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/*
* Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package ch.systemsx.cisd.hdf5;
import hdf.hdf5lib.exceptions.HDF5JavaException;
import ch.systemsx.cisd.base.mdarray.MDFloatArray;
/**
* An interface that provides methods for reading <code>float</code> values from HDF5 files.
* <p>
* Obtain an object implementing this interface by calling {@link IHDF5Reader#float32()}.
* <p>
* <i>Note:</i> 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.
* <p>
* <i>Note:<i> If the values read are unsigned, use the methods in {@link UnsignedIntUtils} to convert
* to a larger Java integer type that can hold all values as unsigned.
*
* @author Bernd Rinn
*/
public interface IHDF5FloatReader
{
// /////////////////////
// Attributes
// /////////////////////
/**
* Reads a <code>float</code> attribute named <var>attributeName</var> from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param attributeName The name of the attribute to read.
* @return The attribute value read from the data set.
*/
public float getAttr(String objectPath, String attributeName);
/**
* Reads a <code>float[]</code> attribute named <var>attributeName</var> from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param attributeName The name of the attribute to read.
* @return The attribute value read from the data set.
*/
public float[] getArrayAttr(String objectPath, String attributeName);
/**
* Reads a multi-dimensional array <code>float</code> attribute named <var>attributeName</var>
* from the data set <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param attributeName The name of the attribute to read.
* @return The attribute array value read from the data set.
*/
public MDFloatArray getMDArrayAttr(String objectPath,
String attributeName);
/**
* Reads a <code>float</code> matrix attribute named <var>attributeName</var>
* from the data set <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param attributeName The name of the attribute to read.
* @return The attribute matrix value read from the data set.
*/
public float[][] getMatrixAttr(String objectPath, String attributeName)
throws HDF5JavaException;
// /////////////////////
// Data Sets
// /////////////////////
/**
* Reads a <code>float</code> value from the data set <var>objectPath</var>. This method
* doesn't check the data space but simply reads the first value.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @return The value read from the data set.
*/
public float read(String objectPath);
/**
* Reads a <code>float</code> array (of rank 1) from the data set <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @return The data read from the data set.
*/
public float[] readArray(String objectPath);
/**
* Reads a multi-dimensional <code>float</code> array data set <var>objectPath</var>
* into a given <var>array</var> in memory.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param array The array to read the data into.
* @param memoryOffset The offset in the array to write the data to.
* @return The effective dimensions of the block in <var>array</var> that was filled.
*/
public int[] readToMDArrayWithOffset(String objectPath,
MDFloatArray array, int[] memoryOffset);
/**
* Reads a multi-dimensional <code>float</code> array data set <var>objectPath</var>
* into a given <var>array</var> in memory.
*
* @param dataSet The data set to read from.
* @param array The array to read the data into.
* @param memoryOffset The offset in the array to write the data to.
* @return The effective dimensions of the block in <var>array</var> that was filled.
*/
public int[] readToMDArrayWithOffset(HDF5DataSet dataSet,
MDFloatArray array, int[] memoryOffset);
/**
* Reads a block of the multi-dimensional <code>float</code> array data set
* <var>objectPath</var> into a given <var>array</var> in memory.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param array The array to read the data into.
* @param blockDimensions The size of the block to read along each axis.
* @param offset The offset of the block in the data set.
* @param memoryOffset The offset of the block in the array to write the data to.
* @return The effective dimensions of the block in <var>array</var> that was filled.
*/
public int[] readToMDArrayBlockWithOffset(String objectPath,
MDFloatArray array, int[] blockDimensions, long[] offset,
int[] memoryOffset);
/**
* Reads a block of the multi-dimensional <code>float</code> array data set
* <var>objectPath</var> into a given <var>array</var> in memory.
*
* @param dataSet The data set to read from.
* @param array The array to read the data into.
* @param blockDimensions The size of the block to read along each axis.
* @param offset The offset of the block in the data set.
* @param memoryOffset The offset of the block in the array to write the data to.
* @return The effective dimensions of the block in <var>array</var> that was filled.
*/
public int[] readToMDArrayBlockWithOffset(HDF5DataSet dataSet,
MDFloatArray array, int[] blockDimensions, long[] offset,
int[] memoryOffset);
/**
* Reads a block from a <code>float</code> array (of rank 1) from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockSize The block size (this will be the length of the <code>float[]</code> returned
* if the data set is long enough).
* @param blockNumber The number of the block to read (starting with 0, offset: multiply with
* <var>blockSize</var>).
* @return The data read from the data set. The length will be min(size - blockSize*blockNumber,
* blockSize).
*/
public float[] readArrayBlock(String objectPath, int blockSize,
long blockNumber);
/**
* Reads a block from a <code>int</code> array (of rank 1) from the <var>dataSet</var>.
* <p>
* <i>This method is faster than {@link #readArrayBlock(String, int, long)}
* when called many times on the same data set.</i>
*
* @param dataSet The data set to read from.
* @param blockSize The block size (this will be the length of the <code>int[]</code> returned
* if the data set is long enough).
* @param blockNumber The number of the block to read (starting with 0, offset: multiply with
* <var>blockSize</var>).
* @return The data read from the data set. The length will be min(size - blockSize*blockNumber,
* blockSize).
*/
public float[] readArrayBlock(HDF5DataSet dataSet, int blockSize,
long blockNumber);
/**
* Reads a block from <code>float</code> array (of rank 1) from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockSize The block size (this will be the length of the <code>float[]</code>
* returned).
* @param offset The offset of the block in the data set to start reading from (starting with 0).
* @return The data block read from the data set.
*/
public float[] readArrayBlockWithOffset(String objectPath, int blockSize,
long offset);
/**
* Reads a block from <code>int</code> array (of rank 1) from the <var>dataSet</var>.
* <p>
* <i>This method is faster than {@link #readArrayBlockWithOffset(String, int, long)}
* when called many times on the same data set.</i>
*
* @param dataSet The data set to read from.
* @param blockSize The block size (this will be the length of the <code>int[]</code>
* returned).
* @param offset The offset of the block in the data set to start reading from (starting with 0).
* @return The data block read from the data set.
*/
public float[] readArrayBlockWithOffset(HDF5DataSet dataSet, int blockSize,
long offset);
/**
* Reads a <code>float</code> matrix (array of arrays) from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @return The data read from the data set.
*
* @throws HDF5JavaException If the data set <var>objectPath</var> is not of rank 2.
*/
public float[][] readMatrix(String objectPath) throws HDF5JavaException;
/**
* Reads a <code>float</code> matrix (array of arrays) from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockSizeX The size of the block in the x dimension.
* @param blockSizeY The size of the block in the y dimension.
* @param blockNumberX The block number in the x dimension (offset: multiply with
* <code>blockSizeX</code>).
* @param blockNumberY The block number in the y dimension (offset: multiply with
* <code>blockSizeY</code>).
* @return The data block read from the data set.
*
* @throws HDF5JavaException If the data set <var>objectPath</var> is not of rank 2.
*/
public float[][] readMatrixBlock(String objectPath, int blockSizeX,
int blockSizeY, long blockNumberX, long blockNumberY)
throws HDF5JavaException;
/**
* Reads a <code>float</code> matrix (array of arrays) from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockSizeX The size of the block in the x dimension.
* @param blockSizeY The size of the block in the y dimension.
* @param offsetX The offset in x dimension in the data set to start reading from.
* @param offsetY The offset in y dimension in the data set to start reading from.
* @return The data block read from the data set.
*
* @throws HDF5JavaException If the data set <var>objectPath</var> is not of rank 2.
*/
public float[][] readMatrixBlockWithOffset(String objectPath,
int blockSizeX, int blockSizeY, long offsetX, long offsetY)
throws HDF5JavaException;
/**
* Reads a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @return The data read from the data set.
*/
public MDFloatArray readMDArray(String objectPath);
/**
* Reads part or all of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param params The parameter block specifying the block or slice to read from the array.
* @return The data read from the data set.
*/
public MDFloatArray readMDArray(String objectPath, HDF5ArrayBlockParams params);
/**
* Reads part or all of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>.
*
* @param dataSet The data set to read from.
* @param params The parameter block specifying the block or slice to read from the array.
* @return The data read from the data set.
*/
public MDFloatArray readMDArray(HDF5DataSet dataSet, HDF5ArrayBlockParams params);
/**
* Reads a slice of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArraySlice(String objectPath, IndexMap boundIndices);
/**
* Reads a slice of a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>. 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.
*
* @param dataSet The data set to read from.
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArraySlice(HDF5DataSet dataSet, IndexMap boundIndices);
/**
* Reads a slice of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArraySlice(String objectPath, long[] boundIndices);
/**
* Reads a slice of a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>. 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.
*
* @param dataSet The data set to read from.
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArraySlice(HDF5DataSet dataSet, long[] boundIndices);
/**
* Reads a block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @return The data block read from the data set.
*/
public MDFloatArray readMDArrayBlock(String objectPath,
int[] blockDimensions, long[] blockNumber);
/**
* Reads a block from a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @return The data block read from the data set.
*/
public MDFloatArray readMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions,
long[] blockNumber);
/**
* Reads a sliced block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions,
long[] blockNumber, IndexMap boundIndices);
/**
* Reads a sliced block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions,
long[] blockNumber, IndexMap boundIndices);
/**
* Reads a sliced block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlock(String objectPath, int[] blockDimensions,
long[] blockNumber, long[] boundIndices);
/**
* Reads a sliced block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param blockNumber The block number in each dimension (offset: multiply with the
* <var>blockDimensions</var> in the according dimension).
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlock(HDF5DataSet dataSet, int[] blockDimensions,
long[] blockNumber, long[] boundIndices);
/**
* Reads a block from a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArrayBlockWithOffset(String objectPath,
int[] blockDimensions, long[] offset);
/**
* Reads a block from a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @return The data block read from the data set.
*/
public MDFloatArray readMDArrayBlockWithOffset(HDF5DataSet dataSet,
int[] blockDimensions, long[] offset);
/**
* Reads a sliced block of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions,
long[] offset, IndexMap boundIndices);
/**
* Reads a sliced block of a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>. 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.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @param boundIndices The mapping of indices to index values which should be bound. For example
* a map of <code>new IndexMap().mapTo(2, 5).mapTo(4, 7)</code> has 2 and 4 as bound
* indices and binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet, int[] blockDimensions,
long[] offset, IndexMap boundIndices);
/**
* Reads a sliced block of a multi-dimensional <code>float</code> array from the data set
* <var>objectPath</var>. 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.
*
* @param objectPath The name (including path information) of the data set object in the file.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlockWithOffset(String objectPath, int[] blockDimensions,
long[] offset, long[] boundIndices);
/**
* Reads a sliced block of a multi-dimensional <code>float</code> array from the data set
* <var>dataSet</var>. 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.
*
* @param dataSet The data set to read from.
* @param blockDimensions The extent of the block in each dimension.
* @param offset The offset in the data set to start reading from in each dimension.
* @param 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
* <code>new long[] { -1, -1, 5, -1, 7, -1 }</code> has 2 and 4 as bound indices and
* binds them to the values 5 and 7, respectively.
* @return The data block read from the data set.
*/
public MDFloatArray readSlicedMDArrayBlockWithOffset(HDF5DataSet dataSet, int[] blockDimensions,
long[] offset, long[] boundIndices);
/**
* Provides all natural blocks of this one-dimensional data set to iterate over.
*
* @see HDF5DataBlock
* @throws HDF5JavaException If the data set is not of rank 1.
*/
public Iterable<HDF5DataBlock<float[]>> getArrayNaturalBlocks(
String dataSetPath)
throws HDF5JavaException;
/**
* Provides all natural blocks of this multi-dimensional data set to iterate over.
*
* @see HDF5MDDataBlock
*/
public Iterable<HDF5MDDataBlock<MDFloatArray>> getMDArrayNaturalBlocks(
String dataSetPath);
}
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