/*
* #%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.IOException;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
/**
* PCXReader is the file format reader for PCX files (originally used by
* PC Paintbrush; now used in Zeiss' LSM Image Browser).
* See http://www.qzx.com/pc-gpe/pcx.txt
*/
public class PCXReader extends FormatReader {
// -- Constants --
public static final byte PCX_MAGIC_BYTE = 10;
// -- Fields --
/** Offset to pixel data. */
private long offset;
/** Number of bytes per scan line - may be different than image width. */
private int bytesPerLine;
private int nColorPlanes;
private byte[][] lut;
// -- Constructor --
/** Constructs a new PCX reader. */
public PCXReader() {
super("PCX", "pcx");
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 1;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.read() == PCX_MAGIC_BYTE;
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() {
FormatTools.assertId(currentId, true, 1);
return lut;
}
/**
* @see loci.formats.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.checkPlaneParameters(this, no, buf.length, x, y, w, h);
in.seek(offset);
// PCX uses a simple RLE compression algorithm
byte[] b = new byte[bytesPerLine * getSizeY() * nColorPlanes];
int pt = 0;
while (pt < b.length) {
int val = in.read() & 0xff;
if (((val & 0xc0) >> 6) == 3) {
int len = val & 0x3f;
val = in.read() & 0xff;
for (int q=0; q<len; q++) {
b[pt++] = (byte) val;
if ((pt % bytesPerLine) == 0) {
break;
}
}
}
else b[pt++] = (byte) (val & 0xff);
}
int src = y * nColorPlanes * bytesPerLine;
for (int row=0; row<h; row++) {
int rowOffset = row * nColorPlanes * bytesPerLine;
for (int c=0; c<nColorPlanes; c++) {
System.arraycopy(b, src + rowOffset + x, buf, c * w * h + row * w, w);
rowOffset += bytesPerLine;
}
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
offset = 0;
bytesPerLine = 0;
nColorPlanes = 0;
lut = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
LOGGER.info("Reading file header");
CoreMetadata m = core.get(0);
m.littleEndian = true;
in.order(isLittleEndian());
in.seek(1);
int version = in.read();
in.skipBytes(1);
int bitsPerPixel = in.read();
int xMin = in.readShort();
int yMin = in.readShort();
int xMax = in.readShort();
int yMax = in.readShort();
m.sizeX = xMax - xMin;
m.sizeY = yMax - yMin;
in.skipBytes(version == 5 ? 53 : 51);
nColorPlanes = in.read();
bytesPerLine = in.readShort();
int paletteType = in.readShort();
offset = in.getFilePointer() + 58;
if (version == 5 && nColorPlanes == 1) {
in.seek(in.length() - 768);
lut = new byte[3][256];
for (int i=0; i<lut[0].length; i++) {
for (int j=0; j<lut.length; j++) {
lut[j][i] = in.readByte();
}
}
m.indexed = true;
}
addGlobalMeta("Palette type", paletteType);
m.sizeZ = 1;
m.sizeT = 1;
m.sizeC = nColorPlanes;
m.rgb = nColorPlanes > 1;
m.imageCount = 1;
m.pixelType = FormatTools.UINT8;
m.dimensionOrder = "XYCZT";
m.interleaved = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}