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| HDF5File [Import/Export of Images and Arrays in HDF5 Format] |

Access to HDF5 files. More...

`#include <vigra/hdf5impex.hxx>`

List of all members.

## Public Types
enum | OpenMode
| Set how a file is opened. OpenMode::New creates a new file. If the file already exists, overwrite it. More...
## Public Member Functions
void | cd (std::string groupName)
| Change the current group. If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
void | cd_mk (std::string groupName)
| Change the current group; create it if nescessary. If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
bool | cd_up ()
| Change the current group to its parent group. returns true if successful, false otherwise.
template<unsigned int N, class T>
void | createDataset (std::string datasetName, typename MultiArrayShape< N >::type shape, T init, int iChunkSize=0, int compressionParameter=0)
| Create a new dataset. This function can be used to create a dataset filled with a default value, for example before writing data into it using writeBlock(). Attention: only atomic datatypes are provided. For spectral data, add an dimension (case RGB: add one dimension of size 3).
std::string | filename ()
| Get the name of the associated file.
void | flushToDisk ()
| Immediately write all data to disk.
std::string | getAttribute (std::string datasetName, std::string attributeName)
| Get an attribute string of an object.
hssize_t | getDatasetDimensions (std::string datasetName)
| Get the number of dimensions of a certain dataset If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
ArrayVector< hsize_t > | getDatasetShape (std::string datasetName)
| Get the shape of each dimension of a certain dataset. Normally, this function is called after determining the dimension of the dataset using getDatasetDimensions(). If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
| HDF5File (std::string filename, OpenMode mode)
| Create a HDF5File object.
std::vector< std::string > | ls ()
| List the content of the current group. The function returns a vector of strings holding the entries of the current group. Only datasets and groups are listed, other objects (e.g. datatypes) are ignored. Group names always have an ending "/".
void | mkdir (std::string groupName)
| Create a new group. If the first character is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
std::string | pwd ()
| Get the path of the current group.
template<unsigned int N, class T>
void | read (std::string datasetName, MultiArrayView< N, T, UnstridedArrayTag > array)
| Read data into a multi array. If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.
template<class T>
void | readAtomic (std::string datasetName, T &data)
| Read a single value. This functions allows to read a single datum of atomic datatype (int, long, double) from the HDF5 file. So it is not nescessary to create a MultiArray of size 1 to read a single number.
template<unsigned int N, class T>
void | readBlock (std::string datasetName, typename MultiArrayShape< N >::type blockOffset, typename MultiArrayShape< N >::type blockShape, MultiArrayView< N, T, UnstridedArrayTag > array)
| Read a block of data into s multi array. This function allows to read a small block out of a larger volume stored in a HDF5 dataset.
void | root ()
| Change current group to "/".
void | setAttribute (std::string datasetName, std::string attributeName, std::string text)
| Attach a string attribute to an existing object. The attribute can be attached to datasets and groups. The string may have arbitrary length.
template<unsigned int N, class T>
void | write (std::string datasetName, const MultiArrayView< N, T, UnstridedArrayTag > &array, typename MultiArrayShape< N >::type chunkSize, int compression=0)
| Write multi arrays. Chunks can be activated by providing a MultiArrayShape as chunkSize. chunkSize must have equal dimension as array.
template<unsigned int N, class T>
void | write (std::string datasetName, const MultiArrayView< N, T, UnstridedArrayTag > &array, int iChunkSize=0, int compression=0)
| Write multi arrays. Chunks can be activated by setting.
template<class T>
void | writeAtomic (std::string datasetName, const T data)
| Write single value as dataset. This functions allows to write data of atomic datatypes (int, long, double) as a dataset in the HDF5 file. So it is not nescessary to create a MultiArray of size 1 to write a single number.
template<unsigned int N, class T>
void | writeBlock (std::string datasetName, typename MultiArrayShape< N >::type blockOffset, const MultiArrayView< N, T, UnstridedArrayTag > &array)
| Write a multi array into a larger volume. blockOffset determines the position, where array is written.
| ~HDF5File ()
| Destructor to make sure that all data is flushed before closing the file.

## Detailed Description

Access to HDF5 files.

HDF5File proviedes a convenient way of accessing data in HDF5 files. vigra::MultiArray structures of any dimension can be stored to / loaded from HDF5 files. Typical HDF5 features like subvolume access, chunks and data compression are available, string attributes can be attached to any dataset or group. Group- or dataset-handles are encapsulated in the class and managed automatically. The internal file-system like structure can be accessed by functions like "cd()" or "mkdir()".

Example: Write the MultiArray out_multi_array to file. Change the current directory to "/group" and read in the same MultiArray as in_multi_array.

    HDF5File file("/path/to/file",HDF5File::New);
    file.mkdir("group");
    file.write("/group/dataset", out_multi_array);

    file.cd("/group");
    file.read("dataset", in_multi_array);

#include <vigra/hdf5impex.hxx>
Namespace: vigra

## Member Enumeration Documentation

enum OpenMode

Set how a file is opened. OpenMode::New creates a new file. If the file already exists, overwrite it.

OpenMode::Open opens a file for reading/writing. The file will be created, if nescessary.

## Constructor & Destructor Documentation

HDF5File | ( | std::string | filename,
|  | OpenMode | mode |
| ) |  |  |

Create a HDF5File object.

Creates or opens HDF5 file at position filename. The current group is set to "/".

## Member Function Documentation

template<unsigned int N, class T>
void createDataset | ( | std::string | datasetName,
|  | typename MultiArrayShape< N >::type | shape,
|  | T | init,
|  | int | iChunkSize = `0`,
|  | int | compressionParameter = `0` |
| ) |  |  |

Create a new dataset. This function can be used to create a dataset filled with a default value, for example before writing data into it using writeBlock(). Attention: only atomic datatypes are provided. For spectral data, add an dimension (case RGB: add one dimension of size 3).

shape determines the dimension and the size of the dataset.

Chunks can be activated by providing a MultiArrayShape as chunkSize. chunkSize must have equal dimension as array.

Compression can be activated by setting

     compression = parameter; // 0 < parameter <= 9

where 0 stands for no compression and 9 for maximum compression.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<class T>
void readAtomic | ( | std::string | datasetName,
|  | T & | data |
| ) |  |  |

Read a single value. This functions allows to read a single datum of atomic datatype (int, long, double) from the HDF5 file. So it is not nescessary to create a MultiArray of size 1 to read a single number.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<unsigned int N, class T>
void readBlock | ( | std::string | datasetName,
|  | typename MultiArrayShape< N >::type | blockOffset,
|  | typename MultiArrayShape< N >::type | blockShape,
|  | MultiArrayView< N, T, UnstridedArrayTag > | array |
| ) |  |  |

Read a block of data into s multi array. This function allows to read a small block out of a larger volume stored in a HDF5 dataset.

blockOffset determines the position of the block. blockSize determines the size in each dimension of the block.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<unsigned int N, class T>
void write | ( | std::string | datasetName,
|  | const MultiArrayView< N, T, UnstridedArrayTag > & | array,
|  | typename MultiArrayShape< N >::type | chunkSize,
|  | int | compression = `0` |
| ) |  |  |

Write multi arrays. Chunks can be activated by providing a MultiArrayShape as chunkSize. chunkSize must have equal dimension as array.

Compression can be activated by setting

     compression = parameter; // 0 < parameter <= 9

where 0 stands for no compression and 9 for maximum compression.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<unsigned int N, class T>
void write | ( | std::string | datasetName,
|  | const MultiArrayView< N, T, UnstridedArrayTag > & | array,
|  | int | iChunkSize = `0`,
|  | int | compression = `0` |
| ) |  |  |

Write multi arrays. Chunks can be activated by setting.

     iChunkSize = size; //size > 0

. The chunks will be hypercubes with edge length size.

Compression can be activated by setting

     compression = parameter; // 0 < parameter <= 9

where 0 stands for no compression and 9 for maximum compression.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<class T>
void writeAtomic | ( | std::string | datasetName,
|  | const T | data |
| ) |  |  |

Write single value as dataset. This functions allows to write data of atomic datatypes (int, long, double) as a dataset in the HDF5 file. So it is not nescessary to create a MultiArray of size 1 to write a single number.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

template<unsigned int N, class T>
void writeBlock | ( | std::string | datasetName,
|  | typename MultiArrayShape< N >::type | blockOffset,
|  | const MultiArrayView< N, T, UnstridedArrayTag > & | array |
| ) |  |  |

Write a multi array into a larger volume. blockOffset determines the position, where array is written.

Chunks can be activated by providing a MultiArrayShape as chunkSize. chunkSize must have equal dimension as array.

Compression can be activated by setting

     compression = parameter; // 0 < parameter <= 9

where 0 stands for no compression and 9 for maximum compression.

If the first character of datasetName is a "/", the path will be interpreted as absolute path, otherwise it will be interpreted as path relative to the current group.

The documentation for this class was generated from the following file:

- vigra/hdf5impex.hxx

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de) Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany | html generated using doxygen and Python vigra 1.7.1 (3 Dec 2010)