Examples with MicroscopeMeasurement cbit.vcell.mapping.MicroscopeMeasurement used on opensource projects

Example 1 with MicroscopeMeasurement

use of cbit.vcell.mapping.MicroscopeMeasurement in project vcell by virtualcell.

the class XmlReader method getMicroscopeMeasurement.

public void getMicroscopeMeasurement(Element element, SimulationContext simContext) {
    MicroscopeMeasurement microscopeMeasurement = simContext.getMicroscopeMeasurement();
    String name = element.getAttributeValue(XMLTags.NameAttrTag);
    microscopeMeasurement.setName(name);
    Element kernelElement = element.getChild(XMLTags.ConvolutionKernel, vcNamespace);
    String type = kernelElement.getAttributeValue(XMLTags.TypeAttrTag);
    ConvolutionKernel ck = null;
    if (type.equals(XMLTags.ConvolutionKernel_Type_ProjectionZKernel)) {
        ck = new ProjectionZKernel();
    } else if (type.equals(XMLTags.ConvolutionKernel_Type_GaussianConvolutionKernel)) {
        Element e = kernelElement.getChild(XMLTags.KernelGaussianSigmaXY, vcNamespace);
        String s = e.getText();
        Expression sigmaXY = unMangleExpression(s);
        e = kernelElement.getChild(XMLTags.KernelGaussianSigmaZ, vcNamespace);
        s = e.getText();
        Expression sigmaZ = unMangleExpression(s);
        ck = new GaussianConvolutionKernel(sigmaXY, sigmaZ);
    }
    microscopeMeasurement.setConvolutionKernel(ck);
    List<Element> children = element.getChildren(XMLTags.FluorescenceSpecies, vcNamespace);
    for (Element c : children) {
        String speciesName = c.getAttributeValue(XMLTags.NameAttrTag);
        SpeciesContext sc = simContext.getModel().getSpeciesContext(speciesName);
        microscopeMeasurement.addFluorescentSpecies(sc);
    }
}

Example 2 with MicroscopeMeasurement

use of cbit.vcell.mapping.MicroscopeMeasurement in project vcell by virtualcell.

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 3 with MicroscopeMeasurement

use of cbit.vcell.mapping.MicroscopeMeasurement in project vcell by virtualcell.

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}

Example 4 with MicroscopeMeasurement

use of cbit.vcell.mapping.MicroscopeMeasurement in project vcell by virtualcell.

the class MicroscopeMeasurementPanel method setKernel.

protected void setKernel() {
    MicroscopeMeasurement microscopeMeasurement = simulationContext.getMicroscopeMeasurement();
    if (rdbtnZprojection.isSelected()) {
        microscopeMeasurement.setConvolutionKernel(new ProjectionZKernel());
        BeanUtils.enableComponents(gaussianPsfPanel, false);
        BeanUtils.enableComponents(experimentalPsfPanel, false);
    } else if (radioButtonGaussian.isSelected()) {
        microscopeMeasurement.setConvolutionKernel(new GaussianConvolutionKernel());
        BeanUtils.enableComponents(gaussianPsfPanel, true);
        BeanUtils.enableComponents(experimentalPsfPanel, false);
    } else if (rdbtnExperimental.isSelected()) {
        String psfName = (String) pointSpreadFunctionsComboBox.getSelectedItem();
        for (DataSymbol dataSymbol : simulationContext.getDataContext().getDataSymbols()) {
            if (dataSymbol.getName().equals(psfName)) {
                microscopeMeasurement.setConvolutionKernel(new ExperimentalPSF(dataSymbol));
                break;
            }
        }
        BeanUtils.enableComponents(gaussianPsfPanel, false);
        BeanUtils.enableComponents(experimentalPsfPanel, true);
    }
}

Example 5 with MicroscopeMeasurement

use of cbit.vcell.mapping.MicroscopeMeasurement in project vcell by virtualcell.

the class MicroscopeMeasurementPanel method refreshInterface.

protected void refreshInterface() {
    if (simulationContext == null) {
        return;
    }
    MicroscopeMeasurement microscopeMeasurement = simulationContext.getMicroscopeMeasurement();
    nameTextField.setText(microscopeMeasurement.getName());
    refreshFluorescenceSpeciesList(microscopeMeasurement);
    refreshAllSpeciesList();
    ConvolutionKernel ck = microscopeMeasurement.getConvolutionKernel();
    if (ck instanceof ProjectionZKernel) {
        rdbtnZprojection.setSelected(true);
        BeanUtils.enableComponents(gaussianPsfPanel, false);
        BeanUtils.enableComponents(experimentalPsfPanel, false);
    } else if (ck instanceof GaussianConvolutionKernel) {
        radioButtonGaussian.setSelected(true);
        BeanUtils.enableComponents(gaussianPsfPanel, true);
        BeanUtils.enableComponents(experimentalPsfPanel, false);
        sigmaXYTextField.setText(((GaussianConvolutionKernel) ck).getSigmaXY_um().infix());
        sigmaZTextField.setText(((GaussianConvolutionKernel) ck).getSigmaZ_um().infix());
    } else if (ck instanceof ExperimentalPSF) {
        rdbtnExperimental.setSelected(true);
        BeanUtils.enableComponents(gaussianPsfPanel, false);
        BeanUtils.enableComponents(experimentalPsfPanel, true);
    }
    pointSpreadFunctionsComboModel.removeAllElements();
    if (simulationContext.getDataContext() != null) {
        for (DataSymbol dataSymbol : simulationContext.getDataContext().getDataSymbols()) {
            if (dataSymbol.getDataSymbolType().equals(DataSymbolType.POINT_SPREAD_FUNCTION)) {
                pointSpreadFunctionsComboModel.addElement(dataSymbol.getName());
            }
        }
    }
}