Basic Operations dealing with semantic structures below the end-user API.

Data Structures
struct	_TimeTableEntry

Typedefs
typedef struct _TimeTableEntry	TimeTableEntry

Functions
F5_API hid_t	F5Bcreate_timetable_type (void)
F5_API hsize_t	F5Bappend_timetable (hid_t loc_id, hid_t timetable_type_location_id, const TimeTableEntry *TTE, hsize_t append_dims)
F5_API hsize_t	F5Bget_timetable_size (hid_t loc_id)
hsize_t	F5Bread_timetable (hid_t loc_id, TimeTableEntry *TTE, hsize_t table_size)
F5_API F5_TimeParameter *	F5BnewTimeParameter (void)
F5_API void	F5deleteTimeParameter (F5_TimeParameter **)
F5_API int	F5setTimeUnit (hid_t file_id, const F5_TimeParameter *)
F5_API int	F5getTimeUnit (hid_t file_id, F5_TimeParameter *)
F5_API char *	F5I_timegroup (const double *time, char *destbuf, size_t len)
F5_API hid_t	F5Bappend_timeslice (hid_t file_id, const F5_TimeParameter *time)
F5_API hid_t	F5Bappend_slice (hid_t file_id, const double *time)
F5_API F5Path *	F5Binitialize_path (hid_t File_id)
F5_API hid_t	F5BgetMostRecentSlice (double *t, hid_t FileID, const char **time_attrib_names)
F5_API hid_t	F5BgetMostRecentFileSlice (double t, const char *filename)
F5_API hid_t	F5BgetGridVertexData (hid_t SliceID, const char *gridname, const char *chartname, const char *fieldname)

Detailed Description

Typedef Documentation

TimeTableEntry

typedef struct _TimeTableEntry TimeTableEntry

Data type entry for time tables.

Function Documentation

F5Bappend_slice()

F5_API hid_t F5Bappend_slice	(	hid_t	file_id,
		const double *	time )

Get the HDF5 identifier for a given time slice. A new group is created in the file if none exists yet.

Parameters

file_id	HDF5 File identifier.
time	The time is specified as a pointer, such that it may be NULL to indicate a static dataset.

Returns

HDF5 identifier for the newly created or opened Time Slice group.

Todo

Maybe move to another header.

Add consistency check on re-open of an existing group

Definition at line 140 of file F5Bslice.c.

{
char    timename[128];
hid_t   Slice_hid = F5Gappend(file_id, F5I_timegroup(time, timename, sizeof(timename) ));
 
        if (time)
                F5printf(30," -- F5Bappend_slice(%lg)", *time);
        else
                F5printf(30," -- F5Bappend_slice( <static> )");
 
        if (time)
        {
                /* TODO: add time slice attribute ONLY if it is not yet
                   //       there. Think about: what if it is there, but is
                   //   not consistent?
                */
        hid_t space_hid = H5Screate(H5S_SCALAR);
        hid_t attr_hid  = F5Aappend(Slice_hid, FIBER_HDF5_TIME_ATTRIB , H5T_NATIVE_DOUBLE, space_hid, H5P_DEFAULT);
                H5Awrite(attr_hid, H5T_NATIVE_DOUBLE,  time);
                H5Sclose(space_hid);
                H5Aclose(attr_hid);
        }
        return Slice_hid;
}

References F5Aappend(), F5Gappend(), F5I_timegroup(), F5printf, and FIBER_HDF5_TIME_ATTRIB.

Referenced by F5Bappend_timeslice(), and F5LTcreateV().

F5Bappend_timeslice()

F5_API hid_t F5Bappend_timeslice	(	hid_t	file_id,
		const F5_TimeParameter *	time )

Append a time slice in the given time unit. Only one time unit is allowed per file. If another time unit has already been defined in the file, the function will return without touching the file.

Definition at line 134 of file F5Bslice.c.

{
        /* ...TODO: Coding....... */
        return F5Bappend_slice(file_id, &time->value);
}

References F5Bappend_slice(), and _F5_TimeParameter::value.

F5Bappend_timetable()

F5_API hsize_t F5Bappend_timetable	(	hid_t	loc_id,
		hid_t	timetable_type_location_id,
		const TimeTableEntry *	TTE,
		hsize_t	append_dims )

Initialize a time table for the given location.

Parameters

timetable_type_id

The type for time table entries, such as provided by F5Bcreate_timetable_type(), but it may well be (and should be) a named type instead of a transient type.

Returns

false if the time table already existed. F5_API int F5Binit_timetable(hid_t loc_id, hid_t timetable_type_id);

Append entries to the time table associated with a certain location.

Parameters

timetable_type_location_id

the location ID where the named datatype for timetable entries will be stored, in case it needs to be created.

Definition at line 261 of file F5Bslice.c.

{
hid_t   mem_space_id;
hid_t   dataset_id;
hsize_t size = 0;
hsize_t current_dim = 0;
 
        if (!TTE) return 0;
 
        mem_space_id = H5Screate_simple( 1, &append_dims, NULL);
 
        H5E_BEGIN_TRY
        dataset_id  = H5Dopen2( loc_id, F5_TIMETABLE_NAME, H5P_DEFAULT);
        H5E_END_TRY
 
/*      printf("F5Bappend_timetable(,,TimeTableEntry={%g,%s},%d)\n",
               TTE->TimeValue, TTE->TimesliceName,
               (int)append_dims );
        fflush(stdout);
*/
        if (dataset_id<=0)
        {
                dataset_id =
                        F5Bcreate_timetable_dataset(loc_id, dtype_location_id, append_dims);
 
                if (dataset_id<=0)
                        return 0;
 
        {
        hid_t   timetable_type_id = F5Bcreate_timetable_type();
                H5Dwrite( dataset_id, timetable_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, TTE);
                H5Tclose( timetable_type_id );
        }
                H5Dclose( dataset_id );
                return append_dims;
        }
 
        {
        hid_t   current_file_space_id = H5Dget_space(dataset_id );
                H5Sget_simple_extent_dims( current_file_space_id, &current_dim, NULL);
                H5Sclose( current_file_space_id );
        }
 
        size = append_dims + current_dim;
        H5Dset_extent( dataset_id, &size);
 
        {
        hid_t   file_space_id = H5Dget_space(dataset_id );
                H5Sselect_hyperslab(file_space_id, H5S_SELECT_SET, &current_dim, NULL, &append_dims, NULL);
 
/*              printf("F5Bappend_timetable(): New extent %d, insert at %d, count = %d\n",
                       (int)size, (int)current_dim, (int)append_dims);
*/
        hid_t   timetable_type_id = F5Bcreate_timetable_type();
                H5Dwrite( dataset_id, timetable_type_id, mem_space_id, file_space_id, H5P_DEFAULT, TTE);
                H5Tclose( timetable_type_id );
                H5Sclose( file_space_id );
        }
 
        H5Dclose( dataset_id );
 
        return size;
}

References F5_TIMETABLE_NAME, F5Bcreate_timetable_type(), and H5Tclose().

Referenced by F5I_add_grid().

F5Bcreate_timetable_type()

F5_API hid_t F5Bcreate_timetable_type

(

void

)

Create a transient type that is compatible with the TimeTableEntry data structure. It must be release via H5Tclose() by the calling code.

Definition at line 167 of file F5Bslice.c.

{
hid_t   dtype_id = H5Tcreate( H5T_COMPOUND, sizeof(TimeTableEntry) );
        {
        hid_t   string_dtype_id = H5Tcreate( H5T_STRING, F5_TIMESLICE_NAME_LENGTH );
                H5Tinsert( dtype_id, FIBER_HDF5_TIME_ATTRIB, 0, H5T_NATIVE_DOUBLE);
                H5Tinsert( dtype_id, "F5::SliceGroup", sizeof(double), string_dtype_id );
                H5Tclose( string_dtype_id );
        }
        return dtype_id;
}

References F5_TIMESLICE_NAME_LENGTH, FIBER_HDF5_TIME_ATTRIB, and H5Tclose().

Referenced by F5Bappend_timetable(), F5Bget_file_timetable_type(), and F5Bread_timetable().

F5Bget_timetable_size()

F5_API hsize_t F5Bget_timetable_size

(

hid_t

loc_id

)

Get the number of entries in the respective time table.

Definition at line 328 of file F5Bslice.c.

{
hid_t   dataset_id;
hsize_t current_dim = 0;
 
        H5E_BEGIN_TRY
        dataset_id  = H5Dopen2( loc_id, F5_TIMETABLE_NAME, H5P_DEFAULT);
        H5E_END_TRY
 
        if (dataset_id<=0)
                return 0;
 
        {
        hid_t   timetable_type_id = H5Dget_type( dataset_id );
        int     type_is_ok = F5check_timetable_Type(timetable_type_id);
                H5Tclose( timetable_type_id );
                if (!type_is_ok)
                {
                        H5Dclose( dataset_id );
                        F5printf(-1, "WARNING: Invalid Time Table time detected!");
                        return 0;
                }
        }
 
 
        {
        hid_t   current_file_space_id = H5Dget_space(dataset_id );
                H5Sget_simple_extent_dims( current_file_space_id, &current_dim, NULL);
                H5Sclose( current_file_space_id );
        }
 
 
        H5Dclose( dataset_id );
 
        return current_dim;
}

References F5_TIMETABLE_NAME, F5printf, and H5Tclose().

F5BgetGridVertexData()

F5_API hid_t F5BgetGridVertexData	(	hid_t	SliceID,
		const char *	gridname,
		const char *	chartname,
		const char *	fieldname )

Get the GridVertexData for given grid-, chart- and fieldnames.

Definition at line 5 of file F5Bgrid.c.

{
hid_t   G_id, T_id, R_id, D_id;
 
        G_id = H5Gopen2(SliceID, gridname, H5P_DEFAULT);
 
        T_id = H5Gopen2(G_id, FIBER_HDF5_POINTS , H5P_DEFAULT);
        H5Gclose(G_id);
        if (T_id<0) return -1;
 
        R_id = H5Gopen2(T_id, chartname, H5P_DEFAULT);
        H5Gclose(T_id);
        if (R_id<0) return -1;
 
        D_id = H5Dopen2(R_id, fieldname, H5P_DEFAULT);
        H5Gclose(R_id);
 
        return D_id;
}

References FIBER_HDF5_POINTS, and H5Gclose.

F5BgetMostRecentFileSlice()

F5_API hid_t F5BgetMostRecentFileSlice	(	double	t,
		const char *	filename )

Get the MostRecentSlice out of a HDF5 file with the given name.

Definition at line 70 of file F5Bslice.c.

{
hid_t   fid = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
 
        if (fid<0)
                return -1;
 
{hid_t  slice_id = F5BgetMostRecentSlice(&t, fid, F5_default_time_attrib_names);
 
        H5Fclose(fid);
 
        if (slice_id>0)
        {
                printf("F5Bslice: got data slice for T=%lg\n", t);
        }
 
        return slice_id;
}
}

References F5_default_time_attrib_names, F5BgetMostRecentSlice(), and slice_info::t.

F5BgetMostRecentSlice()

F5_API hid_t F5BgetMostRecentSlice	(	double *	t,
		hid_t	FileID,
		const char **	time_attrib_names )

Get the next slice for given time attriute names.

Deprecated

Definition at line 55 of file F5Bslice.c.

{
struct slice_info si = { 0, -1, 0 };
        si.time_attribs = time_attribs;
        si.t = t;
 
        H5Giterate(loc_id, ".", 0, slice_iter, &si);
 
        if (si.what>0)
                *t = si.nearest_t;
 
        return si.what;
}

References slice_info::nearest_t, slice_info::t, slice_info::time_attribs, and slice_info::what.

Referenced by F5BgetMostRecentFileSlice().

F5Binitialize_path()

F5_API F5Path * F5Binitialize_path

(

hid_t

File_id

)

Initialize an F5Path from a file for reading. The coordinate system is set to the default cartesian coordinates. No timeslice, grid, field etc. ID's are defined yet, these need to be filled in by iteration. This function is called internally by F5iterate_timeslices() for creating an F5Path object that is then modified to contain a valid group ID for each timeslice, grid, field, ... Currently, it is hard-coded for reading cartesian coordinates only. The preferred way is to employ iterators on reading files.

Definition at line 156 of file F5B.c.

{
/*const char*cs = coordinate_system ? coordinate_system : FIBER_HDF5_DEFAULT_CHART; */
const char*cs = FIBER_HDF5_DEFAULT_CHART;
ChartDomain_IDs*ChartDomain = (strcmp(cs, FIBER_HDF5_DEFAULT_CHART)==0) ? F5B_standard_cartesian_chart3D() : 0;
 
F5Path*f = F5Bopen_coordinate_domain( File_id, ChartDomain);
        if (!f) /* hack for backward compatibility. */
        {
        ChartDomain_IDs*oldChartDomain = F5B_standard_cartesian_chart3D();
                oldChartDomain->domain_name = FIBER_HDF5_DEPRECATED_OLD_CARTESIAN_DOMAIN;
 
                F5printf(10, "*F5Binitialize_path(): Could not initialize with "
                         FIBER_HDF5_DEFAULT_CHART ", now trying " FIBER_HDF5_DEPRECATED_OLD_CARTESIAN_DOMAIN "...");
 
                f = F5Bopen_coordinate_domain(File_id, ChartDomain);
                oldChartDomain->domain_name = FIBER_HDF5_CARTESIAN_CHART_DOMAIN;
 
                if (!f)
                {
                        F5printf(10, "*F5Binitialize_path(): Could not initialize with "
                                 FIBER_HDF5_DEPRECATED_OLD_CARTESIAN_DOMAIN " either... not good.");
 
                        f = F5Bopen_coordinate_domain( File_id, F5B_standard_cartesian_chart3D() );
                }
        }
        return f;
}

References ChartDomain_IDs::domain_name, F5B_standard_cartesian_chart3D(), F5Bopen_coordinate_domain(), F5printf, FIBER_HDF5_CARTESIAN_CHART_DOMAIN, FIBER_HDF5_DEFAULT_CHART, and FIBER_HDF5_DEPRECATED_OLD_CARTESIAN_DOMAIN.

Referenced by F5iterate_timeslices().

F5BnewTimeParameter()

F5_API F5_TimeParameter * F5BnewTimeParameter

(

void

)

Allocate a new F5_TimeParameter structure in memory. Actually, one could also pass a static structure, but using this function and F5deleteTimePArameter(), the call is safe even if the TimeParameter structure is changed in a future version of F5.

References F5_API.

F5Bread_timetable()

hsize_t F5Bread_timetable	(	hid_t	loc_id,
		TimeTableEntry *	TTE,
		hsize_t	table_size )

Read the entries of a time table.

Definition at line 366 of file F5Bslice.c.

{
hid_t   dataset_id;
 
        H5E_BEGIN_TRY
        dataset_id  = H5Dopen2( loc_id, F5_TIMETABLE_NAME, H5P_DEFAULT);
        H5E_END_TRY
 
        if (dataset_id<=0)
                return 0;
 
 
        {
        hid_t   space_id = H5Dget_space(dataset_id );
        hsize_t current_dim = 0;
                H5Sget_simple_extent_dims( space_id, &current_dim, NULL);
                H5Sclose( space_id );
 
                if (table_size<current_dim)
                {
                        H5Dclose( dataset_id );
                        return 0;
                }
 
                {
                hid_t dtype_id  = F5Bcreate_timetable_type();
 
                        H5Dread( dataset_id, dtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, TTE);
                        H5Tclose( dtype_id );
                }
 
                H5Dclose( dataset_id );
                return current_dim;
        }
}

References F5_TIMETABLE_NAME, F5Bcreate_timetable_type(), and H5Tclose().

F5deleteTimeParameter()

F5_API void F5deleteTimeParameter

(

F5_TimeParameter **

)

Deallocate a F5_TimeParameter structure from memory. It needs to be passed a pointer to a pointer, whereby the pointer is set to zero on deallocation. So it is safe to call this function multiple times on the same pointer (just for experimental convenience!).

References F5_API.

F5getTimeUnit()

F5_API int F5getTimeUnit	(	hid_t	file_id,
		F5_TimeParameter *	)

Get the time unit information as specified in the file.

References F5_API.

F5I_timegroup()

F5_API char * F5I_timegroup	(	const double *	time,
		char *	destbuf,
		size_t	len )

Construct the name used for a timeslice, the toplevel hierarchy.

Retrieve the name of the time slice assocciated with the given time. The time is specified as a pointer, such that it may be NULL to indicate a static dataset.

Examples

ObjtoF5.c.

Definition at line 90 of file F5Bslice.c.

{
int     precision = 10;
char    *result = destbuf;
        if (!time)
        {
                return strncpy(destbuf, FIBER_STATIC_DATA, len);
        }
 
#ifdef  _MSC_VER
        _snprintf
#else
        snprintf
#endif
                (destbuf,len,"t=%0*.*f", 2*precision, precision, *time);
 
/*
  (destbuf,len,"t=%0*.*lf", 2*precision, precision, *time);
*/
 
 
/*      printf("TIME %lg -->\n", time); */
        return result;
}

References FIBER_STATIC_DATA.

Referenced by F5Bappend_slice(), F5I_add_grid(), F5Rcreate_relative_vertex_Irefinement3D(), and F5Rcreate_relative_vertex_Qrefinement3D().

F5setTimeUnit()

F5_API int F5setTimeUnit	(	hid_t	file_id,
		const F5_TimeParameter *	TP )

Set the time unit globally for the given file.

Returns

Non-zero indicates that an incompatible time unit has already been set and was not overriden. The caller should take special care to write new data into a different file then.

Definition at line 115 of file F5Bslice.c.

{
/* TODO:
        Create a type which is convertible to "double",
        Open group FIBER_HDF5_GLOBAL_CHARTS
        Commit the type to this group
        Add attributes to this group which describe the type's
        unit
        Close it
 
        And do all that with checking whether such an type
        already exists before.
 
        Only the offset, TimeSemantics and comment members from
        the F5_TimeParameter structure are used.
 */
        return 0;
}