use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class RunRefSimulationOp method saveExternalData.
private static void saveExternalData(Image image, String varName, ExternalDataIdentifier newROIExtDataID, LocalWorkspace localWorkspace) throws ObjectNotFoundException, ImageException, IOException {
Extent extent = image.getExtent();
Origin origin = image.getOrigin();
ISize isize = image.getISize();
VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
int NumTimePoints = 1;
int NumChannels = 1;
// dimensions: time points, channels, whole image ordered by z slices.
double[][][] pixData = new double[NumTimePoints][NumChannels][];
pixData[0][0] = image.getDoublePixels();
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = simpleCartesianMesh;
fdos.doubleSpecData = pixData;
fdos.specEDI = newROIExtDataID;
fdos.varNames = new String[] { varName };
fdos.owner = LocalWorkspace.getDefaultOwner();
fdos.times = new double[] { 0.0 };
fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
fdos.origin = origin;
fdos.extent = extent;
fdos.isize = isize;
localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class DisplayImageOp method displayImage.
public void displayImage(final Image image, String title, WindowListener listener) {
final ImagePlaneManagerPanel imagePanel = new ImagePlaneManagerPanel();
double[] doublePixels = image.getDoublePixels();
double minPixel = Double.MAX_VALUE;
double maxPixel = -Double.MAX_VALUE;
for (int i = 0; i < doublePixels.length; i++) {
double pixel = doublePixels[i];
doublePixels[i] = pixel;
minPixel = Math.min(minPixel, pixel);
maxPixel = Math.max(maxPixel, pixel);
}
Range newRange = new Range(minPixel, maxPixel);
SourceDataInfo source = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, doublePixels, image.getExtent(), image.getOrigin(), newRange, 0, image.getNumX(), 1, image.getNumY(), image.getNumX(), image.getNumZ(), image.getNumX() * image.getNumY());
imagePanel.setDisplayAdapterServicePanelVisible(true);
imagePanel.setCurveValueProvider(new CurveValueProvider() {
@Override
public void curveAdded(Curve curve) {
System.out.println("called curveAdded(" + curve + "), do nothing for now");
}
@Override
public void curveRemoved(Curve curve) {
System.out.println("called curveRemoved(" + curve + ")");
}
@Override
public String getCurveValue(CurveSelectionInfo csi) {
System.out.println("called getCurveValue(CurveSelectionInfo " + csi);
return null;
}
@Override
public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
System.out.println("called getInitialCurveSelection(tool=" + tool + ", coord=" + wc + ")");
return null;
}
@Override
public boolean isAddControlPointOK(int tool, Coordinate wc, Curve addedToThisCurve) {
System.out.println("called isAddControlPointOK");
return true;
}
@Override
public boolean providesInitalCurve(int tool, Coordinate wc) {
System.out.println("called providesInitialCurve(tool=" + tool + " (TOOL_LINE=" + CurveEditorTool.TOOL_LINE + "), coord=" + wc);
return false;
}
@Override
public void setDescription(Curve curve) {
System.out.println("called setDescription(" + curve + ")");
curve.setDescription(CurveValueProvider.DESCRIPTION_VOLUME);
}
@Override
public CurveSelectionInfo findChomboCurveSelectionInfoForPoint(CoordinateIndex ci) {
System.out.println("called find ChomboCurveSelectionInfoForPoint(coord=" + ci + ")");
return null;
}
});
DisplayAdapterService das = imagePanel.getDisplayAdapterServicePanel().getDisplayAdapterService();
das.setValueDomain(null);
das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createGraySpecialColors(), DisplayAdapterService.GRAY);
das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), DisplayAdapterService.BLUERED);
das.setActiveColorModelID(DisplayAdapterService.BLUERED);
final JFrame jframe = new JFrame();
jframe.setTitle(title);
JPanel panel = new JPanel();
panel.setLayout(new GridBagLayout());
GridBagConstraints imageConstraints = new GridBagConstraints();
imageConstraints.gridx = 0;
imageConstraints.gridy = 0;
imageConstraints.weightx = 1.0;
imageConstraints.weighty = 1.0;
imageConstraints.fill = GridBagConstraints.BOTH;
panel.add(imagePanel, imageConstraints);
JButton plotButton = new JButton("plot");
plotButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
Curve curve = imagePanel.getCurveRenderer().getSelection().getCurve();
VariableType variableType = VariableType.VOLUME;
Curve samplerCurve = curve.getSampledCurve();
samplerCurve.setDescription(curve.getDescription());
VCImage vcImage = new VCImageUncompressed(null, new byte[image.getISize().getXYZ()], image.getExtent(), image.getISize().getX(), image.getISize().getY(), image.getISize().getZ());
int dimension = 1 + (image.getISize().getY() > 0 ? 1 : 0) + (image.getISize().getZ() > 0 ? 1 : 0);
RegionImage regionImage = new RegionImage(vcImage, dimension, image.getExtent(), image.getOrigin(), RegionImage.NO_SMOOTHING);
CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(image.getOrigin(), image.getExtent(), image.getISize(), regionImage);
SpatialSelectionVolume ssVolume = new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), variableType, mesh);
String varName = "var";
SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[] { new VolVariable(varName, null) };
PlotData plotData = getLineScan(ssVolume, image, mesh);
PlotPane plotPane = new PlotPane();
DataSymbolMetadataResolver resolver = null;
Plot2D plot2D = new Plot2D(symbolTableEntries, resolver, new String[] { varName }, new PlotData[] { plotData }, new String[] { "Values along curve", "Distance (\u00b5m)", "[" + varName + "]" });
plotPane.setPlot2D(plot2D);
DialogUtils.showComponentCloseDialog(jframe, plotPane, "plot");
} catch (ImageException | IOException | DataAccessException | MathException e1) {
e1.printStackTrace();
}
}
});
GridBagConstraints plotButtonConstraints = new GridBagConstraints();
plotButtonConstraints.gridx = 0;
plotButtonConstraints.gridy = 1;
panel.add(plotButton, plotButtonConstraints);
jframe.getContentPane().add(panel);
jframe.setSize(500, 500);
jframe.addWindowListener(listener);
jframe.setVisible(true);
imagePanel.setSourceDataInfo(source);
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class DisplayTimeSeriesOp method getDataSetControllerProvider.
private DataSetControllerProvider getDataSetControllerProvider(final ImageTimeSeries<? extends Image> imageTimeSeries, final PDEDataViewer pdeDataViewer) throws ImageException, IOException {
ISize size = imageTimeSeries.getISize();
int dimension = (size.getZ() > 0) ? (3) : (2);
Extent extent = imageTimeSeries.getExtent();
Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
// don't care ... no surfaces
double filterCutoffFrequency = 0.5;
VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
final DataSetController dataSetController = new DataSetController() {
@Override
public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_START, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
if (!timeSeriesJobSpec.isCalcSpaceStats() && !timeSeriesJobSpec.isCalcTimeStats()) {
int[][] indices = timeSeriesJobSpec.getIndices();
double[] timeStamps = imageTimeSeries.getImageTimeStamps();
// [var][dataindex+1][timeindex]
double[][][] dataValues = new double[1][indices[0].length + 1][timeStamps.length];
for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
// index 0 is time
dataValues[0][0][timeIndex] = timeStamps[timeIndex];
}
for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
float[] pixelValues = imageTimeSeries.getAllImages()[timeIndex].getFloatPixels();
for (int samplePointIndex = 0; samplePointIndex < indices[0].length; samplePointIndex++) {
int pixelIndex = indices[0][samplePointIndex];
dataValues[0][samplePointIndex + 1][timeIndex] = pixelValues[pixelIndex];
}
}
TSJobResultsNoStats timeSeriesJobResults = new TSJobResultsNoStats(new String[] { "var" }, indices, timeStamps, dataValues);
pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_COMPLETE, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
return timeSeriesJobResults;
}
return null;
}
@Override
public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
double timePoint = time;
double[] timePoints = getDataSetTimes(vcdataID);
int index = -1;
for (int i = 0; i < timePoints.length; i++) {
if (timePoint == timePoints[i]) {
index = i;
break;
}
}
double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
VariableType varType = VariableType.VOLUME;
return new SimDataBlock(pdeDataInfo, data, varType);
}
@Override
public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return false;
}
@Override
public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
return null;
}
@Override
public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return null;
}
@Override
public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return mesh;
}
@Override
public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
return new AnnotatedFunction[0];
}
@Override
public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return imageTimeSeries.getImageTimeStamps();
}
@Override
public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
return new DataIdentifier[] { dataIdentifier };
}
@Override
public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
throw new RuntimeException("not yet implemented");
}
@Override
public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
throw new RuntimeException("not yet implemented");
}
@Override
public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
// TODO Auto-generated method stub
return null;
}
@Override
public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
// TODO Auto-generated method stub
return null;
}
@Override
public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
// TODO Auto-generated method stub
return null;
}
};
DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {
@Override
public DataSetController getDataSetController() throws DataAccessException {
return dataSetController;
}
};
return dataSetControllerProvider;
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class VFrapXmlHelper method LoadVFrapSpecialImages.
// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
//
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
//
// Locate the special images within the vFrap files and load them in memory
//
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
// ------ parse the vfrap file and the log/zip files referred within -----
// many channels of 1 timepoint each
int NumTimePoints = 1;
// the channels: prebleach, postbleach, roi1, roi2 ... roiN
int NumChannels = tokenNames.length;
String[] channelNames = new String[NumChannels];
VariableType[] channelTypes = new VariableType[NumChannels];
DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
double[][][] pixData = new double[NumTimePoints][NumChannels][];
// get the path of the file tagged with "ROIExternalDataInfoTag" and open it
Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
if (roiExternalDataInfoElement == null) {
// can't load FieldData for some reason, fall back to importing the biomodel only
return false;
}
// <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
// <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
// </ImageDatasetExternalDataInfo>
// c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
if (childElement == null) {
// can't load FieldData for some reason, fall back to importing the biomodel only
return false;
}
StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
final ArrayList<String> tokenArray = new ArrayList<String>();
while (tokens.hasMoreElements()) {
tokenArray.add(tokens.nextToken());
}
final String dataID = tokenArray.get(tokenArray.size() - 2);
final String userName = tokenArray.get(tokenArray.size() - 3);
VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {
public String getID() {
return dataID;
}
public KeyValue getDataKey() {
return null;
}
public User getOwner() {
return new User(userName, new KeyValue("123345432334"));
}
};
// ------- recover simulation data for this user name, load the images in memory ------------
// ex c:\\VirtualMicroscopy\\SimulationData
String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
File userDir = new File(userDirName);
SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
// build a valid mesh in 2 steps, what we have in simData is incomplete
CartesianMesh incompleteMesh = simData.getMesh();
Extent extent = incompleteMesh.getExtent();
ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
Origin origin = new Origin(0, 0, 0);
CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
double[] times = simData.getDataTimes();
for (int i = 0; i < dataIdentifiers.length; i++) {
// ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
System.out.println(dataIdentifiers[i].getName());
for (double time : times) {
// this loops only once, we have just 1 timepoint for each "special" image
SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
channelNames[i] = dataIdentifiers[i].getName();
channelTypes[i] = VariableType.VOLUME;
channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
pixData[0][i] = simDataBlock.getData();
// var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
// show a few
for (int j = 0; j < 5; j++) {
System.out.print(pixData[0][i][j] + " ");
}
// show a few
;
// show a few
System.out.println(" ... ");
}
}
hashTable.put("mesh", mesh);
hashTable.put("pixData", pixData);
hashTable.put("channelNames", channelNames);
hashTable.put("channelTypes", channelTypes);
hashTable.put("channelVFrapImageType", channelVFrapImageType);
return true;
}
use of cbit.image.VCImageUncompressed in project vcell by virtualcell.
the class PointSpreadFunctionManagement method importPointSpreadFunction.
public void importPointSpreadFunction() {
AsynchClientTask[] taskArray = new AsynchClientTask[3];
// select the desired PSF file
taskArray[0] = new AsynchClientTask("Select a file", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
ChoosePSFFile(hashTable);
}
};
// create and save the field data object
taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
Component requesterComponent = parentWindow;
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (documentManager == null) {
throw new RuntimeException("Not connected to server.");
}
// the following line of code may modify initialFieldDataName
// normal file name
checkNameAvailability(hashTable, false, documentManager, requesterComponent);
File filePSF = (File) hashTable.get("filePSF");
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ImageDataset imageDataset = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(filePSF.getAbsolutePath(), null);
Extent extent = imageDataset.getExtent();
ISize isize = imageDataset.getISize();
Origin origin = new Origin(0, 0, 0);
CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
// save field data
int NumTimePoints = imageDataset.getImageTimeStamps().length;
int NumChannels = 1;
double[][][] pixData = new double[NumTimePoints][NumChannels][];
for (int i = 0; i < NumTimePoints; i++) {
// images according to zIndex at specific time points(tIndex)
short[] originalData = imageDataset.getPixelsZ(0, i);
double[] doubleData = new double[originalData.length];
for (int j = 0; j < originalData.length; j++) {
doubleData[j] = 0x0000ffff & originalData[j];
}
pixData[i][NumChannels - 1] = doubleData;
}
FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
// try {
// fdos = ClientRequestManager.createFDOSFromImageFile(filePSF, false, null);
// } catch (DataFormatException ex) {
// throw new Exception("Cannot read image " + filePSF.getAbsolutePath()+"\n"+ex.getMessage());
// }
fdos.owner = documentManager.getUser();
fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
fdos.cartesianMesh = cartesianMesh;
fdos.doubleSpecData = pixData;
fdos.specEDI = null;
fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
fdos.times = imageDataset.getImageTimeStamps();
fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
fdos.origin = origin;
fdos.extent = extent;
fdos.isize = isize;
ExternalDataIdentifier pSFImageEDI = documentManager.saveFieldData(fdos, initialFieldDataName);
hashTable.put("pSFImageEDI", pSFImageEDI);
}
};
// create a data symbol for the PSF image saved above as field data
taskArray[2] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
// --- create the data symbols associated with the time series
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ExternalDataIdentifier pSFImageEDI = (ExternalDataIdentifier) hashTable.get("pSFImageEDI");
String fluorName = "psf_" + initialFieldDataName;
DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.POINT_SPREAD_FUNCTION, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), pSFImageEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), 0D);
simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
}
};
Hashtable<String, Object> hash = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(parentWindow, hash, taskArray, false, true, null);
}
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