/*
* #%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.in;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import loci.common.DataTools;
import loci.common.Location;
import loci.formats.ClassList;
import loci.formats.CoreMetadata;
import loci.formats.DelegateReader;
import loci.formats.FileInfo;
import loci.formats.FileStitcher;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.Modulo;
import loci.formats.meta.MetadataStore;
/**
*
*/
public class FilePatternReader extends FormatReader {
// -- Fields --
private FileStitcher helper;
// -- Constructor --
/** Constructs a new pattern reader. */
public FilePatternReader() {
super("File pattern", new String[] {"pattern"});
ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
Class<? extends IFormatReader>[] classArray = classes.getClasses();
ClassList<IFormatReader> newClasses =
new ClassList<IFormatReader>(IFormatReader.class);
for (Class<? extends IFormatReader> c : classArray) {
if (!c.equals(FilePatternReader.class)) {
newClasses.addClass(c);
}
}
helper = new FileStitcher(new ImageReader(newClasses));
suffixSufficient = true;
}
// -- IFormatReader methods --
@Override
public int getImageCount() {
return helper.getImageCount();
}
@Override
public boolean isRGB() {
return helper.isRGB();
}
@Override
public int getSizeX() {
return helper.getSizeX();
}
@Override
public int getSizeY() {
return helper.getSizeY();
}
@Override
public int getSizeZ() {
return helper.getSizeZ();
}
@Override
public int getSizeC() {
return helper.getSizeC();
}
@Override
public int getSizeT() {
return helper.getSizeT();
}
@Override
public int getPixelType() {
return helper.getPixelType();
}
@Override
public int getBitsPerPixel() {
return helper.getBitsPerPixel();
}
@Override
public int getEffectiveSizeC() {
return helper.getEffectiveSizeC();
}
@Override
public int getRGBChannelCount() {
return helper.getRGBChannelCount();
}
@Override
public boolean isIndexed() {
return helper.isIndexed();
}
@Override
public boolean isFalseColor() {
return helper.isFalseColor();
}
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
if (getCurrentFile() == null) {
return null;
}
return helper.get8BitLookupTable();
}
@Override
public short[][] get16BitLookupTable() throws FormatException, IOException {
if (getCurrentFile() == null) {
return null;
}
return helper.get16BitLookupTable();
}
@Override
public Modulo getModuloZ() {
return helper.getModuloZ();
}
@Override
public Modulo getModuloC() {
return helper.getModuloC();
}
@Override
public Modulo getModuloT() {
return helper.getModuloT();
}
@Override
public int getThumbSizeX() {
return helper.getThumbSizeX();
}
@Override
public int getThumbSizeY() {
return helper.getThumbSizeY();
}
@Override
public boolean isLittleEndian() {
return helper.isLittleEndian();
}
@Override
public String getDimensionOrder() {
return helper.getDimensionOrder();
}
@Override
public boolean isOrderCertain() {
return helper.isOrderCertain();
}
@Override
public boolean isThumbnailSeries() {
return helper.isThumbnailSeries();
}
@Override
public boolean isInterleaved() {
return helper.isInterleaved();
}
@Override
public boolean isInterleaved(int subC) {
return helper.isInterleaved(subC);
}
@Override
public byte[] openBytes(int no) throws FormatException, IOException {
return helper.openBytes(no);
}
@Override
public byte[] openBytes(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
return helper.openBytes(no, x, y, w, h);
}
@Override
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
return helper.openBytes(no, buf);
}
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
return helper.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 helper.openPlane(no, x, y, w, h);
}
@Override
public byte[] openThumbBytes(int no) throws FormatException, IOException {
return helper.openThumbBytes(no);
}
@Override
public void close(boolean fileOnly) throws IOException {
helper.close(fileOnly);
}
@Override
public int getSeriesCount() {
return helper.getSeriesCount();
}
@Override
public void setSeries(int no) {
helper.setSeries(no);
}
@Override
public int getSeries() {
return helper.getSeries();
}
@Override
public void setGroupFiles(boolean group) {
helper.setGroupFiles(group);
}
@Override
public boolean isGroupFiles() {
return helper.isGroupFiles();
}
@Override
public boolean isMetadataComplete() {
return helper.isMetadataComplete();
}
@Override
public void setNormalized(boolean normalize) {
helper.setNormalized(normalize);
}
@Override
public boolean isNormalized() { return helper.isNormalized(); }
@Override
public void setOriginalMetadataPopulated(boolean populate) {
helper.setOriginalMetadataPopulated(populate);
}
@Override
public boolean isOriginalMetadataPopulated() {
return helper.isOriginalMetadataPopulated();
}
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
if (noPixels) {
return new String[] {currentId};
}
String[] helperFiles = helper.getSeriesUsedFiles(noPixels);
String[] allFiles = new String[helperFiles.length + 1];
allFiles[0] = currentId;
System.arraycopy(helperFiles, 0, allFiles, 1, helperFiles.length);
return allFiles;
}
@Override
public String[] getUsedFiles(boolean noPixels) {
if (noPixels) {
return new String[] {currentId};
}
String[] helperFiles = helper.getUsedFiles(noPixels);
String[] allFiles = new String[helperFiles.length + 1];
allFiles[0] = currentId;
System.arraycopy(helperFiles, 0, allFiles, 1, helperFiles.length);
return allFiles;
}
@Override
public int getIndex(int z, int c, int t) {
return helper.getIndex(z, c, t);
}
@Override
public int[] getZCTCoords(int index) {
return helper.getZCTCoords(index);
}
@Override
public Object getMetadataValue(String field) {
return helper.getMetadataValue(field);
}
@Override
public Object getSeriesMetadataValue(String field) {
return helper.getSeriesMetadataValue(field);
}
@Override
public Hashtable<String, Object> getGlobalMetadata() {
return helper.getGlobalMetadata();
}
@Override
public Hashtable<String, Object> getSeriesMetadata() {
return helper.getSeriesMetadata();
}
@Override
public List<CoreMetadata> getCoreMetadataList() {
// Only used for determining the object type.
List<CoreMetadata> oldcore = helper.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) {
helper.setMetadataFiltered(filter);
}
@Override
public boolean isMetadataFiltered() { return helper.isMetadataFiltered(); }
@Override
public void setMetadataStore(MetadataStore store) {
helper.setMetadataStore(store);
}
@Override
public MetadataStore getMetadataStore() {
return helper.getMetadataStore();
}
@Override
public Object getMetadataStoreRoot() {
return helper.getMetadataStoreRoot();
}
@Override
public IFormatReader[] getUnderlyingReaders() {
return new IFormatReader[] {helper};
}
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
@Override
public String getDatasetStructureDescription() {
return helper.getDatasetStructureDescription();
}
@Override
public boolean hasCompanionFiles() {
return true;
}
@Override
public String[] getPossibleDomains(String id)
throws FormatException, IOException
{
return helper.getPossibleDomains(id);
}
@Override
public String[] getDomains() {
return helper.getDomains();
}
@Override
public int getOptimalTileWidth() {
return helper.getOptimalTileWidth();
}
@Override
public int getOptimalTileHeight() {
return helper.getOptimalTileHeight();
}
@Override
public int getCoreIndex() {
return helper.getCoreIndex();
}
@Override
public void setCoreIndex(int no) {
helper.setCoreIndex(no);
}
@Override
public int seriesToCoreIndex(int series) {
return helper.seriesToCoreIndex(series);
}
@Override
public int coreIndexToSeries(int index) {
return helper.coreIndexToSeries(index);
}
@Override
public int getResolutionCount() {
return helper.getResolutionCount();
}
@Override
public void setResolution(int no) {
helper.setResolution(no);
}
@Override
public int getResolution() {
return helper.getResolution();
}
@Override
public boolean hasFlattenedResolutions() {
return helper.hasFlattenedResolutions();
}
@Override
public void setFlattenedResolutions(boolean flattened) {
helper.setFlattenedResolutions(flattened);
}
// -- IFormatHandler API methods --
@Override
public Class<?> getNativeDataType() {
return helper.getNativeDataType();
}
@Override
public void close() throws IOException {
if (helper != null) {
helper.close();
}
}
// -- Internal FormatReader methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
// read the pattern from the file
// the file should just contain a single line with the relative or
// absolute file pattern
currentId = new Location(id).getAbsolutePath();
String pattern = DataTools.readFile(id).trim();
String dir = new Location(id).getAbsoluteFile().getParent();
if (new Location(pattern).getParent() == null) {
pattern = dir + File.separator + pattern;
}
helper.setUsingPatternIds(true);
helper.setCanChangePattern(false);
helper.setId(pattern);
core = helper.getCoreMetadataList();
}
}