Examples with ImageTimeSeries org.vcell.vmicro.workflow.data.ImageTimeSeries used on opensource projects

Example 1 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class ExportRawTimeSeriesToVFrap method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get inputs
    File outputFile = context.getData(vfrapFile);
    ImageTimeSeries imageTimeSeries = context.getData(rawTimeSeriesImages);
    // validate that imageTimeSeries is of type ImageTimeSeries<UShortImage>
    Image[] images = imageTimeSeries.getAllImages();
    UShortImage[] usImages = new UShortImage[images.length];
    for (int i = 0; i < usImages.length; i++) {
        if (!(images[i] instanceof UShortImage)) {
            throw new Exception("type mismatch, expecting only UShortImages in time series");
        }
        usImages[i] = (UShortImage) images[i];
    }
    ImageTimeSeries<UShortImage> ushortImageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, usImages, imageTimeSeries.getImageTimeStamps(), imageTimeSeries.getSizeZ());
    ExportRawTimeSeriesToVFrapOp op = new ExportRawTimeSeriesToVFrapOp();
    op.exportToVFRAP(outputFile, ushortImageTimeSeries, clientTaskStatusSupport);
    // write output (just boolean "done" flag)
    context.setData(written, true);
}

Example 2 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class GenerateReducedData method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ROI[] rois = context.getData(imageDataROIs);
    ImageTimeSeries<? extends Image> simData = (ImageTimeSeries<? extends Image>) context.getData(imageTimeSeries);
    // do op
    GenerateReducedDataOp op = new GenerateReducedDataOp();
    RowColumnResultSet reducedData = op.generateReducedData(simData, rois);
    // set output
    context.setData(reducedROIData, reducedData);
}

Example 3 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class WorkflowObjectsPanel method hasDisplayData.

private boolean hasDisplayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet || data instanceof ROI || data instanceof ProfileData[] || data instanceof Image || data instanceof ImageTimeSeries) {
            return true;
        }
    }
    return false;
}

Example 4 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class WorkflowObjectsPanel method displayData.

private void displayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet) {
            RowColumnResultSet rc = (RowColumnResultSet) data;
            try {
                new DisplayPlotOp().displayPlot(rc, title, listener);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        } else if (data instanceof ROI) {
            ROI roi = (ROI) data;
            Image image = roi.getRoiImages()[0];
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ProfileData[]) {
            ProfileData[] profileData = (ProfileData[]) data;
            new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(profileData, title, listener);
        } else if (data instanceof Image) {
            Image image = (Image) data;
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ImageTimeSeries) {
            ImageTimeSeries imageTimeSeries = (ImageTimeSeries) data;
            try {
                DisplayTimeSeries.displayImageTimeSeries(imageTimeSeries, title, listener);
            } catch (ImageException | IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 5 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class RunRefSimulationOp method runRefSimulation.

private static ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, ROI cellROI, double timeStepVal, TimeBounds timeBounds, FloatImage initRefConc, double baseDiffusionRate, ClientTaskStatusSupport progressListener) throws Exception {
    String INITCONC_EXTDATA_NAME = "initConc";
    String INITCONC_EXTDATA_VARNAME = "conc";
    String VAR_NAME = "species";
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    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);
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), baseDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), initialConcentrationExtData.getExternalDataIdentifier(), progressListener, true);
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    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, VAR_NAME, 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;
}