/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.services;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import loci.common.Constants;
import loci.common.Location;
import loci.common.services.AbstractService;
import loci.common.services.ServiceException;
import ch.systemsx.cisd.base.mdarray.MDByteArray;
import ch.systemsx.cisd.base.mdarray.MDIntArray;
import ch.systemsx.cisd.base.mdarray.MDShortArray;
import ch.systemsx.cisd.hdf5.HDF5CompoundDataMap;
import ch.systemsx.cisd.hdf5.HDF5Factory;
import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
/**
* Utility class for working with HDF files.
*/
public class JHDFServiceImpl extends AbstractService
implements JHDFService {
// -- Constants --
public static final String NO_JHDF_MSG
= "JHDF is required to read HDF5 files. "
+ "Please obtain the necessary JAR files from "
+ "http://www.openmicroscopy.org/site/support/bio-formats/developers/java-library.html.\n"
+ "Required JAR files is cisd-jhdf5-batteries_included_lin_win_mac.jar.";
// -- Fields --
private String currentFile;
/**
* Root of the HDF5 file.
*/
private IHDF5Reader hdfReader;
/**
* Root of the HDF5 file.
*/
private IHDF5Writer hdfWriter;
// -- NetCDFService API methods ---
/**
* Default constructor.
*/
public JHDFServiceImpl() {
// One check from each package
checkClassDependency(ch.systemsx.cisd.base.mdarray.MDIntArray.class);
checkClassDependency(ch.systemsx.cisd.hdf5.HDF5Factory.class);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#setFile()
*/
public void setFile(String file) throws IOException {
this.currentFile = file;
this.hdfReader = HDF5Factory.openForReading(file);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#setFileForWrite()
*/
public void setFileForWrite(String file) throws IOException {
this.currentFile = file;
this.hdfWriter = HDF5Factory.open(file);
}
/* (non-Javadoc)
* @see loci.formats.NetCDFService#getFile()
*/
public String getFile() {
return currentFile;
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#getMember()
*/
public List<String> getMember(String path) {
return hdfReader.getGroupMembers(path);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#getShape()
*/
public int[] getShape(String path) {
long[] tmp = hdfReader.getDataSetInformation(path).getDimensions();
// Conversion from long[] to int[]
int[] result = new int[tmp.length];
for (int k = 0; k < tmp.length; k++) {
result[k] = (int) tmp[k];
}
return result;
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readByteArray()
*/
public MDByteArray readByteArray(String path) {
return this.hdfReader.int8().readMDArray(path);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readIntArray()
*/
public MDIntArray readIntArray(String path) {
return this.hdfReader.int32().readMDArray(path);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readIntBlockArray()
*/
//public MDIntArray readIntBlockArray(String path, int z, int c, int t, int h, int w) {
public MDIntArray readIntBlockArray(String path, int[] offset, int[] size) {
long[] longOffset = new long[offset.length];
for (int k = 0; k < offset.length; k++) {
longOffset[k] = (long) offset[k];
}
return this.hdfReader.int32().readMDArrayBlockWithOffset(path, size, longOffset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readIntBlockArray()
*/
public MDByteArray readByteBlockArray(String path, int[] offset, int[] size) {
long[] longOffset = new long[offset.length];
for (int k = 0; k < offset.length; k++) {
longOffset[k] = (long) offset[k];
}
return this.hdfReader.int8().readMDArrayBlockWithOffset(path, size, longOffset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readIntBlockArray()
*/
public MDShortArray readShortBlockArray(String path, int[] offset, int[] size) {
long[] longOffset = new long[offset.length];
for (int k = 0; k < offset.length; k++) {
longOffset[k] = (long) offset[k];
}
return this.hdfReader.int16().readMDArrayBlockWithOffset(path, size, longOffset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readStringArray()
*/
public String[] readStringArray(String path) {
return this.hdfReader.string().readArray(path);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#readCompoundArrayDataMap()
*/
public HDF5CompoundDataMap[] readCompoundArrayDataMap(String path) {
return this.hdfReader.readCompoundArray(path, HDF5CompoundDataMap.class);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#getElementSize()
*/
public int getElementSize(String path) {
return this.hdfReader.getDataSetInformation(path).getTypeInformation().getElementSize();
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#initIntArray()
*/
public void initIntArray(String path, long[] dimensions, long bpp) {
if (bpp == 1) {
this.hdfWriter.uint8().createMDArray(path, dimensions,
new int[] {1,1,1, (int) dimensions[3], (int) dimensions[4]},
HDF5IntStorageFeatures.createDeflationKeep(1));
} else if (bpp == 2) {
this.hdfWriter.uint16().createMDArray(path, dimensions,
new int[] {1,1,1, (int) dimensions[3], (int) dimensions[4]},
HDF5IntStorageFeatures.createDeflationKeep(1));
} else if (bpp == 4) {
this.hdfWriter.int32().createMDArray(path, dimensions,
new int[] {1,1,1, (int) dimensions[3], (int) dimensions[4]},
HDF5IntStorageFeatures.createDeflationKeep(1));
}
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#writeArraySlice()
*/
public void writeArraySlice(String path, MDByteArray image, long[] offset) {
int[] mem_offset = new int[] {0, 0, 0, 0, 0};
this.hdfWriter.uint8().writeMDArrayBlockWithOffset(path, image, image.dimensions(), offset, mem_offset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#writeArraySlice()
*/
public void writeArraySlice(String path, MDShortArray image, long[] offset) {
int[] mem_offset = new int[] {0, 0, 0, 0, 0};
this.hdfWriter.uint16().writeMDArrayBlockWithOffset(path, image, image.dimensions(), offset, mem_offset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#writeArraySlice()
*/
public void writeArraySlice(String path, MDIntArray image, long[] offset) {
int[] mem_offset = new int[] {0, 0, 0, 0, 0};
this.hdfWriter.int32().writeMDArrayBlockWithOffset(path, image, image.dimensions(), offset, mem_offset);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#createGroup()
*/
public void createGroup(String path) throws IOException{
try {
hdfWriter.object().createGroup(path);
}
catch (Exception e) {
throw new IOException("JHDFService: Unable to create group.\n" + e.getMessage());
}
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#exists()
*/
public boolean exists(String path) {
return hdfReader.exists(path);
}
/* (non-Javadoc)
* @see loci.formats.JHDFService#close()
*/
public void close() throws IOException {
if (hdfReader != null) {
hdfReader.close();
}
if (hdfWriter != null) {
hdfWriter.close();
}
currentFile = null;
hdfReader = null;
}
}