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

Example 56 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 57 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 58 with ISize

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

the class FitTimeSeries method fitToGaussian.

static GaussianFitResults fitToGaussian(double init_center_i, double init_center_j, double init_radius2, FloatImage image) {
    // 
    // do some optimization on the image (fitting to a Gaussian)
    // set initial guesses from ROI operation.
    // 
    ISize imageSize = image.getISize();
    final int num_i = imageSize.getX();
    final int num_j = imageSize.getY();
    final float[] floatPixels = image.getFloatPixels();
    // 
    // initial guess based on previous fit of ROI
    // do gaussian fit in index space for center and standard deviation (later to translate it back to world coordinates)
    // 
    final int window_size = (int) Math.sqrt(init_radius2) * 4;
    // final int window_min_i = 0;       // (int) Math.max(0, Math.floor(init_center_i - window_size/2));
    // final int window_max_i = num_i-1; // (int) Math.min(num_i-1, Math.ceil(init_center_i + window_size/2));
    // final int window_min_j = 0;       // (int) Math.max(0, Math.floor(init_center_j - window_size/2));
    // final int window_max_j = num_j-1; // (int) Math.min(num_j-1, Math.ceil(init_center_j + window_size/2));
    final int window_min_i = (int) Math.max(0, Math.floor(init_center_i - window_size / 2));
    final int window_max_i = (int) Math.min(num_i - 1, Math.ceil(init_center_i + window_size / 2));
    final int window_min_j = (int) Math.max(0, Math.floor(init_center_j - window_size / 2));
    final int window_max_j = (int) Math.min(num_j - 1, Math.ceil(init_center_j + window_size / 2));
    final int PARAM_INDEX_CENTER_I = 0;
    final int PARAM_INDEX_CENTER_J = 1;
    final int PARAM_INDEX_K = 2;
    final int PARAM_INDEX_HIGH = 3;
    final int PARAM_INDEX_RADIUS_SQUARED = 4;
    final int NUM_PARAMETERS = 5;
    double[] initParameters = new double[NUM_PARAMETERS];
    initParameters[PARAM_INDEX_CENTER_I] = init_center_i;
    initParameters[PARAM_INDEX_CENTER_J] = init_center_j;
    initParameters[PARAM_INDEX_HIGH] = 1.0;
    initParameters[PARAM_INDEX_K] = 10;
    initParameters[PARAM_INDEX_RADIUS_SQUARED] = init_radius2;
    PowellOptimizer optimizer = new PowellOptimizer(1e-4, 1e-1);
    MultivariateFunction func = new MultivariateFunction() {

        @Override
        public double value(double[] point) {
            double center_i = point[PARAM_INDEX_CENTER_I];
            double center_j = point[PARAM_INDEX_CENTER_J];
            double high = point[PARAM_INDEX_HIGH];
            double K = point[PARAM_INDEX_K];
            double radius2 = point[PARAM_INDEX_RADIUS_SQUARED];
            double error2 = 0;
            for (int j = window_min_j; j <= window_max_j; j++) {
                // double y = j - center_j;
                double y = j;
                for (int i = window_min_i; i <= window_max_i; i++) {
                    // double x = i - center_i;
                    double x = i;
                    double modelValue = high - FastMath.exp(-K * FastMath.exp(-2 * (x * x + y * y) / radius2));
                    double imageValue = floatPixels[j * num_i + i];
                    double error = modelValue - imageValue;
                    error2 += error * error;
                }
            }
            System.out.println(new GaussianFitResults(center_i, center_j, radius2, K, high, error2));
            return error2;
        }
    };
    PointValuePair pvp = optimizer.optimize(new ObjectiveFunction(func), new InitialGuess(initParameters), new MaxEval(100000), GoalType.MINIMIZE);
    double[] fittedParamValues = pvp.getPoint();
    double fitted_center_i = fittedParamValues[PARAM_INDEX_CENTER_I];
    double fitted_center_j = fittedParamValues[PARAM_INDEX_CENTER_J];
    double fitted_radius2 = fittedParamValues[PARAM_INDEX_RADIUS_SQUARED];
    double fitted_K = fittedParamValues[PARAM_INDEX_K];
    double fitted_high = fittedParamValues[PARAM_INDEX_HIGH];
    double objectiveFunctionValue = pvp.getValue();
    return new GaussianFitResults(fitted_center_i, fitted_center_j, fitted_radius2, fitted_K, fitted_high, objectiveFunctionValue);
}

Example 59 with ISize

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

the class FitTimeSeries method fit.

public FitBleachSpotOpResults fit(ROI bleachROI, FloatImage normImage) {
    // 
    // find initial guess by centroid from bleach ROI and total area of bleach ROI (assuming a circle of radius R)
    // 
    int nonzeroPixelsCount = bleachROI.getNonzeroPixelsCount();
    ISize size = bleachROI.getISize();
    if (size.getZ() > 1) {
        throw new RuntimeException("expecting 2D bleach region ROI");
    }
    short[] pixels = bleachROI.getBinaryPixelsXYZ(1);
    long numPixelsInROI = 0;
    Extent extent = bleachROI.getRoiImages()[0].getExtent();
    double totalX_um = 0.0;
    double totalY_um = 0.0;
    double total_I = 0.0;
    double total_J = 0.0;
    int pixelIndex = 0;
    for (int i = 0; i < size.getX(); i++) {
        double x = extent.getX() * (i + 0.5) / (size.getX() - 1);
        for (int j = 0; j < size.getY(); j++) {
            if (pixels[pixelIndex] != 0) {
                double y = extent.getY() * (j + 0.5) / (size.getY() - 1);
                totalX_um += x;
                totalY_um += y;
                total_I += i;
                total_J += j;
                numPixelsInROI++;
            }
            pixelIndex++;
        }
    }
    Origin origin = bleachROI.getRoiImages()[0].getOrigin();
    double roiCenterX_um = origin.getX() + totalX_um / numPixelsInROI;
    double roiCenterY_um = origin.getY() + totalY_um / numPixelsInROI;
    double roiCenterI_pixelscale = total_I / numPixelsInROI;
    double roiCenterJ_pixelscale = total_J / numPixelsInROI;
    // Area = PI * R^2
    // R = sqrt(Area/PI)
    double roiBleachSpotArea_um2 = (extent.getX() * extent.getY() * numPixelsInROI) / (size.getX() * size.getY());
    double roiBleachRadius_um = Math.sqrt(roiBleachSpotArea_um2 / Math.PI);
    double roiBleachRadius_pixelscale = Math.sqrt(numPixelsInROI / Math.PI);
    FitBleachSpotOpResults results = new FitBleachSpotOpResults();
    results.bleachRadius_ROI = roiBleachRadius_um;
    results.centerX_ROI = roiCenterX_um;
    results.centerY_ROI = roiCenterY_um;
    GaussianFitResults gfresults = fitToGaussian(roiCenterI_pixelscale, roiCenterJ_pixelscale, roiBleachRadius_pixelscale * roiBleachRadius_pixelscale, normImage);
    results.bleachFactorK_GaussianFit = gfresults.K;
    results.bleachRadius_GaussianFit = Math.sqrt(gfresults.radius2);
    results.centerX_GaussianFit = origin.getX() + extent.getX() * (gfresults.centerI + 0.5) / size.getX();
    results.centerY_GaussianFit = origin.getY() + extent.getY() * (gfresults.centerJ + 0.5) / size.getY();
    return results;
}

Example 60 with ISize

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

the class ImageJHelper method vcellSendImage.

public static void vcellSendImage(final Component requester, final PDEDataContext pdeDataContext, SubVolume subvolume, Hashtable<SampledCurve, int[]>[] membraneTables, String description, double[] timePoints, String[] channelDescriptions, int[] colormap) throws Exception {
    // xyz, 1 time, 1 var
    final ImageJConnection[] imageJConnectionArr = new ImageJConnection[1];
    AsynchClientTask sendImageTask = new AsynchClientTask("Send image to ImageJ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                ImageJConnection imageJConnection = new ImageJConnection(ExternalCommunicator.IMAGEJ);
                imageJConnectionArr[0] = imageJConnection;
                imageJConnection.openConnection(VCellImageJCommands.vcellSendImage, description);
                // send size of the standard 5 dimensions in this order (width, height, nChannels, nSlices, nFrames)
                ISize xyzSize = pdeDataContext.getCartesianMesh().getISize();
                Extent extent = pdeDataContext.getCartesianMesh().getExtent();
                BasicStackDimensions basicStackDimensions = new BasicStackDimensions(xyzSize.getX(), xyzSize.getY(), xyzSize.getZ(), 1, 1);
                sendData0(imageJConnection, new HyperStackHelper(basicStackDimensions, extent, true, Float.class.getSimpleName(), null, new int[] { subvolume.getHandle() }, timePoints, channelDescriptions, colormap), pdeDataContext.getDataValues(), "'" + pdeDataContext.getVariableName() + "'" + pdeDataContext.getTimePoint());
                sendVolumeDomain0(imageJConnection, pdeDataContext.getCartesianMesh(), null, description);
                sendMembraneOutline(imageJConnection, membraneTables);
            } catch (Exception e) {
                if (e instanceof UserCancelException) {
                    throw e;
                }
                e.printStackTrace();
                hashTable.put("imagejerror", e);
            } finally {
                try {
                    if (imageJConnectionArr[0] != null) {
                        imageJConnectionArr[0].closeConnection();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<>(), new AsynchClientTask[] { sendImageTask }, false, true, new ProgressDialogListener() {

        @Override
        public void cancelButton_actionPerformed(EventObject newEvent) {
            if (imageJConnectionArr[0] != null) {
                imageJConnectionArr[0].closeConnection();
            }
        }
    });
}