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

Example 66 with ROI

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

the class WorkflowObjectsTableModel method getValue.

private String getValue(WorkflowObject workflowObject) {
    if (workflowObject instanceof Task) {
        return "";
    } else {
        Object data = null;
        Class dataType = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            WorkflowDataSource dataSource = taskContext.getWorkflow().getDataSource((DataObject) dataHolder);
            data = taskContext.getRepository().getData(dataSource);
            dataType = dataHolder.getType();
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
            dataType = dataInput.getType();
        }
        if (data instanceof RowColumnResultSet) {
            RowColumnResultSet rc = (RowColumnResultSet) data;
            int N = rc.getColumnDescriptionsCount();
            StringBuffer buffer = new StringBuffer(rc.getRowCount() + " rows of " + N + " {");
            int MAX = 3;
            for (int i = 0; i < N; i++) {
                buffer.append("\"" + rc.getColumnDescriptions(i).getDisplayName() + "\"");
                if (i >= MAX - 1) {
                    buffer.append(", ...");
                    break;
                }
                if (i < N - 1) {
                    buffer.append(", ");
                }
            }
            buffer.append("}");
            return buffer.toString();
        } else if (data instanceof String) {
            return "\"" + (String) data + "\"";
        } else if (data instanceof ROI) {
            return "ROI \"" + ((ROI) data).getROIName() + "\"";
        } else if (data instanceof ROI[]) {
            ROI[] rois = (ROI[]) data;
            int N = rois.length;
            int MAX = 3;
            StringBuffer buffer = new StringBuffer("ROI[" + N + "] { ");
            for (int i = 0; i < N; i++) {
                buffer.append("\"" + rois[i].getROIName() + "\"");
                if (i >= MAX - 1) {
                    buffer.append(", ...");
                    break;
                }
                if (i < N - 1) {
                    buffer.append(", ");
                }
            }
            buffer.append("}");
            return buffer.toString();
        } else if (data instanceof Image) {
            Image image = (Image) data;
            return image.getClass().getSimpleName() + " " + image.getISize().toString();
        } else if (data instanceof ImageTimeSeries) {
            ImageTimeSeries ts = (ImageTimeSeries) data;
            int N = ts.getSizeT();
            double[] times = ts.getImageTimeStamps();
            return ts.getType().getSimpleName() + "[" + N + "] " + ts.getISize() + " times=[" + times[0] + "," + times[N - 1] + "]";
        } else if (data != null) {
            return data.toString();
        } else {
            return "null " + dataType.getSimpleName();
        }
    }
}

Example 67 with ROI

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

the class ComputeMeasurementError method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    ROI[] rois = context.getData(imageDataROIs);
    int indexPostbleach = context.getData(indexFirstPostbleach);
    ImageTimeSeries<UShortImage> rawImageDataset = context.getData(rawImageTimeSeries);
    FloatImage prebleachAvgImage = context.getData(prebleachAverage);
    ArrayList<NormalizedSampleFunction> roiSampleFunctions = new ArrayList<NormalizedSampleFunction>();
    for (int i = 0; i < rois.length; i++) {
        roiSampleFunctions.add(NormalizedSampleFunction.fromROI(rois[i]));
    }
    // do op
    ComputeMeasurementErrorOp op = new ComputeMeasurementErrorOp();
    NormalizedSampleFunction[] roiSampleFunctionArray = roiSampleFunctions.toArray(new NormalizedSampleFunction[0]);
    RowColumnResultSet rowColumnResultSet = op.computeNormalizedMeasurementError(roiSampleFunctionArray, indexPostbleach, rawImageDataset, prebleachAvgImage, clientTaskStatusSupport);
    // set output
    context.setData(normalizedMeasurementError, rowColumnResultSet);
}

Example 68 with ROI

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

the class GenerateBleachROI method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    Image firstPostbleachImage = context.getData(normalizedTimeSeries).getAllImages()[0];
    ROI cellROI = context.getData(cellROI_2D);
    double bleachThresholdValue = context.getData(bleachThreshold);
    // do op
    GenerateBleachRoiOp op = new GenerateBleachRoiOp();
    ROI bleachedROI = op.generateBleachRoi(firstPostbleachImage, cellROI, bleachThresholdValue);
    // set output
    context.setData(bleachedROI_2D, bleachedROI);
    context.setData(bleachedROI_2D_array, new ROI[] { bleachedROI });
}

Example 69 with ROI

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

the class GenerateDependentImageROIs method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ROI cellROI_2D = context.getData(this.cellROI_2D);
    ROI bleachedROI_2D = context.getData(this.bleachedROI_2D);
    // do op
    GenerateDependentImageROIsOp op = new GenerateDependentImageROIsOp();
    ROI[] rois = op.generate(cellROI_2D, bleachedROI_2D);
    // set output
    context.setData(imageDataROIs, rois);
}

Example 70 with ROI

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

the class RunRefSimulationFast method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    ImageTimeSeries<FloatImage> normTimeSeries = context.getData(normalizedTimeSeries);
    ROI cellROI = context.getData(cellROI_2D);
    ROI[] imageDataRois = context.getData(imageDataROIs);
    UShortImage psf = context.getData(this.psf);
    // do op
    RunRefSimulationFastOp op = new RunRefSimulationFastOp();
    RowColumnResultSet reducedData = op.runRefSimFast(cellROI, normTimeSeries, imageDataRois, psf, context.getLocalWorkspace(), clientTaskStatusSupport);
    // set output
    context.setData(reducedROIData, reducedData);
    // always D = 1,
    context.setData(refSimDiffusionRate, op.getReferenceDiffusionCoef());
}