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

Example 31 with VariableType

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

the class FieldUtilities method substituteFieldFuncNames.

public static void substituteFieldFuncNames(Hashtable<String, ExternalDataIdentifier> oldFieldFuncArgsNameNewID, Hashtable<FieldFunctionArguments, Vector<Expression>> fieldFuncArgsExpHash) throws MathException, ExpressionException {
    Enumeration<FieldFunctionArguments> keyEnum = fieldFuncArgsExpHash.keys();
    FunctionFilter functionFilter = new FieldFunctionFilter();
    while (keyEnum.hasMoreElements()) {
        Vector<Expression> value = fieldFuncArgsExpHash.get(keyEnum.nextElement());
        for (int i = 0; i < value.size(); i++) {
            Expression exp = value.elementAt(i);
            FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(functionFilter);
            for (int j = 0; j < functionInvocations.length; j++) {
                Expression[] arguments = functionInvocations[j].getArguments();
                String oldFieldName = removeLiteralQuotes(arguments[0]);
                if (oldFieldFuncArgsNameNewID.containsKey(oldFieldName)) {
                    String varName = removeLiteralQuotes(arguments[1]);
                    Expression timeExp = arguments[2];
                    VariableType varType = VariableType.UNKNOWN;
                    if (arguments.length > 3) {
                        String vt = removeLiteralQuotes(arguments[3]);
                        varType = VariableType.getVariableTypeFromVariableTypeName(vt);
                    }
                    String newFieldName = oldFieldFuncArgsNameNewID.get(oldFieldName).getName();
                    FieldFunctionArguments newFieldFunctionArguments = new FieldFunctionArguments(newFieldName, varName, timeExp, varType);
                    Expression newFunctionExp = new Expression(newFieldFunctionArguments.infix());
                    exp.substituteInPlace(functionInvocations[j].getFunctionExpression(), newFunctionExp);
                }
            }
        }
    }
}

Example 32 with VariableType

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

the class TestingFrameworkWindowManager method compare.

/**
 * Insert the method's description here.
 * Creation date: (1/20/2003 11:52:18 AM)
 * @return boolean
 * @param mathDesc cbit.vcell.math.MathDescription
 */
public void compare(final TestCriteriaNew testCriteria, final SimulationInfo userDefinedRegrSimInfo) {
    final String KEY_MERGEDDATAINFO = "KEY_MERGEDDATAINFO";
    final String KEY_MERGEDDATASETVIEWERCNTRLR = "KEY_MERGEDDATASETVIEWERCNTRLR";
    AsynchClientTask gatherDataTask = new AsynchClientTask("Gathering compare Dta...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // create the merged data for the simulationInfo in testCriteria and the regression simInfo
            SimulationInfo simInfo = testCriteria.getSimInfo();
            SimulationInfo regrSimInfo = null;
            if (userDefinedRegrSimInfo != null) {
                regrSimInfo = userDefinedRegrSimInfo;
            } else {
                regrSimInfo = testCriteria.getRegressionSimInfo();
            }
            if (regrSimInfo == null) {
                return;
            }
            VCDataIdentifier vcSimId1 = new VCSimulationDataIdentifier(simInfo.getAuthoritativeVCSimulationIdentifier(), 0);
            VCDataIdentifier vcSimId2 = new VCSimulationDataIdentifier(regrSimInfo.getAuthoritativeVCSimulationIdentifier(), 0);
            User user = simInfo.getOwner();
            VCDataIdentifier[] vcIdentifierArray = new VCDataIdentifier[] { vcSimId2, vcSimId1 };
            MergedDataInfo mergedDataInfo = new MergedDataInfo(user, vcIdentifierArray, MergedDataInfo.createDefaultPrefixNames(vcIdentifierArray.length));
            hashTable.put(KEY_MERGEDDATAINFO, mergedDataInfo);
            // get the data manager and wire it up
            // 
            // get all "Data1.XXX" data identifiers ... and remove those which are functions
            // add functions of the form DIFF_XXX = (Data1.XXX - Data2.XXX) for convenience in comparing results.
            // 
            Simulation sim1 = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(simInfo);
            Simulation sim2 = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(regrSimInfo);
            boolean isSpatial = sim1.isSpatial();
            if (sim2.isSpatial() != isSpatial) {
                throw new RuntimeException("Cannot compare spatial and non-spatial data sets : " + simInfo + "& " + regrSimInfo);
            }
            DataManager mergedDataManager = getRequestManager().getDataManager(null, mergedDataInfo, isSpatial);
            DataManager data1Manager = getRequestManager().getDataManager(null, vcSimId1, isSpatial);
            DataManager data2Manager = getRequestManager().getDataManager(null, vcSimId2, isSpatial);
            Vector<AnnotatedFunction> functionList = new Vector<AnnotatedFunction>();
            AnnotatedFunction[] data1Functions = data1Manager.getFunctions();
            AnnotatedFunction[] existingFunctions = mergedDataManager.getFunctions();
            DataIdentifier[] data1Identifiers = data1Manager.getDataIdentifiers();
            DataIdentifier[] data2Identifiers = data2Manager.getDataIdentifiers();
            for (int i = 0; i < data1Identifiers.length; i++) {
                // 
                // make sure dataIdentifier is not already a function
                // 
                boolean bIsFunction = false;
                for (int j = 0; j < data1Functions.length; j++) {
                    if (data1Identifiers[i].getName().equals(data1Functions[j].getName())) {
                        bIsFunction = true;
                    }
                }
                if (bIsFunction) {
                    continue;
                }
                // 
                // make sure corresponding identifier exists in "Data2"
                // 
                boolean bIsInData2 = false;
                for (int j = 0; j < data2Identifiers.length; j++) {
                    if (data2Identifiers[j].getName().equals(data1Identifiers[i].getName())) {
                        bIsInData2 = true;
                    }
                }
                if (!bIsInData2) {
                    continue;
                }
                // 
                // create "Diff" function
                // 
                String data1Name = "Data1." + data1Identifiers[i].getName();
                String data2Name = "Data2." + data1Identifiers[i].getName();
                String functionName = "DIFF_" + data1Identifiers[i].getName();
                VariableType varType = data1Identifiers[i].getVariableType();
                Expression exp = new Expression(data1Name + "-" + data2Name);
                AnnotatedFunction newFunction = new AnnotatedFunction(functionName, exp, data1Identifiers[i].getDomain(), "", varType, FunctionCategory.OUTPUTFUNCTION);
                // 
                // make sure new "Diff" function isn't already in existing function list.
                // 
                boolean bDiffFunctionAlreadyHere = false;
                for (int j = 0; j < existingFunctions.length; j++) {
                    if (newFunction.getName().equals(existingFunctions[j].getName())) {
                        bDiffFunctionAlreadyHere = true;
                    }
                }
                if (bDiffFunctionAlreadyHere) {
                    continue;
                }
                functionList.add(newFunction);
            }
            OutputContext outputContext = null;
            if (functionList.size() > 0) {
                AnnotatedFunction[] newDiffFunctions = (AnnotatedFunction[]) BeanUtils.getArray(functionList, AnnotatedFunction.class);
                outputContext = new OutputContext(newDiffFunctions);
            }
            MergedDatasetViewerController mergedDatasetViewerCtr = getRequestManager().getMergedDatasetViewerController(outputContext, mergedDataInfo, !isSpatial);
            hashTable.put(KEY_MERGEDDATASETVIEWERCNTRLR, mergedDatasetViewerCtr);
        }
    };
    AsynchClientTask showResultsTask = new AsynchClientTask("Showing Compare Results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // make the viewer
            MergedDatasetViewerController mergedDatasetViewerCtr = (MergedDatasetViewerController) hashTable.get(KEY_MERGEDDATASETVIEWERCNTRLR);
            addDataListener(mergedDatasetViewerCtr);
            DataViewer viewer = mergedDatasetViewerCtr.createViewer();
            viewer.setDataViewerManager(TestingFrameworkWindowManager.this);
            addExportListener(viewer);
            VCDataIdentifier vcDataIdentifier = (MergedDataInfo) hashTable.get(KEY_MERGEDDATAINFO);
            ChildWindowManager childWindowManager = TFWFinder.findChildWindowManager(getComponent());
            ChildWindow childWindow = childWindowManager.addChildWindow(viewer, vcDataIdentifier, "Comparing ... " + vcDataIdentifier.getID());
            childWindow.pack();
            // childWindow.setSize(450, 450);
            childWindow.setIsCenteredOnParent();
            childWindow.show();
        }
    };
    ClientTaskDispatcher.dispatch(getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { gatherDataTask, showResultsTask }, false);
}

Example 33 with VariableType

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

the class PDEDataViewer method createMultiTimePlotHelper.

// private static class MultiTimePointPropChangeListener implements PropertyChangeListener {
// @Override
// public void propertyChange(PropertyChangeEvent evt) {
// }
// }
private MultiTimePlotHelper createMultiTimePlotHelper(final ClientPDEDataContext copyThisPDEDatacontext, final User user, DataSymbolMetadataResolver argDataSymbolMetadataResolver) throws Exception {
    final ClientPDEDataContext[] copyHolder = new ClientPDEDataContext[1];
    if (PDEDataViewer.this.isPostProcess()) {
        copyHolder[0] = PDEDataViewerPostProcess.createPostProcessPDEDataContext(copyThisPDEDatacontext);
    } else {
        copyHolder[0] = (ClientPDEDataContext) ((PDEDataManager) copyThisPDEDatacontext.getDataManager()).createNewPDEDataManager(copyThisPDEDatacontext.getVCDataIdentifier(), null).getPDEDataContext();
    }
    copyHolder[0].setVariableAndTime(copyThisPDEDatacontext.getDataIdentifier(), copyThisPDEDatacontext.getTimePoint());
    return new PdeTimePlotMultipleVariablesPanel.MultiTimePlotHelper() {

        private DataSymbolMetadataResolver dataSymbolMetadataResolver = argDataSymbolMetadataResolver;

        private ArrayList<PropertyChangeListener> myPropertyChangeHolder = new ArrayList<>();

        private ClientPDEDataContext myPdeDataContext = copyHolder[0];

        private VariableType myVariableType = copyThisPDEDatacontext.getDataIdentifier().getVariableType();

        // catch events from 'this' PDEDataViewer and pass with new source
        private PropertyChangeListener myPropertyChangeListener;

        private User myUser = user;

        // List<AnnotatedFunction> myAnnots;
        // access to anonymous outer class
        private PdeTimePlotMultipleVariablesPanel.MultiTimePlotHelper multiTimePlotHelperThis = this;

        private PDEPlotControlPanel.IdentifierListCellRenderer myListCellRenderer;

        private AnnotatedFunction[] lastAnnotatedFunctions;

        private PDEPlotControlPanel.FunctionListProvider functionListProvider = new PDEPlotControlPanel.FunctionListProvider() {

            @Override
            public List<AnnotatedFunction> getAnnotatedFunctions() {
                if (myPdeDataContext.getDataManager().getOutputContext() != null && myPdeDataContext.getDataManager().getOutputContext().getOutputFunctions() != null && myPdeDataContext.getDataManager().getOutputContext().getOutputFunctions().length > 0) {
                    return new ArrayList<>(Arrays.asList(myPdeDataContext.getDataManager().getOutputContext().getOutputFunctions()));
                }
                return new ArrayList<>();
            }
        };

        private Comparator<AnnotatedFunction> nameComparator = new Comparator<AnnotatedFunction>() {

            @Override
            public int compare(AnnotatedFunction o1, AnnotatedFunction o2) {
                return o2.getName().compareToIgnoreCase(o1.getName());
            }
        };

        @Override
        public void removeDataJobListener(DataJobListener dataJobListener) {
            PDEDataViewer.this.removeDataJobListener(dataJobListener);
        }

        @Override
        public void addDataJobListener(DataJobListener dataJobListener) {
            PDEDataViewer.this.addDataJobListener(dataJobListener);
        }

        @Override
        public User getUser() {
            return myUser;
        }

        @Override
        public PDEDataContext getPdeDatacontext() {
            return myPdeDataContext;
        }

        @Override
        public DataIdentifier[] getCopyOfDisplayedDataIdentifiers() {
            DataIdentifier[] newData = PDEDataViewer.this.getPDEPlotControlPanel1().getDataIdentifierFilter().accept(DefaultDataIdentifierFilter.ALL, functionListProvider.getAnnotatedFunctions(), myPdeDataContext.getDataIdentifiers()).toArray(new DataIdentifier[0]);
            return DataIdentifier.collectSortedSimilarDataTypes(this.getVariableType(), newData);
        }

        @Override
        public PDEPlotControlPanel.IdentifierListCellRenderer getListCellRenderer() {
            if (myListCellRenderer == null) {
                myListCellRenderer = new PDEPlotControlPanel.IdentifierListCellRenderer(functionListProvider);
            }
            return myListCellRenderer;
        }

        @Override
        public Simulation getsimulation() {
            return PDEDataViewer.this.getSimulation();
        }

        private List<AnnotatedFunction> efficiencyFilter(List<AnnotatedFunction> funcs) {
            ArrayList<AnnotatedFunction> outputfunctions = new ArrayList<>();
            Iterator<AnnotatedFunction> iter = funcs.iterator();
            while (iter.hasNext()) {
                AnnotatedFunction theFunc = iter.next();
                if ((isPostProcess() && theFunc.getFunctionType().equals(VariableType.POSTPROCESSING)) || (!isPostProcess() && !theFunc.getFunctionType().equals(VariableType.POSTPROCESSING))) {
                    outputfunctions.add(theFunc);
                }
            }
            return outputfunctions;
        }

        @Override
        public void addPropertyChangeListener(PropertyChangeListener propertyChangeListener) {
            myPropertyChangeHolder.add(propertyChangeListener);
            if (myPropertyChangeListener == null) {
                myPropertyChangeListener = new PropertyChangeListener() {

                    @Override
                    public void propertyChange(PropertyChangeEvent evt) {
                        if (evt.getSource() == PDEDataViewer.this && evt.getPropertyName().equals(PDEDataContext.PROP_PDE_DATA_CONTEXT)) {
                            // List<AnnotatedFunction> currentOutputFunctions = functionListProvider.getAnnotatedFunctions();
                            // currentOutputFunctions = efficiencyFilter(currentOutputFunctions);
                            // currentOutputFunctions.sort(nameComparator);
                            List<AnnotatedFunction> newOutputFunctions0 = Arrays.asList(((ClientPDEDataContext) PDEDataViewer.this.getPdeDataContext()).getDataManager().getOutputContext().getOutputFunctions());
                            List<AnnotatedFunction> newOutputFunctions = efficiencyFilter(newOutputFunctions0);
                            newOutputFunctions.sort(nameComparator);
                            if (lastAnnotatedFunctions != null && Compare.isEqualOrNullStrict(lastAnnotatedFunctions, newOutputFunctions.toArray(new AnnotatedFunction[0]))) {
                                return;
                            }
                            lastAnnotatedFunctions = new AnnotatedFunction[newOutputFunctions.size()];
                            for (int i = 0; i < newOutputFunctions.size(); i++) {
                                lastAnnotatedFunctions[i] = new AnnotatedFunction(newOutputFunctions.get(i));
                            }
                            // lastAnnotatedFunctions = newOutputFunctions0.toArray(new AnnotatedFunction[0]);
                            myPdeDataContext.getDataManager().setOutputContext(new OutputContext(newOutputFunctions0.toArray(new AnnotatedFunction[0])));
                            myPdeDataContext.refreshIdentifiers();
                            for (int i = 0; i < myPropertyChangeHolder.size(); i++) {
                                myPropertyChangeHolder.get(i).propertyChange(new PropertyChangeEvent(multiTimePlotHelperThis, SimDataConstants.PROPERTY_NAME_DATAIDENTIFIERS, null, null));
                            }
                        }
                    }
                };
                PDEDataViewer.this.addPropertyChangeListener(myPropertyChangeListener);
            }
        }

        @Override
        public void removeallPropertyChangeListeners() {
            myPropertyChangeHolder.clear();
            if (myPropertyChangeListener != null) {
                PDEDataViewer.this.removePropertyChangeListener(myPropertyChangeListener);
            }
        }

        @Override
        public VariableType getVariableType() {
            return myVariableType;
        }

        // @Override
        // public void addExtraTasks(AsynchClientTask[] moreTasks) {
        // PDEDataViewer.this.addExtraTasks(moreTasks);
        // }
        @Override
        public DataSymbolMetadataResolver getDataSymbolMetadataResolver() {
            return dataSymbolMetadataResolver;
        }
    };
}

Example 34 with VariableType

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

the class PDEDataViewer method showTimePlot.

// private static final String PROPERTY_PDEDC = "pdedc";
/**
 * Comment
 */
private void showTimePlot() {
    VariableType varType = getPdeDataContext().getDataIdentifier().getVariableType();
    // Collect all sample curves created by user
    SpatialSelection[] spatialSelectionArr = getPDEDataContextPanel1().fetchSpatialSelections(true, true);
    SpatialSelection[] spatialSelectionArr2 = null;
    if (varType.getVariableDomain().equals(VariableDomain.VARIABLEDOMAIN_VOLUME) || varType.getVariableDomain().equals(VariableDomain.VARIABLEDOMAIN_POSTPROCESSING)) {
        spatialSelectionArr2 = getPDEDataContextPanel1().fetchSpatialSelections(varType, true, true);
    } else {
        spatialSelectionArr2 = getPDEDataContextPanel1().fetchSpatialSelections(varType.equals(VariableType.MEMBRANE) ? VariableType.MEMBRANE_REGION : VariableType.MEMBRANE, true, true);
    }
    final Vector<SpatialSelection> singlePointSSOnly = new Vector<SpatialSelection>();
    final Vector<SpatialSelection> singlePointSSOnly2 = new Vector<SpatialSelection>();
    if (spatialSelectionArr != null && spatialSelectionArr.length > 0) {
        for (int i = 0; i < spatialSelectionArr.length; i++) {
            if (spatialSelectionArr[i].isPoint() || (spatialSelectionArr[i] instanceof SpatialSelectionMembrane && ((SpatialSelectionMembrane) spatialSelectionArr[i]).getSelectionSource() instanceof SinglePoint)) {
                singlePointSSOnly.add(spatialSelectionArr[i]);
            }
            if (spatialSelectionArr2[i].isPoint() || (spatialSelectionArr2[i] instanceof SpatialSelectionMembrane && ((SpatialSelectionMembrane) spatialSelectionArr2[i]).getSelectionSource() instanceof SinglePoint)) {
                singlePointSSOnly2.add(spatialSelectionArr2[i]);
            }
        }
    }
    final String varName = getPdeDataContext().getVariableName();
    if (singlePointSSOnly.size() == 0) {
        PopupGenerator.showErrorDialog(this, "No Time sampling points match DataType=" + varType);
        return;
    }
    try {
        int[] indices = null;
        // 
        indices = new int[singlePointSSOnly.size()];
        for (int i = 0; i < singlePointSSOnly.size(); i++) {
            if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                SpatialSelectionVolume ssv = (SpatialSelectionVolume) singlePointSSOnly.get(i);
                indices[i] = ssv.getIndex(0);
            } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) singlePointSSOnly.get(i);
                indices[i] = ssm.getIndex(0);
            }
        }
        double[] timePoints = getPdeDataContext().getTimePoints();
        final TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(new String[] { varName }, new int[][] { indices }, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieving Data for '" + varName + "'...", PDEDataViewer.this, getPdeDataContext());
        AsynchClientTask multiTimePlotHelperTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                PdeTimePlotMultipleVariablesPanel.MultiTimePlotHelper multiTimePlotHelper = createMultiTimePlotHelper((ClientPDEDataContext) PDEDataViewer.this.getPdeDataContext(), PDEDataViewer.this.getDataViewerManager().getUser(), getSimulationModelInfo().getDataSymbolMetadataResolver());
                hashTable.put(MULTITPHELPER_TASK_KEY, multiTimePlotHelper);
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("showing time plot for '" + varName + "'", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(StringKey_timeSeriesJobResults);
                // Make independent Plotviewer that is unaffected by changes (time,var,paramscan) in 'this' PDEDataviewer except to pass-thru OutputContext changes
                PdeTimePlotMultipleVariablesPanel.MultiTimePlotHelper multiTimePlotHelper = (PdeTimePlotMultipleVariablesPanel.MultiTimePlotHelper) hashTable.get(MULTITPHELPER_TASK_KEY);
                try {
                    PdeTimePlotMultipleVariablesPanel pdeTimePlotPanel = new PdeTimePlotMultipleVariablesPanel(multiTimePlotHelper, singlePointSSOnly, singlePointSSOnly2, tsJobResultsNoStats);
                    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(PDEDataViewer.this);
                    String prefix = "Time Plot (" + getPDEPlotControlPanel1().getPlotVariableJList().getSelectedValue().getVariableType().getTypeName() + ") ";
                    ChildWindow childWindow = childWindowManager.addChildWindow(pdeTimePlotPanel, pdeTimePlotPanel, createContextTitle(PDEDataViewer.this.isPostProcess(), prefix, getPdeDataContext(), getSimulationModelInfo(), getSimulation()));
                    childWindow.getParent().addWindowListener(new WindowAdapter() {

                        @Override
                        public void windowClosing(WindowEvent e) {
                            super.windowClosing(e);
                            multiTimePlotHelper.removeallPropertyChangeListeners();
                        }

                        @Override
                        public void windowClosed(WindowEvent e) {
                            super.windowClosed(e);
                            multiTimePlotHelper.removeallPropertyChangeListeners();
                        }
                    });
                    // childWindow.addChildWindowListener(new ChildWindowListener() {
                    // @Override
                    // public void closing(ChildWindow childWindow) {
                    // multiTimePlotHelper.removeallPropertyChangeListeners();
                    // }
                    // @Override
                    // public void closed(ChildWindow childWindow) {
                    // multiTimePlotHelper.removeallPropertyChangeListeners();
                    // }
                    // });
                    childWindow.setSize(900, 550);
                    childWindow.setIsCenteredOnParent();
                    childWindow.show();
                } catch (Exception e) {
                    e.printStackTrace();
                    multiTimePlotHelper.removeallPropertyChangeListeners();
                }
            }
        };
        // ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1,multiTimePlotHelperTask, task2 }, true, true, null);
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, multiTimePlotHelperTask, task2 }, null, false, false, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 35 with VariableType

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

the class PDEDataViewer method showKymograph.

private void showKymograph() {
    String title = createContextTitle(PDEDataViewer.this.isPostProcess(), "Kymograph: ", getPdeDataContext(), getSimulationModelInfo(), getSimulation());
    final String INDICES_KEY = "INDICES_KEY";
    final String CROSSING_KEY = "CROSSING_KEY";
    final String ACCUM_KEY = "ACCUM_KEY";
    AsynchClientTask multiTimePlotHelperTask = new AsynchClientTask("multiTimePlotHelperTask...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Collect all sample curves created by user
            SpatialSelection[] spatialSelectionArr = getPDEDataContextPanel1().fetchSpatialSelections(false, true);
            final Vector<SpatialSelection> lineSSOnly = new Vector<SpatialSelection>();
            if (spatialSelectionArr != null && spatialSelectionArr.length > 0) {
                // 
                for (int i = 0; i < spatialSelectionArr.length; i++) {
                    if (spatialSelectionArr[i].isPoint() || (spatialSelectionArr[i] instanceof SpatialSelectionMembrane && ((SpatialSelectionMembrane) spatialSelectionArr[i]).getSelectionSource() instanceof cbit.vcell.geometry.SinglePoint)) {
                    } else {
                        lineSSOnly.add(spatialSelectionArr[i]);
                    }
                }
            }
            // 
            if (lineSSOnly.size() == 0) {
                throw new Exception("No line samples match DataType=" + getPdeDataContext().getDataIdentifier().getVariableType());
            }
            VariableType varType = getPdeDataContext().getDataIdentifier().getVariableType();
            int[] indices = null;
            int[] crossingMembraneIndices = null;
            double[] accumDistances = null;
            for (int i = 0; i < lineSSOnly.size(); i++) {
                if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                    SpatialSelectionVolume ssv = (SpatialSelectionVolume) lineSSOnly.get(i);
                    SpatialSelection.SSHelper ssh = ssv.getIndexSamples(0.0, 1.0);
                    indices = ssh.getSampledIndexes();
                    crossingMembraneIndices = ssh.getMembraneIndexesInOut();
                    accumDistances = ssh.getWorldCoordinateLengths();
                } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                    SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) lineSSOnly.get(i);
                    SpatialSelection.SSHelper ssh = ssm.getIndexSamples();
                    indices = ssh.getSampledIndexes();
                    accumDistances = ssh.getWorldCoordinateLengths();
                }
            }
            if (indices != null) {
                hashTable.put(INDICES_KEY, indices);
            }
            if (crossingMembraneIndices != null) {
                hashTable.put(CROSSING_KEY, crossingMembraneIndices);
            }
            if (accumDistances != null) {
                hashTable.put(ACCUM_KEY, accumDistances);
            }
            MultiTimePlotHelper multiTimePlotHelper = createMultiTimePlotHelper((ClientPDEDataContext) getPdeDataContext(), getDataViewerManager().getUser(), getSimulationModelInfo().getDataSymbolMetadataResolver());
            hashTable.put(MULTITPHELPER_TASK_KEY, multiTimePlotHelper);
        }
    };
    AsynchClientTask kymographTask = new AsynchClientTask("Kymograph showing...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            KymographPanel kymographPanel = new KymographPanel(PDEDataViewer.this, title, (MultiTimePlotHelper) hashTable.get(MULTITPHELPER_TASK_KEY));
            SymbolTable symbolTable;
            if (getSimulation() != null && getSimulation().getMathDescription() != null) {
                symbolTable = getSimulation().getMathDescription();
            } else {
                symbolTable = new SimpleSymbolTable(new String[] { getPdeDataContext().getDataIdentifier().getName() });
            }
            ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(PDEDataViewer.this);
            ChildWindow childWindow = childWindowManager.addChildWindow(kymographPanel, kymographPanel, title);
            childWindow.setSize(new Dimension(700, 500));
            childWindow.show();
            kymographPanel.initDataManager(getPdeDataContext().getDataIdentifier(), getPdeDataContext().getTimePoints()[0], 1, getPdeDataContext().getTimePoints()[getPdeDataContext().getTimePoints().length - 1], (int[]) hashTable.get(INDICES_KEY), (int[]) hashTable.get(CROSSING_KEY), (double[]) hashTable.get(ACCUM_KEY), true, getPdeDataContext().getTimePoint(), symbolTable);
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { multiTimePlotHelperTask, kymographTask }, null, false, false, true, null, false);
}