/*
* #%L
* Bio-Formats Plugins for ImageJ: a collection of ImageJ plugins including the
* Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
* Data Browser and Stack Slicer.
* %%
* Copyright (C) 2006 - 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.plugins.util;
import ij.VirtualStack;
import ij.process.ImageProcessor;
import java.awt.image.IndexColorModel;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import loci.formats.ChannelMerger;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.Modulo;
import loci.formats.cache.Cache;
import loci.formats.cache.CacheException;
import loci.formats.cache.CacheStrategy;
import loci.formats.cache.CrosshairStrategy;
import loci.plugins.util.RecordedImageProcessor.MethodEntry;
/**
* Subclass of VirtualStack that uses Bio-Formats to read planes on demand.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class BFVirtualStack extends VirtualStack {
// -- Fields --
protected ImageProcessorReader reader;
protected String id;
protected Cache cache;
private List<List<MethodEntry>> methodStacks;
private int currentSlice = -1;
private RecordedImageProcessor currentProcessor;
private boolean colorize;
private boolean merge;
private boolean record;
private int series;
private int[] len;
private int[] planeIndexes;
private float[] calibrationTable;
// -- Static utility methods --
protected static int getWidth(IFormatReader r, String path, int series)
throws FormatException, IOException
{
r.setSeries(series);
return r.getSizeX();
}
protected static int getHeight(IFormatReader r, String path, int series)
throws FormatException, IOException
{
r.setSeries(series);
return r.getSizeY();
}
// -- Constructor --
public BFVirtualStack(String path, IFormatReader r, boolean colorize,
boolean merge, boolean record)
throws FormatException, IOException, CacheException
{
super(getWidth(r, path, r.getSeries()), getHeight(r, path, r.getSeries()),
null, path);
reader = new ImageProcessorReader(r);
id = path;
this.colorize = colorize;
this.merge = merge && !r.isIndexed();
this.record = record;
this.series = r.getSeries();
// set up cache
int[] subC;
Modulo moduloC = r.getModuloC();
if (moduloC.length() > 1) {
subC = new int[] {r.getSizeC() / moduloC.length(), moduloC.length()};
} else {
subC = new int[] {r.getSizeC()};
}
if (merge) subC = new int[] {new ChannelMerger(r).getEffectiveSizeC()};
len = new int[subC.length + 2];
System.arraycopy(subC, 0, len, 0, subC.length);
len[len.length - 2] = r.getSizeZ();
len[len.length - 1] = r.getSizeT();
CacheStrategy strategy = new CrosshairStrategy(len);
cache = new Cache(strategy, new ImageProcessorSource(r), true);
methodStacks = new ArrayList<List<MethodEntry>>();
for (int i=0; i<r.getImageCount(); i++) {
methodStacks.add(new ArrayList<MethodEntry>());
}
}
// -- BFVirtualStack API methods --
public String getPath() { return id; }
public ImageProcessorReader getReader() { return reader; }
public Cache getCache() { return cache; }
public RecordedImageProcessor getRecordedProcessor() {
return currentProcessor;
}
public List<MethodEntry> getMethodStack() {
if (currentSlice >= 0) return methodStacks.get(currentSlice);
return null;
}
public void setPlaneIndexes(int[] planeIndexes) {
this.planeIndexes = planeIndexes;
}
// -- VirtualStack API methods --
@Override
public synchronized ImageProcessor getProcessor(int n) {
reader.setSeries(series);
// check cache first
if (currentSlice >= 0 && currentProcessor != null) {
List<MethodEntry> currentStack = currentProcessor.getMethodStack();
if (currentStack.size() > 1) {
methodStacks.get(currentSlice).addAll(currentStack);
}
}
int sliceIndex = planeIndexes == null ? n - 1 : planeIndexes[n - 1];
int[] pos = reader.getZCTCoords(sliceIndex);
if (merge) pos = new ChannelMerger(reader).getZCTCoords(sliceIndex);
int[] cachePos = FormatTools.rasterToPosition(len, sliceIndex);
ImageProcessor ip = null;
try {
ip = (ImageProcessor) cache.getObject(cachePos);
cache.setCurrentPos(cachePos);
}
catch (CacheException exc) {
exc.printStackTrace();
}
// cache missed
try {
if (ip == null) {
ip = reader.openProcessors(reader.getIndex(pos[0], pos[1], pos[2]))[0];
}
}
catch (FormatException exc) {
exc.printStackTrace();
}
catch (IOException exc) {
exc.printStackTrace();
}
if (colorize) {
// apply color table, if necessary
byte[] lut = new byte[256];
byte[] blank = new byte[256];
for (int i=0; i<lut.length; i++) {
lut[i] = (byte) i;
blank[i] = (byte) 0;
}
IndexColorModel model = null;
if (pos[1] < 3) {
model = new IndexColorModel(8, 256, pos[1] == 0 ? lut : blank,
pos[1] == 1 ? lut : blank, pos[1] == 2 ? lut : blank);
}
else model = new IndexColorModel(8, 256, lut, lut, lut);
if (ip != null) ip.setColorModel(model);
}
else if (merge) {
currentSlice = n - 1;
ImageProcessor[] otherChannels =
new ImageProcessor[reader.getSizeC() - 1];
for (int i=0; i<otherChannels.length; i++) {
int channel = i >= pos[1] ? i + 1 : i;
try {
cachePos[0] = channel;
otherChannels[i] = (ImageProcessor) cache.getObject(cachePos);
}
catch (CacheException exc) {
exc.printStackTrace();
}
if (otherChannels[i] == null) {
try {
int index = reader.getIndex(pos[0], channel, pos[2]);
otherChannels[i] = reader.openProcessors(index)[0];
}
catch (FormatException exc) {
exc.printStackTrace();
}
catch (IOException exc) {
exc.printStackTrace();
}
}
}
currentProcessor = new RecordedImageProcessor(ip, pos[1], otherChannels);
currentProcessor.setDoRecording(record);
if (calibrationTable == null) {
calibrationTable = currentProcessor.getChild().getCalibrationTable();
}
else {
currentProcessor.setCalibrationTable(calibrationTable);
}
return currentProcessor.getChild();
}
if (ip != null) {
currentSlice = n - 1;
currentProcessor = new RecordedImageProcessor(ip);
currentProcessor.setDoRecording(record);
if (calibrationTable == null) {
calibrationTable = currentProcessor.getChild().getCalibrationTable();
}
else {
currentProcessor.setCalibrationTable(calibrationTable);
}
return currentProcessor.getChild();
}
return null;
}
@Override
public int getWidth() {
reader.setSeries(series);
return reader.getSizeX();
}
@Override
public int getHeight() {
reader.setSeries(series);
return reader.getSizeY();
}
@Override
public int getSize() {
if (reader.getCurrentFile() == null) return 0;
reader.setSeries(series);
if (merge) return new ChannelMerger(reader).getImageCount();
return planeIndexes == null ? reader.getImageCount() : planeIndexes.length;
}
}