- *          of type \p mem_type. For example, if data is read from the referenced 
+ *          of type \p mem_type. For example, if data is read from the referenced
- *          region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT 
+ *          region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT
- *          and the buffer must be at least \c sizeof(int) * \p numelem  bytes 
+ *          and the buffer must be at least \c sizeof(int) * \p numelem  bytes
  *          in size. This buffer must be allocated by the application.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -384,10 +358,10 @@ H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
  *
  */
 H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
-				const hdset_reg_ref_t *ref, 
+                 const hdset_reg_ref_t *ref,
-				hid_t mem_type,
+                 hid_t mem_type,
-				size_t *numelem,
+                 size_t *numelem,
-				void *buf );
+                 void *buf );
 
 /*-------------------------------------------------------------------------
  *
@@ -400,40 +374,33 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Retrieves information about the data a region reference 
+ * \brief Retrieves information about the data a region reference points to.
- *        points to.
  *
- * \param[in] obj_id        Identifier of any object in an HDF5 file 
+ * \param[in] obj_id        Identifier of any object in an HDF5 file the region reference belongs to.
- *                          the region reference belongs to.
  * \param[in] ref           Region reference to query
- * \param[in,out] len       Size of the buffer to store \p path in. 
+ * \param[in,out] len       Size of the buffer to store \p path in.
- *                          NOTE: if \p *path is not NULL then \p *len 
+ *                          NOTE: if \p *path is not NULL then \p *len must be the appropriate length
- *                          must be the appropriate length
  * \param[out] path         Full path that a region reference points to
  * \param[out] rank         The number of dimensions of the dataset
- *                          dimensions of the dataset pointed by 
+ *                          dimensions of the dataset pointed by region reference.
- *                          region reference.
+ * \param[out] dtype        Datatype of the dataset pointed by the region reference.
- * \param[out] dtype        Datatype of the dataset pointed by the 
- *                          region reference.
  * \param[out] sel_type     Type of the selection (point or hyperslab)
- * \param[in,out] numelem   Number of coordinate blocks or 
+ * \param[in,out] numelem   Number of coordinate blocks or selected elements.
- *                          selected elements.
+ * \param[out] buf          Buffer containing description of the region pointed by region reference
- * \param[out] buf          Buffer containing description of the region 
- *                          pointed by region reference
  *
  * \return \herr_t
  *
- * \details H5LRget_region_info() queries information about the data 
+ * \details H5LRget_region_info() queries information about the data
- *          pointed by a region reference \p ref. It returns one of the 
+ *          pointed by a region reference \p ref. It returns one of the
- *          absolute paths to a dataset, length of the path, dataset’s rank 
+ *          absolute paths to a dataset, length of the path, dataset’s rank
- *          and datatype, description of the referenced region and type of 
+ *          and datatype, description of the referenced region and type of
- *          the referenced region. Any output argument can be NULL if that 
+ *          the referenced region. Any output argument can be NULL if that
  *          argument does not need to be returned.
  *
- *          The parameter \p obj_id is an identifier for any object in the 
+ *          The parameter \p obj_id is an identifier for any object in the
- *          HDF5 file containing the referenced object. For example, it can 
+ *          HDF5 file containing the referenced object. For example, it can
- *          be an identifier of a dataset the region reference belongs to 
+ *          be an identifier of a dataset the region reference belongs to
- *          or an identifier of an HDF5 file the dataset with region references 
+ *          or an identifier of an HDF5 file the dataset with region references
  *          is stored in.
  *
  *          The parameter \p ref is a region reference to query.
@@ -442,36 +409,36 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  *          buffer of size \p len+1 to return an absolute path to a dataset
  *          the region reference points to.
  *
- *          The parameter \p len is a length of absolute path string plus 
+ *          The parameter \p len is a length of absolute path string plus
- *          the \0 string terminator. If path parameter is NULL, actual 
+ *          the \0 string terminator. If path parameter is NULL, actual
- *          length of the path (+1 for \0 string terminator) is returned to 
+ *          length of the path (+1 for \0 string terminator) is returned to
- *          application and can be used to allocate buffer path of an 
+ *          application and can be used to allocate buffer path of an
  *          appropriate length \p len.
  *
  *          The parameter \p sel_type describes the type of the selected
- *          region. Possible values can be #H5S_SEL_POINTS for point 
+ *          region. Possible values can be #H5S_SEL_POINTS for point
  *          selection and #H5S_SEL_HYPERSLABS for hyperslab selection.
  *
- *          The parameter \p numelem describes how many elements will be 
+ *          The parameter \p numelem describes how many elements will be
- *          placed in the buffer \p buf. The number should be interpreted 
+ *          placed in the buffer \p buf. The number should be interpreted
  *          using the value of \p sel_type.
  *
- *          If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter 
+ *          If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter
- *          \p buf contains \p numelem blocks of the coordinates for each 
+ *          \p buf contains \p numelem blocks of the coordinates for each
- *          simple hyperslab of the referenced region. Each block has 
+ *          simple hyperslab of the referenced region. Each block has
- *          length \c 2*\p rank and is organized as follows: <"start" coordinate>, 
+ *          length \c 2*\p rank and is organized as follows: <"start" coordinate>,
- *          immediately followed by <"opposite" corner coordinate>. 
+ *          immediately followed by <"opposite" corner coordinate>.
- *          The total size of the buffer to hold the description of the 
+ *          The total size of the buffer to hold the description of the
- *          region will be \c 2*\p rank*\p numelem. If region reference 
+ *          region will be \c 2*\p rank*\p numelem. If region reference
- *          points to a contiguous sub-array, then the value of \p numelem 
+ *          points to a contiguous sub-array, then the value of \p numelem
- *          is 1 and the block contains coordinates of the upper left and 
+ *          is 1 and the block contains coordinates of the upper left and
  *          lower right corners of the sub-array (or simple hyperslab).
  *
- *          If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf 
+ *          If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf
- *          contains \p numelem blocks of the coordinates for each selected 
+ *          contains \p numelem blocks of the coordinates for each selected
- *          point of the referenced region. Each block has length \p rank 
+ *          point of the referenced region. Each block has length \p rank
- *          and contains coordinates of the element. The total size of the 
+ *          and contains coordinates of the element. The total size of the
- *          buffer to hold the description of the region will be 
+ *          buffer to hold the description of the region will be
  *          \p rank* \p numelem.
  *
  *
@@ -481,14 +448,14 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
-				    const hdset_reg_ref_t *ref,  
+                     const hdset_reg_ref_t *ref,
-				    size_t *len, 
+                     size_t *len, 
-				    char *path,
+                     char *path,
-				    int *rank,
+                     int *rank,
-				    hid_t *dtype,
+                     hid_t *dtype,
-				    H5S_sel_type *sel_type,
+                     H5S_sel_type *sel_type,
-				    size_t *numelem,
+                     size_t *numelem,
-				    hsize_t *buf );
+                     hsize_t *buf );
 
 
 
@@ -503,35 +470,33 @@ H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Copies data from a specified region in a source dataset 
+ * \brief Copies data from a specified region in a source dataset
  *        to a specified region in a destination dataset
  *
  * \param[in] file_src          Name of the source file
  * \param[in] path_src          Full path to the source dataset
- * \param[in] block_coord_src   Hyperslab coordinates in the 
+ * \param[in] block_coord_src   Hyperslab coordinates in the source dataset
- *                              source dataset
  * \param[in] file_dest         Name of the destination file
  * \param[in] path_dest         Full path to the destination dataset
- * \param[in] block_coord_dset  Hyperslab coordinates in the 
+ * \param[in] block_coord_dset  Hyperslab coordinates in the destination dataset
- *                              destination dataset
  *
  * \return \herr_t
  *
- * \details Given a path to a dataset \p path_src in a file with the 
+ * \details Given a path to a dataset \p path_src in a file with the
- *          name \p file_src, and description of a simple hyperslab of 
+ *          name \p file_src, and description of a simple hyperslab of
- *          the source \p block_coord_src, the function will write data 
+ *          the source \p block_coord_src, the function will write data
- *          to the dataset \p path_dest in file \p file_dest to the 
+ *          to the dataset \p path_dest in file \p file_dest to the
- *          simple hyperslab specified by \p block_coord_dset. 
+ *          simple hyperslab specified by \p block_coord_dset.
- *          The arrays \p block_coord_src and \p block_coord_dset have 
+ *          The arrays \p block_coord_src and \p block_coord_dset have
- *          a length of 2*rank and are the coordinates of the starting 
+ *          a length of 2*rank and are the coordinates of the starting
- *          point following by the coordinates of the ending point of the 
+ *          point following by the coordinates of the ending point of the
- *          hyperslab. For example, to specify a rectangular hyperslab 
+ *          hyperslab. For example, to specify a rectangular hyperslab
- *          destination region starting at element (2,2) to element (5,4) 
+ *          destination region starting at element (2,2) to element (5,4)
  *          then \p block_coord_dset would be {2, 2, 5, 4}.
  *
- *          If \p path_dest does not exist in the destination file 
+ *          If \p path_dest does not exist in the destination file
- *          (as may be the case when writing to a new file) then the 
+ *          (as may be the case when writing to a new file) then the
- *          dataset will be copied directly to the \p path_dest and 
+ *          dataset will be copied directly to the \p path_dest and
  *          \p block_coord_dset will be disregarded.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -540,11 +505,11 @@ H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
  *
  */
 H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
-				const char *path_src,
+                 const char *path_src,
-				const hsize_t *block_coord_src,
+                 const hsize_t *block_coord_src,
-				const char *file_dest,
+                 const char *file_dest,
-				const char *path_dest,
+                 const char *path_dest,
-				const hsize_t *block_coord_dset);
+                 const hsize_t *block_coord_dset);
 
 /*-------------------------------------------------------------------------
  *
@@ -562,27 +527,25 @@ H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
  * \param[in] file          Name of file
  * \param[in] path          Full path to a dataset
  * \param[in] block_coord   Hyperslab coordinates
- * \param[in] mem_type      Memory datatype, describing the buffer 
+ * \param[in] mem_type      Memory datatype, describing the buffer the referenced data will be read into
- *                          the referenced data will be read into
+ * \param[out] buf          Buffer containing data from the referenced region
- * \param[out] buf          Buffer containing data from the 
- *                          referenced region
  *
  * \return \herr_t
  *
- * \details H5LTread_region() reads data from a region described by 
+ * \details H5LTread_region() reads data from a region described by
- *          the hyperslab coordinates in \p block_coord, located in 
+ *          the hyperslab coordinates in \p block_coord, located in
- *          the dataset specified by its absolute path \p path in a 
+ *          the dataset specified by its absolute path \p path in a
- *          file specified by its name \p file. Data is read into a 
+ *          file specified by its name \p file. Data is read into a
- *          buffer \p buf of the datatype that corresponds to the 
+ *          buffer \p buf of the datatype that corresponds to the
  *          HDF5 datatype specified by \p mem_type.
  *
- *          Buffer \p block_coord has size 2*rank and is the coordinates 
+ *          Buffer \p block_coord has size 2*rank and is the coordinates
- *          of the starting point following by the coordinates of the 
+ *          of the starting point following by the coordinates of the
- *          ending point of the hyperslab. For example, to extract a 
+ *          ending point of the hyperslab. For example, to extract a
- *          rectangular hyperslab region starting at element (2,2) to 
+ *          rectangular hyperslab region starting at element (2,2) to
  *          element (5,4) then \p block_coord would be {2, 2, 5, 4}.
  *
- *          Buffer \p buf should be big enough to hold selected elements 
+ *          Buffer \p buf should be big enough to hold selected elements
  *          of the type that corresponds to the \p mem_type
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -591,57 +554,55 @@ H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
  *
  */
 H5_HLRDLL herr_t  H5LTread_region(const char *file,
-				 const char *path,
+                  const char *path,
-				 const hsize_t *block_coord,
+                  const hsize_t *block_coord,
-				 hid_t mem_type,
+                  hid_t mem_type,
-				 void *buf );
+                  void *buf );
 
 /**
  * --------------------------------------------------------------------------
  * \ingroup H5LR
  *
- * \brief Retrieves the values of quality flags for each element 
+ * \brief Retrieves the values of quality flags for each element
  *        to the application provided buffer.
  *
  * \param[in] dset_id   Identifier of the dataset with bit-field values
  * \param[in] num_values    Number of the values to be extracted
- * \param[in] offset        Array of staring bits to be extracted from 
+ * \param[in] offset        Array of staring bits to be extracted from
  *                          the element; valid values: 0 (zero) through 7
- * \param[in] lengths       Array of the number of bits to be extracted 
+ * \param[in] lengths       Array of the number of bits to be extracted for each value
- *                          for each value
+ * \param[in] space         Dataspace identifier, describing the elements
- * \param[in] space         Dataspace identifier, describing the elements 
+ *                          to be read from the dataset with bit-field values
- *                          to be read from the dataset with bit-field 
- *                          values
  * \param[out] buf          Buffer to read the values in
  *
  * \return \herr_t
  *
- * \details H5LTread_bitfield_value() reads selected elements from a 
+ * \details H5LTread_bitfield_value() reads selected elements from a
- *          dataset specified by its identifier \p dset_id, and unpacks 
+ *          dataset specified by its identifier \p dset_id, and unpacks
  *          the bit-field values to a buffer \p buf.
  *
- *          The parameter \p space is a space identifier that indicates 
+ *          The parameter \p space is a space identifier that indicates
  *          which elements of the dataset should be read.
  *
- *          The parameter \p offset is an array of length \p num_values; 
+ *          The parameter \p offset is an array of length \p num_values;
  *          the i<sup>th</sup> element of the array holds the value of the
- *          starting bit of the i<sup>th</sup> bit-field value. 
+ *          starting bit of the i<sup>th</sup> bit-field value.
  *          Valid values are: 0 (zero) through 7.
  *
- *          The parameter \p lengths is an array of length \p num_values; 
+ *          The parameter \p lengths is an array of length \p num_values;
- *          the i<sup>th</sup> element of the array holds the number of 
+ *          the i<sup>th</sup> element of the array holds the number of
- *          bits to be extracted for the i<sup>th</sup> bit-field value. 
+ *          bits to be extracted for the i<sup>th</sup> bit-field value.
- *          Extracted bits will be interpreted as a base-2 integer value. 
+ *          Extracted bits will be interpreted as a base-2 integer value.
- *          Each value will be converted to the base-10 integer value and 
+ *          Each value will be converted to the base-10 integer value and
- *          stored in the application buffer. 
+ *          stored in the application buffer.
  *
- *          Buffer \p buf is allocated by the application and should be big 
+ *          Buffer \p buf is allocated by the application and should be big
- *          enough to hold \c num_sel_elem * \p num_values elements of the 
+ *          enough to hold \c num_sel_elem * \p num_values elements of the
- *          specified type, where \c num_sel_elem is a number of the elements 
+ *          specified type, where \c num_sel_elem is a number of the elements
- *          to be read from the dataset. Data in the buffer is organized 
+ *          to be read from the dataset. Data in the buffer is organized
- *          as \p num_values values for the first element, followed by the 
+ *          as \p num_values values for the first element, followed by the
- *          \p num_values values for the second element, ... , followed by 
+ *          \p num_values values for the second element, ... , followed by
- *          the \p num_values values for the 
+ *          the \p num_values values for the
  *          \c num_selected_elem<sup>th</sup> element.
  *
  * \version 1.1 Fortran wrapper introduced in this release.
@@ -650,5 +611,5 @@ H5_HLRDLL herr_t  H5LTread_region(const char *file,
  *
  */
 H5_HLRDLL herr_t H5LTread_bitfield_value(hid_t dset_id, int num_values, const unsigned *offset,
-					const unsigned *lengths, hid_t space, int *buf);
+                 const unsigned *lengths, hid_t space, int *buf);
 

doxygen/dox/high_level/high_level.dox

@@ -1,29 +0,0 @@
-/** \page high_level High-level library
- * The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
- * facilitate common HDF5 operations.
- *
- * <ul>
- * <li>\ref H5LT "Lite (H5LT, H5LD)"
- * \n
- * Functions to simplify creating and manipulating datasets, attributes and other features
- * <li>\ref H5IM "Image (H5IM)"
- * \n
- * Creating and manipulating HDF5 datasets intended to be interpreted as images
- * <li>\ref H5TB "Table (H5TB)"
- * \n
- * Creating and manipulating HDF5 datasets intended to be interpreted as tables
- * <li>\ref H5PT "Packet Table (H5PT)"
- * \n
- * Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
- * <li>\ref H5DS "Dimension Scale (H5DS)"
- * \n
- * Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
- * <li>\ref H5DO "Optimizations (H5DO)"
- * \n
- * Bypassing default HDF5 behavior in order to optimize for specific use cases
- * <li>\ref H5LR "Extensions (H5LR, H5LT)"
- * \n
- * Working with region references, hyperslab selections, and bit-fields
- * </ul>
- * 
- */

doxygen/dox/rm-template.dox

@@ -96,4 +96,4 @@ the <a href="https://www.oreilly.com/library/view/97-things-every/9780596809515/
      * \version 1.MAJOR.MINOR Function was deprecated in this release
      \endverbatim
 
-*/
+*/

doxygen/examples/H5.format.1.0.html

@@ -139,7 +139,7 @@
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="H5.user.html"><cite>HDF5 User's Guide</cite></a>.
+      in the <a href="H5.user.html"><cite>HDF5 User Guide</cite></a>.
 
 
 <!--

doxygen/examples/H5.format.1.1.html

@@ -172,7 +172,7 @@ TABLE.list TD { border:none; }
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="H5.user.html"><cite>HDF5 User's Guide</cite></a>.
+      in the <a href="H5.user.html"><cite>HDF5 User Guide</cite></a>.
 
     <P>Three levels of information comprise the file format.
       Level 0 contains basic information for identifying and

doxygen/examples/H5.format.html

@@ -418,7 +418,7 @@
 
     <p>This document describes the lower-level data objects;
       the higher-level objects and their properties are described
-      in the <a href="UG/HDF5_Users_Guide-Responsive HTML5/index.html"><cite>HDF5 User&rsquo;s Guide</cite></a>.</p>
+      in the <a href="UG/HDF5_User_Guide-Responsive HTML5/index.html"><cite>HDF5 User Guide</cite></a>.</p>
 
     <p>Three levels of information comprise the file format.
       Level 0 contains basic information for identifying and

doxygen/examples/ThreadSafeLibrary.html

@@ -20,9 +20,9 @@ The following code is placed at the beginning of H5private.h:
 </blockquote>
 
 <p>
-<code>H5_HAVE_THREADSAFE</code> is defined when the HDF-5 library is
+<code>H5_HAVE_THREADSAFE</code> is defined when the HDF5 library is
 compiled with the --enable-threadsafe configuration option. In general,
-code for the non-threadsafe version of HDF-5 library are placed within
+code for the non-threadsafe version of HDF5 library are placed within
 the <code>#else</code> part of the conditional compilation. The exception
 to this rule are the changes to the <code>FUNC_ENTER</code> (in
 H5private.h), <code>HRETURN</code> and <code>HRETURN_ERROR</code> (in
@@ -438,7 +438,7 @@ described in Appendix D and may be found in <code>H5TS.c</code>.
 
 <p>
 Except where stated, all tests involve 16 simultaneous threads that make
-use of HDF-5 API calls without any explicit synchronization typically
+use of HDF5 API calls without any explicit synchronization typically
 required in a non-threadsafe environment.
 </p>
 
@@ -453,7 +453,7 @@ dataset's named value.
 
 <p>
 The main thread would join with all 16 threads and attempt to match the
-resulting HDF-5 file with expected results - that each dataset contains
+resulting HDF5 file with expected results - that each dataset contains
 the correct value (0 for <i>zero</i>, 1 for <i>one</i> etc ...) and all
 datasets were correctly created.
 </p>
@@ -473,7 +473,7 @@ name.
 
 <p>
 The error stack implementation runs correctly if it reports 15 instances
-of the dataset name conflict error and finally generates a correct HDF-5
+of the dataset name conflict error and finally generates a correct HDF5
 containing that single dataset. Each thread should report its own stack
 of errors with a thread number associated with it.
 </p>

doxygen/examples/core_menu.md

@@ -0,0 +1,69 @@
+<b>Core Library</b>
+
+- @ref H5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+- @ref H5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+- @ref H5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+- @ref H5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+- @ref H5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+- @ref H5ES "Event Set (H5ES)"
+<br />
+HDF5 event set life cycle used with HDF5 VOL connectors that enable the asynchronous feature in HDF5.
+
+- @ref H5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+- @ref H5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+- @ref H5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+- @ref H5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+- @ref H5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+- @ref H5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+- @ref H5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+- @ref H5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+- @ref H5PL "Dynamically-loaded Plugins (H5PL)"
+<br />
+Manage the loading behavior of HDF5 plugins.
+
+- @ref H5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
+
+- @ref H5VL "VOL Connector (H5VL)"
+<br />
+Manage HDF5 VOL connector plugins.

doxygen/examples/fortran_menu.md

@@ -0,0 +1,73 @@
+<b>Fortran Library</b>
+
+- @ref FH5A "Attributes (H5A)"
+<br />
+HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object.
+
+- @ref FH5D "Datasets (H5D)"
+<br />
+Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties.
+
+- @ref FH5S "Dataspaces (H5S)"
+<br />
+HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files.
+
+- @ref FH5T "Datatypes (H5T)"
+<br />
+HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+
+- @ref FH5E "Error Handling (H5E)"
+<br />
+HDF5 library error reporting.
+
+- @ref FH5F "Files (H5F)"
+<br />
+Manage HDF5 files.
+
+- @ref FH5Z "Filters (H5Z)"
+<br />
+Manage HDF5 user-defined filters
+
+- @ref FH5G "Groups (H5G)"
+<br />
+Manage HDF5 groups.
+
+- @ref FH5I "Identifiers (H5I)"
+<br />
+Manage identifiers defined by the HDF5 library.
+
+- @ref FH5 "Library General (H5)"
+<br />
+Manage the life cycle of HDF5 library instances.
+
+- @ref FH5L "Links (H5L)"
+<br />
+Manage HDF5 links and link types.
+
+- @ref FH5O "Objects (H5O)"
+<br />
+Manage HDF5 objects (groups, datasets, datatype objects).
+
+- @ref FH5P "Property Lists (H5P)"
+<br />
+HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions.
+
+- @ref FH5R "References (H5R)"
+<br />
+Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions).
+
+- @ref FH5LT "High Level Lite (H5LT)"
+<br />
+Functions to simplify creating and manipulating datasets, attributes and other features
+
+- @ref FH5IM "High Level Image (H5IM)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as images
+
+- @ref FH5TB "High Level Table (H5TB)"
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as tables
+
+- @ref FH5DS "High Level Dimension Scale (H5DS)"
+<br />
+Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset

doxygen/examples/high_level_menu.md

@@ -0,0 +1,30 @@
+<b>High-level library</b>
+<br />
+The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
+facilitate common HDF5 operations.
+
+- @ref H5LT
+<br />
+Functions to simplify creating and manipulating datasets, attributes and other features
+
+- @ref H5IM
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as images
+
+- @ref H5TB
+<br />
+Creating and manipulating HDF5 datasets intended to be interpreted as tables
+
+- @ref H5PT
+<br />
+Creating and manipulating HDF5 datasets to support append- and read-only operations on table data
+
+- @ref H5DS
+<br />
+Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset
+
+- @ref H5DO
+<br />
+Bypassing default HDF5 behavior in order to optimize for specific use cases
+
+- @ref H5LR "Extensions (H5LR, H5LT)"

doxygen/examples/java_menu.md

@@ -0,0 +1,84 @@
+<b>Java Library</b>
+ @ref HDF5LIB
+ 
+- @ref JH5
+<br />
+This package is the Java interface for the HDF5 library.
+ 
+- @ref JH5A
+<br />
+This package is the Java interface for the HDF5 library attribute APIs.
+ 
+- @ref JH5D
+<br />
+This package is the Java interface for the HDF5 library dataset APIs.
+ 
+- @ref JH5S
+<br />
+This package is the Java interface for the HDF5 library dataspace APIs.
+ 
+- @ref JH5T
+<br />
+This package is the Java interface for the HDF5 library datatype APIs.
+ 
+- @ref JH5E
+<br />
+This package is the Java interface for the HDF5 library error APIs.
+ 
+- @ref JH5F
+<br />
+This package is the Java interface for the HDF5 library file APIs.
+ 
+- @ref JH5Z
+<br />
+This package is the Java interface for the HDF5 library filter APIs.
+ 
+- @ref JH5G
+<br />
+This package is the Java interface for the HDF5 library group APIs.
+ 
+- @ref JH5I
+<br />
+This package is the Java interface for the HDF5 library identifier APIs.
+ 
+- @ref JH5L
+<br />
+This package is the Java interface for the HDF5 library links APIs.
+ 
+- @ref JH5O
+<br />
+This package is the Java interface for the HDF5 library object APIs.
+ 
+- @ref JH5P
+<br />
+This package is the Java interface for the HDF5 library property list APIs.
+ 
+- @ref JH5PL
+<br />
+This package is the Java interface for the HDF5 library plugin APIs.
+ 
+- @ref JH5R
+<br />
+This package is the Java interface for the HDF5 library reference APIs.
+
+- @ref JH5VL
+<br />
+This package is the Java interface for the HDF5 library VOL connector APIs.
+
+- @ref HDF5CONST
+<br />
+This class contains C constants and enumerated types of HDF5 library.
+
+- @ref HDFNATIVE
+<br />
+This class encapsulates native methods to deal with arrays of numbers,
+ * converting from numbers to bytes and bytes to numbers.
+
+- @ref HDFARRAY
+<br />
+This is a class for handling multidimensional arrays for HDF.
+
+- @ref ERRORS
+<br />
+The class HDF5Exception returns errors from the Java HDF5 Interface.
+ 

doxygen/hdf5doxy_layout.xml

@@ -3,8 +3,9 @@
   <!-- Navigation index tabs for HTML output -->
   <navindex>
     <tab type="user" url="index.html" title="Overview" />
-    <tab type="user" url="https://portal.hdfgroup.org/display/HDF5/Learning+HDF5" title="Getting started" />
+    <tab type="user" url="@ref GettingStarted" title="Getting started" />
     <tab type="user" url="@ref Cookbook" title="Cookbook" />
+    <tab type="user" url="@ref UG" title="User Guide" />
     <tab type="user" url="https://portal.hdfgroup.org/display/HDF5/HDF5+User+Guides" title="User Guides" />
     <tab type="user" url="https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide" title="Application Developer's Guide" />
     <tab type="user" url="@ref GLS" title="Glossary" />