/** 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);
}
}
}
@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);
}
}
}
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);
}
}