/*
* #%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.StreamTokenizer;
import java.io.IOException;
import java.util.StringTokenizer;
import loci.common.ByteArrayHandle;
import loci.common.DataTools;
import loci.common.RandomAccessInputStream;
import loci.common.RandomAccessOutputStream;
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;
/**
* PGMReader is the file format reader for Portable Gray Map (PGM) images.
*
* Much of this code was adapted from ImageJ (http://rsb.info.nih.gov/ij).
*/
public class PGMReader extends FormatReader {
// -- Constants --
public static final char PGM_MAGIC_CHAR = 'P';
// -- Fields --
private boolean rawBits;
/** Offset to pixel data. */
private long offset;
// -- Constructor --
/** Constructs a new PGMReader. */
public PGMReader() {
super("Portable Any Map",
new String[] {"pbm", "pgm", "ppm"});
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 2;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.read() == PGM_MAGIC_CHAR &&
Character.isDigit((char) stream.read());
}
/**
* @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);
if (rawBits) {
readPlane(in, x, y, w, h, buf);
}
else {
ByteArrayHandle handle = new ByteArrayHandle();
RandomAccessOutputStream out = new RandomAccessOutputStream(handle);
out.order(isLittleEndian());
while (in.getFilePointer() < in.length()) {
String line = in.readLine().trim();
line = line.replaceAll("[^0-9]", " ");
StringTokenizer t = new StringTokenizer(line, " ");
while (t.hasMoreTokens()) {
int q = Integer.parseInt(t.nextToken().trim());
if (getPixelType() == FormatTools.UINT16) {
out.writeShort(q);
}
else out.writeByte(q);
}
}
out.close();
RandomAccessInputStream s = new RandomAccessInputStream(handle);
s.seek(0);
readPlane(s, x, y, w, h, buf);
s.close();
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
rawBits = false;
offset = 0;
}
}
// -- 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);
CoreMetadata m = core.get(0);
// Plain Raw
// B&W P1 P4
// Grayscale P2 P5
// RGB P3 P6
final String magic = in.readString(2);
rawBits = magic.equals("P4") || magic.equals("P5") || magic.equals("P6");
m.sizeC = (magic.equals("P3") || magic.equals("P6")) ? 3 : 1;
final boolean isBlackAndWhite = magic.equals("P1") || magic.equals("P4");
StreamTokenizer st = new StreamTokenizer(in);
st.commentChar('#');
int token;
token = st.nextToken();
m.sizeX = (int) st.nval;
token = st.nextToken();
m.sizeY = (int) st.nval;
if (!isBlackAndWhite) {
token = st.nextToken();
final int max = (int) st.nval;
if (max > 255)
m.pixelType = FormatTools.UINT16;
else
m.pixelType = FormatTools.UINT8;
}
// After reading the 2 or 3 header entries, it is possible that there are
// multiple comments before the actual pixel data.
Byte c;
do {
c = in.readByte();
if (c == 35) {
// Found a # for comment
do {
c = in.readByte();
} while (c != 13 && c != 10); // comment only ends after CR or LF
}
} while (c == 32 || c == 13 || c == 10 || c == 9 || c == 11 || c == 12);
// space CR LF TAB VT FF
offset = in.getFilePointer() -1;
addGlobalMeta("Black and white", isBlackAndWhite);
m.rgb = getSizeC() == 3;
m.dimensionOrder = "XYCZT";
m.littleEndian = true;
m.interleaved = true;
m.sizeZ = 1;
m.sizeT = 1;
m.indexed = false;
m.falseColor = false;
// This may not be true. Multiple images were added to the netpbm
// formats in July 2000.
m.imageCount = 1;
// 1. the comments are being ignored;
// 2. we may be missing some images (allowed in raw)
m.metadataComplete = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}