/*
* #%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;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* OxfordInstrumentsReader is the file format reader for
* Oxford Instruments .top files.
*/
public class OxfordInstrumentsReader extends FormatReader {
// -- Constants --
public static final String OXFORD_MAGIC_STRING = "Oxford Instruments";
// -- Fields --
private long headerSize = 0;
// -- Constructor --
/** Constructs a new Oxford Instruments reader. */
public OxfordInstrumentsReader() {
super("Oxford Instruments", "top");
suffixNecessary = false;
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 = OXFORD_MAGIC_STRING.length();
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).equals(OXFORD_MAGIC_STRING);
}
/**
* @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(headerSize);
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);
m.littleEndian = true;
in.order(isLittleEndian());
in.seek(48);
String comment = in.readString(32);
String dateTime = readDate();
in.skipBytes(8);
double xSize = -in.readFloat() + in.readFloat();
in.skipBytes(20);
double ySize = -in.readFloat() + in.readFloat();
in.skipBytes(24);
double zMin = in.readFloat();
double zMax = in.readFloat();
in.skipBytes(864);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
in.skipBytes(28);
if (getSizeX() == 0 && getSizeY() == 0) {
m.sizeX = in.readInt();
m.sizeY = in.readInt();
in.skipBytes(196);
}
else in.skipBytes(204);
m.pixelType = FormatTools.UINT16;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.rgb = false;
m.indexed = false;
m.dimensionOrder = "XYZCT";
m.interleaved = false;
if (FormatTools.getPlaneSize(this) + in.getFilePointer() > in.length()) {
m.sizeY = 1;
}
int lutSize = in.readInt();
in.skipBytes(lutSize);
headerSize = in.getFilePointer();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
in.skipBytes(FormatTools.getPlaneSize(this));
int nMetadataStrings = in.readInt();
for (int i=0; i<nMetadataStrings; i++) {
int length = in.readInt();
String s = in.readString(length);
if (s.indexOf(":") != -1) {
String key = s.substring(0, s.indexOf(":")).trim();
String value = s.substring(s.indexOf(":") + 1).trim();
if (!value.equals("-")) {
addGlobalMeta(key, value);
}
}
}
addGlobalMeta("Description", comment);
addGlobalMeta("Acquisition date", dateTime);
addGlobalMeta("X size (um)", xSize);
addGlobalMeta("Y size (um)", ySize);
addGlobalMeta("Z minimum (um)", zMin);
addGlobalMeta("Z maximum (um)", zMax);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setImageDescription(comment, 0);
if (dateTime != null) {
store.setImageAcquisitionDate(new Timestamp(dateTime), 0);
}
double physicalSizeX = xSize / getSizeX();
double physicalSizeY = ySize / getSizeY();
Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
// -- Helper methods --
private String readDate() throws IOException {
StringBuffer dateTime = new StringBuffer();
dateTime.append(String.valueOf(in.readInt())); // year
dateTime.append("-");
int month = in.readInt();
dateTime.append(String.format("%02d", month));
dateTime.append("-");
int day = in.readInt();
dateTime.append(String.format("%02d", day));
dateTime.append("T");
int hour = in.readInt();
dateTime.append(String.format("%02d", hour));
dateTime.append(":");
int minute = in.readInt();
dateTime.append(String.format("%02d", minute));
dateTime.append(":");
in.skipBytes(4);
float scanTime = in.readInt() / 100f;
dateTime.append(String.format("%02d", (int) scanTime));
addGlobalMeta("Scan time (s)", scanTime);
return dateTime.toString();
}
}