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

Example 26 with Origin

use of org.vcell.util.Origin 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 27 with Origin

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

the class MicroscopyXmlReader method getUShortImage.

/**
 * This method returns a VCIMage object from a XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @param param org.jdom.Element
 * @return VCImage
 * @throws XmlParseException
 */
private UShortImage getUShortImage(Element param) throws XmlParseException {
    // get the attributes
    Element tempelement = param.getChild(XMLTags.ImageDataTag);
    int aNumX = Integer.parseInt(tempelement.getAttributeValue(XMLTags.XAttrTag));
    int aNumY = Integer.parseInt(tempelement.getAttributeValue(XMLTags.YAttrTag));
    int aNumZ = Integer.parseInt(tempelement.getAttributeValue(XMLTags.ZAttrTag));
    int compressSize = Integer.parseInt(tempelement.getAttributeValue(XMLTags.CompressedSizeTag));
    final int BYTES_PER_SHORT = 2;
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    // getpixels
    String hexEncodedBytes = tempelement.getText();
    byte[] rawBytes = org.vcell.util.Hex.toBytes(hexEncodedBytes);
    ByteArrayInputStream rawByteArrayInputStream = new ByteArrayInputStream(rawBytes);
    InputStream rawInputStream = rawByteArrayInputStream;
    if (compressSize != UNCOMPRESSED_SIZE_BYTES) {
        rawInputStream = new InflaterInputStream(rawByteArrayInputStream);
    }
    byte[] shortsAsBytes = new byte[UNCOMPRESSED_SIZE_BYTES];
    int readCount = 0;
    try {
        while ((readCount += rawInputStream.read(shortsAsBytes, readCount, shortsAsBytes.length - readCount)) != shortsAsBytes.length) {
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image pixels: ", e);
    } finally {
        if (rawInputStream != null) {
            try {
                rawInputStream.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    ByteBuffer byteBuffer = ByteBuffer.wrap(shortsAsBytes);
    short[] shortPixels = new short[aNumX * aNumY * aNumZ];
    for (int i = 0; i < shortPixels.length; i++) {
        shortPixels[i] = byteBuffer.getShort();
    }
    Element extentElement = param.getChild(XMLTags.ExtentTag);
    Extent extent = null;
    if (extentElement != null) {
        extent = vcellXMLReader.getExtent(extentElement);
    }
    Element originElement = param.getChild(XMLTags.OriginTag);
    Origin origin = null;
    if (originElement != null) {
        origin = vcellXMLReader.getOrigin(originElement);
    }
    // //set attributes
    // String name = this.unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // String annotation = param.getChildText(XMLTags.AnnotationTag);
    UShortImage newimage;
    try {
        newimage = new UShortImage(shortPixels, origin, extent, aNumX, aNumY, aNumZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new XmlParseException("error reading image: ", e);
    }
    return newimage;
}

Example 28 with Origin

use of org.vcell.util.Origin 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;
}

Example 29 with Origin

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

the class VFrapXmlHelper method SaveVFrapSpecialImagesAsFieldData.

// 
// save the special images in the database as field data
// 
public static ExternalDataIdentifier SaveVFrapSpecialImagesAsFieldData(Hashtable<String, Object> hashTable, DocumentManager documentManager) throws DataAccessException {
    CartesianMesh mesh = (CartesianMesh) hashTable.get("mesh");
    double[][][] pixData = (double[][][]) hashTable.get("pixData");
    String[] channelNames = (String[]) hashTable.get("channelNames");
    VariableType[] channelTypes = (VariableType[]) hashTable.get("channelTypes");
    // DataSymbolType[] channelVFrapImageType = (DataSymbolType[])hashTable.get("channelVFrapImageType");
    String mixedFieldDataName = (String) hashTable.get("mixedFieldDataName");
    FieldDataFileOperationSpec vfrapMiscFieldDataOpSpec = new FieldDataFileOperationSpec();
    vfrapMiscFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
    vfrapMiscFieldDataOpSpec.cartesianMesh = mesh;
    vfrapMiscFieldDataOpSpec.doubleSpecData = pixData;
    vfrapMiscFieldDataOpSpec.specEDI = null;
    // item name as it comes from vFrap
    vfrapMiscFieldDataOpSpec.varNames = channelNames;
    vfrapMiscFieldDataOpSpec.owner = documentManager.getUser();
    vfrapMiscFieldDataOpSpec.times = new double[] { 0.0 };
    vfrapMiscFieldDataOpSpec.variableTypes = channelTypes;
    vfrapMiscFieldDataOpSpec.origin = new Origin(0, 0, 0);
    vfrapMiscFieldDataOpSpec.extent = mesh.getExtent();
    vfrapMiscFieldDataOpSpec.isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    ExternalDataIdentifier vfrapMisc = documentManager.saveFieldData(vfrapMiscFieldDataOpSpec, mixedFieldDataName);
    return vfrapMisc;
}

Example 30 with Origin

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

the class VCellClientDataServiceImpl method createSimulationDataSetRef.

public static SimulationDataSetRef createSimulationDataSetRef(Simulation simulation, VCDocument modelDocument, int jobIndex, boolean isLocal) {
    SimulationDataSetRef simulationDataSetReference = new SimulationDataSetRef();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    SimulationInfo simInfo = simulation.getSimulationInfo();
    simulationDataSetReference.setSimName(simInfo.getName());
    // String simName = simInfo.getName();
    // if (jobIndex!=0){
    // simName = simName + " job#"+String.valueOf(jobIndex);
    // }
    final String modelId;
    final boolean isMathModel;
    final String modelName;
    final String simContextName;
    if (modelDocument != null) {
        modelId = modelDocument.getVersion().getVersionKey().toString();
        isMathModel = (modelDocument instanceof MathModel);
        modelName = modelDocument.getName();
        if (modelDocument instanceof BioModel && simulation.getSimulationOwner() != null) {
            simContextName = simulation.getSimulationOwner().getName();
        } else {
            simContextName = null;
        }
    } else {
        modelId = "no id";
        isMathModel = false;
        modelName = "no model";
        simContextName = null;
    }
    simulationDataSetReference.setSimId(simInfo.getAuthoritativeVCSimulationIdentifier().getSimulationKey().toString());
    simulationDataSetReference.setModelId(modelId);
    simulationDataSetReference.setUsername(simInfo.getVersion().getOwner().getName());
    simulationDataSetReference.setUserkey(simInfo.getVersion().getOwner().getID().toString());
    simulationDataSetReference.setIsMathModel(isMathModel);
    simulationDataSetReference.setJobIndex(jobIndex);
    simulationDataSetReference.setModelName(modelName);
    simulationDataSetReference.setOriginXYZ(Arrays.asList(new Double[] { origin.getX(), origin.getY(), origin.getZ() }));
    simulationDataSetReference.setExtentXYZ(Arrays.asList(new Double[] { extent.getX(), extent.getY(), extent.getZ() }));
    if (simContextName != null) {
        simulationDataSetReference.setSimulationContextName(simContextName);
    }
    simulationDataSetReference.setSimName(simInfo.getName());
    boolean movingBoundarySolver = simulation.getSolverTaskDescription().getSolverDescription().isMovingBoundarySolver();
    simulationDataSetReference.setIsTimeVaryingMesh(movingBoundarySolver);
    simulationDataSetReference.setIsLocal(isLocal);
    return simulationDataSetReference;
}