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

Example 21 with GeometryThumbnailImageFactoryAWT

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

the class GeometryViewer method resample.

private void resample() {
    AsynchClientTask precomputeCurrentGeometryTask = new AsynchClientTask("computing surfaces for existing geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
            }
        }
    };
    AsynchClientTask sampleSizeTask = new AsynchClientTask("specify sample size", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCImage currSampledImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            int currNumSamples = currSampledImage.getNumXYZ();
            ISize currSize = new ISize(currSampledImage.getNumX(), currSampledImage.getNumY(), currSampledImage.getNumZ());
            ISize sampleSize_times_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples * 10);
            ISize sampleSize_div_ten = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), currNumSamples / 10);
            ISize sampleSize_1e2 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e2);
            ISize sampleSize_1e3 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e3);
            ISize sampleSize_1e4 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e4);
            ISize sampleSize_1e5 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e5);
            ISize sampleSize_1e6 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e6);
            ISize sampleSize_1e7 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e7);
            ISize sampleSize_1e8 = GeometrySpec.calulateResetSamplingSize(3, getGeometry().getExtent(), (int) 1e8);
            String[] columnNames = new String[] { "description", "num samples", "(X,Y,Z)" };
            Object[][] rowData = new Object[][] { new Object[] { "same size", new Integer(currSize.getXYZ()), currSize }, new Object[] { "10 times smaller", new Integer(sampleSize_div_ten.getXYZ()), sampleSize_div_ten }, new Object[] { "10 times bigger", new Integer(sampleSize_times_ten.getXYZ()), sampleSize_times_ten }, new Object[] { "        100 samples", new Integer(sampleSize_1e2.getXYZ()), sampleSize_1e2 }, new Object[] { "      1,000 samples", new Integer(sampleSize_1e3.getXYZ()), sampleSize_1e3 }, new Object[] { "     10,000 samples", new Integer(sampleSize_1e4.getXYZ()), sampleSize_1e4 }, new Object[] { "    100,000 samples", new Integer(sampleSize_1e5.getXYZ()), sampleSize_1e5 }, new Object[] { "  1,000,000 samples", new Integer(sampleSize_1e6.getXYZ()), sampleSize_1e6 }, new Object[] { " 10,000,000 samples", new Integer(sampleSize_1e7.getXYZ()), sampleSize_1e7 }, new Object[] { "100,000,000 samples", new Integer(sampleSize_1e8.getXYZ()), sampleSize_1e8 } };
            int[] selectedRows = DialogUtils.showComponentOKCancelTableList(GeometryViewer.this, "sample size", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
            ISize sampleSize = (ISize) rowData[selectedRows[0]][2];
            hashTable.put("sampleSize", sampleSize);
        }
    };
    AsynchClientTask resampleTask = new AsynchClientTask("resample geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ISize sampleSize = (ISize) hashTable.get("sampleSize");
            Geometry newGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), getGeometry(), sampleSize);
            hashTable.put("newGeometry", newGeometry);
        }
    };
    AsynchClientTask setGeometryTask = new AsynchClientTask("loading geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get("newGeometry");
            if (getGeometryOwner() instanceof SimulationContext) {
                ((SimulationContext) getGeometryOwner()).setGeometry(newGeometry);
            } else if (getGeometryOwner() instanceof MathModel) {
                ((MathModel) getGeometryOwner()).getMathDescription().setGeometry(newGeometry);
            } else {
                throw new RuntimeException("unexpected geometry owner, could not set resampled geometry");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { precomputeCurrentGeometryTask, sampleSizeTask, resampleTask, setGeometryTask }, false);
}

Example 22 with GeometryThumbnailImageFactoryAWT

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

the class CSGObjectPropertiesPanel method updateCSGObject.

private void updateCSGObject(final Object objectToBeSelected) {
    if (csgObject.getRoot() != null) {
        csgObject.setRoot(csgObject.getRoot().clone());
    }
    AsynchClientTask task1 = new AsynchClientTask("regenerating geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            simulationContext.getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("refreshing", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            csgObjectTreeModel.select(objectToBeSelected);
        }
    };
    ClientTaskDispatcher.dispatch(CSGObjectPropertiesPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 23 with GeometryThumbnailImageFactoryAWT

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

the class GeometrySizeDialog method Ok.

/**
 * Comment
 */
private void Ok() throws PropertyVetoException {
    final double worldExtentX = Double.valueOf(getSizeXTextField().getText()).doubleValue();
    final double worldExtentY = Double.valueOf(getSizeYTextField().getText()).doubleValue();
    final double worldExtentZ = Double.valueOf(getSizeZTextField().getText()).doubleValue();
    final double worldOriginX = Double.valueOf(getOriginXTextField().getText()).doubleValue();
    final double worldOriginY = Double.valueOf(getOriginYTextField().getText()).doubleValue();
    final double worldOriginZ = Double.valueOf(getOriginZTextField().getText()).doubleValue();
    final GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    AsynchClientTask extentOriginTask = new AsynchClientTask("Changing domain", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            geometrySpec.setExtent(new Extent(worldExtentX, worldExtentY, worldExtentZ));
            geometrySpec.setOrigin(new Origin(worldOriginX, worldOriginY, worldOriginZ));
            getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT());
        }
    };
    ClientTaskDispatcher.dispatch(this.getParent(), new Hashtable<String, Object>(), new AsynchClientTask[] { extentOriginTask }, false);
}

Example 24 with GeometryThumbnailImageFactoryAWT

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

the class BioModelWindowManager method actionPerformed.

/**
 * Invoked when an action occurs.
 */
public void actionPerformed(java.awt.event.ActionEvent e) {
    String actionCommand = e.getActionCommand();
    final Object source = e.getSource();
    if (source instanceof GeometryViewer && (actionCommand.equals(GuiConstants.ACTIONCMD_CREATE_GEOMETRY) || actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY))) {
        final GeometryViewer geometryViewer = (GeometryViewer) source;
        AsynchClientTask precomputeAllTask = new AsynchClientTask("precomputeAll geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                if (newGeom != null) {
                    newGeom.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                }
            }
        };
        AsynchClientTask setGeomOnSimContextTask = new AsynchClientTask("Setting geometry on application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                for (SimulationContext simulationContext : getBioModel().getSimulationContexts()) {
                    if (simulationContext == geometryViewer.getGeometryOwner()) {
                        if (newGeom.getName() == null) {
                            newGeom.setName(getBioModel().getName() + "_" + (simulationContext.getName() + "_" + BeanUtils.generateDateTimeString()));
                        }
                        simulationContext.setGeometry(newGeom);
                        return;
                    }
                }
                Geometry origGeom = geometryViewer.getGeometryOwner().getGeometry();
                throw new IllegalArgumentException("Couldn't find matching application editor for orig geom '" + origGeom.getName() + "' key=" + origGeom.getKey() + " in application hash.");
            }
        };
        Geometry currentGeometry = geometryViewer.getGeometryOwner().getGeometry();
        createGeometry(currentGeometry, new AsynchClientTask[] { /*oldEditorTask,*/
        precomputeAllTask, setGeomOnSimContextTask }, TopLevelWindowManager.DEFAULT_CREATEGEOM_SELECT_DIALOG_TITLE, TopLevelWindowManager.APPLY_GEOMETRY_BUTTON_TEXT, (actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY) ? new DocumentWindowManager.GeometrySelectionInfo() : null));
    }
    if (source instanceof MathematicsPanel && actionCommand.equals(GuiConstants.ACTIONCMD_CREATE_MATH_MODEL)) {
        SimulationContext sc = ((MathematicsPanel) source).getSimulationContext();
        getRequestManager().createMathModelFromApplication(this, "Untitled", sc);
    }
    if (source instanceof GeometryViewer && actionCommand.equals(GuiConstants.ACTIONCMD_CHANGE_GEOMETRY)) {
        final GeometryViewer geometryViewer = (GeometryViewer) source;
        getRequestManager().changeGeometry(this, (SimulationContext) geometryViewer.getGeometryOwner());
    }
}

Example 25 with GeometryThumbnailImageFactoryAWT

use of cbit.vcell.geometry.GeometryThumbnailImageFactoryAWT 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;
}