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| author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2022-08-09 23:11:14 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-08-09 23:11:14 (GMT) |
| commit | 4c66bf627ec4b963f026bbfa7101127271644f79 (patch) | |
| tree | 4a4352a58dde0a80f7f72eab56484ddd94ec2294 /doxygen | |
| parent | fc9f31ad8c8ff4122e8bb2997e0a2bfa89cb054b (diff) | |
| download | hdf5-4c66bf627ec4b963f026bbfa7101127271644f79.zip hdf5-4c66bf627ec4b963f026bbfa7101127271644f79.tar.gz hdf5-4c66bf627ec4b963f026bbfa7101127271644f79.tar.bz2 | |
Merge UG from 1.10 and add prelim vol section (#1980)
* Merge UG from 1.10 and add prelim vol section
* Spelling fixes
* Merge format and autotools javadoc from 1.10
Diffstat (limited to 'doxygen')
151 files changed, 962 insertions, 576 deletions
diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt index e75c899..17d8da7 100644 --- a/doxygen/CMakeLists.txt +++ b/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) diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in index 6d82765..6f29c0b 100644 --- a/doxygen/Doxyfile.in +++ b/doxygen/Doxyfile.in @@ -874,6 +874,9 @@ FILE_PATTERNS = H5*public.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 @@ -942,7 +945,7 @@ 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 diff --git a/doxygen/dox/DDLBNF110.dox b/doxygen/dox/DDLBNF110.dox index f7e4267..6d6b67e 100644 --- a/doxygen/dox/DDLBNF110.dox +++ b/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>+ diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox index 040769c..64e80c7 100644 --- a/doxygen/dox/Overview.dox +++ b/doxygen/dox/Overview.dox @@ -23,7 +23,7 @@ documents cover a mix of tasks, concepts, and reference, to help a specific \par Versions Version-specific documentation (see the version in the title area) can be found here: - - HDF5 <code>develop</code> branch (this site) + - HDF5 <code>1.12</code> branch (this site) - <a href="https://docs.hdfgroup.org/hdf5/v1_12/index.html">HDF5 1.12.x</a> - <a href="https://docs.hdfgroup.org/hdf5/v1_10/index.html">HDF5 1.10.x</a> - <a href="https://docs.hdfgroup.org/hdf5/v1_8/index.html">HDF5 1.8.x</a> @@ -36,10 +36,6 @@ documents cover a mix of tasks, concepts, and reference, to help a specific \par Offline reading You can <a href="hdf5-doc.tgz">download</a> it as a tgz archive for offline reading. -\par History - A snapshot (~April 2017) of the pre-Doxygen HDF5 documentation can be found - <a href="https://docs.hdfgroup.org/archive/support/HDF5/doc/index.html">here</a>. - \par ToDo List There is plenty of <a href="./todo.html">unfinished business</a>. diff --git a/doxygen/dox/RFC.dox b/doxygen/dox/RFC.dox index c16dcea..3cda309 100644 --- a/doxygen/dox/RFC.dox +++ b/doxygen/dox/RFC.dox @@ -88,4 +88,4 @@ <tr> <td>2004-08-11</td> <td>\ref_rfc20040811</td> <td></td> </tr> </table> -*/
\ No newline at end of file +*/ diff --git a/doxygen/dox/ReferenceManual.dox b/doxygen/dox/ReferenceManual.dox index ad10ba1..7900925 100644 --- a/doxygen/dox/ReferenceManual.dox +++ b/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><td style="border: none;"> -\li \ref H5A "Attributes (H5A)" -\li \ref H5D "Datasets (H5D)" -\li \ref H5S "Dataspaces (H5S)" -\li \ref H5T "Datatypes (H5T)" -\li \ref H5E "Error Handling (H5E)" -\li \ref H5ES "Event Sets (H5ES)" -\li \ref H5F "Files (H5F)" -\li \ref H5Z "Filters (H5Z)" -\li \ref H5G "Groups (H5G)" -</td><td style="border: none;"> -\li \ref H5I "Identifiers (H5I)" -\li \ref H5 "Library General (H5)" -\li \ref H5L "Links (H5L)" -\li \ref H5M "Maps (H5M)" -\li \ref H5O "Objects (H5O)" -\li \ref H5P "Property Lists (H5P)" -\li \ref H5PL "Dynamically-loaded Plugins (H5PL)" -\li \ref H5R "References (H5R)" -\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 valign="top"><td style="border: none;"> +\include{doc} core_menu.md +</td> +</tr> +<tr valign="top"><td style="border: none;"> +<!-- High-level library --> +\include{doc} high_level_menu.md +</td> +</tr> +<tr valign="top"><td style="border: none;"> +<!-- Fortran library --> +\include{doc} fortran_menu.md +</td> +</tr> +<tr valign="top"><td style="border: none;"> +<!-- Java library --> +\include{doc} java_menu.md +</td> +</tr> <tr> <td><a href="./deprecated.html">Deprecated functions</a></td> <td>Functions with \ref ASYNC</td> diff --git a/doxygen/dox/Specifications.dox b/doxygen/dox/Specifications.dox index 5a36d61..e352f40 100644 --- a/doxygen/dox/Specifications.dox +++ b/doxygen/dox/Specifications.dox @@ -2,20 +2,20 @@ \section DDL -\li \ref DDLBNF110 "DDL in BNF through HDF5 1.10" -\li \ref DDLBNF112 "DDL in BNF for HDF5 1.12 and above" +\li \ref DDLBNF110 +\li \ref DDLBNF112 \section File Format -\li \ref FMT1 "HDF5 File Format Specification Version 1.0" -\li \ref FMT11 "HDF5 File Format Specification Version 1.1" -\li \ref FMT2 "HDF5 File Format Specification Version 2.0" -\li \ref FMT3 "HDF5 File Format Specification Version 3.0" +\li \ref FMT1 +\li \ref FMT11 +\li \ref FMT2 +\li \ref FMT3 \section Other -\li \ref IMG "HDF5 Image and Palette Specification Version 1.2" -\li \ref TBL "HDF5 Table Specification Version 1.0" +\li \ref IMG +\li \ref TBL \li <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf"> HDF5 Dimension Scale Specification</a> diff --git a/doxygen/dox/TechnicalNotes.dox b/doxygen/dox/TechnicalNotes.dox index 9bd2802..bca81e4 100644 --- a/doxygen/dox/TechnicalNotes.dox +++ b/doxygen/dox/TechnicalNotes.dox @@ -1,13 +1,13 @@ /** \page TN Technical Notes -\li \link api-compat-macros API Compatibility Macros \endlink -\li \ref APPDBG "Debugging HDF5 Applications" -\li \ref FMTDISC "File Format Walkthrough" -\li \ref FILTER "Filters" -\li \ref IOFLOW "HDF5 Raw I/O Flow Notes" -\li \ref TNMDC "Metadata Caching in HDF5" -\li \ref MT "Thread Safe library" -\li \ref VFL "Virtual File Layer" +\li \ref api-compat-macros +\li \ref APPDBG +\li \ref FMTDISC +\li \ref FILTER +\li \ref IOFLOW +\li \ref TNMDC +\li \ref MT +\li \ref VFL */ diff --git a/doxygen/dox/UsersGuide.dox b/doxygen/dox/UsersGuide.dox new file mode 100644 index 0000000..6b44d21 --- /dev/null +++ b/doxygen/dox/UsersGuide.dox @@ -0,0 +1,400 @@ +/** \page UG HDF5 User Guide + +<center> +HDF5 Release 1.12 + +\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_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><a href="http://www.hdfgroup.org/HDF5/examples/">HDF5 Examples</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>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 + +*/
\ No newline at end of file diff --git a/doxygen/dox/high_level/extension.dox b/doxygen/dox/high_level/extension.dox index c81ac6e..e8471b9 100644 --- a/doxygen/dox/high_level/extension.dox +++ b/doxygen/dox/high_level/extension.dox @@ -1,60 +1,48 @@ /** \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 - * for working with region references, hyperslab selections, and bit-fields. - * These functions were created as part of a project supporting + * The following reference manual entries describe high-level HDF5 C and Fortran APIs + * for working with region references, hyperslab selections, and bit-fields. + * 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>, - * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source"> - * software </a>). - * 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 + * project</a>, software). + * 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 * with region references, hyperslab selections, or bit-fields. * - * Note that these functions are not part of the standard HDF5 distribution; - * the - * <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source"> - * software </a> - * must be separately downloaded and installed. + * Note that these functions are not part of the standard HDF5 distribution; + * the software must be separately downloaded and installed. * - * A comprehensive guide to this library, - * <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf"> + * A comprehensive guide to this library, + * <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 - * creates a reference to it. + * \n Copies data from the specified dataset to a new location and creates a reference to it. * - \ref H5LRcopy_region - * \n Copies data from a referenced region to a region in a - * destination dataset. + * \n Copies data from a referenced region to a region in a destination dataset. * - \ref H5LRcreate_ref_to_all - * \n Creates a dataset with the region references to the data in all - * datasets located under a specified group in a file or creates a - * dataset with object references to all objects (groups or datasets) + * \n Creates a dataset with the region references to the data in all datasets located under a + * specified group in a file or creates a 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 - * region references. + * \n Creates and writes a dataset containing a list of region references. * - \ref H5LRread_region - * \n Retrieves raw data pointed to by a region reference to - * an application buffer. + * \n Retrieves raw data pointed to by a region reference to an application buffer. * - \ref H5LTcopy_region - * \n Copies data from a specified region in a source dataset - * to a specified region in a destination dataset. + * \n Copies data from a specified region in a source dataset to a specified region in a destination dataset. * - \ref H5LTread_bitfield_value - * \n Retrieves the values of quality flags for each element - * to the application provided buffer. + * \n Retrieves the values of quality flags for each element to the application provided buffer. * - \ref H5LTread_region * \n Reads selected data to an application buffer. * @@ -77,24 +65,24 @@ * \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 - * describes to which HDF5 file the corresponding + * \param[in] loc_id_ref Array of object identifiers; each identifier + * 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, - * 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, - * and will write data associated with each region reference in the order - * corresponding to the order of the region references in the buffer. - * It is assumed that all referenced hyperslabs have the same dimensionality, - * and only the size of the slowest changing dimension may differ. - * Each reference in the \p buf array belongs to the file identified + * \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 + * 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 + * corresponding to the order of the region references in the buffer. + * It is assumed that all referenced hyperslabs have the same dimensionality, + * and only the size of the slowest changing dimension may differ. + * 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 +91,10 @@ * */ H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id, - const char *path, - hid_t type_id, const size_t buf_size, - const hid_t *loc_id_ref, - const hdset_reg_ref_t *buf); + const char *path, + hid_t type_id, const size_t buf_size, + const hid_t *loc_id_ref, + const hdset_reg_ref_t *buf); /*------------------------------------------------------------------------- * @@ -119,49 +107,46 @@ 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 - * \p buf arrays - * \param[in] path Array of pointers to strings, which contain - * the paths to the target datasets for the - * region references + * \param[in] num_elem Number of elements in the \p path and \p buf arrays + * \param[in] path Array of pointers to strings, which contain + * 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 - * references + * \param[out] buf Buffer for returning an array of region 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 - * given an array of paths to datasets and another array listing the + * \details H5LRcreate_region_references() creates a list of region references + * 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 - * starting point following by the coordinates of the ending point of - * the hyperslab, repeated \p num_elem times for each hyperslab. - * For example, creating two region references to two hyperslabs, - * one with a rectangular hyperslab region starting at element (2,2) - * to element (5,4) and the second rectangular region starting at - * element (7,7) to element (9,10), results in \p block_coord + * 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 + * the hyperslab, repeated \p num_elem times for each hyperslab. + * For example, creating two region references to two hyperslabs, + * one with a rectangular hyperslab region starting at element (2,2) + * to element (5,4) and the second rectangular region starting at + * 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 - * target dataset. H5LRcreate_region_references() will retrieve - * 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 rank of the hyperslab will be the same as the rank of the + * target dataset. H5LRcreate_region_references() will retrieve + * 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 * dataset to another. * * \version 1.1 Fortran wrapper introduced in this release. @@ -170,43 +155,39 @@ 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, - const char **path, - const hsize_t *block_coord, - hdset_reg_ref_t *buf); + size_t num_elem, + const char **path, + const hsize_t *block_coord, + hdset_reg_ref_t *buf); /** * -------------------------------------------------------------------------- * \ingroup H5LR * - * \brief Copies data from the specified dataset to a new location and - * creates a reference to it. + * \brief Copies data from the specified dataset to a new location and creates a reference to it. * - * \param[in] obj_id Identifier of any object in a file an - * HDF5 reference belongs to + * \param[in] obj_id Identifier of any object in a file an 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 - * dataset - * \param[out] ref_new Region reference to the new location of - * data + * \param[in] block_coord Hyperslab coordinates in the destination dataset + * \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 - * H5LRcopy_reference() will copy the hyperslab data referenced 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 - * specified by the hyperslab coordinates \p block_coord. It will - * 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 + * \details Given a data set pointed to by a region reference, the function + * H5LRcopy_reference() will copy the hyperslab data referenced 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 + * specified by the hyperslab coordinates \p block_coord. It will + * 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 * to be the same. * - * 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 the hyperslab. For example, to extract a rectangular - * hyperslab region starting at element (2,2) to element (5,4) + * 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 the hyperslab. For example, to extract a rectangular + * 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 +196,39 @@ 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, - hdset_reg_ref_t *ref_new); + const char *path, const hsize_t *block_coord, + hdset_reg_ref_t *ref_new); /** * -------------------------------------------------------------------------- * \ingroup H5LR * - * \brief Copies data from a referenced region to a region in a - * destination dataset. + * \brief Copies data from a referenced region to a region in a 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 - * dataset + * \param[in] block_coord Hyperslab coordinates in the destination dataset * * \return \herr_t * - * \details Given a dataset region reference \p ref in a source file - * specified by an identifier of any object in that file - * \p obj_id, the function will write data to the existing - * dataset \p path in file \p file to the simple hyperslab + * \details Given a dataset region reference \p ref in a source file + * specified by an identifier of any object in that file + * \p obj_id, the function will write data to the existing + * 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 - * of the starting point following by the coordinates of the - * ending point of the hyperslab. For example, to specify a - * rectangular hyperslab destination region starting at element + * 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 the hyperslab. For example, to specify a + * 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 - * 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 + * 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 + * copied directly to the \p path and \p block_coord will be * disregarded. * * \version 1.1 Fortran wrapper introduced in this release. @@ -258,71 +237,66 @@ 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, - const char *file, - const char *path, - const hsize_t *block_coord); + hdset_reg_ref_t *ref, + const char *file, + const char *path, + const hsize_t *block_coord); /** * -------------------------------------------------------------------------- * \ingroup H5LR * - * \brief Creates a dataset with the region references to the data - * in all datasets located under a specified group in a file - * or creates a dataset with object references to all objects + * \brief Creates a dataset with the region references to the data + * in all datasets located under a specified group in a file + * 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 - * at which traversal starts - * \param[in] ds_path Absolute or relative path to the dataset - * with region references to be created - * \param[in] index_type Index_type; - * 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 + * \param[in] group_path Absolute or relative path to the group at which traversal starts + * \param[in] ds_path Absolute or relative path to the dataset with region references to be created + * \param[in] index_type Index_type; 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 - * region references to the data in all datasets located - * under a specified group in a file or creates a dataset with - * object references to all objects (groups or datasets) located + * \details H5LRcreate_ref_to_all() creates a dataset with the + * region references to the data in all datasets located + * under a specified group in a file or creates a dataset with + * 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 - * \p loc_id identifier, the function H5LRcreate_ref_to_all() - * will create a contiguous one-dimensional dataset with the - * region references or object references depending on the value - * of the \p ref_type parameter. When \p ref_type is - * #H5R_DATASET_REGION, each region reference points to all data - * in a dataset encountered by an internally called H5Lvisit() - * routine, which starts at the group specified by the \p loc_id + * Given a dataset path \p ds_path in a file specified by the + * \p loc_id identifier, the function H5LRcreate_ref_to_all() + * will create a contiguous one-dimensional dataset with the + * region references or object references depending on the value + * of the \p ref_type parameter. When \p ref_type is + * #H5R_DATASET_REGION, each region reference points to all data + * in a dataset encountered by an internally called H5Lvisit() + * 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 - * inspected along the index specified in \p index_type. + * \p order specifies the order in which objects are to be + * 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, - * see H5Lvisit(). + * For more detailed information on these two parameters, + * @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 +307,7 @@ 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 +326,27 @@ 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 - * in - * \param[in] mem_type Memory datatype of data read from referenced + * \param[in] ref Region reference specifying data to be read in + * \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 - * \p buf - * \param[out] buf Buffer in which data is returned to the - * application + * \param[in,out] numelem Number of elements to be read into buffer \p buf + * \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 - * into \p buf. When the size of the reference region is unknown, - * H5LRread_region() can be called with \p buf set to NULL; - * the number of elements in the referenced region will be returned + * \p numelem specifies the number of elements to be read + * into \p buf. When the size of the reference region is unknown, + * H5LRread_region() can be called with \p buf set to NULL; + * 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 - * 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 - * and the buffer must be at least \c sizeof(int) * \p numelem bytes + * 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 + * 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 * in size. This buffer must be allocated by the application. * * \version 1.1 Fortran wrapper introduced in this release. @@ -384,10 +355,10 @@ 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, - hid_t mem_type, - size_t *numelem, - void *buf ); + const hdset_reg_ref_t *ref, + hid_t mem_type, + size_t *numelem, + void *buf ); /*------------------------------------------------------------------------- * @@ -400,40 +371,33 @@ H5_HLRDLL herr_t H5LRread_region(hid_t obj_id, * -------------------------------------------------------------------------- * \ingroup H5LR * - * \brief Retrieves information about the data a region reference - * points to. + * \brief Retrieves information about the data a region reference points to. * - * \param[in] obj_id Identifier of any object in an HDF5 file - * the region reference belongs to. + * \param[in] obj_id Identifier of any object in an HDF5 file 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. - * NOTE: if \p *path is not NULL then \p *len - * must be the appropriate length + * \param[in,out] len Size of the buffer to store \p path in. + * NOTE: if \p *path is not NULL then \p *len 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 - * region reference. - * \param[out] dtype Datatype of the dataset pointed by the - * region reference. + * dimensions of the dataset pointed by 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 - * selected elements. - * \param[out] buf Buffer containing description of the region - * pointed by region reference + * \param[in,out] numelem Number of coordinate blocks or selected elements. + * \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 - * pointed by a region reference \p ref. It returns one of the - * absolute paths to a dataset, length of the path, dataset’s rank - * and datatype, description of the referenced region and type of - * the referenced region. Any output argument can be NULL if that + * \details H5LRget_region_info() queries information about the data + * pointed by a region reference \p ref. It returns one of the + * absolute paths to a dataset, length of the path, dataset’s rank + * and datatype, description of the referenced region and type of + * 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 - * HDF5 file containing the referenced object. For example, it can - * be an identifier of a dataset the region reference belongs to - * or an identifier of an HDF5 file the dataset with region references + * The parameter \p obj_id is an identifier for any object in the + * HDF5 file containing the referenced object. For example, it can + * be an identifier of a dataset the region reference belongs to + * 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 +406,36 @@ 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 \0 string terminator. If path parameter is NULL, actual - * length of the path (+1 for \0 string terminator) is returned to - * application and can be used to allocate buffer path of an + * The parameter \p len is a length of absolute path string plus + * the \0 string terminator. If path parameter is NULL, actual + * length of the path (+1 for \0 string terminator) is returned to + * 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 - * placed in the buffer \p buf. The number should be interpreted + * The parameter \p numelem describes how many elements will be + * 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 - * \p buf contains \p numelem blocks of the coordinates for each - * simple hyperslab of the referenced region. Each block has - * length \c 2*\p rank and is organized as follows: <"start" coordinate>, - * immediately followed by <"opposite" corner coordinate>. - * The total size of the buffer to hold the description of the - * region will be \c 2*\p rank*\p numelem. If region reference - * points to a contiguous sub-array, then the value of \p numelem - * is 1 and the block contains coordinates of the upper left and + * If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter + * \p buf contains \p numelem blocks of the coordinates for each + * simple hyperslab of the referenced region. Each block has + * length \c 2*\p rank and is organized as follows: <"start" coordinate>, + * immediately followed by <"opposite" corner coordinate>. + * The total size of the buffer to hold the description of the + * region will be \c 2*\p rank*\p numelem. If region reference + * points to a contiguous sub-array, then the value of \p numelem + * 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 - * contains \p numelem blocks of the coordinates for each selected - * point of the referenced region. Each block has length \p rank - * and contains coordinates of the element. The total size of the - * buffer to hold the description of the region will be + * If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf + * contains \p numelem blocks of the coordinates for each selected + * point of the referenced region. Each block has length \p rank + * and contains coordinates of the element. The total size of the + * buffer to hold the description of the region will be * \p rank* \p numelem. * * @@ -481,14 +445,14 @@ 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, - size_t *len, - char *path, - int *rank, - hid_t *dtype, - H5S_sel_type *sel_type, - size_t *numelem, - hsize_t *buf ); + const hdset_reg_ref_t *ref, + size_t *len, + char *path, + int *rank, + hid_t *dtype, + H5S_sel_type *sel_type, + size_t *numelem, + hsize_t *buf ); @@ -503,35 +467,33 @@ 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 - * source dataset + * \param[in] block_coord_src Hyperslab coordinates in the 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 - * destination dataset + * \param[in] block_coord_dset Hyperslab coordinates in the destination dataset * * \return \herr_t * - * \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 - * the source \p block_coord_src, the function will write data - * to the dataset \p path_dest in file \p file_dest to the - * simple hyperslab specified by \p block_coord_dset. - * The arrays \p block_coord_src and \p block_coord_dset have - * a length of 2*rank and are the coordinates of the starting - * point following by the coordinates of the ending point of the - * hyperslab. For example, to specify a rectangular hyperslab - * destination region starting at element (2,2) to element (5,4) + * \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 + * the source \p block_coord_src, the function will write data + * to the dataset \p path_dest in file \p file_dest to the + * simple hyperslab specified by \p block_coord_dset. + * The arrays \p block_coord_src and \p block_coord_dset have + * a length of 2*rank and are the coordinates of the starting + * point following by the coordinates of the ending point of the + * hyperslab. For example, to specify a rectangular hyperslab + * 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 - * (as may be the case when writing to a new file) then the - * dataset will be copied directly to the \p path_dest and + * If \p path_dest does not exist in the destination file + * (as may be the case when writing to a new file) then the + * 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 +502,11 @@ 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 hsize_t *block_coord_src, - const char *file_dest, - const char *path_dest, - const hsize_t *block_coord_dset); + const char *path_src, + const hsize_t *block_coord_src, + const char *file_dest, + const char *path_dest, + const hsize_t *block_coord_dset); /*------------------------------------------------------------------------- * @@ -562,27 +524,25 @@ 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 - * the referenced data will be read into - * \param[out] buf Buffer containing data from the - * referenced region + * \param[in] mem_type Memory datatype, describing the buffer the referenced data will be read into + * \param[out] buf Buffer containing data from the referenced region * * \return \herr_t * - * \details H5LTread_region() reads data from a region described by - * the hyperslab coordinates in \p block_coord, located in - * the dataset specified by its absolute path \p path in a - * file specified by its name \p file. Data is read into a - * buffer \p buf of the datatype that corresponds to the + * \details H5LTread_region() reads data from a region described by + * the hyperslab coordinates in \p block_coord, located in + * the dataset specified by its absolute path \p path in a + * file specified by its name \p file. Data is read into a + * 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 - * of the starting point following by the coordinates of the - * ending point of the hyperslab. For example, to extract a - * rectangular hyperslab region starting at element (2,2) to + * 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 the hyperslab. For example, to extract a + * 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 +551,55 @@ H5_HLRDLL herr_t H5LTcopy_region(const char *file_src, * */ H5_HLRDLL herr_t H5LTread_region(const char *file, - const char *path, - const hsize_t *block_coord, - hid_t mem_type, - void *buf ); + const char *path, + const hsize_t *block_coord, + hid_t mem_type, + 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 - * for each value - * \param[in] space Dataspace identifier, describing the elements - * to be read from the dataset with bit-field - * values + * \param[in] lengths Array of the number of bits to be extracted for each value + * \param[in] space Dataspace identifier, describing the elements + * 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 - * dataset specified by its identifier \p dset_id, and unpacks + * \details H5LTread_bitfield_value() reads selected elements from a + * 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 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. - * Extracted bits will be interpreted as a base-2 integer value. - * Each value will be converted to the base-10 integer value and - * stored in the application buffer. - * - * 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 - * 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 - * as \p num_values values for the first element, followed by the - * \p num_values values for the second element, ... , followed by - * the \p num_values values for the + * 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 + * bits to be extracted for the i<sup>th</sup> bit-field value. + * Extracted bits will be interpreted as a base-2 integer value. + * Each value will be converted to the base-10 integer value and + * stored in the application buffer. + * + * 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 + * 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 + * as \p num_values values for the first element, followed by the + * \p num_values values for the second element, ... , followed by + * 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 +608,5 @@ 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); diff --git a/doxygen/dox/high_level/high_level.dox b/doxygen/dox/high_level/high_level.dox deleted file mode 100644 index c53d298..0000000 --- a/doxygen/dox/high_level/high_level.dox +++ /dev/null @@ -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> - * - */ diff --git a/doxygen/examples/H5.format.1.0.html b/doxygen/examples/H5.format.1.0.html index ff21315..4eb0548 100644 --- a/doxygen/examples/H5.format.1.0.html +++ b/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>. <!-- diff --git a/doxygen/examples/H5.format.1.1.html b/doxygen/examples/H5.format.1.1.html index 0ae31df..9d03a76 100644 --- a/doxygen/examples/H5.format.1.1.html +++ b/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 diff --git a/doxygen/examples/H5.format.2.0.html b/doxygen/examples/H5.format.2.0.html index 4a5fe37..242fdea 100644 --- a/doxygen/examples/H5.format.2.0.html +++ b/doxygen/examples/H5.format.2.0.html @@ -357,7 +357,7 @@ div { page-break-inside:avoid; <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’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 @@ -12861,9 +12861,9 @@ Pipeline Message</a></h4> datatypes).</p> <p>In 1.8.x versions of the library, attributes can be larger than 64KB. See the - <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_Users_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13"> + <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_User_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13"> “Special Issues”</a> section of the Attributes chapter - in the <cite>HDF5 User’s Guide</cite> for more information.</p> + in the <cite>HDF5 User Guide</cite> for more information.</p> <p>Note: Attributes on an object must have unique names: the HDF5 Library currently enforces this by causing the creation of an attribute with a duplicate name to fail. diff --git a/doxygen/examples/H5.format.html b/doxygen/examples/H5.format.html index cbcb387..378f7a3 100644 --- a/doxygen/examples/H5.format.html +++ b/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’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 @@ -14647,9 +14647,9 @@ Data Layout message. datatypes).</p> <p>In 1.8.x versions of the library, attributes can be larger than 64KB. See the - <a href="UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_Users_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13"> + <a href="UG/HDF5_User_Guide-Responsive%20HTML5/index.html#t=HDF5_User_Guide%2FAttributes%2FHDF5_Attributes.htm%3Frhtocid%3Dtoc8.2_1%23TOC_8_5_Special_Issuesbc-13"> “Special Issues”</a> section of the Attributes chapter - in the <cite>HDF5 User’s Guide</cite> for more information.</p> + in the <cite>HDF5 User Guide</cite> for more information.</p> <p>Note: Attributes on an object must have unique names: the HDF5 Library currently enforces this by causing the creation of an attribute with a duplicate name to fail. diff --git a/doxygen/examples/H5R_examples.c b/doxygen/examples/H5R_examples.c deleted file mode 100644 index b40b992..0000000 --- a/doxygen/examples/H5R_examples.c +++ /dev/null @@ -1,171 +0,0 @@ -/* -*- c-file-style: "stroustrup" -*- */ - -#include "hdf5.h" - -#include <assert.h> -#include <stdio.h> -#include <stdlib.h> - -int -main(void) -{ - int ret_val = EXIT_SUCCESS; - - //! <!-- [create] --> - { - __label__ fail_file, fail_fspace, fail_dset, fail_sel, fail_aspace, fail_attr, fail_awrite; - hid_t file, fspace, dset, aspace, attr; - H5R_ref_t ref; - - if ((file = H5Fcreate("reference.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_file; - } - // create a region reference which selects all elements of the dataset at "/data" - if ((fspace = H5Screate_simple(2, (hsize_t[]){10, 20}, NULL)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_fspace; - } - if ((dset = H5Dcreate(file, "data", H5T_STD_I32LE, fspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) == - H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_dset; - } - if (H5Sselect_all(fspace) < 0 || H5Rcreate_region(file, "data", fspace, H5P_DEFAULT, &ref) < 0) { - ret_val = EXIT_FAILURE; - goto fail_sel; - } - // store the region reference in a scalar attribute of the root group called "region" - if ((aspace = H5Screate(H5S_SCALAR)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_aspace; - } - if ((attr = H5Acreate(file, "region", H5T_STD_REF, aspace, H5P_DEFAULT, H5P_DEFAULT)) == - H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_attr; - } - if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) { - ret_val = EXIT_FAILURE; - goto fail_awrite; - } - -fail_awrite: - H5Aclose(attr); -fail_attr: - H5Sclose(aspace); -fail_aspace: - H5Rdestroy(&ref); -fail_sel: - H5Dclose(dset); -fail_dset: - H5Sclose(fspace); -fail_fspace: - H5Fclose(file); -fail_file:; - } - //! <!-- [create] --> - - //! <!-- [read] --> - { - __label__ fail_file, fail_attr, fail_aread; - hid_t file, attr; - H5R_ref_t ref; - - if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_file; - } - - // read the dataset region reference from the attribute - if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_attr; - } - if (H5Aread(attr, H5T_STD_REF, &ref) < 0) { - ret_val = EXIT_FAILURE; - goto fail_aread; - } - assert(H5Rget_type(&ref) == H5R_DATASET_REGION2); - - // get an HDF5 path name for the dataset of the region reference - { - char buf[255]; - if (H5Rget_obj_name(&ref, H5P_DEFAULT, buf, 255) < 0) { - ret_val = EXIT_FAILURE; - } - printf("Object name: \"%s\"\n", buf); - } - - H5Rdestroy(&ref); -fail_aread: - H5Aclose(attr); -fail_attr: - H5Fclose(file); -fail_file:; - } - //! <!-- [read] --> - - //! <!-- [update] --> - { - __label__ fail_file, fail_attr, fail_ref; - hid_t file, attr; - H5R_ref_t ref; - - if ((file = H5Fopen("reference.h5", H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_file; - } - - // H5T_STD_REF is a generic reference type - // we can "update" the attribute value to refer to the attribute itself - if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_attr; - } - if (H5Rcreate_attr(file, "data", "region", H5P_DEFAULT, &ref) < 0) { - ret_val = EXIT_FAILURE; - goto fail_ref; - } - - assert(H5Rget_type(&ref) == H5R_ATTR); - - if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) { - ret_val = EXIT_FAILURE; - } - - H5Rdestroy(&ref); -fail_ref: - H5Aclose(attr); -fail_attr: - H5Fclose(file); -fail_file:; - } - //! <!-- [update] --> - - //! <!-- [delete] --> - { - __label__ fail_file, fail_ref; - hid_t file; - H5R_ref_t ref; - - // create an HDF5 object reference to the root group - if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) { - ret_val = EXIT_FAILURE; - goto fail_file; - } - if (H5Rcreate_object(file, ".", H5P_DEFAULT, &ref) < 0) { - ret_val = EXIT_FAILURE; - goto fail_ref; - } - - // H5Rdestroy() releases all resources associated with an HDF5 reference - H5Rdestroy(&ref); -fail_ref: - H5Fclose(file); -fail_file:; - } - //! <!-- [delete] --> - - return ret_val; -} diff --git a/doxygen/examples/ThreadSafeLibrary.html b/doxygen/examples/ThreadSafeLibrary.html index 97f7742..5824dc6 100644 --- a/doxygen/examples/ThreadSafeLibrary.html +++ b/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> diff --git a/doxygen/examples/core_menu.md b/doxygen/examples/core_menu.md new file mode 100644 index 0000000..8c82cc5 --- /dev/null +++ b/doxygen/examples/core_menu.md @@ -0,0 +1,65 @@ +<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 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. diff --git a/doxygen/examples/fortran_menu.md b/doxygen/examples/fortran_menu.md new file mode 100644 index 0000000..335a21a --- /dev/null +++ b/doxygen/examples/fortran_menu.md @@ -0,0 +1,61 @@ +<b>Fortran Library</b> + +- H5A "Attributes (H5A)" +<br /> +HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary data object. + +- H5D "Datasets (H5D)" +<br /> +Manage HDF5 datasets, including the transfer of data between memory and disk and the description of dataset properties. + +- H5S "Dataspaces (H5S)" +<br /> +HDF5 dataspaces describe the shape of datasets in memory or in HDF5 files. + +- H5T "Datatypes (H5T)" +<br /> +HDF5 datatypes describe the element type of HDF5 datasets and attributes. + +- H5E "Error Handling (H5E)" +<br /> +HDF5 library error reporting. + +- H5F "Files (H5F)" +<br /> +Manage HDF5 files. + +- H5Z "Filters (H5Z)" +<br /> +Manage HDF5 user-defined filters + +- H5G "Groups (H5G)" +<br /> +Manage HDF5 groups. + +- H5I "Identifiers (H5I)" +<br /> +Manage identifiers defined by the HDF5 library. + +- H5 "Library General (H5)" +<br /> +Manage the life cycle of HDF5 library instances. + +- H5L "Links (H5L)" +<br /> +Manage HDF5 links and link types. + +- H5O "Objects (H5O)" +<br /> +Manage HDF5 objects (groups, datasets, datatype objects). + +- H5P "Property Lists (H5P)" +<br /> +HDF5 property lists are the main vehicle to configure the behavior of HDF5 API functions. + +- H5PL "Dynamically-loaded Plugins (H5PL)" +<br /> +Manage the loading behavior of HDF5 plugins. + +- H5R "References (H5R)" +<br /> +Manage HDF5 references (HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions). diff --git a/doxygen/examples/high_level_menu.md b/doxygen/examples/high_level_menu.md new file mode 100644 index 0000000..9e6f696 --- /dev/null +++ b/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 "Lite (H5LT, H5LD)" +<br /> +Functions to simplify creating and manipulating datasets, attributes and other features + +- @ref H5IM "Image (H5IM)" +<br /> +Creating and manipulating HDF5 datasets intended to be interpreted as images + +- @ref H5TB "Table (H5TB)" +<br /> +Creating and manipulating HDF5 datasets intended to be interpreted as tables + +- @ref H5PT "Packet Table (H5PT)" +<br /> +Creating and manipulating HDF5 datasets to support append- and read-only operations on table data + +- @ref H5DS "Dimension Scale (H5DS)" +<br /> +Creating and manipulating HDF5 datasets that are associated with the dimension of another HDF5 dataset + +- @ref H5DO "Optimizations (H5DO)" +<br /> +Bypassing default HDF5 behavior in order to optimize for specific use cases + +- @ref H5LR "Extensions (H5LR, H5LT)" diff --git a/doxygen/examples/java_menu.md b/doxygen/examples/java_menu.md new file mode 100644 index 0000000..1236838 --- /dev/null +++ b/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. +
\ No newline at end of file diff --git a/doxygen/hdf5doxy.css b/doxygen/hdf5doxy.css index 8c03860..639843d 100644 --- a/doxygen/hdf5doxy.css +++ b/doxygen/hdf5doxy.css @@ -244,8 +244,16 @@ a { padding: 2px 1px 0; } -a[href*="http"] { - background: url('https://mdn.mozillademos.org/files/12982/external-link-52.png') no-repeat 100% 0; - background-size: 12px 12px; - padding-right: 16px; +a[href^="http"]::after, +a[href^="https://"]::after +{ + content: ""; + width: 11px; + height: 11px; + margin-left: 4px; + background-image: url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' width='16' height='16' fill='currentColor' viewBox='0 0 16 16'%3E%3Cpath fill-rule='evenodd' d='M8.636 3.5a.5.5 0 0 0-.5-.5H1.5A1.5 1.5 0 0 0 0 4.5v10A1.5 1.5 0 0 0 1.5 16h10a1.5 1.5 0 0 0 1.5-1.5V7.864a.5.5 0 0 0-1 0V14.5a.5.5 0 0 1-.5.5h-10a.5.5 0 0 1-.5-.5v-10a.5.5 0 0 1 .5-.5h6.636a.5.5 0 0 0 .5-.5z'/%3E%3Cpath fill-rule='evenodd' d='M16 .5a.5.5 0 0 0-.5-.5h-5a.5.5 0 0 0 0 1h3.793L6.146 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