PDL::IO::HDF5 - PDL Interface to the HDF5 Data Format.
This package provides an object-oriented interface for PDLs to the HDF5 data-format. Information on the HDF5 Format can be found at the NCSA's web site at http://hdf.ncsa.uiuc.edu/ .
Currently this interface only provides a subset of the total HDF5 library's capability.
Only HDF5 Simple datatypes are supported. No HDF5 Compound datatypes are supported since PDL doesn't support them.
Only HDF5 Simple dataspaces are supported.
Only 0-dimensional (i.e. scalar) attributes are supported. (Support for PDLs as attributes could possibly be added later.)
use PDL::IO::HDF5; # Files ####### my $newfile = new PDL::IO::HDF5("newfile.hdf"); # create new hdf5 or open existing file. my $attrValue = $existingFile->attrGet('AttrName'); # Get attribute value for file $existingFile->attSet('AttrName' => 'AttrValue'); # Set attribute value(s) for file #Groups ###### my $group = $newfile->group("/mygroup"); # create a new or open existing group my @groups = $existingFile->groups; # get a list of all the groups at the root '/' # level. my @groups = $group->groups; # get a list of all the groups at the "mygroup" # level. my $group2 = $group->group('newgroup'); # Create/open a new group in existing group "mygroup" my $attrValue = $group->attrGet('AttrName'); # Get attribute value for a group $group->attrSet('AttrName' => 'AttrValue'); # Set attribute value(s) for a group $group->attrDel('AttrName1', 'AttrName2'); # Delete attribute(s) for a group @attrs = $group->attrs; # Get List of attributes for a group # Data Sets ######## my $dataset = $group->dataset( 'datasetName'); # create a new or open existing dataset # in an existing group my $dataset = $newfile->dataset( 'datasetName'); # create a new or open existing dataset # in the root group of a file my $dataset2 = $newfile->dataset( 'datasetName'); # create a new or open existing dataset # in the root group. my @datasets = $existingFile->datasets; # get a list of all datasets in the root '/' group my @datasets = $group->datasets; # get a list of all datasets in a group @dims = $dataset->dims; # get a list of dimensions for the dataset $pdl = $dataset->get(); # Get the array data in the dataset $dataset->set($pdl); # Set the array data in the dataset my $attrValue = $dataset->attrGet('AttrName'); # Get attribute value for a dataset $dataset->attSet('AttrName' => 'AttrValue'); # Set attribute value(s) for a dataset
ID number given to the file by the HDF5 library
Name of the file.
Access Mode?? ( read /write etc????)
Quick lookup index of group names to attribute values. Autogenerated as-needed by the allAttrValues, allAttrNames, getGroupByAttr methods. Any attribute writes or group creations will delete this data member, because it will no longer be valid.
The index is of this form:
{ groupName1 => { attr1 => value, attr2 => value }. groupName2 => { attr1 => value, attr3 => value }. . . . }
For the purposes of indexing groups by their attributes, the attributes are applied hierarchically. i.e. any attributes of the higher level groups are assumed to be apply for the lower level groups.
Quick lookup index of attribute names/values group names. This index is used by the getGroupByAttr method to quickly find any group(s) that have attribute that match a desired set.
{ "attr1\0attt2" => { "value1\0value2' => [ group1, group2, ...], "value3\0value3' => [ groupA ], . . . }, "att1" => { "value1' => [ group1, group2, ...], "value3' => [ groupA ] . . . }, . . . }
The first level of the index maps the attribute name combinations that have indexes built to their index. The second level maps the corresponding attribute values with the group(s) where these attributes take on these values.
groupName1 => { attr1 => value, attr2 => value }. groupName2 => { attr1 => value, attr3 => value }. . . . }
PDL::IO::HDF5 constructor - creates PDL::IO::HDF5 object for reading or writing data.
Usage:
$a = new PDL::IO::HDF5( $filename );
Arguments: 1) The name of the file.
If this file exists and you want to write to it, prepend the name with the '>' character: ">name.nc"
Returns undef on failure.
Example:
$hdf5obj = new PDL::IO::HDF5( "file.hdf" );
Get the filename for the HDF5 file
my $filename = $HDFfile->filename;
Open or create a group in the root "/" group (i.e. top level) of the HDF5 file.
$HDFfile->group("groupName");
Returns undef on failure, 1 on success.
Get a list of groups in the root "/" group (i.e. top level) of the HDF5 file.
@groups = $HDFfile->groups;
Open or create a dataset in the root "/" group (i.e. top level) of the HDF5 file.
$HDFfile->dataset("groupName");
Note: This is a convienence method that is equivalent to:
$HDFfile->group("/")->dataset("groupName");
Get a list of all dataset names in the root "/" group.
@datasets = $HDF5file->datasets;
$HDFfile->group("/")->datasets;
Set the value of an attribute(s) in the root '/' group of the file.
Currently the only attribute types supported are null-terminated strings.
$HDFfile->attrSet( 'attr1' => 'attr1Value', 'attr2' => 'attr2 value', . . . );
$HDFfile->group("/")->attrSet( 'attr1' => 'attr1Value', 'attr2' => 'attr2 value', . . . );
Get the value of an attribute(s) in the root '/' group of the file.
@attrValues = $HDFfile->attrGet( 'attr1', 'attr2' );
Delete attribute(s) in the root "/" group of the file.
$HDFfile->attrDel( 'attr1', 'attr2', . . . );
$HDFfile->group("/")->attrDel( 'attr1', 'attr2', . . . );
Get a list of all attribute names in the root "/" group of the file.
@attrs = $HDFfile->attrs;
$HDFfile->group("/")->attrs
Internal Method to build the attribute index hash for the object
$hdf5obj->_buildAttrIndex; Output: Updated attrIndex data member
Method to clear the attribute index hash for the object. This is a mostly internal method that is called whenever some part of the HDF5 file has changed and the attrIndex index is no longer valid.
$hdf5obj->clearAttrIndex;
Internal Method to build the groupIndex hash for the object
$hdf5obj->_buildGroupIndex(@attrs); where: @attrs List of attribute names to build a group index on. Output: Updated groupIndex data member
Method to clear the group index hash for the object. This is a mostly internal method that is called whenever some part of the HDF5 file has changed and the groupIndex index is no longer valid.
$hdf5obj->clearGroupIndex;
Get the group names which attributes match a given set of values. This method enables database-like queries to be made. I.e. you can get answers to questions like 'Which groups have attr1 = value1, and attr3 = value2?'.
@groupNames = $hdf5Obj->getGroupsByAttr( 'attr1' => 'value1', 'attr2' => 'value2' );
Returns information about group attributes defined in the HDF5 datafile.
# Single Attr Usage. Returns an array of all # values of attribute 'attrName' in the file. $hdf5obj->allAttrValues('attrName'); # Multiple Attr Usage. Returns an 2D array of all # values of attributes 'attr1', 'attr2' in the file. # Higher-Level $hdf5obj->allAttrValues('attr1', 'attr2');
Returns a sorted list of all the group attribute names that are defined in the file.
my @attrNames = $hdf5obj->allAttrNames;
Returns the HDF5 library ID for this object
my $ID = $hdf5obj->IDget;
Returns the HDF5 Group Name for this object. (Always '/', i.e. the root group for this top-level object)
my $name = $hdf5obj->nameGet;
PDL::IO::HDF5 Desctructor - Closes the HDF5 file
No Usage. Automatically called
John Cerney, j-cerney1@raytheon.com
EOPM
# Read in a modified hdf.h file. Define # a low-level perl interface to hdf from these definitions. sub create_low_level {
# This file must be modified to only include # hdf5 3 function definitions. # Also, all C function declarations must be on one line. my $defn = shift; my @lines = split (/\n/, $defn);
foreach (@lines) { next if (/^\#/); # Skip commented out lines next if (/^\s*$/); # Skip blank lines my ($return_type, $func_name, $parms) = /^(\w+\**)\s+(\w+)\s*\((.*?)\)\;/; my @parms = split (/,/, $parms); my @vars = (); my @types = (); my %output = (); foreach $parm (@parms) { my ($varname) = ($parm =~ /(\w+)$/); $parm =~ s/$varname$//; # parm now contains the full C type $output{$varname} = 1 if (($parm =~ /\*/) && ($parm !~ /const/)); $parm =~ s/const //; # get rid of 'const' in C type $parm =~ s/^\s+//; $parm =~ s/\s+$//; # pare off the variable type from 'parm' push (@vars, $varname); push (@types, $parm); } my $xsout = ''; $xsout .= "$return_type\n"; $xsout .= "$func_name (" . join (", ", @vars) . ")\n"; for (my $i=0;$i<@vars;$i++) { $xsout .= "\t$types[$i]\t$vars[$i]\n"; } $xsout .= "CODE:\n"; $xsout .= "\tRETVAL = $func_name ("; for (my $i=0;$i<@vars;$i++) { if ($types[$i] =~ /PDL/) { ($type = $types[$i]) =~ s/PDL//; # Get rid of PDL type when writine xs CODE section $xsout .= "($type)$vars[$i]"."->data,"; } else { $xsout .= "$vars[$i],"; } } chop ($xsout) if( $xsout =~ /\,$/s); # remove last comma, if present $xsout .= ");\n"; $xsout .= "OUTPUT:\n"; $xsout .= "\tRETVAL\n"; foreach $var (keys %output) { $xsout .= "\t$var\n"; } $xsout .= "\n\n"; pp_addxs ('', $xsout); }
}
#------------------------------------------------------------------------- # Create low level interface from edited hdr5 header file. #-------------------------------------------------------------------------
create_low_level (<<'EODEF'); # HDF5 Functions we create an interface to using the perl XS code # # Note: H5Gget_objinfo arg statbuf has been changed from a H5G_stat_t type to # a const void type to avoid compilation errors. This function only used # to determine if a group exists, so the statbuf variable is not used as # I/O variable as stated in the HDF5 docs.
hid_t H5Fcreate (const char *name, unsigned flags, hid_t create_id, hid_t access_id); hid_t H5Fopen (const char *name, unsigned flags, hid_t access_id); herr_t H5Fclose (hid_t file_id); # # Dataspace functions hid_t H5Screate_simple (int rank, const hsize_t * dims, const hsize_t * maxdims); herr_t H5Sclose(hid_t space_id); int H5Sget_simple_extent_ndims(hid_t space_id); int H5Sget_simple_extent_dims(hid_t space_id, hsize_t *dims, hsize_t *maxdims); # # # Dataset Functions hid_t H5Dcreate (hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t create_plist_id); hid_t H5Dopen (hid_t loc_id, const char *name); herr_t H5Dwrite (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, const char * buf); # H5Dread buf type changed from void * to I8 * so that is can be catergorized separately in the # typemap as a T_PVI traslation herr_t H5Dread (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t xfer_plist_id, I8 * buf); hid_t H5Dclose (hid_t dataset_id); hid_t H5Dget_type(hid_t dataset_id); hid_t H5Dget_space(hid_t dataset_id);
hid_t H5Gcreate(hid_t loc_id, const char *name, size_t size_hint); hid_t H5Gopen(hid_t loc_id, const char *name); herr_t H5Gclose(hid_t group_id); herr_t H5Gget_objinfo(hid_t loc_id, const char *name, hbool_t follow_link, const void *statbuf); herr_t H5errorOn(); herr_t H5errorOff(); # # Attribute Functions hid_t H5Aopen_name(hid_t loc_id, const char *name); hid_t H5Acreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t create_plist); # Note: attrib write only supports char buffer right now herr_t H5Awrite (hid_t attr_id, hid_t mem_type_id, char * buf); herr_t H5Adelete(hid_t loc_id, const char * name); herr_t H5Aclose(hid_t attr_id); int H5Aget_num_attrs(hid_t loc_id); hid_t H5Aopen_idx(hid_t loc_id, unsigned int idx); ssize_t H5Aget_name(hid_t attr_id, size_t buf_size, char *buf); htri_t H5Sis_simple(hid_t space_id); hid_t H5Aget_space(hid_t attr_id); hid_t H5Aget_type(hid_t attr_id); # The Attrib read only supports char buffer right now herr_t H5Aread(hid_t attr_id, hid_t mem_type_id, char *buf);
# Type Functions: herr_t H5Tset_size(hid_t type_id, size_t size); herr_t H5Tclose(hid_t type_id); hid_t H5Tcopy(hid_t type_id); size_t H5Tget_size(hid_t type_id); #hid_t H5Tget_super(hid_t type); htri_t H5Tequal(hid_t type_id1, hid_t type_id2); H5T_class_t H5Tget_class(hid_t type_id);
EODEF
# Add Optional HDF Constants to export list.
pp_add_exported('', <<'EOPM'); H5F_ACC_DEBUG H5F_ACC_EXCL H5F_ACC_RDONLY H5F_ACC_RDWR H5F_ACC_TRUNC H5P_DEFAULT H5S_ALL H5S_UNLIMITED H5T_ALPHA_B16 H5T_ALPHA_B32 H5T_ALPHA_B64 H5T_ALPHA_B8 H5T_ALPHA_F32 H5T_ALPHA_F64 H5T_ALPHA_I16 H5T_ALPHA_I32 H5T_ALPHA_I64 H5T_ALPHA_I8 H5T_ALPHA_U16 H5T_ALPHA_U32 H5T_ALPHA_U64 H5T_ALPHA_U8 H5T_C_S1 H5T_FORTRAN_S1 H5T_IEEE_F32BE H5T_IEEE_F32LE H5T_IEEE_F64BE H5T_IEEE_F64LE H5T_INTEL_B16 H5T_INTEL_B32 H5T_INTEL_B64 H5T_INTEL_B8 H5T_INTEL_F32 H5T_INTEL_F64 H5T_INTEL_I16 H5T_INTEL_I32 H5T_INTEL_I64 H5T_INTEL_I8 H5T_INTEL_U16 H5T_INTEL_U32 H5T_INTEL_U64 H5T_INTEL_U8 H5T_MIPS_B16 H5T_MIPS_B32 H5T_MIPS_B64 H5T_MIPS_B8 H5T_MIPS_F32 H5T_MIPS_F64 H5T_MIPS_I16 H5T_MIPS_I32 H5T_MIPS_I64 H5T_MIPS_I8 H5T_MIPS_U16 H5T_MIPS_U32 H5T_MIPS_U64 H5T_MIPS_U8 H5T_NATIVE_B16 H5T_NATIVE_B32 H5T_NATIVE_B64 H5T_NATIVE_B8 H5T_NATIVE_CHAR H5T_NATIVE_DOUBLE H5T_NATIVE_FLOAT H5T_NATIVE_HBOOL H5T_NATIVE_HERR H5T_NATIVE_HSIZE H5T_NATIVE_HSSIZE H5T_NATIVE_INT H5T_NATIVE_INT16 H5T_NATIVE_INT32 H5T_NATIVE_INT64 H5T_NATIVE_INT8 H5T_NATIVE_INT_FAST16 H5T_NATIVE_INT_FAST32 H5T_NATIVE_INT_FAST64 H5T_NATIVE_INT_FAST8 H5T_NATIVE_INT_LEAST16 H5T_NATIVE_INT_LEAST32 H5T_NATIVE_INT_LEAST64 H5T_NATIVE_INT_LEAST8 H5T_NATIVE_LDOUBLE H5T_NATIVE_LLONG H5T_NATIVE_LONG H5T_NATIVE_OPAQUE H5T_NATIVE_SCHAR H5T_NATIVE_SHORT H5T_NATIVE_UCHAR H5T_NATIVE_UINT H5T_NATIVE_UINT16 H5T_NATIVE_UINT32 H5T_NATIVE_UINT64 H5T_NATIVE_UINT8 H5T_NATIVE_UINT_FAST16 H5T_NATIVE_UINT_FAST32 H5T_NATIVE_UINT_FAST64 H5T_NATIVE_UINT_FAST8 H5T_NATIVE_UINT_LEAST16 H5T_NATIVE_UINT_LEAST32 H5T_NATIVE_UINT_LEAST64 H5T_NATIVE_UINT_LEAST8 H5T_NATIVE_ULLONG H5T_NATIVE_ULONG H5T_NATIVE_USHORT H5T_STD_B16BE H5T_STD_B16LE H5T_STD_B32BE H5T_STD_B32LE H5T_STD_B64BE H5T_STD_B64LE H5T_STD_B8BE H5T_STD_B8LE H5T_STD_I16BE H5T_STD_I16LE H5T_STD_I32BE H5T_STD_I32LE H5T_STD_I64BE H5T_STD_I64LE H5T_STD_I8BE H5T_STD_I8LE H5T_STD_REF_DSETREG H5T_STD_REF_OBJ H5T_STD_U16BE H5T_STD_U16LE H5T_STD_U32BE H5T_STD_U32LE H5T_STD_U64BE H5T_STD_U64LE H5T_STD_U8BE H5T_STD_U8LE H5T_STRING H5T_UNIX_D32BE H5T_UNIX_D32LE H5T_UNIX_D64BE H5T_UNIX_D64LE EOPM
############################################################### # XS Code that implements self-contained turn-on/off for # the h5 library error reporting. We can turn error reporting # selectively on and off to keep the library from complaining # when we are doing things like checking to see if a particular # group name exists.
pp_addhdr(<<'EOXS');
/* ############################################################### # # H5 Library error reporting turn-on/off functions # # */ herr_t H5errorOff() { return H5Eset_auto(NULL, NULL ); }
herr_t H5errorOn() { return H5Eset_auto((herr_t(*)(void*))H5Eprint, stderr ); }
/* ############################################################### # # Operator Interation Functions (Supplied to and called by 'H5Giterate') # used to get the number of datasets in a group, # and the names of the dataset in the group.
# # */ /* * Operator function to get number of datasets */ herr_t incIfDset(hid_t loc_id, const char *name, void *opdata) { H5G_stat_t statbuf; unsigned int * dsetCount;
dsetCount = (unsigned int *) opdata; /* * Get type of the object and increment *dsetCount * if it is a dataset * The name of the object is passed to this function by * the Library. Some magic :-) */ H5Gget_objinfo(loc_id, name, FALSE, &statbuf); if( statbuf.type == H5G_DATASET){ (*dsetCount)++; } return 0; }
/* * Operator function to fill up char array of dataset names * * opdata is a pointer to an Array of strings (i.e. 2D char array) */ herr_t getName_if_Dset(hid_t loc_id, const char *name, void *opdata) { H5G_stat_t statbuf; char ** datasetName;
char *** tempptr; tempptr = (char ***) opdata; datasetName = *tempptr; /* * Get type of the object. * If it is a dataset, get allocate space for it at *datasetName * Increment *tempptr so we will be looking at the next name space when * this function is called again. * * Note: The calling function must take care of freeing memory allocateed * */ H5Gget_objinfo(loc_id, name, FALSE, &statbuf); if( statbuf.type == H5G_DATASET){ *datasetName = (char *) malloc( (strlen(name)+1) * sizeof(char)); if( *datasetName == NULL){ printf("PDL::IO::HDF5; Out of Memory in getName_if_Dset\n"); exit(1); } strcpy(*datasetName,name); (*tempptr)++; } return 0; }
/* * Operator function to get number of groups in a particular location */ herr_t incIfGroup(hid_t loc_id, const char *name, void *opdata) { H5G_stat_t statbuf; unsigned int * groupCount;
groupCount = (unsigned int *) opdata; /* * Get type of the object and increment *groupCount * if it is a group * The name of the object is passed to this function by * the Library. Some magic :-) */ H5Gget_objinfo(loc_id, name, FALSE, &statbuf); if( statbuf.type == H5G_GROUP){ (*groupCount)++; } return 0; }
/* * Operator function to fill up char array of group names * * opdata is a pointer to an Array of strings (i.e. 2D char array) */ herr_t getName_if_Group(hid_t loc_id, const char *name, void *opdata) { H5G_stat_t statbuf; char ** groupName;
char *** tempptr; tempptr = (char ***) opdata; groupName = *tempptr; /* * Get type of the object. * If it is a group, get allocate space for it at *groupName * Increment *tempptr so we will be looking at the next name space when * this function is called again. * * Note: The calling function must take care of freeing memory allocateed * */ H5Gget_objinfo(loc_id, name, FALSE, &statbuf); if( statbuf.type == H5G_GROUP){ *groupName = (char *) malloc( (strlen(name)+1) * sizeof(char)); if( *groupName == NULL){ printf("PDL::IO::HDF5; Out of Memory in getName_if_Group\n"); exit(1); } strcpy(*groupName,name); (*tempptr)++; } return 0; } EOXS ############################################################### # XS Code that implements the HDF constants # Using the AUTOLOAD routine, any calls to hdf5 constants, like # H5F_ACC_RDONLY will call the 'constant' routine here and return # the value of the #defined'ed H5F_ACC_RDONLY
/* ############################################################### # # Functions to handle interfacing HDF5 constants with perl # # This originally generated using h2xs and manually editing # */ static int not_here(s) char *s; { croak("%s not implemented on this architecture", s); return -1; }
double constant(name, arg) char *name; int arg; { errno = 0; switch (*name) { case 'A': break; case 'B': break; case 'C': break; case 'D': break; case 'E': break; case 'F': break; case 'G': break; case 'H': if (strEQ(name, "H5F_ACC_DEBUG")) #ifdef H5F_ACC_DEBUG return H5F_ACC_DEBUG; #else goto not_there; #endif if (strEQ(name, "H5F_ACC_EXCL")) #ifdef H5F_ACC_EXCL return H5F_ACC_EXCL; #else goto not_there; #endif if (strEQ(name, "H5F_ACC_RDONLY")) #ifdef H5F_ACC_RDONLY return H5F_ACC_RDONLY; #else goto not_there; #endif if (strEQ(name, "H5F_ACC_RDWR")) #ifdef H5F_ACC_RDWR return H5F_ACC_RDWR; #else goto not_there; #endif if (strEQ(name, "H5F_ACC_TRUNC")) #ifdef H5F_ACC_TRUNC return H5F_ACC_TRUNC; #else goto not_there; #endif if (strEQ(name, "H5P_DEFAULT")) #ifdef H5P_DEFAULT return H5P_DEFAULT; #else goto not_there; #endif if (strEQ(name, "H5S_ALL")) #ifdef H5S_ALL return H5S_ALL; #else goto not_there; #endif if (strEQ(name, "H5S_UNLIMITED")) #ifdef H5S_UNLIMITED return H5S_UNLIMITED; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_B16")) #ifdef H5T_ALPHA_B16 return H5T_ALPHA_B16; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_B32")) #ifdef H5T_ALPHA_B32 return H5T_ALPHA_B32; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_B64")) #ifdef H5T_ALPHA_B64 return H5T_ALPHA_B64; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_B8")) #ifdef H5T_ALPHA_B8 return H5T_ALPHA_B8; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_F32")) #ifdef H5T_ALPHA_F32 return H5T_ALPHA_F32; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_F64")) #ifdef H5T_ALPHA_F64 return H5T_ALPHA_F64; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_I16")) #ifdef H5T_ALPHA_I16 return H5T_ALPHA_I16; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_I32")) #ifdef H5T_ALPHA_I32 return H5T_ALPHA_I32; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_I64")) #ifdef H5T_ALPHA_I64 return H5T_ALPHA_I64; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_I8")) #ifdef H5T_ALPHA_I8 return H5T_ALPHA_I8; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_U16")) #ifdef H5T_ALPHA_U16 return H5T_ALPHA_U16; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_U32")) #ifdef H5T_ALPHA_U32 return H5T_ALPHA_U32; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_U64")) #ifdef H5T_ALPHA_U64 return H5T_ALPHA_U64; #else goto not_there; #endif if (strEQ(name, "H5T_ALPHA_U8")) #ifdef H5T_ALPHA_U8 return H5T_ALPHA_U8; #else goto not_there; #endif if (strEQ(name, "H5T_C_S1")) #ifdef H5T_C_S1 return H5T_C_S1; #else goto not_there; #endif if (strEQ(name, "H5T_FORTRAN_S1")) #ifdef H5T_FORTRAN_S1 return H5T_FORTRAN_S1; #else goto not_there; #endif if (strEQ(name, "H5T_IEEE_F32BE")) #ifdef H5T_IEEE_F32BE return H5T_IEEE_F32BE; #else goto not_there; #endif if (strEQ(name, "H5T_IEEE_F32LE")) #ifdef H5T_IEEE_F32LE return H5T_IEEE_F32LE; #else goto not_there; #endif if (strEQ(name, "H5T_IEEE_F64BE")) #ifdef H5T_IEEE_F64BE return H5T_IEEE_F64BE; #else goto not_there; #endif if (strEQ(name, "H5T_IEEE_F64LE")) #ifdef H5T_IEEE_F64LE return H5T_IEEE_F64LE; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_B16")) #ifdef H5T_INTEL_B16 return H5T_INTEL_B16; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_B32")) #ifdef H5T_INTEL_B32 return H5T_INTEL_B32; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_B64")) #ifdef H5T_INTEL_B64 return H5T_INTEL_B64; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_B8")) #ifdef H5T_INTEL_B8 return H5T_INTEL_B8; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_F32")) #ifdef H5T_INTEL_F32 return H5T_INTEL_F32; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_F64")) #ifdef H5T_INTEL_F64 return H5T_INTEL_F64; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_I16")) #ifdef H5T_INTEL_I16 return H5T_INTEL_I16; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_I32")) #ifdef H5T_INTEL_I32 return H5T_INTEL_I32; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_I64")) #ifdef H5T_INTEL_I64 return H5T_INTEL_I64; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_I8")) #ifdef H5T_INTEL_I8 return H5T_INTEL_I8; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_U16")) #ifdef H5T_INTEL_U16 return H5T_INTEL_U16; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_U32")) #ifdef H5T_INTEL_U32 return H5T_INTEL_U32; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_U64")) #ifdef H5T_INTEL_U64 return H5T_INTEL_U64; #else goto not_there; #endif if (strEQ(name, "H5T_INTEL_U8")) #ifdef H5T_INTEL_U8 return H5T_INTEL_U8; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_B16")) #ifdef H5T_MIPS_B16 return H5T_MIPS_B16; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_B32")) #ifdef H5T_MIPS_B32 return H5T_MIPS_B32; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_B64")) #ifdef H5T_MIPS_B64 return H5T_MIPS_B64; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_B8")) #ifdef H5T_MIPS_B8 return H5T_MIPS_B8; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_F32")) #ifdef H5T_MIPS_F32 return H5T_MIPS_F32; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_F64")) #ifdef H5T_MIPS_F64 return H5T_MIPS_F64; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_I16")) #ifdef H5T_MIPS_I16 return H5T_MIPS_I16; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_I32")) #ifdef H5T_MIPS_I32 return H5T_MIPS_I32; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_I64")) #ifdef H5T_MIPS_I64 return H5T_MIPS_I64; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_I8")) #ifdef H5T_MIPS_I8 return H5T_MIPS_I8; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_U16")) #ifdef H5T_MIPS_U16 return H5T_MIPS_U16; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_U32")) #ifdef H5T_MIPS_U32 return H5T_MIPS_U32; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_U64")) #ifdef H5T_MIPS_U64 return H5T_MIPS_U64; #else goto not_there; #endif if (strEQ(name, "H5T_MIPS_U8")) #ifdef H5T_MIPS_U8 return H5T_MIPS_U8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_B16")) #ifdef H5T_NATIVE_B16 return H5T_NATIVE_B16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_B32")) #ifdef H5T_NATIVE_B32 return H5T_NATIVE_B32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_B64")) #ifdef H5T_NATIVE_B64 return H5T_NATIVE_B64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_B8")) #ifdef H5T_NATIVE_B8 return H5T_NATIVE_B8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_CHAR")) #ifdef H5T_NATIVE_CHAR return H5T_NATIVE_CHAR; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_DOUBLE")) #ifdef H5T_NATIVE_DOUBLE return H5T_NATIVE_DOUBLE; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_FLOAT")) #ifdef H5T_NATIVE_FLOAT return H5T_NATIVE_FLOAT; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_HBOOL")) #ifdef H5T_NATIVE_HBOOL return H5T_NATIVE_HBOOL; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_HERR")) #ifdef H5T_NATIVE_HERR return H5T_NATIVE_HERR; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_HSIZE")) #ifdef H5T_NATIVE_HSIZE return H5T_NATIVE_HSIZE; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_HSSIZE")) #ifdef H5T_NATIVE_HSSIZE return H5T_NATIVE_HSSIZE; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT")) #ifdef H5T_NATIVE_INT return H5T_NATIVE_INT; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT16")) #ifdef H5T_NATIVE_INT16 return H5T_NATIVE_INT16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT32")) #ifdef H5T_NATIVE_INT32 return H5T_NATIVE_INT32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT64")) #ifdef H5T_NATIVE_INT64 return H5T_NATIVE_INT64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT8")) #ifdef H5T_NATIVE_INT8 return H5T_NATIVE_INT8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_FAST16")) #ifdef H5T_NATIVE_INT_FAST16 return H5T_NATIVE_INT_FAST16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_FAST32")) #ifdef H5T_NATIVE_INT_FAST32 return H5T_NATIVE_INT_FAST32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_FAST64")) #ifdef H5T_NATIVE_INT_FAST64 return H5T_NATIVE_INT_FAST64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_FAST8")) #ifdef H5T_NATIVE_INT_FAST8 return H5T_NATIVE_INT_FAST8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_LEAST16")) #ifdef H5T_NATIVE_INT_LEAST16 return H5T_NATIVE_INT_LEAST16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_LEAST32")) #ifdef H5T_NATIVE_INT_LEAST32 return H5T_NATIVE_INT_LEAST32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_LEAST64")) #ifdef H5T_NATIVE_INT_LEAST64 return H5T_NATIVE_INT_LEAST64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_INT_LEAST8")) #ifdef H5T_NATIVE_INT_LEAST8 return H5T_NATIVE_INT_LEAST8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_LDOUBLE")) #ifdef H5T_NATIVE_LDOUBLE return H5T_NATIVE_LDOUBLE; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_LLONG")) #ifdef H5T_NATIVE_LLONG return H5T_NATIVE_LLONG; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_LONG")) #ifdef H5T_NATIVE_LONG return H5T_NATIVE_LONG; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_OPAQUE")) #ifdef H5T_NATIVE_OPAQUE return H5T_NATIVE_OPAQUE; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_SCHAR")) #ifdef H5T_NATIVE_SCHAR return H5T_NATIVE_SCHAR; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_SHORT")) #ifdef H5T_NATIVE_SHORT return H5T_NATIVE_SHORT; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UCHAR")) #ifdef H5T_NATIVE_UCHAR return H5T_NATIVE_UCHAR; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT")) #ifdef H5T_NATIVE_UINT return H5T_NATIVE_UINT; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT16")) #ifdef H5T_NATIVE_UINT16 return H5T_NATIVE_UINT16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT32")) #ifdef H5T_NATIVE_UINT32 return H5T_NATIVE_UINT32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT64")) #ifdef H5T_NATIVE_UINT64 return H5T_NATIVE_UINT64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT8")) #ifdef H5T_NATIVE_UINT8 return H5T_NATIVE_UINT8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_FAST16")) #ifdef H5T_NATIVE_UINT_FAST16 return H5T_NATIVE_UINT_FAST16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_FAST32")) #ifdef H5T_NATIVE_UINT_FAST32 return H5T_NATIVE_UINT_FAST32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_FAST64")) #ifdef H5T_NATIVE_UINT_FAST64 return H5T_NATIVE_UINT_FAST64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_FAST8")) #ifdef H5T_NATIVE_UINT_FAST8 return H5T_NATIVE_UINT_FAST8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_LEAST16")) #ifdef H5T_NATIVE_UINT_LEAST16 return H5T_NATIVE_UINT_LEAST16; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_LEAST32")) #ifdef H5T_NATIVE_UINT_LEAST32 return H5T_NATIVE_UINT_LEAST32; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_LEAST64")) #ifdef H5T_NATIVE_UINT_LEAST64 return H5T_NATIVE_UINT_LEAST64; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_UINT_LEAST8")) #ifdef H5T_NATIVE_UINT_LEAST8 return H5T_NATIVE_UINT_LEAST8; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_ULLONG")) #ifdef H5T_NATIVE_ULLONG return H5T_NATIVE_ULLONG; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_ULONG")) #ifdef H5T_NATIVE_ULONG return H5T_NATIVE_ULONG; #else goto not_there; #endif if (strEQ(name, "H5T_NATIVE_USHORT")) #ifdef H5T_NATIVE_USHORT return H5T_NATIVE_USHORT; #else goto not_there; #endif if (strEQ(name, "H5T_STRING")) return H5T_STRING; /* This was manually enter to get the enumerated type */ if (strEQ(name, "H5T_STD_B16BE")) #ifdef H5T_STD_B16BE return H5T_STD_B16BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B16LE")) #ifdef H5T_STD_B16LE return H5T_STD_B16LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B32BE")) #ifdef H5T_STD_B32BE return H5T_STD_B32BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B32LE")) #ifdef H5T_STD_B32LE return H5T_STD_B32LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B64BE")) #ifdef H5T_STD_B64BE return H5T_STD_B64BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B64LE")) #ifdef H5T_STD_B64LE return H5T_STD_B64LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B8BE")) #ifdef H5T_STD_B8BE return H5T_STD_B8BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_B8LE")) #ifdef H5T_STD_B8LE return H5T_STD_B8LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I16BE")) #ifdef H5T_STD_I16BE return H5T_STD_I16BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I16LE")) #ifdef H5T_STD_I16LE return H5T_STD_I16LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I32BE")) #ifdef H5T_STD_I32BE return H5T_STD_I32BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I32LE")) #ifdef H5T_STD_I32LE return H5T_STD_I32LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I64BE")) #ifdef H5T_STD_I64BE return H5T_STD_I64BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I64LE")) #ifdef H5T_STD_I64LE return H5T_STD_I64LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I8BE")) #ifdef H5T_STD_I8BE return H5T_STD_I8BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_I8LE")) #ifdef H5T_STD_I8LE return H5T_STD_I8LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_REF_DSETREG")) #ifdef H5T_STD_REF_DSETREG return H5T_STD_REF_DSETREG; #else goto not_there; #endif if (strEQ(name, "H5T_STD_REF_OBJ")) #ifdef H5T_STD_REF_OBJ return H5T_STD_REF_OBJ; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U16BE")) #ifdef H5T_STD_U16BE return H5T_STD_U16BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U16LE")) #ifdef H5T_STD_U16LE return H5T_STD_U16LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U32BE")) #ifdef H5T_STD_U32BE return H5T_STD_U32BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U32LE")) #ifdef H5T_STD_U32LE return H5T_STD_U32LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U64BE")) #ifdef H5T_STD_U64BE return H5T_STD_U64BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U64LE")) #ifdef H5T_STD_U64LE return H5T_STD_U64LE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U8BE")) #ifdef H5T_STD_U8BE return H5T_STD_U8BE; #else goto not_there; #endif if (strEQ(name, "H5T_STD_U8LE")) #ifdef H5T_STD_U8LE return H5T_STD_U8LE; #else goto not_there; #endif if (strEQ(name, "H5T_UNIX_D32BE")) #ifdef H5T_UNIX_D32BE return H5T_UNIX_D32BE; #else goto not_there; #endif if (strEQ(name, "H5T_UNIX_D32LE")) #ifdef H5T_UNIX_D32LE return H5T_UNIX_D32LE; #else goto not_there; #endif if (strEQ(name, "H5T_UNIX_D64BE")) #ifdef H5T_UNIX_D64BE return H5T_UNIX_D64BE; #else goto not_there; #endif if (strEQ(name, "H5T_UNIX_D64LE")) #ifdef H5T_UNIX_D64LE return H5T_UNIX_D64LE; #else goto not_there; #endif break; case 'I': break; case 'J': break; case 'K': break; case 'L': break; case 'M': break; case 'N': break; case 'O': break; case 'P': break; case 'Q': break; case 'R': break; case 'S': break; case 'T': break; case 'U': break; case 'V': break; case 'W': break; case 'X': break; case 'Y': break; case 'Z': break; } errno = EINVAL; return 0;
not_there: errno = ENOENT; return 0; }
/* ############################################################# */ EOXS
pp_addxs('',<<'EOXS');
double constant(name,arg) char * name int arg
EOXS ############### Add Autoload Routine for the hdf5 constants ##########
pp_addpm( {At => Top}, <<'EOPM');
use PDL::Lite; use PDL::Char;
use PDL::IO::HDF5::Group;
# Require needed here becuase dataset uses some of the XS # calls that are defined in PDL::IO::HDF5 (like PDL::IO::HDF5::H5T_NATIVE_CHAR() ) # Doing a 'use' would make use of the calls before they are defined. # require PDL::IO::HDF5::Dataset;
use Carp;
sub AUTOLOAD { # This AUTOLOAD is used to 'autoload' constants from the constant() # XS function. If a constant is not found then control is passed # to the AUTOLOAD in AutoLoader.
my $constname; ($constname = $AUTOLOAD) =~ s/.*:://; croak "& not defined" if $constname eq 'constant'; my $val = constant($constname, @_ ? $_[0] : 0); if ($! != 0) { if ($! =~ /Invalid/) { $AutoLoader::AUTOLOAD = $AUTOLOAD; goto &AutoLoader::AUTOLOAD; } else { croak "Your vendor has not defined hdf5 macro $constname"; } } *$AUTOLOAD = sub { $val }; goto &$AUTOLOAD; } EOPM
# Code that implements the dataset count and dataset name functions pp_addxs('',<<'EOXS');
# Code to get the number of datasets in a group
int H5GgetDatasetCount( groupID, groupName ) hid_t groupID char * groupName CODE: int dsetCount = 0; H5Giterate(groupID, groupName, NULL, incIfDset, &dsetCount); RETVAL = dsetCount; OUTPUT: RETVAL
# Code to get the names of the datasets in a group
void H5GgetDatasetNames( groupID, groupName ) hid_t groupID char * groupName PREINIT: int dsetCount = 0; char ** datasetNames; /* Array of dataset names */ char ** datasetPtr; /* temp pointer to datasetNames */ int i; /* Index variable */ PPCODE: /* Get the number of datasets */ H5Giterate(groupID, groupName, NULL, incIfDset, &dsetCount);
if( dsetCount > 0){ /* Datasets found */ /* Allocate Space for array of strings */ datasetNames = (char **) malloc( dsetCount * sizeof(char *)); if( datasetNames == NULL){ printf("PDL::IO::HDF5; out of Memory in H5GgetDatasetNames\n"); exit(1); } datasetPtr = datasetNames; H5Giterate(groupID, groupName, NULL, getName_if_Dset, &datasetPtr); EXTEND(SP, dsetCount); /* Make room for results on the return stack */ for( i = 0; i< dsetCount; i++){ /* Push Names onto return stack */ /* printf("Name found = '%s'\n",datasetNames[i]); */ PUSHs(sv_2mortal(newSVpv(datasetNames[i],0))); free(datasetNames[i]); /* Release Memory */ } free(datasetNames); }
# Code to get the number of groups in a group/file
int H5GgetGroupCount( groupID, groupName ) hid_t groupID char * groupName CODE: int groupCount = 0; H5Giterate(groupID, groupName, NULL, incIfGroup, &groupCount); RETVAL = groupCount; OUTPUT: RETVAL
# Code to get the names of the groups in a group/file
void H5GgetGroupNames( groupID, groupName ) hid_t groupID char * groupName PREINIT: int groupCount = 0; char ** groupNames; /* Array of group names */ char ** groupPtr; /* temp pointer to groupnames */ int i; /* Index variable */ PPCODE: /* Get the number of datasets */ H5Giterate(groupID, groupName, NULL, incIfGroup, &groupCount);
if( groupCount > 0){ /* Groups found */ /* Allocate Space for array of strings */ groupNames = (char **) malloc( groupCount * sizeof(char *)); if( groupNames == NULL){ printf("PDL::IO::HDF5; out of Memory in H5GgetGroupNames\n"); exit(1); } groupPtr = groupNames; H5Giterate(groupID, groupName, NULL, getName_if_Group, &groupPtr); EXTEND(SP, groupCount); /* Make room for results on the return stack */ for( i = 0; i< groupCount; i++){ /* Push Names onto return stack */ /* printf("Name found = '%s'\n",datasetNames[i]); */ PUSHs(sv_2mortal(newSVpv(groupNames[i],0))); free(groupNames[i]); /* Release Memory */ } free(groupNames); }
EOXS
# Don't import anything from core but barf # (Don't wan't to pollute our namespace) pp_core_importList(' qw/ barf/'); # set to not export anything. (This is a OO package, it doesn't need to export any methods.) pp_export_nothing;
pp_done();
To install PDL::IO::HDF5::Group, copy and paste the appropriate command in to your terminal.
cpanm
cpanm PDL::IO::HDF5::Group
CPAN shell
perl -MCPAN -e shell install PDL::IO::HDF5::Group
For more information on module installation, please visit the detailed CPAN module installation guide.