Examples with ISize org.vcell.util.ISize used on opensource projects

Example 36 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method resizeDataset.

private void resizeDataset() {
    final ISize currentISize = new ISize(roiComposite[0].getWidth(), roiComposite[0].getHeight(), roiComposite.length);
    ImageSizeInfo origImageSizeInfo = new ImageSizeInfo(null, currentISize, 0, new double[] { 0 }, 0);
    ImageSizeInfo newImageSizeInfo = null;
    try {
        newImageSizeInfo = ClientRequestManager.queryImageResize(overlayEditorPanelJAI, origImageSizeInfo, false);
    } catch (UserCancelException e) {
        return;
    }
    final ISize newImageSize = newImageSizeInfo.getiSize();
    AsynchClientTask resizeTask = new AsynchClientTask("Resizing...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            resizeImpl(ResizeInfo.createScaleResizeInfo(currentISize, newImageSize), getClientTaskStatusSupport());
        }
    };
    final AsynchClientTask updatePanelTask = getUpdateDisplayAfterCropTask();
    ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { resizeTask, updatePanelTask }, false, false, null, true);
}

Example 37 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class RunRefSimulationFastOp method runRefSimulation.

private RowColumnResultSet runRefSimulation(ROI cellROI, ROI[] imageDataROIs, UShortImage psf, FloatImage initRefConc, double experimentalRecoveryTime, LocalWorkspace localWorkspace, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    // 
    // save first image from normalized time series as the initial concentration field data
    // 
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    // 
    // save ROIs as a multivariate field data
    // 
    ExternalDataInfo roiExtData = createNewExternalDataInfo(localWorkspace, ROI_EXTDATA_NAME);
    saveROIsAsExternalData(imageDataROIs, localWorkspace, roiExtData.getExternalDataIdentifier());
    ArrayList<FieldFunctionArguments> roiFFAs = new ArrayList<FieldFunctionArguments>();
    for (ROI roi : imageDataROIs) {
        roiFFAs.add(new FieldFunctionArguments(ROI_EXTDATA_NAME, ROI_MASK_NAME_PREFIX + roi.getROIName(), new Expression(0.0), VariableType.VOLUME));
    }
    // 
    // save PSF as a field data
    // 
    ExternalDataInfo psfExtData = createNewExternalDataInfo(localWorkspace, PSF_EXTDATA_NAME);
    savePsfAsExternalData(psf, PSF_EXTDATA_VARNAME, psfExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments psfFFA = new FieldFunctionArguments(PSF_EXTDATA_NAME, PSF_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    TimeBounds timeBounds = getEstimatedRefTimeBound(experimentalRecoveryTime);
    double timeStepVal = REFERENCE_DIFF_DELTAT;
    Expression chirpedDiffusionRate = new Expression(REFERENCE_DIFF_RATE_COEFFICIENT + "*(t+" + REFERENCE_DIFF_DELTAT + ")");
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), psfFFA, chirpedDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    Simulation simulation = bioModel.getSimulation(0);
    ROIDataGenerator roiDataGenerator = getROIDataGenerator(localWorkspace, imageDataROIs);
    simulation.getMathDescription().getPostProcessingBlock().addDataGenerator(roiDataGenerator);
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, initialConcentrationExtData.getExternalDataIdentifier(), roiExtData.getExternalDataIdentifier(), psfExtData.getExternalDataIdentifier(), progressListener, true);
    KeyValue referenceSimKeyValue = simulation.getVersion().getVersionKey();
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(referenceSimKeyValue, LocalWorkspace.getDefaultOwner());
    VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, 0);
    File hdf5File = new File(localWorkspace.getDefaultSimDataDirectory(), vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
    // get post processing info (time points, variable sizes)
    DataOperation.DataProcessingOutputInfoOP dataOperationInfo = new DataOperation.DataProcessingOutputInfoOP(null, /*no vcDataIdentifier OK*/
    false, null);
    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(dataOperationInfo, hdf5File);
    // get post processing data
    DataOperation.DataProcessingOutputDataValuesOP dataOperationDataValues = new DataOperation.DataProcessingOutputDataValuesOP(null, /*no vcDataIdentifier OK*/
    ROI_EXTDATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null);
    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataOperationDataValues, hdf5File);
    // 
    // delete the simulation files
    // 
    // 
    // remove reference simulation files and field data files
    // 
    File userDir = new File(localWorkspace.getDefaultSimDataDirectory());
    File[] oldSimFilesToDelete = getSimulationFileNames(userDir, referenceSimKeyValue);
    for (int i = 0; oldSimFilesToDelete != null && i < oldSimFilesToDelete.length; i++) {
        oldSimFilesToDelete[i].delete();
    }
    deleteCanonicalExternalData(localWorkspace, initialConcentrationExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    // get ref sim time points (distorted by time dilation acceleration)
    double[] rawRefDataTimePoints = dataProcessingOutputInfo.getVariableTimePoints();
    // get shifted time points
    double[] correctedRefDataTimePoints = shiftTimeForBaseDiffRate(rawRefDataTimePoints);
    double[][] refData = dataProcessingOutputDataValues.getDataValues();
    // 
    // for rowColumnResultSet with { "t", "roi1", .... , "roiN" } for reference data
    // 
    int numROIs = imageDataROIs.length;
    String[] columnNames = new String[numROIs + 1];
    columnNames[0] = "t";
    for (int i = 0; i < numROIs; i++) {
        columnNames[i + 1] = imageDataROIs[i].getROIName();
    }
    RowColumnResultSet reducedData = new RowColumnResultSet(columnNames);
    for (int i = 0; i < correctedRefDataTimePoints.length; i++) {
        double[] row = new double[numROIs + 1];
        row[0] = correctedRefDataTimePoints[i];
        double[] roiData = refData[i];
        for (int j = 0; j < numROIs; j++) {
            // roiData[0] is the average over the cell .. postbleach this shouldn't change for pure diffusion
            row[j + 1] = roiData[j + 1];
        }
        reducedData.addRow(row);
    }
    return reducedData;
}

Example 38 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class RunRefSimulationFastOp method saveROIsAsExternalData.

private void saveROIsAsExternalData(ROI[] rois, LocalWorkspace localWorkspace, ExternalDataIdentifier newROIExtDataID) throws ObjectNotFoundException, ImageException, IOException {
    ISize isize = rois[0].getISize();
    Origin origin = rois[0].getRoiImages()[0].getOrigin();
    Extent extent = rois[0].getRoiImages()[0].getExtent();
    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 cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    int NumTimePoints = 1;
    int NumChannels = rois.length;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    int index = 0;
    for (ROI roi : rois) {
        pixData[0][index++] = createDoubleArray(roi.getBinaryPixelsXYZ(1));
    }
    // Origin origin = new Origin(0,0,0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    ArrayList<String> varNames = new ArrayList<String>();
    ArrayList<VariableType> varTypes = new ArrayList<VariableType>();
    for (ROI roi : rois) {
        varNames.add(ROI_MASK_NAME_PREFIX + roi.getROIName());
        varTypes.add(VariableType.VOLUME);
    }
    fdos.varNames = varNames.toArray(new String[0]);
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = varTypes.toArray(new VariableType[0]);
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 39 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class RunRefSimulationFastOp method savePsfAsExternalData.

private void savePsfAsExternalData(UShortImage psf, String varName, ExternalDataIdentifier newPsfExtDataID, LocalWorkspace localWorkspace) throws IOException, ImageException, ObjectNotFoundException {
    Origin origin = new Origin(0, 0, 0);
    Extent ext = new Extent(1, 1, 1);
    ISize isize = new ISize(3, 3, 1);
    VCImageUncompressed vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ());
    RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
    CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, regionImage);
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psf.getPixels();
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.shortSpecData = pixData;
    fdos.specEDI = newPsfExtDataID;
    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 = ext;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 40 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class RunSimulation2DOp method runRefSimulation.

public ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, String varName, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, varName, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}