@Override
public void writeDisplaySettings() {
for (MultipageTiffReader r : new HashSet<MultipageTiffReader>(tiffReadersByLabel_.values())) {
try {
r.rewriteDisplaySettings(displayAndComments_.getJSONArray("Channels"));
r.rewriteComments(displayAndComments_.getJSONObject("Comments"));
} catch (JSONException ex) {
ReportingUtils.logError("Error writing display settings");
} catch (IOException ex) {
ReportingUtils.logError(ex);
}
}
}
@Override
public void putImage(TaggedImage taggedImage) throws MMException {
if (!newDataSet_) {
throw new MMException("This ImageFileManager is read-only.");
}
int fileSetIndex = 0;
if (splitByXYPosition_) {
try {
fileSetIndex = MDUtils.getPositionIndex(taggedImage.tags);
} catch (JSONException ex) {
ReportingUtils.logError(ex);
}
}
String label = MDUtils.getLabel(taggedImage.tags);
if (fileSets_ == null) {
try {
fileSets_ = new HashMap<Integer, FileSet>();
createDirectory(directory_);
} catch (Exception ex) {
ReportingUtils.logError(ex);
}
}
if (omeTiff_) {
if (omeMetadata_ == null) {
omeMetadata_ = new OMEMetadata(this);
}
}
if (fileSets_.get(fileSetIndex) == null) {
fileSets_.put(fileSetIndex, new FileSet(taggedImage.tags, this));
}
FileSet set = fileSets_.get(fileSetIndex);
try {
set.writeImage(taggedImage);
} catch (IOException ex) {
ReportingUtils.showError("problem writing image to file");
}
tiffReadersByLabel_.put(label, set.getCurrentReader());
int frame;
try {
frame = MDUtils.getFrameIndex(taggedImage.tags);
} catch (JSONException ex) {
frame = 0;
}
lastFrameOpenedDataSet_ = Math.max(frame, lastFrameOpenedDataSet_);
cached_.add(taggedImage, label);
}
/** Disposes of the tagged images in the imagestorage */
@Override
public void close() {
shutdownHook_.run();
Runtime.getRuntime().removeShutdownHook(shutdownHook_);
for (MultipageTiffReader r : new HashSet<MultipageTiffReader>(tiffReadersByLabel_.values())) {
try {
r.close();
} catch (IOException ex) {
ReportingUtils.logError(ex);
}
}
}
// <editor-fold defaultstate="collapsed" desc=" Metadata ">
//
private void processSummaryMD() {
// TODO displayAndComments_ =
// VirtualAcquisitionDisplay.getDisplaySettingsFromSummary(summaryMetadata_);
try {
numPositions_ = MDUtils.getNumPositions(summaryMetadata_);
if (numPositions_ <= 0) {
numPositions_ = 1;
}
} catch (JSONException ex) {
ReportingUtils.logError(ex);
numPositions_ = 1;
}
try {
// Estimate of max number of image planes
numChannels_ = MDUtils.getNumChannels(summaryMetadata_);
numSlices_ = MDUtils.getNumSlices(summaryMetadata_);
totalNumImagePlanes_ =
numChannels_ * MDUtils.getNumFrames(summaryMetadata_) * numPositions_ * numSlices_;
} catch (Exception ex) {
ReportingUtils.logError("Error estimating total number of image planes");
totalNumImagePlanes_ = 1;
}
}
@Override
public void setSummaryMetadata(JSONObject md) {
summaryMetadata_ = md;
if (summaryMetadata_ != null) {
try {
boolean slicesFirst = summaryMetadata_.getBoolean("SlicesFirst");
boolean timeFirst = summaryMetadata_.getBoolean("TimeFirst");
TreeMap<String, MultipageTiffReader> oldImageMap = tiffReadersByLabel_;
tiffReadersByLabel_ =
new TreeMap<String, MultipageTiffReader>(
new ImageLabelComparator(slicesFirst, timeFirst));
tiffReadersByLabel_.putAll(oldImageMap);
} catch (JSONException ex) {
ReportingUtils.logError("Couldn't find SlicesFirst or TimeFirst in summary metadata");
}
if (summaryMetadata_ != null && summaryMetadata_.length() > 0) {
processSummaryMD();
}
}
}
/**
* Call this function when no more images are expected Finishes writing the metadata file and
* closes it. After calling this function, the imagestorage is read-only
*/
@Override
public synchronized void finished() {
if (finished_) {
return;
}
newDataSet_ = false;
try {
if (fileSets_ != null) {
for (FileSet p : fileSets_.values()) {
p.finishAbortedAcqIfNeeded();
}
for (FileSet p : fileSets_.values()) {
p.finished();
}
}
} catch (IOException ex) {
ReportingUtils.logError(ex);
}
finished_ = true;
}
private void openExistingDataSet() throws IOException {
// Need to throw error if file not found
MultipageTiffReader reader = null;
File dir = new File(directory_);
for (File f : dir.listFiles()) {
if (f.getName().endsWith(".tif") || f.getName().endsWith(".TIF")) {
reader = new MultipageTiffReader(f);
Set<String> labels = reader.getIndexKeys();
for (String label : labels) {
tiffReadersByLabel_.put(label, reader);
int frameIndex = Integer.parseInt(label.split("_")[2]);
lastFrameOpenedDataSet_ = Math.max(frameIndex, lastFrameOpenedDataSet_);
}
}
}
try {
setSummaryMetadata(reader.getSummaryMetadata());
numPositions_ = MDUtils.getNumPositions(summaryMetadata_);
displayAndComments_ = reader.getDisplayAndComments();
} catch (JSONException ex) {
ReportingUtils.logError(ex);
}
}