/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 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.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;
/**
* VGSAMReader is the file format reader for VG SAM .dti files.
*/
public class VGSAMReader extends FormatReader {
// -- Constants --
public static final String VG_MAGIC_STRING = "VGS";
public static final int PIXEL_OFFSET = 368;
// -- Fields --
// -- Constructor --
/** Constructs a new VG SAM reader. */
public VGSAMReader() {
super("VG SAM", "dti");
domains = new String[] {FormatTools.SPM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 3;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(VG_MAGIC_STRING) >= 0;
}
/**
* @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(PIXEL_OFFSET);
readPlane(in, x, y, w, h, buf);
return buf;
}
// -- 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);
in.seek(348);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
in.skipBytes(4);
int bpp = in.readInt();
addGlobalMeta("Bytes per pixel", bpp);
m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, bpp == 4);
m.littleEndian = false;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.rgb = false;
m.interleaved = false;
m.dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}