use of loci.formats.FormatException in project bioformats by openmicroscopy.
the class MINCReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
try {
ServiceFactory factory = new ServiceFactory();
netcdf = factory.getInstance(NetCDFService.class);
netcdf.setFile(id);
} catch (DependencyException e) {
throw new MissingLibraryException(e);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Vector<String> variableList = netcdf.getVariableList();
for (String variable : variableList) {
Hashtable<String, Object> attributes = netcdf.getVariableAttributes(variable);
String[] keys = attributes.keySet().toArray(new String[0]);
Arrays.sort(keys);
for (String key : keys) {
if (attributes.get(key) instanceof Object[]) {
final StringBuilder sb = new StringBuilder();
Object[] o = (Object[]) attributes.get(key);
for (Object q : o) {
sb.append(q.toString());
}
addGlobalMeta(variable + " " + key, sb.toString());
} else {
addGlobalMeta(variable + " " + key, attributes.get(key));
}
}
}
}
CoreMetadata m = core.get(0);
try {
Object pixels = netcdf.getVariableValue("/image");
if (pixels == null) {
pixels = netcdf.getVariableValue("/minc-2.0/image/0/image");
isMINC2 = true;
}
m.littleEndian = isMINC2;
boolean signed = false;
if (isMINC2) {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/image/0/image");
String unsigned = attrs.get("_Unsigned").toString();
if (!unsigned.startsWith("true")) {
signed = true;
}
} else {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/image");
String signtype = attrs.get("signtype").toString();
if (signtype.startsWith("signed")) {
signed = true;
}
}
if (pixels instanceof byte[][][]) {
m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
pixelData = (byte[][][]) pixels;
} else if (pixels instanceof byte[][][][]) {
byte[][][][] actualPixels = (byte[][][][]) pixels;
m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
pixelData = new byte[actualPixels.length * actualPixels[0].length][][];
int nextPlane = 0;
for (int t = 0; t < actualPixels.length; t++) {
for (int z = 0; z < actualPixels[t].length; z++) {
pixelData[nextPlane++] = actualPixels[t][z];
}
}
} else if (pixels instanceof short[][][]) {
m.pixelType = signed ? FormatTools.INT16 : FormatTools.UINT16;
short[][][] s = (short[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.shortsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof int[][][]) {
m.pixelType = signed ? FormatTools.INT32 : FormatTools.UINT32;
int[][][] s = (int[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.intsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof float[][][]) {
m.pixelType = FormatTools.FLOAT;
float[][][] s = (float[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.floatsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof double[][][]) {
m.pixelType = FormatTools.DOUBLE;
double[][][] s = (double[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.doublesToBytes(s[i][j], isLittleEndian());
}
}
}
} catch (ServiceException e) {
throw new FormatException(e);
}
Length physicalX = null;
Length physicalY = null;
Length physicalZ = null;
Length xPosition = null;
Length yPosition = null;
Length zPosition = null;
if (isMINC2) {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/xspace");
m.sizeX = Integer.parseInt(attrs.get("length").toString());
physicalX = getStepSize(attrs);
xPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/yspace");
m.sizeY = Integer.parseInt(attrs.get("length").toString());
physicalY = getStepSize(attrs);
yPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/zspace");
m.sizeZ = Integer.parseInt(attrs.get("length").toString());
physicalZ = getStepSize(attrs);
zPosition = getStart(attrs);
} else {
m.sizeX = netcdf.getDimension("/xspace");
m.sizeY = netcdf.getDimension("/yspace");
m.sizeZ = netcdf.getDimension("/zspace");
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/xspace");
physicalX = getStepSize(attrs);
xPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/yspace");
physicalY = getStepSize(attrs);
yPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/zspace");
physicalZ = getStepSize(attrs);
zPosition = getStart(attrs);
}
try {
m.sizeT = netcdf.getDimension("/time");
} catch (NullPointerException e) {
m.sizeT = 1;
}
m.sizeC = 1;
m.imageCount = getSizeZ() * getSizeT() * getSizeC();
m.rgb = false;
m.indexed = false;
m.dimensionOrder = "XYZCT";
String history = null;
if (isMINC2) {
history = netcdf.getAttributeValue("/minc-2.0/ident");
} else {
history = netcdf.getAttributeValue("/history");
}
addGlobalMeta("Comment", history);
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, xPosition != null || yPosition != null || zPosition != null);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(history, 0);
if (physicalX != null) {
store.setPixelsPhysicalSizeX(physicalX, 0);
}
if (physicalY != null) {
store.setPixelsPhysicalSizeY(physicalY, 0);
}
if (physicalZ != null) {
store.setPixelsPhysicalSizeZ(physicalZ, 0);
}
for (int i = 0; i < getImageCount(); i++) {
if (xPosition != null) {
store.setPlanePositionX(xPosition, 0, i);
}
if (yPosition != null) {
store.setPlanePositionY(yPosition, 0, i);
}
if (zPosition != null) {
int z = getZCTCoords(i)[0];
Double pos = zPosition.value().doubleValue();
if (physicalZ != null && z > 0) {
pos += z * physicalZ.value().doubleValue();
}
store.setPlanePositionZ(FormatTools.createLength(pos, zPosition.unit()), 0, i);
}
}
}
}
use of loci.formats.FormatException in project bioformats by openmicroscopy.
the class MetamorphReader method initStandardMetadata.
// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
CoreMetadata ms0 = core.get(0);
ms0.sizeZ = 1;
ms0.sizeT = 0;
int rgbChannels = getSizeC();
// Now that the base TIFF standard metadata has been parsed, we need to
// parse out the STK metadata from the UIC4TAG.
TiffIFDEntry uic1tagEntry = null;
TiffIFDEntry uic2tagEntry = null;
TiffIFDEntry uic4tagEntry = null;
try {
uic1tagEntry = tiffParser.getFirstIFDEntry(UIC1TAG);
uic2tagEntry = tiffParser.getFirstIFDEntry(UIC2TAG);
uic4tagEntry = tiffParser.getFirstIFDEntry(UIC4TAG);
} catch (IllegalArgumentException exc) {
LOGGER.debug("Unknown tag", exc);
}
try {
if (uic4tagEntry != null) {
mmPlanes = uic4tagEntry.getValueCount();
}
if (mmPlanes == 0) {
mmPlanes = ifds.size();
}
if (uic2tagEntry != null) {
parseUIC2Tags(uic2tagEntry.getValueOffset());
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (uic4tagEntry != null) {
parseUIC4Tags(uic4tagEntry.getValueOffset());
}
if (uic1tagEntry != null) {
parseUIC1Tags(uic1tagEntry.getValueOffset(), uic1tagEntry.getValueCount());
}
}
in.seek(uic4tagEntry.getValueOffset());
} catch (NullPointerException exc) {
LOGGER.debug("", exc);
} catch (IOException exc) {
LOGGER.debug("Failed to parse proprietary tags", exc);
}
try {
// copy ifds into a new array of Hashtables that will accommodate the
// additional image planes
IFD firstIFD = ifds.get(0);
long[] uic2 = firstIFD.getIFDLongArray(UIC2TAG);
if (uic2 == null) {
throw new FormatException("Invalid Metamorph file. Tag " + UIC2TAG + " not found.");
}
ms0.imageCount = uic2.length;
Object entry = firstIFD.getIFDValue(UIC3TAG);
TiffRational[] uic3 = entry instanceof TiffRational[] ? (TiffRational[]) entry : new TiffRational[] { (TiffRational) entry };
wave = new double[uic3.length];
final List<Double> uniqueWavelengths = new ArrayList<Double>();
for (int i = 0; i < uic3.length; i++) {
wave[i] = uic3[i].doubleValue();
addSeriesMeta("Wavelength [" + intFormatMax(i, mmPlanes) + "]", wave[i]);
final Double v = wave[i];
if (!uniqueWavelengths.contains(v))
uniqueWavelengths.add(v);
}
if (getSizeC() == 1) {
ms0.sizeC = uniqueWavelengths.size();
if (getSizeC() < getImageCount() && getSizeC() > (getImageCount() - getSizeC()) && (getImageCount() % getSizeC()) != 0) {
ms0.sizeC = getImageCount();
}
}
IFDList tempIFDs = new IFDList();
long[] oldOffsets = firstIFD.getStripOffsets();
long[] stripByteCounts = firstIFD.getStripByteCounts();
int rowsPerStrip = (int) firstIFD.getRowsPerStrip()[0];
int stripsPerImage = getSizeY() / rowsPerStrip;
if (stripsPerImage * rowsPerStrip != getSizeY())
stripsPerImage++;
PhotoInterp check = firstIFD.getPhotometricInterpretation();
if (check == PhotoInterp.RGB_PALETTE) {
firstIFD.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION, PhotoInterp.BLACK_IS_ZERO);
}
emWavelength = firstIFD.getIFDLongArray(UIC3TAG);
// for each image plane, construct an IFD hashtable
IFD temp;
for (int i = 0; i < getImageCount(); i++) {
// copy data from the first IFD
temp = new IFD(firstIFD);
// now we need a StripOffsets entry - the original IFD doesn't have this
long[] newOffsets = new long[stripsPerImage];
if (stripsPerImage * (i + 1) <= oldOffsets.length) {
System.arraycopy(oldOffsets, stripsPerImage * i, newOffsets, 0, stripsPerImage);
} else {
System.arraycopy(oldOffsets, 0, newOffsets, 0, stripsPerImage);
long image = (stripByteCounts[0] / rowsPerStrip) * getSizeY();
for (int q = 0; q < stripsPerImage; q++) {
newOffsets[q] += i * image;
}
}
temp.putIFDValue(IFD.STRIP_OFFSETS, newOffsets);
long[] newByteCounts = new long[stripsPerImage];
if (stripsPerImage * i < stripByteCounts.length) {
System.arraycopy(stripByteCounts, stripsPerImage * i, newByteCounts, 0, stripsPerImage);
} else {
Arrays.fill(newByteCounts, stripByteCounts[0]);
}
temp.putIFDValue(IFD.STRIP_BYTE_COUNTS, newByteCounts);
tempIFDs.add(temp);
}
ifds = tempIFDs;
} catch (IllegalArgumentException exc) {
LOGGER.debug("Unknown tag", exc);
} catch (NullPointerException exc) {
LOGGER.debug("", exc);
} catch (FormatException exc) {
LOGGER.debug("Failed to build list of IFDs", exc);
}
// parse (mangle) TIFF comment
String descr = ifds.get(0).getComment();
if (descr != null) {
String[] lines = descr.split("\n");
final StringBuilder sb = new StringBuilder();
for (int i = 0; i < lines.length; i++) {
String line = lines[i].trim();
if (line.startsWith("<") && line.endsWith(">")) {
// XML comment; this will have already been parsed so can be ignored
break;
}
int colon = line.indexOf(':');
if (colon < 0) {
// normal line (not a key/value pair)
if (line.length() > 0) {
// not a blank line
sb.append(line);
sb.append(" ");
}
} else {
String descrValue = null;
if (i == 0) {
// first line could be mangled; make a reasonable guess
int dot = line.lastIndexOf(".", colon);
if (dot >= 0) {
descrValue = line.substring(0, dot + 1);
}
line = line.substring(dot + 1);
colon -= dot + 1;
}
// append value to description
if (descrValue != null) {
sb.append(descrValue);
if (!descrValue.endsWith("."))
sb.append(".");
sb.append(" ");
}
// add key/value pair embedded in comment as separate metadata
String key = line.substring(0, colon);
String value = line.substring(colon + 1).trim();
addSeriesMeta(key, value);
if (key.equals("Exposure")) {
if (value.indexOf('=') != -1) {
value = value.substring(value.indexOf('=') + 1).trim();
}
if (value.indexOf(' ') != -1) {
value = value.substring(0, value.indexOf(' '));
}
try {
value = value.replace(',', '.');
double exposure = Double.parseDouble(value);
exposureTime = exposure / 1000;
} catch (NumberFormatException e) {
}
} else if (key.equals("Bit Depth")) {
if (value.indexOf('-') != -1) {
value = value.substring(0, value.indexOf('-'));
}
try {
ms0.bitsPerPixel = Integer.parseInt(value);
} catch (NumberFormatException e) {
}
} else if (key.equals("Gain")) {
int space = value.indexOf(' ');
if (space != -1) {
int nextSpace = value.indexOf(" ", space + 1);
if (nextSpace < 0) {
nextSpace = value.length();
}
try {
gain = new Double(value.substring(space, nextSpace));
} catch (NumberFormatException e) {
}
}
}
}
}
// replace comment with trimmed version
descr = sb.toString().trim();
if (descr.equals(""))
metadata.remove("Comment");
else
addSeriesMeta("Comment", descr);
}
ms0.sizeT = getImageCount() / (getSizeZ() * (getSizeC() / rgbChannels));
if (getSizeT() * getSizeZ() * (getSizeC() / rgbChannels) != getImageCount()) {
ms0.sizeT = 1;
ms0.sizeZ = getImageCount() / (getSizeC() / rgbChannels);
}
// if '_t' is present in the file name, swap Z and T sizes
// this file was probably part of a larger dataset, but the .nd file is
// missing
String filename = currentId.substring(currentId.lastIndexOf(File.separator) + 1);
if (filename.contains("_t") && getSizeT() > 1) {
int z = getSizeZ();
ms0.sizeZ = getSizeT();
ms0.sizeT = z;
}
if (getSizeZ() == 0)
ms0.sizeZ = 1;
if (getSizeT() == 0)
ms0.sizeT = 1;
if (getSizeZ() * getSizeT() * (isRGB() ? 1 : getSizeC()) != getImageCount()) {
ms0.sizeZ = getImageCount();
ms0.sizeT = 1;
if (!isRGB())
ms0.sizeC = 1;
}
}
use of loci.formats.FormatException in project bioformats by openmicroscopy.
the class MetamorphReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (checkSuffix(id, ND_SUFFIX)) {
LOGGER.info("Initializing " + id);
// find an associated STK file
String stkFile = id.substring(0, id.lastIndexOf("."));
if (stkFile.indexOf(File.separatorChar) != -1) {
stkFile = stkFile.substring(stkFile.lastIndexOf(File.separator) + 1);
}
Location parent = new Location(id).getAbsoluteFile().getParentFile();
LOGGER.info("Looking for STK file in {}", parent.getAbsolutePath());
String[] dirList = parent.list(true);
Arrays.sort(dirList);
for (String f : dirList) {
int underscore = f.indexOf('_');
if (underscore < 0)
underscore = f.indexOf('.');
if (underscore < 0)
underscore = f.length();
String prefix = f.substring(0, underscore);
if ((f.equals(stkFile) || stkFile.startsWith(prefix)) && checkSuffix(f, STK_SUFFIX)) {
stkFile = new Location(parent.getAbsolutePath(), f).getAbsolutePath();
break;
}
}
if (!checkSuffix(stkFile, STK_SUFFIX)) {
throw new FormatException("STK file not found in " + parent.getAbsolutePath() + ".");
}
super.initFile(stkFile);
} else
super.initFile(id);
Location ndfile = null;
if (checkSuffix(id, ND_SUFFIX))
ndfile = new Location(id);
else if (canLookForND && isGroupFiles()) {
// an STK file was passed to initFile
// let's check the parent directory for an .nd file
Location stk = new Location(id).getAbsoluteFile();
String stkName = stk.getName();
String stkPrefix = stkName;
if (stkPrefix.indexOf('_') >= 0) {
stkPrefix = stkPrefix.substring(0, stkPrefix.indexOf('_') + 1);
}
Location parent = stk.getParentFile();
String[] list = parent.list(true);
int matchingChars = 0;
for (String f : list) {
if (checkSuffix(f, ND_SUFFIX)) {
String prefix = f.substring(0, f.lastIndexOf("."));
if (prefix.indexOf('_') >= 0) {
prefix = prefix.substring(0, prefix.indexOf('_') + 1);
}
if (stkName.startsWith(prefix) || prefix.equals(stkPrefix)) {
int charCount = 0;
for (int i = 0; i < f.length(); i++) {
if (i >= stkName.length()) {
break;
}
if (f.charAt(i) == stkName.charAt(i)) {
charCount++;
} else {
break;
}
}
if (charCount > matchingChars || (charCount == matchingChars && f.charAt(charCount) == '.')) {
ndfile = new Location(parent, f).getAbsoluteFile();
matchingChars = charCount;
}
}
}
}
}
String creationTime = null;
if (ndfile != null && ndfile.exists() && (fileGroupOption(id) == FormatTools.MUST_GROUP || isGroupFiles())) {
// parse key/value pairs from .nd file
int zc = getSizeZ(), cc = getSizeC(), tc = getSizeT();
int nstages = 0;
String z = null, c = null, t = null;
final List<Boolean> hasZ = new ArrayList<Boolean>();
waveNames = new ArrayList<String>();
stageNames = new ArrayList<String>();
boolean useWaveNames = true;
ndFilename = ndfile.getAbsolutePath();
String[] lines = DataTools.readFile(ndFilename).split("\n");
boolean globalDoZ = true;
boolean doTimelapse = false;
StringBuilder currentValue = new StringBuilder();
String key = "";
for (String line : lines) {
int comma = line.indexOf(',');
if (comma <= 0) {
currentValue.append("\n");
currentValue.append(line);
continue;
}
String value = currentValue.toString();
addGlobalMeta(key, value);
if (key.equals("NZSteps"))
z = value;
else if (key.equals("DoTimelapse")) {
doTimelapse = Boolean.parseBoolean(value);
} else if (key.equals("NWavelengths"))
c = value;
else if (key.equals("NTimePoints"))
t = value;
else if (key.startsWith("WaveDoZ")) {
hasZ.add(Boolean.parseBoolean(value));
} else if (key.startsWith("WaveName")) {
String waveName = value.substring(1, value.length() - 1);
if (waveName.equals("Both lasers") || waveName.startsWith("DUAL")) {
bizarreMultichannelAcquisition = true;
}
waveNames.add(waveName);
} else if (key.startsWith("Stage")) {
stageNames.add(value);
} else if (key.startsWith("StartTime")) {
creationTime = value;
} else if (key.equals("ZStepSize")) {
value = value.replace(',', '.');
stepSize = Double.parseDouble(value);
} else if (key.equals("NStagePositions")) {
nstages = Integer.parseInt(value);
} else if (key.equals("WaveInFileName")) {
useWaveNames = Boolean.parseBoolean(value);
} else if (key.equals("DoZSeries")) {
globalDoZ = Boolean.parseBoolean(value);
}
key = line.substring(1, comma - 1).trim();
currentValue.delete(0, currentValue.length());
currentValue.append(line.substring(comma + 1).trim());
}
if (!globalDoZ) {
for (int i = 0; i < hasZ.size(); i++) {
hasZ.set(i, false);
}
}
if (z != null)
zc = Integer.parseInt(z);
if (c != null)
cc = Integer.parseInt(c);
if (t != null)
tc = Integer.parseInt(t);
else if (!doTimelapse) {
tc = 1;
}
if (cc == 0)
cc = 1;
if (cc == 1 && bizarreMultichannelAcquisition) {
cc = 2;
}
if (tc == 0) {
tc = 1;
}
int numFiles = cc * tc;
if (nstages > 0)
numFiles *= nstages;
// determine series count
int stagesCount = nstages == 0 ? 1 : nstages;
int seriesCount = stagesCount;
firstSeriesChannels = new boolean[cc];
Arrays.fill(firstSeriesChannels, true);
boolean differentZs = false;
for (int i = 0; i < cc; i++) {
boolean hasZ1 = i < hasZ.size() && hasZ.get(i);
boolean hasZ2 = i != 0 && (i - 1 < hasZ.size()) && hasZ.get(i - 1);
if (i > 0 && hasZ1 != hasZ2 && globalDoZ) {
if (!differentZs)
seriesCount *= 2;
differentZs = true;
}
}
int channelsInFirstSeries = cc;
if (differentZs) {
channelsInFirstSeries = 0;
for (int i = 0; i < cc; i++) {
if ((!hasZ.get(0) && i == 0) || (hasZ.get(0) && hasZ.get(i))) {
channelsInFirstSeries++;
} else
firstSeriesChannels[i] = false;
}
}
stks = new String[seriesCount][];
if (seriesCount == 1)
stks[0] = new String[numFiles];
else if (differentZs) {
for (int i = 0; i < stagesCount; i++) {
stks[i * 2] = new String[channelsInFirstSeries * tc];
stks[i * 2 + 1] = new String[(cc - channelsInFirstSeries) * tc];
}
} else {
for (int i = 0; i < stks.length; i++) {
stks[i] = new String[numFiles / stks.length];
}
}
String prefix = ndfile.getPath();
prefix = prefix.substring(prefix.lastIndexOf(File.separator) + 1, prefix.lastIndexOf("."));
// build list of STK files
boolean anyZ = hasZ.contains(Boolean.TRUE);
int[] pt = new int[seriesCount];
for (int i = 0; i < tc; i++) {
for (int s = 0; s < stagesCount; s++) {
for (int j = 0; j < cc; j++) {
boolean validZ = j >= hasZ.size() || hasZ.get(j);
int seriesNdx = s * (seriesCount / stagesCount);
if ((seriesCount != 1 && (!validZ || (hasZ.size() > 0 && !hasZ.get(0)))) || (nstages == 0 && ((!validZ && cc > 1) || seriesCount > 1))) {
if (anyZ && j > 0 && seriesNdx < seriesCount - 1 && (!validZ || !hasZ.get(0))) {
seriesNdx++;
}
}
if (seriesNdx >= stks.length || seriesNdx >= pt.length || pt[seriesNdx] >= stks[seriesNdx].length) {
continue;
}
stks[seriesNdx][pt[seriesNdx]] = prefix;
if (j < waveNames.size() && waveNames.get(j) != null) {
stks[seriesNdx][pt[seriesNdx]] += "_w" + (j + 1);
if (useWaveNames) {
String waveName = waveNames.get(j);
// If there are underscores in the wavelength name, translate
// them to hyphens. (See #558)
waveName = waveName.replace('_', '-');
// If there are slashes (forward or backward) in the wavelength
// name, translate them to hyphens. (See #5922)
waveName = waveName.replace('/', '-');
waveName = waveName.replace('\\', '-');
waveName = waveName.replace('(', '-');
waveName = waveName.replace(')', '-');
stks[seriesNdx][pt[seriesNdx]] += waveName;
}
}
if (nstages > 0) {
stks[seriesNdx][pt[seriesNdx]] += "_s" + (s + 1);
}
if (tc > 1 || doTimelapse) {
stks[seriesNdx][pt[seriesNdx]] += "_t" + (i + 1) + ".STK";
} else
stks[seriesNdx][pt[seriesNdx]] += ".STK";
pt[seriesNdx]++;
}
}
}
ndfile = ndfile.getAbsoluteFile();
for (int s = 0; s < stks.length; s++) {
for (int f = 0; f < stks[s].length; f++) {
Location l = new Location(ndfile.getParent(), stks[s][f]);
stks[s][f] = getRealSTKFile(l);
}
}
String file = locateFirstValidFile();
if (file == null) {
throw new FormatException("Unable to locate at least one valid STK file!");
}
RandomAccessInputStream s = new RandomAccessInputStream(file, 16);
TiffParser tp = new TiffParser(s);
IFD ifd = tp.getFirstIFD();
CoreMetadata ms0 = core.get(0);
s.close();
ms0.sizeX = (int) ifd.getImageWidth();
ms0.sizeY = (int) ifd.getImageLength();
if (bizarreMultichannelAcquisition) {
ms0.sizeX /= 2;
}
ms0.sizeZ = hasZ.size() > 0 && !hasZ.get(0) ? 1 : zc;
ms0.sizeC = cc;
ms0.sizeT = tc;
ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
ms0.dimensionOrder = "XYZCT";
if (stks != null && stks.length > 1) {
// Note that core can't be replaced with newCore until the end of this block.
ArrayList<CoreMetadata> newCore = new ArrayList<CoreMetadata>();
for (int i = 0; i < stks.length; i++) {
CoreMetadata ms = new CoreMetadata();
newCore.add(ms);
ms.sizeX = getSizeX();
ms.sizeY = getSizeY();
ms.sizeZ = getSizeZ();
ms.sizeC = getSizeC();
ms.sizeT = getSizeT();
ms.pixelType = getPixelType();
ms.imageCount = getImageCount();
ms.dimensionOrder = getDimensionOrder();
ms.rgb = isRGB();
ms.littleEndian = isLittleEndian();
ms.interleaved = isInterleaved();
ms.orderCertain = true;
}
if (stks.length > nstages) {
for (int j = 0; j < stagesCount; j++) {
int idx = j * 2 + 1;
CoreMetadata midx = newCore.get(idx);
CoreMetadata pmidx = newCore.get(j * 2);
pmidx.sizeC = stks[j * 2].length / getSizeT();
midx.sizeC = stks[idx].length / midx.sizeT;
midx.sizeZ = hasZ.size() > 1 && hasZ.get(1) && core.get(0).sizeZ == 1 ? zc : 1;
pmidx.imageCount = pmidx.sizeC * pmidx.sizeT * pmidx.sizeZ;
midx.imageCount = midx.sizeC * midx.sizeT * midx.sizeZ;
}
}
core = newCore;
}
}
if (stks == null) {
stkReaders = new MetamorphReader[1][1];
stkReaders[0][0] = new MetamorphReader();
stkReaders[0][0].setCanLookForND(false);
} else {
stkReaders = new MetamorphReader[stks.length][];
for (int i = 0; i < stks.length; i++) {
stkReaders[i] = new MetamorphReader[stks[i].length];
for (int j = 0; j < stkReaders[i].length; j++) {
stkReaders[i][j] = new MetamorphReader();
stkReaders[i][j].setCanLookForND(false);
if (j > 0) {
stkReaders[i][j].setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
}
}
}
}
// check stage labels for plate data
int rows = 0;
int cols = 0;
Map<String, Integer> rowMap = null;
Map<String, Integer> colMap = null;
isHCS = true;
if (null == stageLabels) {
isHCS = false;
} else {
Set<Map.Entry<Integer, Integer>> uniqueWells = new HashSet<Map.Entry<Integer, Integer>>();
rowMap = new HashMap<String, Integer>();
colMap = new HashMap<String, Integer>();
for (String label : stageLabels) {
if (null == label) {
isHCS = false;
break;
}
Map.Entry<Integer, Integer> wellCoords = getWellCoords(label);
if (null == wellCoords) {
isHCS = false;
break;
}
uniqueWells.add(wellCoords);
rowMap.put(label, wellCoords.getKey());
colMap.put(label, wellCoords.getValue());
}
if (uniqueWells.size() != stageLabels.length) {
isHCS = false;
} else {
rows = Collections.max(rowMap.values());
cols = Collections.max(colMap.values());
CoreMetadata c = core.get(0);
core.clear();
c.sizeZ = 1;
c.sizeT = 1;
c.imageCount = 1;
for (int s = 0; s < uniqueWells.size(); s++) {
CoreMetadata toAdd = new CoreMetadata(c);
if (s > 0) {
toAdd.seriesMetadata.clear();
}
core.add(toAdd);
}
seriesToIFD = true;
}
}
List<String> timestamps = null;
MetamorphHandler handler = null;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (isHCS) {
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateRows(new PositiveInteger(rows), 0);
store.setPlateColumns(new PositiveInteger(cols), 0);
store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
}
int nextObjective = 0;
String instrumentID = MetadataTools.createLSID("Instrument", 0);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setInstrumentID(instrumentID, 0);
store.setDetectorID(detectorID, 0, 0);
store.setDetectorType(getDetectorType("Other"), 0, 0);
for (int i = 0; i < getSeriesCount(); i++) {
setSeries(i);
// do not reparse the same XML for every well
if (i == 0 || !isHCS) {
handler = new MetamorphHandler(getSeriesMetadata());
}
if (isHCS) {
String label = stageLabels[i];
String wellID = MetadataTools.createLSID("Well", 0, i);
store.setWellID(wellID, 0, i);
store.setWellColumn(new NonNegativeInteger(colMap.get(label)), 0, i);
store.setWellRow(new NonNegativeInteger(rowMap.get(label)), 0, i);
store.setWellSampleID(MetadataTools.createLSID("WellSample", 0, i, 0), 0, i, 0);
store.setWellSampleImageRef(MetadataTools.createLSID("Image", i), 0, i, 0);
store.setWellSampleIndex(new NonNegativeInteger(i), 0, i, 0);
}
store.setImageInstrumentRef(instrumentID, i);
String comment = getFirstComment(i);
if (i == 0 || !isHCS) {
if (comment != null && comment.startsWith("<MetaData>")) {
try {
XMLTools.parseXML(XMLTools.sanitizeXML(comment), handler);
} catch (IOException e) {
}
}
}
if (creationTime != null) {
String date = DateTools.formatDate(creationTime, SHORT_DATE_FORMAT, ".");
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
store.setImageName(makeImageName(i).trim(), i);
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
continue;
}
store.setImageDescription("", i);
store.setImagingEnvironmentTemperature(new Temperature(handler.getTemperature(), UNITS.CELSIUS), i);
if (sizeX == null)
sizeX = handler.getPixelSizeX();
if (sizeY == null)
sizeY = handler.getPixelSizeY();
Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX);
Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY);
if (physicalSizeX != null) {
store.setPixelsPhysicalSizeX(physicalSizeX, i);
}
if (physicalSizeY != null) {
store.setPixelsPhysicalSizeY(physicalSizeY, i);
}
if (zDistances != null) {
stepSize = zDistances[0];
} else {
List<Double> zPositions = new ArrayList<Double>();
final List<Double> uniqueZ = new ArrayList<Double>();
for (IFD ifd : ifds) {
MetamorphHandler zPlaneHandler = new MetamorphHandler();
String zComment = ifd.getComment();
if (zComment != null && zComment.startsWith("<MetaData>")) {
try {
XMLTools.parseXML(XMLTools.sanitizeXML(zComment), zPlaneHandler);
} catch (IOException e) {
}
}
zPositions = zPlaneHandler.getZPositions();
for (Double z : zPositions) {
if (!uniqueZ.contains(z))
uniqueZ.add(z);
}
}
if (uniqueZ.size() > 1 && uniqueZ.size() == getSizeZ()) {
BigDecimal lastZ = BigDecimal.valueOf(uniqueZ.get(uniqueZ.size() - 1));
BigDecimal firstZ = BigDecimal.valueOf(uniqueZ.get(0));
BigDecimal zRange = (lastZ.subtract(firstZ)).abs();
BigDecimal zSize = BigDecimal.valueOf((double) (getSizeZ() - 1));
MathContext mc = new MathContext(10, RoundingMode.HALF_UP);
stepSize = zRange.divide(zSize, mc).doubleValue();
}
}
Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
if (physicalSizeZ != null) {
store.setPixelsPhysicalSizeZ(physicalSizeZ, i);
}
if (handler.getLensNA() != 0 || handler.getLensRI() != 0) {
String objectiveID = MetadataTools.createLSID("Objective", 0, nextObjective);
store.setObjectiveID(objectiveID, 0, nextObjective);
if (handler.getLensNA() != 0) {
store.setObjectiveLensNA(handler.getLensNA(), 0, nextObjective);
}
store.setObjectiveSettingsID(objectiveID, i);
if (handler.getLensRI() != 0) {
store.setObjectiveSettingsRefractiveIndex(handler.getLensRI(), i);
}
nextObjective++;
}
int waveIndex = 0;
for (int c = 0; c < getEffectiveSizeC(); c++) {
if (firstSeriesChannels == null || (stageNames != null && stageNames.size() == getSeriesCount())) {
waveIndex = c;
} else if (firstSeriesChannels != null) {
int s = i % 2;
while (firstSeriesChannels[waveIndex] == (s == 1) && waveIndex < firstSeriesChannels.length) {
waveIndex++;
}
}
if (waveNames != null && waveIndex < waveNames.size()) {
store.setChannelName(waveNames.get(waveIndex).trim(), i, c);
}
if (handler.getBinning() != null)
binning = handler.getBinning();
if (binning != null) {
store.setDetectorSettingsBinning(getBinning(binning), i, c);
}
if (handler.getReadOutRate() != 0) {
store.setDetectorSettingsReadOutRate(new Frequency(handler.getReadOutRate(), UNITS.HERTZ), i, c);
}
if (gain == null) {
gain = handler.getGain();
}
if (gain != null) {
store.setDetectorSettingsGain(gain, i, c);
}
store.setDetectorSettingsID(detectorID, i, c);
if (wave != null && waveIndex < wave.length) {
Length wavelength = FormatTools.getWavelength(wave[waveIndex]);
if ((int) wave[waveIndex] >= 1) {
// link LightSource to Image
int laserIndex = i * getEffectiveSizeC() + c;
String lightSourceID = MetadataTools.createLSID("LightSource", 0, laserIndex);
store.setLaserID(lightSourceID, 0, laserIndex);
store.setChannelLightSourceSettingsID(lightSourceID, i, c);
store.setLaserType(getLaserType("Other"), 0, laserIndex);
store.setLaserLaserMedium(getLaserMedium("Other"), 0, laserIndex);
if (wavelength != null) {
store.setChannelLightSourceSettingsWavelength(wavelength, i, c);
}
}
}
waveIndex++;
}
timestamps = handler.getTimestamps();
for (int t = 0; t < timestamps.size(); t++) {
String date = DateTools.convertDate(DateTools.getTime(timestamps.get(t), SHORT_DATE_FORMAT, "."), DateTools.UNIX, SHORT_DATE_FORMAT + ".SSS");
addSeriesMetaList("timestamp", date);
}
long startDate = 0;
if (timestamps.size() > 0) {
startDate = DateTools.getTime(timestamps.get(0), SHORT_DATE_FORMAT, ".");
}
final Length positionX = handler.getStagePositionX();
final Length positionY = handler.getStagePositionY();
final List<Double> exposureTimes = handler.getExposures();
if (exposureTimes.size() == 0) {
for (int p = 0; p < getImageCount(); p++) {
exposureTimes.add(exposureTime);
}
} else if (exposureTimes.size() == 1 && exposureTimes.size() < getSizeC()) {
for (int c = 1; c < getSizeC(); c++) {
MetamorphHandler channelHandler = new MetamorphHandler();
String channelComment = getComment(i, c);
if (channelComment != null && channelComment.startsWith("<MetaData>")) {
try {
XMLTools.parseXML(XMLTools.sanitizeXML(channelComment), channelHandler);
} catch (IOException e) {
}
}
final List<Double> channelExpTime = channelHandler.getExposures();
exposureTimes.add(channelExpTime.get(0));
}
}
int lastFile = -1;
IFDList lastIFDs = null;
IFD lastIFD = null;
double distance = zStart;
TiffParser tp = null;
RandomAccessInputStream stream = null;
for (int p = 0; p < getImageCount(); p++) {
int[] coords = getZCTCoords(p);
Double deltaT = 0d;
Double expTime = exposureTime;
Double xmlZPosition = null;
int fileIndex = getIndex(0, coords[1], coords[2]) / getSizeZ();
if (fileIndex >= 0) {
String file = stks == null ? currentId : stks[i][fileIndex];
if (file != null) {
if (fileIndex != lastFile) {
if (stream != null) {
stream.close();
}
stream = new RandomAccessInputStream(file, 16);
tp = new TiffParser(stream);
tp.checkHeader();
IFDList f = tp.getIFDs();
if (f.size() > 0) {
lastFile = fileIndex;
lastIFDs = f;
} else {
file = null;
stks[i][fileIndex] = null;
}
}
}
if (file != null) {
lastIFD = lastIFDs.get(p % lastIFDs.size());
Object commentEntry = lastIFD.get(IFD.IMAGE_DESCRIPTION);
if (commentEntry != null) {
if (commentEntry instanceof String) {
comment = (String) commentEntry;
} else if (commentEntry instanceof TiffIFDEntry) {
comment = tp.getIFDValue((TiffIFDEntry) commentEntry).toString();
}
}
if (comment != null)
comment = comment.trim();
if (comment != null && comment.startsWith("<MetaData>")) {
String[] lines = comment.split("\n");
timestamps = new ArrayList<String>();
for (String line : lines) {
line = line.trim();
if (line.startsWith("<prop")) {
int firstQuote = line.indexOf("\"") + 1;
int lastQuote = line.lastIndexOf("\"");
String key = line.substring(firstQuote, line.indexOf("\"", firstQuote));
String value = line.substring(line.lastIndexOf("\"", lastQuote - 1) + 1, lastQuote);
if (key.equals("z-position")) {
xmlZPosition = new Double(value);
} else if (key.equals("acquisition-time-local")) {
timestamps.add(value);
}
}
}
}
}
}
int index = 0;
if (timestamps.size() > 0) {
if (coords[2] < timestamps.size())
index = coords[2];
String stamp = timestamps.get(index);
long ms = DateTools.getTime(stamp, SHORT_DATE_FORMAT, ".");
deltaT = (ms - startDate) / 1000.0;
} else if (internalStamps != null && p < internalStamps.length) {
long delta = internalStamps[p] - internalStamps[0];
deltaT = delta / 1000.0;
if (coords[2] < exposureTimes.size())
index = coords[2];
}
if (index == 0 && p > 0 && exposureTimes.size() > 0) {
index = coords[1] % exposureTimes.size();
}
if (index < exposureTimes.size()) {
expTime = exposureTimes.get(index);
}
if (deltaT != null) {
store.setPlaneDeltaT(new Time(deltaT, UNITS.SECOND), i, p);
}
if (expTime != null) {
store.setPlaneExposureTime(new Time(expTime, UNITS.SECOND), i, p);
}
if (stageX != null && p < stageX.length) {
store.setPlanePositionX(stageX[p], i, p);
} else if (positionX != null) {
store.setPlanePositionX(positionX, i, p);
}
if (stageY != null && p < stageY.length) {
store.setPlanePositionY(stageY[p], i, p);
} else if (positionY != null) {
store.setPlanePositionY(positionY, i, p);
}
if (zDistances != null && p < zDistances.length) {
if (p > 0) {
if (zDistances[p] != 0d)
distance += zDistances[p];
else
distance += zDistances[0];
}
final Length zPos = new Length(distance, UNITS.REFERENCEFRAME);
store.setPlanePositionZ(zPos, i, p);
} else if (xmlZPosition != null) {
final Length zPos = new Length(xmlZPosition, UNITS.REFERENCEFRAME);
store.setPlanePositionZ(zPos, i, p);
}
}
if (stream != null) {
stream.close();
}
}
setSeries(0);
}
use of loci.formats.FormatException in project bioformats by openmicroscopy.
the class ND2Handler method startElement.
@Override
public void startElement(String uri, String localName, String qName, Attributes attributes) {
String runtype = attributes.getValue("runtype");
if ("CLxListVariant".equals(runtype) || "RLxIRect".equals(runtype)) {
prevElement = qName;
}
String value = attributes.getValue("value");
CoreMetadata ms0 = core.get(0);
try {
if (qName.equals("uiWidth")) {
int x = Integer.parseInt(value);
if (x != 0 && populateXY) {
ms0.sizeX = x;
}
} else if (qName.equals("uiCamPxlCountX")) {
if (ms0.sizeX == 0 && populateXY) {
ms0.sizeX = Integer.parseInt(value);
}
} else if (qName.equals("uiCamPxlCountY")) {
if (ms0.sizeY == 0 && populateXY) {
ms0.sizeY = Integer.parseInt(value);
}
} else if (qName.equals("iXFields")) {
int fields = Integer.parseInt(value);
nXFields += fields;
} else if (qName.equals("iYFields")) {
int fields = Integer.parseInt(value);
nYFields += fields;
} else if ("rectSensorUser".equals(prevElement) && populateXY) {
if (qName.equals("left") && ms0.sizeX == 0) {
ms0.sizeX = -1 * Integer.parseInt(value);
} else if (qName.equals("top") && ms0.sizeY == 0) {
ms0.sizeY = -1 * Integer.parseInt(value);
} else if (qName.equals("right") && ms0.sizeX <= 0) {
ms0.sizeX += Integer.parseInt(value);
} else if (qName.equals("bottom") && ms0.sizeY <= 0) {
ms0.sizeY += Integer.parseInt(value);
}
} else if ("LoopState".equals(prevElement) && value != null) {
long v = Long.parseLong(value);
validLoopState.add(v != 529 && v < 0xfffff);
} else if ("LoopSize".equals(prevElement) && value != null) {
int v = Integer.parseInt(value);
int loopIndex = 0;
while (validLoopState.get(loopIndex) == null) {
loopIndex++;
}
boolean loop = validLoopState.get(loopIndex);
if (!loop && validLoopState.contains(true)) {
v = 1;
}
if (ms0.sizeT == 0 || (ms0.sizeT * ms0.sizeZ > nImages && v < ms0.sizeT)) {
ms0.sizeT = v;
} else if (qName.equals("no_name") && v > 1 && core.size() == 1) {
core = new ArrayList<CoreMetadata>();
for (int q = 0; q < v; q++) {
core.add(ms0);
}
} else if (ms0.sizeZ == 0) {
ms0.sizeZ = v;
} else {
canAdjustDimensions = false;
}
ms0.dimensionOrder = "CZT";
} else if ("pPosName".equals(prevElement) && value != null) {
posNames.add(value);
} else if (qName.equals("FramesBefore")) {
if (ms0.sizeZ == 0) {
ms0.sizeZ = 1;
}
// only adjust if we haven't parsed all of the dimensions already
if (canAdjustDimensions && core.size() == 1 && (ms0.sizeT <= 1 || ms0.sizeT * ms0.sizeZ != nImages)) {
ms0.sizeZ *= Integer.parseInt(value);
}
} else if (qName.equals("FramesAfter")) {
int loopIndex = 0;
while (validLoopState.get(loopIndex) == null) {
loopIndex++;
}
boolean loop = validLoopState.get(loopIndex);
validLoopState.set(loopIndex, null);
if (canAdjustDimensions && core.size() == 1) {
ms0.sizeZ *= Integer.parseInt(value);
if (ms0.sizeT * ms0.sizeZ > nImages && ms0.sizeT <= nImages && ms0.sizeT != ms0.sizeZ) {
ms0.sizeZ = ms0.sizeT;
ms0.sizeT = 1;
}
}
} else if (qName.equals("TimeBefore") && canAdjustDimensions) {
if (ms0.sizeT == 0) {
ms0.sizeT = 1;
}
ms0.sizeT *= Integer.parseInt(value);
} else if (qName.equals("TimeAfter") && canAdjustDimensions) {
ms0.sizeT *= Integer.parseInt(value);
} else if (qName.equals("uiMaxDst")) {
int maxPixelValue = Integer.parseInt(value) + 1;
int bits = 0;
while (maxPixelValue > 0) {
maxPixelValue /= 2;
bits++;
}
try {
if (ms0.pixelType == 0) {
ms0.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
}
} catch (FormatException e) {
LOGGER.warn("Could not set the pixel type", e);
}
} else if (qName.equals("uiWidthBytes") || qName.startsWith("uiBpcInMemory") || qName.startsWith("uiBpcSignificant")) {
int div = qName.equals("uiWidthBytes") ? ms0.sizeX : 8;
if (div > 0) {
int bits = Integer.parseInt(value);
int bytes = bits / div;
if (bytes * div == bits) {
try {
ms0.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
} catch (FormatException e) {
}
}
parseKeyAndValue(qName, value, prevRuntype);
}
} else if ("dPosX".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posX.add(new Length(number, UNITS.REFERENCEFRAME));
metadata.put("X position for position #" + posX.size(), value);
} else if ("dPosY".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posY.add(new Length(number, UNITS.REFERENCEFRAME));
metadata.put("Y position for position #" + posY.size(), value);
} else if ("dPosZ".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posZ.add(new Length(number, UNITS.REFERENCEFRAME));
metadata.put("Z position for position #" + posZ.size(), value);
} else if (qName.startsWith("item_")) {
int v = Integer.parseInt(qName.substring(qName.indexOf('_') + 1));
if (v == numSeries) {
numSeries++;
}
} else if (qName.equals("uiCompCount")) {
int v = Integer.parseInt(value);
ms0.sizeC = (int) Math.max(ms0.sizeC, v);
} else if (qName.equals("uiHeight") && populateXY) {
int y = Integer.parseInt(value);
if (y != 0) {
ms0.sizeY = y;
}
} else if (qName.startsWith("TextInfo")) {
parseKeyAndValue(qName, attributes.getValue("Text"), prevRuntype);
parseKeyAndValue(qName, value, prevRuntype);
} else if (qName.equals("dCompressionParam")) {
isLossless = Double.parseDouble(value) > 0;
parseKeyAndValue(qName, value, prevRuntype);
} else if (qName.equals("CalibrationSeq") || qName.equals("MetadataSeq")) {
prefix = qName + " " + attributes.getValue("_SEQUENCE_INDEX");
} else if (qName.equals("HorizontalLine") || qName.equals("VerticalLine") || qName.equals("Text")) {
Hashtable<String, String> roi = new Hashtable<String, String>();
roi.put("ROIType", qName);
for (int q = 0; q < attributes.getLength(); q++) {
roi.put(attributes.getQName(q), attributes.getValue(q));
}
rois.add(roi);
} else if (qName.equals("dPinholeRadius")) {
pinholeSize = DataTools.parseDouble(value);
metadata.put("Pinhole size", value);
} else if (qName.endsWith("ChannelColor")) {
String name = qName.substring(0, qName.indexOf("Channel"));
colors.put(name, new Integer(value));
} else if (qName.endsWith("DyeName")) {
int channelIndex = qName.indexOf("Channel");
if (channelIndex < 0)
channelIndex = 0;
dyes.put(qName.substring(0, channelIndex), value);
} else if (qName.equals("uiSequenceCount")) {
int imageCount = Integer.parseInt(value);
if (core.size() > 0) {
int newCount = imageCount / core.size();
if (newCount * core.size() == imageCount) {
imageCount = newCount;
}
}
if (ms0.sizeZ * ms0.sizeT != imageCount && ms0.sizeZ * ms0.sizeC * ms0.sizeT != imageCount) {
if (ms0.sizeZ > 1 && ms0.sizeT <= 1) {
ms0.sizeZ = imageCount;
ms0.sizeT = 1;
ms0.imageCount = imageCount;
} else if (ms0.sizeT > 1 && ms0.sizeZ <= 1) {
ms0.sizeT = imageCount;
ms0.sizeZ = 1;
ms0.imageCount = imageCount;
} else if (imageCount == 0) {
ms0.sizeT = 0;
ms0.sizeZ = 0;
ms0.imageCount = 0;
}
}
metadata.put(qName, value);
} else {
final StringBuilder sb = new StringBuilder();
if (prefix != null) {
sb.append(prefix);
sb.append(" ");
}
sb.append(qName);
parseKeyAndValue(sb.toString(), value, prevRuntype);
}
} catch (NumberFormatException exc) {
LOGGER.warn("Could not parse {} value: {}", qName, value);
}
prevRuntype = attributes.getValue("runtype");
}
use of loci.formats.FormatException in project bioformats by openmicroscopy.
the class NDPIReader method openBytes.
/**
* @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);
if (x == 0 && y == 0 && w == 1 && h == 1) {
return buf;
} else if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
int ifdIndex = getIFDIndex(getCoreIndex(), no);
in = new RandomAccessInputStream(currentId);
tiffParser = new TiffParser(in);
tiffParser.setUse64BitOffsets(true);
tiffParser.setYCbCrCorrection(false);
byte[] b = tiffParser.getSamples(ifds.get(ifdIndex), buf, x, y, w, h);
in.close();
tiffParser.getStream().close();
return b;
}
if (initializedSeries != getCoreIndex() || initializedPlane != no) {
IFD ifd = ifds.get(getIFDIndex(getCoreIndex(), no));
long offset = ifd.getStripOffsets()[0];
long byteCount = ifd.getStripByteCounts()[0];
if (in != null) {
in.close();
}
in = new RandomAccessInputStream(currentId);
in.seek(offset);
in.setLength(offset + byteCount);
try {
service.close();
long[] markers = ifd.getIFDLongArray(MARKER_TAG);
if (!use64Bit) {
for (int i = 0; i < markers.length; i++) {
markers[i] = markers[i] & 0xffffffffL;
}
}
if (markers != null) {
service.setRestartMarkers(markers);
}
service.initialize(in, getSizeX(), getSizeY());
} catch (ServiceException e) {
throw new FormatException(e);
}
initializedSeries = getCoreIndex();
initializedPlane = no;
}
service.getTile(buf, x, y, w, h);
return buf;
}
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