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

Example 26 with RegionImage

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

the class MeshDisplayAdapter method generateMeshRegionSurfaces.

/**
 * Insert the method's description here.
 * Creation date: (9/18/2005 10:42:24 AM)
 */
public MeshRegionSurfaces generateMeshRegionSurfaces(ClientTaskStatusSupport clientTaskStatusSupport) throws cbit.image.ImageException, UserCancelException {
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("Generating region image...");
    }
    RegionImage meshRegionImage = generateRegionImage(getMesh(), clientTaskStatusSupport);
    cbit.vcell.geometry.surface.SurfaceCollection surfaceCollection = meshRegionImage.getSurfacecollection();
    MembraneElement[] membraneElements = (MembraneElement[]) getMesh().getMembraneElements().clone();
    int[][] surface_polygon_MembraneIndexes = new int[surfaceCollection.getSurfaceCount()][];
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("Generating surfaces...");
    }
    int totalPolygons = surfaceCollection.getTotalPolygonCount();
    int counter = 0;
    // Assign membraneIndexes to Polygons
    for (int i = 0; i < surfaceCollection.getSurfaceCount(); i += 1) {
        cbit.vcell.geometry.surface.Surface surface = surfaceCollection.getSurfaces(i);
        surface_polygon_MembraneIndexes[i] = new int[surface.getPolygonCount()];
        for (int j = 0; j < surface.getPolygonCount(); j += 1) {
            if (clientTaskStatusSupport != null && (j % 1000 == 0)) {
                if (clientTaskStatusSupport.isInterrupted()) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
                clientTaskStatusSupport.setProgress(counter * 100 / totalPolygons);
            }
            counter++;
            cbit.vcell.geometry.surface.Quadrilateral quad = (cbit.vcell.geometry.surface.Quadrilateral) surface.getPolygons(j);
            int membraneIndex = -1;
            for (int k = 0; k < membraneElements.length; k += 1) {
                if (membraneElements[k] == null) {
                    continue;
                }
                if ((membraneElements[k].getInsideVolumeIndex() == quad.getVolIndexNeighbor1() && membraneElements[k].getOutsideVolumeIndex() == quad.getVolIndexNeighbor2()) || (membraneElements[k].getInsideVolumeIndex() == quad.getVolIndexNeighbor2() && membraneElements[k].getOutsideVolumeIndex() == quad.getVolIndexNeighbor1())) {
                    membraneIndex = k;
                    break;
                }
            }
            if (membraneIndex == -1) {
                throw new RuntimeException("Couldn't find membraneIndex for quad=" + quad);
            } else if (membraneElements[membraneIndex] == null) {
                throw new RuntimeException("More than 1 MembraneElement found for quad=" + quad);
            }
            surface_polygon_MembraneIndexes[i][j] = membraneIndex;
            membraneElements[membraneIndex] = null;
        }
    }
    // All MembraneElements should have been assigned
    for (int i = 0; i < membraneElements.length; i += 1) {
        if (membraneElements[i] != null) {
            throw new RuntimeException("Some MembraneElements were not assigned to surface");
        }
    }
    return new MeshRegionSurfaces(surfaceCollection, surface_polygon_MembraneIndexes);
}

Example 27 with RegionImage

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

the class FunctionRangeGenerator method main.

public static void main(String[] args) {
    try {
        Expression exp = new Expression("a+log(b)+c");
        VarStatistics[] varStats = new VarStatistics[3];
        varStats[0] = new VarStatistics("a", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[1] = new VarStatistics("b", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[2] = new VarStatistics("c", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        double[] times = new double[] { 0.0, 1.0, 2.0 };
        Extent extent = new Extent(5, 5, 5);
        Origin origin = new Origin(0, 0, 0);
        // int numSamplesPerDim = 10;
        byte[] pixels = new byte[3 * 3 * 3];
        BitSet indomain = new BitSet(pixels.length);
        for (int i = 0; i < pixels.length; i++) {
            indomain.set(i);
        }
        VCImageUncompressed vcImage = new VCImageUncompressed(null, pixels, extent, 3, 3, 3);
        RegionImage regionImage = new RegionImage(vcImage, 3, extent, origin, RegionImage.NO_SMOOTHING);
        CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, new ISize(regionImage.getNumX(), regionImage.getNumY(), regionImage.getNumZ()), regionImage, true);
        FunctionStatistics results = FunctionRangeGenerator.getFunctionStatistics(exp, varStats, times, mesh, indomain, VariableType.VOLUME);
        System.out.println(results.getDefaultDatasetRange().toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 28 with RegionImage

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

the class FieldDataGUIPanel method addNewExternalData.

public static AsynchClientTask[] addNewExternalData(final Component requester, final FieldDataGUIPanel fieldDataGUIPanel, final boolean isFromSimulation) {
    final RequestManager clientRequestManager = fieldDataGUIPanel.fieldDataWindowManager.getLocalRequestManager();
    AsynchClientTask task1 = new AsynchClientTask("creating field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            String initialExtDataName = (String) hashTable.get("initFDName");
            fdos.specEDI = null;
            FieldDataInfoPanel fdip = new FieldDataInfoPanel();
            fdip.setSimulationMode(isFromSimulation);
            fdip.initISize(fdos.isize);
            fdip.initIOrigin(fdos.origin);
            fdip.initIExtent(fdos.extent);
            fdip.initTimes(fdos.times);
            fdip.initNames(TokenMangler.fixTokenStrict(initialExtDataName), fdos.varNames);
            fdip.setAnnotation(fdos.annotation);
            FieldDataFileOperationSpec userDefinedFDOS = new FieldDataFileOperationSpec();
            while (true) {
                int choice = PopupGenerator.showComponentOKCancelDialog(requester, fdip, "Create new field data");
                if (choice == JOptionPane.OK_OPTION) {
                    // Check values
                    try {
                        userDefinedFDOS.extent = fdip.getExtent();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Extent values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.origin = fdip.getOrigin();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Origin values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.varNames = fdip.getVariableNames();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Variable names. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    userDefinedFDOS.annotation = fdip.getAnnotation();
                    userDefinedFDOS.times = fdip.getTimes();
                    try {
                        if (fdip.getFieldName() == null || fdip.getFieldName().length() == 0 || !fdip.getFieldName().equals(TokenMangler.fixTokenStrict(fdip.getFieldName()))) {
                            throw new Exception("Field Data names can contain only letters,digits and underscores");
                        }
                        // Check to see if this name is already used
                        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot();
                        for (int i = 0; i < rootNode.getChildCount(); i += 1) {
                            ExternalDataIdentifier extDataID = ((FieldDataMainList) ((DefaultMutableTreeNode) rootNode.getChildAt(i)).getUserObject()).externalDataIdentifier;
                            if (fdip.getFieldName().equals(extDataID.getName())) {
                                throw new Exception("New Field Data name " + fdip.getFieldName() + " already used.");
                            }
                        }
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Error saving Field Data Name to Database. Try again.\n" + e.getMessage(), e);
                        continue;
                    }
                    hashTable.put("userDefinedFDOS", userDefinedFDOS);
                    hashTable.put("fieldName", fdip.getFieldName());
                    break;
                } else {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("saving field data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Add to Server Disk
            // save Database
            FieldDataFileOperationSpec tempFDOS = (FieldDataFileOperationSpec) hashTable.get("userDefinedFDOS");
            String fieldName = (String) hashTable.get("fieldName");
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DocumentManager documentManager = clientRequestManager.getDocumentManager();
            FieldDataDBOperationSpec newExtDataIDSpec = FieldDataDBOperationSpec.createSaveNewExtDataIDSpec(documentManager.getUser(), fieldName, tempFDOS.annotation);
            tempFDOS.specEDI = documentManager.fieldDataDBOperation(newExtDataIDSpec).extDataID;
            fdos.specEDI = tempFDOS.specEDI;
            fdos.annotation = tempFDOS.annotation;
            try {
                if (!isFromSimulation) {
                    fdos.extent = tempFDOS.extent;
                    fdos.origin = tempFDOS.origin;
                    fdos.varNames = tempFDOS.varNames;
                    fdos.times = tempFDOS.times;
                    // 
                    // Subvolumes and Regions NOT implemented now
                    // 
                    fdos.cartesianMesh = CartesianMesh.createSimpleCartesianMesh(fdos.origin, fdos.extent, fdos.isize, new RegionImage(new // empty regions
                    VCImageUncompressed(// empty regions
                    null, // empty regions
                    new byte[fdos.isize.getXYZ()], fdos.extent, fdos.isize.getX(), fdos.isize.getY(), fdos.isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
                }
                // Add to Server Disk
                documentManager.fieldDataFileOperation(fdos);
            } catch (Exception e) {
                try {
                    // try to cleanup new ExtDataID
                    documentManager.fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(fdos.specEDI));
                } catch (Exception e2) {
                // ignore
                }
                fdos.specEDI = null;
                throw e;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("refreshing field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DefaultMutableTreeNode root = ((DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot());
            if (root.getChildCount() == 0) {
                fieldDataGUIPanel.updateJTree(clientRequestManager);
            } else {
                int alphabeticalIndex = -1;
                for (int i = 0; i < root.getChildCount(); i += 1) {
                    if ((((FieldDataMainList) ((DefaultMutableTreeNode) root.getChildAt(i)).getUserObject())).externalDataIdentifier.getName().compareToIgnoreCase(fdos.specEDI.getName()) > 0) {
                        alphabeticalIndex = i;
                        break;
                    }
                }
                if (alphabeticalIndex == -1) {
                    alphabeticalIndex = root.getChildCount();
                }
                DefaultMutableTreeNode mainNode = new DefaultMutableTreeNode(new FieldDataMainList(fdos.specEDI, fdos.annotation));
                mainNode.add(new DefaultMutableTreeNode(new FieldDataVarMainList()));
                ((DefaultTreeModel) fieldDataGUIPanel.getJTree1().getModel()).insertNodeInto(mainNode, root, alphabeticalIndex);
            }
        }
    };
    return new AsynchClientTask[] { task1, task2, task3 };
}

Example 29 with RegionImage

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

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}

Example 30 with RegionImage

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

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}