Examples with Geometry cbit.vcell.geometry.Geometry used on opensource projects

Example 36 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryFilamentCurvePanel method setGeometry.

/**
 * Sets the geometry property (cbit.vcell.geometry.Geometry) value.
 * @param geometry The new value for the property.
 * @see #getGeometry
 */
public void setGeometry(cbit.vcell.geometry.Geometry geometry) {
    cbit.vcell.geometry.Geometry oldValue = fieldGeometry;
    fieldGeometry = geometry;
    firePropertyChange("geometry", oldValue, geometry);
}

Example 37 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryGuiTest method main.

public static void main(java.lang.String[] args) {
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        GeometryViewer aGeometryViewer;
        aGeometryViewer = new GeometryViewer();
        frame.setContentPane(aGeometryViewer);
        frame.setSize(aGeometryViewer.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        Geometry csGeometry = getExampleGeometryCSG();
        // try to convert this CSG geometry to image
        ISize imageSize = csGeometry.getGeometrySpec().getDefaultSampledImageSize();
        Geometry imageGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), csGeometry, imageSize);
        // aGeometryViewer.setGeometry(csGeometry);
        aGeometryViewer.setGeometry(imageGeometry);
        frame.setSize(600, 600);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 38 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryGuiTest method getExampleGeometryCSG.

public static Geometry getExampleGeometryCSG() throws PropertyVetoException, ExpressionException, GeometryException, ImageException {
    // translated rotated cube
    CSGPrimitive cube = new CSGPrimitive("cube", CSGPrimitive.PrimitiveType.CUBE);
    CSGRotation rotatedCube = new CSGRotation("Rotation", new Vect3d(1, 2, 3), Math.PI / 4.0);
    rotatedCube.setChild(cube);
    // translated sphere
    CSGTranslation translatedSphere = new CSGTranslation("translation", new Vect3d(0.5, 0.5, 0.5));
    CSGPrimitive sphere = new CSGPrimitive("sphere", CSGPrimitive.PrimitiveType.SPHERE);
    translatedSphere.setChild(sphere);
    // union
    CSGSetOperator csgSetOperator = new CSGSetOperator("difference", OperatorType.DIFFERENCE);
    csgSetOperator.addChild(rotatedCube);
    csgSetOperator.addChild(translatedSphere);
    // scaled union
    CSGScale csgScale = new CSGScale("scale", new Vect3d(3, 3, 3));
    csgScale.setChild(csgSetOperator);
    CSGTranslation csgTranslatedUnion = new CSGTranslation("translationUnion", new Vect3d(5, 5, 5));
    csgTranslatedUnion.setChild(csgScale);
    Geometry geometry = new Geometry("csg", 3);
    CSGObject csgObject = new CSGObject(null, "obj1", 1);
    csgObject.setRoot(csgTranslatedUnion);
    geometry.getGeometrySpec().addSubVolume(new AnalyticSubVolume("background", new Expression(1.0)));
    geometry.getGeometrySpec().addSubVolume(csgObject, true);
    geometry.refreshDependencies();
    geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
    return geometry;
}

Example 39 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class BioModelTreeModel method propertyChange.

/**
 * Insert the method's description here.
 * Creation date: (5/9/01 8:28:22 AM)
 * @param evt java.beans.PropertyChangeEvent
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    try {
        if (evt.getSource() == getBioModel() && evt.getPropertyName().equals("simulations")) {
            refreshTree();
            Simulation[] oldSims = (Simulation[]) evt.getOldValue();
            if (oldSims != null) {
                for (int i = 0; i < oldSims.length; i++) {
                    oldSims[i].removePropertyChangeListener(this);
                }
            }
            Simulation[] newSims = (Simulation[]) evt.getNewValue();
            if (newSims != null) {
                for (int i = 0; i < newSims.length; i++) {
                    newSims[i].addPropertyChangeListener(this);
                }
            }
        } else if (evt.getSource() == getBioModel() && evt.getPropertyName().equals("simulationContexts")) {
            refreshTree();
            SimulationContext[] oldSCs = (SimulationContext[]) evt.getOldValue();
            if (oldSCs != null) {
                for (int i = 0; i < oldSCs.length; i++) {
                    oldSCs[i].removePropertyChangeListener(this);
                }
            }
            SimulationContext[] newSCs = (SimulationContext[]) evt.getNewValue();
            if (newSCs != null) {
                for (int i = 0; i < newSCs.length; i++) {
                    newSCs[i].addPropertyChangeListener(this);
                }
            }
        } else if (evt.getSource() == getBioModel() && evt.getPropertyName().equals("description")) {
            BioModel bioModel = (BioModel) evt.getSource();
            BioModelNode bioModelNode = ((BioModelNode) getRoot()).findNodeByUserObject(bioModel);
            BioModelNode annotNode = bioModelNode.findNodeByUserObject(new Annotation((String) evt.getOldValue()));
            if (annotNode == null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                // 
                // must add annotation node (was null string)
                // 
                bioModelNode.insert(new BioModelNode(new Annotation((String) evt.getNewValue()), false), 0);
                nodeStructureChanged(bioModelNode);
            } else if (annotNode != null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                // 
                // change annotation content for annotation node
                // 
                annotNode.setUserObject(new Annotation((String) evt.getNewValue()));
                nodeChanged(annotNode);
            } else if (annotNode != null && (evt.getNewValue() == null || ((String) evt.getNewValue()).equals(""))) {
                // 
                // delete annotation node
                // 
                removeNodeFromParent(annotNode);
            }
        } else if (evt.getSource() instanceof Simulation) {
            if (evt.getPropertyName().equals("name")) {
                Simulation sim = (Simulation) evt.getSource();
                BioModelNode simNode = ((BioModelNode) getRoot()).findNodeByUserObject(sim);
                nodeChanged(simNode);
            } else if (evt.getPropertyName().equals("description")) {
                Simulation sim = (Simulation) evt.getSource();
                BioModelNode simNode = ((BioModelNode) getRoot()).findNodeByUserObject(sim);
                BioModelNode annotNode = simNode.findNodeByUserObject(new Annotation((String) evt.getOldValue()));
                if (annotNode == null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                    // 
                    // must add annotation node (was null string)
                    // 
                    simNode.insert(new BioModelNode(new Annotation((String) evt.getNewValue()), false), 0);
                    nodeStructureChanged(simNode);
                } else if (annotNode != null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                    // 
                    // change annotation content for annotation node
                    // 
                    annotNode.setUserObject(new Annotation((String) evt.getNewValue()));
                    nodeChanged(annotNode);
                } else if (annotNode != null && (evt.getNewValue() == null || ((String) evt.getNewValue()).equals(""))) {
                    // 
                    // delete annotation node
                    // 
                    removeNodeFromParent(annotNode);
                }
            }
        } else if (evt.getSource() instanceof SimulationContext) {
            if (evt.getPropertyName().equals("geometry")) {
                Geometry oldGeometry = (Geometry) evt.getOldValue();
                Geometry newGeometry = (Geometry) evt.getNewValue();
                BioModelNode geoNode = ((BioModelNode) getRoot()).findNodeByUserObject(oldGeometry);
                geoNode.setUserObject(newGeometry);
                nodeChanged(geoNode);
            } else if (evt.getPropertyName().equals("name")) {
                SimulationContext simContext = (SimulationContext) evt.getSource();
                BioModelNode scNode = ((BioModelNode) getRoot()).findNodeByUserObject(simContext);
                nodeChanged(scNode);
            } else if (evt.getPropertyName().equals("description")) {
                SimulationContext simContext = (SimulationContext) evt.getSource();
                BioModelNode scNode = ((BioModelNode) getRoot()).findNodeByUserObject(simContext);
                BioModelNode annotNode = scNode.findNodeByUserObject(new Annotation((String) evt.getOldValue()));
                if (annotNode == null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                    // 
                    // must add annotation node (was null string)
                    // 
                    scNode.insert(new BioModelNode(new Annotation((String) evt.getNewValue()), false), 0);
                    nodeStructureChanged(scNode);
                } else if (annotNode != null && evt.getNewValue() != null && !((String) evt.getNewValue()).equals("")) {
                    // 
                    // change annotation content for annotation node
                    // 
                    annotNode.setUserObject(new Annotation((String) evt.getNewValue()));
                    nodeChanged(annotNode);
                } else if (annotNode != null && (evt.getNewValue() == null || ((String) evt.getNewValue()).equals(""))) {
                    // 
                    // delete annotation node
                    // 
                    removeNodeFromParent(annotNode);
                }
            } else if (evt.getPropertyName().equals("mathDescription")) {
                SimulationContext simContext = (SimulationContext) evt.getSource();
                BioModelNode scNode = ((BioModelNode) getRoot()).findNodeByUserObject(simContext);
                nodeStructureChanged(scNode);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 40 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class BioModelTreePanel method actionsOnClick.

/**
 * Comment
 */
private void actionsOnClick(MouseEvent mouseEvent) {
    DefaultMutableTreeNode currentTreeSelection = (DefaultMutableTreeNode) getJTree2().getLastSelectedPathComponent();
    Object selectedObject = null;
    if (currentTreeSelection == null) {
        return;
    }
    selectedObject = currentTreeSelection.getUserObject();
    // double click
    if (mouseEvent.getClickCount() == 2) {
        if (selectedObject instanceof SimulationContext) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Annotation) {
            editAnnotation();
        } else if (selectedObject instanceof MathDescription) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_MATH, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Geometry) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_GEOMETRY, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof Simulation) {
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_SIMULATION, mouseEvent.getModifiers()));
        } else if (selectedObject instanceof MathType) {
            // deterministic or stochastic or rule-bsaed
            fireActionPerformed(new ActionEvent(this, mouseEvent.getID(), GuiConstants.ACTIONCMD_OPEN_APPLICATION_DETSTOCH, mouseEvent.getModifiers()));
        }
        return;
    }
    // right click
    if (mouseEvent.isPopupTrigger()) {
        Point mousePoint = mouseEvent.getPoint();
        if (selectedObject instanceof BioModel) {
            getBioModelPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        } else if (selectedObject instanceof SimulationContext) {
            getAppPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        } else if (selectedObject instanceof Simulation) {
            getSimPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        }
        if (selectedObject instanceof Annotation) {
            getEditAnnotationPopupMenu().show(getJTree2(), mousePoint.x, mousePoint.y);
        }
    }
}