/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package loci.formats;
import java.io.IOException;
import java.lang.reflect.Array;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Set;
import loci.common.RandomAccessInputStream;
import loci.formats.in.MetadataLevel;
import loci.formats.in.MetadataOptions;
import loci.formats.meta.MetadataStore;
/**
* Abstract superclass of reader logic that wraps other readers.
* All methods are simply delegated to the wrapped reader.
*/
public abstract class ReaderWrapper implements IFormatReader {
// -- Fields --
/** FormatReader used to read the file. */
protected IFormatReader reader;
// -- Constructors --
/** Constructs a reader wrapper around a new image reader. */
public ReaderWrapper() { this(new ImageReader()); }
/** Constructs a reader wrapper around the given reader. */
public ReaderWrapper(IFormatReader r) {
if (r == null) {
throw new IllegalArgumentException("Format reader cannot be null");
}
reader = r;
}
// -- ReaderWrapper API methods --
/** Gets the wrapped reader. */
public IFormatReader getReader() { return reader; }
/**
* Unwraps nested wrapped readers until the core reader (i.e., not
* a {@link ReaderWrapper} or {@link ImageReader}) is found.
*/
public IFormatReader unwrap() throws FormatException, IOException {
return unwrap(null, null);
}
/**
* Unwraps nested wrapped readers until the core reader (i.e., not
* a {@link ReaderWrapper} or {@link ImageReader}) is found.
*
* @param id Id to use as a basis when unwrapping any nested
* {@link ImageReader}s. If null, the current id is used.
*/
public IFormatReader unwrap(String id)
throws FormatException, IOException
{
return unwrap(null, id);
}
/**
* Unwraps nested wrapped readers until the given reader class is found.
*
* @param readerClass Class of the desired nested reader. If null, the
* core reader (i.e., deepest wrapped reader) will be returned.
* @param id Id to use as a basis when unwrapping any nested
* {@link ImageReader}s. If null, the current id is used.
*/
public IFormatReader unwrap(Class<? extends IFormatReader> readerClass,
String id) throws FormatException, IOException
{
IFormatReader r = this;
while (r instanceof ReaderWrapper || r instanceof ImageReader) {
if (readerClass != null && readerClass.isInstance(r)) break;
if (r instanceof ImageReader) {
ImageReader ir = (ImageReader) r;
r = id == null ? ir.getReader() : ir.getReader(id);
}
else r = ((ReaderWrapper) r).getReader();
}
if (readerClass != null && !readerClass.isInstance(r)) return null;
return r;
}
/**
* Performs a deep copy of the reader, including nested wrapped readers.
* Most of the reader state is preserved as well, including:<ul>
* <li>{@link #isNormalized()}</li>
* <li>{@link #isMetadataFiltered()}</li>
* <li>{@link DelegateReader#isLegacy()}</li>
* </ul>
*
* @param imageReaderClass If non-null, any {@link ImageReader}s in the
* reader stack will be replaced with instances of the given class.
* @throws FormatException If something goes wrong during the duplication.
*/
public ReaderWrapper duplicate(
Class<? extends IFormatReader> imageReaderClass) throws FormatException
{
ReaderWrapper wrapperCopy = duplicateRecurse(imageReaderClass);
// sync top-level configuration with original reader
boolean normalized = isNormalized();
boolean metadataFiltered = isMetadataFiltered();
wrapperCopy.setNormalized(normalized);
wrapperCopy.setMetadataFiltered(metadataFiltered);
return wrapperCopy;
}
// -- IMetadataConfigurable API methods --
/* (non-Javadoc)
* @see loci.formats.IMetadataConfigurable#getSupportedMetadataLevels()
*/
@Override
public Set<MetadataLevel> getSupportedMetadataLevels() {
return reader.getSupportedMetadataLevels();
}
/* (non-Javadoc)
* @see loci.formats.IMetadataConfigurable#getMetadataOptions()
*/
@Override
public MetadataOptions getMetadataOptions() {
return reader.getMetadataOptions();
}
/* (non-Javadoc)
* @see loci.formats.IMetadataConfigurable#setMetadataOptions(loci.formats.in.MetadataOptions)
*/
@Override
public void setMetadataOptions(MetadataOptions options) {
reader.setMetadataOptions(options);
}
// -- IFormatReader API methods --
@Override
public boolean isThisType(String name, boolean open) {
return reader.isThisType(name, open);
}
@Override
public boolean isThisType(byte[] block) {
return reader.isThisType(block);
}
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException{
return reader.isThisType(stream);
}
@Override
public int getImageCount() {
return reader.getImageCount();
}
@Override
public boolean isRGB() {
return reader.isRGB();
}
@Override
public int getSizeX() {
return reader.getSizeX();
}
@Override
public int getSizeY() {
return reader.getSizeY();
}
@Override
public int getSizeZ() {
return reader.getSizeZ();
}
@Override
public int getSizeC() {
return reader.getSizeC();
}
@Override
public int getSizeT() {
return reader.getSizeT();
}
@Override
public int getPixelType() {
return reader.getPixelType();
}
@Override
public int getBitsPerPixel() {
return reader.getBitsPerPixel();
}
@Override
public int getEffectiveSizeC() {
//return reader.getEffectiveSizeC();
int sizeZT = getSizeZ() * getSizeT();
if (sizeZT == 0) return 0;
return getImageCount() / sizeZT;
}
@Override
public int getRGBChannelCount() {
//return reader.getRGBChannelCount();
int effSizeC = getEffectiveSizeC();
if (effSizeC == 0) return 0;
return getSizeC() / effSizeC;
}
@Override
public boolean isIndexed() {
return reader.isIndexed();
}
@Override
public boolean isFalseColor() {
return reader.isFalseColor();
}
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
return reader.get8BitLookupTable();
}
@Override
public short[][] get16BitLookupTable() throws FormatException, IOException {
return reader.get16BitLookupTable();
}
@Override
public Modulo getModuloZ() {
return reader.getModuloZ();
}
@Override
public Modulo getModuloC() {
return reader.getModuloC();
}
@Override
public Modulo getModuloT() {
return reader.getModuloT();
}
@Override
public int getThumbSizeX() {
return reader.getThumbSizeX();
}
@Override
public int getThumbSizeY() {
return reader.getThumbSizeY();
}
@Override
public boolean isLittleEndian() {
return reader.isLittleEndian();
}
@Override
public String getDimensionOrder() {
return reader.getDimensionOrder();
}
@Override
public boolean isOrderCertain() {
return reader.isOrderCertain();
}
@Override
public boolean isThumbnailSeries() {
return reader.isThumbnailSeries();
}
@Override
public boolean isInterleaved() {
return reader.isInterleaved();
}
@Override
public boolean isInterleaved(int subC) {
return reader.isInterleaved(subC);
}
@Override
public byte[] openBytes(int no) throws FormatException, IOException {
return reader.openBytes(no);
}
@Override
public byte[] openBytes(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
return reader.openBytes(no, x, y, w, h);
}
@Override
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
return reader.openBytes(no, buf);
}
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
return reader.openBytes(no, buf, x, y, w, h);
}
@Override
public Object openPlane(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
return reader.openPlane(no, x, y, w, h);
}
@Override
public byte[] openThumbBytes(int no) throws FormatException, IOException {
return reader.openThumbBytes(no);
}
@Override
public void close(boolean fileOnly) throws IOException {
reader.close(fileOnly);
}
@Override
public int getSeriesCount() {
return reader.getSeriesCount();
}
@Override
public void setSeries(int no) {
reader.setSeries(no);
}
@Override
public int getSeries() {
return reader.getSeries();
}
@Override
public void setGroupFiles(boolean group) {
reader.setGroupFiles(group);
}
@Override
public boolean isGroupFiles() {
return reader.isGroupFiles();
}
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return reader.fileGroupOption(id);
}
@Override
public boolean isMetadataComplete() {
return reader.isMetadataComplete();
}
@Override
public void setNormalized(boolean normalize) {
reader.setNormalized(normalize);
}
@Override
public boolean isNormalized() { return reader.isNormalized(); }
@Override
public void setOriginalMetadataPopulated(boolean populate) {
reader.setOriginalMetadataPopulated(populate);
}
@Override
public boolean isOriginalMetadataPopulated() {
return reader.isOriginalMetadataPopulated();
}
@Override
public String[] getUsedFiles() {
return reader.getUsedFiles();
}
@Override
public String[] getUsedFiles(boolean noPixels) {
return reader.getUsedFiles(noPixels);
}
@Override
public String[] getSeriesUsedFiles() {
return reader.getSeriesUsedFiles();
}
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
return reader.getSeriesUsedFiles(noPixels);
}
@Override
public FileInfo[] getAdvancedUsedFiles(boolean noPixels) {
return reader.getAdvancedUsedFiles(noPixels);
}
@Override
public FileInfo[] getAdvancedSeriesUsedFiles(boolean noPixels) {
return reader.getAdvancedSeriesUsedFiles(noPixels);
}
@Override
public String getCurrentFile() { return reader.getCurrentFile(); }
@Override
public int getIndex(int z, int c, int t) {
return reader.getIndex(z, c, t);
}
@Override
public int getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT) {
return reader.getIndex(z, c, t, moduloZ, moduloC, moduloT);
}
@Override
public int[] getZCTCoords(int index) {
return reader.getZCTCoords(index);
}
@Override
public int[] getZCTModuloCoords(int index) {
return reader.getZCTModuloCoords(index);
}
@Override
public Object getMetadataValue(String field) {
return reader.getMetadataValue(field);
}
@Override
public Object getSeriesMetadataValue(String field) {
return reader.getSeriesMetadataValue(field);
}
@Override
public Hashtable<String, Object> getGlobalMetadata() {
return reader.getGlobalMetadata();
}
@Override
public Hashtable<String, Object> getSeriesMetadata() {
return reader.getSeriesMetadata();
}
@Override
public List<CoreMetadata> getCoreMetadataList() {
// Only used for determining the object type.
List<CoreMetadata> oldcore = reader.getCoreMetadataList();
List<CoreMetadata> newcore = new ArrayList<CoreMetadata>();
for (int s=0; s<oldcore.size(); s++) {
CoreMetadata newMeta = oldcore.get(s).clone(this, s);
newMeta.resolutionCount = oldcore.get(s).resolutionCount;
newcore.add(newMeta);
}
return newcore;
}
@Override
public void setMetadataFiltered(boolean filter) {
reader.setMetadataFiltered(filter);
}
@Override
public boolean isMetadataFiltered() { return reader.isMetadataFiltered(); }
@Override
public void setMetadataStore(MetadataStore store) {
reader.setMetadataStore(store);
}
@Override
public MetadataStore getMetadataStore() {
return reader.getMetadataStore();
}
@Override
public Object getMetadataStoreRoot() {
return reader.getMetadataStoreRoot();
}
@Override
public IFormatReader[] getUnderlyingReaders() {
return new IFormatReader[] {reader};
}
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return reader.isSingleFile(id);
}
@Override
public int getRequiredDirectories(String[] files)
throws FormatException, IOException
{
return reader.getRequiredDirectories(files);
}
@Override
public String getDatasetStructureDescription() {
return reader.getDatasetStructureDescription();
}
@Override
public boolean hasCompanionFiles() {
return reader.hasCompanionFiles();
}
@Override
public String[] getPossibleDomains(String id)
throws FormatException, IOException
{
return reader.getPossibleDomains(id);
}
@Override
public String[] getDomains() {
return reader.getDomains();
}
@Override
public int getOptimalTileWidth() {
return reader.getOptimalTileWidth();
}
@Override
public int getOptimalTileHeight() {
return reader.getOptimalTileHeight();
}
@Override
public int getCoreIndex() {
return reader.getCoreIndex();
}
@Override
public void setCoreIndex(int no) {
reader.setCoreIndex(no);
}
@Override
public int seriesToCoreIndex(int series) {
return reader.seriesToCoreIndex(series);
}
@Override
public int coreIndexToSeries(int index) {
return reader.coreIndexToSeries(index);
}
@Override
public int getResolutionCount() {
return reader.getResolutionCount();
}
@Override
public void setResolution(int no) {
reader.setResolution(no);
}
@Override
public int getResolution() {
return reader.getResolution();
}
@Override
public boolean hasFlattenedResolutions() {
return reader.hasFlattenedResolutions();
}
@Override
public void setFlattenedResolutions(boolean flattened) {
reader.setFlattenedResolutions(flattened);
}
// -- IFormatHandler API methods --
@Override
public boolean isThisType(String name) {
return reader.isThisType(name);
}
@Override
public String getFormat() {
return reader.getFormat();
}
@Override
public String[] getSuffixes() {
return reader.getSuffixes();
}
@Override
public Class<?> getNativeDataType() {
return reader.getNativeDataType();
}
@Override
public void setId(String id) throws FormatException, IOException {
reader.setId(id);
}
@Override
public void reopenFile() throws IOException {
reader.reopenFile();
}
@Override
public void close() throws IOException {
reader.close();
}
// -- Helper methods --
private ReaderWrapper duplicateRecurse(
Class<? extends IFormatReader> imageReaderClass) throws FormatException
{
IFormatReader childCopy = null;
if (reader instanceof ReaderWrapper) {
// found a nested reader layer; duplicate via recursion
childCopy = ((ReaderWrapper) reader).duplicateRecurse(imageReaderClass);
}
else {
Class<? extends IFormatReader> c = null;
if (reader instanceof ImageReader) {
// found an image reader; if given, substitute the reader class
c = imageReaderClass == null ? ImageReader.class : imageReaderClass;
}
else {
// bottom of the reader stack; duplicate the core reader
c = reader.getClass();
}
try {
childCopy = c.newInstance();
}
catch (IllegalAccessException exc) { throw new FormatException(exc); }
catch (InstantiationException exc) { throw new FormatException(exc); }
// preserve reader-specific configuration with original reader
if (reader instanceof DelegateReader) {
DelegateReader delegateOriginal = (DelegateReader) reader;
DelegateReader delegateCopy = (DelegateReader) childCopy;
delegateCopy.setLegacy(delegateOriginal.isLegacy());
}
}
// use crazy reflection to instantiate a reader of the proper type
Class<? extends ReaderWrapper> wrapperClass = getClass();
ReaderWrapper wrapperCopy = null;
try {
wrapperCopy = wrapperClass.getConstructor(new Class[]
{IFormatReader.class}).newInstance(new Object[] {childCopy});
}
catch (InstantiationException exc) { throw new FormatException(exc); }
catch (IllegalAccessException exc) { throw new FormatException(exc); }
catch (NoSuchMethodException exc) { throw new FormatException(exc); }
catch (InvocationTargetException exc) { throw new FormatException(exc); }
return wrapperCopy;
}
}