Examples with Point2D java.awt.geom.Point2D used on opensource projects

Example 91 with Point2D

use of java.awt.geom.Point2D 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 92 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class UShortImage method createCircularBinaryKernel.

public static KernelJAI createCircularBinaryKernel(int radius) {
    int enclosingBoxSideLength = radius * 2 + 1;
    float[] kernalData = new float[enclosingBoxSideLength * enclosingBoxSideLength];
    Point2D kernalPoint = new Point2D.Float(0f, 0f);
    int index = 0;
    for (int y = -radius; y <= radius; y++) {
        for (int x = -radius; x <= radius; x++) {
            if (kernalPoint.distance(x, y) <= radius) {
                kernalData[index] = 1.0f;
            }
            index++;
        }
    }
    return new KernelJAI(enclosingBoxSideLength, enclosingBoxSideLength, radius, radius, kernalData);
}

Example 93 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class EdgeShape method getParameterAtArcLength.

protected static double getParameterAtArcLength(CubicCurve2D curve, double startT, double endT, double arcLength, int numIntervals) {
    double currentT = startT;
    double totalLength = 0.0;
    double deltaT = (endT - startT) / numIntervals;
    Point2D curr = evaluate(curve, currentT);
    for (int i = 0; i < numIntervals && totalLength < arcLength; i++) {
        currentT = startT + i * deltaT;
        Point2D next = evaluate(curve, currentT);
        double dx = next.getX() - curr.getX();
        double dy = next.getY() - curr.getY();
        totalLength += Math.sqrt(dx * dx + dy * dy);
        curr = next;
    }
    return currentT;
}

Example 94 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class BioPaxShape method paintSelf.

@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
    RenderingHints oldRenderingHints = g.getRenderingHints();
    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    int shapeHeight = getSpaceManager().getSize().height;
    int shapeWidth = getSpaceManager().getSize().width;
    int offsetX = (shapeWidth - getPreferredWidth()) / 2;
    int offsetY = (shapeHeight - getPreferredHeight()) / 2;
    Graphics2D g2D = g;
    if (icon == null) {
        icon = new Area();
        icon.add(new Area(new Ellipse2D.Double(offsetX, offsetY, getPreferredWidth(), getPreferredHeight())));
    }
    Area movedIcon = icon.createTransformedArea(AffineTransform.getTranslateInstance(absPosX, absPosY));
    g.setColor((!hasPCLink() && !isSelected() ? darkerBackground : backgroundColor));
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    Color exterior = !hasPCLink() && !isSelected() ? darkerBackground : backgroundColor;
    Color interior = exterior.brighter();
    exterior = exterior.darker();
    Point2D center = new Point2D.Float(absPosX + getPreferredWidth() / 2, absPosY + getPreferredWidth() / 2);
    float radius = getPreferredWidth() * 0.5f;
    Point2D focus = new Point2D.Float(absPosX + getPreferredWidth() / 2 - 2, absPosY + getPreferredWidth() / 2 - 2);
    float[] dist = { 0.1f, 1.0f };
    // Color[] colors = {Color.white, exterior};
    Color[] colors = { interior, exterior };
    RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
    g2D.setPaint(p);
    g2D.fill(movedIcon);
    g.setColor(forgroundColor);
    g2D.draw(movedIcon);
    // draw label
    if (getLabel() != null && getLabel().length() > 0) {
        if (isSelected()) {
            // clear background and outline to make selected label stand out
            drawRaisedOutline(getLabelPos().x + absPosX - 5, getLabelPos().y + absPosY - getLabelSize().height + 3, getLabelSize().width + 10, getLabelSize().height, g, Color.white, forgroundColor, Color.gray);
        }
        g.setColor(forgroundColor);
        g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y + absPosY);
    }
    if (hasRelationships) {
        ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
    }
    g.setRenderingHints(oldRenderingHints);
}

Example 95 with Point2D

use of java.awt.geom.Point2D in project vcell by virtualcell.

the class MolecularTypeSmallShape method paintSpecies.

// --------------------------------------------------------------------------------------
// paintComponent is being overridden in the renderer
// 
private void paintSpecies(Graphics g) {
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g2.getColor();
    Color primaryColor = null;
    Color border = Color.black;
    int finalHeight = baseHeight;
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    if (mt == null && mtp == null) {
        if (shapeManager == null) {
            primaryColor = Color.green.darker().darker();
        } else {
            primaryColor = shapeManager.isEditable() ? Color.green.darker().darker() : Color.gray;
        }
        finalHeight = baseHeight + 3;
        Point2D center = new Point2D.Float(xPos + finalHeight / 3, yPos + finalHeight / 3);
        float radius = finalHeight * 0.5f;
        Point2D focus = new Point2D.Float(xPos + finalHeight / 3 - 1, yPos + finalHeight / 3 - 1);
        float[] dist = { 0.1f, 1.0f };
        Color[] colors = { Color.white, primaryColor };
        RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
        g2.setPaint(p);
        Ellipse2D circle = new Ellipse2D.Double(xPos, yPos, finalHeight, finalHeight);
        g2.fill(circle);
        Ellipse2D circle2 = new Ellipse2D.Double(xPos - 1, yPos - 1, finalHeight, finalHeight);
        g2.setPaint(getDefaultColor(Color.darkGray));
        g2.draw(circle2);
        g.setColor(colorOld);
        return;
    } else {
        // molecular type, species pattern, observable
        if (mt == null || mt.getModel() == null) {
            primaryColor = Color.blue.darker().darker();
        } else {
            if (shapeManager != null) {
                if (shapeManager.isShowMoleculeColor()) {
                    RbmModelContainer rbmmc = mt.getModel().getRbmModelContainer();
                    List<MolecularType> mtList = rbmmc.getMolecularTypeList();
                    int index = mtList.indexOf(mt);
                    index = index % 7;
                    primaryColor = MolecularTypeLargeShape.colorTable[index].darker().darker();
                } else {
                    primaryColor = Color.gray;
                }
                border = shapeManager.isEditable() ? Color.black : LargeShapeCanvas.uneditableShape;
            } else {
                RbmModelContainer rbmmc = mt.getModel().getRbmModelContainer();
                List<MolecularType> mtList = rbmmc.getMolecularTypeList();
                int index = mtList.indexOf(mt);
                index = index % 7;
                primaryColor = MolecularTypeLargeShape.colorTable[index].darker().darker();
            }
        }
        if (owner instanceof MolecularType && hasErrorIssues(owner, mt)) {
            primaryColor = Color.red;
        }
    }
    GradientPaint p = new GradientPaint(xPos, yPos, primaryColor, xPos, yPos + finalHeight / 2, Color.WHITE, true);
    g2.setPaint(p);
    RoundRectangle2D rect = new RoundRectangle2D.Float(xPos, yPos, width, finalHeight, cornerArc, cornerArc);
    g2.fill(rect);
    RoundRectangle2D inner = new RoundRectangle2D.Float(xPos + 1, yPos + 1, width - 2, finalHeight - 2, cornerArc - 3, cornerArc - 3);
    g2.setPaint(border);
    g2.draw(rect);
    g.setColor(colorOld);
    for (MolecularComponentSmallShape mcss : componentShapes) {
        mcss.paintSelf(g);
    }
    g.setColor(colorOld);
}