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

Example 81 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 82 with UShortImage

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

the class ImportRawTimeSeriesFromExperimentImage method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    File expTimeSeriesFile = context.getData(this.expTimeSeriesFile);
    // do op
    ImportRawTimeSeriesFromExperimentImageOp op = new ImportRawTimeSeriesFromExperimentImageOp();
    ImageTimeSeries<UShortImage> imageTimeSeries = op.importRawTimeSeries(expTimeSeriesFile);
    // set output
    context.setData(rawTimeSeriesImages, imageTimeSeries);
}

Example 83 with UShortImage

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

the class ImportRawTimeSeriesFromHdf5Fluor method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    int zSlice = context.getDataWithDefault(zSliceIndex, 0);
    File hdf5File = new File(context.getData(this.vcellHdf5File));
    String fluorName = context.getData(this.fluorDataName);
    Double maxFluor = context.getData(this.maxIntensity);
    Boolean isNoise = context.getData(this.bNoise);
    // do op
    ImportRawTimeSeriesFromHdf5FluorOp op = new ImportRawTimeSeriesFromHdf5FluorOp();
    ImageTimeSeries<UShortImage> timeRawData = op.importTimeSeriesFromHDF5Data(hdf5File, fluorName, maxFluor, isNoise, zSlice);
    // set output
    context.setData(rawTimeSeriesImages, timeRawData);
}

Example 84 with UShortImage

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

the class GenerateTrivial2DPsf method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // do op
    GenerateTrivial2DPsfOp op = new GenerateTrivial2DPsfOp();
    UShortImage psf = op.generateTrivial2D_Psf();
    // set output
    context.setData(psf_2D, psf);
}

Example 85 with UShortImage

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

the class ImportRawTimeSeriesFromExperimentImages method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    File[] files = context.getData(expTimeSeriesFiles);
    Double tInterval = context.getData(timeInterval);
    // do op
    ImportRawTimeSeriesFromExperimentImagesOp op = new ImportRawTimeSeriesFromExperimentImagesOp();
    ImageTimeSeries<UShortImage> imageTimeSeries = op.importRawTimeSeries(files, tInterval);
    // set output
    context.setData(rawTimeSeriesImages, imageTimeSeries);
}