/**
* Constructs a special JComboBox with all cameras that have only 1 channel
*
* @param deviceName
* @return
*/
public JComboBox makeSingleCameraDeviceBox(Devices.Keys deviceName, int maximumWidth) {
List<String> singleCameras = new ArrayList<String>();
singleCameras.add(0, "");
String originalCamera = core_.getCameraDevice();
try {
StrVector strvDevices = core_.getLoadedDevicesOfType(mmcorej.DeviceType.CameraDevice);
for (int i = 0; i < strvDevices.size(); i++) {
String test = strvDevices.get(i);
core_.setCameraDevice(test);
if (core_.getNumberOfCameraChannels() == 1) {
singleCameras.add(test);
}
}
} catch (Exception ex) {
MyDialogUtils.showError("Error detecting single camera devices");
} finally {
try {
core_.setCameraDevice(originalCamera);
} catch (Exception e) {
MyDialogUtils.showError(e);
}
}
JComboBox deviceBox = new JComboBox(singleCameras.toArray());
deviceBox.addActionListener(new DeviceBoxListener(deviceName, deviceBox));
deviceBox.setSelectedItem(
devices_.getMMDevice(deviceName)); // selects whatever device was read in by prefs
deviceBox.setMaximumSize(new Dimension(maximumWidth, 30));
return deviceBox;
}
/**
* Sets the current position to be the origin.
*
* @param devKey
* @param dir
* @param pos
*/
public void setOrigin(Devices.Keys devKey, Joystick.Directions dir) {
try {
String mmDevice = devices_.getMMDeviceException(devKey);
switch (dir) {
case X:
if (devices_.isXYStage(devKey)) {
double ypos = getUpdatedPosition(devKey, Joystick.Directions.Y);
core_.setAdapterOriginXY(
mmDevice, 0.0, ypos); // so serial com, since adapter keeps own origin
}
break;
case Y:
if (devices_.isXYStage(devKey)) {
double xpos = getUpdatedPosition(devKey, Joystick.Directions.X);
core_.setAdapterOriginXY(
mmDevice, xpos, 0.0); // so serial com, since adapter keeps own origin
}
break;
case NONE:
default:
if (devices_.is1DStage(devKey)) {
core_.setOrigin(mmDevice);
}
break;
}
} catch (Exception ex) {
MyDialogUtils.showError(ex);
}
}
/**
* Constructs a special JComboBox with all cameras that have more than 1 channel, which we expect
* to just be a single Multicamera device
*
* @param deviceName
* @return
*/
public JComboBox makeMultiCameraDeviceBox(Devices.Keys deviceName, int maximumWidth) {
List<String> multiCameras = new ArrayList<String>();
multiCameras.add(0, "");
try {
StrVector strvDevices = core_.getLoadedDevicesOfType(mmcorej.DeviceType.CameraDevice);
for (int i = 0; i < strvDevices.size(); i++) {
// find all Multi-camera devices (usually just one)
String test = strvDevices.get(i);
if (core_.getDeviceLibrary(test).equals(Devices.Libraries.UTILITIES.toString())
&& core_
.getDeviceDescription(test)
.equals("Combine multiple physical cameras into a single logical camera")) {
multiCameras.add(strvDevices.get(i));
}
}
} catch (Exception ex) {
MyDialogUtils.showError("Error detecting multi camera devices");
}
JComboBox deviceBox = new JComboBox(multiCameras.toArray());
deviceBox.addActionListener(new DeviceBoxListener(deviceName, deviceBox));
// if we have one and only one multi-camera then set box to it
if (multiCameras.size() == 2) { // recall we added empty string as the first entry
deviceBox.setSelectedIndex(1);
} else {
deviceBox.setSelectedItem(
devices_.getMMDevice(deviceName)); // selects whatever device was read in by prefs
}
deviceBox.setMaximumSize(new Dimension(maximumWidth, 30));
return deviceBox;
}
/**
* Returns the current position of the specified stage, or 0 if the stage wasn't found. Updates
* the cache with the value as well.
*
* @param devKey
* @param dir
* @return
*/
public double getUpdatedPosition(Devices.Keys devKey, Joystick.Directions dir) {
String mmDevice = devices_.getMMDevice(devKey);
if (mmDevice == null) {
return 0;
}
try {
if (devices_.is1DStage(devKey)) {
double pt = core_.getPosition(mmDevice);
oneAxisDrivePositions_.put(devKey, pt);
return pt;
}
Point2D.Double pt;
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);
if (dir == Joystick.Directions.X) {
return pt.x;
} else if (dir == Joystick.Directions.Y) {
return pt.y;
}
} catch (Exception ex) {
MyDialogUtils.showError(ex);
}
return 0;
}
public void enableContinuousFocus(boolean enable) throws MMException {
try {
core_.setAutoFocusDevice(devName_);
core_.enableContinuousFocus(enable);
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
public boolean isContinuousFocusLocked() throws MMException {
try {
core_.setAutoFocusDevice(devName_);
return core_.isContinuousFocusLocked();
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
public double getCurrentFocusScore() {
try {
core_.setAutoFocusDevice(devName_);
} catch (Exception e) {
ReportingUtils.logError(e);
return 0;
}
return core_.getCurrentFocusScore();
}
public void readFromCore(CMMCore core, String deviceName, String propertyName, boolean cached) {
device = deviceName;
name = propertyName;
try {
readOnly = core.isPropertyReadOnly(deviceName, propertyName);
preInit = core.isPropertyPreInit(deviceName, propertyName);
hasRange = core.hasPropertyLimits(deviceName, propertyName);
lowerLimit = core.getPropertyLowerLimit(deviceName, propertyName);
upperLimit = core.getPropertyUpperLimit(deviceName, propertyName);
type = core.getPropertyType(deviceName, propertyName);
StrVector values = core.getAllowedPropertyValues(deviceName, propertyName);
allowed = new String[(int) values.size()];
for (int k = 0; k < values.size(); k++) {
allowed[k] = values.get(k);
}
sort();
String coreVal;
if (cached) coreVal = core.getPropertyFromCache(deviceName, propertyName);
else coreVal = core.getProperty(deviceName, propertyName);
setValueFromCoreString(coreVal);
} catch (Exception e) {
ReportingUtils.logError(e);
}
}
public String[] getPropertyNames() {
Vector<String> propNames = new Vector<String>();
try {
core_.setAutoFocusDevice(devName_);
StrVector propNamesVect = core_.getDevicePropertyNames(devName_);
for (int i = 0; i < propNamesVect.size(); i++)
if (!core_.isPropertyReadOnly(devName_, propNamesVect.get(i))
&& !core_.isPropertyPreInit(devName_, propNamesVect.get(i)))
propNames.add(propNamesVect.get(i));
} catch (Exception e) {
ReportingUtils.logError(e);
}
return (String[]) propNames.toArray();
}
/**
* Sets the position of specified stage to the specified value using appropriate core calls
*
* @param devKey
* @param dir
* @param pos new position of the stage
* @param ignoreErrors true will return without any errors (or any action) if device is missing
*/
public boolean setPosition(
Devices.Keys devKey, Joystick.Directions dir, double pos, boolean ignoreErrors) {
try {
if (ignoreErrors && !devices_.isValidMMDevice(devKey)) {
return false;
}
String mmDevice = devices_.getMMDeviceException(devKey);
if (devices_.is1DStage(devKey)) {
core_.setPosition(mmDevice, pos);
} else if (devices_.isXYStage(devKey)) {
if (dir == Joystick.Directions.X) {
// would prefer setXPosition but it doesn't exist so we stop any Y motion
double ypos = core_.getYPosition(mmDevice);
core_.setXYPosition(mmDevice, pos, ypos);
} else if (dir == Joystick.Directions.Y) {
double xpos = core_.getXPosition(mmDevice);
// would prefer setYPosition but it doesn't exist so we stop any X motion
core_.setXYPosition(mmDevice, xpos, pos);
}
} else if (devices_.isGalvo(devKey)) {
Point2D.Double pos2D = core_.getGalvoPosition(mmDevice);
if (dir == Joystick.Directions.X) {
core_.setGalvoPosition(mmDevice, pos, pos2D.y);
} else if (dir == Joystick.Directions.Y) {
core_.setGalvoPosition(mmDevice, pos2D.x, pos);
}
}
return true;
} catch (Exception ex) {
MyDialogUtils.showError(ex);
return false;
}
}
public PropertyItem[] getProperties() {
StrVector propNamesVect;
Vector<PropertyItem> props = new Vector<PropertyItem>();
try {
core_.setAutoFocusDevice(devName_);
propNamesVect = core_.getDevicePropertyNames(devName_);
for (int i = 0; i < propNamesVect.size(); i++) {
PropertyItem p = new PropertyItem();
p.device = devName_;
p.name = propNamesVect.get(i);
p.value = core_.getProperty(devName_, p.name);
p.readOnly = core_.isPropertyReadOnly(devName_, p.name);
if (core_.hasPropertyLimits(devName_, p.name)) {
p.lowerLimit = core_.getPropertyLowerLimit(devName_, p.name);
p.upperLimit = core_.getPropertyUpperLimit(devName_, p.name);
}
StrVector vals = core_.getAllowedPropertyValues(devName_, p.name);
p.allowed = new String[(int) vals.size()];
for (int j = 0; j < vals.size(); j++) p.allowed[j] = vals.get(j);
props.add(p);
}
} catch (Exception e) {
ReportingUtils.logError(e);
}
return props.toArray(new PropertyItem[0]);
}
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_);
}
public void setProperty(PropertyItem p) throws MMException {
try {
core_.setProperty(devName_, p.name, p.value);
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
public void setPropertyValue(String name, String value) throws MMException {
try {
core_.setProperty(devName_, name, value);
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
public String getPropertyValue(String name) throws MMException {
try {
return core_.getProperty(devName_, name);
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
public double incrementalFocus() throws MMException {
if (core_ == null) return 0.0;
try {
core_.setAutoFocusDevice(devName_);
core_.incrementalFocus();
} catch (Exception e) {
throw new MMException(e.getMessage());
}
try {
return core_.getLastFocusScore();
} catch (Exception e) {
ReportingUtils.logError(e);
return 0.0;
}
}
// Set ImageJ pixel calibration
public void setIJCal() {
double pixSizeUm = core_.getPixelSizeUm();
Calibration cal = new Calibration();
if (pixSizeUm > 0) {
cal.setUnit("um");
cal.pixelWidth = pixSizeUm;
cal.pixelHeight = pixSizeUm;
}
getImagePlus().setCalibration(cal);
}
private static Image5D createImage5D(CMMCore core, String wndTitle) throws Exception {
core_ = core;
ImageProcessor ip;
int type = 0;
int width_ = (int) core_.getImageWidth();
int height_ = (int) core_.getImageHeight();
long byteDepth = core_.getBytesPerPixel();
long channels = core_.getNumberOfChannels();
if (byteDepth == 1 && channels == 1) {
type = ImagePlus.GRAY8;
ip = new ByteProcessor(width_, height_);
if (contrastSettings8_.getRange() == 0.0) ip.setMinAndMax(0, 255);
else ip.setMinAndMax(contrastSettings8_.min, contrastSettings8_.max);
} else if (byteDepth == 2 && channels == 1) {
type = ImagePlus.GRAY16;
ip = new ShortProcessor(width_, height_);
if (contrastSettings16_.getRange() == 0.0) ip.setMinAndMax(0, 65535);
else ip.setMinAndMax(contrastSettings16_.min, contrastSettings16_.max);
} else if (byteDepth == 0) {
throw (new Exception(logError("Imaging device not initialized")));
} else if (byteDepth == 1 && channels == 4) {
// assuming RGB32 format
ip = new ColorProcessor(width_, height_);
if (contrastSettings8_.getRange() == 0.0) ip.setMinAndMax(0, 255);
else ip.setMinAndMax(contrastSettings8_.min, contrastSettings8_.max);
} else {
String message =
"Unsupported pixel depth: "
+ core_.getBytesPerPixel()
+ " byte(s) and "
+ channels
+ " channel(s).";
throw (new Exception(logError(message)));
}
ip.setColor(Color.black);
if (currentColorModel_ != null) ip.setColorModel(currentColorModel_);
ip.fill();
Image5D img5d = new Image5D(wndTitle, type, width_, height_, 1, 1, 1, false);
@SuppressWarnings("unused")
Image5DWindow i5dw = new Image5DWindow(img5d);
return img5d;
}
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);
}
}
}
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);
}
}
}
/**
* Constructs a JComboBox populated with devices of specified Micro-Manager type Attaches a
* listener and sets selected item to what is specified in the Devices class.
*
* @param deviceType - Micro-Manager device type (mmcorej.DeviceType)
* @param deviceKey - ASi diSPIM device key (see Devices class)
* @param maximumWidth -
* @return final JComboBox
*/
public JComboBox makeDeviceSelectionBox(
mmcorej.DeviceType deviceType, Devices.Keys deviceKey, int maximumWidth) {
// when editing this method do the same to the one with array argument too
JComboBox deviceBox = new JComboBox();
ArrayList<String> devices = new ArrayList<String>();
StrVector strvDevices = core_.getLoadedDevicesOfType(deviceType);
devices.addAll(Arrays.asList(strvDevices.toArray()));
devices.add(0, "");
deviceBox.removeAllItems();
for (String device : devices) {
deviceBox.addItem(device);
}
deviceBox.addActionListener(new DeviceBoxListener(deviceKey, deviceBox));
deviceBox.setSelectedItem(
devices_.getMMDevice(deviceKey)); // selects whatever device was read in by prefs
deviceBox.setMaximumSize(new Dimension(maximumWidth, 30));
return deviceBox;
}
public PropertyItem getProperty(String name) throws MMException {
try {
if (core_.hasProperty(devName_, name)) {
PropertyItem p = new PropertyItem();
p.device = devName_;
p.name = name;
p.value = core_.getProperty(devName_, p.name);
p.readOnly = core_.isPropertyReadOnly(devName_, p.name);
if (core_.hasPropertyLimits(devName_, p.name)) {
p.lowerLimit = core_.getPropertyLowerLimit(devName_, p.name);
p.upperLimit = core_.getPropertyUpperLimit(devName_, p.name);
}
StrVector vals = core_.getAllowedPropertyValues(devName_, p.name);
p.allowed = new String[(int) vals.size()];
for (int j = 0; j < vals.size(); j++) p.allowed[j] = vals.get(j);
return p;
} else {
throw new MMException("Unknown property: " + name);
}
} catch (Exception e) {
throw new MMException(e.getMessage());
}
}
/**
* Sets the relative position of specified stage to the specified value using appropriate core
* calls
*
* @param devKey
* @param dir
* @param pos new position of the stage
*/
public void setPositionRelative(Devices.Keys devKey, Joystick.Directions dir, double delta) {
try {
String mmDevice = devices_.getMMDeviceException(devKey);
if (devices_.is1DStage(devKey)) {
core_.setRelativePosition(mmDevice, delta);
} else if (devices_.isXYStage(devKey)) {
if (dir == Joystick.Directions.X) {
core_.setRelativeXYPosition(mmDevice, delta, 0);
} else if (dir == Joystick.Directions.Y) {
core_.setRelativeXYPosition(mmDevice, 0, delta);
}
} else if (devices_.isGalvo(devKey)) {
Point2D.Double pos2D = core_.getGalvoPosition(mmDevice);
if (dir == Joystick.Directions.X) {
core_.setGalvoPosition(mmDevice, pos2D.x + delta, pos2D.y);
} else if (dir == Joystick.Directions.Y) {
core_.setGalvoPosition(mmDevice, pos2D.x, pos2D.y + delta);
}
}
} catch (Exception ex) {
MyDialogUtils.showError(ex);
}
}
public int getNumberOfImages() {
return core_.getRemainingImageCount();
}
public void setApp(ScriptInterface app) {
core_ = app.getMMCore();
devName_ = core_.getAutoFocusDevice();
}
