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);
}
}
public DisplayPlus(
final ImageCache stitchedCache,
AcquisitionEngine eng,
JSONObject summaryMD,
boolean invX,
boolean invY,
boolean swapXY) {
eng_ = eng;
invertX_ = invX;
invertY_ = invY;
swapXY_ = swapXY;
try {
MultiStagePosition pos0 = MMStudioMainFrame.getInstance().getPositionList().getPosition(0);
pos0x_ = pos0.getX();
pos0y_ = pos0.getY();
tileWidth_ = MDUtils.getHeight(summaryMD);
tileHeight_ = MDUtils.getWidth(summaryMD);
} catch (Exception e) {
ReportingUtils.showError("Couldnt get grid info");
}
vad_ =
new VirtualAcquisitionDisplay(stitchedCache, eng, WINDOW_TITLE) {
public void showImage(final JSONObject tags, boolean waitForDisplay)
throws InterruptedException, InvocationTargetException {
// Since this is multichannel camera, only show when last channel arrives
try {
if (MDUtils.getChannelIndex(tags) == super.getNumChannels() - 1) {
super.showImage(tags, waitForDisplay);
} else {
ImagePlus ip = super.getHyperImage();
if (ip != null) {
// canvas never gets painted so need to set painpending false
ip.getCanvas().setPaintPending(false);
}
}
} catch (JSONException ex) {
}
}
};
DisplayControls controls = new Controls();
// Add in custom controls
try {
JavaUtils.setRestrictedFieldValue(
vad_, VirtualAcquisitionDisplay.class, "controls_", controls);
} catch (NoSuchFieldException ex) {
ReportingUtils.showError("Couldn't create display controls");
}
vad_.show();
// Zoom to 100%
vad_.getImagePlus().getWindow().getCanvas().unzoom();
// add mouse listeners for moving grids
addMouseListeners();
stitchedCache.addImageCacheListener(this);
}
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;
}
}
@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");
}
}
protected void initializeFlags() {
flags_ = new ShowFlags();
if (showFlagsPanelVisible) {
flags_.load(getPrefsNode());
Configuration cfg;
try {
if (presetName_.length() == 0) cfg = new Configuration();
else cfg = core_.getConfigState(groupName_, presetName_);
showFlagsPanel_ = new ShowFlagsPanel(data_, flags_, core_, cfg);
} catch (Exception e) {
ReportingUtils.showError(e);
}
getContentPane().add(showFlagsPanel_);
springLayout_.putConstraint(
SpringLayout.EAST, showFlagsPanel_, 440, SpringLayout.WEST, getContentPane());
springLayout_.putConstraint(
SpringLayout.WEST, showFlagsPanel_, 290, SpringLayout.WEST, getContentPane());
springLayout_.putConstraint(
SpringLayout.SOUTH, showFlagsPanel_, 135, SpringLayout.NORTH, getContentPane());
springLayout_.putConstraint(
SpringLayout.NORTH, showFlagsPanel_, 5, SpringLayout.NORTH, getContentPane());
}
data_.setFlags(flags_);
}
private JSONObject readMMMetadata(IFDData data) throws IOException {
try {
return readJSONObject(data.mdOffset, data.mdLength);
} catch (JSONException ex) {
ReportingUtils.showError("Error reading image metadata");
return new JSONObject();
}
}
@Override
public void setValueAt(Object value, int row, int col) {
if (col == 1) {
try {
labels_[row] = (String) value;
curDevice_.setSetupLabel(row, (String) value);
fireTableCellUpdated(row, col);
} catch (Exception e) {
ReportingUtils.showError(e);
}
}
}
@Override
public void imageReceived(TaggedImage taggedImage) {
try {
// duplicate so image storage doesnt see incorrect tags
JSONObject newTags = new JSONObject(taggedImage.tags.toString());
MDUtils.setPositionIndex(newTags, 0);
taggedImage = new TaggedImage(taggedImage.pix, newTags);
} catch (JSONException ex) {
ReportingUtils.showError("Couldn't manipulate image tags for display");
}
vad_.imageReceived(taggedImage);
}
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 void start() {
for (DataProcessor<E> processor : processors_) {
if (!processor.isAlive()) {
if (processor.isStarted()) {
ReportingUtils.showError(
"Processor: "
+ processor.getName()
+ " is no longer running. Remove and re-insert to get it to go again");
} else {
processor.start();
}
}
}
}
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;
}
private void refreshOneAxisStagePositions() {
for (Devices.Keys devKey : Devices.STAGES1D) {
String mmDevice = devices_.getMMDevice(devKey);
if (mmDevice == null) { // skip devices not set in devices tab
oneAxisDrivePositions_.put(devKey, null);
continue;
}
try {
if (devices_.is1DStage(devKey)) {
double pt = core_.getPosition(mmDevice);
oneAxisDrivePositions_.put(devKey, pt);
}
} catch (Exception ex) {
ReportingUtils.logMessage("Problem getting position of " + mmDevice);
}
}
}
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;
}
}
private void refreshTwoAxisStagePositions() {
for (Devices.Keys devKey : Devices.STAGES2D) {
String mmDevice = devices_.getMMDevice(devKey);
if (mmDevice == null) { // skip devices not set in devices tab
twoAxisDrivePositions_.put(devKey, null);
continue;
}
Point2D.Double pt;
try {
if (devices_.isXYStage(devKey)) {
pt = core_.getXYStagePosition(mmDevice);
} else if (devices_.isGalvo(devKey)) {
pt = core_.getGalvoPosition(mmDevice);
} else {
pt = new Point2D.Double();
}
twoAxisDrivePositions_.put(devKey, pt);
} catch (Exception ex) {
ReportingUtils.logMessage("Problem getting position of " + mmDevice);
}
}
}
protected void handleException(Exception e) {
ReportingUtils.showError(e);
}