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

Example 1 with CSGTranslation

use of cbit.vcell.geometry.CSGTranslation 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 2 with CSGTranslation

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

the class ComsolModelBuilder method csgVisitor.

private static VCCGeomFeature csgVisitor(CSGNode node, ArrayList<VCCGeomFeature> geomFeatureList, String namePrefix) {
    final VCCGeomFeature newFeature;
    if (node instanceof CSGPrimitive) {
        CSGPrimitive csg = (CSGPrimitive) node;
        switch(csg.getType()) {
            case CONE:
                {
                    newFeature = new VCCCone(namePrefix + csg.getName());
                    break;
                }
            case CUBE:
                {
                    String[] size = new String[] { "2", "2", "2" };
                    String[] pos = new String[] { "-1", "-1", "-1" };
                    VCCBlock vccblock = new VCCBlock(namePrefix + csg.getName(), size, pos);
                    newFeature = vccblock;
                    break;
                }
            case CYLINDER:
                {
                    newFeature = new VCCCylinder(namePrefix + csg.getName());
                    break;
                }
            case SPHERE:
                {
                    String r = "1";
                    String[] pos = new String[] { "0", "0", "0" };
                    newFeature = new VCCSphere(namePrefix + csg.getName(), pos, r);
                    break;
                }
            default:
                {
                    throw new RuntimeException("csg primative type '" + csg.getType().name() + "' not yet supported in COMSOL model builder");
                }
        }
    } else if (node instanceof CSGSetOperator) {
        CSGSetOperator setOp = (CSGSetOperator) node;
        ArrayList<VCCGeomFeature> childSubtrees = new ArrayList<VCCGeomFeature>();
        for (CSGNode child : setOp.getChildren()) {
            VCCGeomFeature vccChild = csgVisitor(child, geomFeatureList, namePrefix);
            childSubtrees.add(vccChild);
        }
        switch(setOp.getOpType()) {
            case DIFFERENCE:
                {
                    if (childSubtrees.size() != 2) {
                        throw new RuntimeException("expecting exactly two children for CSG difference operator");
                    }
                    VCCDifference diff = new VCCDifference(namePrefix + setOp.getName(), Keep.off);
                    diff.input.add(childSubtrees.get(0));
                    diff.input2.add(childSubtrees.get(1));
                    newFeature = diff;
                    break;
                }
            case INTERSECTION:
                {
                    if (childSubtrees.size() < 2) {
                        throw new RuntimeException("expecting two or more children for CSG intersection operator");
                    }
                    VCCIntersection intersection = new VCCIntersection(namePrefix + setOp.getName(), Keep.off);
                    intersection.input.add(childSubtrees.get(0));
                    newFeature = intersection;
                    break;
                }
            case UNION:
                {
                    if (childSubtrees.size() < 2) {
                        throw new RuntimeException("expecting two or more children for CSG union operator");
                    }
                    VCCUnion union = new VCCUnion(namePrefix + setOp.getName(), Keep.off);
                    union.input.add(childSubtrees.get(0));
                    newFeature = union;
                    break;
                }
            default:
                {
                    throw new RuntimeException("csg set operator '" + setOp.getOpType().name() + "' not yet supported in COMSOL model builder");
                }
        }
    } else if (node instanceof CSGTransformation) {
        CSGTransformation transformation = (CSGTransformation) node;
        VCCGeomFeature vccChild = csgVisitor(transformation.getChild(), geomFeatureList, namePrefix);
        if (transformation instanceof CSGHomogeneousTransformation) {
            throw new RuntimeException("unsupported CSG transformation type Homogeneous transformation");
        } else if (transformation instanceof CSGRotation) {
            CSGRotation rotation = (CSGRotation) transformation;
            String[] axis = new String[] { Double.toString(rotation.getAxis().getX()), Double.toString(rotation.getAxis().getY()), Double.toString(rotation.getAxis().getZ()) };
            String[] pos = new String[] { "0.0", "0.0", "0.0" };
            String rot = Double.toString(rotation.getRotationRadians());
            VCCRotate vccrotate = new VCCRotate(namePrefix + rotation.getName(), axis, pos, rot, Keep.off);
            vccrotate.input.add(vccChild);
            newFeature = vccrotate;
        } else if (transformation instanceof CSGScale) {
            CSGScale scale = (CSGScale) transformation;
            String[] factor = new String[] { Double.toString(scale.getScale().getX()), Double.toString(scale.getScale().getY()), Double.toString(scale.getScale().getZ()) };
            String[] pos = new String[] { "0.0", "0.0", "0.0" };
            VCCScale vccscale = new VCCScale(namePrefix + scale.getName(), pos, factor, Keep.off);
            vccscale.input.add(vccChild);
            newFeature = vccscale;
        } else if (transformation instanceof CSGTranslation) {
            CSGTranslation translation = (CSGTranslation) transformation;
            String[] displ = new String[] { Double.toString(translation.getTranslation().getX()), Double.toString(translation.getTranslation().getY()), Double.toString(translation.getTranslation().getZ()) };
            VCCMove vccmove = new VCCMove(namePrefix + translation.getName(), displ, Keep.off);
            vccmove.input.add(vccChild);
            newFeature = vccmove;
        } else {
            throw new RuntimeException("unsupported CSG transformation type '" + transformation.getClass().getSimpleName() + "'");
        }
    } else {
        throw new RuntimeException("unsupported CSGNode type '" + node.getClass().getSimpleName() + "'");
    }
    geomFeatureList.add(newFeature);
    return newFeature;
}

Example 3 with CSGTranslation

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

the class XmlReader method getCSGTranslation.

private CSGTranslation getCSGTranslation(Element param) throws XmlParseException {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String translateXStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationXTag));
    String translateYStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationYTag));
    String translateZStr = unMangle(param.getAttributeValue(XMLTags.CSGTranslationZTag));
    Vect3d translateAxis = new Vect3d(Double.parseDouble(translateXStr), Double.parseDouble(translateYStr), Double.parseDouble(translateZStr));
    CSGTranslation csgTranslation = new CSGTranslation(name, translateAxis);
    // Retrieve CSGNode - CSGScale element should have one child
    Object[] elements = param.getChildren().toArray();
    if (elements.length > 1) {
        throw new XmlParseException("CSGScale element cannot have more than one child element");
    }
    CSGNode csgChildNode = getCSGNode((Element) elements[0]);
    csgTranslation.setChild(csgChildNode);
    return csgTranslation;
}

Example 4 with CSGTranslation

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

the class ClientRequestManager method createNewDocument.

/**
 * Insert the method's description here. Creation date: (5/10/2004 3:48:16 PM)
 */
public AsynchClientTask[] createNewDocument(final TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo) {
    // throws UserCancelException, Exception {
    /* asynchronous and not blocking any window */
    AsynchClientTask[] taskArray = null;
    final int createOption = documentCreationInfo.getOption();
    switch(documentCreationInfo.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                AsynchClientTask task1 = new AsynchClientTask("creating biomodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        BioModel bioModel = createDefaultBioModelDocument(null);
                        hashTable.put("doc", bioModel);
                    }
                };
                taskArray = new AsynchClientTask[] { task1 };
                break;
            }
        case MATHMODEL_DOC:
            {
                if ((createOption == VCDocument.MATH_OPTION_NONSPATIAL) || (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS)) {
                    AsynchClientTask task2 = new AsynchClientTask("creating mathmodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = null;
                            if (createOption == VCDocument.MATH_OPTION_NONSPATIAL) {
                                geometry = new Geometry("Untitled", 0);
                            } else {
                                geometry = (Geometry) hashTable.get(GEOMETRY_KEY);
                            }
                            MathModel mathModel = createMathModel("Untitled", geometry);
                            mathModel.setName("MathModel" + (getMdiManager().getNumCreatedDocumentWindows() + 1));
                            hashTable.put("doc", mathModel);
                        }
                    };
                    if (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS) {
                        AsynchClientTask task1 = createSelectDocTask(requester);
                        AsynchClientTask task1b = createSelectLoadGeomTask(requester);
                        taskArray = new AsynchClientTask[] { task1, task1b, task2 };
                    } else {
                        taskArray = new AsynchClientTask[] { task2 };
                    }
                    break;
                } else if (createOption == VCDocument.MATH_OPTION_FROMBIOMODELAPP) {
                    AsynchClientTask task1 = new AsynchClientTask("select biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            BioModelInfo bioModelInfo = (BioModelInfo) DialogUtils.getDBTreePanelSelection(requester.getComponent(), getMdiManager().getDatabaseWindowManager().getBioModelDbTreePanel(), "Open", "Select BioModel");
                            if (bioModelInfo != null) {
                                // may throw UserCancelException
                                hashTable.put("bioModelInfo", bioModelInfo);
                            }
                        }
                    };
                    AsynchClientTask task2 = new AsynchClientTask("find sim contexts in biomodel application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            // Get the simContexts in the corresponding BioModel
                            BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                            SimulationContext[] simContexts = getDocumentManager().getBioModel(bioModelInfo).getSimulationContexts();
                            if (simContexts != null) {
                                // may throw UserCancelException
                                hashTable.put("simContexts", simContexts);
                            }
                        }
                    };
                    AsynchClientTask task3 = new AsynchClientTask("create math model from biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            SimulationContext[] simContexts = (SimulationContext[]) hashTable.get("simContexts");
                            String[] simContextNames = new String[simContexts.length];
                            if (simContextNames.length == 0) {
                                throw new RuntimeException("no application is available");
                            } else {
                                for (int i = 0; i < simContexts.length; i++) {
                                    simContextNames[i] = simContexts[i].getName();
                                }
                                Component component = requester.getComponent();
                                // Get the simContext names, so that user can choose which simContext math to
                                // import
                                String simContextChoice = (String) PopupGenerator.showListDialog(component, simContextNames, "Please select Application");
                                if (simContextChoice == null) {
                                    throw UserCancelException.CANCEL_DB_SELECTION;
                                }
                                SimulationContext chosenSimContext = null;
                                for (int i = 0; i < simContexts.length; i++) {
                                    if (simContexts[i].getName().equals(simContextChoice)) {
                                        chosenSimContext = simContexts[i];
                                        break;
                                    }
                                }
                                Objects.requireNonNull(chosenSimContext);
                                BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                                // Get corresponding mathDesc to create new mathModel and return.
                                String newName = bioModelInfo.getVersion().getName() + "_" + chosenSimContext.getName();
                                MathDescription bioMathDesc = chosenSimContext.getMathDescription();
                                MathDescription newMathDesc = null;
                                newMathDesc = new MathDescription(newName + "_" + (new Random()).nextInt());
                                newMathDesc.setGeometry(bioMathDesc.getGeometry());
                                newMathDesc.read_database(new CommentStringTokenizer(bioMathDesc.getVCML_database()));
                                newMathDesc.isValid();
                                MathModel newMathModel = new MathModel(null);
                                newMathModel.setName(newName);
                                newMathModel.setMathDescription(newMathDesc);
                                hashTable.put("doc", newMathModel);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1, task2, task3 };
                    break;
                } else {
                    throw new RuntimeException("Unknown MathModel Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        case GEOMETRY_DOC:
            {
                if (createOption == VCDocument.GEOM_OPTION_1D || createOption == VCDocument.GEOM_OPTION_2D || createOption == VCDocument.GEOM_OPTION_3D) {
                    // analytic
                    AsynchClientTask task1 = new AsynchClientTask("creating analytic geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), documentCreationInfo.getOption());
                            geometry.getGeometrySpec().addSubVolume(new AnalyticSubVolume("subdomain0", new Expression(1.0)));
                            geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                            hashTable.put("doc", geometry);
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                }
                if (createOption == VCDocument.GEOM_OPTION_CSGEOMETRY_3D) {
                    // constructed solid geometry
                    AsynchClientTask task1 = new AsynchClientTask("creating constructed solid geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), 3);
                            Extent extent = geometry.getExtent();
                            if (extent != null) {
                                // create a CSGPrimitive of type cube and scale it to the 'extent' components.
                                // Use this as the default or background CSGObject (subdomain).
                                // This can be considered as the equivalent of subdomain (with expression) 1.0
                                // for analyticSubvolume.
                                // basic cube
                                CSGPrimitive cube = new CSGPrimitive("cube", CSGPrimitive.PrimitiveType.CUBE);
                                // scaled cube
                                double x = extent.getX();
                                double y = extent.getY();
                                double z = extent.getZ();
                                CSGScale scaledCube = new CSGScale("scale", new Vect3d(x / 2.0, y / 2.0, z / 2.0));
                                scaledCube.setChild(cube);
                                // translated scaled cube
                                CSGTranslation translatedScaledCube = new CSGTranslation("translation", new Vect3d(x / 2, y / 2, z / 2));
                                translatedScaledCube.setChild(scaledCube);
                                CSGObject csgObject = new CSGObject(null, "subdomain0", 0);
                                csgObject.setRoot(translatedScaledCube);
                                geometry.getGeometrySpec().addSubVolume(csgObject, false);
                                geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                                hashTable.put("doc", geometry);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                } else {
                    throw new RuntimeException("Unknown Geometry Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        default:
            {
                throw new RuntimeException("Unknown default document type: " + documentCreationInfo.getDocumentType());
            }
    }
    return taskArray;
}

Example 5 with CSGTranslation

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

the class CSGObjectTreeCellEditor method getTreeCellEditorComponent.

@Override
public Component getTreeCellEditorComponent(JTree tree, Object value, boolean isSelected, boolean expanded, boolean leaf, int row) {
    if (!(value instanceof BioModelNode)) {
        return null;
    }
    Object userObject = ((BioModelNode) value).getUserObject();
    CSGObjectTreeCellRenderer.CSGNodeLabel csgNodeLabel = new CSGObjectTreeCellRenderer.CSGNodeLabel();
    CSGObjectTreeCellRenderer.getCSGNodeLabel(userObject, csgNodeLabel);
    renderer.setOpenIcon(csgNodeLabel.icon);
    renderer.setClosedIcon(csgNodeLabel.icon);
    renderer.setLeafIcon(csgNodeLabel.icon);
    Component component = null;
    if (bRenaming) {
        realEditor = defaultCellEditor;
        component = super.getTreeCellEditorComponent(tree, value, isSelected, expanded, leaf, row);
        if (editingComponent instanceof JTextField) {
            String text = null;
            JTextField textField = (JTextField) editingComponent;
            if (userObject instanceof CSGObject) {
                text = ((CSGObject) userObject).getName();
            } else if (userObject instanceof CSGNode) {
                text = ((CSGNode) userObject).getName();
            }
            textField.setText(text);
        }
    } else {
        if (userObject instanceof CSGScale || userObject instanceof CSGTranslation) {
            realEditor = getVect3dCellEditor();
            Vect3d vect3d = null;
            if (userObject instanceof CSGScale) {
                vect3d = ((CSGScale) userObject).getScale();
            } else if (userObject instanceof CSGTranslation) {
                vect3d = ((CSGTranslation) userObject).getTranslation();
            }
            component = super.getTreeCellEditorComponent(tree, vect3d, isSelected, expanded, leaf, row);
        } else if (userObject instanceof CSGRotation) {
            realEditor = getRotationCellEditor();
            component = super.getTreeCellEditorComponent(tree, value, isSelected, expanded, leaf, row);
        }
    }
    return component;
}