hdf5File

C++ Class Reference

1 Overview

Constructor with path and filename.

2 Detailed Description

routeDirectory path filenFilename overwriteWhether to overwrite existing file

3 Class Hierarchy

4 Public Interface

4.1 Methods

4.1.1 `hdf5File()`

BigDataStatMeth::hdf5File::hdf5File(H5::H5File *file)

Constructor with file pointer.

Parameters:

file (H5::H5File *): HDF5 file pointer

fileHDF5 file pointer

4.1.2 `createFile()`

int BigDataStatMeth::hdf5File::createFile()

Create a new HDF5 file.

Returns: EXEC_OK on success, EXEC_ERROR on error, EXEC_WARNING if file exists

Creates a new HDF5 file at the specified location. If the file exists and overwrite is true, it will be truncated.

4.1.3 `openFile()`

H5::H5File * BigDataStatMeth::hdf5File::openFile(std::string opentype)

Open an existing HDF5 file.

Parameters:

opentype (std::string): Access mode (“r” for read-only, “rw” for read-write)

Returns: Pointer to opened file or nullptr on error

Opens an HDF5 file in read or read/write mode.

4.1.4 `getFileptr()`

H5::H5File * BigDataStatMeth::hdf5File::getFileptr()

Get file pointer.

Returns: Pointer to HDF5 file

Pointer to HDF5 file

4.1.5 `getFilename()`

std::string BigDataStatMeth::hdf5File::getFilename()

Get filename.

Returns: Filename without path

Filename without path

4.1.6 `getPath()`

std::string BigDataStatMeth::hdf5File::getPath()

Get file path.

Returns: Directory path without filename

Directory path without filename

4.1.7 `getFullPath()`

std::string BigDataStatMeth::hdf5File::getFullPath()

Get full file path.

Returns: Complete path including filename

Complete path including filename

4.1.8 `checkFile()`

bool BigDataStatMeth::hdf5File::checkFile()

Check if file exists.

Returns: True if file exists, false otherwise

True if file exists, false otherwise

4.1.9 `getDatasetNames()`

Rcpp::StringVector BigDataStatMeth::hdf5File::getDatasetNames(std::string strgroup, std::string strprefix, std::string strsufix)

Get list of dataset names.

Parameters:

strgroup (std::string): Group path
strprefix (std::string): Prefix filter
strsufix (std::string): Suffix filter

Returns: Vector of dataset names

strgroupGroup path strprefixPrefix filter strsufixSuffix filter Vector of dataset names

4.1.10 `getAllDatasetNames()`

Rcpp::StringVector BigDataStatMeth::hdf5File::getAllDatasetNames(std::string strgroup, std::string strprefix, bool recursive)

List datasets in a group, optionally recursing into subgroups.

Parameters:

strgroup (std::string): HDF5 group path. Use “/” for the file root.
strprefix (std::string): Only return names starting with this prefix (empty = all).
recursive (bool): If true, recurse into every subgroup and return full paths relative to strgroup (e.g. “SUB/dataset”).

Returns: StringVector of dataset names (or relative paths when recursive).

strgroupHDF5 group path. Use “/” for the file root. strprefixOnly return names starting with this prefix (empty = all). recursiveIf true, recurse into every subgroup and return full paths relative to strgroup (e.g. “SUB/dataset”). StringVector of dataset names (or relative paths when recursive).

4.1.11 `close_file()`

void BigDataStatMeth::hdf5File::close_file()

Close file and cleanup resources.

Closes all open objects and the file itself. Used for emergency cleanup.

4.1.12 `~hdf5File()`

BigDataStatMeth::hdf5File::~hdf5File()

Destructor.

Closes the file and releases resources

5 Protected Members

Details

5.1 Attributes

5.1.1 `pfile`

Type: H5::H5File *

5.1.2 `filename`

Type: std::string

5.1.3 `path`

Type: std::string

5.1.4 `bOwnsFile`

Type: bool

6 Private Implementation

Note

Internal implementation details for advanced users and contributors.

Details

6.1 Methods

6.1.1 `ResFileExist_filestream()`

bool BigDataStatMeth::hdf5File::ResFileExist_filestream()

Check if file exists using file stream.

Returns: True if file exists and is accessible

True if file exists and is accessible

6.1.2 `checkHDF5File()`

bool BigDataStatMeth::hdf5File::checkHDF5File()

Check if file is corrupt, open, accessible or has_valid_structure.

Returns: True if file exists and is accessible

True if file exists and is accessible

6.1.3 `lockedByOtherProcess()`

bool BigDataStatMeth::hdf5File::lockedByOtherProcess()

Return true if existing HDF5 file appears locked/busy.

Requires HDF5 file locking enabled (env var set above).

6.1.4 `isOpenInCurrentProcess()`

bool BigDataStatMeth::hdf5File::isOpenInCurrentProcess()

Check if file is already open in the current process.

Returns: true if this process already has the file open.

Uses HDF5 C API to enumerate all file IDs open in this process and compare their paths against fullPath. This avoids false positives from lockedByOtherProcess() when the same R session already has the file open via another HDF5Matrix object. true if this process already has the file open.

6.1.5 `isHDF5FileOpen()`

bool BigDataStatMeth::hdf5File::isHDF5FileOpen()

Check if HDF5 file is already open.

Returns: True if file is open

True if file is open

6.1.6 `collect_datasets_recursive()`

void BigDataStatMeth::hdf5File::collect_datasets_recursive(const std::string &group_path, const std::string &rel_prefix, const std::string &strprefix, Rcpp::StringVector &results)

Recursive helper: walk group_path and collect dataset paths.

Parameters:

group_path (const std::string &): Current group being visited.
rel_prefix (const std::string &): Path prefix accumulated so far (empty at root call).
strprefix (const std::string &): User-supplied name filter (empty = accept all).
results (Rcpp::StringVector &): Accumulator vector — paths appended in-place.

group_pathCurrent group being visited. rel_prefixPath prefix accumulated so far (empty at root call). strprefixUser-supplied name filter (empty = accept all). resultsAccumulator vector — paths appended in-place.

6.1.7 `get_dataset_names_from_group()`

Rcpp::StringVector BigDataStatMeth::hdf5File::get_dataset_names_from_group(std::string strgroup, std::string strprefix, std::string strsufix)

Get dataset names from group.

Parameters:

strgroup (std::string): Group path
strprefix (std::string): Prefix filter
strsufix (std::string): Suffix filter

Returns: Vector of dataset names

strgroupGroup path strprefixPrefix filter strsufixSuffix filter Vector of dataset names

6.2 Attributes

6.2.1 `opentype`

Type: std::string

6.2.2 `fullPath`

Type: std::string

6.2.3 `boverwrite`

Type: bool

7 Usage Example

#include "hdf5File.hpp"

// Example usage
hdf5File obj;
// Your code here

--- title: "hdf5File" subtitle: "C++ Class Reference" --- ## Overview Constructor with path and filename. ## Detailed Description routeDirectory path filenFilename overwriteWhether to overwrite existing file ## Class Hierarchy ::: {.diagram-section} ![Class diagram](images/class_big_data_stat_meth_1_1hdf5_file__inherit__graph_org.svg){.class-diagram} ::: ## Public Interface ### Methods #### `hdf5File()` ```cpp BigDataStatMeth::hdf5File::hdf5File(H5::H5File *file) ``` Constructor with file pointer. **Parameters:** - `file` (`H5::H5File *`): HDF5 file pointer fileHDF5 file pointer --- #### `createFile()` ```cpp int BigDataStatMeth::hdf5File::createFile() ``` Create a new HDF5 file. **Returns:** EXEC_OK on success, EXEC_ERROR on error, EXEC_WARNING if file exists Creates a new HDF5 file at the specified location. If the file exists and overwrite is true, it will be truncated. --- #### `openFile()` ```cpp H5::H5File * BigDataStatMeth::hdf5File::openFile(std::string opentype) ``` Open an existing HDF5 file. **Parameters:** - `opentype` (`std::string`): Access mode ("r" for read-only, "rw" for read-write) **Returns:** Pointer to opened file or nullptr on error Opens an HDF5 file in read or read/write mode. --- #### `getFileptr()` ```cpp H5::H5File * BigDataStatMeth::hdf5File::getFileptr() ``` Get file pointer. **Returns:** Pointer to HDF5 file Pointer to HDF5 file --- #### `getFilename()` ```cpp std::string BigDataStatMeth::hdf5File::getFilename() ``` Get filename. **Returns:** Filename without path Filename without path --- #### `getPath()` ```cpp std::string BigDataStatMeth::hdf5File::getPath() ``` Get file path. **Returns:** Directory path without filename Directory path without filename --- #### `getFullPath()` ```cpp std::string BigDataStatMeth::hdf5File::getFullPath() ``` Get full file path. **Returns:** Complete path including filename Complete path including filename --- #### `checkFile()` ```cpp bool BigDataStatMeth::hdf5File::checkFile() ``` Check if file exists. **Returns:** True if file exists, false otherwise True if file exists, false otherwise --- #### `getDatasetNames()` ```cpp Rcpp::StringVector BigDataStatMeth::hdf5File::getDatasetNames(std::string strgroup, std::string strprefix, std::string strsufix) ``` Get list of dataset names. **Parameters:** - `strgroup` (`std::string`): Group path - `strprefix` (`std::string`): Prefix filter - `strsufix` (`std::string`): Suffix filter **Returns:** Vector of dataset names strgroupGroup path strprefixPrefix filter strsufixSuffix filter Vector of dataset names --- #### `getAllDatasetNames()` ```cpp Rcpp::StringVector BigDataStatMeth::hdf5File::getAllDatasetNames(std::string strgroup, std::string strprefix, bool recursive) ``` List datasets in a group, optionally recursing into subgroups. **Parameters:** - `strgroup` (`std::string`): HDF5 group path. Use "/" for the file root. - `strprefix` (`std::string`): Only return names starting with this prefix (empty = all). - `recursive` (`bool`): If true, recurse into every subgroup and return full paths relative to strgroup (e.g. "SUB/dataset"). **Returns:** StringVector of dataset names (or relative paths when recursive). strgroupHDF5 group path. Use "/" for the file root. strprefixOnly return names starting with this prefix (empty = all). recursiveIf true, recurse into every subgroup and return full paths relative to strgroup (e.g. "SUB/dataset"). StringVector of dataset names (or relative paths when recursive). --- #### `close_file()` ```cpp void BigDataStatMeth::hdf5File::close_file() ``` Close file and cleanup resources. Closes all open objects and the file itself. Used for emergency cleanup. --- #### `~hdf5File()` ```cpp BigDataStatMeth::hdf5File::~hdf5File() ``` Destructor. Closes the file and releases resources --- ## Protected Members ::: {.callout-note collapse="true"} ### Details ### Attributes #### `pfile` **Type:** `H5::H5File *` --- #### `filename` **Type:** `std::string` --- #### `path` **Type:** `std::string` --- #### `bOwnsFile` **Type:** `bool` --- ::: ## Private Implementation ::: {.callout-note} Internal implementation details for advanced users and contributors. ::: ::: {.callout-note collapse="true"} ### Details ### Methods #### `ResFileExist_filestream()` ```cpp bool BigDataStatMeth::hdf5File::ResFileExist_filestream() ``` Check if file exists using file stream. **Returns:** True if file exists and is accessible True if file exists and is accessible --- #### `checkHDF5File()` ```cpp bool BigDataStatMeth::hdf5File::checkHDF5File() ``` Check if file is corrupt, open, accessible or has_valid_structure. **Returns:** True if file exists and is accessible True if file exists and is accessible --- #### `lockedByOtherProcess()` ```cpp bool BigDataStatMeth::hdf5File::lockedByOtherProcess() ``` Return true if existing HDF5 file appears locked/busy. Requires HDF5 file locking enabled (env var set above). --- #### `isOpenInCurrentProcess()` ```cpp bool BigDataStatMeth::hdf5File::isOpenInCurrentProcess() ``` Check if file is already open in the current process. **Returns:** true if this process already has the file open. Uses HDF5 C API to enumerate all file IDs open in this process and compare their paths against fullPath. This avoids false positives from lockedByOtherProcess() when the same R session already has the file open via another HDF5Matrix object. true if this process already has the file open. --- #### `isHDF5FileOpen()` ```cpp bool BigDataStatMeth::hdf5File::isHDF5FileOpen() ``` Check if HDF5 file is already open. **Returns:** True if file is open True if file is open --- #### `collect_datasets_recursive()` ```cpp void BigDataStatMeth::hdf5File::collect_datasets_recursive(const std::string &group_path, const std::string &rel_prefix, const std::string &strprefix, Rcpp::StringVector &results) ``` Recursive helper: walk group_path and collect dataset paths. **Parameters:** - `group_path` (`const std::string &`): Current group being visited. - `rel_prefix` (`const std::string &`): Path prefix accumulated so far (empty at root call). - `strprefix` (`const std::string &`): User-supplied name filter (empty = accept all). - `results` (`Rcpp::StringVector &`): Accumulator vector — paths appended in-place. group_pathCurrent group being visited. rel_prefixPath prefix accumulated so far (empty at root call). strprefixUser-supplied name filter (empty = accept all). resultsAccumulator vector — paths appended in-place. --- #### `get_dataset_names_from_group()` ```cpp Rcpp::StringVector BigDataStatMeth::hdf5File::get_dataset_names_from_group(std::string strgroup, std::string strprefix, std::string strsufix) ``` Get dataset names from group. **Parameters:** - `strgroup` (`std::string`): Group path - `strprefix` (`std::string`): Prefix filter - `strsufix` (`std::string`): Suffix filter **Returns:** Vector of dataset names strgroupGroup path strprefixPrefix filter strsufixSuffix filter Vector of dataset names --- ### Attributes #### `opentype` **Type:** `std::string` --- #### `fullPath` **Type:** `std::string` --- #### `boverwrite` **Type:** `bool` --- ::: ## Usage Example ```cpp #include "hdf5File.hpp" // Example usage hdf5File obj; // Your code here ```

1 Overview

2 Detailed Description

3 Class Hierarchy

4 Public Interface

4.1 Methods

4.1.1 hdf5File()

4.1.2 createFile()

4.1.3 openFile()

4.1.4 getFileptr()

4.1.5 getFilename()

4.1.6 getPath()

4.1.7 getFullPath()

4.1.8 checkFile()

4.1.9 getDatasetNames()

4.1.10 getAllDatasetNames()

4.1.11 close_file()

4.1.12 ~hdf5File()

5 Protected Members

5.1 Attributes

5.1.1 pfile

5.1.2 filename

5.1.3 path

5.1.4 bOwnsFile

6 Private Implementation

6.1 Methods

6.1.1 ResFileExist_filestream()

6.1.2 checkHDF5File()

6.1.3 lockedByOtherProcess()

6.1.4 isOpenInCurrentProcess()

6.1.5 isHDF5FileOpen()

6.1.6 collect_datasets_recursive()

6.1.7 get_dataset_names_from_group()

6.2 Attributes

6.2.1 opentype

6.2.2 fullPath

6.2.3 boverwrite

7 Usage Example

4.1.1 `hdf5File()`

4.1.2 `createFile()`

4.1.3 `openFile()`

4.1.4 `getFileptr()`

4.1.5 `getFilename()`

4.1.6 `getPath()`

4.1.7 `getFullPath()`

4.1.8 `checkFile()`

4.1.9 `getDatasetNames()`

4.1.10 `getAllDatasetNames()`

4.1.11 `close_file()`

4.1.12 `~hdf5File()`

5.1.1 `pfile`

5.1.2 `filename`

5.1.3 `path`

5.1.4 `bOwnsFile`

6.1.1 `ResFileExist_filestream()`

6.1.2 `checkHDF5File()`

6.1.3 `lockedByOtherProcess()`

6.1.4 `isOpenInCurrentProcess()`

6.1.5 `isHDF5FileOpen()`

6.1.6 `collect_datasets_recursive()`

6.1.7 `get_dataset_names_from_group()`

6.2.1 `opentype`

6.2.2 `fullPath`

6.2.3 `boverwrite`