Examples with SimpleSymbolTable cbit.vcell.parser.SimpleSymbolTable used on opensource projects

Example 6 with SimpleSymbolTable

use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.

the class FunctionRangeGenerator method getFunctionStatistics.

// 
// note: functionExp should already be flattened to only have symbols for state variables, x, y, z, and t
// 
public static FunctionStatistics getFunctionStatistics(Expression functionExp, VarStatistics[] varStatistics, double[] times, CartesianMesh cartesianMesh, BitSet inDomainBitSetOrig, VariableType variableType) throws /*,int numSamplesPerDim*/
Exception {
    ArrayList<Integer> inDomainIndexesInit = new ArrayList<>();
    // make list of all indexes in domain
    for (int i = inDomainBitSetOrig.nextSetBit(0); i >= 0; i = inDomainBitSetOrig.nextSetBit(i + 1)) {
        if (i == Integer.MAX_VALUE) {
            break;
        }
        inDomainIndexesInit.add(i);
    }
    if (varStatistics.length == 0) {
        double constantValue = functionExp.evaluateConstant();
        double[] minValues = new double[times.length];
        Arrays.fill(minValues, constantValue);
        double[] maxValues = new double[times.length];
        Arrays.fill(maxValues, constantValue);
        return new FunctionStatistics(minValues, maxValues);
    }
    if (varStatistics[0].minValuesOverTime.length != times.length) {
        // happens if viewing data of running sim
        double[] temp = new double[varStatistics[0].minValuesOverTime.length];
        System.arraycopy(times, 0, temp, 0, temp.length);
        times = temp;
    }
    // int numVars = varStatistics.length;
    // Math.min(1000, b)
    long numSamples = (inDomainIndexesInit.size() < 10000 ? inDomainIndexesInit.size() : 10000);
    // long numSamples = numVars*numSamplesPerDim;
    ArrayList<String> symbols = new ArrayList<>();
    // if (functionExp.hasSymbol("x")){
    // numSamples *= numSamplesPerDim;
    // }
    // if (functionExp.hasSymbol("y")){
    // numSamples *= numSamplesPerDim;
    // }
    // if (functionExp.hasSymbol("z")){
    // numSamples *= numSamplesPerDim;
    // }
    // boolean bSampleSpace = functionExp.hasSymbol(ReservedVariable.X.getSyntax()) || functionExp.hasSymbol(ReservedVariable.Y.getSyntax()) || functionExp.hasSymbol(ReservedVariable.Z.getSyntax());
    // 
    // establishes order of values when evaluating, values={t,x,y,z,var1,var2, ... varN}
    // 
    symbols.add("t");
    symbols.add("x");
    symbols.add("y");
    symbols.add("z");
    for (VarStatistics varStat : varStatistics) {
        symbols.add(varStat.stateVariableName);
    }
    SimpleSymbolTable symTable = new SimpleSymbolTable(symbols.toArray(new String[0]));
    functionExp.bindExpression(symTable);
    // loop through time, at each time sample state variables (and x,y,z if necessary) to estimate
    // the min and max values for that time.
    Random rand = new Random(0);
    double[] values = new double[symbols.size()];
    double[] minFunctionValues = new double[times.length];
    double[] maxFunctionValues = new double[times.length];
    // Extent extent = cartesianMesh.getExtent();
    for (int tIndex = 0; tIndex < times.length; tIndex++) {
        ArrayList<Integer> inDomainIndexes = new ArrayList<>(inDomainIndexesInit);
        values[0] = times[tIndex];
        double minValue = Double.POSITIVE_INFINITY;
        double maxValue = Double.NEGATIVE_INFINITY;
        for (int sample = 0; sample < numSamples; sample++) {
            Coordinate coord = null;
            int rndIndex = rand.nextInt(inDomainIndexes.size());
            int index = inDomainIndexes.remove(rndIndex);
            if (variableType.equals(VariableType.MEMBRANE)) {
                coord = cartesianMesh.getCoordinateFromMembraneIndex(index);
            } else if (variableType.equals(VariableType.VOLUME)) {
                coord = cartesianMesh.getCoordinateFromVolumeIndex(index);
            } else {
                throw new Exception("Not implemented " + variableType.getTypeName());
            }
            values[1] = coord.getX();
            values[2] = coord.getY();
            values[3] = coord.getZ();
            for (int varIndex = 0; varIndex < varStatistics.length; varIndex++) {
                double s = rand.nextDouble();
                values[4 + varIndex] = s * varStatistics[varIndex].minValuesOverTime[tIndex] + (1 - s) * varStatistics[varIndex].maxValuesOverTime[tIndex];
            }
            double evaluation = functionExp.evaluateVector(values);
            minValue = Math.min(minValue, evaluation);
            maxValue = Math.max(maxValue, evaluation);
        }
        minFunctionValues[tIndex] = minValue;
        maxFunctionValues[tIndex] = maxValue;
    // System.out.println("tIndex="+tIndex+" min="+minValue+" max="+maxValue);
    }
    FunctionStatistics functionStats = new FunctionStatistics(minFunctionValues, maxFunctionValues);
    return functionStats;
}

Example 7 with SimpleSymbolTable

use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.

the class OptimizationSpec method read.

/**
 * Insert the method's description here.
 * Creation date: (3/3/00 3:59:31 PM)
 * @return cbit.vcell.opt.OptimizationSpec
 * @param vcmlString java.lang.String
 */
public void read(CommentStringTokenizer tokens) {
    try {
        String token = null;
        while (tokens.hasMoreTokens()) {
            token = tokens.nextToken();
            if (token.equalsIgnoreCase("Parameter")) {
                String name = tokens.nextToken();
                String lowerBound = tokens.nextToken();
                double lowerBoundDouble = 0.0;
                try {
                    lowerBoundDouble = Double.parseDouble(lowerBound);
                } catch (NumberFormatException e) {
                    if (lowerBound.equalsIgnoreCase("-Infinity") || lowerBound.equalsIgnoreCase("-Inf")) {
                        lowerBoundDouble = Double.NEGATIVE_INFINITY;
                    }
                }
                String upperBound = tokens.nextToken();
                double upperBoundDouble = 0.0;
                try {
                    upperBoundDouble = Double.parseDouble(upperBound);
                } catch (NumberFormatException e) {
                    if (upperBound.equalsIgnoreCase("Infinity") || upperBound.equalsIgnoreCase("Inf")) {
                        upperBoundDouble = Double.POSITIVE_INFINITY;
                    }
                }
                String scale = tokens.nextToken();
                String initialValue = tokens.nextToken();
                Parameter parameter = new Parameter(name, lowerBoundDouble, upperBoundDouble, Double.parseDouble(scale), Double.parseDouble(initialValue));
                addParameter(parameter);
                continue;
            }
            if (token.equalsIgnoreCase("ExplicitObjectiveFunction")) {
                ObjectiveFunction objFunction = ExplicitObjectiveFunction.fromVCML(tokens);
                setObjectiveFunction(objFunction);
                continue;
            }
            if (token.equalsIgnoreCase("OdeObjectiveFunction")) {
                throw new RuntimeException("OdeObjectiveFunction no longer supported");
            }
            if (token.equalsIgnoreCase(ConstraintType.LinearEquality.toString())) {
                Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
                SimpleSymbolTable symbolTable = new SimpleSymbolTable(getParameterNames());
                exp.bindExpression(symbolTable);
                Constraint constraint = new Constraint(ConstraintType.LinearEquality, exp);
                addConstraint(constraint);
                continue;
            }
            if (token.equalsIgnoreCase(ConstraintType.LinearInequality.toString())) {
                Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
                SimpleSymbolTable symbolTable = new SimpleSymbolTable(getParameterNames());
                exp.bindExpression(symbolTable);
                Constraint constraint = new Constraint(ConstraintType.LinearInequality, exp);
                addConstraint(constraint);
                continue;
            }
            if (token.equalsIgnoreCase(ConstraintType.NonlinearInequality.toString())) {
                Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
                SimpleSymbolTable symbolTable = new SimpleSymbolTable(getParameterNames());
                exp.bindExpression(symbolTable);
                Constraint constraint = new Constraint(ConstraintType.NonlinearInequality, exp);
                addConstraint(constraint);
                continue;
            }
            if (token.equalsIgnoreCase(ConstraintType.NonlinearEquality.toString())) {
                Expression exp = MathFunctionDefinitions.fixFunctionSyntax(tokens);
                SimpleSymbolTable symbolTable = new SimpleSymbolTable(getParameterNames());
                exp.bindExpression(symbolTable);
                Constraint constraint = new Constraint(ConstraintType.NonlinearEquality, exp);
                addConstraint(constraint);
                continue;
            }
            throw new RuntimeException("unexpected identifier " + token);
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("line #" + (tokens.lineIndex() + 1) + " Exception: " + e.getMessage());
    }
}

Example 8 with SimpleSymbolTable

use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.

the class TimeFunctionPanel method refreshPlot.

private void refreshPlot() throws Exception {
    // try {
    Expression exp = new Expression(funcTextField.getText());
    exp.flatten();
    SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "pi" /*, "x", "y", "z"*/
    });
    exp.bindExpression(symbolTable);
    double[] valueArray = new double[2];
    valueArray[1] = Math.PI;
    // valueArray[ReservedVariable.Z.getIndex()] = 0 ;
    // valueArray[ReservedVariable.Y.getIndex()] = 0 ;
    // valueArray[ReservedVariable.X.getIndex()] = 0 ;
    int totalTimePoints = 0;
    double beginTime = 0;
    double timeStep = 0;
    double parseEndTime = 0;
    try {
        beginTime = Double.parseDouble(timeBegTextField.getText());
    } catch (Exception e) {
        throw new Exception("Couldn't evaluate 'Time Begin' as number\n" + e.getMessage());
    }
    try {
        timeStep = Double.parseDouble(timeStepTextField.getText());
        if (timeStep <= 0) {
            throw new Exception("timestep value = " + timeStep);
        }
    } catch (Exception e) {
        throw new Exception("'Time Step' must be > 0\n" + e.getMessage());
    }
    try {
        parseEndTime = Double.parseDouble(endTimeTextField.getText());
    } catch (Exception e) {
        throw new Exception("Couldn't evaluate 'Time End' as number\n" + e.getMessage());
    }
    try {
        if (beginTime > parseEndTime || beginTime == parseEndTime) {
            throw new Exception("endTime must be greater than beginTime");
        }
        totalTimePoints = (int) Math.ceil((parseEndTime - beginTime) / timeStep);
    // if(totalTimePoints <= 0){
    // throw new Exception("calculated number of time points ="+totalTimePoints);
    // }
    } catch (Exception e) {
        throw new Exception("check beginTime, endTime and timeStep: ((endTime-beginTime)/timeStep) must be greater than 0" + "\n" + e.getMessage());
    }
    double[] timePoints = new double[totalTimePoints];
    double[] funcVals = new double[totalTimePoints];
    for (int i = 0; i < totalTimePoints; i++) {
        valueArray[ReservedVariable.TIME.getIndex()] = beginTime + i * timeStep;
        timePoints[i] = valueArray[ReservedVariable.TIME.getIndex()];
        funcVals[i] = exp.evaluateVector(valueArray);
    }
    PlotData plotData = new PlotData(timePoints, funcVals);
    Plot2D plot2D = new Plot2D(null, null, new String[] { "Time Function" }, new PlotData[] { plotData }, new String[] { "Time Function Value", "Time", "[" + "Time Function" + "]" });
    plotPane.setPlot2D(plot2D);
// } catch (Exception e) {
// e.printStackTrace();
// DialogUtils.showErrorDialog(this, "Error refreshing Plot:\n"+e.getMessage(), e);
// plotPane.setPlot2D(	null);
// }
}

Example 9 with SimpleSymbolTable

use of cbit.vcell.parser.SimpleSymbolTable in project vcell by virtualcell.

the class PDEDataViewer method plotSpaceStats.

void plotSpaceStats(TSJobResultsSpaceStats tsjrss) {
    // Determine if Volume or Membrane
    DataIdentifier[] diArr = getPdeDataContext().getDataIdentifiers();
    boolean bVolume = true;
    for (int i = 0; i < diArr.length; i += 1) {
        if (diArr[i].getName().equals(tsjrss.getVariableNames()[0])) {
            if (diArr[i].getVariableType().equals(VariableType.MEMBRANE) || diArr[i].getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                bVolume = false;
                break;
            }
        }
    }
    SymbolTableEntry[] symbolTableEntries = null;
    if (tsjrss.getVariableNames().length == 1) {
        // max.mean.min,sum
        symbolTableEntries = new SymbolTableEntry[3];
        if (getSimulation() != null && getSimulation().getMathDescription() != null) {
            symbolTableEntries[0] = getSimulation().getMathDescription().getEntry(tsjrss.getVariableNames()[0]);
        } else {
            symbolTableEntries[0] = new SimpleSymbolTable(tsjrss.getVariableNames()).getEntry(tsjrss.getVariableNames()[0]);
        }
        symbolTableEntries[1] = symbolTableEntries[0];
        symbolTableEntries[2] = symbolTableEntries[0];
    }
    SymbolTableEntry[] finalSymbolTableEntries = symbolTableEntries;
    boolean finalBVolume = bVolume;
    PlotPane plotPane = new cbit.plot.gui.PlotPane();
    plotPane.setPlot2D(new SingleXPlot2D(finalSymbolTableEntries, getSimulationModelInfo().getDataSymbolMetadataResolver(), "Time", new String[] { "Max", (tsjrss.getWeightedMean() != null ? "WeightedMean" : "UnweightedMean"), "Min" /*,
				(tsjrss.getWeightedSum() != null?"WeightedSum":"UnweightedSum")*/
    }, new double[][] { tsjrss.getTimes(), tsjrss.getMaximums()[0], (tsjrss.getWeightedMean() != null ? tsjrss.getWeightedMean()[0] : tsjrss.getUnweightedMean()[0]), tsjrss.getMinimums()[0] /*,
				(tsjrss.getWeightedSum() != null?tsjrss.getWeightedSum()[0]:tsjrss.getUnweightedSum()[0])*/
    }, new String[] { "Statistics Plot for " + tsjrss.getVariableNames()[0] + (tsjrss.getTotalSpace() != null ? " (ROI " + (finalBVolume ? "volume" : "area") + "=" + tsjrss.getTotalSpace()[0] + ")" : ""), ReservedVariable.TIME.getName(), "[" + tsjrss.getVariableNames()[0] + "]" }));
    String title = "Statistics: (" + tsjrss.getVariableNames()[0] + ") ";
    if (getSimulationModelInfo() != null) {
        title += getSimulationModelInfo().getContextName() + " " + getSimulationModelInfo().getSimulationName();
    }
    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(PDEDataViewer.this);
    ChildWindow childWindow = childWindowManager.addChildWindow(plotPane, plotPane, title);
    childWindow.setIsCenteredOnParent();
    childWindow.pack();
    childWindow.show();
}

Example 10 with SimpleSymbolTable

use of cbit.vcell.parser.SimpleSymbolTable 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);
}