Examples with SourceDataInfo cbit.image.SourceDataInfo used on opensource projects

Example 1 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class ImageContainerPanel method refreshImage.

/**
 * This method was created by a SmartGuide.
 */
public void refreshImage() {
    if (getImageContainer() == null) {
        getImagePaneScroller().getImagePaneView().clear();
        return;
    }
    try {
        int nX = getImageContainer().getDisplayWidth();
        int nY = getImageContainer().getDisplayHeight();
        int nZ = 1;
        SourceDataInfo sourceData = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, getImageContainer().getPixels(), new org.vcell.util.Extent(1, 1, 1), new org.vcell.util.Origin(0, 0, 0), getImageContainer().getDataRange(), 0, nX, 1, nY, nX, nZ, nX * nY);
        getImagePaneScroller().getImagePaneModel().setSourceData(sourceData);
    } catch (Exception e) {
        getImagePaneScroller().getImagePaneView().clear();
        e.printStackTrace(System.out);
    }
}

Example 2 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class GeometryViewer method refreshSourceDataInfo.

/**
 * connEtoM2:  (Geometry.this --> ImagePlaneManagerPanel1.sourceDataInfo)
 * @param value cbit.vcell.geometry.Geometry
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void refreshSourceDataInfo() {
    if (getGeometry() == null) {
        return;
    }
    GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
    if (geometrySpec.getSampledImage().isDirty()) {
        return;
    }
    VCImage sampledImage = geometrySpec.getSampledImage().getCurrentValue();
    try {
        SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INDEX_TYPE, sampledImage.getPixels(), geometrySpec.getExtent(), geometrySpec.getOrigin(), null, 0, sampledImage.getNumX(), 1, sampledImage.getNumY(), sampledImage.getNumX(), sampledImage.getNumZ(), sampledImage.getNumX() * sampledImage.getNumY());
        getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
    } catch (ImageException e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage());
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 3 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class GeometrySummaryPanel method initGeometry.

/**
 * Comment
 */
private void initGeometry(Geometry arg1) {
    final boolean bSpatial = getGeometry() != null && getGeometry().getDimension() > 0;
    getImagePlaneManagerPanel1().setVisible(bSpatial);
    getJPanelOrigin().setVisible(bSpatial);
    getJPanelSize().setVisible(bSpatial);
    if (getGeometry() != null) {
        try {
            if (getGeometry().getGeometrySpec().getSampledImage().isDirty()) {
                return;
            }
            VCImage vcImage = getGeometry().getGeometrySpec().getSampledImage().getCurrentValue();
            byte[] pixels = vcImage.getPixels();
            DisplayAdapterService das = new DisplayAdapterService();
            das.setActiveScaleRange(new org.vcell.util.Range(0, 255));
            das.setValueDomain(new org.vcell.util.Range(0, 255));
            das.addColorModelForValues(DisplayAdapterService.createContrastColorModel(), DisplayAdapterService.createGraySpecialColors(), "Contrast");
            das.setActiveColorModelID("Contrast");
            int[] rgb = new int[pixels.length];
            for (int i = 0; i < rgb.length; i += 1) {
                rgb[i] = das.getColorFromIndex(pixels[i]);
            }
            SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, rgb, getGeometry().getExtent(), getGeometry().getOrigin(), new org.vcell.util.Range(0, 255), 0, vcImage.getNumX(), 1, vcImage.getNumY(), vcImage.getNumX(), vcImage.getNumZ(), vcImage.getNumX() * vcImage.getNumY());
            getImagePlaneManagerPanel1().setSourceDataInfo(sdi);
        } catch (Exception e) {
            PopupGenerator.showErrorDialog(GeometrySummaryPanel.this, e.getMessage(), e);
        }
    } else {
        getImagePlaneManagerPanel1().setSourceDataInfo(null);
    }
}

Example 4 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class PDEDataContextPanel method calculateSourceDataInfo.

/**
 * Comment
 */
private SourceDataInfo calculateSourceDataInfo(CartesianMesh mesh, double[] sdiData, VariableType sdiVarType, Range newRange) {
    SourceDataInfo sdi = null;
    // 
    if (sdiVarType.equals(VariableType.VOLUME) || sdiVarType.equals(VariableType.POSTPROCESSING)) {
        // Set data to display
        int yIncr = mesh.getSizeX();
        int zIncr = mesh.getSizeX() * mesh.getSizeY();
        sdi = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, sdiData, mesh.getExtent(), mesh.getOrigin(), newRange, 0, mesh.getSizeX(), 1, mesh.getSizeY(), yIncr, mesh.getSizeZ(), zIncr);
    } else if (sdiVarType.equals(VariableType.VOLUME_REGION)) {
        // 
        double[] expandedVolumeRegionValues = new double[mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ()];
        double[] volumeRegionDataValues = sdiData;
        for (int i = 0; i < expandedVolumeRegionValues.length; i += 1) {
            expandedVolumeRegionValues[i] = volumeRegionDataValues[mesh.getVolumeRegionIndex(i)];
        }
        // 
        int yIncr = mesh.getSizeX();
        int zIncr = mesh.getSizeX() * mesh.getSizeY();
        sdi = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, expandedVolumeRegionValues, mesh.getExtent(), mesh.getOrigin(), newRange, 0, mesh.getSizeX(), 1, mesh.getSizeY(), yIncr, mesh.getSizeZ(), zIncr);
    } else {
        // Membranes
        // Create placeholder SDI with null data
        sdi = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, null, mesh.getExtent(), mesh.getOrigin(), newRange, 0, mesh.getSizeX(), 0, mesh.getSizeY(), 0, mesh.getSizeZ(), 0);
    }
    if (mesh.isChomboMesh()) {
        sdi.setIsChombo(true);
    } else if (mesh instanceof CartesianMeshMovingBoundary) {
        sdi.setSolverDataType(SolverDataType.MBSData);
    }
    return sdi;
}

Example 5 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class PDEDataContextPanel method recodeDataForDomain.

public void recodeDataForDomain() {
    // 
    if (getPdeDataContext() == null) {
        return;
    }
    recodeDataForDomain0();
    VariableType vt = getPdeDataContext().getDataIdentifier().getVariableType();
    // This creates an appropriate volume data data holder for volume data types
    // or creates a dummy background for membrane data types
    SourceDataInfo recodedSourceDataInfo = calculateSourceDataInfo(getPdeDataContext().getCartesianMesh(), recodeDataForDomainInfo.getRecodedDataForDomain(), getPdeDataContext().getDataIdentifier().getVariableType(), recodeDataForDomainInfo.getRecodedDataRange());
    getImagePlaneManagerPanel().setSourceDataInfo(recodedSourceDataInfo);
}