Examples with PostProcessingBlock cbit.vcell.math.PostProcessingBlock used on opensource projects

Example 1 with PostProcessingBlock

use of cbit.vcell.math.PostProcessingBlock in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a MathDescription object.
 * Creation date: (3/2/2001 10:57:25 AM)
 * @return Element
 * @param mathdes cbit.vcell.math.MathDescription
 */
Element getXML(MathDescription mathdes) throws XmlParseException {
    Element math = new Element(XMLTags.MathDescriptionTag);
    // Add attributes
    math.setAttribute(XMLTags.NameAttrTag, mangle(mathdes.getName()));
    // Add annotation
    if (mathdes.getDescription() != null && mathdes.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(mathdes.getDescription()));
        math.addContent(annotationElem);
    }
    List<ParticleMolecularType> particleMolecularTypes = mathdes.getParticleMolecularTypes();
    for (ParticleMolecularType particleMolecularType : particleMolecularTypes) {
        math.addContent(getXML(particleMolecularType));
    }
    // Add Constant subelements
    Enumeration<Variable> enum1 = mathdes.getVariables();
    /*java.util.Iterator k;
    try {
    	VariableHash varHash = new VariableHash();
    	while (enum1.hasMoreElements()) 
    	 	varHash.addVariable((Variable)enum1.nextElement());
    	Variable vars [] = varHash.getReorderedVariables();
    	k = new ArrayList(java.util.Arrays.asList(vars)).iterator();
    } catch (cbit.vcell.mapping.MappingException e) {
		e.printStackTrace();
		return null;
    }*/
    while (enum1.hasMoreElements()) {
        Variable var = enum1.nextElement();
        Element element = null;
        if (var instanceof Constant) {
            element = getXML((Constant) var);
        } else if (var instanceof FilamentRegionVariable) {
            element = getXML((FilamentRegionVariable) var);
        } else if (var instanceof FilamentVariable) {
            element = getXML((FilamentVariable) var);
        } else if (var instanceof PointVariable) {
            element = getXML((PointVariable) var);
        } else if (var instanceof Function) {
            element = getXML((Function) var);
        } else if (var instanceof RandomVariable) {
            element = getXML((RandomVariable) var);
        } else if (var instanceof InsideVariable) {
            // *** for internal use! Ignore it ***
            continue;
        } else if (var instanceof MembraneRegionVariable) {
            element = getXML((MembraneRegionVariable) var);
        } else if (var instanceof MemVariable) {
            element = getXML((MemVariable) var);
        } else if (var instanceof OutsideVariable) {
            // *** for internal use! Ignore it ****
            continue;
        } else if (var instanceof VolumeRegionVariable) {
            element = getXML((VolumeRegionVariable) var);
        } else if (var instanceof VolVariable) {
            element = getXML((VolVariable) var);
        } else if (var instanceof StochVolVariable) {
            // added for stochastic volumn variables
            element = getXML((StochVolVariable) var);
        } else if (var instanceof ParticleVariable) {
            element = getXML((ParticleVariable) var);
        } else if (var instanceof ParticleObservable) {
            element = getXML((ParticleObservable) var);
        } else {
            throw new XmlParseException("An unknown variable type " + var.getClass().getName() + " was found when parsing the mathdescription " + mathdes.getName() + "!");
        }
        transcribeComments(var, element);
        math.addContent(element);
    }
    // this was moved to the simspec!
    /*	buffer.append("\n");
    	if (geometry != null){
    		buffer.append(geometry.getXML());
    	}	
    	buffer.append("\n");*/
    // Add subdomains
    Enumeration<SubDomain> enum2 = mathdes.getSubDomains();
    while (enum2.hasMoreElements()) {
        SubDomain subDomain = enum2.nextElement();
        math.addContent(getXML(subDomain));
    }
    // Add Metadata (Version) if there is!
    if (mathdes.getVersion() != null) {
        math.addContent(getXML(mathdes.getVersion(), mathdes));
    }
    Iterator<Event> iter = mathdes.getEvents();
    while (iter.hasNext()) {
        math.addContent(getXML(iter.next()));
    }
    PostProcessingBlock postProcessingBlock = mathdes.getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() > 0) {
        math.addContent(getXML(postProcessingBlock));
    }
    return math;
}

Example 2 with PostProcessingBlock

use of cbit.vcell.math.PostProcessingBlock 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();
}