Examples with Generate2DSimBioModelOp org.vcell.vmicro.op.Generate2DSimBioModelOp used on opensource projects

Example 1 with Generate2DSimBioModelOp

use of org.vcell.vmicro.op.Generate2DSimBioModelOp 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);
}