/*
* #%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;
/**
* SMCameraReader is the file format reader for SM camera files.
*/
public class SMCameraReader extends FormatReader {
// -- Constants --
private static final byte[] SMC_MAGIC = new byte[] {
0, 0, 0, 0, 2, 0, 0, 5, (byte) 0xc9, (byte) 0x88, 0, 5, (byte) 0xcb,
(byte) 0x88, 0, 0
};
private static final int HEADER_SIZE = 548;
// -- Fields --
// -- Constructor --
/** Constructs a new SM camera reader. */
public SMCameraReader() {
super("SM Camera", "");
domains = new String[] {FormatTools.SEM_DOMAIN};
suffixSufficient = false;
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 16;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
byte[] magic = new byte[blockLen];
stream.read(magic);
for (int i=0; i<magic.length; i++) {
if (magic[i] != SMC_MAGIC[i]) return false;
}
return true;
}
/**
* @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(HEADER_SIZE);
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(524);
m.sizeY = in.readShort();
in.skipBytes(6);
m.sizeX = in.readShort();
m.pixelType = FormatTools.UINT8;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYZCT";
m.littleEndian = false;
addGlobalMeta("Image width", getSizeX());
addGlobalMeta("Image height", getSizeY());
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
}