/*
* #%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.Constants;
import loci.common.DateTools;
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;
import ome.units.quantity.Temperature;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
*/
public class KodakReader extends FormatReader {
// -- Constants --
private static final String MAGIC_STRING = "DTag";
private static final String PIXELS_STRING = "BSfD";
private static final String DIMENSIONS_STRING = "GBiH";
private static final String FILEINFO_STRING = "DLFi";
private static final String DATE_FORMAT = "HH:mm:ss 'on' MM/dd/yyyy";
// -- Fields --
private long pixelOffset;
// -- Constructor --
/** Constructs a new Kodak reader. */
public KodakReader() {
super("Kodak Molecular Imaging", "bip");
domains = new String[] {FormatTools.GEL_DOMAIN};
}
// -- 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;
return (stream.readString(blockLen)).indexOf(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(pixelOffset);
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pixelOffset = 0;
}
}
// -- 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 = false;
findString(DIMENSIONS_STRING);
in.skipBytes(DIMENSIONS_STRING.length() + 20);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
findString(PIXELS_STRING);
pixelOffset = in.getFilePointer() + PIXELS_STRING.length() + 20;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYCZT";
m.pixelType = FormatTools.FLOAT;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
readExtraMetadata(store);
readFileInfoMetadata(store);
}
// -- Helper methods --
private void findString(String marker) throws IOException {
byte[] buf = new byte[8192];
int overlap = marker.length();
in.read(buf, 0, overlap);
while (in.getFilePointer() < in.length()) {
int length = in.read(buf, overlap, buf.length - overlap);
for (int i=0; i<length; i++) {
if (marker.equals(
new String(buf, i, marker.length(), Constants.ENCODING)))
{
in.seek(in.getFilePointer() - (length + overlap) + i);
return;
}
}
System.arraycopy(buf, length, buf, 0, overlap);
}
}
private void readExtraMetadata(MetadataStore store) throws IOException {
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
return;
}
in.seek(0);
findString("Image Capture Source");
String metadata = in.readCString();
if (metadata == null) {
return;
}
String[] lines = metadata.split("\n");
for (String line : lines) {
int index = line.indexOf(":");
if (index < 0 || line.startsWith("#") || line.startsWith("-")) {
continue;
}
String key = line.substring(0, index).trim();
String value = line.substring(index + 1).trim();
addGlobalMeta(key, value);
if (key.equals("Image Capture Source")) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
store.setMicroscopeModel(value, 0);
}
else if (key.equals("Capture Time/Date")) {
String date = DateTools.formatDate(value, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
else if (key.equals("Exposure Time")) {
Double exposureTime = new Double(value.substring(0, value.indexOf(" ")));
if (exposureTime != null) {
store.setPlaneExposureTime(new Time(exposureTime, UNITS.S), 0, 0);
}
}
else if (key.equals("Vertical Resolution")) {
// resolution stored in pixels per inch
if (value.indexOf(" ") > 0) {
value = value.substring(0, value.indexOf(" "));
}
Double size = new Double(value);
size = 1.0 / (size * (1.0 / 25400));
Length sizeY = FormatTools.getPhysicalSizeY(size);
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
else if (key.equals("Horizontal Resolution")) {
// resolution stored in pixels per inch
if (value.indexOf(" ") > 0) {
value = value.substring(0, value.indexOf(" "));
}
Double size = new Double(value);
size = 1.0 / (size * (1.0 / 25400));
Length sizeX = FormatTools.getPhysicalSizeX(size);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
}
else if (key.equals("CCD Temperature")) {
Double temp = new Double(value.substring(0, value.indexOf(" ")));
store.setImagingEnvironmentTemperature(
new Temperature(temp, UNITS.DEGREEC), 0);
}
}
}
private void readFileInfoMetadata(MetadataStore store) throws IOException {
in.seek(0);
findString(FILEINFO_STRING);
int tagLength = FILEINFO_STRING.length();
if (in.length() - in.getFilePointer() < tagLength + 20) {
return;
}
in.skipBytes(tagLength + 16);
int dataLength = in.readInt() - tagLength - 20;
if (in.length() - in.getFilePointer() < dataLength) {
return;
}
byte[] data = new byte[dataLength];
if (in.read(data) != dataLength) {
return;
}
String info = new String(data, Constants.ENCODING);
info = info.trim().replaceAll("(\\r|\\n)+", " | ");
if (info.isEmpty()) {
return;
}
addGlobalMeta("FileInfo", info);
}
}