Examples with ROI cbit.vcell.VirtualMicroscopy.ROI used on opensource projects

Example 21 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class DisplayDependentROIs method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get inputs
    ROI[] imagerois = context.getData(imageROIs);
    ROI cellroi = context.getData(cellROI);
    String titleString = context.getDataWithDefault(title, "no title");
    // do op
    DisplayDependentROIsOp op = new DisplayDependentROIsOp();
    op.displayDependentROIs(imagerois, cellroi, titleString, null);
    // set output
    context.setData(displayed, true);
}

Example 22 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI 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 23 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI 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 24 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class GenerateNormalizedFrapData method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ImageTimeSeries<UShortImage> rawTimeSeries = context.getData(rawImageTimeSeries);
    ROI backgroundROI = context.getData(backgroundROI_2D);
    Integer indexPostbleach = context.getData(indexOfFirstPostbleach);
    // do op
    GenerateNormalizedFrapDataOp op = new GenerateNormalizedFrapDataOp();
    NormalizedFrapDataResults results = op.generate(rawTimeSeries, backgroundROI, indexPostbleach);
    // set output
    context.setData(normalizedFrapData, results.normalizedFrapData);
    context.setData(this.prebleachAverage, results.prebleachAverage);
}

Example 25 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class Generate2DSimBioModel method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get inputs
    Extent extent = context.getData(this.extent);
    ROI cellROI_2D = context.getData(this.cellROI_2D);
    double[] timeStamps = context.getData(this.timeStamps);
    Integer indexFirstPostbleach = context.getData(this.indexFirstPostbleach);
    double primaryDiffusionRate = context.getData(this.primaryDiffusionRate);
    double primaryFraction = context.getData(this.primaryFraction);
    double bleachMonitorRate = context.getData(this.bleachMonitorRate);
    Double secondaryDiffusionRate = context.getData(this.secondaryDiffusionRate);
    double secondaryFraction = context.getData(this.secondaryFraction);
    double bindingSiteConcentration = context.getData(this.bindingSiteConcentration);
    double bindingOnRate = context.getData(this.bindingOnRate);
    double bindingOffRate = context.getData(this.bindingOffRate);
    String extracellularName = context.getData(this.extracellularName);
    String cytosolName = context.getData(this.cytosolName);
    User owner = context.getData(this.owner);
    KeyValue simKey = context.getData(this.simKey);
    // do op
    Generate2DSimBioModelOp op = new Generate2DSimBioModelOp();
    BioModel bioModel = op.generateBioModel(extent, cellROI_2D, timeStamps, indexFirstPostbleach, primaryDiffusionRate, primaryFraction, bleachMonitorRate, secondaryDiffusionRate, secondaryFraction, bindingSiteConcentration, bindingOnRate, bindingOffRate, extracellularName, cytosolName, owner, simKey);
    // set output
    context.setData(this.bioModel_2D, bioModel);
}