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

Example 46 with ISize

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

the class FRAPStudy method getROIDataGenerator.

public ROIDataGenerator getROIDataGenerator(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] roiFieldData = null;
    ROI[] rois = getFrapData().getRois();
    if (rois.length > 0) {
        Extent extent = rois[0].getRoiImages()[0].getExtent();
        ISize isize = rois[0].getISize();
        int numROIX = rois[0].getISize().getX();
        int numROIY = rois[0].getISize().getY();
        roiFieldData = new short[numROIX * numROIY];
        short regionCounter = 1;
        for (int roiIdx = FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.ordinal(); roiIdx < rois.length; roiIdx++) {
            short[] roiImg = rois[roiIdx].getPixelsXYZ();
            for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
                if (roiImg[pixelIdx] > 0) {
                    roiFieldData[pixelIdx] = regionCounter;
                }
            }
            regionCounter++;
        }
        // create field data
        int NumTimePoints = 1;
        // 8 rois integrated into 1 image
        int NumChannels = 1;
        short[][][] pixData = new short[NumTimePoints][NumChannels][];
        pixData[0][0] = roiFieldData;
        // get extental data id
        ExternalDataIdentifier newROIExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_SUMDATA_NAME).getExternalDataIdentifier();
        CartesianMesh cartesianMesh;
        try {
            cartesianMesh = getCartesianMesh();
            Origin origin = new Origin(0, 0, 0);
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.shortSpecData = pixData;
            fdos.specEDI = newROIExtDataID;
            fdos.varNames = new String[] { "roiSumDataVar" };
            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);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
        new int[] { 0 }, /* volumePoints*/
        new int[0], /* membranePoints*/
        regionCounter, /*numRegions*/
        0, /*zSlice*/
        newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
        new FieldFunctionArguments(FRAPStudy.ROI_SUMDATA_NAME, "roiSumDataVar", new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}

Example 47 with ISize

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

the class MeshSpecification method getVCML.

/**
 * This method was created by a SmartGuide.
 * @return java.lang.String
 */
public String getVCML() {
    StringBuffer buffer = new StringBuffer();
    buffer.append(VCML.MeshSpecification + " {\n");
    ISize size = getSamplingSize();
    buffer.append("\t" + VCML.Size + " " + size.getX() + " " + size.getY() + " " + size.getZ() + "\n");
    buffer.append("}\n");
    return buffer.toString();
}

Example 48 with ISize

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

the class XmlReader method getMeshSpecification.

/**
 * This method returns a MeshSpecification object from a XML Element.
 * Creation date: (5/22/2001 12:05:21 PM)
 * @return cbit.vcell.mesh.MeshSpecification
 * @param param org.jdom.Element
 */
private MeshSpecification getMeshSpecification(Element param, Geometry geometry) throws XmlParseException {
    // *** create new MeshSpecification ***
    MeshSpecification meshSpec = new MeshSpecification(geometry);
    // get ISize
    Element size = param.getChild(XMLTags.SizeTag, vcNamespace);
    int x = Integer.parseInt(size.getAttributeValue(XMLTags.XAttrTag));
    int y = Integer.parseInt(size.getAttributeValue(XMLTags.YAttrTag));
    int z = Integer.parseInt(size.getAttributeValue(XMLTags.ZAttrTag));
    ISize newsize = new ISize(x, y, z);
    // set ISize
    try {
        meshSpec.setSamplingSize(newsize);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the ISize object to a new MeshSpecification", e);
    }
    return meshSpec;
}

Example 49 with ISize

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

the class Xmlproducer method getXML.

private Element getXML(GeometrySurfaceDescription param) throws XmlParseException {
    Element gsd = new Element(XMLTags.SurfaceDescriptionTag);
    // add attributes
    ISize isize = param.getVolumeSampleSize();
    if (isize == null) {
        throw new XmlParseException("Unable to retrieve dimensions for surface descriptions for Geometry: " + param.getGeometry().getName());
    }
    gsd.setAttribute(XMLTags.NumSamplesXAttrTag, String.valueOf(isize.getX()));
    gsd.setAttribute(XMLTags.NumSamplesYAttrTag, String.valueOf(isize.getY()));
    gsd.setAttribute(XMLTags.NumSamplesZAttrTag, String.valueOf(isize.getZ()));
    Double coFrequency = param.getFilterCutoffFrequency();
    if (coFrequency == null) {
        throw new XmlParseException("Unable to retrieve cutoff frequency for surface descriptions for Geometry: " + param.getGeometry().getName());
    }
    double cutoffFrequency = coFrequency.doubleValue();
    gsd.setAttribute(XMLTags.CutoffFrequencyAttrTag, String.valueOf(cutoffFrequency));
    // add subelements
    GeometricRegion[] geomRegions = param.getGeometricRegions();
    if (geomRegions != null) {
        for (int i = 0; i < geomRegions.length; i++) {
            if (geomRegions[i] instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) geomRegions[i];
                Element membraneRegion = new Element(XMLTags.MembraneRegionTag);
                membraneRegion.setAttribute(XMLTags.NameAttrTag, sgr.getName());
                GeometricRegion[] adjacents = sgr.getAdjacentGeometricRegions();
                if (adjacents == null || adjacents.length != 2) {
                    throw new XmlParseException("Wrong number of adjacent regions for surface descriptions for location: " + sgr.getName() + " in Geometry: " + param.getGeometry().getName());
                }
                membraneRegion.setAttribute(XMLTags.VolumeRegion_1AttrTag, adjacents[0].getName());
                membraneRegion.setAttribute(XMLTags.VolumeRegion_2AttrTag, adjacents[1].getName());
                double size = sgr.getSize();
                if (size != -1) {
                    membraneRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
                    VCUnitDefinition unit = sgr.getSizeUnit();
                    if (unit != null) {
                        membraneRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                    }
                }
                gsd.addContent(membraneRegion);
            } else if (geomRegions[i] instanceof VolumeGeometricRegion) {
                VolumeGeometricRegion vgr = (VolumeGeometricRegion) geomRegions[i];
                Element volumeRegion = new Element(XMLTags.VolumeRegionTag);
                volumeRegion.setAttribute(XMLTags.NameAttrTag, vgr.getName());
                volumeRegion.setAttribute(XMLTags.RegionIDAttrTag, String.valueOf(vgr.getRegionID()));
                volumeRegion.setAttribute(XMLTags.SubVolumeAttrTag, vgr.getSubVolume().getName());
                double size = vgr.getSize();
                if (size != -1) {
                    volumeRegion.setAttribute(XMLTags.SizeAttrTag, String.valueOf(size));
                    VCUnitDefinition unit = vgr.getSizeUnit();
                    if (unit != null) {
                        volumeRegion.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                    }
                }
                gsd.addContent(volumeRegion);
            }
        }
    }
    return gsd;
}

Example 50 with ISize

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

the class Xmlproducer method getXML.

/**
 * Insert the method's description here.
 * Creation date: (3/3/2001 12:24:59 AM)
 * @return Element
 * @param param cbit.vcell.mesh.MeshSpecification
 */
private Element getXML(MeshSpecification param) {
    Element meshspec = new Element(XMLTags.MeshSpecTag);
    Element size = new Element(XMLTags.SizeTag);
    // Add extent attributes
    ISize sampling = param.getSamplingSize();
    size.setAttribute(XMLTags.XAttrTag, String.valueOf(sampling.getX()));
    size.setAttribute(XMLTags.YAttrTag, String.valueOf(sampling.getY()));
    size.setAttribute(XMLTags.ZAttrTag, String.valueOf(sampling.getZ()));
    meshspec.addContent(size);
    return meshspec;
}