Examples with ConvolutionDataGeneratorKernel cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel used on opensource projects

Example 1 with ConvolutionDataGeneratorKernel

use of cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel in project vcell by virtualcell.

the class XmlReader method getConvolutionDataGenerator.

private ConvolutionDataGenerator getConvolutionDataGenerator(Element element) {
    String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag));
    Expression volumeFunction = null;
    Element volumeFunctionElement = element.getChild(XMLTags.FunctionTag, vcNamespace);
    if (volumeFunctionElement == null) {
        volumeFunctionElement = element.getChild(XMLTags.VolumeFunctionTag, vcNamespace);
    }
    if (volumeFunctionElement != null) {
        String s = volumeFunctionElement.getText();
        volumeFunction = unMangleExpression(s);
    }
    Expression membraneFunction = null;
    Element membraneFunctionElement = element.getChild(XMLTags.MembraneFunctionTag, vcNamespace);
    if (membraneFunctionElement != null) {
        String s = membraneFunctionElement.getText();
        membraneFunction = unMangleExpression(s);
    }
    ConvolutionDataGeneratorKernel kernel = null;
    Element kernelElement = element.getChild(XMLTags.Kernel, vcNamespace);
    String kernelType = kernelElement.getAttributeValue(XMLTags.TypeAttrTag);
    if (kernelType.equals(XMLTags.KernelType_Gaussian)) {
        Element e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace);
        String s = e0.getText();
        Expression sigmaXY = unMangleExpression(s);
        e0 = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace);
        s = e0.getText();
        Expression sigmaZ = unMangleExpression(s);
        kernel = new GaussianConvolutionDataGeneratorKernel(sigmaXY, sigmaZ);
    }
    ConvolutionDataGenerator cdg = new ConvolutionDataGenerator(name, kernel, volumeFunction, membraneFunction);
    return cdg;
}

Example 2 with ConvolutionDataGeneratorKernel

use of cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel in project vcell by virtualcell.

the class Xmlproducer method getXML.

private Element getXML(ConvolutionDataGenerator convolutionDataGenerator) {
    Element element = new Element(XMLTags.ConvolutionDataGenerator);
    element.setAttribute(XMLTags.NameAttrTag, mangle(convolutionDataGenerator.getName()));
    Element kernelElement = new Element(XMLTags.Kernel);
    ConvolutionDataGeneratorKernel kernel = convolutionDataGenerator.getKernel();
    if (kernel instanceof GaussianConvolutionDataGeneratorKernel) {
        kernelElement.setAttribute(XMLTags.TypeAttrTag, XMLTags.KernelType_Gaussian);
        GaussianConvolutionDataGeneratorKernel gck = (GaussianConvolutionDataGeneratorKernel) kernel;
        Element e = new Element(XMLTags.KernelGaussianSigmaXY);
        e.addContent(mangleExpression(gck.getSigmaXY_um()));
        kernelElement.addContent(e);
        e = new Element(XMLTags.KernelGaussianSigmaZ);
        e.addContent(mangleExpression(gck.getSigmaZ_um()));
        kernelElement.addContent(e);
    }
    element.addContent(kernelElement);
    if (convolutionDataGenerator.getVolFunction() != null) {
        Element e = new Element(XMLTags.VolumeFunctionTag);
        e.addContent(mangleExpression(convolutionDataGenerator.getVolFunction()));
        element.addContent(e);
    }
    if (convolutionDataGenerator.getMemFunction() != null) {
        Element e = new Element(XMLTags.MembraneFunctionTag);
        e.addContent(mangleExpression(convolutionDataGenerator.getMemFunction()));
        element.addContent(e);
    }
    return element;
}

Example 3 with ConvolutionDataGeneratorKernel

use of cbit.vcell.math.ConvolutionDataGenerator.ConvolutionDataGeneratorKernel in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writePostProcessingBlock.

private void writePostProcessingBlock() throws Exception {
    // SolverException, ExpressionException and exceptions from roiDataGenerator.getROIDataGeneratorDescription()
    PostProcessingBlock postProcessingBlock = simTask.getSimulation().getMathDescription().getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() == 0) {
        // to make c++ code write default var statisitcs, without the token it won't write anything
        printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_BEGIN);
        printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_END);
        printWriter.println();
        return;
    }
    if (bChomboSolver && postProcessingBlock.getDataGeneratorList().size() > 0) {
        throw new Exception("Data generators are not supported by " + simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel());
    }
    printWriter.println(" # Post Processing Block");
    printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_BEGIN);
    for (DataGenerator dataGenerator : postProcessingBlock.getDataGeneratorList()) {
        String varName = dataGenerator.getName();
        Domain domain = dataGenerator.getDomain();
        String domainName = domain == null ? null : domain.getName();
        if (dataGenerator instanceof ProjectionDataGenerator) {
            ProjectionDataGenerator pdg = (ProjectionDataGenerator) dataGenerator;
            Expression function = subsituteExpression(pdg.getFunction(), VariableDomain.VARIABLEDOMAIN_VOLUME);
            printWriter.println(FVInputFileKeyword.PROJECTION_DATA_GENERATOR + " " + varName + " " + domainName + " " + pdg.getAxis() + " " + pdg.getOperation() + " " + function.infix() + ";");
        } else if (dataGenerator instanceof ConvolutionDataGenerator) {
            ConvolutionDataGenerator convolutionDataGenerator = (ConvolutionDataGenerator) dataGenerator;
            ConvolutionDataGeneratorKernel kernel = convolutionDataGenerator.getKernel();
            if (kernel instanceof GaussianConvolutionDataGeneratorKernel) {
                GaussianConvolutionDataGeneratorKernel gck = (GaussianConvolutionDataGeneratorKernel) kernel;
                Expression volFunction = subsituteExpression(convolutionDataGenerator.getVolFunction(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                Expression memFunction = subsituteExpression(convolutionDataGenerator.getMemFunction(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
                Expression sigmaXY = subsituteExpression(gck.getSigmaXY_um(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                Expression sigmaZ = subsituteExpression(gck.getSigmaZ_um(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                String volFuncStr = volFunction.infix();
                String memFuncStr = memFunction.infix();
                printWriter.println(FVInputFileKeyword.GAUSSIAN_CONVOLUTION_DATA_GENERATOR + " " + varName + " " + domainName + " " + sigmaXY.infix() + " " + sigmaZ.infix() + " " + FVInputFileKeyword.GAUSSIAN_CONVOLUTION_VOL_FUNCTION + " " + volFuncStr + "; " + FVInputFileKeyword.GAUSSIAN_CONVOLUTION_MEM_FUNCTION + " " + memFuncStr + ";");
            }
        } else if (dataGenerator instanceof cbit.vcell.microscopy.ROIDataGenerator) {
            /*
			ROI_DATA_GENERATOR_BEGIN roidata
			VolumePoints 20
			2667 2676 2679 2771 2969 2877 3067 3277 3185 3283 3473 3580 3690 3687 3878 4086 3990 4182 4193 1077 (all points in one line)
			SampleImage 9 0 1341426862190 vcField('sumROIData','roiSumDataVar',0.0,'Volume')
			StoreEnabled false

			SampleImageFile roiSumDataVar 0.0 C:\Users\abcde\VirtualMicroscopy\SimulationData\SimID_1341426862125_0_sumROIData_roiSumDataVar_0_0_Volume.fdat
			DATA_PROCESSOR_END
			*/
            cbit.vcell.microscopy.ROIDataGenerator roiDataGenerator = (cbit.vcell.microscopy.ROIDataGenerator) dataGenerator;
            printWriter.println(roiDataGenerator.getROIDataGeneratorDescription(workingDirectory, simTask.getSimulationJob()));
        } else if (dataGenerator instanceof org.vcell.vmicro.workflow.data.ROIDataGenerator) {
            /*
			ROI_DATA_GENERATOR_BEGIN roidata
			VolumePoints 20
			2667 2676 2679 2771 2969 2877 3067 3277 3185 3283 3473 3580 3690 3687 3878 4086 3990 4182 4193 1077 (all points in one line)
			SampleImage 9 0 1341426862190 vcField('sumROIData','roiSumDataVar',0.0,'Volume')
			StoreEnabled false

			SampleImageFile roiSumDataVar 0.0 C:\Users\abcde\VirtualMicroscopy\SimulationData\SimID_1341426862125_0_sumROIData_roiSumDataVar_0_0_Volume.fdat
			DATA_PROCESSOR_END
			*/
            org.vcell.vmicro.workflow.data.ROIDataGenerator roiDataGenerator = (org.vcell.vmicro.workflow.data.ROIDataGenerator) dataGenerator;
            printWriter.println(roiDataGenerator.getROIDataGeneratorDescription(workingDirectory, simTask.getSimulationJob()));
        } else {
            throw new SolverException(dataGenerator.getClass() + " : data generator not supported yet.");
        }
    }
    printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_END);
    printWriter.println();
}