hdf5DatasetInternal

C++ Class Reference

1 Overview

Constructor with file, group, and dataset name.

2 Detailed Description

fileHDF5 file pointer groupGroup path datasetnameDataset name overwriteWhether to overwrite existing dataset

3 Class Hierarchy

4 Inheritance

Inherits from:

BigDataStatMeth::hdf5Dataset

5 Public Interface

5.1 Methods

5.1.1 `hdf5DatasetInternal()`

BigDataStatMeth::hdf5DatasetInternal::hdf5DatasetInternal(std::string filename, std::string group, std::string datasetname, bool overwrite)

Constructor with filename, group, and dataset name.

Parameters:

filename (std::string): Name of HDF5 file
group (std::string): Group path
datasetname (std::string): Dataset name
overwrite (bool): Whether to overwrite existing dataset

filenameName of HDF5 file groupGroup path datasetnameDataset name overwriteWhether to overwrite existing dataset

5.1.2 `createDataset()`

virtual void BigDataStatMeth::hdf5Dataset::createDataset(BigDataStatMeth::hdf5Dataset *dsLike, std::string strdatatype, int compression_level=6)

Create a dataset based on another dataset’s dimensions with optional compression.

Parameters:

dsLike (BigDataStatMeth::hdf5Dataset *): Reference dataset to copy dimensions from
strdatatype (std::string): Data type for the new dataset (“int”, “numeric”, “real”, “string”)
compression_level (int): Compression level (0=none, 1-9=gzip level, 6=balanced default) 0 = No compression 1-3 = Light compression (fast) 4-6 = Balanced compression (recommended) 7-9 = Maximum compression (slower)

Creates a new dataset with the same dimensions as the reference dataset but with a specified data type and compression settings. This is useful for creating derived datasets or transformations while maintaining dimensional consistency.

5.1.3 `createUnlimitedDataset()`

void BigDataStatMeth::hdf5DatasetInternal::createUnlimitedDataset(size_t rows, size_t cols, std::string strdatatype, int compression_level=6)

Create an unlimited internal dataset with optional compression.

Parameters:

rows (size_t): Initial number of rows
cols (size_t): Initial number of columns
strdatatype (std::string): Data type for the dataset
compression_level (int): Compression level (0=none, 1-9=gzip level, 6=balanced default)

Creates a new internal HDF5 dataset with unlimited dimensions. The dataset is marked as internal and unlimited and can grow in size.

5.1.4 `extendUnlimitedDataset()`

void BigDataStatMeth::hdf5DatasetInternal::extendUnlimitedDataset(const size_t rows, const size_t cols)

Extend an unlimited internal dataset.

Parameters:

rows (const size_t): New number of rows
cols (const size_t): New number of columns

Increases the dimensions of an unlimited internal dataset. Only works with datasets created as unlimited.

5.1.5 `writeDataset()`

void BigDataStatMeth::hdf5DatasetInternal::writeDataset(Rcpp::RObject DatasetValues)

Write data to the internal dataset.

Parameters:

DatasetValues (Rcpp::RObject): R object containing the data to write

Writes data to the internal dataset, handling different data types and formats. Optimized for internal storage patterns.

5.1.6 `writeDatasetBlock()`

void BigDataStatMeth::hdf5DatasetInternal::writeDatasetBlock(std::vector< double > DatasetValues, std::vector< hsize_t > vOffset, std::vector< hsize_t > vCount, std::vector< hsize_t > vStride, std::vector< hsize_t > vBlock)

Write block of vector data to internal dataset.

Parameters:

DatasetValues (std::vector< double >): Vector data to write
vOffset (std::vector< hsize_t >): Starting position
vCount (std::vector< hsize_t >): Number of elements
vStride (std::vector< hsize_t >): Stride between elements
vBlock (std::vector< hsize_t >): Block size

Writes a block of vector data to the internal dataset. Optimized for vector operations.

5.1.7 `readDatasetBlock()`

double * BigDataStatMeth::hdf5DatasetInternal::readDatasetBlock(std::vector< hsize_t > ivoffset, std::vector< hsize_t > ivcount, std::vector< hsize_t > ivstride, std::vector< hsize_t > ivblock, double *rdatablock)

Read a block of data from internal dataset.

Parameters:

ivoffset (std::vector< hsize_t >): Starting position for read
ivcount (std::vector< hsize_t >): Number of elements to read
ivstride (std::vector< hsize_t >): Stride between elements
ivblock (std::vector< hsize_t >): Size of blocks
rdatablock (double *): Pointer to read data (double*)

Returns: Pointer to read data (double*)

Reads a specified block of data from the internal dataset. Optimized for internal data access patterns.

5.1.8 `getDatasetptr()`

H5::DataSet * BigDataStatMeth::hdf5DatasetInternal::getDatasetptr()

5.1.9 `getDatasetName()`

std::string BigDataStatMeth::hdf5DatasetInternal::getDatasetName()

Get dataset name.

Returns: Name of the internal dataset

Name of the internal dataset

5.1.10 `getGroup()`

std::string BigDataStatMeth::hdf5DatasetInternal::getGroup()

Get group name.

Returns: Name of the group containing the internal dataset

Name of the group containing the internal dataset

5.1.11 `getFileName()`

std::string BigDataStatMeth::hdf5DatasetInternal::getFileName()

Get file name.

Returns: Name of the file containing the internal dataset

Name of the file containing the internal dataset

5.1.12 `nrows()`

hsize_t BigDataStatMeth::hdf5DatasetInternal::nrows()

5.1.13 `ncols()`

hsize_t BigDataStatMeth::hdf5DatasetInternal::ncols()

5.1.14 `dim()`

hsize_t * BigDataStatMeth::hdf5DatasetInternal::dim()

5.1.15 `isUnlimited()`

bool BigDataStatMeth::hdf5DatasetInternal::isUnlimited()

5.1.16 `~hdf5DatasetInternal()`

BigDataStatMeth::hdf5DatasetInternal::~hdf5DatasetInternal()

Destructor.

Closes the internal dataset and releases resources

6 Private Implementation

Note

Internal implementation details for advanced users and contributors.

Details

6.1 Methods

6.1.1 `close_dataset()`

void BigDataStatMeth::hdf5DatasetInternal::close_dataset()

Close the dataset.

Closes the internal dataset and releases associated resources

6.1.2 `close_dataset_file()`

void BigDataStatMeth::hdf5DatasetInternal::close_dataset_file()

Close dataset and file.

Closes both the internal dataset and its associated file

6.1.3 `convert_DataFrame_to_RangeList()`

names * BigDataStatMeth::hdf5DatasetInternal::convert_DataFrame_to_RangeList(Rcpp::RObject DatasetValues, bool bFullDataset)

Convert DataFrame to range list.

Parameters:

DatasetValues (Rcpp::RObject): R DataFrame to convert
bFullDataset (bool): Whether to convert entire dataset

Returns: Array of name structures

Converts R DataFrame to HDF5-compatible range list format for internal storage.

6.1.4 `getDimensExistingDataset()`

void BigDataStatMeth::hdf5DatasetInternal::getDimensExistingDataset()

Get dimensions of existing dataset.

Retrieves and stores the dimensions of an existing internal dataset

7 Usage Example

#include "hdf5DatasetInternal.hpp"

// Example usage
hdf5DatasetInternal obj;
// Your code here

--- title: "hdf5DatasetInternal" subtitle: "C++ Class Reference" --- ## Overview Constructor with file, group, and dataset name. ## Detailed Description fileHDF5 file pointer groupGroup path datasetnameDataset name overwriteWhether to overwrite existing dataset ## Class Hierarchy ::: {.diagram-section} ![Class diagram](images/class_big_data_stat_meth_1_1hdf5_dataset_internal__inherit__graph_org.svg){.class-diagram} ::: ## Inheritance Inherits from: * BigDataStatMeth::hdf5Dataset ## Public Interface ### Methods #### `hdf5DatasetInternal()` ```cpp BigDataStatMeth::hdf5DatasetInternal::hdf5DatasetInternal(std::string filename, std::string group, std::string datasetname, bool overwrite) ``` Constructor with filename, group, and dataset name. **Parameters:** - `filename` (`std::string`): Name of HDF5 file - `group` (`std::string`): Group path - `datasetname` (`std::string`): Dataset name - `overwrite` (`bool`): Whether to overwrite existing dataset filenameName of HDF5 file groupGroup path datasetnameDataset name overwriteWhether to overwrite existing dataset --- #### `createDataset()` ```cpp virtual void BigDataStatMeth::hdf5Dataset::createDataset(BigDataStatMeth::hdf5Dataset *dsLike, std::string strdatatype, int compression_level=6) ``` Create a dataset based on another dataset's dimensions with optional compression. **Parameters:** - `dsLike` (`BigDataStatMeth::hdf5Dataset *`): Reference dataset to copy dimensions from - `strdatatype` (`std::string`): Data type for the new dataset ("int", "numeric", "real", "string") - `compression_level` (`int`): Compression level (0=none, 1-9=gzip level, 6=balanced default) 0 = No compression 1-3 = Light compression (fast) 4-6 = Balanced compression (recommended) 7-9 = Maximum compression (slower) Creates a new dataset with the same dimensions as the reference dataset but with a specified data type and compression settings. This is useful for creating derived datasets or transformations while maintaining dimensional consistency. --- #### `createUnlimitedDataset()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::createUnlimitedDataset(size_t rows, size_t cols, std::string strdatatype, int compression_level=6) ``` Create an unlimited internal dataset with optional compression. **Parameters:** - `rows` (`size_t`): Initial number of rows - `cols` (`size_t`): Initial number of columns - `strdatatype` (`std::string`): Data type for the dataset - `compression_level` (`int`): Compression level (0=none, 1-9=gzip level, 6=balanced default) Creates a new internal HDF5 dataset with unlimited dimensions. The dataset is marked as internal and unlimited and can grow in size. --- #### `extendUnlimitedDataset()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::extendUnlimitedDataset(const size_t rows, const size_t cols) ``` Extend an unlimited internal dataset. **Parameters:** - `rows` (`const size_t`): New number of rows - `cols` (`const size_t`): New number of columns Increases the dimensions of an unlimited internal dataset. Only works with datasets created as unlimited. --- #### `writeDataset()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::writeDataset(Rcpp::RObject DatasetValues) ``` Write data to the internal dataset. **Parameters:** - `DatasetValues` (`Rcpp::RObject`): R object containing the data to write Writes data to the internal dataset, handling different data types and formats. Optimized for internal storage patterns. --- #### `writeDatasetBlock()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::writeDatasetBlock(std::vector< double > DatasetValues, std::vector< hsize_t > vOffset, std::vector< hsize_t > vCount, std::vector< hsize_t > vStride, std::vector< hsize_t > vBlock) ``` Write block of vector data to internal dataset. **Parameters:** - `DatasetValues` (`std::vector< double >`): Vector data to write - `vOffset` (`std::vector< hsize_t >`): Starting position - `vCount` (`std::vector< hsize_t >`): Number of elements - `vStride` (`std::vector< hsize_t >`): Stride between elements - `vBlock` (`std::vector< hsize_t >`): Block size Writes a block of vector data to the internal dataset. Optimized for vector operations. --- #### `readDatasetBlock()` ```cpp double * BigDataStatMeth::hdf5DatasetInternal::readDatasetBlock(std::vector< hsize_t > ivoffset, std::vector< hsize_t > ivcount, std::vector< hsize_t > ivstride, std::vector< hsize_t > ivblock, double *rdatablock) ``` Read a block of data from internal dataset. **Parameters:** - `ivoffset` (`std::vector< hsize_t >`): Starting position for read - `ivcount` (`std::vector< hsize_t >`): Number of elements to read - `ivstride` (`std::vector< hsize_t >`): Stride between elements - `ivblock` (`std::vector< hsize_t >`): Size of blocks - `rdatablock` (`double *`): Pointer to read data (double*) **Returns:** Pointer to read data (double*) Reads a specified block of data from the internal dataset. Optimized for internal data access patterns. --- #### `getDatasetptr()` ```cpp H5::DataSet * BigDataStatMeth::hdf5DatasetInternal::getDatasetptr() ``` --- #### `getDatasetName()` ```cpp std::string BigDataStatMeth::hdf5DatasetInternal::getDatasetName() ``` Get dataset name. **Returns:** Name of the internal dataset Name of the internal dataset --- #### `getGroup()` ```cpp std::string BigDataStatMeth::hdf5DatasetInternal::getGroup() ``` Get group name. **Returns:** Name of the group containing the internal dataset Name of the group containing the internal dataset --- #### `getFileName()` ```cpp std::string BigDataStatMeth::hdf5DatasetInternal::getFileName() ``` Get file name. **Returns:** Name of the file containing the internal dataset Name of the file containing the internal dataset --- #### `nrows()` ```cpp hsize_t BigDataStatMeth::hdf5DatasetInternal::nrows() ``` --- #### `ncols()` ```cpp hsize_t BigDataStatMeth::hdf5DatasetInternal::ncols() ``` --- #### `dim()` ```cpp hsize_t * BigDataStatMeth::hdf5DatasetInternal::dim() ``` --- #### `isUnlimited()` ```cpp bool BigDataStatMeth::hdf5DatasetInternal::isUnlimited() ``` --- #### `~hdf5DatasetInternal()` ```cpp BigDataStatMeth::hdf5DatasetInternal::~hdf5DatasetInternal() ``` Destructor. Closes the internal dataset and releases resources --- ## Private Implementation ::: {.callout-note} Internal implementation details for advanced users and contributors. ::: ::: {.callout-note collapse="true"} ### Details ### Methods #### `close_dataset()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::close_dataset() ``` Close the dataset. Closes the internal dataset and releases associated resources --- #### `close_dataset_file()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::close_dataset_file() ``` Close dataset and file. Closes both the internal dataset and its associated file --- #### `convert_DataFrame_to_RangeList()` ```cpp names * BigDataStatMeth::hdf5DatasetInternal::convert_DataFrame_to_RangeList(Rcpp::RObject DatasetValues, bool bFullDataset) ``` Convert DataFrame to range list. **Parameters:** - `DatasetValues` (`Rcpp::RObject`): R DataFrame to convert - `bFullDataset` (`bool`): Whether to convert entire dataset **Returns:** Array of name structures Converts R DataFrame to HDF5-compatible range list format for internal storage. --- #### `getDimensExistingDataset()` ```cpp void BigDataStatMeth::hdf5DatasetInternal::getDimensExistingDataset() ``` Get dimensions of existing dataset. Retrieves and stores the dimensions of an existing internal dataset --- ::: ## Usage Example ```cpp #include "hdf5DatasetInternal.hpp" // Example usage hdf5DatasetInternal obj; // Your code here ```

1 Overview

2 Detailed Description

3 Class Hierarchy

4 Inheritance

5 Public Interface

5.1 Methods

5.1.1 hdf5DatasetInternal()

5.1.2 createDataset()

5.1.3 createUnlimitedDataset()

5.1.4 extendUnlimitedDataset()

5.1.5 writeDataset()

5.1.6 writeDatasetBlock()

5.1.7 readDatasetBlock()

5.1.8 getDatasetptr()

5.1.9 getDatasetName()

5.1.10 getGroup()

5.1.11 getFileName()

5.1.12 nrows()

5.1.13 ncols()

5.1.14 dim()

5.1.15 isUnlimited()

5.1.16 ~hdf5DatasetInternal()

6 Private Implementation

6.1 Methods

6.1.1 close_dataset()

6.1.2 close_dataset_file()

6.1.3 convert_DataFrame_to_RangeList()

6.1.4 getDimensExistingDataset()

7 Usage Example

5.1.1 `hdf5DatasetInternal()`

5.1.2 `createDataset()`

5.1.3 `createUnlimitedDataset()`

5.1.4 `extendUnlimitedDataset()`

5.1.5 `writeDataset()`

5.1.6 `writeDatasetBlock()`

5.1.7 `readDatasetBlock()`

5.1.8 `getDatasetptr()`

5.1.9 `getDatasetName()`

5.1.10 `getGroup()`

5.1.11 `getFileName()`

5.1.12 `nrows()`

5.1.13 `ncols()`

5.1.14 `dim()`

5.1.15 `isUnlimited()`

5.1.16 `~hdf5DatasetInternal()`

6.1.1 `close_dataset()`

6.1.2 `close_dataset_file()`

6.1.3 `convert_DataFrame_to_RangeList()`

6.1.4 `getDimensExistingDataset()`