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

Example 1 with ColumnDescription

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

the class ODEDataViewer method updateMetadata.

private void updateMetadata() {
    /* Set the target from the source */
    if (getOdeSolverResultSet() == null) {
        return;
    }
    final HashMap<String, DataSymbolMetadata> auxDataSymbolMap = new HashMap();
    for (ColumnDescription columnDescription : getOdeSolverResultSet().getColumnDescriptions()) {
        if (columnDescription.getName().startsWith("sens_") && columnDescription.getName().contains("_wrt_")) {
            DataSymbolMetadata dataSymbolMetadata = sensitivityMetaDataParser(columnDescription.getName());
            auxDataSymbolMap.put(columnDescription.getName(), dataSymbolMetadata);
        }
    }
    // check if clienttaskdispatcher is busy, if so schedule this method to run later (workaround spurious threading problem)
    if ((odeDataViewersetupTimer = ClientTaskDispatcher.getBlockingTimer(ODEDataViewer.this, null, null, odeDataViewersetupTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            updateMetadata();
        }
    }, "ODEDataViewer Setup...")) != null) {
        return;
    }
    try {
        AsynchClientTask filterCategoriesTask = new AsynchClientTask("Calculating Filter...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (ODEDataViewer.this.getSimulationModelInfo() != null) {
                    SimulationModelInfo simulationModelInfo = ODEDataViewer.this.getSimulationModelInfo();
                    simulationModelInfo.getDataSymbolMetadataResolver().populateDataSymbolMetadata(auxDataSymbolMap);
                }
            }
        };
        AsynchClientTask firePropertyChangeTask = new AsynchClientTask("Fire Property Change...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                SimulationModelInfo simulationModelInfo = ODEDataViewer.this.getSimulationModelInfo();
                ODEDataInterfaceImpl oDEDataInterfaceImpl = new ODEDataInterfaceImpl(getOdeSolverResultSet(), simulationModelInfo);
                getODESolverPlotSpecificationPanel1().setMyDataInterface(oDEDataInterfaceImpl);
            // new Thread(new Runnable() {
            // @Override
            // public void run() {
            // while(ClientTaskDispatcher.isBusy()){
            // try{Thread.sleep(200);}catch(Exception e){e.printStackTrace();}
            // }
            // SwingUtilities.invokeLater(new Runnable() {
            // @Override
            // public void run() {
            // ((Window)BeanUtils.findTypeParentOfComponent(ODEDataViewer.this, Window.class)).toFront();
            // }
            // });
            // }
            // }).start();
            }
        };
        ClientTaskDispatcher.dispatch(ODEDataViewer.this, new Hashtable<String, Object>(), new AsynchClientTask[] { filterCategoriesTask, firePropertyChangeTask }, false, false, false, null, true);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 2 with ColumnDescription

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

the class RowColumnResultSet method createResultSetSymbolTable.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2003 4:32:00 PM)
 * @return cbit.vcell.parser.SymbolTable
 */
private VariableSymbolTable createResultSetSymbolTable(boolean bIncludeFunctions) {
    // 
    // create symbol table for binding expression against data columns and functions (of data columns)
    // 
    VariableSymbolTable resultSetSymbolTable = new VariableSymbolTable();
    for (int i = 0; i < getColumnDescriptionsCount(); i++) {
        ColumnDescription colDesc = getColumnDescriptions(i);
        if (colDesc instanceof ODESolverResultSetColumnDescription) {
            Domain domain = null;
            VolVariable vVar = new VolVariable(colDesc.getName(), domain);
            vVar.setIndex(i);
            resultSetSymbolTable.addVar(vVar);
        } else if (bIncludeFunctions && colDesc instanceof FunctionColumnDescription) {
            FunctionColumnDescription funcColDesc = (FunctionColumnDescription) colDesc;
            Domain domain = null;
            Function func = new Function(funcColDesc.getName(), new Expression(funcColDesc.getExpression()), domain);
            func.setIndex(i);
            resultSetSymbolTable.addVar(func);
        }
    }
    return resultSetSymbolTable;
}

Example 3 with ColumnDescription

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

the class RowColumnResultSet method extractColumn.

/**
 * getVariableNames method comment.
 *  If column is empty, return null or an empty array?
 *  For now, null...
 */
public synchronized double[] extractColumn(int c) throws ExpressionException {
    double[] values = null;
    if (getRowCount() > 0) {
        ColumnDescription colDescription = getColumnDescriptions(c);
        if (colDescription instanceof FunctionColumnDescription) {
            Expression exp = ((FunctionColumnDescription) colDescription).getExpression();
            // 
            // must rebind expression due to transient nature of expression binding (see ASTIdNode.symbolTableEntry)
            // 
            exp.bindExpression(getResultSetSymbolTableWithoutFunction());
            values = new double[getRowCount()];
            for (int r = 0; r < getRowCount(); r++) {
                try {
                    values[r] = exp.evaluateVector(getRow(r));
                } catch (DivideByZeroException e) {
                    e.printStackTrace(System.out);
                    values[r] = Double.NaN;
                } catch (FunctionDomainException e) {
                    e.printStackTrace(System.out);
                    values[r] = Double.NaN;
                }
            }
        } else {
            values = new double[getRowCount()];
            for (int r = 0; r < getRowCount(); r++) {
                values[r] = getRow(r)[c];
            }
        }
    }
    return (values);
}

Example 4 with ColumnDescription

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

the class ODESolverPlotSpecificationPanel method regeneratePlot2D.

/**
 * Comment
 */
private void regeneratePlot2D() throws ExpressionException, ObjectNotFoundException {
    if (getMyDataInterface() == null) {
        return;
    }
    if (!getMyDataInterface().isMultiTrialData()) {
        if (getXAxisComboBox_frm().getSelectedIndex() < 0) {
            return;
        } else {
            // double[] xData = getOdeSolverResultSet().extractColumn(getPlottableColumnIndices()[getXIndex()]);
            // getUnfilteredSortedXAxisNames
            double[] xData = getMyDataInterface().extractColumn((String) getXAxisComboBox_frm().getSelectedItem());
            double[][] allData = new double[((DefaultListModel) getYAxisChoice().getModel()).size() + 1][xData.length];
            String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
            allData[0] = xData;
            double[] yData = new double[xData.length];
            double currParamValue = 0.0;
            double deltaParamValue = 0.0;
            // Extrapolation calculations!
            if (getSensitivityParameter() != null) {
                int val = getSensitivityParameterSlider().getValue();
                double nominalParamValue = getSensitivityParameter().getConstantValue();
                double pMax = nominalParamValue * 1.1;
                double pMin = nominalParamValue * 0.9;
                int iMax = getSensitivityParameterSlider().getMaximum();
                int iMin = getSensitivityParameterSlider().getMinimum();
                double slope = (pMax - pMin) / (iMax - iMin);
                currParamValue = slope * val + pMin;
                deltaParamValue = currParamValue - nominalParamValue;
                getMaxLabel().setText(Double.toString(pMax));
                getMinLabel().setText(Double.toString(pMin));
                getCurLabel().setText(Double.toString(currParamValue));
            }
            if (!getLogSensCheckbox().getModel().isSelected()) {
                // When log sensitivity check box is not selected.
                for (int i = 0; i < allData.length - 1; i++) {
                    // If sensitivity analysis is enabled, extrapolate values for State vars and non-sensitivity functions
                    if (getSensitivityParameter() != null) {
                        ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                        double[] sens = getSensValues(cd);
                        yData = getMyDataInterface().extractColumn(cd.getName());
                        // sens array != null for non-sensitivity state vars and functions, so extrapolate
                        if (sens != null) {
                            for (int j = 0; j < sens.length; j++) {
                                if (Math.abs(yData[j]) > 1e-6) {
                                    // away from zero, exponential extrapolation
                                    allData[i + 1][j] = yData[j] * Math.exp(deltaParamValue * sens[j] / yData[j]);
                                } else {
                                    // around zero - linear extrapolation
                                    allData[i + 1][j] = yData[j] + sens[j] * deltaParamValue;
                                }
                            }
                        // sens array == null for sensitivity state vars and functions, so don't change their original values
                        } else {
                            allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                        }
                    } else {
                        // No sensitivity analysis case, so do not alter the original values for any variable or function
                        allData[i + 1] = getMyDataInterface().extractColumn((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                    }
                    yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
                }
            } else {
                // When log sensitivity checkbox is selected.
                // Get sensitivity parameter and its value to compute log sensitivity
                Constant sensParam = getSensitivityParameter();
                double sensParamValue = sensParam.getConstantValue();
                getJLabelSensitivityParameter().setText("Sensitivity wrt Parameter " + sensParam.getName());
                // 
                for (int i = 0; i < allData.length - 1; i++) {
                    // Finding sensitivity var column for each column in result set.
                    ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
                    String sensVarName = null;
                    ColumnDescription[] allColumnDescriptions = getMyDataInterface().getAllColumnDescriptions();
                    for (int j = 0; j < allColumnDescriptions.length; j++) {
                        String obj = "sens_" + cd.getName() + "_wrt_" + sensParam.getName();
                        if (allColumnDescriptions[j].getName().equals(obj)) {
                            sensVarName = obj;
                            break;
                        }
                    }
                    int sensIndex = -1;
                    if (sensVarName != null) {
                        for (int j = 0; j < ((DefaultListModel) getYAxisChoice().getModel()).getSize(); j++) {
                            if (((String) ((DefaultListModel) getYAxisChoice().getModel()).get(j)).equals(sensVarName)) {
                                sensIndex = j;
                                break;
                            }
                        }
                    }
                    yData = getMyDataInterface().extractColumn(cd.getName());
                    // If sensitivity var exists, compute log sensitivity
                    if (sensVarName != null) {
                        double[] sens = getMyDataInterface().extractColumn(sensVarName);
                        for (int k = 0; k < yData.length; k++) {
                            // Extrapolated statevars and functions
                            if (Math.abs(yData[k]) > 1e-6) {
                                // away from zero, exponential extrapolation
                                allData[i + 1][k] = yData[k] * Math.exp(deltaParamValue * sens[k] / yData[k]);
                            } else {
                                // around zero - linear extrapolation
                                allData[i + 1][k] = yData[k] + sens[k] * deltaParamValue;
                            }
                            // Log sensitivity for the state variables and functions
                            // default if floating point problems
                            double logSens = 0.0;
                            if (Math.abs(yData[k]) > 0) {
                                double tempLogSens = sens[k] * sensParamValue / yData[k];
                                if (tempLogSens != Double.NEGATIVE_INFINITY && tempLogSens != Double.POSITIVE_INFINITY && tempLogSens != Double.NaN) {
                                    logSens = tempLogSens;
                                }
                            }
                            if (sensIndex > -1) {
                                allData[sensIndex + 1][k] = logSens;
                            }
                        }
                    // If sensitivity var does not exist, retain  original value of column (var or function).
                    } else {
                        if (!cd.getName().startsWith("sens_")) {
                            allData[i + 1] = yData;
                        }
                    }
                    yNames[i] = (String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i);
                }
            }
            String title = "";
            String xLabel = (String) getXAxisComboBox_frm().getSelectedItem();
            String yLabel = "";
            if (yNames.length == 1) {
                yLabel = yNames[0];
            }
            // Update Sensitivity parameter label depending on whether Log sensitivity check box is checked or not.
            if (!getLogSensCheckbox().getModel().isSelected()) {
                getJLabelSensitivityParameter().setText("");
            }
            SymbolTableEntry[] symbolTableEntries = null;
            if (getSymbolTable() != null && yNames != null && yNames.length > 0) {
                symbolTableEntries = new SymbolTableEntry[yNames.length];
                for (int i = 0; i < yNames.length; i += 1) {
                    SymbolTableEntry ste = getSymbolTable().getEntry(yNames[i]);
                    symbolTableEntries[i] = ste;
                }
            }
            SingleXPlot2D plot2D = new SingleXPlot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), xLabel, yNames, allData, new String[] { title, xLabel, yLabel });
            refreshVisiblePlots(plot2D);
            // here fire "singleXPlot2D" event, ODEDataViewer's event handler listens to it.
            setPlot2D(plot2D);
        }
    } else // end of none MultitrialData
    // multitrial data
    {
        // a column of data get from ODESolverRestultSet, which is actually the results for a specific variable during multiple trials
        double[] rowData = new double[getMyDataInterface().getRowCount()];
        PlotData[] plotData = new PlotData[((DefaultListModel) getYAxisChoice().getModel()).size()];
        for (int i = 0; i < plotData.length; i++) {
            ColumnDescription cd = getMyDataInterface().getColumnDescription((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
            rowData = getMyDataInterface().extractColumn(cd.getName());
            Point2D[] histogram = generateHistogram(rowData);
            double[] x = new double[histogram.length];
            double[] y = new double[histogram.length];
            for (int j = 0; j < histogram.length; j++) {
                x[j] = histogram[j].getX();
                y[j] = histogram[j].getY();
            }
            plotData[i] = new PlotData(x, y);
        }
        SymbolTableEntry[] symbolTableEntries = null;
        if (getSymbolTable() != null && ((DefaultListModel) getYAxisChoice().getModel()).size() > 0) {
            symbolTableEntries = new SymbolTableEntry[((DefaultListModel) getYAxisChoice().getModel()).size()];
            for (int i = 0; i < symbolTableEntries.length; i += 1) {
                symbolTableEntries[i] = getSymbolTable().getEntry((String) ((DefaultListModel) getYAxisChoice().getModel()).elementAt(i));
            }
        }
        String title = "Probability Distribution of Species";
        String xLabel = "Number of Particles";
        String yLabel = "";
        String[] yNames = new String[((DefaultListModel) getYAxisChoice().getModel()).size()];
        ((DefaultListModel) getYAxisChoice().getModel()).copyInto(yNames);
        Plot2D plot2D = new Plot2D(symbolTableEntries, getMyDataInterface().getDataSymbolMetadataResolver(), yNames, plotData, new String[] { title, xLabel, yLabel });
        refreshVisiblePlots(plot2D);
        setPlot2D(plot2D);
    }
}

Example 5 with ColumnDescription

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

the class ODESolverPlotSpecificationPanel method updateChoices.

/**
 * Insert the method's description here.
 * Creation date: (2/8/2001 4:56:15 PM)
 * @param cbit.vcell.solver.ode.ODESolverResultSet
 */
private synchronized void updateChoices(ODEDataInterface oDEDataInterface) throws ExpressionException, ObjectNotFoundException {
    if (oDEDataInterface == null) {
        return;
    }
    Object xAxisSelection = getXAxisComboBox_frm().getSelectedItem();
    Object[] yAxisSelections = getYAxisChoice().getSelectedValues();
    ArrayList<ColumnDescription> variableColumnDescriptions = new ArrayList<ColumnDescription>();
    ArrayList<ColumnDescription> sensitivityColumnDescriptions = new ArrayList<ColumnDescription>();
    ColumnDescription timeColumnDescription = null;
    // find TIME columnDescription
    ColumnDescription[] columnDescriptions = getMyDataInterface().getAllColumnDescriptions();
    for (int i = 0; i < columnDescriptions.length; i++) {
        if (columnDescriptions[i].getName().equals(ReservedVariable.TIME.getName())) {
            timeColumnDescription = columnDescriptions[i];
        }
    }
    // find filtered columnDescriptions
    columnDescriptions = getMyDataInterface().getFilteredColumnDescriptions();
    for (int i = 0; i < columnDescriptions.length; i++) {
        ColumnDescription cd = columnDescriptions[i];
        // If the column is "_initConnt" generated when using concentration as initial condition, we dont' put the function in list. amended again in August, 2008.
        if (cd.getParameterName() == null) {
            if (!cd.getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME) && !cd.getName().contains(DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT)) {
                variableColumnDescriptions.add(cd);
            }
        } else {
            sensitivityColumnDescriptions.add(cd);
        }
    }
    sortColumnDescriptions(variableColumnDescriptions);
    sortColumnDescriptions(sensitivityColumnDescriptions);
    // Hack this here, Later we can use an array utility...
    ArrayList<ColumnDescription> sortedColumndDescriptions = new ArrayList<ColumnDescription>();
    if (timeColumnDescription != null) {
        // add time first
        sortedColumndDescriptions.add(timeColumnDescription);
    }
    boolean bMultiTrialData = oDEDataInterface.isMultiTrialData();
    sortedColumndDescriptions.addAll(variableColumnDescriptions);
    if (!bMultiTrialData) {
        sortedColumndDescriptions.addAll(sensitivityColumnDescriptions);
    }
    // finally, update widgets
    try {
        getXAxisComboBox_frm().removeItemListener(ivjEventHandler);
        getYAxisChoice().removeListSelectionListener(ivjEventHandler);
        getComboBoxModelX_frm().removeAllElements();
        if (!bMultiTrialData) {
            // Don't put anything in X Axis, if the results of multiple trials are being displayed.
            ArrayList<ColumnDescription> xColumnDescriptions = new ArrayList<ColumnDescription>(Arrays.asList(getMyDataInterface().getAllColumnDescriptions()));
            sortColumnDescriptions(xColumnDescriptions);
            if (timeColumnDescription != null) {
                getComboBoxModelX_frm().addElement(timeColumnDescription.getName());
            }
            for (ColumnDescription columnDescription : xColumnDescriptions) {
                if (!columnDescription.getName().equals((timeColumnDescription == null ? null : timeColumnDescription.getName()))) {
                    getComboBoxModelX_frm().addElement(columnDescription.getName());
                }
            }
        }
        getDefaultListModelY().removeAllElements();
        for (int i = 0; i < sortedColumndDescriptions.size(); i++) {
            if (sortedColumndDescriptions.get(i).getName().equals(ReservedVariable.TIME.getName())) {
                continue;
            }
            getDefaultListModelY().addElement(sortedColumndDescriptions.get(i).getName());
        }
        if (sortedColumndDescriptions.size() > 0) {
            // Don't put anything in X Axis, if the results of multifple trials are being displayed.
            if (!bMultiTrialData) {
                getXAxisComboBox_frm().setSelectedItem(xAxisSelection);
                if (getXAxisComboBox_frm().getSelectedIndex() == -1) {
                    getXAxisComboBox_frm().setSelectedIndex(0);
                }
            }
            if (yAxisSelections != null && yAxisSelections.length > 0) {
                ArrayList<Integer> carryoverSelections = new ArrayList<Integer>();
                for (int i = 0; i < getYAxisChoice().getModel().getSize(); i++) {
                    for (int j = 0; j < yAxisSelections.length; j++) {
                        if (getYAxisChoice().getModel().getElementAt(i).equals(yAxisSelections[j])) {
                            carryoverSelections.add(i);
                            break;
                        }
                    }
                }
                if (carryoverSelections.size() > 0) {
                    int[] carryoverInts = new int[carryoverSelections.size()];
                    for (int i = 0; i < carryoverInts.length; i++) {
                        carryoverInts[i] = carryoverSelections.get(i);
                    }
                    getYAxisChoice().setSelectedIndices(carryoverInts);
                } else {
                    getYAxisChoice().setSelectedIndex((getYAxisChoice().getModel().getSize() > 1 ? 1 : 0));
                }
            } else {
                getYAxisChoice().setSelectedIndex(sortedColumndDescriptions.size() > 1 ? 1 : 0);
            }
        }
    } finally {
        getXAxisComboBox_frm().addItemListener(ivjEventHandler);
        getYAxisChoice().addListSelectionListener(ivjEventHandler);
    }
    regeneratePlot2D();
}