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

Example 1 with Extent

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

the class ImageJHelper method vcellSendNRRD.

public static void vcellSendNRRD(final Component requester, BufferedInputStream bis, ClientTaskStatusSupport clientTaskStatusSupport, ImageJConnection imageJConnection, String description, double[] timePoints, String[] channelDescriptions) throws Exception {
    if (clientTaskStatusSupport != null) {
        clientTaskStatusSupport.setMessage("reading format... ");
    }
    // read nrrd file format (See NRRDWriter.writeNRRD(...) for header format)
    DataInputStream dis = new DataInputStream(bis);
    // magic nrrd
    readLine(bis);
    // endian
    readLine(bis);
    // comment
    readLine(bis);
    // "double"
    String type = extract(readLine(bis));
    // integer (dimension)
    Integer.parseInt(extract(readLine(bis)));
    // "raw" (encoding)
    extract(readLine(bis));
    BasicStackDimensions basicStackDimensions = extractArr(readLine(bis));
    // read other text header elements until exhausted
    String unused = "";
    while ((unused = readLine(bis)).length() != 0) {
        System.out.println(unused);
    }
    try {
        if (clientTaskStatusSupport != null) {
            clientTaskStatusSupport.setMessage("Sending data to ImageJ...");
        }
        imageJConnection.openConnection(VCellImageJCommands.vcellSendImage, description);
        double[] data = new double[basicStackDimensions.getTotalSize()];
        for (int i = 0; i < data.length; i++) {
            data[i] = dis.readDouble();
        }
        sendData0(imageJConnection, new HyperStackHelper(basicStackDimensions, new Extent(1, 1, 1), false, Float.class.getSimpleName(), null, null, timePoints, channelDescriptions, null), data, description);
    } finally {
        try {
            if (imageJConnection != null) {
                imageJConnection.closeConnection();
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

Example 2 with Extent

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

the class RunRefSimulationOp method saveExternalData.

private static void saveExternalData(Image image, String varName, ExternalDataIdentifier newROIExtDataID, LocalWorkspace localWorkspace) throws ObjectNotFoundException, ImageException, IOException {
    Extent extent = image.getExtent();
    Origin origin = image.getOrigin();
    ISize isize = image.getISize();
    VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
    RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
    CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    int NumTimePoints = 1;
    int NumChannels = 1;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    pixData[0][0] = image.getDoublePixels();
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = simpleCartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    fdos.varNames = new String[] { varName };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 3 with Extent

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

the class BioformatsImageDatasetReader method getImageDataset.

private ImageDataset getImageDataset(org.vcell.imagedataset.ImageDataset t_imageDataset) throws ImageException {
    List<org.vcell.imagedataset.UShortImage> t_images = t_imageDataset.getImages();
    UShortImage[] images = new UShortImage[t_images.size()];
    for (int i = 0; i < t_images.size(); i++) {
        org.vcell.imagedataset.UShortImage t_image = t_images.get(i);
        short[] pixels = new short[t_image.getPixels().size()];
        for (int p = 0; p < t_image.getPixelsSize(); p++) {
            pixels[p] = t_image.getPixels().get(p);
        }
        Origin origin = new Origin(t_image.getOrigin().x, t_image.getOrigin().y, t_image.getOrigin().z);
        Extent extent = new Extent(t_image.getExtent().x, t_image.getExtent().y, t_image.getExtent().z);
        int numX = t_image.getSize().x;
        int numY = t_image.getSize().y;
        int numZ = t_image.getSize().z;
        UShortImage image = new UShortImage(pixels, origin, extent, numX, numY, numZ);
        images[i] = image;
    }
    ;
    List<Double> t_imageTimeStamps = t_imageDataset.getImageTimeStamps();
    double[] timestamps = new double[t_imageTimeStamps.size()];
    for (int t = 0; t < t_imageTimeStamps.size(); t++) {
        timestamps[t] = t_imageTimeStamps.get(t);
    }
    ImageDataset imageDataset = new ImageDataset(images, timestamps, t_imageDataset.numZ);
    return imageDataset;
}

Example 4 with Extent

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

the class ClientRequestManager method getParseImageTask.

public static AsynchClientTask getParseImageTask(final Component requesterComp, final VCDocument.DocumentCreationInfo documentCreationInfo, final MDIManager mdiManager) {
    AsynchClientTask parseImageTask = new AsynchClientTask("read and parse image file", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            final Component guiParent = (Component) hashTable.get(ClientRequestManager.GUI_PARENT);
            try {
                FieldDataFileOperationSpec fdfos = null;
                // }
                if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FILE) // || documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIJI_IMAGEJ ||
                // documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_BLENDER
                {
                    File imageFile = (File) hashTable.get(IMAGE_FILE);
                    if (imageFile == null) {
                        throw new Exception("No file selected");
                    }
                    if (ExtensionFilter.isMatchingExtension(imageFile, ".nrrd")) {
                        DataInputStream dis = null;
                        try {
                            dis = new DataInputStream(new BufferedInputStream(new FileInputStream(imageFile)));
                            int xsize = 1;
                            int ysize = 1;
                            int zsize = 1;
                            double xspace = 1.0;
                            double yspace = 1.0;
                            double zspace = 1.0;
                            NRRDTYPE type = null;
                            NRRDENCODING encoding = null;
                            int dimension = -1;
                            // read header lines
                            while (true) {
                                @SuppressWarnings("deprecation") String line = dis.readLine();
                                if (line == null || line.length() == 0) {
                                    break;
                                }
                                StringTokenizer stringTokenizer = new StringTokenizer(line, ": ");
                                String headerParam = stringTokenizer.nextToken();
                                // System.out.println(headerParam);
                                if (headerParam.equals("sizes")) {
                                    if (dimension != -1) {
                                        xsize = Integer.parseInt(stringTokenizer.nextToken());
                                        if (dimension >= 2) {
                                            ysize = Integer.parseInt(stringTokenizer.nextToken());
                                        }
                                        if (dimension >= 3) {
                                            zsize = Integer.parseInt(stringTokenizer.nextToken());
                                        }
                                        for (int i = 4; i < dimension; i++) {
                                            if (Integer.parseInt(stringTokenizer.nextToken()) != 1) {
                                                throw new Exception("Dimensions > 3 not supported");
                                            }
                                        }
                                    } else {
                                        throw new Exception("dimension expected to be set before reading sizes");
                                    }
                                } else if (headerParam.equals("spacings")) {
                                    if (dimension != -1) {
                                        xspace = Double.parseDouble(stringTokenizer.nextToken());
                                        if (dimension >= 2) {
                                            yspace = Double.parseDouble(stringTokenizer.nextToken());
                                        }
                                        if (dimension >= 3) {
                                            zspace = Double.parseDouble(stringTokenizer.nextToken());
                                        }
                                    // ignore other dimension spacings
                                    } else {
                                        throw new Exception("dimension expected to be set before reading spacings");
                                    }
                                } else if (headerParam.equals("type")) {
                                    String nextToken = stringTokenizer.nextToken();
                                    if (nextToken.equalsIgnoreCase("double")) {
                                        type = NRRDTYPE.DOUBLE;
                                    } else if (nextToken.equalsIgnoreCase("float")) {
                                        type = NRRDTYPE.FLOAT;
                                    } else if (nextToken.equalsIgnoreCase("unsigned")) {
                                        nextToken = stringTokenizer.nextToken();
                                        if (nextToken.equalsIgnoreCase("char")) {
                                            type = NRRDTYPE.UNSIGNEDCHAR;
                                        } else {
                                            throw new Exception("Unknown nrrd data type=" + nextToken);
                                        }
                                    } else {
                                        throw new Exception("Unknown nrrd data type=" + nextToken);
                                    }
                                } else if (headerParam.equals("dimension")) {
                                    dimension = Integer.parseInt(stringTokenizer.nextToken());
                                    if (dimension < 1) {
                                        throw new Exception("unexpected dimension=" + dimension);
                                    }
                                } else if (headerParam.equals("encoding")) {
                                    encoding = NRRDENCODING.valueOf(stringTokenizer.nextToken().toUpperCase());
                                }
                            }
                            BufferedInputStream bis = null;
                            if (encoding == NRRDENCODING.GZIP) {
                                dis.close();
                                bis = new BufferedInputStream(new FileInputStream(imageFile));
                                boolean bnewLine = false;
                                while (true) {
                                    int currentChar = bis.read();
                                    if (currentChar == '\n') {
                                        if (bnewLine) {
                                            // 2 newlines end header
                                            break;
                                        }
                                        bnewLine = true;
                                    } else {
                                        bnewLine = false;
                                    }
                                }
                                GZIPInputStream gzipInputStream = new GZIPInputStream(bis);
                                dis = new DataInputStream(gzipInputStream);
                            }
                            double[] data = new double[xsize * ysize * zsize];
                            double minValue = Double.POSITIVE_INFINITY;
                            double maxValue = Double.NEGATIVE_INFINITY;
                            for (int i = 0; i < data.length; i++) {
                                if (i % 262144 == 0) {
                                    if (getClientTaskStatusSupport() != null) {
                                        getClientTaskStatusSupport().setMessage("Reading " + encoding + " " + type + " NRRD data " + (((long) i * (long) 100) / (long) data.length) + " % done.");
                                    }
                                }
                                if (type == NRRDTYPE.DOUBLE) {
                                    data[i] = dis.readDouble();
                                } else if (type == NRRDTYPE.FLOAT) {
                                    data[i] = dis.readFloat();
                                } else if (type == NRRDTYPE.UNSIGNEDCHAR) {
                                    data[i] = dis.readUnsignedByte();
                                } else {
                                    throw new Exception("Unexpected data type=" + type.toString());
                                }
                                minValue = Math.min(minValue, data[i]);
                                maxValue = Math.max(maxValue, data[i]);
                            }
                            dis.close();
                            if (getClientTaskStatusSupport() != null) {
                                getClientTaskStatusSupport().setMessage("Scaling " + encoding + " " + type + " NRRD data.");
                            }
                            short[] dataToSegment = new short[data.length];
                            double scaleShort = Math.pow(2, Short.SIZE) - 1;
                            for (int i = 0; i < data.length; i++) {
                                dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
                            }
                            fdfos = new FieldDataFileOperationSpec();
                            fdfos.origin = new Origin(0, 0, 0);
                            fdfos.extent = new Extent((xsize == 1 ? .5 : (xsize) * xspace), (ysize == 1 ? .5 : (ysize) * yspace), (zsize == 1 ? .5 : (zsize) * zspace));
                            fdfos.isize = new ISize(xsize, ysize, zsize);
                            fdfos.shortSpecData = new short[][][] { { dataToSegment } };
                        } finally {
                            if (dis != null) {
                                try {
                                    dis.close();
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                            }
                        }
                    } else if ((fdfos = createFDOSFromSurfaceFile(imageFile)) != null) {
                    // try surface file formats
                    // work already done at this point
                    } else {
                        File[] dirFiles = null;
                        ImageSizeInfo origImageSizeInfo = null;
                        ImageDatasetReaderService imageDatasetReaderServiceInstance = ImageDatasetReaderService.getInstance();
                        ImageDatasetReader imageDatasetReader = imageDatasetReaderServiceInstance.getImageDatasetReader();
                        if (imageFile.isDirectory()) {
                            dirFiles = imageFile.listFiles(new java.io.FileFilter() {

                                public boolean accept(File pathname) {
                                    // exclude windows Thumbs.db
                                    return pathname.isFile() && !pathname.isHidden();
                                }
                            });
                            if (dirFiles.length == 0) {
                                throw new Exception("No valid files in selected directory");
                            }
                            String fileExt0 = null;
                            for (int i = 0; i < dirFiles.length; i++) {
                                int lastDot = dirFiles[i].getName().lastIndexOf('.');
                                String fileExt = (lastDot != -1 ? dirFiles[i].getName().substring(lastDot) : null);
                                if (dirFiles[i].isDirectory()) {
                                    fileExt = "dir";
                                }
                                if (i == 0) {
                                    fileExt0 = fileExt;
                                } else if (!Compare.isEqualOrNull(fileExt, fileExt0)) {
                                    String result = DialogUtils.showWarningDialog(requesterComp, "Files in '" + imageFile.getAbsolutePath() + "' have different name extensions, continue?", new String[] { "OK", "Cancel" }, "Cancel");
                                    if (!"OK".equals(result)) {
                                        throw UserCancelException.CANCEL_FILE_SELECTION;
                                    }
                                    break;
                                }
                            }
                            hashTable.put(IMPORT_SOURCE_NAME, "Directory: " + imageFile.getAbsolutePath());
                            origImageSizeInfo = imageDatasetReader.getImageSizeInfoForceZ(dirFiles[0].getAbsolutePath(), dirFiles.length);
                            if (dirFiles.length > 1) {
                                final String importZ = "Import Z-Sections";
                                final String cancelOption = "Cancel";
                                String result = DialogUtils.showWarningDialog(guiParent, "Import all files in directory '" + imageFile.getAbsolutePath() + "' as Z-Sections", new String[] { importZ, cancelOption }, importZ);
                                if (result.equals(cancelOption)) {
                                    throw UserCancelException.CANCEL_GENERIC;
                                }
                            }
                            hashTable.put(DIR_FILES, dirFiles);
                        } else {
                            origImageSizeInfo = imageDatasetReader.getImageSizeInfoForceZ(imageFile.getAbsolutePath(), null);
                            hashTable.put(IMPORT_SOURCE_NAME, "File: " + imageFile.getAbsolutePath());
                        }
                        hashTable.put(ORIG_IMAGE_SIZE_INFO, origImageSizeInfo);
                        return;
                    }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FIELDDATA) {
                    getClientTaskStatusSupport().setMessage("Reading data from VCell server.");
                    VCDocument.GeomFromFieldDataCreationInfo docInfo = (VCDocument.GeomFromFieldDataCreationInfo) documentCreationInfo;
                    PDEDataContext pdeDataContext = mdiManager.getFieldDataWindowManager().getPDEDataContext(docInfo.getExternalDataID(), null);
                    ImageSizeInfo newImageSizeInfo = (ImageSizeInfo) hashTable.get(NEW_IMAGE_SIZE_INFO);
                    pdeDataContext.setVariableNameAndTime(docInfo.getVarName(), newImageSizeInfo.getTimePoints()[newImageSizeInfo.getSelectedTimeIndex()]);
                    double[] data = pdeDataContext.getDataValues();
                    hashTable.put(INITIAL_ANNOTATION, hashTable.get(IMPORT_SOURCE_NAME));
                    CartesianMesh mesh = (CartesianMesh) hashTable.get(FD_MESH);
                    ISize meshISize = (ISize) hashTable.get(FD_MESHISIZE);
                    double minValue = Double.POSITIVE_INFINITY;
                    double maxValue = Double.NEGATIVE_INFINITY;
                    for (int i = 0; i < data.length; i++) {
                        minValue = Math.min(minValue, data[i]);
                        maxValue = Math.max(maxValue, data[i]);
                    }
                    short[] dataToSegment = new short[data.length];
                    double scaleShort = Math.pow(2, Short.SIZE) - 1;
                    for (int i = 0; i < data.length; i++) {
                        dataToSegment[i] |= (int) ((data[i] - minValue) / (maxValue - minValue) * scaleShort);
                    }
                    fdfos = new FieldDataFileOperationSpec();
                    fdfos.origin = mesh.getOrigin();
                    fdfos.extent = mesh.getExtent();
                    fdfos.isize = meshISize;
                    fdfos.shortSpecData = new short[][][] { { dataToSegment } };
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_SCRATCH) {
                    ISize isize = getISizeFromUser(guiParent, new ISize(256, 256, 8), "Enter # of pixels for  x,y,z (e.g. 3D{256,256,8}, 2D{256,256,1}, 1D{256,1,1})");
                    fdfos = new FieldDataFileOperationSpec();
                    fdfos.origin = new Origin(0, 0, 0);
                    fdfos.extent = new Extent(1, 1, 1);
                    fdfos.isize = isize;
                    hashTable.put(IMPORT_SOURCE_NAME, "Scratch: New Geometry");
                // final int SCRATCH_SIZE_LIMIT = 512*512*20;
                // if(isize.getXYZ() > (SCRATCH_SIZE_LIMIT)){
                // throw new Exception("Total pixels (x*y*z) cannot be >"+SCRATCH_SIZE_LIMIT+".");
                // }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_ANALYTIC) {
                    if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
                        Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
                        ISize defaultISize = workspaceGeom.getGeometrySpec().getDefaultSampledImageSize();
                        ISize isize = getISizeFromUser(guiParent, defaultISize, "Warning: converting analytic expression geometry into an image based geometry\nwill remove analytic expressions after new image is created.\n\n" + "Enter size (x,y,z) for new geometry image (e.g. " + defaultISize.getX() + "," + defaultISize.getY() + "," + defaultISize.getZ() + ")");
                        hashTable.put(IMPORT_SOURCE_NAME, "Workspace from Analytic Geometry");
                        VCImage img = workspaceGeom.getGeometrySpec().createSampledImage(isize);
                        Enumeration<SubVolume> enumSubvolume = workspaceGeom.getGeometrySpec().getAnalyticOrCSGSubVolumes();
                        ArrayList<VCPixelClass> vcPixelClassArrList = new ArrayList<VCPixelClass>();
                        while (enumSubvolume.hasMoreElements()) {
                            SubVolume subVolume = enumSubvolume.nextElement();
                            vcPixelClassArrList.add(new VCPixelClass(null, subVolume.getName(), subVolume.getHandle()));
                        }
                        if (vcPixelClassArrList.size() > img.getPixelClasses().length) {
                            String result = DialogUtils.showOKCancelWarningDialog(requesterComp, null, "Warning: sampling size is too small to include all subvolumes.");
                            if (result == null || !result.equals(SimpleUserMessage.OPTION_OK)) {
                                throw UserCancelException.CANCEL_GENERIC;
                            }
                        }
                        hashTable.put(VCPIXELCLASSES, vcPixelClassArrList.toArray(new VCPixelClass[0]));
                        fdfos = createFDOSFromVCImage(img);
                    } else {
                        throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE_ANALYTIC");
                    }
                } else if (documentCreationInfo.getOption() == VCDocument.GEOM_OPTION_FROM_WORKSPACE_IMAGE) {
                    if (hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE) != null) {
                        Geometry workspaceGeom = (Geometry) hashTable.get(ClientRequestManager.GEOM_FROM_WORKSPACE);
                        hashTable.put(IMPORT_SOURCE_NAME, "Workspace Image");
                        fdfos = createFDOSFromVCImage(workspaceGeom.getGeometrySpec().getImage());
                        if (workspaceGeom.getGeometrySpec().getImage().getDescription() != null) {
                            hashTable.put(INITIAL_ANNOTATION, workspaceGeom.getGeometrySpec().getImage().getDescription());
                        }
                        GeometryClass[] myGeometryClasses = workspaceGeom.getGeometryClasses();
                        VCPixelClass[] myPixelClasses = workspaceGeom.getGeometrySpec().getImage().getPixelClasses();
                        VCPixelClass[] newPixelClasses = new VCPixelClass[myPixelClasses.length];
                        for (int i = 0; i < myPixelClasses.length; i++) {
                            for (int j = 0; j < myGeometryClasses.length; j++) {
                                if (myGeometryClasses[j] instanceof ImageSubVolume && myPixelClasses[i].getPixel() == ((ImageSubVolume) myGeometryClasses[j]).getPixelValue()) {
                                    newPixelClasses[i] = new VCPixelClass(null, myGeometryClasses[j].getName(), myPixelClasses[i].getPixel());
                                    break;
                                }
                            }
                        }
                        hashTable.put(VCPIXELCLASSES, newPixelClasses);
                    } else {
                        throw new Exception("Expecting image source for GEOM_OPTION_FROM_WORKSPACE");
                    }
                }
                hashTable.put(FDFOS, fdfos);
            } catch (DataFormatException ex) {
                throw new Exception("Cannot read image file.\n" + ex.getMessage());
            }
        }
    };
    return parseImageTask;
}

Example 5 with Extent

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

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = 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));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}