Examples with ColumnDescription cbit.vcell.util.ColumnDescription used on opensource projects

Example 6 with ColumnDescription

use of cbit.vcell.util.ColumnDescription in project vcell by virtualcell.

the class ODESolverPlotSpecificationPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
@SuppressWarnings({ "serial", "unchecked" })
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getFilterPanel().addPropertyChangeListener(ivjEventHandler);
    getYAxisChoice().addListSelectionListener(ivjEventHandler);
    this.addPropertyChangeListener(ivjEventHandler);
    getXAxisComboBox_frm().addItemListener(ivjEventHandler);
    getLogSensCheckbox().addActionListener(ivjEventHandler);
    getSensitivityParameterSlider().addChangeListener(ivjEventHandler);
    connPtoP1SetTarget();
    connPtoP3SetTarget();
    getYAxisChoice().setCellRenderer(new DefaultListCellRenderer() {

        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            ODEDataInterface mdi = getMyDataInterface();
            if (mdi == null) {
                return this;
            }
            String varName = (String) value;
            ColumnDescription cd = null;
            try {
                cd = mdi.getColumnDescription(varName);
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
            }
            if (cd instanceof FunctionColumnDescription && ((FunctionColumnDescription) cd).getIsUserDefined()) {
                if (function_icon == null) {
                    function_icon = new ImageIcon(getClass().getResource("/icons/function_icon.png"));
                }
                setIcon(function_icon);
            }
            if (mdi.getDataSymbolMetadataResolver() != null && mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName) != null) {
                DataSymbolMetadata dsm = mdi.getDataSymbolMetadataResolver().getDataSymbolMetadata(varName);
                String tooltipString = dsm.tooltipString;
                if (tooltipString == null) {
                    tooltipString = varName;
                }
                setToolTipText(tooltipString);
            }
            return this;
        }
    });
}

Example 7 with ColumnDescription

use of cbit.vcell.util.ColumnDescription in project vcell by virtualcell.

the class MathTestingUtilities method compareUnEqualResultSets.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:48:36 PM)
 * @param testResultSet cbit.vcell.solver.ode.ODESolverResultSet
 * @param referenceResultSet cbit.vcell.solver.ode.ODESolverResultSet
 */
public static SimulationComparisonSummary compareUnEqualResultSets(ODESolverResultSet testResultSet, ODESolverResultSet referenceResultSet, String[] varsToTest, double absErrorThreshold, double relErrorThreshold, int interpolationOrder) throws Exception {
    if (varsToTest == null) {
        throw new IllegalArgumentException("varsToTest must not be null");
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    int testTimeOrHistogramIndex = testResultSet.findColumn(ReservedVariable.TIME.getName());
    int refTimeOrHistogramIndex = referenceResultSet.findColumn(ReservedVariable.TIME.getName());
    if (testTimeOrHistogramIndex < 0 && refTimeOrHistogramIndex < 0) {
        testTimeOrHistogramIndex = testResultSet.findColumn(SimDataConstants.HISTOGRAM_INDEX_NAME);
        refTimeOrHistogramIndex = referenceResultSet.findColumn(SimDataConstants.HISTOGRAM_INDEX_NAME);
    }
    double[] testRSTimes = testResultSet.extractColumn(testTimeOrHistogramIndex);
    double[] refRSTimes = referenceResultSet.extractColumn(refTimeOrHistogramIndex);
    for (int i = 0; i < varsToTest.length; i++) {
        int refRSIndex = referenceResultSet.findColumn(varsToTest[i]);
        if (refRSIndex == -1) {
            if (varsToTest[i].endsWith(AbstractMathMapping.MATH_VAR_SUFFIX_SPECIES_COUNT)) {
                String varNameWithoutCount = varsToTest[i].replace(AbstractMathMapping.MATH_VAR_SUFFIX_SPECIES_COUNT, "");
                refRSIndex = referenceResultSet.findColumn(varNameWithoutCount);
                if (refRSIndex == -1) {
                    throw new RuntimeException("neither variable '" + varsToTest[i] + "' nor '" + varNameWithoutCount + "' found in reference dataset");
                }
            } else {
                throw new RuntimeException("variable '" + varsToTest[i] + "' not found in reference dataset");
            }
        }
        ColumnDescription refColDesc = referenceResultSet.getColumnDescriptions(refRSIndex);
        double[] refData = referenceResultSet.extractColumn(refRSIndex);
        int testRSIndex = testResultSet.findColumn(varsToTest[i]);
        if (testRSIndex == -1) {
            throw new RuntimeException("variable '" + varsToTest[i] + "' not found in test dataset");
        }
        double[] testData = testResultSet.extractColumn(testRSIndex);
        // Resampling test data
        double[] resampledTestData = interpolateArray(refRSTimes, testRSTimes, testData, interpolationOrder);
        DataErrorSummary tempVar = new DataErrorSummary();
        for (int j = 0; j < refData.length; j++) {
            tempVar.addDataValues(refData[j], resampledTestData[j], refRSTimes[j], 0, absErrorThreshold, relErrorThreshold);
        }
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(refColDesc.getName(), tempVar.getMinRef(), tempVar.getMaxRef(), tempVar.getMaxAbsoluteError(), tempVar.getMaxRelativeError(), tempVar.getL2Norm(), tempVar.getTimeAtMaxAbsoluteError(), tempVar.getIndexAtMaxAbsoluteError(), tempVar.getTimeAtMaxRelativeError(), tempVar.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 8 with ColumnDescription

use of cbit.vcell.util.ColumnDescription in project vcell by virtualcell.

the class MathTestingUtilities method compareResultSets.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:48:36 PM)
 * @param testResultSet cbit.vcell.solver.ode.ODESolverResultSet
 * @param referenceResultSet cbit.vcell.solver.ode.ODESolverResultSet
 */
public static SimulationComparisonSummary compareResultSets(ODESolverResultSet testResultSet, ODESolverResultSet referenceResultSet, String[] varsToTest, String type, double absErrorThreshold, double relErrorThreshold) throws Exception {
    if (varsToTest == null) {
        throw new IllegalArgumentException("varsToTest must not be null");
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    double[] timeData = referenceResultSet.extractColumn(referenceResultSet.findColumn(ODESolverResultSet.TIME_COLUMN));
    for (int i = 0; i < varsToTest.length; i++) {
        int refRSIndex = referenceResultSet.findColumn(varsToTest[i]);
        if (refRSIndex == -1) {
            throw new RuntimeException("variable '" + varsToTest[i] + "' not found in reference dataset");
        }
        ColumnDescription refColDesc = referenceResultSet.getColumnDescriptions(refRSIndex);
        double[] refData = referenceResultSet.extractColumn(refRSIndex);
        int testRSIndex = testResultSet.findColumn(varsToTest[i]);
        if (testRSIndex == -1) {
            throw new RuntimeException("variable '" + varsToTest[i] + "' not found in test dataset");
        }
        double[] testData = testResultSet.extractColumn(testRSIndex);
        DataErrorSummary tempVar = new DataErrorSummary();
        for (int j = 0; j < refData.length; j++) {
            if (type.equals(TestCaseNew.EXACT_STEADY)) {
                if (j != (refData.length - 1)) {
                    continue;
                }
            }
            tempVar.addDataValues(refData[j], testData[j], timeData[j], 0, absErrorThreshold, relErrorThreshold);
        }
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(refColDesc.getName(), tempVar.getMinRef(), tempVar.getMaxRef(), tempVar.getMaxAbsoluteError(), tempVar.getMaxRelativeError(), tempVar.getL2Norm(), tempVar.getTimeAtMaxAbsoluteError(), tempVar.getIndexAtMaxAbsoluteError(), tempVar.getTimeAtMaxRelativeError(), tempVar.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 9 with ColumnDescription

use of cbit.vcell.util.ColumnDescription in project vcell by virtualcell.

the class ODESolverPlotSpecificationPanel method getSensitivityParameter.

/**
 * // Method to obtain the sensitivity parameter (if applicable). The method checks the column description names in the
 * // result set to find any column description that begins with the substring "sens" and contains the substring "wrt_".
 * // If there is, then the last portion of that column description name is the parameter name. The sensitivity parameter
 * // is also stored as a function column description in the result set (as a constant function). The value is extracted
 * // from the result set, and a new Constant is created (with the name and value of the parameter) and returned. If no
 * // column description starts with the substring "sens" or if the column for the parameter does not exist in the result
 * // set, the method returns null.
 */
private Constant getSensitivityParameter() throws ExpressionException {
    String sensParamName = "";
    ColumnDescription[] fcds = getMyDataInterface().getAllColumnDescriptions();
    // Check for any column description name that starts with the substring "sens" and contains "wrt_".
    for (int i = 0; i < fcds.length; i++) {
        if (fcds[i].getName().startsWith("sens_")) {
            int c = fcds[i].getName().indexOf("wrt_");
            sensParamName = fcds[i].getName().substring(c + 4);
            if (!sensParamName.equals(null) || !sensParamName.equals("")) {
                break;
            }
        }
    }
    double sensParamValue = 0.0;
    if (sensParamName.equals("")) {
        return null;
    }
    // If the sens param column exists in the result set, create a Constant and return it, else return null.
    try {
        sensParamValue = getMyDataInterface().extractColumn(sensParamName)[1];
    } catch (ObjectNotFoundException e) {
        // System.out.println("REUSULT SET DOES NOT HAVE SENSITIVITY ANALYSIS");
        return null;
    }
    Constant sensParam = new Constant(sensParamName, new Expression(sensParamValue));
    return sensParam;
}

Example 10 with ColumnDescription

use of cbit.vcell.util.ColumnDescription in project vcell by virtualcell.

the class ODEDataInterfaceImpl method getFilteredColumnDescriptions.

@Override
public ColumnDescription[] getFilteredColumnDescriptions() {
    if (selectedFilters == null || simulationModelInfo == null) {
        return getOdeSolverResultSet().getColumnDescriptions();
    } else {
        ArrayList<ColumnDescription> selectedColumnDescriptions = new ArrayList<ColumnDescription>();
        for (int i = 0; i < getOdeSolverResultSet().getColumnDescriptions().length; i++) {
            DataSymbolMetadata dataSymbolMetadata = simulationModelInfo.getDataSymbolMetadataResolver().getDataSymbolMetadata(getOdeSolverResultSet().getColumnDescriptions()[i].getName());
            ModelCategoryType selectedFilterCategory = null;
            if (dataSymbolMetadata != null) {
                selectedFilterCategory = dataSymbolMetadata.filterCategory;
            }
            for (int j = 0; j < selectedFilters.length; j++) {
                if (selectedFilters[j].equals(selectedFilterCategory)) {
                    selectedColumnDescriptions.add(getOdeSolverResultSet().getColumnDescriptions()[i]);
                    break;
                }
            }
        }
        return selectedColumnDescriptions.toArray(new ColumnDescription[0]);
    }
}