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HISReader.java
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HISReader.java
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/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2016 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 ome.xml.model.primitives.Timestamp;
import loci.common.DataTools;
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.units.quantity.Time;
import ome.units.UNITS;
/**
* HISReader is the file format reader for Hamamatsu .his files.
*/
public class HISReader extends FormatReader {
// -- Constants --
public static final String HIS_MAGIC_STRING = "IM";
// -- Fields --
/** Offsets to pixel data for each series. */
private long[] pixelOffset;
// -- Constructor --
/** Constructs a new Hamamatsu .his reader. */
public HISReader() {
super("Hamamatsu HIS", "his");
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 2;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(HIS_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[getSeries()]);
if ((getBitsPerPixel() % 8) == 0) {
readPlane(in, x, y, w, h, buf);
}
else {
int bits = getBitsPerPixel();
int bpp = FormatTools.getBytesPerPixel(getPixelType());
in.skipBits(y * getSizeX() * getSizeC() * bits);
for (int row=0; row<h; row++) {
int rowOffset = row * w * getSizeC() * bpp;
in.skipBits(x * getSizeC() * bits);
for (int col=0; col<w; col++) {
int colOffset = col * getSizeC() * bpp;
for (int c=0; c<getSizeC(); c++) {
int sample = in.readBits(bits);
DataTools.unpackBytes(sample, buf, rowOffset + colOffset + c * bpp,
bpp, isLittleEndian());
}
}
in.skipBits(getSizeC() * bits * (getSizeX() - w - x));
}
}
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);
in.order(true);
in.skipBytes(14);
int nSeries = in.readShort();
pixelOffset = new long[nSeries];
String[] date = new String[nSeries];
String[] binning = new String[nSeries];
double[] offset = new double[nSeries];
double[] exposureTime = new double[nSeries];
boolean adjustedBitDepth = false;
in.seek(0);
core.clear();
for (int i=0; i<nSeries; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
String checkString = in.readString(2);
if (!checkString.equals("IM") && i > 0) {
if (getBitsPerPixel() == 12) {
core.get(i - 1).bitsPerPixel = 16;
int prevSkip = (getSizeX() * getSizeY() * getSizeC() * 12) / 8;
int totalBytes = FormatTools.getPlaneSize(this);
in.skipBytes(totalBytes - prevSkip);
adjustedBitDepth = true;
}
}
setSeries(i);
int commentBytes = in.readShort();
ms.sizeX = in.readShort();
ms.sizeY = in.readShort();
in.skipBytes(4);
int dataType = in.readShort();
switch (dataType) {
case 1:
ms.pixelType = FormatTools.UINT8;
break;
case 2:
ms.pixelType = FormatTools.UINT16;
break;
case 6:
ms.pixelType = FormatTools.UINT16;
ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
break;
case 11:
ms.pixelType = FormatTools.UINT8;
ms.sizeC = 3;
break;
case 12:
ms.pixelType = FormatTools.UINT16;
ms.sizeC = 3;
break;
case 14:
ms.pixelType = FormatTools.UINT16;
ms.sizeC = 3;
ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
break;
}
in.skipBytes(50);
String comment = in.readString(commentBytes);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String[] data = comment.split(";");
for (String token : data) {
int eq = token.indexOf("=");
if (eq != -1) {
String key = token.substring(0, eq);
String value = token.substring(eq + 1);
addSeriesMeta(key, value);
if (key.equals("vDate")) {
date[i] = value;
}
else if (key.equals("vTime")) {
date[i] += " " + value;
date[i] = DateTools.formatDate(date[i], "yyyy/MM/dd HH:mm:ss");
}
else if (key.equals("vOffset")) {
offset[i] = Double.parseDouble(value);
}
else if (key.equals("vBinX")) {
binning[i] = value;
}
else if (key.equals("vBinY")) {
binning[i] += "x" + value;
}
else if (key.equals("vExpTim1")) {
exposureTime[i] = Double.parseDouble(value) * 100;
}
}
}
}
pixelOffset[i] = in.getFilePointer();
ms.littleEndian = true;
if (ms.sizeC == 0) ms.sizeC = 1;
ms.sizeT = 1;
ms.sizeZ = 1;
ms.imageCount = 1;
ms.rgb = ms.sizeC > 1;
ms.interleaved = isRGB();
ms.dimensionOrder = "XYCZT";
in.skipBytes(
(getSizeX() * getSizeY() * getSizeC() * getBitsPerPixel()) / 8);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
for (int i=0; i<nSeries; i++) {
store.setImageInstrumentRef(instrumentID, i);
if (date[i] != null) {
store.setImageAcquisitionDate(new Timestamp(date[i]), i);
}
store.setPlaneExposureTime(new Time(exposureTime[i], UNITS.S), i, 0);
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorOffset(offset[i], 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
store.setDetectorSettingsID(detectorID, i, 0);
store.setDetectorSettingsBinning(getBinning(binning[i]), i, 0);
}
}
}
}