use of loci.common.services.DependencyException in project bioformats by openmicroscopy.
the class VolocityReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "mvd2")) {
Location file = new Location(id).getAbsoluteFile();
Location parent = file.getParentFile().getParentFile();
String[] files = parent.list(true);
for (String f : files) {
if (checkSuffix(f, "mvd2")) {
id = new Location(parent, f).getAbsolutePath();
break;
}
}
}
super.initFile(id);
stacks = new ArrayList<Stack>();
extraFiles = new ArrayList<String>();
Location file = new Location(id).getAbsoluteFile();
extraFiles.add(file.getAbsolutePath());
Location parentDir = file.getParentFile();
dir = new Location(parentDir, DATA_DIR);
if (dir.exists()) {
String[] files = dir.list(true);
for (String f : files) {
if (!checkSuffix(f, "aisf") && !checkSuffix(f, "atsf")) {
extraFiles.add(new Location(dir, f).getAbsolutePath());
}
}
}
try {
ServiceFactory factory = new ServiceFactory();
MetakitService reader = factory.getInstance(MetakitService.class);
reader.initialize(id);
sampleTable = reader.getTableData(1);
stringTable = reader.getTableData(2);
reader.close();
} catch (DependencyException e) {
throw new MissingLibraryException("Could not find Metakit library", e);
}
ArrayList<String> stackNames = new ArrayList<String>();
ArrayList<Integer> parentIDs = new ArrayList<Integer>();
for (int i = 0; i < sampleTable.length; i++) {
Integer stringID = (Integer) sampleTable[i][11];
String name = getString(stringID);
int channelIndex = getChildIndex((Integer) sampleTable[i][0], "Channels");
if (i > 0 && (Integer) sampleTable[i][2] == 1 && (channelIndex >= 0 || (sampleTable[i][14] != null && !sampleTable[i][14].equals(0)) || ((byte[]) sampleTable[i][13]).length > 21)) {
if (channelIndex < 0) {
RandomAccessInputStream s = getStream(i);
s.seek(0);
if (s.read() != 'I') {
s.order(false);
}
s.seek(22);
int x = s.readInt();
int y = s.readInt();
int z = s.readInt();
if (x * y * z > 0 && x * y * z < (s.length() * 3)) {
stackNames.add(name);
parentIDs.add((Integer) sampleTable[i][0]);
}
s.close();
} else {
stackNames.add(name);
parentIDs.add((Integer) sampleTable[i][0]);
}
}
}
for (int i = 0; i < parentIDs.size(); i++) {
Stack stack = new Stack();
stack.core = new CoreMetadata();
Integer parent = parentIDs.get(i);
int channelIndex = getChildIndex(parent, "Channels");
if (channelIndex >= 0) {
Integer[] channels = getAllChildren((Integer) sampleTable[channelIndex][0]);
stack.core.sizeC = channels.length;
stack.pixelsFiles = new String[stack.core.sizeC];
stack.channelNames = new String[channels.length];
for (int c = 0; c < channels.length; c++) {
stack.channelNames[c] = getString((Integer) sampleTable[channels[c]][11]);
RandomAccessInputStream data = getStream(channels[c]);
if (data.length() > 22) {
data.seek(22);
int stackID = data.readInt();
Location f = new Location(dir, stackID + ".aisf");
if (!f.exists()) {
f = new Location(dir, DataTools.swap(stackID) + ".aisf");
}
stack.pixelsFiles[c] = f.getAbsolutePath();
} else {
Integer child = getAllChildren((Integer) sampleTable[channels[c]][0])[0];
stack.pixelsFiles[c] = getFile((Integer) sampleTable[child][0], dir);
}
data.close();
}
} else {
stack.pixelsFiles = new String[1];
stack.pixelsFiles[0] = getFile(parent, dir);
if (stack.pixelsFiles[0] == null || !new Location(stack.pixelsFiles[0]).exists()) {
int row = -1;
for (int r = 0; r < sampleTable.length; r++) {
if (sampleTable[r][0].equals(parent)) {
row = r;
break;
}
}
stack.pixelsFiles[0] = EMBEDDED_STREAM;
IRandomAccess data = new ByteArrayHandle((byte[]) sampleTable[row][13]);
Location.mapFile(stack.pixelsFiles[0], data);
}
}
RandomAccessInputStream data = null;
int timestampIndex = getChildIndex(parent, "Timepoint times stream");
if (timestampIndex >= 0) {
data = getStream(timestampIndex);
data.seek(22);
int timestampID = data.readInt();
Location f = new Location(dir, timestampID + ".atsf");
if (!f.exists()) {
f = new Location(dir, DataTools.swap(timestampID) + ".atsf");
}
stack.timestampFile = f.getAbsolutePath();
data.close();
}
int xIndex = getChildIndex(parent, "um/pixel (X)");
if (xIndex >= 0) {
data = getStream(xIndex);
data.seek(SIGNATURE_SIZE);
stack.physicalX = data.readDouble();
data.close();
}
int yIndex = getChildIndex(parent, "um/pixel (Y)");
if (yIndex >= 0) {
data = getStream(yIndex);
data.seek(SIGNATURE_SIZE);
stack.physicalY = data.readDouble();
data.close();
}
int zIndex = getChildIndex(parent, "um/pixel (Z)");
if (zIndex >= 0) {
data = getStream(zIndex);
data.seek(SIGNATURE_SIZE);
stack.physicalZ = data.readDouble();
data.close();
}
timestampIndex = getChildIndex(parent, "TimepointTimes");
if (timestampIndex >= 0) {
data = getStream(timestampIndex);
data.seek(SIGNATURE_SIZE);
data.close();
}
int objectiveIndex = getChildIndex(parent, "Microscope Objective");
if (objectiveIndex >= 0) {
data = getStream(objectiveIndex);
data.seek(SIGNATURE_SIZE);
stack.magnification = data.readDouble();
data.close();
}
int detectorIndex = getChildIndex(parent, "Camera/Detector");
if (detectorIndex >= 0) {
data = getStream(detectorIndex);
data.seek(SIGNATURE_SIZE);
int len = data.readInt();
stack.detector = data.readString(len);
data.close();
}
int descriptionIndex = getChildIndex(parent, "Experiment Description");
if (descriptionIndex >= 0) {
data = getStream(descriptionIndex);
data.seek(SIGNATURE_SIZE);
int len = data.readInt();
stack.description = data.readString(len);
data.close();
}
int xLocationIndex = getChildIndex(parent, "X Location");
if (xLocationIndex >= 0) {
data = getStream(xLocationIndex);
data.seek(SIGNATURE_SIZE);
stack.xLocation = data.readDouble();
data.close();
}
int yLocationIndex = getChildIndex(parent, "Y Location");
if (yLocationIndex >= 0) {
data = getStream(yLocationIndex);
data.seek(SIGNATURE_SIZE);
stack.yLocation = data.readDouble();
data.close();
}
int zLocationIndex = getChildIndex(parent, "Z Location");
if (zLocationIndex >= 0) {
data = getStream(zLocationIndex);
data.seek(SIGNATURE_SIZE);
stack.zLocation = data.readDouble();
data.close();
}
stacks.add(stack);
}
for (int i = 0; i < stacks.size(); i++) {
Stack stack = stacks.get(i);
if (!new Location(stack.pixelsFiles[0]).exists()) {
stacks.remove(i);
i--;
continue;
}
RandomAccessInputStream base = new RandomAccessInputStream(stack.pixelsFiles[0]);
long baseLength = base.length();
base.close();
for (int q = 1; q < stack.pixelsFiles.length; q++) {
if (!new Location(stack.pixelsFiles[q]).exists()) {
continue;
}
base = new RandomAccessInputStream(stack.pixelsFiles[q]);
long length = base.length();
base.close();
if (length > baseLength) {
// split the stack
Stack newStack = new Stack();
newStack.timestampFile = stack.timestampFile;
newStack.core = new CoreMetadata();
newStack.physicalX = stack.physicalX;
newStack.physicalY = stack.physicalY;
newStack.physicalZ = stack.physicalZ;
newStack.magnification = stack.magnification;
newStack.detector = stack.detector;
newStack.description = stack.description;
newStack.xLocation = stack.xLocation;
newStack.yLocation = stack.yLocation;
newStack.zLocation = stack.zLocation;
String[] pixels = stack.pixelsFiles;
newStack.pixelsFiles = new String[pixels.length - q];
System.arraycopy(pixels, q, newStack.pixelsFiles, 0, newStack.pixelsFiles.length);
stack.pixelsFiles = new String[q];
System.arraycopy(pixels, 0, stack.pixelsFiles, 0, q);
String[] channels = stack.channelNames;
newStack.channelNames = new String[channels.length - q];
System.arraycopy(channels, q, newStack.channelNames, 0, newStack.channelNames.length);
stack.channelNames = new String[q];
System.arraycopy(channels, 0, stack.channelNames, 0, q);
newStack.core.sizeC = newStack.channelNames.length;
stack.core.sizeC = stack.channelNames.length;
stacks.add(i + 1, newStack);
stackNames.add(i + 1, stackNames.get(i));
}
}
}
int seriesCount = stacks.size();
core.clear();
for (int i = 0; i < seriesCount; i++) {
Stack stack = stacks.get(i);
CoreMetadata ms = stack.core;
core.add(ms);
setSeries(i);
ms.littleEndian = true;
if (stack.timestampFile != null) {
RandomAccessInputStream s = new RandomAccessInputStream(stack.timestampFile);
s.seek(0);
if (s.read() != 'I') {
ms.littleEndian = false;
}
s.seek(17);
s.order(isLittleEndian());
ms.sizeT = s.readInt();
Double firstStamp = null;
Double[] stamps = new Double[ms.sizeT];
for (int t = 0; t < ms.sizeT; t++) {
// timestamps are stored in microseconds
double timestamp = s.readLong() / 1000000.0;
if (firstStamp == null) {
firstStamp = timestamp;
}
stamps[t] = timestamp - firstStamp;
}
timestamps.add(stamps);
s.close();
} else {
ms.sizeT = 1;
}
ms.rgb = false;
ms.interleaved = true;
ms.dimensionOrder = "XYCZT";
RandomAccessInputStream s = new RandomAccessInputStream(stack.pixelsFiles[0]);
s.order(isLittleEndian());
if (checkSuffix(stack.pixelsFiles[0], "aisf")) {
s.seek(18);
stack.blockSize = s.readShort() * 256;
s.skipBytes(5);
int x = s.readInt();
int y = s.readInt();
int zStart = s.readInt();
int w = s.readInt();
int h = s.readInt();
if (w - x < 0 || h - y < 0 || (w - x) * (h - y) < 0) {
ms.littleEndian = !isLittleEndian();
s.order(isLittleEndian());
s.seek(s.getFilePointer() - 20);
x = s.readInt();
y = s.readInt();
zStart = s.readInt();
w = s.readInt();
h = s.readInt();
}
ms.sizeX = w - x;
ms.sizeY = h - y;
ms.sizeZ = s.readInt() - zStart;
ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
ms.pixelType = FormatTools.INT8;
int planesPerFile = getSizeZ() * getSizeT();
int planeSize = FormatTools.getPlaneSize(this);
int bytesPerPlane = (int) ((s.length() - stack.blockSize) / planesPerFile);
int bytesPerPixel = 0;
while (bytesPerPlane >= planeSize) {
bytesPerPixel++;
bytesPerPlane -= planeSize;
}
if ((bytesPerPixel % 3) == 0) {
ms.sizeC *= 3;
ms.rgb = true;
bytesPerPixel /= 3;
}
ms.pixelType = FormatTools.pixelTypeFromBytes(bytesPerPixel, false, bytesPerPixel > 2);
// full timepoints are padded to have a multiple of 256 bytes
int timepoint = FormatTools.getPlaneSize(this) * getSizeZ();
stack.planePadding = stack.blockSize - (timepoint % stack.blockSize);
if (stack.planePadding == stack.blockSize) {
stack.planePadding = 0;
}
} else {
boolean embedded = Location.getMappedFile(EMBEDDED_STREAM) != null;
s.seek(0);
if (s.read() != 'I') {
ms.littleEndian = false;
s.order(false);
}
s.seek(22);
ms.sizeX = s.readInt();
ms.sizeY = s.readInt();
ms.sizeZ = s.readInt();
ms.sizeC = embedded ? 1 : 4;
ms.imageCount = getSizeZ() * getSizeT();
ms.rgb = ms.sizeC > 1;
ms.pixelType = FormatTools.UINT8;
stack.blockSize = embedded ? (int) s.getFilePointer() : 99;
stack.planePadding = 0;
if (s.length() > ms.sizeX * ms.sizeY * ms.sizeZ * 6) {
ms.pixelType = FormatTools.UINT16;
ms.sizeC = 3;
ms.rgb = true;
}
if (s.length() < (ms.sizeX * ms.sizeY * ms.sizeZ * ms.sizeC)) {
ms.rgb = false;
ms.sizeC = 1;
long pixels = ms.sizeX * ms.sizeY * ms.sizeZ;
double approximateBytes = (double) s.length() / pixels;
int bytes = (int) Math.ceil(approximateBytes);
if (bytes == 0) {
bytes = 1;
} else if (bytes == 3) {
bytes = 2;
}
ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
s.seek(70);
stack.blockSize = s.readInt();
stack.clippingData = true;
}
}
s.close();
}
setSeries(0);
for (int i = 0; i < getSeriesCount(); i++) {
setSeries(i);
Stack stack = stacks.get(i);
addSeriesMeta("Name", stackNames.get(i));
addSeriesMeta("Pixel width (in microns)", stack.physicalX);
addSeriesMeta("Pixel height (in microns)", stack.physicalY);
addSeriesMeta("Z step (in microns)", stack.physicalZ);
addSeriesMeta("Objective magnification", stack.magnification);
addSeriesMeta("Camera/Detector", stack.detector);
addSeriesMeta("Description", stack.description);
addSeriesMeta("X Location", stack.xLocation);
addSeriesMeta("Y Location", stack.yLocation);
addSeriesMeta("Z Location", stack.zLocation);
if (stack.channelNames != null) {
for (int c = 0; c < stack.channelNames.length; c++) {
addSeriesMetaList("Channel", stack.channelNames[c]);
}
}
}
setSeries(0);
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageInstrumentRef(instrument, i);
setSeries(i);
Stack stack = stacks.get(i);
store.setImageName(stackNames.get(i), i);
store.setImageDescription(stack.description, i);
if (stack.channelNames != null) {
for (int c = 0; c < getEffectiveSizeC(); c++) {
store.setChannelName(stack.channelNames[c], i, c);
}
}
Length sizeX = FormatTools.getPhysicalSizeX(stack.physicalX);
Length sizeY = FormatTools.getPhysicalSizeY(stack.physicalY);
Length sizeZ = FormatTools.getPhysicalSizeZ(stack.physicalZ);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, i);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, i);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, i);
}
String objective = MetadataTools.createLSID("Objective", 0, i);
store.setObjectiveID(objective, 0, i);
store.setObjectiveNominalMagnification(stack.magnification, 0, i);
store.setObjectiveCorrection(getCorrection("Other"), 0, i);
store.setObjectiveImmersion(getImmersion("Other"), 0, i);
store.setObjectiveSettingsID(objective, i);
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorModel(stack.detector, 0, i);
for (int c = 0; c < getEffectiveSizeC(); c++) {
store.setDetectorSettingsID(detectorID, i, c);
}
for (int img = 0; img < getImageCount(); img++) {
int[] coords = getZCTCoords(img);
int z = coords[0];
final Length xLoc = new Length(stack.xLocation, UNITS.REFERENCEFRAME);
final Length yLoc = new Length(stack.yLocation, UNITS.REFERENCEFRAME);
store.setPlanePositionX(xLoc, i, img);
store.setPlanePositionY(yLoc, i, img);
if (stack.physicalZ != null) {
final double zLocNumber = stack.zLocation + z * stack.physicalZ;
final Length zLoc = new Length(zLocNumber, UNITS.REFERENCEFRAME);
store.setPlanePositionZ(zLoc, i, img);
}
if (i < timestamps.size() && coords[2] < timestamps.get(i).length && timestamps.get(i)[coords[2]] != null) {
store.setPlaneDeltaT(new Time(timestamps.get(i)[coords[2]], UNITS.SECOND), i, img);
}
}
}
setSeries(0);
}
use of loci.common.services.DependencyException in project bioformats by openmicroscopy.
the class WlzReader 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();
wlz = factory.getInstance(WlzService.class);
} catch (DependencyException e) {
throw new FormatException(NO_WLZ_MSG, e);
}
if (wlz != null) {
wlz.open(id, "r");
CoreMetadata md = core.get(0);
MetadataStore store = makeFilterMetadata();
md.rgb = wlz.isRGB();
md.interleaved = false;
md.indexed = false;
md.sizeX = wlz.getSizeX();
md.sizeY = wlz.getSizeY();
md.sizeZ = wlz.getSizeZ();
md.sizeC = wlz.getSizeC();
md.sizeT = wlz.getSizeT();
md.dimensionOrder = "XYZCT";
md.imageCount = wlz.getSizeZ();
md.pixelType = wlz.getPixelType();
PositiveFloat x = new PositiveFloat(Math.abs(wlz.getVoxSzX()));
PositiveFloat y = new PositiveFloat(Math.abs(wlz.getVoxSzY()));
PositiveFloat z = new PositiveFloat(Math.abs(wlz.getVoxSzZ()));
store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0);
store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0);
store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0);
store.setStageLabelName(wlz.getWlzOrgLabelName(), 0);
store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
store.setStageLabelY(new Length(wlz.getOrgY(), UNITS.REFERENCEFRAME), 0);
store.setStageLabelZ(new Length(wlz.getOrgZ(), UNITS.REFERENCEFRAME), 0);
MetadataTools.populatePixels(store, this);
}
}
use of loci.common.services.DependencyException in project bioformats by openmicroscopy.
the class WlzReader 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 (wlz != null) {
buf = wlz.readBytes(no, buf, x, y, w, h);
} else {
try {
ServiceFactory factory = new ServiceFactory();
wlz = factory.getInstance(WlzService.class);
} catch (DependencyException e) {
throw new FormatException(NO_WLZ_MSG, e);
}
if (wlz != null) {
wlz.open(currentId, "r");
buf = wlz.readBytes(no, buf, x, y, w, h);
}
}
return buf;
}
use of loci.common.services.DependencyException in project bioformats by openmicroscopy.
the class TillVisionReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "vws")) {
Location pst = new Location(id).getAbsoluteFile();
String name = pst.getParentFile().getName();
Location parent = pst.getParentFile().getParentFile();
Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
if (vwsFile.exists() && !vwsFile.isDirectory()) {
id = vwsFile.getAbsolutePath();
} else if (vwsFile.isDirectory()) {
parent = pst.getParentFile();
String[] list = parent.list(true);
boolean foundVWS = false;
for (String f : list) {
if (checkSuffix(f, "vws")) {
id = new Location(parent, f).getAbsolutePath();
foundVWS = true;
break;
}
}
if (!foundVWS) {
throw new FormatException("Could not find .vws file.");
}
} else
throw new FormatException("Could not find .vws file.");
}
super.initFile(id);
exposureTimes = new HashMap<Integer, Double>();
POIService poi = null;
try {
ServiceFactory factory = new ServiceFactory();
poi = factory.getInstance(POIService.class);
} catch (DependencyException de) {
throw new FormatException("POI library not found", de);
}
poi.initialize(id);
Vector<String> documents = poi.getDocumentList();
int nImages = 0;
final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
for (String name : documents) {
LOGGER.debug("Reading {}", name);
if (name.equals("Root Entry" + File.separator + "Contents")) {
RandomAccessInputStream s = poi.getDocumentStream(name);
s.order(true);
boolean specialCImage = false;
int nFound = 0;
Long[] cimages = null;
Location dir = new Location(id).getAbsoluteFile().getParentFile();
String[] list = dir.list(true);
boolean hasPST = false;
for (String f : list) {
if (checkSuffix(f, "pst")) {
hasPST = true;
break;
}
}
if (!hasPST) {
cimages = findImages(s);
nFound = cimages.length;
if (nFound == 0) {
s.seek(13);
int len = s.readShort();
String type = s.readString(len);
if (type.equals("CImage")) {
nFound = 1;
cimages = new Long[] { s.getFilePointer() + 6 };
specialCImage = true;
}
}
embeddedImages = nFound > 0;
}
LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
if (embeddedImages) {
core.clear();
embeddedOffset = new long[nFound];
for (int i = 0; i < nFound; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
s.seek(cimages[i]);
int len = s.read();
String imageName = s.readString(len);
imageNames.add(imageName);
if (specialCImage) {
s.seek(1280);
} else {
while (true) {
if (s.readString(2).equals("sB")) {
break;
} else
s.seek(s.getFilePointer() - 1);
}
}
s.skipBytes(20);
ms.sizeX = s.readInt();
ms.sizeY = s.readInt();
ms.sizeZ = s.readInt();
ms.sizeC = s.readInt();
ms.sizeT = s.readInt();
ms.pixelType = convertPixelType(s.readInt());
if (specialCImage) {
embeddedOffset[i] = s.getFilePointer() + 27;
} else {
embeddedOffset[i] = s.getFilePointer() + 31;
}
}
if (in != null)
in.close();
in = poi.getDocumentStream(name);
s.close();
break;
}
s.seek(0);
int lowerBound = 0;
int upperBound = 0x1000;
while (s.getFilePointer() < s.length() - 2) {
LOGGER.debug(" Looking for image at {}", s.getFilePointer());
s.order(false);
int nextOffset = findNextOffset(s);
if (nextOffset < 0 || nextOffset >= s.length())
break;
s.seek(nextOffset);
s.skipBytes(3);
int len = s.readShort();
if (len <= 0)
continue;
imageNames.add(s.readString(len));
if (s.getFilePointer() + 8 >= s.length())
break;
s.skipBytes(6);
s.order(true);
len = s.readShort();
if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
lowerBound = 512;
upperBound = 0x4000;
}
if (len < lowerBound || len > upperBound)
continue;
String description = s.readString(len);
LOGGER.debug("Description: {}", description);
// parse key/value pairs from description
String dateTime = "";
String[] lines = description.split("[\r\n]");
for (String line : lines) {
line = line.trim();
int colon = line.indexOf(':');
if (colon != -1 && !line.startsWith(";")) {
String key = line.substring(0, colon).trim();
String value = line.substring(colon + 1).trim();
String metaKey = "Series " + nImages + " " + key;
addMeta(metaKey, value, tmpSeriesMetadata);
if (key.equals("Start time of experiment")) {
// HH:mm:ss aa OR HH:mm:ss.sss aa
dateTime += " " + value;
} else if (key.equals("Date")) {
// mm/dd/yy ?
dateTime = value + " " + dateTime;
} else if (key.equals("Exposure time [ms]")) {
double exp = Double.parseDouble(value) / 1000;
exposureTimes.put(nImages, exp);
} else if (key.equals("Image type")) {
types.add(value);
}
}
}
dateTime = dateTime.trim();
if (!dateTime.equals("")) {
boolean success = false;
for (String format : DATE_FORMATS) {
try {
dateTime = DateTools.formatDate(dateTime, format, ".");
success = true;
} catch (NullPointerException e) {
}
}
dates.add(success ? dateTime : "");
}
nImages++;
}
s.close();
}
}
Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
String[] pixelsFile = new String[nImages];
if (!embeddedImages) {
if (nImages == 0) {
throw new FormatException("No images found.");
}
// look for appropriate pixels files
String[] files = directory.list(true);
String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
int nextFile = 0;
for (String f : files) {
if (checkSuffix(f, "pst")) {
Location pst = new Location(directory, f);
if (pst.isDirectory() && f.startsWith(name)) {
String[] subfiles = pst.list(true);
Arrays.sort(subfiles);
for (String q : subfiles) {
if (checkSuffix(q, "pst") && nextFile < nImages) {
pixelsFile[nextFile++] = f + File.separator + q;
}
}
}
}
}
if (nextFile == 0) {
for (String f : files) {
if (checkSuffix(f, "pst")) {
pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
}
}
if (nextFile == 0)
throw new FormatException("No image files found.");
}
}
Arrays.sort(pixelsFile);
int nSeries = core.size();
if (!embeddedImages) {
core.clear();
nSeries = nImages;
}
pixelsFiles = new String[nSeries];
infFiles = new String[nSeries];
Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
IniParser parser = new IniParser();
for (int i = 0; i < nSeries; i++) {
CoreMetadata ms;
if (!embeddedImages) {
ms = new CoreMetadata();
core.add(ms);
setSeries(i);
// make sure that pixels file exists
String file = pixelsFile[i];
file = file.replace('/', File.separatorChar);
file = file.replace('\\', File.separatorChar);
String oldFile = file;
Location f = new Location(directory, oldFile);
if (!f.exists()) {
oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
f = new Location(directory, oldFile);
if (!f.exists()) {
throw new FormatException("Could not find pixels file '" + file);
}
}
file = f.getAbsolutePath();
pixelsFiles[i] = file;
// read key/value pairs from .inf files
int dot = file.lastIndexOf(".");
String inf = file.substring(0, dot) + ".inf";
infFiles[i] = inf;
BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
IniList data = parser.parseINI(reader);
reader.close();
IniTable infoTable = data.getTable("Info");
ms.sizeX = Integer.parseInt(infoTable.get("Width"));
ms.sizeY = Integer.parseInt(infoTable.get("Height"));
ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
int dataType = Integer.parseInt(infoTable.get("Datatype"));
ms.pixelType = convertPixelType(dataType);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
HashMap<String, String> iniMap = data.flattenIntoHashMap();
ms.seriesMetadata.putAll(iniMap);
}
} else {
ms = core.get(i);
setSeries(i);
}
ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
ms.rgb = false;
ms.littleEndian = true;
ms.dimensionOrder = "XYCZT";
ms.seriesMetadata = new Hashtable<String, Object>();
for (Object key : metadataKeys) {
String keyName = key.toString();
if (keyName.startsWith("Series " + i + " ")) {
keyName = keyName.replaceAll("Series " + i + " ", "");
ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
}
}
}
setSeries(0);
populateMetadataStore();
poi.close();
poi = null;
}
use of loci.common.services.DependencyException in project bioformats by openmicroscopy.
the class ZeissZVIReader method initPOIService.
private void initPOIService() throws FormatException, IOException {
try {
ServiceFactory factory = new ServiceFactory();
poi = factory.getInstance(POIService.class);
} catch (DependencyException de) {
throw new FormatException("POI library not found", de);
}
poi.initialize(Location.getMappedId(getCurrentFile()));
}
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