Examples with Extent org.vcell.util.Extent used on opensource projects

Example 51 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}

Example 52 with Extent

use of org.vcell.util.Extent 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 53 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class ClientRequestManager method createFDOSWithChannels.

public static FieldDataFileOperationSpec createFDOSWithChannels(ImageDataset[] imagedataSets, Integer saveOnlyThisTimePointIndex) {
    final FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    // [time][var][data]
    int numXY = imagedataSets[0].getISize().getX() * imagedataSets[0].getISize().getY();
    int numXYZ = imagedataSets[0].getSizeZ() * numXY;
    fdos.variableTypes = new VariableType[imagedataSets.length];
    fdos.varNames = new String[imagedataSets.length];
    short[][][] shortData = new short[(saveOnlyThisTimePointIndex != null ? 1 : imagedataSets[0].getSizeT())][imagedataSets.length][numXYZ];
    for (int c = 0; c < imagedataSets.length; c += 1) {
        fdos.variableTypes[c] = VariableType.VOLUME;
        fdos.varNames[c] = "Channel" + c;
        for (int t = 0; t < imagedataSets[c].getSizeT(); t += 1) {
            if (saveOnlyThisTimePointIndex != null && saveOnlyThisTimePointIndex.intValue() != t) {
                continue;
            }
            int zOffset = 0;
            for (int z = 0; z < imagedataSets[c].getSizeZ(); z += 1) {
                UShortImage ushortImage = imagedataSets[c].getImage(z, 0, t);
                System.arraycopy(ushortImage.getPixels(), 0, shortData[(saveOnlyThisTimePointIndex != null ? 0 : t)][c], zOffset, numXY);
                // shortData[t][c] = ushortImage.getPixels();
                zOffset += numXY;
            }
        }
    }
    fdos.shortSpecData = shortData;
    fdos.times = imagedataSets[0].getImageTimeStamps();
    if (fdos.times == null) {
        fdos.times = new double[imagedataSets[0].getSizeT()];
        for (int i = 0; i < fdos.times.length; i += 1) {
            fdos.times[i] = i;
        }
    }
    fdos.origin = (imagedataSets[0].getAllImages()[0].getOrigin() != null ? imagedataSets[0].getAllImages()[0].getOrigin() : new Origin(0, 0, 0));
    fdos.extent = (imagedataSets[0].getExtent() != null) ? (imagedataSets[0].getExtent()) : (new Extent(1, 1, 1));
    fdos.isize = imagedataSets[0].getISize();
    return fdos;
}

Example 54 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class MeshSpecificationPanel method autoUpdateSizes.

private void autoUpdateSizes(DocumentEvent e) {
    if (bInProgress) {
        return;
    }
    final int dimension = getMeshSpecification().getGeometry().getDimension();
    if (!getAutoMeshSizeCheckBox().isSelected()) {
        updateTotalSizeAndSpatialStep();
        return;
    }
    JTextField input = null;
    try {
        bInProgress = true;
        Extent extent = getMeshSpecification().getGeometry().getExtent();
        if (e.getDocument() == getXTextField().getDocument()) {
            input = getXTextField();
            String xtext = getXTextField().getText();
            if (xtext == null || xtext.trim().length() == 0) {
                getYTextField().setText(xtext);
                getZTextField().setText(xtext);
                clearTotalSizeAndSpatialStep();
                return;
            }
            int numX = Integer.parseInt(xtext);
            if (dimension > 1) {
                double yxRatio = extent.getY() / extent.getX();
                long numY = computeAnotherSizeWRTAspectRatio(numX, yxRatio);
                getYTextField().setText("" + numY);
                if (dimension > 2) {
                    double zxRatio = extent.getZ() / extent.getX();
                    long numZ = computeAnotherSizeWRTAspectRatio(numX, zxRatio);
                    getZTextField().setText("" + numZ);
                }
            }
        } else if (e.getDocument() == getYTextField().getDocument()) {
            input = getYTextField();
            String ytext = getYTextField().getText();
            if (ytext == null || ytext.trim().length() == 0) {
                getXTextField().setText(ytext);
                getZTextField().setText(ytext);
                clearTotalSizeAndSpatialStep();
                return;
            }
            int numY = Integer.parseInt(ytext);
            double xyRatio = extent.getX() / extent.getY();
            long numX = computeAnotherSizeWRTAspectRatio(numY, xyRatio);
            getXTextField().setText("" + numX);
            if (dimension > 2) {
                double zyRatio = extent.getZ() / extent.getY();
                long numZ = computeAnotherSizeWRTAspectRatio(numY, zyRatio);
                getZTextField().setText("" + numZ);
            }
        } else if (e.getDocument() == getZTextField().getDocument()) {
            input = getZTextField();
            String ztext = getZTextField().getText();
            if (ztext == null || ztext.trim().length() == 0) {
                getXTextField().setText(ztext);
                getYTextField().setText(ztext);
                clearTotalSizeAndSpatialStep();
                return;
            }
            int numZ = Integer.parseInt(ztext);
            if (dimension > 2) {
                double xzRatio = extent.getX() / extent.getZ();
                double yzRatio = extent.getY() / extent.getZ();
                long numX = computeAnotherSizeWRTAspectRatio(numZ, xzRatio);
                long numY = computeAnotherSizeWRTAspectRatio(numZ, yzRatio);
                getXTextField().setText("" + numX);
                getYTextField().setText("" + numY);
            }
        }
        input.setBorder(UIManager.getBorder("TextField.border"));
        updateTotalSizeAndSpatialStep();
    } catch (NumberFormatException ex) {
        DialogUtils.showErrorDialog(this, "Wrong number format " + ex.getMessage().toLowerCase());
        input.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createLineBorder(Color.red), BorderFactory.createEmptyBorder(2, 2, 2, 2)));
        clearTotalSizeAndSpatialStep();
    } finally {
        bInProgress = false;
    }
}

Example 55 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class ChomboMeshSpecificationPanel method updateDisplay.

private void updateDisplay(boolean bSolverChanged) throws ChomboGeometryException, ChomboInvalidGeometryException {
    if (!simulation.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
        setVisible(false);
        return;
    }
    Geometry geometry = simulation.getMathDescription().getGeometry();
    Extent extent = geometry.getExtent();
    int dimension = geometry.getDimension();
    switch(dimension) {
        case 0:
            setVisible(false);
            break;
        case 1:
            getGeometrySizeTextField().setText("" + extent.getX());
            NyLabel.setVisible(false);
            NyComboBox.setVisible(false);
            NzLabel.setVisible(false);
            NzComboBox.setVisible(false);
            break;
        case 2:
            getGeometrySizeTextField().setText("(" + extent.getX() + ", " + extent.getY() + ")");
            NzLabel.setVisible(false);
            NzComboBox.setVisible(false);
            break;
        case 3:
            getGeometrySizeTextField().setText("(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")");
            break;
    }
    String error;
    ChomboMeshRecommendation meshRecommendation = new ChomboMeshValidator(geometry.getDimension(), geometry.getExtent(), simulation.getSolverTaskDescription().getChomboSolverSpec().getBlockFactor()).computeMeshSpecs();
    if (meshRecommendation.validate()) {
        // remove ActionListener, here we only want to set values
        removeComboBoxListener();
        HComboBox.removeAll();
        NxComboBox.removeAll();
        NyComboBox.removeAll();
        NzComboBox.removeAll();
        for (ChomboMeshSpec meshSpec : meshRecommendation.validMeshSpecList) {
            HComboBox.addItem((float) meshSpec.H);
            NxComboBox.addItem(meshSpec.Nx[0]);
            if (geometry.getDimension() > 1) {
                NyComboBox.addItem(meshSpec.Nx[1]);
                if (geometry.getDimension() == 3) {
                    NzComboBox.addItem(meshSpec.Nx[2]);
                }
            }
        }
        addComboBoxListener();
        if (bSolverChanged) {
            NxComboBox.setSelectedIndex(0);
        } else {
            ISize samplingSize = simulation.getMeshSpecification().getSamplingSize();
            NxComboBox.setSelectedItem(samplingSize.getX());
            // double check if existing mesh size is an option in drop down
            Integer selectedNx = (Integer) NxComboBox.getSelectedItem();
            Integer selectedNy = geometry.getDimension() > 1 ? (Integer) NyComboBox.getSelectedItem() : 1;
            Integer selectedNz = geometry.getDimension() > 2 ? (Integer) NzComboBox.getSelectedItem() : 1;
            boolean bMatchFound = selectedNx == samplingSize.getX() && (dimension < 2 || selectedNy == samplingSize.getY()) && (dimension < 3 || selectedNz == samplingSize.getZ());
            if (!bMatchFound) {
                NxComboBox.setSelectedIndex(0);
                throw new ChomboGeometryException(ChomboMeshValidator.ERROR_MESSAGE_INCOMPATIBLE_MESH_SIZE);
            }
        }
    } else {
        throw new ChomboInvalidGeometryException(meshRecommendation);
    }
}