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

Example 76 with Extent

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

the class RayCaster method createGeometryFromSTL.

public static Geometry createGeometryFromSTL(GeometryThumbnailImageFactory geometryThumbnailImageFactory, SurfaceCollection surfaceCollection, int numSamples) throws ImageException, PropertyVetoException, GeometryException, ExpressionException, IOException {
    Node[] nodes = surfaceCollection.getNodes();
    double minX = Double.MAX_VALUE;
    double maxX = -Double.MAX_VALUE;
    double minY = Double.MAX_VALUE;
    double maxY = -Double.MAX_VALUE;
    double minZ = Double.MAX_VALUE;
    double maxZ = -Double.MAX_VALUE;
    for (Node node : nodes) {
        double nx = node.getX();
        double ny = node.getY();
        double nz = node.getZ();
        minX = Math.min(minX, nx);
        maxX = Math.max(maxX, nx);
        minY = Math.min(minY, ny);
        maxY = Math.max(maxY, ny);
        minZ = Math.min(minZ, nz);
        maxZ = Math.max(maxZ, nz);
    }
    Extent extent = new Extent((maxX - minX) * 1.4, (maxY - minY) * 1.4, (maxZ - minZ) * 1.4);
    Origin origin = new Origin(minX - 0.2 * extent.getX(), minY - 0.2 * extent.getY(), minZ - 0.2 * extent.getZ());
    ISize sampleSize = GeometrySpec.calulateResetSamplingSize(3, extent, numSamples);
    Geometry geometry = createGeometry(geometryThumbnailImageFactory, surfaceCollection, origin, extent, sampleSize);
    return geometry;
}

Example 77 with Extent

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

the class NonGUIFRAPTest method runSolver.

/**
 * @param args
 */
public static void runSolver(String[] args) throws Exception {
    String startingIndexForRecovery = args[0];
    String freeDiffusionRateStr = args[1];
    String freeMobileFractionStr = args[2];
    String complexDiffusionRateStr = args[3];
    String complexMobileFractionStr = args[4];
    String bleachWhileMonitoringRateString = args[5];
    String immobileFractionStr = args[6];
    String bindingSiteConcentrationStr = args[7];
    String reacOnRateStr = args[8];
    String reacOffRateStr = args[9];
    String workingDirectoryPath = args[10];
    String inputFRAPDataFileName = args[11];
    String inputCellROIFileName = args[12];
    String inputBleachROIFileName = args[13];
    String inputBackgroundROIFileName = args[14];
    String outputXMLFileName = args[15];
    String commaSepTimeStamps = args[16];
    String commaSepExtentXYZ = args[17];
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDirectoryPath));
    ExternalDataFileContents extDataFileContents = readExternalDataContents(inputFRAPDataFileName, inputCellROIFileName, inputBleachROIFileName, inputBackgroundROIFileName);
    ROI cellROI = new ROI(extDataFileContents.cellROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = new ROI(extDataFileContents.bleachROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = new ROI(extDataFileContents.backgroundROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // Insert Time information
    double[] timeStamps = new double[extDataFileContents.imageData.getAllImages().length];
    StringTokenizer commaStringTokenizer = new StringTokenizer(commaSepTimeStamps, ",");
    int timeCount = 0;
    while (commaStringTokenizer.hasMoreTokens()) {
        timeStamps[timeCount] = Double.parseDouble(commaStringTokenizer.nextToken());
        timeCount++;
    }
    ImageDataset frapDataImageDataSet = new ImageDataset(extDataFileContents.imageData.getAllImages(), timeStamps, 1);
    // Insert Extent information
    commaStringTokenizer = new StringTokenizer(commaSepExtentXYZ, ",");
    Extent extent = new Extent(Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()));
    frapDataImageDataSet.setExtent(extent);
    bleachROI.getRoiImages()[0].setExtent(extent);
    cellROI.getRoiImages()[0].setExtent(extent);
    backgroundROI.getRoiImages()[0].setExtent(extent);
    FRAPData frapData = FrapDataUtils.importFRAPDataFromImageDataSet(frapDataImageDataSet);
    frapData.addReplaceRoi(bleachROI);
    frapData.addReplaceRoi(cellROI);
    frapData.addReplaceRoi(backgroundROI);
    FRAPStudy frapStudy = new FRAPStudy();
    frapStudy.setFrapData(frapData);
    // old model parameters, need to rewrite
    // FRAPStudy.FRAPModelParameters frapModelParameters = new FRAPStudy.FRAPModelParameters(
    // new FRAPStudy.InitialModelParameters(freeDiffusionRateStr, freeMobileFractionStr, bleachWhileMonitoringRateString, startingIndexForRecovery),
    // null,
    // null);
    // frapStudy.setFrapModelParameters(frapModelParameters);
    frapStudy.refreshDependentROIs();
    ExternalDataInfo imageDatasetExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME);
    ExternalDataInfo roiExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME);
    frapStudy.setFrapDataExternalDataInfo(imageDatasetExternalDataInfo);
    frapStudy.setRoiExternalDataInfo(roiExternalDataInfo);
    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    // Double bleachWhileMonitoringRate =
    // (!bleachWhileMonitoringRateString.equals("-")
    // ?Double.parseDouble(bleachWhileMonitoringRateString)
    // :null);
    double fd, ff, bwmr, cd, cf, imf, bs, on, off;
    try {
        fd = Double.parseDouble(freeDiffusionRateStr);
        ff = Double.parseDouble(freeMobileFractionStr);
        bwmr = Double.parseDouble(bleachWhileMonitoringRateString);
        cd = Double.parseDouble(complexDiffusionRateStr);
        cf = Double.parseDouble(complexMobileFractionStr);
        imf = Double.parseDouble(immobileFractionStr);
        bs = Double.parseDouble(bindingSiteConcentrationStr);
        on = Double.parseDouble(reacOnRateStr);
        off = Double.parseDouble(reacOffRateStr);
    } catch (NumberFormatException e) {
        throw new Exception("Input parameters are not all valid. Check if they are empty or in illegal forms.");
    }
    BioModel bioModel = FRAPStudy.createNewSimBioModel(frapStudy, createParameterArray(fd, ff, bwmr, cd, cf, imf, bs, on, off), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), new Integer(frapStudy.getStartingIndexForRecovery()));
    frapStudy.setBioModel(bioModel);
    // no progress listener, need to change
    MicroscopyXmlproducer.writeXMLFile(frapStudy, new File(outputXMLFileName), true, null, false);
    FRAPStudy.runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), imageDatasetExternalDataInfo.getExternalDataIdentifier(), roiExternalDataInfo.getExternalDataIdentifier(), null);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(bioModel.getSimulations()[0].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
    PDEDataManager simulationDataManager = new PDEDataManager(null, localWorkspace.getVCDataManager(), vcSimulationDataIdentifier);
    double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
    VCDataManager testVCDataManager = localWorkspace.getVCDataManager();
    double[] prebleachAverage = testVCDataManager.getSimDataBlock(null, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), "prebleach_avg", 0).getData();
    // TODO: need to create parameters here.
    Parameter[] parameters = null;
    SpatialAnalysisResults spatialAnalysisResults = FRAPStudy.spatialAnalysis(simulationDataManager, new Integer(frapStudy.getStartingIndexForRecovery()), frapDataTimeStamps[new Integer(frapStudy.getStartingIndexForRecovery())], parameters, frapData, prebleachAverage);
    dumpSummaryReport(spatialAnalysisResults, frapDataTimeStamps, new Integer(startingIndexForRecovery).intValue(), new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
    dumpSpatialResults(spatialAnalysisResults, frapDataTimeStamps, new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
}

Example 78 with Extent

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

the class FrapDataUtils method saveImageDatasetAsExternalData.

public static void saveImageDatasetAsExternalData(FRAPData frapData, LocalWorkspace localWorkspace, ExternalDataIdentifier newImageExtDataID, int startingIndexForRecovery, CartesianMesh cartesianMesh) throws ObjectNotFoundException, FileNotFoundException {
    ImageDataset imageDataset = frapData.getImageDataset();
    if (imageDataset.getSizeC() > 1) {
        throw new RuntimeException("FRAPData.saveImageDatasetAsExternalData(): multiple channels not yet supported");
    }
    Extent extent = imageDataset.getExtent();
    ISize isize = imageDataset.getISize();
    // not include the prebleach
    int numImageToStore = imageDataset.getSizeT() - startingIndexForRecovery;
    // original fluor data and back ground average
    double[][][] pixData = new double[numImageToStore][2][];
    double[] timesArray = new double[numImageToStore];
    double[] bgAvg = frapData.getAvgBackGroundIntensity();
    for (int tIndex = startingIndexForRecovery; tIndex < imageDataset.getSizeT(); tIndex++) {
        // images according to zIndex at specific time points(tIndex)
        short[] originalData = imageDataset.getPixelsZ(0, tIndex);
        double[] doubleData = new double[originalData.length];
        double[] expandBgAvg = new double[originalData.length];
        for (int i = 0; i < originalData.length; i++) {
            doubleData[i] = 0x0000ffff & originalData[i];
            expandBgAvg[i] = bgAvg[tIndex];
        }
        pixData[tIndex - startingIndexForRecovery][0] = doubleData;
        pixData[tIndex - startingIndexForRecovery][1] = expandBgAvg;
        timesArray[tIndex - startingIndexForRecovery] = imageDataset.getImageTimeStamps()[tIndex] - imageDataset.getImageTimeStamps()[startingIndexForRecovery];
    }
    // changed in March 2008. Though biomodel is not created, we still let user save to xml file.
    Origin origin = new Origin(0, 0, 0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newImageExtDataID;
    fdos.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME, "bg_average" };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = timesArray;
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME, VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 79 with Extent

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

the class FrapDataUtils method saveROIsAsExternalData.

public static void saveROIsAsExternalData(FRAPData frapData, LocalWorkspace localWorkspace, ExternalDataIdentifier newROIExtDataID, int startingIndexForRecovery, CartesianMesh cartesianMesh) throws ObjectNotFoundException, FileNotFoundException {
    ImageDataset imageDataset = frapData.getImageDataset();
    Extent extent = imageDataset.getExtent();
    ISize isize = imageDataset.getISize();
    int NumTimePoints = 1;
    // actually it is total number of ROIs(cell,bleached + 8 rings)+prebleach+firstPostBleach+lastPostBleach
    int NumChannels = 13;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    double[] temp_background = frapData.getAvgBackGroundIntensity();
    double[] avgPrebleachDouble = calculatePreBleachAverageXYZ(frapData, startingIndexForRecovery);
    // average of prebleach with background subtracted
    pixData[0][0] = avgPrebleachDouble;
    // first post-bleach with background subtracted
    pixData[0][1] = createDoubleArray(imageDataset.getPixelsZ(0, startingIndexForRecovery), temp_background[startingIndexForRecovery], true);
    // adjustPrebleachAndPostbleachData(avgPrebleachDouble, pixData[0][1]);
    // last post-bleach image (at last time point) with background subtracted
    pixData[0][2] = createDoubleArray(imageDataset.getPixelsZ(0, imageDataset.getSizeT() - 1), temp_background[imageDataset.getSizeT() - 1], true);
    // below are ROIs, we don't need to subtract background for them.
    pixData[0][3] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getBinaryPixelsXYZ(1), 0, false);
    pixData[0][4] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()).getBinaryPixelsXYZ(1), 0, false);
    if (frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name()) == null) {
        // throw new RuntimeException("must first generate \"derived masks\"");
        pixData[0][5] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][6] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][7] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][8] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][9] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][10] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][11] = new double[imageDataset.getISize().getXYZ()];
        pixData[0][12] = new double[imageDataset.getISize().getXYZ()];
    } else {
        pixData[0][5] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][6] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][7] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][8] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][9] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][10] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][11] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name()).getBinaryPixelsXYZ(1), 0, false);
        pixData[0][12] = createDoubleArray(frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name()).getBinaryPixelsXYZ(1), 0, false);
    }
    Origin origin = new Origin(0, 0, 0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    fdos.varNames = new String[] { "prebleach_avg", "postbleach_first", "postbleach_last", "bleached_mask", "cell_mask", "ring1_mask", "ring2_mask", "ring3_mask", "ring4_mask", "ring5_mask", "ring6_mask", "ring7_mask", "ring8_mask" };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME, VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 80 with Extent

use of org.vcell.util.Extent 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;
}