/* @see IFormatHandler#setId(String) */
public void setId(String id) throws FormatException, IOException {
try {
super.setId(id);
} catch (CMMException e) {
// strip out all but the first application marker
// ImageIO isn't too keen on supporting multiple application markers
// in the same stream, as evidenced by:
//
// http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6488904
in = new RandomAccessInputStream(id);
ByteArrayOutputStream v = new ByteArrayOutputStream();
byte[] tag = new byte[2];
in.read(tag);
v.write(tag);
in.read(tag);
int tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
boolean appNoteFound = false;
while (tagValue != 0xffdb) {
if (!appNoteFound || (tagValue < 0xffe0 && tagValue >= 0xfff0)) {
v.write(tag);
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
byte[] tagContents = new byte[len - 2];
in.read(tagContents);
v.write(tag);
v.write(tagContents);
} else {
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
in.skipBytes(len - 2);
}
if (tagValue >= 0xffe0 && tagValue < 0xfff0 && !appNoteFound) {
appNoteFound = true;
}
in.read(tag);
tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
}
v.write(tag);
byte[] remainder = new byte[(int) (in.length() - in.getFilePointer())];
in.read(remainder);
v.write(remainder);
ByteArrayHandle bytes = new ByteArrayHandle(v.toByteArray());
Location.mapFile(currentId + ".fixed", bytes);
super.setId(currentId + ".fixed");
}
if (getSizeX() > MAX_SIZE && getSizeY() > MAX_SIZE && !legacyReaderInitialized) {
close();
useLegacy = true;
super.setId(id);
}
currentId = id;
}
private void writePixels(String chunk, byte[] stream, int x, int y, int width, int height)
throws FormatException, IOException {
MetadataRetrieve r = getMetadataRetrieve();
int sizeC = getSamplesPerPixel();
String type = r.getPixelsType(series).toString();
int pixelType = FormatTools.pixelTypeFromString(type);
boolean signed = FormatTools.isSigned(pixelType);
if (!isFullPlane(x, y, width, height)) {
throw new FormatException("APNGWriter does not support writing tiles.");
}
ByteArrayOutputStream s = new ByteArrayOutputStream();
s.write(chunk.getBytes());
if (chunk.equals("fdAT")) {
s.write(DataTools.intToBytes(nextSequenceNumber++, false));
}
DeflaterOutputStream deflater = new DeflaterOutputStream(s);
int planeSize = stream.length / sizeC;
int rowLen = stream.length / height;
int bytesPerPixel = stream.length / (width * height * sizeC);
byte[] rowBuf = new byte[rowLen];
for (int i = 0; i < height; i++) {
deflater.write(0);
if (interleaved) {
if (littleEndian) {
for (int col = 0; col < width * sizeC; col++) {
int offset = (i * sizeC * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
DataTools.unpackBytes(pixel, rowBuf, col * bytesPerPixel, bytesPerPixel, false);
}
} else System.arraycopy(stream, i * rowLen, rowBuf, 0, rowLen);
} else {
int max = (int) Math.pow(2, bytesPerPixel * 8 - 1);
for (int col = 0; col < width; col++) {
for (int c = 0; c < sizeC; c++) {
int offset = c * planeSize + (i * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
if (signed) {
if (pixel < max) pixel += max;
else pixel -= max;
}
int output = (col * sizeC + c) * bytesPerPixel;
DataTools.unpackBytes(pixel, rowBuf, output, bytesPerPixel, false);
}
}
}
deflater.write(rowBuf);
}
deflater.finish();
byte[] b = s.toByteArray();
// write chunk length
out.writeInt(b.length - 4);
out.write(b);
// write checksum
out.writeInt(crc(b));
}
/* @see loci.formats.IFormatHandler#setId(String) */
public void setId(String id) throws FormatException, IOException {
super.setId(id);
if (out.length() == 0) {
MetadataRetrieve r = getMetadataRetrieve();
int width = r.getPixelsSizeX(series).getValue().intValue();
int height = r.getPixelsSizeY(series).getValue().intValue();
int bytesPerPixel = FormatTools.getBytesPerPixel(r.getPixelsType(series).toString());
int nChannels = getSamplesPerPixel();
boolean indexed = getColorModel() != null && (getColorModel() instanceof IndexColorModel);
littleEndian = !r.getPixelsBinDataBigEndian(series, 0);
// write 8-byte PNG signature
out.write(PNG_SIG);
// write IHDR chunk
out.writeInt(13);
byte[] b = new byte[17];
b[0] = 'I';
b[1] = 'H';
b[2] = 'D';
b[3] = 'R';
DataTools.unpackBytes(width, b, 4, 4, false);
DataTools.unpackBytes(height, b, 8, 4, false);
b[12] = (byte) (bytesPerPixel * 8);
if (indexed) b[13] = (byte) 3;
else if (nChannels == 1) b[13] = (byte) 0;
else if (nChannels == 2) b[13] = (byte) 4;
else if (nChannels == 3) b[13] = (byte) 2;
else if (nChannels == 4) b[13] = (byte) 6;
b[14] = (byte) 0;
b[15] = (byte) 0;
b[16] = (byte) 0;
out.write(b);
out.writeInt(crc(b));
// write acTL chunk
out.writeInt(8);
out.writeBytes("acTL");
numFramesPointer = out.getFilePointer();
out.writeInt(0);
out.writeInt(0);
out.writeInt(0); // save a place for the CRC
}
}
private void parsePosition(int posIndex) throws IOException, FormatException {
Position p = positions.get(posIndex);
String s = DataTools.readFile(p.metadataFile);
parsePosition(s, posIndex);
buildTIFFList(posIndex);
}
private void parseROIs(MetadataStore store) throws IOException {
if (roiFile == null) return;
String roiData = DataTools.readFile(roiFile);
String[] lines = roiData.split("\r\n");
int firstRow = 0;
while (firstRow < lines.length && !lines[firstRow].startsWith("ROI")) {
firstRow++;
}
firstRow += 2;
if (firstRow >= lines.length) return;
for (int i = firstRow; i < lines.length; i++) {
String[] cols = lines[i].split("\t");
if (cols.length < 6) break;
if (cols[2].trim().length() > 0) {
String rectangleID = MetadataTools.createLSID("Shape", i - firstRow, 0);
store.setRectangleID(rectangleID, i - firstRow, 0);
store.setRectangleX(new Double(cols[2]), i - firstRow, 0);
store.setRectangleY(new Double(cols[3]), i - firstRow, 0);
store.setRectangleWidth(new Double(cols[4]), i - firstRow, 0);
store.setRectangleHeight(new Double(cols[5]), i - firstRow, 0);
String roiID = MetadataTools.createLSID("ROI", i - firstRow);
store.setROIID(roiID, i - firstRow);
for (int s = 0; s < getSeriesCount(); s++) {
store.setImageROIRef(roiID, s, i - firstRow);
}
}
}
}
/** Parse metadata values from the Acqusition.xml file. */
private void parseXMLFile() throws IOException {
Position p = positions.get(getSeries());
String xmlData = DataTools.readFile(p.xmlFile);
xmlData = XMLTools.sanitizeXML(xmlData);
DefaultHandler handler = new MicromanagerHandler();
XMLTools.parseXML(xmlData, handler);
}
/**
* Calculates a SHA-1 digest on a byte array.
*
* @param buf Byte array to calculate a SHA-1 digest for.
* @return Hex string of the SHA-1 digest for <code>buf</code>.
*/
private String sha1(byte[] buf) {
try {
MessageDigest md = MessageDigest.getInstance("SHA-1");
return DataTools.bytesToHex(md.digest(buf));
} catch (Exception e) {
throw new RuntimeException(e);
}
}
private void writeFooter() throws IOException {
// write IEND chunk
out.writeInt(0);
out.writeBytes("IEND");
out.writeInt(crc("IEND".getBytes()));
// update frame count
out.seek(numFramesPointer);
out.writeInt(numFrames);
out.skipBytes(4);
byte[] b = new byte[12];
b[0] = 'a';
b[1] = 'c';
b[2] = 'T';
b[3] = 'L';
DataTools.unpackBytes(numFrames, b, 4, 4, false);
DataTools.unpackBytes(0, b, 8, 4, false);
out.writeInt(crc(b));
}
private static double decodeWord(byte[] plane, int index, int pixelType, boolean little) {
final double value;
switch (pixelType) {
case FormatTools.UINT8:
value = plane[index] & 0xff;
break;
case FormatTools.INT8:
value = plane[index];
break;
case FormatTools.UINT16:
value = DataTools.bytesToShort(plane, 2 * index, 2, little) & 0xffff;
break;
case FormatTools.INT16:
value = DataTools.bytesToShort(plane, 2 * index, 2, little);
break;
case FormatTools.UINT32:
value = DataTools.bytesToInt(plane, 4 * index, 4, little) & 0xffffffffL;
break;
case FormatTools.INT32:
value = DataTools.bytesToInt(plane, 4 * index, 4, little);
break;
case FormatTools.FLOAT:
value = DataTools.bytesToFloat(plane, 4 * index, 4, little);
break;
case FormatTools.DOUBLE:
value = DataTools.bytesToDouble(plane, 8 * index, 8, little);
break;
default:
value = Double.NaN;
}
return value;
}
@SuppressWarnings({"rawtypes", "unchecked"})
private void populatePlane(IFormatReader r, int no, byte[] plane, PlanarAccess planarAccess) {
final int pixelType = r.getPixelType();
final int bpp = FormatTools.getBytesPerPixel(pixelType);
final boolean fp = FormatTools.isFloatingPoint(pixelType);
final boolean little = r.isLittleEndian();
Object planeArray = DataTools.makeDataArray(plane, bpp, fp, little);
if (planeArray == plane) {
// array was returned by reference; make a copy
final byte[] planeCopy = new byte[plane.length];
System.arraycopy(plane, 0, planeCopy, 0, plane.length);
planeArray = planeCopy;
}
planarAccess.setPlane(no, makeArray(planeArray));
}
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
// read the pattern from the file
// the file should just contain a single line with the relative or
// absolute file pattern
currentId = new Location(id).getAbsolutePath();
String pattern = DataTools.readFile(id).trim();
String dir = new Location(id).getAbsoluteFile().getParent();
if (new Location(pattern).getParent() == null) {
pattern = dir + File.separator + pattern;
}
helper.setUsingPatternIds(true);
helper.setCanChangePattern(false);
helper.setId(pattern);
core = helper.getCoreMetadataList();
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
Location parent = new Location(id).getAbsoluteFile().getParentFile();
String[] lines = DataTools.readFile(currentId).split("\r\n");
for (String line : lines) {
int eq = line.indexOf("=");
if (eq < 0) {
continue;
}
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
if (key.equals("NoImages")) {
ndpiFiles = new String[Integer.parseInt(value)];
readers = new ChannelSeparator[ndpiFiles.length];
} else if (key.startsWith("Image")) {
int index = Integer.parseInt(key.replaceAll("Image", ""));
ndpiFiles[index] = new Location(parent, value).getAbsolutePath();
readers[index] = new ChannelSeparator(new NDPIReader());
}
}
readers[0].setMetadataStore(getMetadataStore());
readers[0].setId(ndpiFiles[0]);
core = readers[0].getCoreMetadata();
for (int i = 0; i < getSeriesCount(); i++) {
core[i].sizeC = readers.length;
core[i].rgb = false;
core[i].imageCount = core[i].sizeC * core[i].sizeZ * core[i].sizeT;
core[i].cLengths = new int[] {getSizeC()};
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
private void writeFCTL(int width, int height) throws IOException {
out.writeInt(26);
byte[] b = new byte[30];
b[0] = 'f';
b[1] = 'c';
b[2] = 'T';
b[3] = 'L';
DataTools.unpackBytes(nextSequenceNumber++, b, 4, 4, false);
DataTools.unpackBytes(width, b, 8, 4, false);
DataTools.unpackBytes(height, b, 12, 4, false);
DataTools.unpackBytes(0, b, 16, 4, false);
DataTools.unpackBytes(0, b, 20, 4, false);
DataTools.unpackBytes(1, b, 24, 2, false);
DataTools.unpackBytes(fps, b, 26, 2, false);
b[28] = (byte) 1;
b[29] = (byte) 0;
out.write(b);
out.writeInt(crc(b));
}
private void parseROIs(MetadataStore store) throws FormatException, IOException {
if (MetadataTools.isOMEXMLMetadata(store) || MetadataTools.isOMEXMLRoot(store.getRoot())) {
return;
}
String roiID = MetadataTools.createLSID("ROI", 0, 0);
String maskID = MetadataTools.createLSID("Shape", 0, 0);
store.setROIID(roiID, 0);
store.setMaskID(maskID, 0, 0);
String positionData = DataTools.readFile(roiDrawFile);
String[] coordinates = positionData.split("[ ,]");
double x1 = Double.parseDouble(coordinates[1]);
double y1 = Double.parseDouble(coordinates[2]);
double x2 = Double.parseDouble(coordinates[3]);
double y2 = Double.parseDouble(coordinates[5]);
store.setMaskX(x1, 0, 0);
store.setMaskY(y1, 0, 0);
store.setMaskWidth(x2 - x1, 0, 0);
store.setMaskHeight(y2 - y1, 0, 0);
store.setImageROIRef(roiID, 0, 0);
ImageReader roiReader = new ImageReader();
roiReader.setId(roiFile);
byte[] roiPixels = roiReader.openBytes(0);
roiReader.close();
BitWriter bits = new BitWriter(roiPixels.length / 8);
for (int i = 0; i < roiPixels.length; i++) {
bits.write(roiPixels[i] == 0 ? 0 : 1, 1);
}
store.setMaskBinData(bits.toByteArray(), 0, 0);
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
// make sure we have the experiment file
id = locateExperimentFile(id);
super.initFile(id);
Location dir = new Location(id).getAbsoluteFile().getParentFile();
for (String file : dir.list(true)) {
Location f = new Location(dir, file);
if (!f.isDirectory()) {
if (checkSuffix(file, META_EXT)) {
metadataFiles.add(f.getAbsolutePath());
}
}
}
// parse Experiment metadata
IniList experiment = readMetaData(id);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
objective = experiment.getTable("Geometry").get("Name");
IniTable camera = experiment.getTable("Camera");
binning = camera.get("BinX") + "x" + camera.get("BinY");
parseChannelData(dir);
addGlobalMeta("Objective", objective);
addGlobalMeta("Camera binning", binning);
}
Vector<String> uniqueRows = new Vector<String>();
Vector<String> uniqueColumns = new Vector<String>();
for (String well : wellLabels) {
String row = well.substring(0, 1).trim();
String column = well.substring(1).trim();
if (!uniqueRows.contains(row) && row.length() > 0) uniqueRows.add(row);
if (!uniqueColumns.contains(column) && column.length() > 0) {
uniqueColumns.add(column);
}
}
int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
int nTimepoints = getSizeT();
int nWells = wellLabels.size();
int nChannels = getSizeC() == 0 ? channelNames.size() : getSizeC();
if (nChannels == 0) nChannels = 1;
tiffs = getTiffs(dir.getAbsolutePath());
reader = new MinimalTiffReader();
reader.setId(tiffs[0][0]);
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int pixelType = reader.getPixelType();
boolean rgb = reader.isRGB();
boolean interleaved = reader.isInterleaved();
boolean indexed = reader.isIndexed();
boolean littleEndian = reader.isLittleEndian();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
IniParser parser = new IniParser();
for (String metadataFile : metadataFiles) {
String filename = new Location(metadataFile).getName();
if (!checkSuffix(metadataFile, "txt")) {
String data = DataTools.readFile(metadataFile);
IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
HashMap<String, String> h = ini.flattenIntoHashMap();
for (String key : h.keySet()) {
addGlobalMeta(filename + " " + key, h.get(key));
}
}
}
}
for (int i = 0; i < getSeriesCount(); i++) {
core[i] = new CoreMetadata();
core[i].sizeC = nChannels;
core[i].sizeZ = nSlices;
core[i].sizeT = nTimepoints;
core[i].sizeX = sizeX / fieldCols;
core[i].sizeY = sizeY / fieldRows;
core[i].pixelType = pixelType;
core[i].rgb = rgb;
core[i].interleaved = interleaved;
core[i].indexed = indexed;
core[i].littleEndian = littleEndian;
core[i].dimensionOrder = "XYZTC";
core[i].imageCount = nSlices * nTimepoints * nChannels;
}
MetadataStore store = makeFilterMetadata();
boolean populatePlanes = getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM;
MetadataTools.populatePixels(store, this, populatePlanes);
String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
store.setPlateAcquisitionID(plateAcqID, 0, 0);
if (fieldRows * fieldCols > 0) {
store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(fieldRows * fieldCols), 0, 0);
} else {
LOGGER.warn("Expected positive value for MaximumFieldCount; got {}", fieldRows * fieldCols);
}
for (int row = 0; row < wellRows; row++) {
for (int col = 0; col < wellCols; col++) {
int index = row * wellCols + col;
store.setWellID(MetadataTools.createLSID("Well", 0, index), 0, index);
store.setWellRow(new NonNegativeInteger(row), 0, index);
store.setWellColumn(new NonNegativeInteger(col), 0, index);
}
}
for (int i = 0; i < getSeriesCount(); i++) {
int well = i / (fieldRows * fieldCols);
int field = i % (fieldRows * fieldCols);
MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i);
String name = wellLabels.get(well);
String row = name.substring(0, 1);
Integer col = Integer.parseInt(name.substring(1));
int index = (row.charAt(0) - 'A') * wellCols + col - 1;
String wellSampleID = MetadataTools.createLSID("WellSample", 0, index, field);
store.setWellSampleID(wellSampleID, 0, index, field);
store.setWellSampleIndex(new NonNegativeInteger(i), 0, index, field);
String imageID = MetadataTools.createLSID("Image", i);
store.setWellSampleImageRef(imageID, 0, index, field);
store.setImageID(imageID, i);
store.setImageName(name + " Field #" + (field + 1), i);
store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, i);
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objectiveID, 0, 0);
if (objective != null) {
String[] tokens = objective.split(" ");
String mag = tokens[0].replaceAll("[xX]", "");
String na = null;
int naIndex = 0;
for (int i = 0; i < tokens.length; i++) {
if (tokens[i].equals("NA")) {
naIndex = i + 1;
na = tokens[naIndex];
break;
}
}
Integer magnification = new Integer(mag);
if (magnification > 0) {
store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0);
} else {
LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification);
}
if (na != null) {
na = na.substring(0, 1) + "." + na.substring(1);
store.setObjectiveLensNA(new Double(na), 0, 0);
}
if (naIndex + 1 < tokens.length) {
store.setObjectiveManufacturer(tokens[naIndex + 1], 0, 0);
}
}
// populate LogicalChannel data
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageInstrumentRef(instrumentID, i);
store.setObjectiveSettingsID(objectiveID, i);
for (int c = 0; c < getSizeC(); c++) {
store.setChannelName(channelNames.get(c), i, c);
if (emWave[c] > 0) {
store.setChannelEmissionWavelength(new PositiveInteger(emWave[c]), i, c);
} else {
LOGGER.warn("Expected positive value for EmissionWavelength; got {}", emWave[c]);
}
if (exWave[c] > 0) {
store.setChannelExcitationWavelength(new PositiveInteger(exWave[c]), i, c);
} else {
LOGGER.warn("Expected positive value for ExcitationWavelength; got {}", exWave[c]);
}
String detectorID = MetadataTools.createLSID("Detector", 0, c);
store.setDetectorID(detectorID, 0, c);
store.setDetectorSettingsID(detectorID, i, c);
store.setDetectorSettingsGain(gain[c], i, c);
store.setDetectorSettingsOffset(offset[c], i, c);
store.setDetectorSettingsBinning(getBinning(binning), i, c);
}
long firstPlane = 0;
for (int p = 0; p < getImageCount(); p++) {
int[] zct = getZCTCoords(p);
store.setPlaneExposureTime(exposure[zct[1]], i, p);
String file = getFilename(i, p);
if (file != null) {
long plane = getTimestamp(file);
if (p == 0) {
firstPlane = plane;
}
double timestamp = (plane - firstPlane) / 1000.0;
store.setPlaneDeltaT(timestamp, i, p);
}
}
}
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
store.setPlateName(plateName, 0);
store.setPlateDescription(plateDescription, 0);
if (level != MetadataLevel.NO_OVERLAYS) {
parseROIs(store);
}
}
}