Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*-
* 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.FileNotFoundException;
import java.io.IOException;
import java.util.Iterator;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;
import org.eclipse.dawnsci.analysis.api.io.ScanFileHolderException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
/**
* This contains method to access low level HDF5 file IDs and allows them to
* be held open for a set period (default of 5s) before being closed.
*/
public class HDF5FileFactory {
private static final Logger logger = LoggerFactory.getLogger(HDF5FileFactory.class);
private static long heldPeriod = 5000; // 5 seconds
private static long finishPeriod = heldPeriod / 5; // 1 seconds
private static boolean verbose = false;
/**
* @param verbose if true, print to standard error when opening, closing, creating or deleting files
*/
public static void setVerbose(boolean verbose) {
HDF5FileFactory.verbose = verbose;
}
private final static HDF5FileFactory INSTANCE;
static {
INSTANCE = new HDF5FileFactory();
}
private ConcurrentMap map;
// Need singleton to add finalizer
private HDF5FileFactory() {
map = new ConcurrentHashMap<>();
}
@Override
protected void finalize() throws Throwable {
synchronized (map) {
Iterator iter = map.keySet().iterator();
while (iter.hasNext()) {
String f = iter.next();
HDF5File a = map.remove(f);
a.flushWrites();
a.finish(finishPeriod);
try {
H5.H5Fclose(a.getID());
} catch (HDF5LibraryException e) {
logger.error("Could not close file: {}", f);
}
}
}
super.finalize();
}
/**
* Canonicalise path so that we can use it as a standard key
* @param absolutePath
* @return
* @throws IOException
*/
public static String canonicalisePath(String absolutePath) throws IOException {
try {
return new File(absolutePath).getCanonicalPath();
} catch (IOException e) {
logger.error("Could not get canonical path: {}", absolutePath);
throw e;
}
}
/**
* Set period of time a file ID is held open for. The period specified must be greater
* than or equal to 100 ms.
* @param heldPeriod in milliseconds
*/
public static void setHeldPeriod(long heldPeriod) {
if (heldPeriod < 100) {
throw new IllegalArgumentException();
}
finishPeriod = heldPeriod/10l;
HDF5FileFactory.heldPeriod = heldPeriod;
}
/**
* Get period of time a file ID is held open for.
* @return period held in milliseconds
*/
public static long getHeldPeriod() {
return heldPeriod;
}
private static void closeFile(HDF5File f) throws HDF5LibraryException {
f.flushWrites();
f.finish(finishPeriod);
long fid = f.getID();
long openObjects = H5.H5Fget_obj_count(fid,
HDF5Constants.H5F_OBJ_LOCAL |
HDF5Constants.H5F_OBJ_DATASET |
HDF5Constants.H5F_OBJ_DATATYPE |
HDF5Constants.H5F_OBJ_GROUP |
HDF5Constants.H5F_OBJ_ATTR);
if (openObjects > 0) {
logger.error("There are {} hdf5 objects left open in {}", openObjects, f);
}
H5.H5Fclose(fid);
}
static {
new Thread(new Runnable() {
@Override
public void run() {
long waitPeriod = heldPeriod;
while (true) {
if (waitPeriod >= 0) {
try {
Thread.sleep(waitPeriod);
} catch (InterruptedException e) {
}
}
long now = System.currentTimeMillis();
long next = now + heldPeriod;
synchronized (INSTANCE.map) {
Iterator iter = INSTANCE.map.keySet().iterator();
while (iter.hasNext()) {
String f = iter.next();
HDF5File a = INSTANCE.map.get(f);
if (a.getCount() <= 0) {
if (a.getTime() <= now) {
try {
closeFile(a);
INSTANCE.map.remove(f);
// FIXME for CustomTomoConverter, etc
// HierarchicalDataFactory.releaseLowLevelReadingAccess(f);
} catch (HDF5LibraryException e) {
logger.error("Could not close file {}", f, e);
}
} else if (a.getTime() < next) {
next = a.getTime(); // reduce waiting to next earliest between now and next
}
}
}
}
waitPeriod = next - System.currentTimeMillis();
}
}
}, "File ID releaser").start();
// make sure all files are closed on shutdown
Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() {
@Override
public void run() {
try {
INSTANCE.finalize();
} catch (Throwable e) {
}
}
}, "File ID closer"));
}
/**
* Acquire file ID
* @param fileName
* @param writeable
* @param asNew
* @param withLatestVersion if true, use latest object format version for writing
* @return file ID
* @throws ScanFileHolderException
*/
private synchronized static HDF5File acquireFile(String fileName, boolean writeable, boolean asNew, boolean withLatestVersion) throws ScanFileHolderException {
final String cPath;
try {
cPath = canonicalisePath(fileName);
} catch (IOException e) {
String msg = String.format("Problem canonicalising file path %s", fileName);
logger.error(msg, e);
throw new ScanFileHolderException(msg, e);
}
HDF5File access = null;
long fid = -1;
long fapl = -1;
boolean canSWMR = false;
synchronized (INSTANCE.map) {
try {
if (INSTANCE.map.containsKey(cPath)) {
access = INSTANCE.map.get(cPath);
if (asNew) {
// we should be able to create if nobody is actually using the old file handle,
// even though it hasn't been disposed yet
if (access.getCount() > 0) {
String msg = String.format("File %s already open and will need to closed", cPath);
logger.error(msg);
throw new ScanFileHolderException(msg);
} else {
// close and allow fall through to file creation below
closeFile(access);
INSTANCE.map.remove(cPath);
}
} else {
if (writeable && !access.isWriteable()) {
String msg = String.format("Could not get file %s in writeable state as it has been opened read-only", cPath);
logger.error(msg);
throw new ScanFileHolderException(msg);
}
access.incrementCount();
return access;
}
}
// FIXME for CustomTomoConverter, etc
// HierarchicalDataFactory.acquireLowLevelReadingAccess(cPath);
try {
fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
if (writeable && withLatestVersion) {
canSWMR = true;
H5.H5Pset_libver_bounds(fapl, HDF5Constants.H5F_LIBVER_LATEST, HDF5Constants.H5F_LIBVER_LATEST);
}
if (asNew) {
if (verbose) {
System.err.println("Creating " + cPath + " with latest " + withLatestVersion);
}
fid = H5.H5Fcreate(cPath, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl);
} else {
if (new File(cPath).exists()) {
if (verbose) {
System.err.println("Opening " + cPath + " with writeable " + writeable + " with latest " + withLatestVersion);
}
if (!writeable) {
// attempt to read with SWMR access first
int a = HDF5Constants.H5F_ACC_RDONLY | HDF5Constants.H5F_ACC_SWMR_READ;
try {
fid = H5.H5Fopen(cPath, a, fapl);
} catch (HDF5LibraryException e) {
// this can happen when someone else has already
// opened the file without SWMR
// i.e. high-level API access (e.g. its use in PersistentFileImpl)
a = HDF5Constants.H5F_ACC_RDONLY;
fid = H5.H5Fopen(cPath, a, fapl);
}
} else {
int a = HDF5Constants.H5F_ACC_RDWR;
fid = H5.H5Fopen(cPath, a, fapl);
}
} else if (!writeable) {
String msg = String.format("File %s does not exist!", cPath);
logger.error(msg);
throw new FileNotFoundException(msg);
} else {
if (verbose) {
System.err.println("Creating " + cPath + " with latest " + withLatestVersion);
}
fid = H5.H5Fcreate(cPath, HDF5Constants.H5F_ACC_EXCL, HDF5Constants.H5P_DEFAULT, fapl);
}
}
} finally {
if (fapl != -1) {
H5.H5Pclose(fapl);
}
}
access = new HDF5File(cPath, fid, asNew || writeable, canSWMR);
INSTANCE.map.put(cPath, access);
return access;
} catch (Throwable le) {
// FIXME for CustomTomoConverter, etc
// if (!IDS.containsKey(cPath)) {
// HierarchicalDataFactory.releaseLowLevelReadingAccess(cPath);
// }
String msg = String.format("Could not acquire access to file %s", cPath);
logger.error(msg, le);
throw new ScanFileHolderException(msg, le);
}
}
}
/**
* Acquire file
* @param fileName
* @param writeable
* @return file
* @throws ScanFileHolderException
*/
public static HDF5File acquireFile(String fileName, boolean writeable) throws ScanFileHolderException {
return acquireFile(fileName, writeable, false, false);
}
/**
* Acquire file
* @param fileName
* @param writeable
* @param withLatestVersion if true, use latest object format version for writing
* @return file
* @throws ScanFileHolderException
*/
public static HDF5File acquireFile(String fileName, boolean writeable, boolean withLatestVersion) throws ScanFileHolderException {
return acquireFile(fileName, writeable, false, withLatestVersion);
}
/**
* Acquire file as a newly created one. This deletes extant files
* @param fileName
* @return file
* @throws ScanFileHolderException
*/
public static HDF5File acquireFileAsNew(String fileName) throws ScanFileHolderException {
return acquireFile(fileName, true, true, false);
}
/**
* Acquire file as a newly created one. This deletes extant files
* @param fileName
* @param withLatestVersion if true, use latest object format version for writing
* @return file
* @throws ScanFileHolderException
*/
public static HDF5File acquireFileAsNew(String fileName, boolean withLatestVersion) throws ScanFileHolderException {
return acquireFile(fileName, true, true, withLatestVersion);
}
/**
* Delete file
* @param fileName
* @throws ScanFileHolderException
*/
public static void deleteFile(String fileName) throws ScanFileHolderException {
final String cPath;
try {
cPath = canonicalisePath(fileName);
} catch (IOException e) {
String msg = String.format("Problem canonicalising file path %s", fileName);
logger.error(msg, e);
throw new ScanFileHolderException(msg, e);
}
synchronized (INSTANCE.map) {
if (INSTANCE.map.containsKey(cPath)) {
try {
HDF5File access = INSTANCE.map.get(cPath);
if (access.getCount() <= 0) {
try {
access.finish(finishPeriod);
if (verbose) {
System.err.println("Closing and deleting " + cPath);
}
H5.H5Fclose(access.getID());
INSTANCE.map.remove(cPath);
// FIXME for CustomTomoConverter, etc
// HierarchicalDataFactory.releaseLowLevelReadingAccess(cPath);
} catch (HDF5LibraryException e) {
logger.error("Could not close file", e);
throw e;
}
} else {
if (verbose) {
System.err.println("Could not close as file being used " + cPath);
}
String msg = String.format("File %s currently being used", cPath);
logger.error(msg);
throw new ScanFileHolderException(msg);
}
} catch (Throwable le) {
String msg = String.format("Problem releasing access to file %s", cPath);
logger.error(msg, le);
throw new ScanFileHolderException(msg, le);
}
}
}
File f = new File(cPath);
if (f.exists()) {
f.delete();
}
}
/**
* Release file
* @param fileName
* @throws ScanFileHolderException
*/
public static void releaseFile(String fileName) throws ScanFileHolderException {
releaseFile(fileName, false);
}
/**
* Release file associated with file name
* @param fileName
* @param close if true then close it too
* @throws ScanFileHolderException
*/
public static void releaseFile(String fileName, boolean close) throws ScanFileHolderException {
final String cPath;
try {
cPath = canonicalisePath(fileName);
} catch (IOException e) {
String msg = String.format("Problem canonicalising file path %s", fileName);
logger.error(msg, e);
throw new ScanFileHolderException(msg, e);
}
synchronized (INSTANCE.map) {
if (!INSTANCE.map.containsKey(cPath)) {
logger.debug("File not known - has it already been released?");
return;
}
try {
HDF5File access = INSTANCE.map.get(cPath);
if (access.decrementCount() <= 0) {
if (close) {
try {
if (verbose) {
System.err.println("Finishing writes for " + cPath);
}
access.finish(access.getID());
tryToCloseOpenObjects(access.getID());
if (verbose) {
System.err.println("Closing " + cPath);
}
H5.H5Fclose(access.getID());
INSTANCE.map.remove(cPath);
// FIXME for CustomTomoConverter, etc
// HierarchicalDataFactory.releaseLowLevelReadingAccess(cPath);
} catch (HDF5LibraryException e) {
logger.error("Could not close file", e);
throw e;
}
} else {
access.setTime(System.currentTimeMillis() + heldPeriod); // update release time
}
}
} catch (Throwable le) {
String msg = String.format("Problem releasing access to file %s", cPath);
logger.error(msg, le);
throw new ScanFileHolderException(msg, le);
}
}
}
private static void tryToCloseOpenObjects(long fileId) throws ScanFileHolderException {
try {
//try datasets, datatypes and groups (things that can be closed with H5Oclose)
int typeIdentifier = HDF5Constants.H5F_OBJ_DATASET |
HDF5Constants.H5F_OBJ_DATATYPE |
HDF5Constants.H5F_OBJ_GROUP |
HDF5Constants.H5F_OBJ_LOCAL;
int openObjectCount = (int) H5.H5Fget_obj_count(fileId, typeIdentifier);
if (openObjectCount > 0) {
logger.debug("Trying to close hdf5 file with open objects");
long[] openIds = new long[openObjectCount];
H5.H5Fget_obj_ids(fileId, typeIdentifier, openObjectCount, openIds);
for (int i = 0; i < openObjectCount; i++) {
long id = openIds[i];
try {
H5.H5Oclose(id);
openIds[i] = -1;
} catch (HDF5LibraryException e) {
logger.error("Error closing hdf5 file - could not close open object");
}
}
}
//try attributes
typeIdentifier = HDF5Constants.H5F_OBJ_ATTR | HDF5Constants.H5F_OBJ_LOCAL;
openObjectCount = (int) H5.H5Fget_obj_count(fileId, typeIdentifier);
if (openObjectCount > 0) {
logger.debug("Trying to close hdf5 file with open attributes");
long[] attrIds = new long[openObjectCount];
H5.H5Fget_obj_ids(fileId, typeIdentifier, openObjectCount, attrIds);
for (int i = 0; i < openObjectCount; i++) {
long id = attrIds[i];
try {
H5.H5Aclose(id);
attrIds[i] = -1;
} catch (HDF5LibraryException e) {
logger.error("Error closing hdf5 file - could not close open attribute");
}
}
}
} catch (HDF5LibraryException e) {
throw new ScanFileHolderException("Could not query for open objects", e);
}
}
/**
* Flush writes to file associated with file name
* @param fileName
* @throws ScanFileHolderException
*/
public static void flushWrites(String fileName) throws ScanFileHolderException {
final String cPath;
try {
cPath = canonicalisePath(fileName);
} catch (IOException e) {
String msg = String.format("Problem canonicalising file path %s", fileName);
logger.error(msg, e);
throw new ScanFileHolderException(msg, e);
}
HDF5File access = null;
synchronized (INSTANCE.map) {
if (!INSTANCE.map.containsKey(cPath)) {
// logger.debug("File not known - has it already been released?");
return;
}
access = INSTANCE.map.get(cPath);
}
synchronized(access) {
try {
if (verbose) {
System.err.println("Flushing writes for " + cPath);
}
access.flushWrites();
int status = H5.H5Fflush(access.getID(), HDF5Constants.H5F_SCOPE_GLOBAL);
if (status < 0) {
throw new HDF5LibraryException("H5Fflush returned an error value: " + status);
}
} catch (Throwable le) {
String msg = String.format("Problem flushing file %s", cPath);
logger.error(msg, le);
throw new ScanFileHolderException(msg, le);
}
}
}
}
