Add H5Fed changes in h5fed api.
This commit is contained in:
Patrik Leidenberger
+165
-100
@@ -341,127 +341,159 @@ public:
|
||||
// Set dimension of an elements vector.
|
||||
unsigned int elemDim = H5FED_TET_N_NODE;
|
||||
// Set the name of the dataset, we want to operate.
|
||||
string datasetName = H5FED_D_TETMESH + stringify(level);
|
||||
string datasetName = H5FED_D_TETMESH;
|
||||
// This function does the real work for all elements.
|
||||
element_(level, elem, datasetName, elemDim);
|
||||
return OKCODE;
|
||||
|
||||
}
|
||||
|
||||
// This function gets some attributes of the element, it should insert and
|
||||
// insert it to the given dataset.
|
||||
// Here we do the index mapping.
|
||||
int element_(unsigned int level,
|
||||
std::vector< std::vector<unsigned int> >* elem,
|
||||
std::string datasetName,
|
||||
std::string datasetNameBlank,
|
||||
unsigned int elemDim )
|
||||
{
|
||||
// All these operations are only allowed, if there is a valid file
|
||||
// identifier.
|
||||
if (hdf5FileIdent_ >= 0)
|
||||
{
|
||||
rDebug("Insert a check, if the selected level exits,");
|
||||
rDebug("and if it is consecutive.");
|
||||
// Define the rank of the different dataspaces.
|
||||
const int rank = 2;
|
||||
// Hdf5 error handling variable for Hdf5 actions.
|
||||
herr_t hdf5Status;
|
||||
// Hdf5 dataspace identifier.
|
||||
hid_t hdf5DataspaceId;
|
||||
// Hdf5 dataset identifier.
|
||||
hid_t hdf5DatasetId;
|
||||
// Define the dimension of the data array.
|
||||
hsize_t dim[2];
|
||||
// Number of rows: as much as elements.
|
||||
dim[0] = elem->size();
|
||||
// Number of colums: dimenstion of an elements vector.
|
||||
dim[1] = elemDim;
|
||||
|
||||
// We copy the element nodes from a element in an standart array,
|
||||
// so that hdf5 can handle it.
|
||||
// We do this for every element separate, so we save memory.
|
||||
|
||||
// Subdimension of hyperslab in memory: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_mem[2];
|
||||
dim_sub_mem[0] = 1;
|
||||
dim_sub_mem[1] = elemDim;
|
||||
// Subdimension of hyperslab in file: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_file[2];
|
||||
dim_sub_file[0] = 1;
|
||||
dim_sub_file[1] = elemDim;
|
||||
// Define the offset for reading from the memory.
|
||||
// Always fixed, because memory has exactly the same size.
|
||||
hsize_t offset_mem[2];
|
||||
offset_mem[0] = 0;
|
||||
offset_mem[1] = 0;
|
||||
// Define the offset for writing into the file.
|
||||
hsize_t offset_file[2];
|
||||
offset_file[0] = 0; // Row ofsett zero only at the beginning.
|
||||
offset_file[1] = 0; // We have no offset respective to the column.
|
||||
|
||||
// Array for single elements of an element vector.
|
||||
unsigned int element[elemDim];
|
||||
|
||||
// Dimesion and datatype of the file dataset, read out form file.
|
||||
// This is not the fastest, but the most robust way.
|
||||
hsize_t dim_out[2];
|
||||
hid_t dataType;
|
||||
// Make datasetName with the datasetNameBlank and the level.
|
||||
string datasetName = datasetNameBlank + stringify(level);
|
||||
|
||||
// Create dataspace of full size.
|
||||
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
|
||||
|
||||
// Create dataset of full size.
|
||||
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, datasetName.c_str(),
|
||||
H5T_STD_U32LE, hdf5DataspaceId, H5P_DEFAULT);
|
||||
|
||||
// Loop over all rows of the dataset (file) and copy the elem vector
|
||||
// row wise.
|
||||
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out,
|
||||
H5P_DEFAULT);
|
||||
// Get the datatype of the datas we want to write.
|
||||
dataType = H5Dget_type(hdf5DatasetId);
|
||||
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
|
||||
// Check if the dataset with the given datasetName already exists:
|
||||
// if it exists, abort;
|
||||
// if not, check if the previouse level exists:
|
||||
// if not, prompt warning
|
||||
// if it exits, every thing is correct.
|
||||
if (existsDataspace(datasetName))
|
||||
{
|
||||
// Iterate over the rows in file dataspace.
|
||||
offset_file[0] = varI;
|
||||
|
||||
// Copy every element of a coordinate.
|
||||
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
|
||||
rError("Dataspace %s already exists!", datasetName.c_str());
|
||||
rError("You cannot insert it twice.");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
else
|
||||
{
|
||||
// INSERT COMMENT HERE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
if (level > 0)
|
||||
{
|
||||
// Here is the only special case for automated mapping:
|
||||
// Do not copy the next in the input vector, copy the coord
|
||||
// with the next following number.
|
||||
if (doIndexMapping_ == true)
|
||||
if (!(existsDataspace(datasetNameBlank + stringify(level-1))))
|
||||
{
|
||||
std::map<unsigned int, unsigned int>::iterator iter;
|
||||
iter = indexMap_.find((*elem)[varI][varJ]);
|
||||
element[varJ] = iter->second;
|
||||
rError("You insert level %d while level %d does not exists.",
|
||||
level, level-1);
|
||||
rError("So the %s levels will be not consective.",
|
||||
datasetNameBlank);
|
||||
rError("Exit.");
|
||||
exit(ERRORCODE);
|
||||
}
|
||||
else
|
||||
element[varJ] = (*elem)[varI][varJ];
|
||||
}
|
||||
|
||||
// Select hyperslab ('region') in file dataspace.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
|
||||
offset_file, H5P_DEFAULT,
|
||||
dim_sub_file, H5P_DEFAULT);
|
||||
// Define memory Dataspace.
|
||||
hid_t hdf5MemspaceId;
|
||||
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
|
||||
// Select hyperslab ('region') in memory.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
|
||||
offset_mem, H5P_DEFAULT,
|
||||
dim_sub_mem, H5P_DEFAULT);
|
||||
// Copy dataset to dataset from memory to file.
|
||||
hdf5Status = H5Dwrite(hdf5DatasetId, dataType,
|
||||
hdf5MemspaceId, hdf5DataspaceId,
|
||||
H5P_DEFAULT, element);
|
||||
// Close the memory space identifier.
|
||||
H5Sclose(hdf5MemspaceId);
|
||||
}
|
||||
|
||||
// Close hdf5 identifier.
|
||||
hdf5Status = H5Dclose(hdf5DatasetId);
|
||||
hdf5Status = H5Sclose(hdf5DataspaceId);
|
||||
|
||||
return OKCODE;
|
||||
// Define the rank of the different dataspaces.
|
||||
const int rank = 2;
|
||||
// Hdf5 error handling variable for Hdf5 actions.
|
||||
herr_t hdf5Status;
|
||||
// Hdf5 dataspace identifier.
|
||||
hid_t hdf5DataspaceId;
|
||||
// Hdf5 dataset identifier.
|
||||
hid_t hdf5DatasetId;
|
||||
// Define the dimension of the data array.
|
||||
hsize_t dim[2];
|
||||
// Number of rows: as much as elements.
|
||||
dim[0] = elem->size();
|
||||
// Number of colums: dimenstion of an elements vector.
|
||||
dim[1] = elemDim;
|
||||
|
||||
// We copy the element nodes from a element in an standart array,
|
||||
// so that hdf5 can handle it.
|
||||
// We do this for every element separate, so we save memory.
|
||||
|
||||
// Subdimension of hyperslab in memory: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_mem[2];
|
||||
dim_sub_mem[0] = 1;
|
||||
dim_sub_mem[1] = elemDim;
|
||||
// Subdimension of hyperslab in file: 1 line, elemDim columns.
|
||||
hsize_t dim_sub_file[2];
|
||||
dim_sub_file[0] = 1;
|
||||
dim_sub_file[1] = elemDim;
|
||||
// Define the offset for reading from the memory.
|
||||
// Always fixed, because memory has exactly the same size.
|
||||
hsize_t offset_mem[2];
|
||||
offset_mem[0] = 0;
|
||||
offset_mem[1] = 0;
|
||||
// Define the offset for writing into the file.
|
||||
hsize_t offset_file[2];
|
||||
offset_file[0] = 0; // Row ofsett zero only at the beginning.
|
||||
offset_file[1] = 0; // We have no offset respective to the column.
|
||||
|
||||
// Array for single elements of an element vector.
|
||||
unsigned int element[elemDim];
|
||||
|
||||
// Dimesion and datatype of the file dataset, read out form file.
|
||||
// This is not the fastest, but the most robust way.
|
||||
hsize_t dim_out[2];
|
||||
hid_t dataType;
|
||||
|
||||
// Create dataspace of full size.
|
||||
hdf5DataspaceId = H5Screate_simple(rank, dim, H5P_DEFAULT);
|
||||
|
||||
// Create dataset of full size.
|
||||
hdf5DatasetId = H5Dcreate(hdf5FileIdent_, datasetName.c_str(),
|
||||
H5T_STD_U32LE, hdf5DataspaceId, H5P_DEFAULT);
|
||||
|
||||
// Loop over all rows of the dataset (file) and copy the elem vector
|
||||
// row wise.
|
||||
hdf5Status = H5Sget_simple_extent_dims(hdf5DataspaceId, dim_out,
|
||||
H5P_DEFAULT);
|
||||
// Get the datatype of the datas we want to write.
|
||||
dataType = H5Dget_type(hdf5DatasetId);
|
||||
for (unsigned int varI = 0; varI < dim_out[0]; varI++)
|
||||
{
|
||||
// Iterate over the rows in file dataspace.
|
||||
offset_file[0] = varI;
|
||||
|
||||
// Copy every element of a coordinate.
|
||||
for (unsigned int varJ = 0; varJ < dim_out[1]; varJ++)
|
||||
{
|
||||
// Here is the only special case for automated mapping:
|
||||
// Do not copy the next in the input vector, copy the coord
|
||||
// with the next following number.
|
||||
if (doIndexMapping_ == true)
|
||||
{
|
||||
std::map<unsigned int, unsigned int>::iterator iter;
|
||||
iter = indexMap_.find((*elem)[varI][varJ]);
|
||||
element[varJ] = iter->second;
|
||||
}
|
||||
else
|
||||
element[varJ] = (*elem)[varI][varJ];
|
||||
}
|
||||
|
||||
// Select hyperslab ('region') in file dataspace.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5DataspaceId, H5S_SELECT_SET,
|
||||
offset_file, H5P_DEFAULT,
|
||||
dim_sub_file, H5P_DEFAULT);
|
||||
// Define memory Dataspace.
|
||||
hid_t hdf5MemspaceId;
|
||||
hdf5MemspaceId = H5Screate_simple(rank, dim_sub_mem, H5P_DEFAULT);
|
||||
// Select hyperslab ('region') in memory.
|
||||
hdf5Status = H5Sselect_hyperslab(hdf5MemspaceId, H5S_SELECT_SET,
|
||||
offset_mem, H5P_DEFAULT,
|
||||
dim_sub_mem, H5P_DEFAULT);
|
||||
// Copy dataset to dataset from memory to file.
|
||||
hdf5Status = H5Dwrite(hdf5DatasetId, dataType,
|
||||
hdf5MemspaceId, hdf5DataspaceId,
|
||||
H5P_DEFAULT, element);
|
||||
// Close the memory space identifier.
|
||||
H5Sclose(hdf5MemspaceId);
|
||||
}
|
||||
|
||||
// Close hdf5 identifier.
|
||||
hdf5Status = H5Dclose(hdf5DatasetId);
|
||||
hdf5Status = H5Sclose(hdf5DataspaceId);
|
||||
|
||||
return OKCODE;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
@@ -473,6 +505,39 @@ public:
|
||||
|
||||
|
||||
|
||||
// Write 3dim coordinates to h5fed file.
|
||||
bool existsDataspace (std::string dataspaceName)
|
||||
{
|
||||
// All these operations are only allowed, if there is a valid file
|
||||
// identifier.
|
||||
if (hdf5FileIdent_ >= 0)
|
||||
{
|
||||
// Hdf5 error handling variable for Hdf5 actions.
|
||||
herr_t hdf5Status;
|
||||
// Hdf5 dataspace identifier.
|
||||
hid_t hdf5DataspaceId;
|
||||
|
||||
hdf5DataspaceId = H5Dopen(hdf5FileIdent_, dataspaceName.c_str());
|
||||
if (hdf5DataspaceId < 0)
|
||||
{
|
||||
//rDebug("This dataspace exists NOT in this file: %s",
|
||||
// dataspaceName.c_str());
|
||||
return false;
|
||||
}
|
||||
else
|
||||
{
|
||||
//rDebug("This dataspace exists in this file: %s",
|
||||
// dataspaceName.c_str());
|
||||
return true;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
rError("You cannot check if the dataspace exists.");
|
||||
rError("There is no valid file identifier.");
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user