//
// BurleighReader.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;
import ome.xml.model.primitives.PositiveFloat;
/**
* BurleighReader is the file format reader for Burleigh .img files.
*
* <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/BurleighReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/BurleighReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class BurleighReader extends FormatReader {
// -- Fields --
private int pixelsOffset;
// -- Constructor --
/** Constructs a new Burleigh reader. */
public BurleighReader() {
super("Burleigh", "img");
domains = new String[] {FormatTools.SEM_DOMAIN};
suffixSufficient = false;
suffixNecessary = false;
}
// -- 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[] magic = new byte[blockLen];
stream.read(magic);
return magic[0] == 0x66 && magic[1] == 0x66 && magic[3] == 0x40 &&
(magic[2] == 0x46 || magic[2] == 0x06);
}
/**
* @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(pixelsOffset);
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pixelsOffset = 0;
}
}
// -- 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);
core[0].littleEndian = true;
in.order(isLittleEndian());
int version = (int) in.readFloat() - 1;
core[0].sizeX = in.readShort();
core[0].sizeY = in.readShort();
double xSize = 0d, ySize = 0d, zSize = 0d;
pixelsOffset = version == 1 ? 8 : 260;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
double timePerPixel = 0d;
int mode = 0, gain = 0, mag = 0;
double sampleVolts = 0d, tunnelCurrent = 0d;
if (version == 1) {
in.seek(in.length() - 40);
in.skipBytes(12);
xSize = in.readInt();
ySize = in.readInt();
zSize = in.readInt();
timePerPixel = in.readShort() * 50;
mag = in.readShort();
switch (mag) {
case 3:
mag = 10;
break;
case 4:
mag = 50;
break;
case 5:
mag = 250;
break;
}
xSize /= mag;
ySize /= mag;
zSize /= mag;
mode = in.readShort();
gain = in.readShort();
sampleVolts = in.readFloat() / 1000;
tunnelCurrent = in.readFloat();
}
else if (version == 2) {
in.skipBytes(14);
xSize = in.readInt();
ySize = in.readInt();
zSize = in.readInt();
mode = in.readShort();
in.skipBytes(4);
gain = in.readShort();
timePerPixel = in.readShort() * 50;
in.skipBytes(12);
sampleVolts = in.readFloat();
tunnelCurrent = in.readFloat();
addGlobalMeta("Force", in.readFloat());
}
addGlobalMeta("Version", version);
addGlobalMeta("Image mode", mode);
addGlobalMeta("Z gain", gain);
addGlobalMeta("Time per pixel (s)", timePerPixel);
addGlobalMeta("Sample volts", sampleVolts);
addGlobalMeta("Tunnel current", tunnelCurrent);
addGlobalMeta("Magnification", mag);
}
core[0].pixelType = FormatTools.UINT16;
core[0].sizeZ = 1;
core[0].sizeC = 1;
core[0].sizeT = 1;
core[0].imageCount = 1;
core[0].dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setPixelsPhysicalSizeX(new PositiveFloat(xSize / getSizeX()), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(ySize / getSizeY()), 0);
store.setPixelsPhysicalSizeZ(new PositiveFloat(zSize / getSizeZ()), 0);
}
}
}