/*
* #%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 loci.common.DataTools;
/**
* Logic to automatically merge channels in a file.
*/
public class ChannelMerger extends ReaderWrapper {
// -- Utility methods --
/** Converts the given reader into a ChannelMerger, wrapping if needed. */
public static ChannelMerger makeChannelMerger(IFormatReader r) {
if (r instanceof ChannelMerger) return (ChannelMerger) r;
return new ChannelMerger(r);
}
// -- Constructor --
/** Constructs a ChannelMerger around a new image reader. */
public ChannelMerger() { super(); }
/** Constructs a ChannelMerger with the given reader. */
public ChannelMerger(IFormatReader r) { super(r); }
// -- ChannelMerger API methods --
/** Determines whether the channels in the file can be merged. */
public boolean canMerge() {
int c = getSizeC();
return c > 1 && c <= 4 && !reader.isRGB();
}
// -- ChannelMerger API methods --
/**
* Returns the image number in the original dataset that corresponds to the
* given image number.
*
* @param no is an image number greater than or equal to 0 and less than
* getImageCount()
* @return the corresponding image number in the original (unmerged) data.
*/
public int getOriginalIndex(int no) throws FormatException, IOException {
int imageCount = getImageCount();
int originalCount = reader.getImageCount();
if (imageCount == originalCount) return no;
int[] coords = getZCTCoords(no);
return reader.getIndex(coords[0], coords[1], coords[2]);
}
// -- IFormatReader API methods --
/* @see IFormatReader#getImageCount() */
@Override
public int getImageCount() {
FormatTools.assertId(getCurrentFile(), true, 2);
int no = reader.getImageCount();
if (canMerge()) no /= getSizeC();
return no;
}
/* @see IFormatReader#getDimensionOrder() */
@Override
public String getDimensionOrder() {
FormatTools.assertId(getCurrentFile(), true, 2);
String order = reader.getDimensionOrder();
if (canMerge()) {
StringBuffer sb = new StringBuffer(order);
while (order.indexOf("C") != 2) {
char pre = order.charAt(order.indexOf("C") - 1);
sb.setCharAt(order.indexOf("C"), pre);
sb.setCharAt(order.indexOf(pre), 'C');
order = sb.toString();
}
}
return order;
}
/* @see IFormatReader#isInterleaved() */
@Override
public boolean isInterleaved() {
FormatTools.assertId(getCurrentFile(), true, 2);
return canMerge() ? false : reader.isInterleaved();
}
/* @see IFormatReader#isRGB() */
@Override
public boolean isRGB() {
FormatTools.assertId(getCurrentFile(), true, 2);
return canMerge() || reader.isRGB();
}
/* @see IFormatReader#isIndexed() */
@Override
public boolean isIndexed() {
FormatTools.assertId(getCurrentFile(), true, 2);
return !canMerge() && reader.isIndexed();
}
/* @see IFormatReader#openBytes(int) */
@Override
public byte[] openBytes(int no) throws FormatException, IOException {
return openBytes(no, 0, 0, getSizeX(), getSizeY());
}
/* @see IFormatReader#openBytes(int, byte[]) */
@Override
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
return openBytes(no , buf, 0, 0, getSizeX(), getSizeY());
}
/* @see IFormatReader#openBytes(int, int, int, int, int) */
@Override
public byte[] openBytes(int no, int x, int y, int w, int h)
throws FormatException, IOException
{
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int ch = getRGBChannelCount();
byte[] newBuffer = DataTools.allocate(w, h, ch, bpp);
return openBytes(no, newBuffer, x, y, w, h);
}
/* @see IFormatReader#openBytes(int, byte[], int, int, int, int) */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.assertId(getCurrentFile(), true, 2);
if (!canMerge()) return super.openBytes(no, buf, x, y, w, h);
int sizeC = getSizeC();
int[] nos = getZCTCoords(no);
int z = nos[0], t = nos[2];
for (int c=0; c<sizeC; c++) {
byte[] b = reader.openBytes(reader.getIndex(z, c, t), x, y, w, h);
System.arraycopy(b, 0, buf, c * b.length, b.length);
}
return buf;
}
@Override
public int getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT) {
return FormatTools.getIndex(this, z, c, t, moduloZ, moduloC, moduloT);
}
@Override
public int getIndex(int z, int c, int t) {
return FormatTools.getIndex(this, z, c, t);
}
@Override
public int[] getZCTCoords(int index) {
return FormatTools.getZCTCoords(this, index);
}
@Override
public int[] getZCTModuloCoords(int index) {
return FormatTools.getZCTModuloCoords(this, index);
}
// -- IFormatHandler API methods --
/* @see IFormatHandler#getNativeDataType() */
@Override
public Class<?> getNativeDataType() {
return byte[].class;
}
}