iRoCS Toolbox  1.1.0
Functions
HDF5IOWrapper Namespace Reference

Functions

template<typename DataT , typename ElSizeT , int Dim>
void readDataset (blitz::Array< DataT, Dim > &data, blitz::TinyVector< ElSizeT, Dim > &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, iRoCS::ProgressReporter *pr=NULL)
 Read a scalar n-dimensional dataset with element size. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void readDataset (blitz::Array< DataT, Dim > &data, blitz::TinyVector< ElSizeT, Dim > &elSize, BlitzH5File const &inFile, std::string const &dsName, iRoCS::ProgressReporter *pr=NULL)
 Read a scalar n-dimensional dataset with element size. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void readDataset (blitz::Array< DataT, Dim > &data, blitz::TinyVector< ElSizeT, Dim-1 > &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, iRoCS::ProgressReporter *pr=NULL)
 Read a scalar n-dimensional timelapse dataset with element size. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void readDataset (blitz::Array< DataT, Dim > &data, blitz::TinyVector< ElSizeT, Dim-1 > &elSize, BlitzH5File const &inFile, std::string const &dsName, iRoCS::ProgressReporter *pr=NULL)
 Read a scalar n-dimensional timelapse dataset with element size. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim > const &elSize, std::string const &fileName, std::string const &dsName, DataT displayMin, DataT displayMax, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim > const &elSize, BlitzH5File &outFile, std::string const &dsName, DataT displayMin, DataT displayMax, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim >const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim >const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, std::string const &fileName, std::string const &dsName, DataT displayMin, DataT displayMax, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, DataT displayMin, DataT displayMax, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void writeDataset (blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &data, blitz::TinyVector< ElSizeT, OuterDim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, std::string const &fileName, std::string const &dsName, DataT displayMin, DataT displayMax, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, BlitzH5File &outFile, std::string const &dsName, DataT displayMin, DataT displayMax, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int Dim>
void writeDataset (blitz::Array< unsigned char, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int Dim>
void writeDataset (blitz::Array< unsigned char, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< std::complex< DataT >, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a complex n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< std::complex< DataT >, Dim > const &data, blitz::TinyVector< ElSizeT, Dim > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a complex n-dimensional dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, std::string const &fileName, std::string const &dsName, DataT displayMin, DataT displayMax, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< DataT, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, DataT displayMin, DataT displayMax, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int Dim>
void writeDataset (blitz::Array< unsigned char, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename ElSizeT , int Dim>
void writeDataset (blitz::Array< unsigned char, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a scalar n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< std::complex< DataT >, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, std::string const &fileName, std::string const &dsName, bool throwErrors=false, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a complex n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 
template<typename DataT , typename ElSizeT , int Dim>
void writeDataset (blitz::Array< std::complex< DataT >, Dim > const &data, blitz::TinyVector< ElSizeT, Dim-1 > const &elSize, BlitzH5File &outFile, std::string const &dsName, int compression=0, iRoCS::ProgressReporter *pr=NULL, std::string const &dim_interpretation="")
 Write a complex n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation. More...
 

Function Documentation

◆ readDataset() [1/4]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::readDataset ( blitz::Array< DataT, Dim > &  data,
blitz::TinyVector< ElSizeT, Dim > &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
iRoCS::ProgressReporter pr = NULL 
)

Read a scalar n-dimensional dataset with element size.

Parameters
dataThe blitz::Array to read the dataset to
elSizeThe blitz::TinyVector to read the element size to
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
prIf given, progress will be reported via the given iRoCS::ProgressReporter
Exceptions
BlitzH5ErrorIf throwErrors is true

Referenced by BlitzH5File::name().

◆ readDataset() [2/4]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::readDataset ( blitz::Array< DataT, Dim > &  data,
blitz::TinyVector< ElSizeT, Dim > &  elSize,
BlitzH5File const &  inFile,
std::string const &  dsName,
iRoCS::ProgressReporter pr = NULL 
)

Read a scalar n-dimensional dataset with element size.

Parameters
dataThe blitz::Array to read the dataset to
elSizeThe blitz::TinyVector to read the element size to
inFileThe BlitzH5File containing the dataset to read
dsNameThe full path of the hdf5 dataset
prIf given, progress will be reported via the given iRoCS::ProgressReporter
Exceptions
BlitzH5ErrorIf the dataset cannot be read for any reason

◆ readDataset() [3/4]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::readDataset ( blitz::Array< DataT, Dim > &  data,
blitz::TinyVector< ElSizeT, Dim-1 > &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
iRoCS::ProgressReporter pr = NULL 
)

Read a scalar n-dimensional timelapse dataset with element size.

Parameters
dataThe blitz::Array to read the dataset to
elSizeThe blitz::TinyVector to read the element size to
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
prIf given, progress will be reported via the given iRoCS::ProgressReporter
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ readDataset() [4/4]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::readDataset ( blitz::Array< DataT, Dim > &  data,
blitz::TinyVector< ElSizeT, Dim-1 > &  elSize,
BlitzH5File const &  inFile,
std::string const &  dsName,
iRoCS::ProgressReporter pr = NULL 
)

Read a scalar n-dimensional timelapse dataset with element size.

Parameters
dataThe blitz::Array to read the dataset to
elSizeThe blitz::TinyVector to read the element size to
inFileThe BlitzH5File containing the dataset to read
dsNameThe full path of the hdf5 dataset
prIf given, progress will be reported via the given iRoCS::ProgressReporter
Exceptions
BlitzH5ErrorIf the dataset cannot be read for any reason

◆ writeDataset() [1/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

Referenced by BlitzH5File::name().

◆ writeDataset() [2/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be writen for any reason

◆ writeDataset() [3/26]

template<typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim >const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [4/26]

template<typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim >const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [5/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [6/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [7/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [8/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [9/26]

template<typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D vectorial timelapse datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [10/26]

template<typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< unsigned char, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D vectorial timelapse datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [11/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [12/26]

template<typename DataT , typename ElSizeT , int InnerDim, int OuterDim>
void HDF5IOWrapper::writeDataset ( blitz::Array< blitz::TinyVector< DataT, InnerDim >, OuterDim > const &  data,
blitz::TinyVector< ElSizeT, OuterDim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a vectorial n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D vectorial datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]xc" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [13/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [14/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [15/26]

template<typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< unsigned char, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [16/26]

template<typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< unsigned char, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity", display_min := 0, display_max := 255

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [17/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [18/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := min(0, min(data)), display_max := max(data)

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [19/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< std::complex< DataT >, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a complex n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := max(0, min(Re(data))) + i * max(0, min(Im(data))), display_max := max(Re(data)) + i * max(Im(data))

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [20/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< std::complex< DataT >, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a complex n-dimensional dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := max(0, min(Re(data))) + i * max(0, min(Im(data))), display_max := max(Re(data)) + i * max(Im(data))

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [21/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [22/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< DataT, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
DataT  displayMin,
DataT  displayMax,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity"

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
displayMinThe value to use as minimum value in visualizations
displayMaxThe value to use as maximum value in visualizations
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [23/26]

template<typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< unsigned char, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity", displayMin = 0, displayMax = 255

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [24/26]

template<typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< unsigned char, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a scalar n-dimensional timelapse 8Bit unsigned integer dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "intensity", displayMin = 0, displayMax = 255

Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason

◆ writeDataset() [25/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< std::complex< DataT >, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
std::string const &  fileName,
std::string const &  dsName,
bool  throwErrors = false,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a complex n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := max(0, min(Re(data))) + i * max(0, min(Im(data))), display_max := max(Re(data)) + i * max(Im(data))

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
fileNameThe name of the hdf5 file
dsNameThe full path of the hdf5 dataset
throwErrorsIf given, BlitzH5Error will be thrown on failure otherwise an error message is written to std::cout and the program terminated.
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf throwErrors is true

◆ writeDataset() [26/26]

template<typename DataT , typename ElSizeT , int Dim>
void HDF5IOWrapper::writeDataset ( blitz::Array< std::complex< DataT >, Dim > const &  data,
blitz::TinyVector< ElSizeT, Dim-1 > const &  elSize,
BlitzH5File outFile,
std::string const &  dsName,
int  compression = 0,
iRoCS::ProgressReporter pr = NULL,
std::string const &  dim_interpretation = "" 
)

Write a complex n-dimensional timelapse dataset with element size and additional meta-information for dataset interpretation.

Meta-Information which are stored as local attributes are:

  • element_size_um - The element size in micrometers
  • display_min - Hint on the minimum value for visualization
  • display_max - Hint on the maximum value for visualization
  • dim_interpretation - Hint on how to interpret the different dimensions of the dataset (string made up of 'x', 'y', 'z', 'c', 't' characters)
  • value_interpretation - Hint on how to interpret the channels

Written fixed metadata using this function: value_interpretation := "vector", display_min := max(0, min(Re(data))) + i * max(0, min(Im(data))), display_max := max(Re(data)) + i * max(Im(data))

Remarks
This function is a convenience function calling the general version for n-D datasets of arbitrary datatype.
Parameters
dataThe blitz::Array to write
elSizeThe blitz::TinyVector containing the element size in micrometers to write
outFileThe hdf5 file to write the dataset to
dsNameThe full path of the hdf5 dataset
compressionThe compression level to use (0-9). 0 means no compression
prIf given, progress will be reported via the given iRoCS::ProgressReporter
dim_interpretationA hint of how to interpret the dimensions of the dataset. E.g. "zyxc" means that the first three dimensions are ordinary coordinates and the last is a channel index. If not provided by the user a default of "t[z][y]x" will be generated.
Exceptions
BlitzH5ErrorIf the dataset cannot be written for any reason