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Cleaning up doxygen warnings

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This commit is contained in:
Mark Berrill 2021-09-13 11:51:21 -04:00
parent 50f77fb2d3
commit 88dda8d914
15 changed files with 37 additions and 52 deletions
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2
CMakeLists.txt
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@ -90,7 +90,7 @@ CHECK_ENABLE_FLAG( USE_DOXYGEN 1 )
CHECK_ENABLE_FLAG( USE_LATEX 1 )
FILE( MAKE_DIRECTORY "${${PROJ}_INSTALL_DIR}/doc" )
IF ( USE_DOXYGEN )
SET( DOXYFILE_LATEX YES )
SET( DOXYFILE_LATEX NO )
SET( DOXYFILE_IN "${${PROJ}_SOURCE_DIR}/doxygen/Doxyfile.in" )
SET( DOXY_HEADER_FILE "${${PROJ}_SOURCE_DIR}/doxygen/html/header.html" )
SET( DOXY_FOOTER_FILE "${${PROJ}_SOURCE_DIR}/doxygen/html/footer.html" )

2
IO/Reader.h
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@ -87,7 +87,7 @@ std::shared_ptr<IO::Variable> getVariable( const std::string &path, const std::s
* @brief Reformat the variable to match the mesh
* @details This function modifies the dimensions of the array to match the mesh
* @param[in] mesh The underlying mesh
* @param[in/out] variable The variable name to read
* @param[in,out] var The variable name to read
*/
void reformatVariable( const IO::Mesh &mesh, IO::Variable &var );

1
IO/Xdmf.h
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@ -105,6 +105,7 @@ public:
* @param[in] type The element type
* @param[in] NumElements The number of elements
* @param[in] dofMap The connectivity information (type x NumElements)
* @param[in] NumNodes The number of nodes
* @param[in] x The x coordinates or the xy/xyz coordinates
* @param[in] y The y coordinates (may be null)
* @param[in] z The z coordinates (may be null)

6
IO/netcdf.h
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@ -123,6 +123,8 @@ Array<TYPE> getAtt( int fid, const std::string &att );
* @brief Write the dimensions
* @details This function writes the grid dimensions to netcdf.
* @param fid Handle to the open file
* @param names
* @param dims
*/
std::vector<int> defDim(
int fid, const std::vector<std::string> &names, const std::vector<int> &dims );
@ -132,6 +134,10 @@ std::vector<int> defDim(
* @brief Write a variable
* @details This function writes a variable to netcdf.
* @param fid Handle to the open file
* @param var Variable to read
* @param dimids
* @param data
* @param rank_info
*/
template<class TYPE>
void write( int fid, const std::string &var, const std::vector<int> &dimids,

4
IO/silo.h
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@ -49,7 +49,7 @@ void close( DBfile *fid );
* @param[in] fid Handle to the open file
* @param[in] name Name of variable
*/
DataType varDataType( DBfile *dbfile, const std::string &name );
DataType varDataType( DBfile *fid, const std::string &name );
/*!
@ -250,8 +250,6 @@ void writeMultiMesh( DBfile *fid, const std::string &meshname,
* @param[in] varname Mesh name
* @param[in] subVarNames Names of the sub meshes in the form "filename:meshname"
* @param[in] subVarTypes Type of each submesh
* @param[in] ndim Dimension of variable (used to determine suffix)
* @param[in] nvar Number of subvariables (used to determine suffix)
*/
void writeMultiVar( DBfile *fid, const std::string &varname,
const std::vector<std::string> &subVarNames, const std::vector<int> &subVarTypes );

26
analysis/analysis.h
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@ -22,8 +22,8 @@ typedef Array<BlobIDType> BlobIDArray;
* @param[in] SignDist SignDist
* @param[in] vF vF
* @param[in] vS vS
* @param[in] S S
* @param[out] LocalBlobID The ids of the blobs
* @param[in] periodic Optional value
* @return Returns the number of blobs
*/
int ComputeLocalBlobIDs( const DoubleArray& Phase, const DoubleArray& SignDist,
@ -48,12 +48,13 @@ int ComputeLocalPhaseComponent( const IntArray &PhaseID, int &VALUE, IntArray &C
* @param[in] nx Number of elements in the x-direction
* @param[in] ny Number of elements in the y-direction
* @param[in] nz Number of elements in the z-direction
* @param[in] rank_info MPI communication info
* @param[in] Phase Phase
* @param[in] SignDist SignDist
* @param[in] vF vF
* @param[in] vS vS
* @param[in] S S
* @param[out] LocalBlobID The ids of the blobs
* @param[out] GlobalBlobID The ids of the blobs
* @param[in] comm MPI communicator
* @return Returns the number of blobs
*/
int ComputeGlobalBlobIDs( int nx, int ny, int nz, const RankInfoStruct& rank_info,
@ -68,10 +69,11 @@ int ComputeGlobalBlobIDs( int nx, int ny, int nz, const RankInfoStruct& rank_inf
* @param[in] nx Number of elements in the x-direction
* @param[in] ny Number of elements in the y-direction
* @param[in] nz Number of elements in the z-direction
* @param[in] rank_in MPI communication info
* @param[in] rank_info MPI communication info
* @param[in] PhaseID Array that identifies the phases
* @param[in] VALUE Identifier for the phase to decompose
* @param[out] GlobalBlobID The ids of the blobs for the phase
* @param[in] comm The communicator to use
* @return Return the number of components in the specified phase
*/
int ComputeGlobalPhaseComponent( int nx, int ny, int nz, const RankInfoStruct& rank_info,
@ -82,10 +84,8 @@ int ComputeGlobalPhaseComponent( int nx, int ny, int nz, const RankInfoStruct& r
* @brief Reorder the blobs
* @details Reorder the blobs based on the number of cells they contain
* largest first.
* @param[in] nx Number of elements in the x-direction
* @param[in] ny Number of elements in the y-direction
* @param[in] nz Number of elements in the z-direction
* @param[in/out] ID The ids of the blobs
* @param[in,out] ID The ids of the blobs
* @param[in] comm MPI communicator
*/
void ReorderBlobIDs( BlobIDArray& ID, const Utilities::MPI& comm );
@ -117,8 +117,12 @@ struct ID_map_struct {
* @details This functions computes the map of blob ids between iterations
* @return Returns the map of the blob ids. Each final blob may have no source
* ids, one parent, or multiple parents. Each src id may be a parent for multiple blobs.
* @param[in] nx Number of elements in the x-direction
* @param[in] ny Number of elements in the y-direction
* @param[in] nz Number of elements in the z-direction
* @param[in] ID1 The blob ids at the first timestep
* @param[in] ID2 The blob ids at the second timestep
* @param[in] comm The communicator to use
*/
ID_map_struct computeIDMap( int nx, int ny, int nz, const BlobIDArray& ID1, const BlobIDArray& ID2, const Utilities::MPI& comm );
@ -127,7 +131,7 @@ ID_map_struct computeIDMap( int nx, int ny, int nz, const BlobIDArray& ID1, cons
* @brief Compute the new global ids based on the map
* @details This functions computes the time-consistent global ids for the
* current global id index
* @param[in/out] map The timestep mapping for the ids
* @param[in,out] map The timestep mapping for the ids
* @param[in] id_max The globally largest id used previously
* @param[out] new_ids The newly renumbered blob ids (0:ids.max())
*/
@ -139,9 +143,9 @@ void getNewIDs( ID_map_struct& map, BlobIDType& id_max, std::vector<BlobIDType>&
* @details This functions computes the map of blob ids between iterations.
* Note: we also update the map to reflect the new ids
* @param[out] new_ids The newly renumbered blob ids (0:ids.max())
* @param[in/out] IDs The blob ids to renumber
* @param[in,out] IDs The blob ids to renumber
*/
void renumberIDs( const std::vector<BlobIDType>& new_id_list, BlobIDArray& IDs );
void renumberIDs( const std::vector<BlobIDType>& new_ids, BlobIDArray& IDs );
/*!

2
analysis/distance.h
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@ -24,6 +24,7 @@ inline bool operator<(const Vec& l, const Vec& r){ return l.x*l.x+l.y*l.y+l.z*l.
* @param[in] ID Segmentation id
* @param[in] Dm Domain information
* @param[in] periodic Directions that are periodic
* @param[in] dx Cell size
*/
template<class TYPE>
void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
@ -36,6 +37,7 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
* @param[in] ID Domain id
* @param[in] Dm Domain information
* @param[in] periodic Directions that are periodic
* @param[in] dx Cell size
*/
void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm,
const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );

3
analysis/filters.h
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@ -25,7 +25,10 @@ void Med3D( const Array<float> &Input, Array<float> &Output );
* @details This routine performs a non-linear local means filter
* @param[in] Input Input image
* @param[in] Mean Mean value
* @param[in] Distance Distance
* @param[out] Output Output image
* @param[in] d
* @param[in] h
*/
int NLM3D( const Array<float> &Input, Array<float> &Mean,
const Array<float> &Distance, Array<float> &Output, const int d, const float h);

3
analysis/imfilter.h
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@ -89,7 +89,7 @@ Array<TYPE> imfilter_separable( const Array<TYPE>& A, const std::vector<Array<TY
* multidimensional filter H. The result B has the same size and class as A.
* This version works with separable filters and is more efficient than a single filter.
* @param[in] A The input array (Nx,Ny,Nz)
* @param[in] H The filter [2*Nhx+1,2*Nhy+1,...]
* @param[in] Nh The filter size
* @param[in] boundary The boundary conditions to apply (ndim):
* fixed - Input array values outside the bounds of the array are
* implicitly assumed to have the value X
@ -114,6 +114,7 @@ Array<TYPE> imfilter_separable( const Array<TYPE>& A, const std::vector<int>& Nh
* This version works with separable filters and is more efficient than a single filter.
* @param[in] A The input array (Nx,Ny,Nz)
* @param[in] H The filter [2*Nhx+1,2*Nhy+1,...]
* @param[in] Nh The filter size
* @param[in] boundary The boundary conditions to apply (ndim):
* fixed - Input array values outside the bounds of the array are
* implicitly assumed to have the value X

1
common/Communication.h
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@ -51,6 +51,7 @@ class fillHalo
public:
/*!
* @brief Default constructor
* @param[in] comm Communicator to use
* @param[in] info Rank and neighbor rank info
* @param[in] n Number of local cells
* @param[in] ng Number of ghost cells

2
common/MPI.h
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@ -821,7 +821,7 @@ public: // Member functions
* @return Output array for allGather
*/
template<class type>
std::vector<type> allGather( const std::vector<type> &x_in ) const;
std::vector<type> allGather( const std::vector<type> &x ) const;
/*!

1
common/Utilities.h
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@ -30,6 +30,7 @@ using StackTrace::Utilities::sleep_s;
* \details This routine will peform the default startup sequence
* \param argc argc from main
* \param argv argv from main
* \param multiple Intialize mpi with MPI_THREAD_MULTIPLE support?
*/
void startup( int argc, char **argv, bool multiple=true );

33
doxygen/Doxyfile.in
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@ -379,12 +379,6 @@ MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = YES
# If the sources in your project are distributed over multiple directories
# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
# in the documentation. The default is NO.
SHOW_DIRECTORIES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
# This will remove the Files entry from the Quick Index and from the
# Folder Tree View (if specified). The default is YES.
@ -467,7 +461,7 @@ INPUT_ENCODING = UTF-8
# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
# *.f90 *.f *.for *.vhd *.vhdl
FILE_PATTERNS = *.h *.hh *.cu
FILE_PATTERNS = *.h *.hh
# The RECURSIVE tag can be used to turn specify whether or not subdirectories
# should be searched for input files as well. Possible values are YES and NO.
@ -728,12 +722,6 @@ HTML_COLORSTYLE_GAMMA = 80
HTML_TIMESTAMP = YES
# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
# files or namespaces will be aligned in HTML using tables. If set to
# NO a bullet list will be used.
HTML_ALIGN_MEMBERS = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded. For this to work a browser that supports
@ -850,7 +838,7 @@ TREEVIEW_WIDTH = 250
# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.
GENERATE_LATEX = YES
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be
@ -1005,18 +993,6 @@ GENERATE_XML = NO
XML_OUTPUT = xml
# The XML_SCHEMA tag can be used to specify an XML schema,
# which can be used by a validating XML parser to check the
# syntax of the XML files.
XML_SCHEMA =
# The XML_DTD tag can be used to specify an XML DTD,
# which can be used by a validating XML parser to check the
# syntax of the XML files.
XML_DTD =
# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
# dump the program listings (including syntax highlighting
# and cross-referencing information) to the XML output. Note that
@ -1174,11 +1150,6 @@ ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
# The PERL_PATH should be the absolute path and name of the perl script
# interpreter (i.e. the result of `which perl').
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------

2
doxygen/DoxygenMainpage.h
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@ -4,8 +4,6 @@
*
* - \ref IO "IO routines"
* - \ref Utilities "Utility routines"
* - \ref silo "Access to silo routines"
* - \ref netcdf "Access to netcdf routines"
*
* \author James McClure
*/

1
threadpool/atomic_helpers.h
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@ -222,7 +222,6 @@ inline int32_atomic atomic_fetch_and_or( int32_atomic volatile *v, int32_atomic
* \brief Fetch the current value and "ou" with given value
* \details Perform *v = (*v) | x, returning the previous value
* \return Returns the previous value before the "and" operation
* \param[in] v The pointer to the value to check and swap
* \param[in] v The pointer to the value to check and or
* \param[in] x The value to or
*/