HDF5GroupObjects* HDF5Dataset::HDF5FindDatasetObjects
( HDF5GroupObjects *poH5Objects, const char* pszDatasetName )
{
int i;
HDF5Dataset *poDS;
HDF5GroupObjects *poObjectsFound;
poDS=this;
if( poH5Objects->nType == H5G_DATASET &&
EQUAL( poH5Objects->pszName,pszDatasetName ) ) {
/* printf("found it! %ld\n",(long) poH5Objects);*/
return( poH5Objects );
}
if( poH5Objects->nbObjs >0 )
for( i=0; i <poH5Objects->nbObjs; i++ ) {
poObjectsFound=
poDS->HDF5FindDatasetObjects( poH5Objects->poHchild+i,
pszDatasetName );
/* -------------------------------------------------------------------- */
/* Is this our dataset?? */
/* -------------------------------------------------------------------- */
if( poObjectsFound != NULL ) return( poObjectsFound );
}
/* -------------------------------------------------------------------- */
/* Dataset has not been found! */
/* -------------------------------------------------------------------- */
return( NULL );
}
HDF5GroupObjects *
HDF5Dataset::HDF5FindDatasetObjects( HDF5GroupObjects *poH5Objects,
const char *pszDatasetName )
{
if( poH5Objects->nType == H5G_DATASET &&
EQUAL(poH5Objects->pszName, pszDatasetName) )
{
#ifdef DEBUG_VERBOSE
printf("found it! %p\n", poH5Objects); /*ok*/
#endif
return poH5Objects;
}
HDF5Dataset *poDS = this;
if( poH5Objects->nbObjs > 0 )
{
for( unsigned int i = 0; i <poH5Objects->nbObjs; i++ )
{
HDF5GroupObjects *poObjectsFound = poDS->HDF5FindDatasetObjects(
poH5Objects->poHchild + i, pszDatasetName);
// Is this our dataset?
if( poObjectsFound != nullptr )
return poObjectsFound;
}
}
// Dataset has not been found.
return nullptr;
}
// writing attribute to the file
void WriteAttribute( RString& rFilename,
RString& rPath,
RVector<int> rIntdata,
RVector<double> rDoubledata,
RString rStrdata,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),StringUtils::CompareNoCase(ExtractAttribute(inAttributes,NEWFILE),"true"));
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
// read the compress level
string compressStr = ExtractAttribute(inAttributes,COMPRESSLEVEL);
int compressedLevel = 0;
if ((compressStr.size()>0))
compressedLevel = atoi(compressStr.c_str());
// the dimension of the data to be read
string strRow = ExtractAttribute(inAttributes,ROW);
string strCol = ExtractAttribute(inAttributes,COL);
size_t row=0;
size_t col=0;
if ((strRow.size()>0) && (strCol.size()>0))
{
row = atoi(strRow.c_str());
col = atoi(strCol.c_str());
}
string::size_type index = strPath.find_last_of('/');
if((index == string::npos )||(index==0))
throw RException("Attribute can only be directly under an existing dataset or group.");
string parent = strPath.substr(0,index);
string attr = strPath.substr(index+1,string::npos);
// are we going to overwrite an existing attribute
bool overwrite = StringUtils::CompareNoCase(ExtractAttribute(inAttributes,OVERWRITE),"true");
if(rIntdata.Size()>0)
{
// obtain the data from input
rIntdata.Dimensions(row,col);
Matrix<int> intdata;
rIntdata.Extract(intdata);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,intdata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,intdata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
else if(rDoubledata.Size()>0)
{
// obtain the data from input
rDoubledata.Dimensions(row,col);
Matrix<double> doubledata;
rDoubledata.Extract(doubledata);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,doubledata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,doubledata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
else if(rStrdata.Size()>0)
{
// obtain the data from input
rStrdata.Dimensions(row,col);
Matrix<string> strdata;
rStrdata.Extract(strdata,row,col);
if(CheckDataset(da,parent))
{
HDF5Dataset ds = da.OpenDatasetByFullPath(parent);
if (overwrite)
ds.DeleteAttribute(attr);
ds.CreateAttribute(attr,strdata, compressedLevel);
}
else if(CheckGroup(da,parent))
{
HDF5Group gp = da.OpenGroupByFullPath(parent);
if (overwrite)
gp.DeleteAttribute(attr);
gp.CreateAttribute(attr,strdata, compressedLevel);
}
else
throw RException("Attribute can only be directly under an existing dataset or group.");
}
}
// Read data from file
void ReadData( RString& rFilename,
RString& rPath,
vector<STLTypes::NameValuePair>& inAttributes, SEXP& results)
{
HDF5DA da(rFilename.Data(0),false);
HDF5OutputConverter oc;
string strPath(rPath.Data(0));
// check if this is a valid dataset
vector<string> dasummary=da.GetDatasetNamesFullPath();
bool isDataset = (find( dasummary.begin( ), dasummary.end( ), strPath)!=dasummary.end( ));
if(!isDataset)
throw RException("path - "+strPath+" is not dataset.");
HDF5Dataset ds = da.OpenDatasetByFullPath(strPath);
string startStr = ExtractAttribute(inAttributes,STARTINDEX);
string nrowsStr = ExtractAttribute(inAttributes,NROWS);
size_t start=0;
size_t nRows=ds.NumberOfRows();
// if only start index is supplied, we need to figure out the nrows.
if ((startStr.size()>0))
{
start = atoi(startStr.c_str());
nRows = nRows-start;
}
// nrows is supplied as well
if (nrowsStr.size()>0)
nRows = atoi(nrowsStr.c_str());
switch (ds.GetDataType())
{
case HDF5DataType::CHAR:{
Matrix<char> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT:{
Matrix<int> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertIntMatrix(data);
break;}
case HDF5DataType::INT64:{
Matrix<__int64> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::FLOAT:{
Matrix<float> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::DOUBLE:{
Matrix<double> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertDoubleMatrix(data);
break;}
case HDF5DataType::STRING:{
Matrix<string> data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertStrMatrix(data);
break;}
case HDF5DataType::COMPOUND:{
HDF5CompoundType data;
da.ReadDataByFullPath(strPath, start, nRows, data);
results=oc.ConvertCompoundType(data);
break;}
default:
throw RException("Unknown data type");
}
}
CPLErr HDF5Dataset::HDF5ListGroupObjects( HDF5GroupObjects *poRootGroup,
int bSUBDATASET )
{
int i;
char szTemp[8192];
char szDim[8192];
HDF5Dataset *poDS;
poDS=this;
if( poRootGroup->nbObjs >0 )
for( i=0; i < poRootGroup->nbObjs; i++ ) {
poDS->HDF5ListGroupObjects( poRootGroup->poHchild+i, bSUBDATASET );
}
if( poRootGroup->nType == H5G_GROUP ) {
CreateMetadata( poRootGroup, H5G_GROUP );
}
/* -------------------------------------------------------------------- */
/* Create Sub dataset list */
/* -------------------------------------------------------------------- */
if( (poRootGroup->nType == H5G_DATASET ) && bSUBDATASET
&& poDS->GetDataType( poRootGroup->native ) == GDT_Unknown )
{
CPLDebug( "HDF5", "Skipping unsupported %s of type %s",
poRootGroup->pszUnderscorePath,
poDS->GetDataTypeName( poRootGroup->native ) );
}
else if( (poRootGroup->nType == H5G_DATASET ) && bSUBDATASET )
{
szDim[0]='\0';
switch( poRootGroup->nRank ) {
case 3:
sprintf( szTemp,"%dx%dx%d",
(int)poRootGroup->paDims[0],
(int)poRootGroup->paDims[1],
(int)poRootGroup->paDims[2] );
break;
case 2:
sprintf( szTemp,"%dx%d",
(int)poRootGroup->paDims[0],
(int)poRootGroup->paDims[1] );
break;
default:
return CE_None;
}
strcat( szDim,szTemp );
sprintf( szTemp, "SUBDATASET_%d_NAME", ++(poDS->nSubDataCount) );
poDS->papszSubDatasets =
CSLSetNameValue( poDS->papszSubDatasets, szTemp,
CPLSPrintf( "HDF5:\"%s\":%s",
poDS->GetDescription(),
poRootGroup->pszUnderscorePath ) );
sprintf( szTemp, "SUBDATASET_%d_DESC", poDS->nSubDataCount );
poDS->papszSubDatasets =
CSLSetNameValue( poDS->papszSubDatasets, szTemp,
CPLSPrintf( "[%s] %s (%s)",
szDim,
poRootGroup->pszUnderscorePath,
poDS->GetDataTypeName
( poRootGroup->native ) ) );
}
return CE_None;
}
GDALDataset *HDF5Dataset::Open( GDALOpenInfo * poOpenInfo )
{
HDF5Dataset *poDS;
CPLErr Err;
if( !Identify( poOpenInfo ) )
return NULL;
/* -------------------------------------------------------------------- */
/* Create datasource. */
/* -------------------------------------------------------------------- */
poDS = new HDF5Dataset();
poDS->SetDescription( poOpenInfo->pszFilename );
/* -------------------------------------------------------------------- */
/* Try opening the dataset. */
/* -------------------------------------------------------------------- */
poDS->hHDF5 = H5Fopen( poOpenInfo->pszFilename,
H5F_ACC_RDONLY,
H5P_DEFAULT );
if( poDS->hHDF5 < 0 ) {
delete poDS;
return NULL;
}
poDS->hGroupID = H5Gopen( poDS->hHDF5, "/" );
if( poDS->hGroupID < 0 ){
poDS->bIsHDFEOS=false;
delete poDS;
return NULL;
}
poDS->bIsHDFEOS=true;
Err = poDS->ReadGlobalAttributes( true );
poDS->SetMetadata( poDS->papszMetadata );
if ( CSLCount( poDS->papszSubDatasets ) / 2 >= 1 )
poDS->SetMetadata( poDS->papszSubDatasets, "SUBDATASETS" );
// Make sure we don't try to do any pam stuff with this dataset.
poDS->nPamFlags |= GPF_NOSAVE;
/* -------------------------------------------------------------------- */
/* If we have single subdataset only, open it immediately */
/* -------------------------------------------------------------------- */
int nSubDatasets = CSLCount( poDS->papszSubDatasets ) / 2;
if( nSubDatasets == 1 )
{
CPLString osDSName = CSLFetchNameValue( poDS->papszSubDatasets,
"SUBDATASET_1_NAME" );
delete poDS;
return (GDALDataset *) GDALOpen( osDSName, poOpenInfo->eAccess );
}
else
{
/* -------------------------------------------------------------------- */
/* Confirm the requested access is supported. */
/* -------------------------------------------------------------------- */
if( poOpenInfo->eAccess == GA_Update )
{
delete poDS;
CPLError( CE_Failure, CPLE_NotSupported,
"The HDF5 driver does not support update access to existing"
" datasets.\n" );
return NULL;
}
}
return( poDS );
}
CPLErr HDF5Dataset::HDF5ListGroupObjects( HDF5GroupObjects *poRootGroup,
int bSUBDATASET )
{
HDF5Dataset *poDS = this;
if( poRootGroup->nbObjs > 0 )
for( hsize_t i = 0; i < poRootGroup->nbObjs; i++ )
{
poDS->HDF5ListGroupObjects(poRootGroup->poHchild + i, bSUBDATASET);
}
if( poRootGroup->nType == H5G_GROUP ) {
CreateMetadata(poRootGroup, H5G_GROUP);
}
// Create Sub dataset list.
if( poRootGroup->nType == H5G_DATASET && bSUBDATASET &&
poDS->GetDataType(poRootGroup->native) == GDT_Unknown )
{
CPLDebug("HDF5", "Skipping unsupported %s of type %s",
poRootGroup->pszUnderscorePath,
poDS->GetDataTypeName(poRootGroup->native));
}
else if( poRootGroup->nType == H5G_DATASET && bSUBDATASET )
{
CreateMetadata(poRootGroup, H5G_DATASET);
char szTemp[8192]; // TODO(schwehr): Get this off of the stack.
switch( poRootGroup->nRank )
{
case 2:
snprintf(szTemp, sizeof(szTemp), "%dx%d",
static_cast<int>(poRootGroup->paDims[0]),
static_cast<int>(poRootGroup->paDims[1]));
break;
case 3:
snprintf(szTemp, sizeof(szTemp), "%dx%dx%d",
static_cast<int>(poRootGroup->paDims[0]),
static_cast<int>(poRootGroup->paDims[1]),
static_cast<int>(poRootGroup->paDims[2]));
break;
default:
return CE_None;
}
const std::string osDim = szTemp;
snprintf(szTemp, sizeof(szTemp), "SUBDATASET_%d_NAME",
++(poDS->nSubDataCount));
poDS->papszSubDatasets =
CSLSetNameValue(poDS->papszSubDatasets, szTemp,
CPLSPrintf("HDF5:\"%s\":%s",
poDS->GetDescription(),
poRootGroup->pszUnderscorePath));
snprintf(szTemp, sizeof(szTemp), "SUBDATASET_%d_DESC",
poDS->nSubDataCount);
poDS->papszSubDatasets = CSLSetNameValue(
poDS->papszSubDatasets, szTemp,
CPLSPrintf("[%s] %s (%s)", osDim.c_str(),
poRootGroup->pszUnderscorePath,
poDS->GetDataTypeName(poRootGroup->native)));
}
return CE_None;
}
