Hello,
I just made a modification to the PDL::IO::HDF5 package
so it can now read slices or hyperslabs of the file instead
of the whole array
Use the following patch by untarring the PDL-IO-HDF5-0.5.tar.gz file
and "cd PDL-IO-HDF5-0.5" and then
patch -p1 < ../PDL-IO-HDF5-0.5-hyperslab.patch
patch file attached
Cheers,
Xavier
diff -ur PDL-IO-HDF5-0.5/HDF5/Dataset.pm PDL-IO-HDF5-0.5-new/HDF5/Dataset.pm
--- PDL-IO-HDF5-0.5/HDF5/Dataset.pm 2006-01-10 18:57:43.000000000 +0000
+++ PDL-IO-HDF5-0.5-new/HDF5/Dataset.pm 2007-02-20 14:50:59.301516735 +0000
@@ -345,6 +345,9 @@
sub get{
my $self = shift;
+ my $start = shift;
+ my $length = shift;
+ my $stride = shift;
my $pdl;
@@ -423,39 +426,79 @@
}
- # Initialize Dims structure:
my @dims = ( 0..($Ndims-1));
- my $dims = PDL::IO::HDF5::packList(@dims);
- my $dims2 = PDL::IO::HDF5::packList(@dims);
-
- my $rc = PDL::IO::HDF5::H5Sget_simple_extent_dims($dataspaceID, $dims, $dims2 );
-
- if( $rc != $Ndims){
+ my ($mem_space,$file_space);
+ if (not defined $start) {
+ # Initialize Dims structure:
+ my $dims = PDL::IO::HDF5::packList(@dims);
+ my $dims2 = PDL::IO::HDF5::packList(@dims);
+
+ my $rc = PDL::IO::HDF5::H5Sget_simple_extent_dims($dataspaceID, $dims, $dims2 );
+
+ if( $rc != $Ndims){
carp("Error getting number of dims in dataspace in ".__PACKAGE__.":get\n");
carp("Can't close Datatype in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Tclose($HDF5type) < 0);
carp("Can't close DataSpace in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Sclose($dataspaceID) < 0);
return undef;
- }
+ }
+
+ @dims = PDL::IO::HDF5::unpackList($dims); # get the dim sizes from the binary structure
+
+ } else {
+
+ carp("Wrong dimensions in start PDL in ".__PACKAGE__."\n") if ( ($start->getndims != 1) || ($start->getdim(0) != $Ndims) );
+ my $start2 = PDL::IO::HDF5::packList(reverse($start->list));
+ carp("No length supplied in ".__PACKAGE__."\n") if (not defined $length);
+ carp("Wrong dimensions in length PDL in ".__PACKAGE__."\n") if ( ($length->getndims != 1) || ($length->getdim(0) != $Ndims) );
+ my $length2 = PDL::IO::HDF5::packList(reverse($length->list));
+
+ if (defined $stride) {
+ carp("Wrong dimensions in stride in ".__PACKAGE__."\n") if ( ($stride->getndims != 1) || ($stride->getdim(0) != $Ndims) );
+ @dims=reverse(($length/$stride)->list);
+ } else {
+ @dims=reverse($length->list);
+ $stride=PDL::Core::ones($Ndims);
+ }
+ my $mem_dims = PDL::IO::HDF5::packList(@dims);
+ my $stride2 = PDL::IO::HDF5::packList(reverse($stride->list));
+ my $block=PDL::Core::ones($Ndims);
+ my $block2 = PDL::IO::HDF5::packList(reverse($block->list));
+
+ # Slice the data
+ $file_space = PDL::IO::HDF5::H5Dget_space($datasetID);
+ $rc=PDL::IO::HDF5::H5Sselect_hyperslab($file_space, 0,
+ $start2, $stride2, $length2, $block2);
- @dims = PDL::IO::HDF5::unpackList($dims); # get the dim sizes from the binary structure
+
+ if( $rc < 0 ){
+ carp("Error slicing data from file in ".__PACKAGE__.":get\n");
+ carp("Can't close Datatype in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Tclose($HDF5type) < 0);
+ carp("Can't close DataSpace in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Sclose($dataspaceID) < 0);
+ return undef;
+ }
+
+ $mem_space = PDL::IO::HDF5::H5Screate_simple($Ndims, $mem_dims,
+ $mem_dims);
+ }
+
$pdl = $ReturnType->null;
$pdl->set_datatype($PDLtype);
my @pdldims; # dims of the PDL
if( defined( $stringSize )){ # String types
-
- @pdldims = ($stringSize,reverse(@dims)); # HDF5 stores columns/rows in reverse order than pdl,
- # 1st PDL dim is the string length (for PDL::Char)
+
+ @pdldims = ($stringSize,reverse(@dims)); # HDF5 stores columns/rows in reverse order than pdl,
+ # 1st PDL dim is the string length (for PDL::Char)
}
else{ # Normal Numeric types
- @pdldims = (reverse(@dims)); # HDF5 stores columns/rows in reverse order than pdl,
+ @pdldims = (reverse(@dims)); # HDF5 stores columns/rows in reverse order than pdl,
}
-
+
$pdl->setdims([EMAIL PROTECTED]);
-
+
my $nelems = 1;
foreach (@pdldims){ $nelems *= $_; }; # calculate the number of elements
-
+
my $datasize = $nelems * PDL::howbig($pdl->get_datatype);
# Create empty space for the data
@@ -463,21 +506,29 @@
my $howBig = PDL::howbig($pdl->get_datatype);
my $data = ' ' x $howBig;
foreach my $dim(@pdldims){
- $data = $data x $dim;
+ $data = $data x $dim;
}
-
# Read the data:
- $rc = PDL::IO::HDF5::H5Dread($datasetID, $internalhdf5_type, PDL::IO::HDF5::H5S_ALL(), PDL::IO::HDF5::H5S_ALL(),
- PDL::IO::HDF5::H5P_DEFAULT(),
- $data);
+ if (not defined $start) {
+ $rc = PDL::IO::HDF5::H5Dread($datasetID, $internalhdf5_type, PDL::IO::HDF5::H5S_ALL(), PDL::IO::HDF5::H5S_ALL(),
+ PDL::IO::HDF5::H5P_DEFAULT(),
+ $data);
+ } else {
+
+ $rc = PDL::IO::HDF5::H5Dread($datasetID, $internalhdf5_type,
+ $mem_space, $file_space,
+ PDL::IO::HDF5::H5P_DEFAULT(),
+ $data);
+ }
+
if( $rc < 0 ){
- carp("Error reading data from file in ".__PACKAGE__.":get\n");
- carp("Can't close Datatype in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Tclose($HDF5type) < 0);
- carp("Can't close DataSpace in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Sclose($dataspaceID) < 0);
+ carp("Error reading data from file in ".__PACKAGE__.":get\n");
+ carp("Can't close Datatype in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Tclose($HDF5type) < 0);
+ carp("Can't close DataSpace in ".__PACKAGE__.":get\n") if( PDL::IO::HDF5::H5Sclose($dataspaceID) < 0);
return undef;
}
-
+
# Update the PDL data with the data read from the file
${$pdl->get_dataref()} = $data;
$pdl->upd_data();
diff -ur PDL-IO-HDF5-0.5/hdf5.pd PDL-IO-HDF5-0.5-new/hdf5.pd
--- PDL-IO-HDF5-0.5/hdf5.pd 2006-03-24 20:37:34.000000000 +0000
+++ PDL-IO-HDF5-0.5-new/hdf5.pd 2007-02-20 09:46:01.788379776 +0000
@@ -1166,6 +1166,7 @@
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);
+herr_t H5Sselect_hyperslab(hid_t space_id, int op, const hsize_t *start, const hsize_t *stride, const hsize_t *count, const hsize_t *block);
#
#
# Dataset Functions
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