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org.eclipse.dawnsci.hdf5.HDF5Utils Maven / Gradle / Ivy
/*-
* Copyright 2015 Diamond Light Source Ltd.
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*/
package org.eclipse.dawnsci.hdf5;
import java.io.File;
import java.io.Serializable;
import java.net.InetAddress;
import java.net.UnknownHostException;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.TimeoutException;
import org.eclipse.dawnsci.analysis.api.io.ScanFileHolderException;
import org.eclipse.dawnsci.analysis.api.tree.Node;
import org.eclipse.dawnsci.analysis.api.tree.Tree;
import org.eclipse.dawnsci.nexus.NexusException;
import org.eclipse.dawnsci.nexus.NexusFile;
import org.eclipse.january.dataset.DTypeUtils;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.DatasetFactory;
import org.eclipse.january.dataset.DatasetUtils;
import org.eclipse.january.dataset.IDataset;
import org.eclipse.january.dataset.LazyWriteableDataset;
import org.eclipse.january.dataset.SliceND;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import hdf.hdf5lib.structs.H5O_info_t;
public class HDF5Utils {
private static final Logger logger = LoggerFactory.getLogger(HDF5Utils.class);
private static String host;
/**
* Gracefully gets the local host name (if there is a mis-configuration or any other issue, "localhost" is returned)
* @return local host name
*/
public static String getLocalHostName() {
if (host == null) {
ExecutorService ex = Executors.newSingleThreadExecutor();
Future fu = ex.submit(new Callable() {
@Override
public String call() throws Exception {
try { // this can block for a long while
return InetAddress.getLocalHost().getHostName();
} catch (UnknownHostException e) {
logger.error("Could not find host name", e);
}
return null;
}
});
try { // time-out after 5 seconds
host = fu.get(5, TimeUnit.SECONDS);
} catch (TimeoutException e) {
logger.error("Timed out finding host name", e);
} catch (InterruptedException e) {
logger.error("Thread interrupted on finding host name", e);
Thread.currentThread().interrupt();
} catch (ExecutionException e) {
logger.error("Task aborted on finding host name", e);
}
if (host == null) {
host = "localhost";
}
}
return host;
}
/**
* Check if file is a HDF5 file
* @param fileName
* @return true if it can be read as an HDF5 file
*/
public static boolean isHDF5(final String fileName) {
if (fileName == null || !new File(fileName).canRead()) {
return false;
}
try {
return H5.H5Fis_hdf5(fileName);
} catch (HDF5LibraryException e) {
logger.error("Problem using HDF5 library when checking if a file is HDF5: {}", fileName, e);
}
return false;
}
/**
* Create a dataset from the given data object
* @param data
* @param shape
* @param dtype
* @param extend true dataset for unsigned types
* @return dataset
*/
public static Dataset createDataset(final Object data, final int[] shape, final int dtype,
final boolean extend) {
Dataset ds = DatasetFactory.createFromObject(dtype, data);
if (extend) {
ds = DatasetUtils.makeUnsigned(ds);
}
ds.setShape(shape);
return ds;
}
/**
* Translate between data type and dataset type
* @param dclass data type class
* @param dsize data type element size in bytes
* @return dataset type
*/
public static int getDType(final int dclass, final int dsize) {
if (dclass == HDF5Constants.H5T_STRING) {
return Dataset.STRING;
} else if (dclass == HDF5Constants.H5T_INTEGER) {
switch (dsize) {
case 1:
return Dataset.INT8;
case 2:
return Dataset.INT16;
case 4:
return Dataset.INT32;
case 8:
return Dataset.INT64;
}
} else if (dclass == HDF5Constants.H5T_BITFIELD) {
switch (dsize) {
case 1:
return Dataset.INT8;
case 2:
return Dataset.INT16;
case 4:
return Dataset.INT32;
case 8:
return Dataset.INT64;
}
} else if (dclass == HDF5Constants.H5T_FLOAT) {
switch (dsize) {
case 4:
return Dataset.FLOAT32;
case 8:
return Dataset.FLOAT64;
}
}
return -1;
}
/**
* Get HDF5 data type constants for boxed primitives
* @param clazz
* @return
*/
public static long getHDF5type(Class clazz) {
if (clazz.equals(String.class)) {
return HDF5Constants.H5T_C_S1;
} else if (clazz.equals(Boolean.class)) {
return HDF5Constants.H5T_NATIVE_INT8;
} else if (clazz.equals(Byte.class)) {
return HDF5Constants.H5T_NATIVE_INT8;
} else if (clazz.equals(Short.class)) {
return HDF5Constants.H5T_NATIVE_INT16;
} else if (clazz.equals(Integer.class)) {
return HDF5Constants.H5T_NATIVE_INT32;
} else if (clazz.equals(Long.class)) {
return HDF5Constants.H5T_NATIVE_INT64;
} else if (clazz.equals(Float.class)) {
return HDF5Constants.H5T_NATIVE_FLOAT;
} else if (clazz.equals(Double.class)) {
return HDF5Constants.H5T_NATIVE_DOUBLE;
}
throw new IllegalArgumentException("Invalid datatype requested");
}
/**
* Get HDF5 data type constants for dataset types
* @param dtype
* @return
*/
public static long getHDF5type(int dtype) {
switch (dtype) {
case Dataset.STRING:
return HDF5Constants.H5T_C_S1;
case Dataset.BOOL:
case Dataset.INT8:
case Dataset.ARRAYINT8:
return HDF5Constants.H5T_NATIVE_INT8;
case Dataset.INT16:
case Dataset.ARRAYINT16:
return HDF5Constants.H5T_NATIVE_INT16;
case Dataset.INT32:
case Dataset.ARRAYINT32:
return HDF5Constants.H5T_NATIVE_INT32;
case Dataset.INT64:
case Dataset.ARRAYINT64:
return HDF5Constants.H5T_NATIVE_INT64;
case Dataset.FLOAT32:
case Dataset.ARRAYFLOAT32:
case Dataset.COMPLEX64:
return HDF5Constants.H5T_NATIVE_FLOAT;
case Dataset.FLOAT64:
case Dataset.ARRAYFLOAT64:
case Dataset.COMPLEX128:
return HDF5Constants.H5T_NATIVE_DOUBLE;
default:
throw new IllegalArgumentException("Invalid datatype requested");
}
}
/**
* Load dataset from given file
* @param fileName
* @param node
* @param start
* @param count
* @param step
* @param dtype
* @param isize
* @param extend
* @return dataset
* @throws Exception
*/
public static Dataset loadDatasetWithClose(final String fileName, final String node,
final int[] start, final int[] count, final int[] step,
final int dtype, final int isize, final boolean extend)
throws ScanFileHolderException {
return loadDataset(fileName, node, start, count, step, dtype, isize, extend, true);
}
/**
* Load entire dataset from given file
* @param fileName
* @param node
* @return dataset
* @throws Exception
*/
public static Dataset loadDataset(final String fileName, final String node)
throws ScanFileHolderException {
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
return loadDataset(fid, node);
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
/**
* Load entire dataset from given file
* @param fileName
* @param node
* @return dataset
* @throws Exception
*/
public static Dataset loadDataset(final HDF5File fid, final String node)
throws ScanFileHolderException {
Dataset data = null;
try {
int[][] shapes = readDatasetShape(fid, node);
int[] shape = shapes[0];
int[] start = new int[shape.length];
int[] step = new int[shape.length];
Arrays.fill(step, 1);
data = readDataset(fid, node, start, shape, step, -1, -1, false);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem loading dataset %s in %s", node, fid);
}
return data;
}
/**
* Check whether a dataset exists in a file
* @param fileName
* @param node
* @return dataset
* @throws Exception
*/
public static boolean hasDataset(final String fileName, String node)
throws ScanFileHolderException {
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
StringBuilder build = new StringBuilder();
if (node.startsWith(Tree.ROOT)) {
node = node.substring(1);
build.append(Tree.ROOT);
}
String[] split = node.split(Node.SEPARATOR);
for (String s : split) {
build.append(s);
if (!H5.H5Lexists(fid.getID(), build.toString(), HDF5Constants.H5P_DEFAULT)) {
return false;
}
build.append(Node.SEPARATOR);
}
build.deleteCharAt(build.length()-1);
String full = build.toString();
if (!H5.H5Oexists_by_name(fid.getID(), full, HDF5Constants.H5P_DEFAULT)) {
return false;
}
H5O_info_t info = H5.H5Oget_info_by_name(fid.getID(), full,HDF5Constants.H5O_INFO_BASIC, HDF5Constants.H5P_DEFAULT);
return info.type == HDF5Constants.H5O_TYPE_DATASET;
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
private static void logAndThrowSFHException(Throwable e, String format, Object... args) throws ScanFileHolderException {
String msg = String.format(format, args);
if (e == null) {
logger.error(msg);
throw new ScanFileHolderException(msg);
}
logger.error(msg, e);
throw new ScanFileHolderException(msg, e);
}
private static void logAndThrowNexusException(Throwable e, String format, Object... args) throws NexusException {
String msg = String.format(format, args);
if (e == null) {
logger.error(msg);
throw new NexusException(msg);
}
logger.error(msg, e);
throw new NexusException(msg, e);
}
/**
* Load dataset from given file
* @param fileName
* @param node
* @param start
* @param count
* @param step
* @param dtype
* @param isize
* @param extend
* @return dataset
* @throws Exception
*/
public static Dataset loadDataset(final String fileName, final String node,
final int[] start, final int[] count, final int[] step,
final int dtype, final int isize, final boolean extend)
throws ScanFileHolderException {
return loadDataset(fileName, node, start, count, step, dtype, isize, extend, false);
}
/**
* Load dataset from given file
* @param fileName
* @param node
* @param start
* @param count
* @param step
* @param dtype
* @param isize
* @param extend
* @return dataset
* @throws Exception
*/
private static Dataset loadDataset(final String fileName, final String node,
final int[] start, final int[] count, final int[] step,
final int dtype, final int isize, final boolean extend, final boolean close)
throws ScanFileHolderException {
Dataset data = null;
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
data = readDataset(fid, node, start, count, step, dtype, isize, extend);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem loading dataset from file");
} finally {
HDF5FileFactory.releaseFile(fileName, close);
}
return data;
}
/**
* Get dataset shape information from given file
* @param fileName
* @param dataPath
* @return null for when there's no data; two empty arrays for a zero-rank dataset;
* shape, max shape otherwise
* @throws ScanFileHolderException
*/
public static int[][] getDatasetShape(final String fileName, final String node)
throws ScanFileHolderException {
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
return readDatasetShape(fid, node);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem loading dataset shape in file");
return null;
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
/**
* Read shape information from a dataset
* @param f
* @param dataPath
* @return null for when there's no data; two empty arrays for a zero-rank dataset;
* shape, max shape otherwise
* @throws NexusException
*/
public static int[][] readDatasetShape(HDF5File f, String dataPath) throws NexusException {
long hdfDatasetId = -1;
try {
try {
hdfDatasetId = H5.H5Dopen(f.getID(), dataPath, HDF5Constants.H5P_DEFAULT);
long hdfDataspaceId = -1;
try {
H5.H5Drefresh(hdfDatasetId);
hdfDataspaceId = H5.H5Dget_space(hdfDatasetId);
int type = H5.H5Sget_simple_extent_type(hdfDataspaceId);
if (type == HDF5Constants.H5S_NULL) {
return null;
} else if (type == HDF5Constants.H5S_SCALAR) {
return new int[][] {new int[0], new int[0]};
}
int rank = H5.H5Sget_simple_extent_ndims(hdfDataspaceId);
long[] dims = new long[rank];
long[] mdims = new long[rank];
H5.H5Sget_simple_extent_dims(hdfDataspaceId, dims, mdims);
int[] shape = new int[rank];
int[] mshape = new int[rank];
for (int i = 0; i < rank; i++) {
shape[i] = (int) dims[i];
mshape[i] = (int) mdims[i];
}
return new int[][] { shape, mshape};
} finally {
if (hdfDataspaceId != -1) {
try {
H5.H5Sclose(hdfDataspaceId);
} catch (HDF5Exception ex) {
}
}
}
} finally {
if (hdfDatasetId != -1) {
try {
H5.H5Dclose(hdfDatasetId);
} catch (HDF5Exception ex) {
}
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not read dataset shape for %s in %s", dataPath, f);
}
return null;
}
/**
* Read dataset from given file ID
* @param f
* @param dataPath
* @param start
* @param count
* @param step
* @param dtype (can be -1 for dataset type from file)
* @param isize (can be -1 for item size from file)
* @param extend
* @return dataset
* @throws NexusException
*/
public static Dataset readDataset(HDF5File f, final String dataPath, final int[] start, final int[] count,
final int[] step, final int dtype, final int isize, final boolean extend)
throws NexusException {
Dataset data = null;
try {
H5O_info_t info = H5.H5Oget_info_by_name(f.getID(), dataPath, HDF5Constants.H5O_INFO_BASIC, HDF5Constants.H5P_DEFAULT);
int t = info.type;
if (t != HDF5Constants.H5O_TYPE_DATASET) {
logger.error("Path {} was not a dataset in {}", dataPath, f);
return data;
}
} catch (HDF5Exception ex) {
logger.error("Could not find info about object {} in {}", dataPath, f);
return data;
}
long did = -1;
long tid = -1;
long ntid = -1;
try {
did = H5.H5Dopen(f.getID(), dataPath, HDF5Constants.H5P_DEFAULT);
tid = H5.H5Dget_type(did);
if (H5.H5Tequal(tid, HDF5Constants.H5T_STD_REF_OBJ)) {
logAndThrowNexusException(null, "Could not handle reference object data for %s in %s", dataPath, f);
}
ntid = H5.H5Tget_native_type(tid);
DatasetType type = getDatasetType(tid, ntid);
if (type == null) {
logAndThrowNexusException(null, "Datatype not supported for %s in %s", dataPath, f);
}
long sid = -1;
long msid = -1;
int rank;
// create a new scalar dataset
try {
sid = H5.H5Dget_space(did);
rank = H5.H5Sget_simple_extent_ndims(sid);
final long[] sstart = new long[rank]; // source start
final long[] sstride = new long[rank]; // source steps
final long[] dsize = new long[rank]; // destination size
for (int i = 0; i < rank; i++) {
sstart[i] = start[i];
sstride[i] = step[i];
dsize[i] = count[i];
}
if (rank == 0) {
msid = H5.H5Screate(HDF5Constants.H5S_SCALAR);
} else {
H5.H5Sselect_hyperslab(sid, HDF5Constants.H5S_SELECT_SET, sstart, sstride, dsize, null);
msid = H5.H5Screate_simple(rank, dsize, null);
H5.H5Sselect_all(msid);
}
final int ldtype = dtype >= 0 ? dtype : type.dtype;
final int lisize = isize >= 0 ? isize : type.isize;
data = DatasetFactory.zeros(lisize, count, ldtype);
Object odata = data.getBuffer();
try {
if (type.isVariableLength) {
H5.H5Dread_VLStrings(did, tid, msid, sid, HDF5Constants.H5P_DEFAULT, (Object[]) odata);
} else if (type.dtype == Dataset.STRING) {
H5.H5Dread_string(did, tid, msid, sid, HDF5Constants.H5P_DEFAULT, (String[]) odata);
} else {
H5.H5Dread(did, tid, msid, sid, HDF5Constants.H5P_DEFAULT, odata);
}
if (extend) {
data = DatasetUtils.makeUnsigned(data, true);
}
} catch (HDF5LibraryException e) {
logAndThrowNexusException(e, "Could not read data from %s in %s", dataPath, f);
}
} catch (HDF5Exception ex) {
logAndThrowNexusException(ex, "Could not get data space information from %s in %s", dataPath, f);
} finally {
if (msid != -1) {
try {
H5.H5Sclose(msid);
} catch (HDF5Exception ex2) {
}
}
if (sid != -1) {
try {
H5.H5Sclose(sid);
} catch (HDF5Exception ex2) {
}
}
}
} catch (HDF5Exception ex) {
logAndThrowNexusException(ex, "Could not open dataset %s in %s", dataPath, f);
} finally {
if (ntid != -1) {
try {
H5.H5Tclose(ntid);
} catch (HDF5Exception ex) {
}
}
if (tid != -1) {
try {
H5.H5Tclose(tid);
} catch (HDF5Exception ex) {
}
}
if (did != -1) {
try {
H5.H5Dclose(did);
} catch (HDF5Exception ex) {
}
}
}
return data;
}
/**
* @return the absolute path to data
*/
public static String absolutePathToData(String parentPath, String name) {
if (parentPath == null || parentPath.isEmpty()) {
parentPath = Tree.ROOT;
} else if (!parentPath.startsWith(Tree.ROOT)) {
parentPath = Tree.ROOT.concat(parentPath);
}
if (!parentPath.endsWith(Node.SEPARATOR)) {
parentPath = parentPath.concat(Node.SEPARATOR);
}
return parentPath.concat(name);
}
/**
* Create a dataset in HDF5 file. Create the file if necessary
* @param fileName
* @param parentPath path to group containing dataset
* @param name name of dataset
* @param initialShape
* @param maxShape
* @param chunking
* @param dtype dataset type
* @param fill
* @param asUnsigned
* @throws ScanFileHolderException
*/
public static void createDataset(final String fileName, final String parentPath, final String name, final int[] initialShape, final int[] maxShape, final int[] chunking, final int dtype, final Object fill, final boolean asUnsigned) throws ScanFileHolderException {
createDataset(fileName, parentPath, name, initialShape, maxShape, chunking, dtype, fill, asUnsigned, false);
}
/**
* Create a dataset in HDF5 file. Create the file if necessary
* @param fileName
* @param parentPath path to group containing dataset
* @param name name of dataset
* @param initialShape
* @param maxShape
* @param chunking
* @param dtype dataset type
* @param fill
* @param asUnsigned
* @param close
* @throws ScanFileHolderException
*/
private static void createDataset(final String fileName, final String parentPath, final String name, final int[] initialShape, final int[] maxShape, final int[] chunking, final int dtype, final Object fill, final boolean asUnsigned, final boolean close) throws ScanFileHolderException {
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, true);
requireDestination(fid, parentPath);
String dataPath = absolutePathToData(parentPath, name);
createDataset(fid, NexusFile.COMPRESSION_NONE, dataPath, dtype, initialShape, maxShape, chunking, fill);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem creating dataset in file: %s", fileName);
} finally {
HDF5FileFactory.releaseFile(fileName, close);
}
}
/**
* Create a lazy dataset in HDF5 file
* @param fileName
* @param parentPath
* @param name
* @param initialShape
* @param maxShape
* @param chunking
* @param dtype
* @param fill
* @param asUnsigned
* @return
*/
public static LazyWriteableDataset createLazyDataset(final String fileName, final String parentPath, final String name, final int[] initialShape, final int[] maxShape, final int[] chunking, final int dtype, final Object fill, final boolean asUnsigned) {
HDF5LazySaver saver = new HDF5LazySaver(null, fileName,
parentPath + Node.SEPARATOR + name, name, initialShape, 1, dtype, asUnsigned, maxShape, chunking, fill);
saver.setCreateOnInitialization(true);
LazyWriteableDataset lazy = new LazyWriteableDataset(name, dtype, initialShape, maxShape, chunking, saver);
lazy.setFillValue(fill);
return lazy;
}
/**
* Create a dataset in HDF5 file. Create the file if necessary
* @param fileName
* @param parentPath path to group containing dataset
* @param name name of dataset
* @param initialShape
* @param maxShape
* @param chunking
* @param dtype dataset type
* @param fill
* @param asUnsigned
* @throws ScanFileHolderException
*/
static void createDatasetWithClose(final String fileName, final String parentPath, final String name, final int[] initialShape, final int[] maxShape, final int[] chunking, final int dtype, final Object fill, final boolean asUnsigned) throws ScanFileHolderException {
createDataset(fileName, parentPath, name, initialShape, maxShape, chunking, dtype, fill, asUnsigned, true);
}
/**
* Check if group exists in file and create group if not
* @param file
* id
* @param group
* @throws HDF5Exception
*/
private static void requireDestination(HDF5File fid, String group) throws HDF5Exception {
boolean exists = false;
long gid = -1;
try {
try {
gid = H5.H5Gopen(fid.getID(), group, HDF5Constants.H5P_DEFAULT);
exists = true;
} catch (Exception e) {
} finally {
if (!exists) {
gid = createDestination(fid.getID(), group);
}
}
} finally {
if (gid != -1) {
try {
H5.H5Gclose(gid);
} catch (HDF5Exception ex) {
}
}
}
}
private static long createDestination(long fileID, String group) throws HDF5Exception {
long gcpid = -1;
long gid = -1;
try {
gcpid = H5.H5Pcreate(HDF5Constants.H5P_LINK_CREATE);
H5.H5Pset_create_intermediate_group(gcpid, true);
gid = H5.H5Gcreate(fileID, group, gcpid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
} catch (HDF5Exception e) {
logger.error("Could not create destination", e);
throw e;
} finally {
if (gcpid != -1) {
try {
H5.H5Pclose(gcpid);
} catch (HDF5Exception ex) {
}
}
}
return gid;
}
/**
* Create a dataset in given file
* @param f
* @param compression
* @param dataPath
* @param dtype
* @param iShape
* @param iMaxShape
* @param iChunks
* @param fillValue
* @throws NexusException
*/
public static void createDataset(HDF5File f, int compression, String dataPath, int dtype, int[] iShape, int[] iMaxShape, int[] iChunks,
Object fillValue) throws NexusException {
long[] shape = toLongArray(iShape);
long[] maxShape = toLongArray(iMaxShape);
long[] chunks = toLongArray(iChunks);
boolean stringDataset = dtype == Dataset.STRING;
long hdfType = getHDF5type(dtype);
try {
long hdfDatatypeId = -1;
long hdfDataspaceId = -1;
long hdfPropertiesId = -1;
try {
hdfDatatypeId = H5.H5Tcopy(hdfType);
hdfDataspaceId = H5.H5Screate_simple(shape.length, shape, maxShape);
hdfPropertiesId = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
if (stringDataset) {
H5.H5Tset_cset(hdfDatatypeId, HDF5Constants.H5T_CSET_UTF8);
H5.H5Tset_size(hdfDatatypeId, HDF5Constants.H5T_VARIABLE);
} else if (fillValue != null) {
// Strings must not have a fill value set
H5.H5Pset_fill_value(hdfPropertiesId, hdfDatatypeId, fillValue);
}
if (chunks != null) {
// these have to be set in this order
H5.H5Pset_layout(hdfPropertiesId, HDF5Constants.H5D_CHUNKED);
H5.H5Pset_chunk(hdfPropertiesId, chunks.length, chunks);
}
int deflateLevel = 0;
switch (compression) {
case NexusFile.COMPRESSION_LZW_L1:
deflateLevel = 1;
break;
default:
compression = NexusFile.COMPRESSION_NONE;
break;
}
if (compression != NexusFile.COMPRESSION_NONE) {
H5.H5Pset_deflate(hdfPropertiesId, deflateLevel);
}
long hdfDatasetId = -1;
try {
hdfDatasetId = H5.H5Dcreate(f.getID(), dataPath, hdfDatatypeId, hdfDataspaceId,
HDF5Constants.H5P_DEFAULT, hdfPropertiesId, HDF5Constants.H5P_DEFAULT);
} finally {
if (hdfDatasetId != -1) {
try {
H5.H5Dclose(hdfDatasetId);
} catch (HDF5Exception ex) {
}
}
}
} finally {
if (hdfPropertiesId != -1) {
try {
H5.H5Pclose(hdfPropertiesId);
} catch (HDF5Exception ex) {
}
}
if (hdfDataspaceId != -1) {
try {
H5.H5Sclose(hdfDataspaceId);
} catch (HDF5Exception ex) {
}
}
if (hdfDatatypeId != -1) {
try {
H5.H5Tclose(hdfDatatypeId);
} catch (HDF5Exception ex) {
}
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not create dataset %s in %s", dataPath, f);
}
}
/**
* Write a dataset in HDF5 file. Create the file if necessary
* @param fileName
* @param parentPath path to group containing dataset
* @param data
* @throws ScanFileHolderException
* @throws IllegalArgumentException when data has null or empty name
*/
public static void writeDataset(String fileName, String parentPath, IDataset data) throws ScanFileHolderException {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, true);
try {
requireDestination(fid, parentPath);
String dataName = data.getName();
if (dataName == null || dataName.isEmpty()) {
throw new IllegalArgumentException("Dataset must have a name");
}
String dataPath = absolutePathToData(parentPath, data.getName());
writeDataset(fid, dataPath, data);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem writing dataset to file: %s", fileName);
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
/**
* Write a dataset in given file
* @param f
* @param dataPath
* @param data
* @throws NexusException
*/
public static void writeDataset(HDF5File f, String dataPath, IDataset data) throws NexusException {
Dataset dataset = DatasetUtils.convertToDataset(data);
long[] shape = toLongArray(dataset.getShapeRef());
int dtype = dataset.getDType();
boolean stringDataset = dtype == Dataset.STRING;
long hdfType = getHDF5type(dtype);
try {
long hdfDatatypeId = -1;
long hdfDataspaceId = -1;
long hdfPropertiesId = -1;
try {
hdfDatatypeId = H5.H5Tcopy(hdfType);
hdfDataspaceId = shape.length == 0 ? H5.H5Screate(HDF5Constants.H5S_SCALAR) : H5.H5Screate_simple(shape.length, shape, null);
hdfPropertiesId = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
if (stringDataset) {
H5.H5Tset_cset(hdfDatatypeId, HDF5Constants.H5T_CSET_UTF8);
H5.H5Tset_size(hdfDatatypeId, HDF5Constants.H5T_VARIABLE);
}
long hdfDatasetId = -1;
try {
hdfDatasetId = H5.H5Dcreate(f.getID(), dataPath, hdfDatatypeId, hdfDataspaceId,
HDF5Constants.H5P_DEFAULT, hdfPropertiesId, HDF5Constants.H5P_DEFAULT);
if (stringDataset) {
String[] strings = (String[])DatasetUtils.serializeDataset(data);
H5.H5Dwrite_VLStrings(hdfDatasetId, hdfDatatypeId, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, strings);
} else {
Serializable buffer = DatasetUtils.serializeDataset(data);
H5.H5Dwrite(hdfDatasetId, hdfDatatypeId, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, buffer);
}
} finally {
if (hdfDatasetId != -1) {
try {
H5.H5Dclose(hdfDatasetId);
} catch (HDF5Exception ex) {
}
}
}
} finally {
if (hdfPropertiesId != -1) {
try {
H5.H5Pclose(hdfPropertiesId);
} catch (HDF5Exception ex) {
}
}
if (hdfDataspaceId != -1) {
try {
H5.H5Sclose(hdfDataspaceId);
} catch (HDF5Exception ex) {
}
}
if (hdfDatatypeId != -1) {
try {
H5.H5Tclose(hdfDatatypeId);
} catch (HDF5Exception ex) {
}
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not write dataset %s in %s", dataPath, f);
}
}
private static final Charset UTF8 = Charset.forName("UTF-8");
private static final Charset ASCII = Charset.forName("US-ASCII");
/**
* Write attributes to a group or dataset in given file. When writing to group,
* this checks if group exists in file and creates group if not
*
* @param fileName
* @param path
* @param isGroup
* @param attributes
* @throws ScanFileHolderException
*/
public static void writeAttributes(String fileName, String path, boolean isGroup, IDataset... attributes)
throws ScanFileHolderException {
HDF5File f = HDF5FileFactory.acquireFile(fileName, true);
try {
if (isGroup) {
requireDestination(f, path);
}
writeAttributes(f, path, attributes);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem writing attributes in %s", path);
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
/**
* Write attributes to a group or dataset in given file
* @param f
* @param path
* @param attributes
* @throws NexusException
* @throws IllegalArgumentException when any attribute has null or empty name
*/
public static void writeAttributes(HDF5File f, String path, IDataset... attributes) throws NexusException {
for (IDataset attr : attributes) {
String attrName = attr.getName();
if (attrName == null || attrName.isEmpty()) {
throw new IllegalArgumentException("Attribute must have a name");
}
long fileID = f.getID();
try {
// if an attribute with the same name already exists, we delete it to be consistent with NAPI
if (H5.H5Aexists_by_name(fileID, path, attrName, HDF5Constants.H5P_DEFAULT)) {
try {
H5.H5Adelete_by_name(fileID, path, attrName, HDF5Constants.H5P_DEFAULT);
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not delete existing attribute %s for %s in %s", attrName, path, f);
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not check for existing attribute %s for %s in %s", attrName, path, f);
}
Dataset attrData = DatasetUtils.convertToDataset(attr);
long baseHdf5Type = getHDF5type(attrData.getDType());
final boolean isScalar = attrData.getRank() == 0;
final long[] shape = toLongArray(attrData.getShapeRef());
long datatypeID = -1;
long dataspaceID = -1;
try {
datatypeID = H5.H5Tcopy(baseHdf5Type);
dataspaceID = isScalar ? H5.H5Screate(HDF5Constants.H5S_SCALAR) : H5.H5Screate_simple(shape.length, shape, shape);
boolean stringDataset = attrData.getDType() == Dataset.STRING;
Serializable buffer = DatasetUtils.serializeDataset(attrData);
if (stringDataset) {
String[] strings = (String[]) buffer;
int strCount = strings.length;
int maxLength = 0;
byte[][] stringbuffers = new byte[strCount][];
int i = 0;
for (String str : strings) {
stringbuffers[i] = str.getBytes(UTF8);
int l = stringbuffers[i].length;
if (l > maxLength) maxLength = l;
i++;
}
maxLength++; //we require null terminators
buffer = new byte[maxLength * strCount];
int offset = 0;
for (byte[] str: stringbuffers) {
System.arraycopy(str, 0, buffer, offset, str.length);
offset += maxLength;
}
//deliberate choice, mis-labelling to work around h5py/numpy
//handling of non ascii strings
H5.H5Tset_cset(datatypeID, HDF5Constants.H5T_CSET_ASCII);
H5.H5Tset_size(datatypeID, maxLength);
}
long attrID = -1;
try {
attrID = H5.H5Acreate_by_name(fileID, path, attrName, datatypeID, dataspaceID,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Awrite(attrID, datatypeID, buffer);
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not create or write attribute %s for %s in %s", attrName, path, f);
} finally {
if (attrID != -1) {
try {
H5.H5Aclose(attrID);
} catch (HDF5Exception e) {
}
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not make data type or space for attribute %s for %s in %s", attrName, path, f);
} finally {
if (dataspaceID != -1) {
try {
H5.H5Sclose(dataspaceID);
} catch (HDF5Exception e) {
}
}
if (datatypeID != -1) {
try {
H5.H5Tclose(datatypeID);
} catch (HDF5Exception e) {
}
}
}
}
}
/**
* Set slice of dataset in HDF5 file. Create file if necessary
* @param fileName
* @param parentPath
* @param name
* @param slice
* @param value
* @throws ScanFileHolderException
*/
static void setDatasetSliceWithClose(final String fileName, final String parentPath, final String name, final SliceND slice, final IDataset value) throws ScanFileHolderException {
setDatasetSlice(fileName, parentPath, name, slice, value, true, false);
}
/**
* Set slice of dataset in HDF5 file. Create file if necessary
* @param fileName
* @param parentPath
* @param name
* @param slice
* @param value
* @throws ScanFileHolderException
*/
public static void setDatasetSlice(final String fileName, final String parentPath, final String name, final SliceND slice, final IDataset value) throws ScanFileHolderException {
setDatasetSlice(fileName, parentPath, name, slice, value, false, false);
}
/**
* Set slice of dataset in HDF5 file. Create file if necessary
* @param fileName
* @param parentPath
* @param name
* @param slice
* @param value
* @throws ScanFileHolderException
*/
public static void setExistingDatasetSlice(final String fileName, final String parentPath, final String name, final SliceND slice, final IDataset value) throws ScanFileHolderException {
setDatasetSlice(fileName, parentPath, name, slice, value, false, true);
}
/**
* Set slice of dataset in HDF5 file. Create file if necessary
* @param fileName
* @param parentPath
* @param name
* @param slice
* @param value
* @param close
* @param exists
* @throws ScanFileHolderException
*/
private static void setDatasetSlice(final String fileName, final String parentPath, final String name, final SliceND slice, final IDataset value, final boolean close, boolean exists) throws ScanFileHolderException {
try {
if (!exists) {
prepareFile(fileName, parentPath, name, slice, value);
}
HDF5File fid = HDF5FileFactory.acquireFile(fileName, true);
String dataPath = absolutePathToData(parentPath, name);
writeDatasetSlice(fid, dataPath, slice, value);
} catch (Throwable le) {
logAndThrowSFHException(le, "Problem setting slice of dataset in file: %s", fileName);
} finally {
HDF5FileFactory.releaseFile(fileName, close);
}
}
private static void prepareFile(final String fileName, final String parentPath, final String name, final SliceND slice, final IDataset value) throws Exception {
if (!new File(fileName).exists()) {
int[] mshape = slice.getMaxShape();
if (mshape == null) {
mshape = slice.getShape();
}
createDataset(fileName, parentPath, name, slice.getStart(), mshape, slice.getShape(),
DTypeUtils.getDType(value), null, false);
}
}
/**
*
* @param f
* @param dataPath
* @return
* @throws NexusException
*/
public static long[] openDataset(HDF5File f, String dataPath) throws NexusException {
long hdfDatasetId = -1;
long hdfDataspaceId = -1;
try {
hdfDatasetId = H5.H5Dopen(f.getID(), dataPath, HDF5Constants.H5P_DEFAULT);
hdfDataspaceId = H5.H5Dget_space(hdfDatasetId);
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not open dataset %s in %s", dataPath, f);
}
return new long[] {hdfDatasetId, hdfDataspaceId};
}
/**
*
* @param ids
* @throws NexusException
*/
public static void flushDataset(long[] ids) throws NexusException {
long id = ids[0];
if (id != -1) {
try {
H5.H5Dflush(id);
} catch (HDF5Exception ex) {
logAndThrowNexusException(ex, "Could not flush data");
}
}
}
/**
*
* @param ids
* @throws NexusException
*/
public static void closeDataset(long[] ids) throws NexusException {
long id = ids[1];
if (id != -1) {
ids[1] = -1;
try {
H5.H5Sclose(id);
} catch (HDF5Exception ex) {
logger.error("Could not close file space", ex);
}
}
try {
flushDataset(ids);
} finally {
id = ids[0];
if (id != -1) {
ids[0] = -1;
try {
H5.H5Dclose(id);
} catch (HDF5Exception ex) {
logAndThrowNexusException(ex, "Could not close data");
}
}
}
}
/**
* Write to a slice in a dataset
* @param f
* @param dataPath
* @param slice
* @param value
* @throws NexusException
*/
public static void writeDatasetSlice(HDF5File f, String dataPath, SliceND slice, IDataset value) throws NexusException {
long[] ids = null;
try {
ids = f.openDataset(dataPath);
long hdfDatasetId = ids[0];
long hdfDataspaceId = ids[1];
long hdfMemspaceId = -1;
long hdfDatatypeId = -1;
try {
int rank = H5.H5Sget_simple_extent_ndims(hdfDataspaceId);
long[] dims = new long[rank];
long[] mdims = new long[rank];
H5.H5Sget_simple_extent_dims(hdfDataspaceId, dims, mdims);
long[] start = toLongArray(slice.getStart());
long[] stride = toLongArray(slice.getStep());
long[] shape = toLongArray(slice.getShape());
long[] newShape = null;
if (slice.isExpanded()) {
newShape = toLongArray(slice.getSourceShape());
} else {
long[] mShape = toLongArray(slice.getStop());
if (expandToGreatestShape(mShape, dims)) {
newShape = mShape;
}
}
if (newShape != null) {
H5.H5Dset_extent(hdfDatasetId, newShape);
try {
H5.H5Sclose(hdfDataspaceId);
} catch (HDF5Exception ex) {
}
hdfDataspaceId = H5.H5Screate_simple(rank, newShape, mdims);
ids[1] = hdfDataspaceId;
}
if (rank != 0) { // not a scalar (or null) dataspace
H5.H5Sselect_hyperslab(hdfDataspaceId, HDF5Constants.H5S_SELECT_SET, start, stride, shape, null);
}
Dataset data = DatasetUtils.convertToDataset(value);
int dtype = data.getDType();
long memtype = getHDF5type(dtype);
Serializable buffer = DatasetUtils.serializeDataset(data);
// convert boolean[] data to byte[]
// the HDF5 library cannot handle boolean[]
if (data.getElementClass().equals(Boolean.class)) {
boolean[] original = (boolean[]) buffer;
int length = original.length;
byte[] converted = new byte[length];
for (int i = 0; i < length; i++) {
converted[i] = (byte) (original[i] ? 1 : 0);
}
buffer = converted;
}
hdfMemspaceId = H5.H5Screate_simple(rank, HDF5Utils.toLongArray(data.getShape()), null);
if (dtype == Dataset.STRING) {
//use the properties from the existing dataset for a string,
//not the memtype of the dataset.
boolean vlenString = false;
hdfDatatypeId = H5.H5Dget_type(hdfDatasetId);
int typeSize = -1;
typeSize = (int) H5.H5Tget_size(hdfDatatypeId);
vlenString = H5.H5Tis_variable_str(hdfDatatypeId);
if (vlenString) {
H5.H5Dwrite_VLStrings(hdfDatasetId, hdfDatatypeId, hdfMemspaceId, hdfDataspaceId, HDF5Constants.H5P_DEFAULT, (String[]) buffer);
} else {
String[] strings = (String[]) buffer;
byte[] strBuffer = new byte[typeSize * strings.length];
int idx = 0;
for (String str : (String[]) strings) {
//typesize - 1 since we always want to leave room for \0 at the end of the string
if (str.length() > typeSize - 1) {
logger.warn("String does not fit into space allocated in HDF5 file in {} - string will be truncated", dataPath);
}
byte[] src = str.getBytes(ASCII);
int length = Math.min(typeSize - 1, src.length);
System.arraycopy(src, 0, strBuffer, idx, length);
idx += typeSize;
}
H5.H5Dwrite(hdfDatasetId, hdfDatatypeId, hdfMemspaceId, hdfDataspaceId, HDF5Constants.H5P_DEFAULT, strBuffer);
}
} else {
H5.H5Dwrite(hdfDatasetId, memtype, hdfMemspaceId, hdfDataspaceId, HDF5Constants.H5P_DEFAULT, buffer);
}
} finally {
if (hdfDatatypeId != -1) {
try {
H5.H5Tclose(hdfDatatypeId);
} catch (HDF5Exception ex) {
logger.error("Could not close datatype", ex);
throw ex;
}
}
if (hdfMemspaceId != -1) {
try {
H5.H5Sclose(hdfMemspaceId);
} catch (HDF5Exception ex) {
logger.error("Could not close memory space", ex);
throw ex;
}
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not write dataset slice (%s) to %s in %s", slice, dataPath, f);
} finally {
if (!f.containsDataset(dataPath)) {
closeDataset(ids);
}
}
}
private static boolean expandToGreatestShape(long[] a, long[] b) {
int rank = a.length;
boolean isExpanded = false;
for (int i = 0; i < rank; i++) {
if (a[i] > b[i]) {
isExpanded = true;
} else { // ensure shape is maximal
a[i] = b[i];
}
}
return isExpanded;
}
/**
* Wrapper to fix super block status flag issue
* @param filePath
* @param flags
* @param fapl
* @return file ID
* @throws HDF5LibraryException
* @throws NullPointerException
* @deprecated Use {@link H5#H5Fopen(String,int,long)} directly
*/
public static long H5Fopen(String filePath, int flags, long fapl) throws HDF5LibraryException, NullPointerException {
return H5.H5Fopen(filePath, flags, fapl);
}
private static final Map HDF_TYPES_TO_DATASET_TYPES;
private static final Map DATASET_TYPES_TO_HDF_TYPES;
private static final Map ENUM_SIZE_TO_HDF_TYPES;
private static final Set UNSIGNED_HDF_TYPES;
private static long getTypeRepresentation(long nativeHdfTypeId) throws NexusException {
try {
for (long type : HDF_TYPES_TO_DATASET_TYPES.keySet()) {
if (H5.H5Tequal(nativeHdfTypeId, type)) {
return type;
}
}
} catch (HDF5LibraryException e) {
logAndThrowNexusException(e, "Could not compare types");
}
return -1;
}
static {
HDF_TYPES_TO_DATASET_TYPES = new HashMap();
DATASET_TYPES_TO_HDF_TYPES = new HashMap();
ENUM_SIZE_TO_HDF_TYPES = new HashMap();
UNSIGNED_HDF_TYPES = new HashSet();
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_INT8, Dataset.INT8);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.INT8, HDF5Constants.H5T_NATIVE_INT8);
ENUM_SIZE_TO_HDF_TYPES.put(1l, HDF5Constants.H5T_NATIVE_INT8);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_INT16, Dataset.INT16);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.INT16, HDF5Constants.H5T_NATIVE_INT16);
ENUM_SIZE_TO_HDF_TYPES.put(2l, HDF5Constants.H5T_NATIVE_INT16);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_INT32, Dataset.INT32);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.INT32, HDF5Constants.H5T_NATIVE_INT32);
ENUM_SIZE_TO_HDF_TYPES.put(4l, HDF5Constants.H5T_NATIVE_INT32);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B8, Dataset.INT8);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B16, Dataset.INT16);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B32, Dataset.INT32);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B64, Dataset.INT8);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_INT64, Dataset.INT64);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.INT64, HDF5Constants.H5T_NATIVE_INT64);
ENUM_SIZE_TO_HDF_TYPES.put(8l, HDF5Constants.H5T_NATIVE_INT64);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_UINT8, Dataset.INT8);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_UINT8);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_UINT16, Dataset.INT16);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_UINT16);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_UINT32, Dataset.INT32);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_UINT32);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_UINT64, Dataset.INT64);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_UINT64);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_FLOAT, Dataset.FLOAT32);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.FLOAT32, HDF5Constants.H5T_NATIVE_FLOAT);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_DOUBLE, Dataset.FLOAT64);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.FLOAT64, HDF5Constants.H5T_NATIVE_DOUBLE);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_C_S1, Dataset.STRING);
DATASET_TYPES_TO_HDF_TYPES.put(Dataset.STRING, HDF5Constants.H5T_C_S1);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B8, Dataset.INT8);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_B8);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B16, Dataset.INT16);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_B16);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B32, Dataset.INT32);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_B32);
HDF_TYPES_TO_DATASET_TYPES.put(HDF5Constants.H5T_NATIVE_B64, Dataset.INT64);
UNSIGNED_HDF_TYPES.add(HDF5Constants.H5T_NATIVE_B64);
}
public static class DatasetType {
public int dtype = -1; // dataset type number
public int isize = 1; // number of elements per item
public long size; // size of string in bytes
public int bits = -1; // max number of bits for bit-fields (-1 for other types)
public int nEnum; // number of enumerations
public String name;
public boolean isVariableLength; // is variable length
public boolean isComplex = false;
public boolean unsigned; // is unsigned
}
public static Dataset[] readAttributes(long oid) throws NexusException {
return readAttributes(oid, HERE);
}
private static final String HERE = ".";
/**
* Read attributes from group or dataset in given file
*
* @param fileName
* @param groupPath
* @throws ScanFileHolderException
*/
public static Dataset[] readAttributes(String fileName, String path)
throws NexusException, ScanFileHolderException {
long id = -1;
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
id = H5.H5Oopen(fid.getID(), path, HDF5Constants.H5P_DEFAULT);
return readAttributes(id);
} finally {
if (id != -1) {
try {
H5.H5Oclose(id);
} catch (HDF5Exception ex) {
}
}
HDF5FileFactory.releaseFile(fileName);
}
}
public static Dataset[] readAttributes(long oid, String path) throws NexusException {
H5O_info_t info = null;
try {
info = H5.H5Oget_info(oid, HDF5Constants.H5O_INFO_NUM_ATTRS);
} catch (HDF5LibraryException e) {
logAndThrowNexusException(e, "Could not get info from object");
}
int n = (int) info.num_attrs;
if (n <= 0) {
return new Dataset[0];
}
Dataset[] attrs = new Dataset[n];
for (int i = 0; i < n; i++) {
attrs[i] = getAttrDataset(oid, path, i);
}
return attrs;
}
/**
* Create a link to a source node in an external file
* @param fileName file name where link will be created
* @param destination path of created link
* @param externalFileName external file
* @param source path of source node
* @throws ScanFileHolderException
*/
public static void createExternalLink(String fileName, String destination, String externalFileName, String source) throws ScanFileHolderException {
try {
HDF5File fid = HDF5FileFactory.acquireFile(fileName, false);
createExternalLink(fid, destination, externalFileName, source);
} catch (Throwable t) {
logAndThrowSFHException(t, "Could not create external link in %s", fileName);
} finally {
HDF5FileFactory.releaseFile(fileName);
}
}
/**
* Create a link to a source node in an external file
* @param f
* @param destination path of created link (if ends with {@value Node#SEPARATOR} then use name from source)
* @param externalFileName external file
* @param source path of source node
* @throws ScanFileHolderException
*/
public static void createExternalLink(HDF5File f, String destination, String externalFileName, String source) throws NexusException {
String parent;
if (destination.endsWith(Node.SEPARATOR)) { // use name from source
parent = destination.substring(0, destination.length() - 1);
if (source.endsWith(Node.SEPARATOR)) {
source = source.substring(0, source.length() - 1);
}
int l = source.lastIndexOf(Node.SEPARATOR);
if (l < 0) {
// no group left!
} else {
destination = destination.concat(source.substring(l));
}
} else {
int l = destination.lastIndexOf(Node.SEPARATOR);
parent = l <= 0 ? Tree.ROOT : destination.substring(0, l);
}
long fapl = -1;
long lapl = -1;
try {
if (!Tree.ROOT.equals(parent)) {
requireDestination(f, parent);
}
fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
lapl = H5.H5Pcreate(HDF5Constants.H5P_LINK_ACCESS);
H5.H5Pset_libver_bounds(fapl, HDF5Constants.H5F_LIBVER_LATEST, HDF5Constants.H5F_LIBVER_LATEST);
H5.H5Pset_elink_fapl(lapl, fapl);
H5.H5Pset_elink_acc_flags(lapl, HDF5Constants.H5F_ACC_RDONLY | HDF5Constants.H5F_ACC_SWMR_READ);
H5.H5Lcreate_external(externalFileName, source, f.getID(), destination, HDF5Constants.H5P_DEFAULT, lapl);
} catch (Throwable le) {
logAndThrowNexusException(le, "Problem creating external link (%s) to %s in file: %s", source, destination, f);
} finally {
if (lapl != -1) {
H5.H5Pclose(lapl);
}
if (fapl != -1) {
H5.H5Pclose(fapl);
}
}
}
/**
* Find classes in composite data type
* @param tid
* @return
* @throws HDF5LibraryException
* @throws NexusException
*/
public static DatasetType findClassesInComposite(long tid) throws HDF5LibraryException, NexusException {
List names = new ArrayList();
List classes = new ArrayList();
List dtypes = new ArrayList();
List widths = new ArrayList();
List signs = new ArrayList();
flattenCompositeDatasetType(tid, "", names, classes, dtypes, widths, signs);
DatasetType comp = new DatasetType();
comp.isize = classes.size();
if (comp.isize > 0) {
int tclass = classes.get(0);
for (int i = 1; i < comp.isize; i++) {
if (tclass != classes.get(i)) {
logger.error("Could not load inhomogeneous compound datatype");
return null;
}
}
comp.dtype = dtypes.get(0);
if (comp.isize == 2 && tclass == HDF5Constants.H5T_FLOAT) {
if (getLastComponent(names.get(0)).toLowerCase().startsWith("r") && getLastComponent(names.get(1)).toLowerCase().startsWith("i")) {
comp.isComplex = true;
comp.dtype = comp.dtype == Dataset.FLOAT32 ? Dataset.COMPLEX64 : Dataset.COMPLEX128;
}
}
if (!comp.isComplex) {
comp.dtype *= Dataset.ARRAYMUL;
}
StringBuilder name = new StringBuilder(comp.isComplex ? "Complex = {" : "Composite of {");
for (int i = 0; i < comp.isize; i++) {
name.append(names.get(i));
name.append(constructType(classes.get(i), widths.get(i), signs.get(i)));
name.append(", ");
}
name.delete(name.length() - 2, name.length());
name.append("}");
comp.name = name.toString();
Collections.sort(widths);
comp.bits = widths.get(widths.size() - 1);
}
return comp;
}
private static final String COLON = ":";
private static String getLastComponent(String n) {
String[] bits = n.split(COLON);
int l = bits.length - 1;
while (bits[l].trim().length() == 0) {
l--;
}
return bits[l];
}
private static String constructType(int c, int w, boolean s) {
StringBuilder n = new StringBuilder(":");
if (!s) {
n.append("U");
}
if (c == HDF5Constants.H5T_BITFIELD) {
n.append("INT");
n.append(w);
} else if (c == HDF5Constants.H5T_INTEGER) {
n.append("INT");
n.append(-w*8);
} else if (c == HDF5Constants.H5T_FLOAT) {
n.append("FLOAT");
n.append(-w*8);
}
return n.toString();
}
/**
* This flattens compound and array
* @param tid
* @param prefix
* @param names
* @param classes
* @param dtypes
* @param widths bits (positive) or bytes (negative)
* @param signs
* @throws HDF5LibraryException
* @throws NexusException
*/
private static void flattenCompositeDatasetType(long tid, String prefix, List names, List classes, List dtypes, List widths, List signs) throws HDF5LibraryException, NexusException {
int tclass = H5.H5Tget_class(tid);
if (tclass == HDF5Constants.H5T_ARRAY) {
long btid = -1;
try {
btid = H5.H5Tget_super(tid);
tclass = H5.H5Tget_class(btid);
// deal with array of composite
if (tclass == HDF5Constants.H5T_COMPOUND || tclass == HDF5Constants.H5T_ARRAY) {
flattenCompositeDatasetType(btid, prefix, names, classes, dtypes, widths, signs);
return;
}
int r = H5.H5Tget_array_ndims(tid);
long[] shape = new long[r];
H5.H5Tget_array_dims(tid, shape);
long size = calcLongSize(shape);
for (long i = 0; i < size; i++) {
names.add(prefix + i);
classes.add(tclass);
}
} catch (HDF5Exception ex) {
} finally {
if (btid != -1) {
try {
H5.H5Tclose(btid);
} catch (HDF5LibraryException e) {
}
}
}
} else {
int n = H5.H5Tget_nmembers(tid);
if (n <= 0)
return;
int mclass = 0;
long tmptid = -1;
for (int i = 0; i < n; i++) {
long mtype = -1;
try {
mtype = H5.H5Tget_member_type(tid, i);
try {
tmptid = mtype;
mtype = H5.H5Tget_native_type(tmptid);
} catch (HDF5Exception ex) {
continue;
} finally {
if (tmptid != -1) {
try {
H5.H5Tclose(tmptid);
} catch (HDF5LibraryException e) {
}
}
}
try {
mclass = H5.H5Tget_class(mtype);
} catch (HDF5Exception ex) {
continue;
}
String mname = prefix;
if (prefix.length() > 0) {
mname += COLON;
}
mname += H5.H5Tget_member_name(tid, i);
if (mclass == HDF5Constants.H5T_COMPOUND || mclass == HDF5Constants.H5T_ARRAY) {
// deal with composite
flattenCompositeDatasetType(mtype, mname, names, classes, dtypes, widths, signs);
} else if (mclass == HDF5Constants.H5T_VLEN) {
continue;
} else {
names.add(mname);
classes.add(mclass);
if (mclass == HDF5Constants.H5T_BITFIELD) {
int p = -1;
try {
p = H5.H5Tget_precision(mtype);
} catch (HDF5Exception ex) {
continue;
} finally {
widths.add(p);
}
signs.add(false);
} else {
int w = 1;
try {
w = (int) H5.H5Tget_size(mtype);
} catch (HDF5Exception ex) {
continue;
} finally {
widths.add(-w);
}
if (mclass == HDF5Constants.H5T_INTEGER) {
boolean s = true;
try {
s = H5.H5Tget_sign(mtype) == HDF5Constants.H5T_SGN_2;
} catch (HDF5Exception ex) {
continue;
} finally {
signs.add(s);
}
} else {
signs.add(true);
}
}
dtypes.add(HDF_TYPES_TO_DATASET_TYPES.get(getTypeRepresentation(mtype)));
}
} finally {
if (mtype != -1) {
try {
H5.H5Tclose(mtype);
} catch (HDF5LibraryException e) {
}
}
}
}
}
}
public static DatasetType getDatasetType(long typeId, long nativeTypeId) throws NexusException, HDF5LibraryException {
DatasetType type = new DatasetType();
int tclass = H5.H5Tget_class(nativeTypeId);
if (tclass == HDF5Constants.H5T_ARRAY || tclass == HDF5Constants.H5T_COMPOUND) {
type = findClassesInComposite(typeId);
} else {
type.size = H5.H5Tget_size(nativeTypeId);
long typeRepresentation;
if (tclass == HDF5Constants.H5T_STRING) {
type.isVariableLength = H5.H5Tis_variable_str(nativeTypeId);
typeRepresentation = HDF5Constants.H5T_C_S1;
} else if (tclass == HDF5Constants.H5T_ENUM) {
// TODO maybe convert to string dataset eventually
type.nEnum = H5.H5Tget_nmembers(nativeTypeId);
typeRepresentation = ENUM_SIZE_TO_HDF_TYPES.get(type.size);
} else if (tclass == HDF5Constants.H5T_REFERENCE) {
return null;
} else {
type.isVariableLength = tclass == HDF5Constants.H5T_VLEN;
typeRepresentation = getTypeRepresentation(nativeTypeId);
}
type.dtype = HDF_TYPES_TO_DATASET_TYPES.get(typeRepresentation);
type.unsigned = UNSIGNED_HDF_TYPES.contains(typeRepresentation);
type.name = DTypeUtils.getDTypeName(type.dtype, type.isize);
if (type.unsigned) {
type.name = "U" + type.name;
}
}
// isRegRef = H5.H5Tequal(tid, HDF5Constants.H5T_STD_REF_DSETREG);
return type;
}
public static Dataset getAttrDataset(long locId, String path, long i) throws NexusException {
Dataset dataset = null;
String name = null;
try {
try (HDF5Resource attrResource = new HDF5AttributeResource(
H5.H5Aopen_by_idx(locId, path, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, i,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT))) {
long[] shape = null;
long[] maxShape = null;
long attrId = attrResource.getResource();
name = H5.H5Aget_name(attrId);
try (HDF5Resource spaceResource = new HDF5DataspaceResource(H5.H5Aget_space(attrId));
HDF5Resource typeResource = new HDF5DatatypeResource(H5.H5Aget_type(attrId));
HDF5Resource nativeTypeResource = new HDF5DatatypeResource(H5.H5Tget_native_type(typeResource.getResource()))) {
final long spaceId = spaceResource.getResource();
final long nativeTypeId = nativeTypeResource.getResource();
DatasetType type = getDatasetType(typeResource.getResource(), nativeTypeId);
if (type == null) {
logAndThrowNexusException(null, "Unknown data type");
}
final int nDims = H5.H5Sget_simple_extent_ndims(spaceId);
shape = new long[nDims];
maxShape = new long[nDims];
H5.H5Sget_simple_extent_dims(spaceId, shape, maxShape);
final int[] iShape = toIntArray(shape);
int strCount = 1;
for (int d : iShape) {
strCount *= d;
}
if (type.dtype == Dataset.STRING) {
if (type.isVariableLength) {
String[] buffer = new String[strCount];
H5.H5AreadVL(attrId, nativeTypeId, buffer);
dataset = DatasetFactory.createFromObject(buffer).reshape(iShape);
} else {
byte[] buffer = new byte[(int) (strCount * type.size)];
H5.H5Aread(attrId, nativeTypeId, buffer);
String[] strings = new String[strCount];
int strIndex = 0;
for (int j = 0; j < buffer.length; j += type.size) {
int strLength = 0;
//Java doesn't strip null bytes during string construction
for (int k = j; k < j + type.size && buffer[k] != '\0'; k++) strLength++;
strings[strIndex++] = new String(buffer, j, strLength, UTF8);
}
dataset = DatasetFactory.createFromObject(strings).reshape(iShape);
}
} else {
dataset = DatasetFactory.zeros(iShape, type.dtype);
Serializable buffer = dataset.getBuffer();
H5.H5Aread(attrId, nativeTypeId, buffer);
}
dataset.setName(name);
}
}
} catch (HDF5Exception e) {
logAndThrowNexusException(e, "Could not retrieve attribute %s for %s", name, path);
}
return dataset;
}
public static long calcLongSize(final long[] shape) {
double dsize = 1.0;
for (int i = 0; i < shape.length; i++) {
// make sure the indexes isn't zero or negative
if (shape[i] == 0) {
return 0;
} else if (shape[i] < 0) {
throw new IllegalArgumentException(String.format(
"The %d-th is %d which is an illegal argument as it is negative", i, shape[i]));
}
dsize *= shape[i];
}
// check to see if the size is larger than an integer, i.e. we can't allocate it
if (dsize > Long.MAX_VALUE) {
throw new IllegalArgumentException("Size of the dataset is too large to allocate");
}
return (long) dsize;
}
/**
* Convert integer array to long array
* @param in
* @return long array
*/
public static final long[] toLongArray(final int[] in) {
if (in == null)
return null;
long[] out = new long[in.length];
for (int i = 0; i < in.length; i++) {
out[i] = in[i];
}
return out;
}
/**
* Convert long array to integer array
* @param in
* @return integer array
*/
public static int[] toIntArray(long[] in) {
int[] out = new int[in.length];
for (int i = 0; i < out.length; i++) {
long value = in[i];
if (value == Long.MAX_VALUE) {
value = -1; // stopgap fix for incorrectly written maximum shape
}
if (value > Integer.MAX_VALUE || value < Integer.MIN_VALUE) {
throw new IllegalArgumentException("Cannot convert to int array without data loss");
}
out[i] = (int)value;
}
return out;
}
}
