ch.systemsx.cisd.hdf5

Interface IHDF5DoubleReader

All Known Subinterfaces:

IHDF5DoubleWriter

public interface IHDF5DoubleReader

An interface that provides methods for reading double values from HDF5 files.

Obtain an object implementing this interface by calling IHDF5Reader.float64().

Note: This interface supports block access and sliced access (which is a special cases of block access) to arrays. The performance of this block access can vary greatly depending on how the data are layed out in the HDF5 file. For best performance, the block (or slice) dimension should be chosen to be equal to the chunk dimensions of the array, as in this case the block written / read are stored as consecutive value in the HDF5 file and one write / read access will suffice.

Note: If the values read are unsigned, use the methods in UnsignedIntUtils to convert to a larger Java integer type that can hold all values as unsigned.

Method Summary

Modifier and Type	Method and Description
double[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a double[] attribute named attributeName from the data set objectPath.
java.lang.Iterable<HDF5DataBlock<double[]>>	getArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this one-dimensional data set to iterate over.
double	getAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a double attribute named attributeName from the data set objectPath.
double[][]	getMatrixAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a double matrix attribute named attributeName from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	getMDArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Reads a multi-dimensional array double attribute named attributeName from the data set objectPath.
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDDoubleArray>>	getMDArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this multi-dimensional data set to iterate over.
double	read(java.lang.String objectPath) Reads a double value from the data set objectPath.
double[]	readArray(java.lang.String objectPath) Reads a double array (of rank 1) from the data set objectPath.
double[]	readArrayBlock(HDF5DataSet dataSet, int blockSize, long blockNumber) Reads a block from a int array (of rank 1) from the dataSet.
double[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block from a double array (of rank 1) from the data set objectPath.
double[]	readArrayBlockWithOffset(HDF5DataSet dataSet, int blockSize, long offset) Reads a block from int array (of rank 1) from the dataSet.
double[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset) Reads a block from double array (of rank 1) from the data set objectPath.
double[][]	readMatrix(java.lang.String objectPath) Reads a double matrix (array of arrays) from the data set objectPath.
double[][]	readMatrixBlock(java.lang.String objectPath, int blockSizeX, int blockSizeY, long blockNumberX, long blockNumberY) Reads a double matrix (array of arrays) from the data set objectPath.
double[][]	readMatrixBlockWithOffset(java.lang.String objectPath, int blockSizeX, int blockSizeY, long offsetX, long offsetY) Reads a double matrix (array of arrays) from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArray(HDF5DataSet dataSet, HDF5ArrayBlockParams params) Reads part or all of a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArray(java.lang.String objectPath) Reads a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArray(java.lang.String objectPath, HDF5ArrayBlockParams params) Reads part or all of a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions, long[] blockNumber) Reads a block from a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber) Reads a block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArrayBlockWithOffset(HDF5DataSet dataSet, int[] blockDimensions, long[] offset) Reads a block from a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset) Reads a block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArraySlice(HDF5DataSet dataSet, IndexMap boundIndices) Reads a slice of a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArraySlice(HDF5DataSet dataSet, long[] boundIndices) Reads a slice of a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArraySlice(java.lang.String objectPath, IndexMap boundIndices) Reads a slice of a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readMDArraySlice(java.lang.String objectPath, long[] boundIndices) Reads a slice of a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) Reads a sliced block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions, long[] blockNumber, long[] boundIndices) Reads a sliced block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber, IndexMap boundIndices) Reads a sliced block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber, long[] boundIndices) Reads a sliced block from a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet, int[] blockDimensions, long[] offset, IndexMap boundIndices) Reads a sliced block of a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet, int[] blockDimensions, long[] offset, long[] boundIndices) Reads a sliced block of a multi-dimensional double array from the data set dataSet.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset, IndexMap boundIndices) Reads a sliced block of a multi-dimensional double array from the data set objectPath.
ch.systemsx.cisd.base.mdarray.MDDoubleArray	readSlicedMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset, long[] boundIndices) Reads a sliced block of a multi-dimensional double array from the data set objectPath.
int[]	readToMDArrayBlockWithOffset(HDF5DataSet dataSet, ch.systemsx.cisd.base.mdarray.MDDoubleArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) Reads a block of the multi-dimensional double array data set objectPath into a given array in memory.
int[]	readToMDArrayBlockWithOffset(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDDoubleArray array, int[] blockDimensions, long[] offset, int[] memoryOffset) Reads a block of the multi-dimensional double array data set objectPath into a given array in memory.
int[]	readToMDArrayWithOffset(HDF5DataSet dataSet, ch.systemsx.cisd.base.mdarray.MDDoubleArray array, int[] memoryOffset) Reads a multi-dimensional double array data set objectPath into a given array in memory.
int[]	readToMDArrayWithOffset(java.lang.String objectPath, ch.systemsx.cisd.base.mdarray.MDDoubleArray array, int[] memoryOffset) Reads a multi-dimensional double array data set objectPath into a given array in memory.

Method Detail

getAttr

double getAttr(java.lang.String objectPath,
               java.lang.String attributeName)

Reads a double attribute named attributeName from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

attributeName - The name of the attribute to read.

Returns:

The attribute value read from the data set.

getArrayAttr

double[] getArrayAttr(java.lang.String objectPath,
                      java.lang.String attributeName)

Reads a double[] attribute named attributeName from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

attributeName - The name of the attribute to read.

Returns:

The attribute value read from the data set.

getMDArrayAttr

ch.systemsx.cisd.base.mdarray.MDDoubleArray getMDArrayAttr(java.lang.String objectPath,
                                                           java.lang.String attributeName)

Reads a multi-dimensional array double attribute named attributeName from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

attributeName - The name of the attribute to read.

Returns:

The attribute array value read from the data set.

getMatrixAttr

double[][] getMatrixAttr(java.lang.String objectPath,
                         java.lang.String attributeName)
                  throws HDF5JavaException

Reads a double matrix attribute named attributeName from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

attributeName - The name of the attribute to read.

Returns:

The attribute matrix value read from the data set.

Throws:

HDF5JavaException

read

double read(java.lang.String objectPath)

Reads a double value from the data set objectPath. This method doesn't check the data space but simply reads the first value.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The value read from the data set.

readArray

double[] readArray(java.lang.String objectPath)

Reads a double array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readToMDArrayWithOffset

int[] readToMDArrayWithOffset(java.lang.String objectPath,
                              ch.systemsx.cisd.base.mdarray.MDDoubleArray array,
                              int[] memoryOffset)

Reads a multi-dimensional double array data set objectPath into a given array in memory.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

array - The array to read the data into.

memoryOffset - The offset in the array to write the data to.

Returns:

The effective dimensions of the block in array that was filled.

readToMDArrayWithOffset

int[] readToMDArrayWithOffset(HDF5DataSet dataSet,
                              ch.systemsx.cisd.base.mdarray.MDDoubleArray array,
                              int[] memoryOffset)

Reads a multi-dimensional double array data set objectPath into a given array in memory.

Parameters:

dataSet - The data set to read from.

array - The array to read the data into.

memoryOffset - The offset in the array to write the data to.

Returns:

The effective dimensions of the block in array that was filled.

readToMDArrayBlockWithOffset

int[] readToMDArrayBlockWithOffset(java.lang.String objectPath,
                                   ch.systemsx.cisd.base.mdarray.MDDoubleArray array,
                                   int[] blockDimensions,
                                   long[] offset,
                                   int[] memoryOffset)

Reads a block of the multi-dimensional double array data set objectPath into a given array in memory.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

array - The array to read the data into.

blockDimensions - The size of the block to read along each axis.

offset - The offset of the block in the data set.

memoryOffset - The offset of the block in the array to write the data to.

Returns:

The effective dimensions of the block in array that was filled.

readToMDArrayBlockWithOffset

int[] readToMDArrayBlockWithOffset(HDF5DataSet dataSet,
                                   ch.systemsx.cisd.base.mdarray.MDDoubleArray array,
                                   int[] blockDimensions,
                                   long[] offset,
                                   int[] memoryOffset)

Reads a block of the multi-dimensional double array data set objectPath into a given array in memory.

Parameters:

dataSet - The data set to read from.

array - The array to read the data into.

blockDimensions - The size of the block to read along each axis.

offset - The offset of the block in the data set.

memoryOffset - The offset of the block in the array to write the data to.

Returns:

The effective dimensions of the block in array that was filled.

readArrayBlock

double[] readArrayBlock(java.lang.String objectPath,
                        int blockSize,
                        long blockNumber)

Reads a block from a double array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size (this will be the length of the double[] returned if the data set is long enough).

blockNumber - The number of the block to read (starting with 0, offset: multiply with blockSize).

Returns:

The data read from the data set. The length will be min(size - blockSize*blockNumber, blockSize).

readArrayBlock

double[] readArrayBlock(HDF5DataSet dataSet,
                        int blockSize,
                        long blockNumber)

Reads a block from a int array (of rank 1) from the dataSet.

This method is faster than readArrayBlock(String, int, long) when called many times on the same data set.

Parameters:

dataSet - The data set to read from.

blockSize - The block size (this will be the length of the int[] returned if the data set is long enough).

blockNumber - The number of the block to read (starting with 0, offset: multiply with blockSize).

Returns:

The data read from the data set. The length will be min(size - blockSize*blockNumber, blockSize).

readArrayBlockWithOffset

double[] readArrayBlockWithOffset(java.lang.String objectPath,
                                  int blockSize,
                                  long offset)

Reads a block from double array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size (this will be the length of the double[] returned).

offset - The offset of the block in the data set to start reading from (starting with 0).

Returns:

The data block read from the data set.

readArrayBlockWithOffset

double[] readArrayBlockWithOffset(HDF5DataSet dataSet,
                                  int blockSize,
                                  long offset)

Reads a block from int array (of rank 1) from the dataSet.

This method is faster than readArrayBlockWithOffset(String, int, long) when called many times on the same data set.

Parameters:

dataSet - The data set to read from.

blockSize - The block size (this will be the length of the int[] returned).

offset - The offset of the block in the data set to start reading from (starting with 0).

Returns:

The data block read from the data set.

readMatrix

double[][] readMatrix(java.lang.String objectPath)
               throws HDF5JavaException

Reads a double matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the data set objectPath is not of rank 2.

readMatrixBlock

double[][] readMatrixBlock(java.lang.String objectPath,
                           int blockSizeX,
                           int blockSizeY,
                           long blockNumberX,
                           long blockNumberY)
                    throws HDF5JavaException

Reads a double matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSizeX - The size of the block in the x dimension.

blockSizeY - The size of the block in the y dimension.

blockNumberX - The block number in the x dimension (offset: multiply with blockSizeX).

blockNumberY - The block number in the y dimension (offset: multiply with blockSizeY).

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set objectPath is not of rank 2.

readMatrixBlockWithOffset

double[][] readMatrixBlockWithOffset(java.lang.String objectPath,
                                     int blockSizeX,
                                     int blockSizeY,
                                     long offsetX,
                                     long offsetY)
                              throws HDF5JavaException

Reads a double matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSizeX - The size of the block in the x dimension.

blockSizeY - The size of the block in the y dimension.

offsetX - The offset in x dimension in the data set to start reading from.

offsetY - The offset in y dimension in the data set to start reading from.

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set objectPath is not of rank 2.

readMDArray

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArray(java.lang.String objectPath)

Reads a multi-dimensional double array from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readMDArray

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArray(java.lang.String objectPath,
                                                        HDF5ArrayBlockParams params)

Reads part or all of a multi-dimensional double array from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

params - The parameter block specifying the block or slice to read from the array.

Returns:

The data read from the data set.

readMDArray

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArray(HDF5DataSet dataSet,
                                                        HDF5ArrayBlockParams params)

Reads part or all of a multi-dimensional double array from the data set objectPath.

Parameters:

dataSet - The data set to read from.

params - The parameter block specifying the block or slice to read from the array.

Returns:

The data read from the data set.

readMDArraySlice

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArraySlice(java.lang.String objectPath,
                                                             IndexMap boundIndices)

Reads a slice of a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readMDArraySlice

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArraySlice(HDF5DataSet dataSet,
                                                             IndexMap boundIndices)

Reads a slice of a multi-dimensional double array from the data set dataSet. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readMDArraySlice

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArraySlice(java.lang.String objectPath,
                                                             long[] boundIndices)

Reads a slice of a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readMDArraySlice

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArraySlice(HDF5DataSet dataSet,
                                                             long[] boundIndices)

Reads a slice of a multi-dimensional double array from the data set dataSet. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArrayBlock(java.lang.String objectPath,
                                                             int[] blockDimensions,
                                                             long[] blockNumber)

Reads a block from a multi-dimensional double array from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

Returns:

The data block read from the data set.

readMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArrayBlock(HDF5DataSet dataSet,
                                                             int[] blockDimensions,
                                                             long[] blockNumber)

Reads a block from a multi-dimensional double array from the data set dataSet.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

Returns:

The data block read from the data set.

readSlicedMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlock(java.lang.String objectPath,
                                                                   int[] blockDimensions,
                                                                   long[] blockNumber,
                                                                   IndexMap boundIndices)

Reads a sliced block from a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlock(HDF5DataSet dataSet,
                                                                   int[] blockDimensions,
                                                                   long[] blockNumber,
                                                                   IndexMap boundIndices)

Reads a sliced block from a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlock(java.lang.String objectPath,
                                                                   int[] blockDimensions,
                                                                   long[] blockNumber,
                                                                   long[] boundIndices)

Reads a sliced block from a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlock

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlock(HDF5DataSet dataSet,
                                                                   int[] blockDimensions,
                                                                   long[] blockNumber,
                                                                   long[] boundIndices)

Reads a sliced block from a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

blockNumber - The block number in each dimension (offset: multiply with the blockDimensions in the according dimension).

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArrayBlockWithOffset(java.lang.String objectPath,
                                                                       int[] blockDimensions,
                                                                       long[] offset)

Reads a block from a multi-dimensional double array from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

Returns:

The data block read from the data set.

readMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readMDArrayBlockWithOffset(HDF5DataSet dataSet,
                                                                       int[] blockDimensions,
                                                                       long[] offset)

Reads a block from a multi-dimensional double array from the data set dataSet.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

Returns:

The data block read from the data set.

readSlicedMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlockWithOffset(java.lang.String objectPath,
                                                                             int[] blockDimensions,
                                                                             long[] offset,
                                                                             IndexMap boundIndices)

Reads a sliced block of a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet,
                                                                             int[] blockDimensions,
                                                                             long[] offset,
                                                                             IndexMap boundIndices)

Reads a sliced block of a multi-dimensional double array from the data set dataSet. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

boundIndices - The mapping of indices to index values which should be bound. For example a map of new IndexMap().mapTo(2, 5).mapTo(4, 7) has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlockWithOffset(java.lang.String objectPath,
                                                                             int[] blockDimensions,
                                                                             long[] offset,
                                                                             long[] boundIndices)

Reads a sliced block of a multi-dimensional double array from the data set objectPath. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

readSlicedMDArrayBlockWithOffset

ch.systemsx.cisd.base.mdarray.MDDoubleArray readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet,
                                                                             int[] blockDimensions,
                                                                             long[] offset,
                                                                             long[] boundIndices)

Reads a sliced block of a multi-dimensional double array from the data set dataSet. The slice is defined by "bound indices", each of which is fixed to a given value. The returned data block only contains the free (i.e. non-fixed) indices.

Parameters:

dataSet - The data set to read from.

blockDimensions - The extent of the block in each dimension.

offset - The offset in the data set to start reading from in each dimension.

boundIndices - The array containing the values of the bound indices at the respective index positions, and -1 at the free index positions. For example an array of new long[] { -1, -1, 5, -1, 7, -1 } has 2 and 4 as bound indices and binds them to the values 5 and 7, respectively.

Returns:

The data block read from the data set.

getArrayNaturalBlocks

java.lang.Iterable<HDF5DataBlock<double[]>> getArrayNaturalBlocks(java.lang.String dataSetPath)
                                                           throws HDF5JavaException

Provides all natural blocks of this one-dimensional data set to iterate over.

Throws:

HDF5JavaException - If the data set is not of rank 1.

See Also:

HDF5DataBlock

getMDArrayNaturalBlocks

java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDDoubleArray>> getMDArrayNaturalBlocks(java.lang.String dataSetPath)

Provides all natural blocks of this multi-dimensional data set to iterate over.

See Also:

HDF5MDDataBlock