private void readIndexMap() throws IOException {
MappedByteBuffer mapOffset = makeReadOnlyBuffer(8, 8);
if (mapOffset.getInt() != MultipageTiffWriter.INDEX_MAP_OFFSET_HEADER) {
ReportingUtils.logError("Image map offset header incorrect");
indexMap_ = null;
return;
}
long offset = unsignInt(mapOffset.getInt());
MappedByteBuffer mapHeader = makeReadOnlyBuffer(offset, 8);
int headerCode = mapHeader.getInt();
if (headerCode != MultipageTiffWriter.INDEX_MAP_HEADER) {
ReportingUtils.logError("Image index map header incorrect");
indexMap_ = null;
return;
}
int numMappings = mapHeader.getInt();
MappedByteBuffer mapData = makeReadOnlyBuffer(offset + 8, 24 * numMappings);
for (int i = 0; i < numMappings; i++) {
int channel = mapData.getInt();
int slice = mapData.getInt();
int frame = mapData.getInt();
int position = mapData.getInt();
long imageOffset = mapData.getLong();
indexMap_.put(MDUtils.generateLabel(channel, slice, frame, position), imageOffset);
}
}
@Override
public void newImageUpdate(JSONObject tags) {
if (tags == null) {
return;
}
updateLabels(tags);
try {
if (vad_.acquisitionIsRunning() && vad_.getNextWakeTime() > 0) {
final long nextImageTime = vad_.getNextWakeTime();
if (System.nanoTime() / 1000000 < nextImageTime) {
final java.util.Timer timer = new java.util.Timer("Next frame display");
TimerTask task =
new TimerTask() {
public void run() {
double timeRemainingS = (nextImageTime - System.nanoTime() / 1000000) / 1000;
if (timeRemainingS > 0 && vad_.acquisitionIsRunning()) {
setStatusLabel(
"Next frame: "
+ NumberUtils.doubleToDisplayString(1 + timeRemainingS)
+ " s");
} else {
timer.cancel();
setStatusLabel("");
}
}
};
timer.schedule(task, 2000, 100);
}
}
} catch (Exception ex) {
ReportingUtils.logError(ex);
}
}
private void updateLabels(JSONObject tags) {
// Z position label
String zPosition = "";
try {
zPosition = NumberUtils.doubleStringCoreToDisplay(tags.getString("ZPositionUm"));
} catch (Exception e) {
try {
zPosition = NumberUtils.doubleStringCoreToDisplay(tags.getString("Z-um"));
} catch (Exception e1) {
// Do nothing...
}
}
zPosLabel_.setText("Z Position: " + zPosition + " um ");
// time label
try {
int ms = (int) tags.getDouble("ElapsedTime-ms");
int s = ms / 1000;
int min = s / 60;
int h = min / 60;
String time =
twoDigitFormat(h)
+ ":"
+ twoDigitFormat(min % 60)
+ ":"
+ twoDigitFormat(s % 60)
+ "."
+ threeDigitFormat(ms % 1000);
timeStampLabel_.setText("Elapsed time: " + time + " ");
} catch (JSONException ex) {
ReportingUtils.logError("MetaData did not contain ElapsedTime-ms field");
}
}
public void readFromHardware() {
LabelTableModel labelTableModel = (LabelTableModel) labelTable_.getModel();
Device selectedDevice = labelTableModel.getCurrentDevice();
if (selectedDevice != null) {
try {
selectedDevice.getSetupLabelsFromHardware(core_);
labelTableModel.setData(model_, selectedDevice.getName());
labelTableModel.fireTableStructureChanged();
} catch (Exception e) {
ReportingUtils.logError(e);
}
}
}
public JSONObject readSummaryMD() throws IOException {
MappedByteBuffer mdInfo = makeReadOnlyBuffer(16, 8);
if (mdInfo.getInt() != MultipageTiffWriter.SUMMARY_MD_HEADER) {
ReportingUtils.logError("Summary Metadata Header Incorrect");
return null;
}
long length = unsignInt(mdInfo.getInt());
try {
return readJSONObject(24, length);
} catch (JSONException ex) {
ReportingUtils.showError("Error reading summary metadata");
return null;
}
}
public TaggedImage readImage(String label) {
if (indexMap_.containsKey(label)) {
try {
long byteOffset = indexMap_.get(label);
IFDData data = readIFD(byteOffset);
Object pixels = readPixels(data);
JSONObject md = readMMMetadata(data);
return new TaggedImage(pixels, md);
} catch (IOException ex) {
ReportingUtils.logError(ex);
return null;
}
} else {
// label not in map--maybe parse whole file?
return null;
}
}
public boolean enterPage(boolean next) {
DevTableModel tm = (DevTableModel) devTable_.getModel();
tm.setData(model_);
try {
try {
model_.loadStateLabelsFromHardware(core_);
} catch (Throwable t) {
ReportingUtils.logError(t);
}
// default the selection to the first row
if (devTable_.getSelectedRowCount() < 1) {
TableModel m2 = devTable_.getModel();
if (0 < m2.getRowCount()) devTable_.setRowSelectionInterval(0, 0);
}
} catch (Exception e) {
ReportingUtils.showError(e);
return false;
}
resetLabels();
return true;
}
