package PDL::IO::HDF5::Group; use Carp; use strict; =head1 NAME PDL::IO::HDF5::Group - PDL::IO::HDF5 Helper Object representing HDF5 groups. =head1 DESCRIPTION This is a helper-object used by PDL::IO::HDF5 to interface with HDF5 format's group objects. Information on the HDF5 Format can be found at the HDF Group's web site at http://www.hdfgroup.org . =head1 SYNOPSIS See L =head1 MEMBER DATA =over 1 =item ID ID number given to the group by the HDF5 library =item name Name of the group. (Absolute to the root group '/'. e.g. /maingroup/subgroup) =item parent Ref to parent object (file or group) that owns this group. =item fileObj Ref to the L object that owns this object. =back =head1 METHODS =head2 new =for ref PDL::IO::HDF5::Group Constructor - creates new object B =for usage This object will usually be created using the calling format detailed in the L. The following syntax is used by the L object to build the object. $a = new PDL::IO::HDF5:Group( name => $name, parent => $parent, fileObj => $fileObj ); Args: $name Name of the group (relative to the parent) $parent Parent Object that owns this group $fileObj PDL::HDF (Top Level) object that owns this group. =cut sub new{ my $type = shift; my %parms = @_; my $self = {}; my @DataMembers = qw( name parent fileObj); my %DataMembers; @DataMembers{ @DataMembers } = @DataMembers; # hash for quick lookup # check for proper supplied names: my $varName; foreach $varName(keys %parms){ unless( defined($DataMembers{$varName})){ carp("Error Calling ".__PACKAGE__." Constuctor\n \'$varName\' not a valid data member\n"); return undef; } $self->{$varName} = $parms{$varName}; } my $parent = $self->{parent}; my $parentID = $parent->IDget; my $parentName = $parent->nameGet; my $groupName = $self->{name}; my $groupID; # Adjust groupname to be absolute: if( $parentName ne '/') { # Parent is not the root group $self->{name} = "$parentName/$groupName"; } else{ # Parent is root group $self->{name} = "$parentName$groupName"; } # Turn Error Reporting off for the following, so H5 lib doesn't complain # if the group isn't found. PDL::IO::HDF5::H5errorOff(); my $rc = PDL::IO::HDF5::H5Gget_objinfo($parentID, $groupName,1,0); PDL::IO::HDF5::H5errorOn(); # See if the group exists: if( $rc >= 0){ #Group Exists open it: $groupID = PDL::IO::HDF5::H5Gopen($parentID, $groupName); } else{ # group didn't exist, create it: $groupID = PDL::IO::HDF5::H5Gcreate($parentID, $groupName, 0); # Clear-out the attribute index, it is no longer valid with the updates # we just made. $self->{fileObj}->clearAttrIndex; } # Try Opening the Group First (Assume it already exists) if($groupID < 0 ){ carp "Error Calling ".__PACKAGE__." Constuctor: Can't open or create group '$groupName'\n"; return undef; } $self->{ID} = $groupID; bless $self, $type; return $self; } =head2 DESTROY =for ref PDL::IO::HDF5 Destructor - Closes the HDF5::Group Object. B =for usage No Usage. Automatically called =cut sub DESTROY { my $self = shift; #print "In Group Destroy\n"; if( PDL::IO::HDF5::H5Gclose($self->{ID}) < 0){ warn("Error closing HDF5 Group '".$self->{name}."' in file '".$self->{parentName}."'\n"); } } =head2 attrSet =for ref Set the value of an attribute(s) Supports null-terminated strings, integers and floating point scalar and 1D array attributes. B =for usage $group->attrSet( 'attr1' => 'attr1Value', 'attr2' => 'attr2 value', 'attr3' => $pdl, . . . ); Returns undef on failure, 1 on success. =cut sub attrSet { my $self = shift; # Attribute setting for groups is exactly like datasets # Call datasets directly (This breaks OO inheritance, but is # better than duplicating code from the dataset object here return $self->PDL::IO::HDF5::Dataset::attrSet(@_); } =head2 attrGet =for ref Get the value of an attribute(s) Supports null-terminated strings, integer and floating point scalar and 1D array attributes. B =for usage my @attrs = $group->attrGet( 'attr1', 'attr2'); =cut sub attrGet { my $self = shift; # Attribute reading for groups is exactly like datasets # Call datasets directly (This breaks OO inheritance, but is # better than duplicating code from the dataset object here return $self->PDL::IO::HDF5::Dataset::attrGet(@_); } =head2 attrDel =for ref Delete attribute(s) B =for usage $group->attrDel( 'attr1', 'attr2', . . . ); Returns undef on failure, 1 on success. =cut sub attrDel { my $self = shift; my @attrs = @_; # get atribute names my $groupID = $self->{ID}; my $attr; my $rc; #Return code returned by H5Adelete foreach $attr( @attrs ){ # Note: We don't consider errors here as cause for aborting, we just # complain using carp if( PDL::IO::HDF5::H5Adelete($groupID, $attr) < 0){ carp "Error in ".__PACKAGE__." attrDel; Error Deleting attribute '$attr'\n"; } } # Clear-out the attribute index, it is no longer valid with the updates # we just made. $self->{fileObj}->clearAttrIndex; return 1; } =head2 attrs =for ref Get a list of all attribute names in a group B =for usage @attrs = $group->attrs; =cut sub attrs { my $self = shift; my $groupID = $self->{ID}; my $defaultMaxSize = 256; # default max size of a attribute name my $noAttr = PDL::IO::HDF5::H5Aget_num_attrs($groupID); # get the number of attributes my $attrIndex = 0; # attribute Index my @attrNames = (); my $attributeID; my $attrNameSize; # size of the attribute name my $attrName; # attribute name # Go thru each attribute and get the name for( $attrIndex = 0; $attrIndex < $noAttr; $attrIndex++){ $attributeID = PDL::IO::HDF5::H5Aopen_idx($groupID, $attrIndex ); if( $attributeID < 0){ carp "Error in ".__PACKAGE__." attrs; Error Opening attribute number $attrIndex\n"; next; } #init attrname to 256 length string (Maybe this not necessary with # the typemap) $attrName = ' ' x 256; # Get the name $attrNameSize = PDL::IO::HDF5::H5Aget_name($attributeID, 256, $attrName ); # If the name is greater than 256, try again with the proper size: if( $attrNameSize > 256 ){ $attrName = ' ' x $attrNameSize; $attrNameSize = PDL::IO::HDF5::H5Aget_name($attributeID, $attrNameSize, $attrName ); } push @attrNames, $attrName; # Close the attr: PDL::IO::HDF5::H5Aclose($attributeID); } return @attrNames; } =head2 dataset =for ref Open an existing or create a new dataset in a group. B =for usage $dataset = $group->dataset('newdataset'); Returns undef on failure, 1 on success. =cut sub dataset { my $self = shift; my $name = $_[0]; my $groupID = $self->{ID}; # get the group name of the current group my $dataset = PDL::IO::HDF5::Dataset->new( name=> $name, parent => $self, fileObj => $self->{fileObj} ); } =head2 datasets =for ref Get a list of all dataset names in a group. (Relative to the current group) B =for usage @datasets = $group->datasets; =cut sub datasets { my $self = shift; my $groupID = $self->{ID}; my @totalDatasets = PDL::IO::HDF5::H5GgetDatasetNames($groupID,"."); return @totalDatasets; } =head2 group =for ref Open an existing or create a new group in an existing group. B =for usage $newgroup = $oldgroup->group("newgroup"); Returns undef on failure, 1 on success. =cut sub group { my $self = shift; my $name = $_[0]; # get the group name my $group = new PDL::IO::HDF5::Group( name=> $name, parent => $self, fileObj => $self->{fileObj} ); return $group; } =head2 groups =for ref Get a list of all group names in a group. (Relative to the current group) B =for usage @groupNames = $group->groups; =cut sub groups { my $self = shift; my $groupID = $self->{ID}; my @totalgroups = PDL::IO::HDF5::H5GgetGroupNames($groupID,'.'); return @totalgroups; } =head2 _buildAttrIndex =for ref Internal Recursive Method to build the attribute index hash for the object For the purposes of indexing groups by their attributes, the attributes are applied hierarchial. i.e. any attributes of the higher level groups are assumed to be apply for the lower level groups. B =for usage $group->_buildAttrIndex($index, $currentAttrs); Input/Output: $index: Total Index hash ref $currentAttrs: Hash refs of the attributes valid for the current group. =cut sub _buildAttrIndex{ my ($self, $index, $currentAttrs) = @_; # Take care of any attributes in the current group my @attrs = $self->attrs; my @attrValues = $self->attrGet(@attrs); # Get the group name my $groupName = $self->nameGet; my %indexElement; # element of the index for this group %indexElement = %$currentAttrs; # Initialize index element # with attributes valid at the # group above # Add (or overwrite) attributes for this group # i.e. local group attributes take precedence over # higher-level attributes @indexElement{@attrs} = @attrValues; $index->{$groupName} = \%indexElement; # Now Do any subgroups: my @subGroups = $self->groups; my $subGroup; foreach $subGroup(@subGroups){ $self->group($subGroup)->_buildAttrIndex($index,\%indexElement); } } =head2 IDget =for ref Returns the HDF5 library ID for this object B =for usage my $ID = $groupObj->IDget; =cut sub IDget{ my $self = shift; return $self->{ID}; } =head2 nameGet =for ref Returns the HDF5 Group Name for this object. (Relative to the root group) B =for usage my $name = $groupObj->nameGet; =cut sub nameGet{ my $self = shift; return $self->{name}; } ####--------------------------------------------------------- =head2 reference =for ref Creates a reference to a region of a dataset. B =for usage $groupObj->reference($referenceName,$datasetObj,@regionStart,@regionCount); Create a reference named $referenceName within the group $groupObj to a subroutine of the dataset $datasetObj. The region to be referenced is defined by the @regionStart and @regionCount arrays. =cut sub reference{ my $self = shift; my $datasetObj = shift; my $referenceName = shift; my @regionStart = shift; my @regionCount = shift; # Get the dataset ID. my $dataSubsetID = $datasetObj->IDget; # Get the dataspace of the dataset. my $dataSubsetSpaceID = PDL::IO::HDF5::H5Dget_space($dataSubsetID); if( $dataSubsetSpaceID <= 0 ){ carp("Can't get dataspacein ".__PACKAGE__.":reference\n"); return undef; } # Select a hyperslab from this dataspace. my $Ndims = $#regionStart+1; my $start = new PDL @regionStart; my $length = new PDL @regionCount; my $start2 = PDL::IO::HDF5::packList(reverse($start->list)); my $length2 = PDL::IO::HDF5::packList(reverse($length->list)); my $stride = PDL::Core::ones($Ndims); my $stride2 = PDL::IO::HDF5::packList(reverse($stride->list)); my $block = PDL::Core::ones($Ndims); my $block2 = PDL::IO::HDF5::packList(reverse($block->list)); my $rc = PDL::IO::HDF5::H5Sselect_hyperslab($dataSubsetSpaceID,0,$start2,$stride2,$length2,$block2); if ( $rc < 0 ) { carp("Error slicing data space in ".__PACKAGE__.":reference\n"); carp("Can't close DataSpace in ".__PACKAGE__.":reference\n") if( PDL::IO::HDF5::H5Sclose($dataSubsetSpaceID) < 0); return undef; } # Create a dataspace for the reference dataset. my $dataspaceID = PDL::IO::HDF5::H5Screate_simple(0,0,0); if( $dataspaceID < 0 ){ carp("Can't Open Dataspace in ".__PACKAGE__.":reference\n"); return undef; } # Create the reference dataset. my $dataSetID = PDL::IO::HDF5::H5Dcreate($self->{ID},$referenceName, PDL::IO::HDF5::H5T_STD_REF_DSETREG(), $dataspaceID, PDL::IO::HDF5::H5P_DEFAULT()); if( $dataSetID < 0){ carp("Can't Create Dataset in ".__PACKAGE__.":reference\n"); return undef; } # Create the reference. my $howBig = PDL::IO::HDF5::H5Tget_size(PDL::IO::HDF5::H5T_STD_REF_DSETREG()); my $datasetReference = ' ' x $howBig; if ( PDL::IO::HDF5::H5Rcreate($datasetReference,$datasetObj->{parent}->{ID},$datasetObj->{name},PDL::IO::HDF5::H5R_DATASET_REGION(),$dataSubsetSpaceID) < 0 ) { carp("Can't Create Reference Dataset in ".__PACKAGE__.":reference\n"); return undef; } # Write the reference dataset. if( PDL::IO::HDF5::H5Dwrite($dataSetID,PDL::IO::HDF5::H5T_STD_REF_DSETREG(),PDL::IO::HDF5::H5S_ALL(),PDL::IO::HDF5::H5S_ALL(),PDL::IO::HDF5::H5P_DEFAULT(),$datasetReference) < 0 ){ carp("Error Writing to dataset in ".__PACKAGE__.":reference\n"); return undef; } # Close the dataset dataspace. PDL::IO::HDF5::H5Sclose($dataspaceID); PDL::IO::HDF5::H5Sclose($dataSubsetSpaceID); PDL::IO::HDF5::H5Dclose($dataSetID); return 1; } ####--------------------------------------------------------- =head2 unlink =for ref Unlink an object from a group. B =for usage $groupObj->unlink($objectName); Unlink the named object from the group. =cut sub unlink{ my $self = shift; my $objectName = shift; # Get the dataset ID. my $groupID = $self->{ID}; # Do the unlink. if ( PDL::IO::HDF5::H5Ldelete($groupID,$objectName,PDL::IO::HDF5::H5P_DEFAULT()) < 0 ) { carp("Can't unlink object in ".__PACKAGE__.":unlink\n"); return undef; } return 1; } 1;