//
// ARFReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.IOException;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
/**
* ARFReader is the file format reader for Axon Raw Format (ARF) files,
* produced by INDEC BioSystems's
* <a href="http://www.imagingworkbench.com/">Imaging Workbench</a>
* software.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/ARFReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/ARFReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Johannes Schindelin johannes.schindelin at gmx.de
*/
public class ARFReader extends FormatReader {
// -- Constants --
private static final long PIXELS_OFFSET = 524;
// -- Constructor --
/** Constructs a new ARF reader. */
public ARFReader() {
super("ARF", "arf");
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
byte endian1 = stream.readByte();
byte endian2 = stream.readByte();
return ((endian1 == 1 && endian2 == 0) || (endian1 == 0 && endian2 == 1)) &&
stream.readString(2).equals("AR");
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
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(PIXELS_OFFSET + no * FormatTools.getPlaneSize(this));
readPlane(in, x, y, w, h, buf);
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
// parse file header
LOGGER.info("Reading file header");
byte endian1 = in.readByte();
byte endian2 = in.readByte();
boolean little;
if (endian1 == 1 && endian2 == 0) little = true;
else if (endian1 == 0 && endian2 == 1) little = false;
else throw new FormatException("Undefined endianness");
in.order(little);
in.skipBytes(2); // 'AR' signature
int version = in.readUnsignedShort();
int width = in.readUnsignedShort();
int height = in.readUnsignedShort();
int bitsPerPixel = in.readUnsignedShort();
int numImages = version == 2 ? in.readUnsignedShort() : 1;
// NB: The next 510 bytes are unused 'application dependent' data,
// followed by raw image data with no padding.
// populate core metadata
core[0].sizeX = width;
core[0].sizeY = height;
core[0].sizeZ = 1;
core[0].sizeC = 1;
core[0].sizeT = numImages;
int bpp = bitsPerPixel / 8;
if ((bitsPerPixel % 8) != 0) bpp++;
core[0].pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
core[0].bitsPerPixel = bitsPerPixel;
core[0].imageCount = numImages;
core[0].dimensionOrder = "XYCZT";
core[0].orderCertain = true;
core[0].littleEndian = little;
core[0].rgb = false;
core[0].interleaved = false;
core[0].indexed = false;
core[0].metadataComplete = true;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
// populate original metadata
addGlobalMeta("Endianness", little ? "little" : "big");
addGlobalMeta("Version", version);
addGlobalMeta("Width", width);
addGlobalMeta("Height", height);
addGlobalMeta("Bits per pixel", bitsPerPixel);
addGlobalMeta("Image count", numImages);
}
// populate OME metadata
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
}
}