/**
* Creates and returns a laser. This will have to be linked to an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Laser createLaser() throws Exception {
Laser laser = new LaserI();
laser.setManufacturer(omero.rtypes.rstring("manufacturer"));
laser.setModel(omero.rtypes.rstring("model"));
laser.setLotNumber(omero.rtypes.rstring("lot number"));
laser.setSerialNumber(omero.rtypes.rstring("serial number"));
// type
List<IObject> types = pixelsService.getAllEnumerations(LaserType.class.getName());
laser.setType((LaserType) types.get(0));
// laser medium
types = pixelsService.getAllEnumerations(LaserMedium.class.getName());
laser.setLaserMedium((LaserMedium) types.get(0));
// pulse
types = pixelsService.getAllEnumerations(Pulse.class.getName());
laser.setPulse((Pulse) types.get(0));
laser.setFrequencyMultiplication(omero.rtypes.rint(1));
laser.setPockelCell(omero.rtypes.rbool(false));
laser.setTuneable(omero.rtypes.rbool(true));
laser.setWavelength(omero.rtypes.rint(500));
laser.setPower(omero.rtypes.rdouble(1));
laser.setRepetitionRate(omero.rtypes.rdouble(1));
return laser;
}
/**
* Creates a pixels object.
*
* @param sizeX The size along the X-axis.
* @param sizeY The size along the Y-axis.
* @param sizeZ The number of Z-sections.
* @param sizeT The number of time-points.
* @param sizeC The number of channels.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Pixels createPixels(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC)
throws Exception {
List<IObject> types = pixelsService.getAllEnumerations(PixelsType.class.getName());
Iterator<IObject> i = types.iterator();
PixelsType object;
PixelsType type = null;
while (i.hasNext()) {
object = (PixelsType) i.next();
if (UINT16.equals(object.getValue().getValue())) {
type = object;
break;
}
}
if (type == null) type = (PixelsType) types.get(0);
types = pixelsService.getAllEnumerations(DimensionOrder.class.getName());
i = types.iterator();
DimensionOrder o;
DimensionOrder order = null;
while (i.hasNext()) {
o = (DimensionOrder) i.next();
if (XYZCT.equals(o.getValue().getValue())) {
order = o;
break;
}
}
if (order == null) order = (DimensionOrder) types.get(0);
Pixels pixels = new PixelsI();
pixels.setPhysicalSizeX(omero.rtypes.rdouble(1.0));
pixels.setPhysicalSizeY(omero.rtypes.rdouble(1.0));
pixels.setPhysicalSizeZ(omero.rtypes.rdouble(1.0));
pixels.setSizeX(omero.rtypes.rint(sizeX));
pixels.setSizeY(omero.rtypes.rint(sizeY));
pixels.setSizeZ(omero.rtypes.rint(sizeZ));
pixels.setSizeT(omero.rtypes.rint(sizeT));
pixels.setSizeC(omero.rtypes.rint(sizeC));
pixels.setSha1(omero.rtypes.rstring("Pending..."));
pixels.setPixelsType(type);
pixels.setDimensionOrder(order);
List<Channel> channels = new ArrayList<Channel>();
for (int j = 0; j < sizeC; j++) {
channels.add(createChannel(j));
}
pixels.addAllChannelSet(channels);
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
PlaneInfo info = new PlaneInfoI();
pixels.addPlaneInfo(createPlaneInfo(z, t, c));
}
}
}
return pixels;
}
/**
* Creates and returns the settings of the specified source of light.
*
* @param light The light to link the settings to.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public LightSettings createLightSettings(LightSource light) throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types =
pixelsService.getAllEnumerations(MicrobeamManipulationType.class.getName());
LightSettings settings = new LightSettingsI();
settings.setLightSource(light);
settings.setAttenuation(omero.rtypes.rdouble(1));
MicrobeamManipulation mm = new MicrobeamManipulationI();
mm.setType((MicrobeamManipulationType) types.get(0));
Experiment exp = new ExperimentI();
types = pixelsService.getAllEnumerations(ExperimentType.class.getName());
exp.setType((ExperimentType) types.get(0));
mm.setExperiment(exp);
// settings.setMicrobeamManipulation(mm);
settings.setWavelength(omero.rtypes.rint(500));
return settings;
}
/**
* Creates and returns the settings of the specified objective.
*
* @param objective The objective to link the settings to.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public ObjectiveSettings createObjectiveSettings(Objective objective) throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(Medium.class.getName());
ObjectiveSettings settings = new ObjectiveSettingsI();
settings.setCorrectionCollar(omero.rtypes.rdouble(1));
settings.setRefractiveIndex(omero.rtypes.rdouble(1));
settings.setMedium((Medium) types.get(0));
settings.setObjective(objective);
return settings;
}
/**
* Creates and returns a filament. This will have to be linked to an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Arc createArc() throws Exception {
List<IObject> types = pixelsService.getAllEnumerations(ArcType.class.getName());
Arc arc = new ArcI();
arc.setManufacturer(omero.rtypes.rstring("manufacturer"));
arc.setModel(omero.rtypes.rstring("model"));
arc.setPower(omero.rtypes.rdouble(1));
arc.setSerialNumber(omero.rtypes.rstring("serial number"));
arc.setLotNumber(omero.rtypes.rstring("lot number"));
arc.setType((ArcType) types.get(0));
return arc;
}
/**
* Creates and returns a filament. This will have to be linked to an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Filament createFilament() throws Exception {
List<IObject> types = pixelsService.getAllEnumerations(FilamentType.class.getName());
Filament filament = new FilamentI();
filament.setManufacturer(omero.rtypes.rstring("manufacturer"));
filament.setModel(omero.rtypes.rstring("model"));
filament.setPower(omero.rtypes.rdouble(1));
filament.setSerialNumber(omero.rtypes.rstring("serial number"));
filament.setLotNumber(omero.rtypes.rstring("lot number"));
filament.setType((FilamentType) types.get(0));
return filament;
}
/**
* Creates a channel.
*
* @param w The wavelength in nanometers.
* @return See Above.
* @throws Exception
*/
public Channel createChannel(int w) throws Exception {
Channel channel = new ChannelI();
LogicalChannel lc = new LogicalChannelI();
lc.setEmissionWave(omero.rtypes.rint(200));
List<IObject> types = pixelsService.getAllEnumerations(ContrastMethod.class.getName());
ContrastMethod cm = (ContrastMethod) types.get(0);
types = pixelsService.getAllEnumerations(Illumination.class.getName());
Illumination illumination = (Illumination) types.get(0);
types = pixelsService.getAllEnumerations(AcquisitionMode.class.getName());
AcquisitionMode mode = (AcquisitionMode) types.get(0);
lc.setContrastMethod(cm);
lc.setIllumination(illumination);
lc.setMode(mode);
channel.setLogicalChannel(lc);
StatsInfo info = new StatsInfoI();
info.setGlobalMin(omero.rtypes.rdouble(0.0));
info.setGlobalMax(omero.rtypes.rdouble(1.0));
channel.setStatsInfo(info);
return channel;
}
/**
* Creates and returns an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Instrument createInstrument() throws Exception {
List<IObject> types = pixelsService.getAllEnumerations(MicroscopeType.class.getName());
Instrument instrument = new InstrumentI();
MicroscopeI microscope = new MicroscopeI();
microscope.setManufacturer(omero.rtypes.rstring("manufacturer"));
microscope.setModel(omero.rtypes.rstring("model"));
microscope.setSerialNumber(omero.rtypes.rstring("serial number"));
microscope.setLotNumber(omero.rtypes.rstring("lot number"));
microscope.setType((MicroscopeType) types.get(0));
instrument.setMicroscope(microscope);
return instrument;
}
/**
* Creates and returns the settings of the specified detector.
*
* @param detector The detector to link the settings to.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
DetectorSettings createDetectorSettings(Detector detector) throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(Binning.class.getName());
DetectorSettings settings = new DetectorSettingsI();
settings.setBinning((Binning) types.get(0));
settings.setDetector(detector);
settings.setGain(omero.rtypes.rdouble(1));
settings.setOffsetValue(omero.rtypes.rdouble(1));
settings.setReadOutRate(omero.rtypes.rdouble(1));
settings.setVoltage(omero.rtypes.rdouble(1));
return settings;
}
/**
* Creates and returns an objective. This will have to be linked to an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Objective createObjective() throws Exception {
Objective objective = new ObjectiveI();
objective.setManufacturer(omero.rtypes.rstring("manufacturer"));
objective.setModel(omero.rtypes.rstring("model"));
objective.setSerialNumber(omero.rtypes.rstring("serial number"));
objective.setLotNumber(omero.rtypes.rstring("lot number"));
objective.setCalibratedMagnification(omero.rtypes.rdouble(1));
// correction
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(Correction.class.getName());
objective.setCorrection((Correction) types.get(0));
// immersion
types = pixelsService.getAllEnumerations(Immersion.class.getName());
objective.setImmersion((Immersion) types.get(0));
objective.setIris(omero.rtypes.rbool(true));
objective.setLensNA(omero.rtypes.rdouble(0.5));
objective.setNominalMagnification(omero.rtypes.rdouble(1));
objective.setWorkingDistance(omero.rtypes.rdouble(1));
return objective;
}
/**
* Creates an Optical Transfer Function object.
*
* @param filterSet The filter set linked to it.
* @param objective The objective linked to it.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public OTF createOTF(FilterSet filterSet, Objective objective) throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(PixelsType.class.getName());
OTF otf = new OTFI();
otf.setFilterSet(filterSet);
otf.setObjective(objective);
otf.setPath(omero.rtypes.rstring("/OMERO"));
otf.setOpticalAxisAveraged(omero.rtypes.rbool(true));
otf.setPixelsType((PixelsType) types.get(0));
otf.setSizeX(omero.rtypes.rint(10));
otf.setSizeY(omero.rtypes.rint(10));
return otf;
}
/**
* Creates and returns a detector. This will have to be linked to an instrument.
*
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Detector createDetector() throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(DetectorType.class.getName());
Detector detector = new DetectorI();
detector.setAmplificationGain(omero.rtypes.rdouble(0));
detector.setGain(omero.rtypes.rdouble(1));
detector.setManufacturer(omero.rtypes.rstring("manufacturer"));
detector.setModel(omero.rtypes.rstring("model"));
detector.setSerialNumber(omero.rtypes.rstring("serial number"));
detector.setLotNumber(omero.rtypes.rstring("lot number"));
detector.setOffsetValue(omero.rtypes.rdouble(0));
detector.setType((DetectorType) types.get(0));
return detector;
}
/**
* Creates and returns a filter. This will have to be linked to an instrument.
*
* @param cutIn The cut in value.
* @param cutOut The cut out value.
* @return See above.
* @throws Exception Thrown if an error occurred.
*/
public Filter createFilter(int cutIn, int cutOut) throws Exception {
// already tested see PixelsService enumeration.
List<IObject> types = pixelsService.getAllEnumerations(FilterType.class.getName());
Filter filter = new FilterI();
filter.setLotNumber(omero.rtypes.rstring("lot number"));
filter.setSerialNumber(omero.rtypes.rstring("serial number"));
filter.setManufacturer(omero.rtypes.rstring("manufacturer"));
filter.setModel(omero.rtypes.rstring("model"));
filter.setType((FilterType) types.get(0));
TransmittanceRangeI transmittance = new TransmittanceRangeI();
transmittance.setCutIn(omero.rtypes.rint(cutIn));
transmittance.setCutOut(omero.rtypes.rint(cutOut));
transmittance.setCutInTolerance(omero.rtypes.rint(1));
transmittance.setCutOutTolerance(omero.rtypes.rint(1));
filter.setTransmittanceRange(transmittance);
return filter;
}
/**
* Creates a new image with one channel from a source image.
*
* @param info The information about the data to handle.
*/
private void CreateNewImage(ConfigurationInfo info) throws Exception {
PixelsData pixels = image.getDefaultPixels();
int sizeZ = pixels.getSizeZ();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
int sizeX = pixels.getSizeX();
int sizeY = pixels.getSizeY();
long pixelsId = pixels.getId();
if (sizeC <= 1) throw new Exception("The image must have at least 2 channels.");
RawPixelsStorePrx store = null;
// Create a new image.
Map<Integer, byte[]> map = new LinkedHashMap<Integer, byte[]>();
try {
store = connector.getRawPixelsStore();
store.setPixelsId(pixelsId, false);
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
byte[] planeC1 = store.getPlane(z, 0, t);
byte[] planeC2 = store.getPlane(z, 1, t);
byte[] newPlane = new byte[planeC1.length];
for (int i = 0; i < planeC1.length; i++) {
newPlane[i] = (byte) ((planeC1[i] + planeC2[i]) / 2);
}
map.put(linearize(z, t, sizeZ), newPlane);
}
}
} catch (Exception e) {
throw new Exception("Cannot retrieve the plane", e);
} finally {
if (store != null) store.close();
}
// Now we are going to create the new image.
IPixelsPrx proxy = connector.getPixelsService();
List<IObject> l = proxy.getAllEnumerations(PixelsType.class.getName());
Iterator<IObject> i = l.iterator();
PixelsType type = null;
String original = pixels.getPixelType();
while (i.hasNext()) {
PixelsType o = (PixelsType) i.next();
String value = o.getValue().getValue();
if (value.equals(original)) {
type = o;
break;
}
}
if (type == null) throw new Exception("Pixels Type not valid.");
String name = "newImageFrom" + image.getId();
RLong idNew =
proxy.createImage(
sizeX,
sizeY,
sizeZ,
sizeT,
Arrays.asList(0),
type,
name,
"From Image ID: " + image.getId());
if (idNew == null) throw new Exception("New image could not be created.");
ImageData newImage = loadImage(idNew.getValue());
// link the new image and the dataset hosting the source image.
DatasetImageLink link = new DatasetImageLinkI();
link.setParent(new DatasetI(info.getDatasetId(), false));
link.setChild(new ImageI(newImage.getId(), false));
connector.getUpdateService().saveAndReturnObject(link);
// Write the data.
try {
store = connector.getRawPixelsStore();
store.setPixelsId(newImage.getDefaultPixels().getId(), false);
int index = 0;
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
index = linearize(z, t, sizeZ);
store.setPlane(map.get(index), z, 0, t);
}
}
store.save();
System.err.println("image created");
} catch (Exception e) {
throw new Exception("Cannot set the plane", e);
} finally {
if (store != null) store.close();
}
}
