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

Example 46 with Coordinate

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

the class PDEDataContextPanel method getCurveValue.

/**
 * Insert the method's description here.
 * Creation date: (3/13/2001 12:53:10 PM)
 * @return java.lang.String
 * @param csi cbit.vcell.geometry.CurveSelectionInfo
 */
public String getCurveValue(CurveSelectionInfo csi) {
    String infoS = null;
    if (csi.getType() == CurveSelectionInfo.TYPE_SEGMENT) {
        if (membranesAndIndexes != null) {
            java.util.Enumeration<SampledCurve> keysEnum = membranesAndIndexes.keys();
            while (keysEnum.hasMoreElements()) {
                Curve curve = (Curve) keysEnum.nextElement();
                if (csi.getCurve() == curve) {
                    int[] membraneIndexes = (int[]) membranesAndIndexes.get(curve);
                    if (meshDisplayAdapter != null) {
                        double[] membraneValues = meshDisplayAdapter.getDataValuesForMembraneIndexes(membraneIndexes, getPdeDataContext().getDataValues(), getPdeDataContext().getDataIdentifier().getVariableType());
                        if (membraneValues != null) {
                            Coordinate segmentWC = getPdeDataContext().getCartesianMesh().getCoordinateFromMembraneIndex(membraneIndexes[csi.getSegment()]);
                            String xCoordString = NumberUtils.formatNumber(segmentWC.getX());
                            String yCoordString = NumberUtils.formatNumber(segmentWC.getY());
                            String zCoordString = NumberUtils.formatNumber(segmentWC.getZ());
                            boolean bDefined = getDataInfoProvider() == null || getDataInfoProvider().isDefined(membraneIndexes[csi.getSegment()]);
                            infoS = "(" + xCoordString + "," + yCoordString + "," + zCoordString + ")  [" + membraneIndexes[csi.getSegment()] + "]  Value = " + (bDefined ? membraneValues[csi.getSegment()] : "Undefined");
                            if (getPdeDataContext().getCartesianMesh() != null && getPdeDataContext().getCartesianMesh().isChomboMesh()) {
                                if (bDefined && getDataInfoProvider() != null) {
                                    StructureMetricsEntry structure = ((CartesianMeshChombo) getDataInfoProvider().getPDEDataContext().getCartesianMesh()).getStructureInfo(getDataInfoProvider().getPDEDataContext().getDataIdentifier());
                                    if (structure != null) {
                                        infoS += " || " + structure.getDisplayLabel();
                                    }
                                }
                            } else {
                                if (getDataInfoProvider() != null) {
                                    MembraneDataInfo membraneDataInfo = getDataInfoProvider().getMembraneDataInfo(membraneIndexes[csi.getSegment()]);
                                    infoS += "          ";
                                    infoS += " \"" + membraneDataInfo.membraneName + "\"";
                                    infoS += " mrID=" + membraneDataInfo.membraneRegionID;
                                }
                                String curveDescr = CurveRenderer.getROIDescriptions(segmentWC, getImagePlaneManagerPanel().getCurveRenderer());
                                if (curveDescr != null) {
                                    infoS += "     " + curveDescr;
                                }
                            }
                            break;
                        }
                    }
                }
            }
        }
    }
    return infoS;
}

Example 47 with Coordinate

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

the class ImageJHelper method sendMembraneOutline.

private static void sendMembraneOutline(ImageJConnection imageJConnection, Hashtable<SampledCurve, int[]>[] membraneTables) throws Exception {
    if (membraneTables != null) {
        // num slices
        imageJConnection.dos.writeInt(membraneTables.length);
        for (Hashtable<SampledCurve, int[]> membraneTable : membraneTables) {
            // System.out.println();
            if (membraneTable != null) {
                // some slices have no membrane outline
                // num polygons on slice
                imageJConnection.dos.writeInt(membraneTable.size());
                Enumeration<SampledCurve> sliceMembranes = membraneTable.keys();
                while (sliceMembranes.hasMoreElements()) {
                    SampledCurve sampledCurve = sliceMembranes.nextElement();
                    Vector<Coordinate> polygonPoints = sampledCurve.getControlPointsVector();
                    // System.out.println(polygonPoints.size());
                    // num points for polygon
                    imageJConnection.dos.writeInt(polygonPoints.size());
                    // isClosed
                    imageJConnection.dos.writeInt((sampledCurve.isClosed() ? 1 : 0));
                    for (Coordinate coord : polygonPoints) {
                        imageJConnection.dos.writeDouble(coord.getX());
                        imageJConnection.dos.writeDouble(coord.getY());
                        imageJConnection.dos.writeDouble(coord.getZ());
                    }
                }
            } else {
                imageJConnection.dos.writeInt(0);
            }
        }
    } else {
        imageJConnection.dos.writeInt(0);
    }
}

Example 48 with Coordinate

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

the class ImagePlaneManager method snapWorldCoordinate.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2004 1:52:04 PM)
 */
public org.vcell.util.Coordinate snapWorldCoordinate(org.vcell.util.Coordinate targetC) {
    if (getSourceDataInfo() != null) {
        double distance = 0;
        org.vcell.util.CoordinateIndex centerCI = getSourceDataInfo().getDataIndexFromWorldCoordinate(targetC);
        Coordinate centerCoord = getSourceDataInfo().getWorldCoordinateFromIndex(centerCI);
        return centerCoord;
    }
    return null;
}

Example 49 with Coordinate

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

the class PDEOffscreenRenderer method getPixelsRGB.

/**
 * Insert the method's description here.
 * Creation date: (3/1/2001 11:54:44 PM)
 * @return int[]
 */
public int[] getPixelsRGB(int imageScale, int membrScale, int meshMode, int volVarMembrOutlineThickness) {
    if (getServerPDEDataContext().getDataIdentifier().getVariableType().equals(VariableType.VOLUME) || getServerPDEDataContext().getDataIdentifier().getVariableType().equals(VariableType.POSTPROCESSING)) {
        CartesianMesh mesh = getServerPDEDataContext().getCartesianMesh();
        MeshDisplayAdapter meshDisplayAdapter = new MeshDisplayAdapter(mesh);
        BufferedImage bufferedImage = getScaledRGBVolume(mesh, meshMode, imageScale, false);
        // 
        if (!getServerPDEDataContext().getDataIdentifier().getVariableType().equals(VariableType.POSTPROCESSING) && volVarMembrOutlineThickness > 0) {
            cbit.vcell.geometry.CurveRenderer curveRenderer = new cbit.vcell.geometry.CurveRenderer(getDisplayAdapterService());
            curveRenderer.setNormalAxis(getNormalAxis());
            org.vcell.util.Origin origin = mesh.getOrigin();
            org.vcell.util.Extent extent = mesh.getExtent();
            curveRenderer.setWorldOrigin(new org.vcell.util.Coordinate(origin.getX(), origin.getY(), origin.getZ()));
            Coordinate pixeldelta = getPixelDelta(extent, mesh, meshMode, imageScale);
            curveRenderer.setWorldDelta(new org.vcell.util.Coordinate(pixeldelta.getX(), pixeldelta.getY(), pixeldelta.getZ()));
            Hashtable<SampledCurve, int[]> curvesAndMembraneIndexes = meshDisplayAdapter.getCurvesAndMembraneIndexes(getNormalAxis(), getSlice());
            if (curvesAndMembraneIndexes != null) {
                Curve[] curves = (Curve[]) org.vcell.util.BeanUtils.getArray(curvesAndMembraneIndexes.keys(), Curve.class);
                for (int i = 0; curves != null && i < curves.length; i++) {
                    curveRenderer.addCurve(curves[i]);
                    curveRenderer.renderPropertySegmentColors(curves[i], null);
                    curveRenderer.renderPropertyLineWidthMultiplier(curves[i], volVarMembrOutlineThickness);
                }
                Graphics2D g = (Graphics2D) bufferedImage.getGraphics();
                // must be false or could get more than 256 colors
                curveRenderer.setAntialias(false);
                curveRenderer.draw(g);
            }
        }
        return ((DataBufferInt) bufferedImage.getData().getDataBuffer()).getData();
    } else if (getServerPDEDataContext().getDataIdentifier().getVariableType().equals(VariableType.MEMBRANE)) {
        CartesianMesh mesh = getServerPDEDataContext().getCartesianMesh();
        MeshDisplayAdapter meshDisplayAdapter = new MeshDisplayAdapter(mesh);
        BufferedImage bufferedImage = getScaledRGBVolume(mesh, meshMode, imageScale, true);
        // 
        // apply curve renderer
        // 
        cbit.vcell.geometry.CurveRenderer curveRenderer = new cbit.vcell.geometry.CurveRenderer(getDisplayAdapterService());
        curveRenderer.setNormalAxis(getNormalAxis());
        org.vcell.util.Origin origin = mesh.getOrigin();
        org.vcell.util.Extent extent = mesh.getExtent();
        curveRenderer.setWorldOrigin(new org.vcell.util.Coordinate(origin.getX(), origin.getY(), origin.getZ()));
        Coordinate pixeldelta = getPixelDelta(extent, mesh, meshMode, imageScale);
        curveRenderer.setWorldDelta(new org.vcell.util.Coordinate(pixeldelta.getX(), pixeldelta.getY(), pixeldelta.getZ()));
        Hashtable<SampledCurve, int[]> curvesAndMembraneIndexes = meshDisplayAdapter.getCurvesAndMembraneIndexes(getNormalAxis(), getSlice());
        if (curvesAndMembraneIndexes != null) {
            Curve[] curves = (Curve[]) org.vcell.util.BeanUtils.getArray(curvesAndMembraneIndexes.keys(), Curve.class);
            for (int i = 0; curves != null && i < curves.length; i++) {
                curveRenderer.addCurve(curves[i]);
                curveRenderer.renderPropertySegmentColors(curves[i], getCurveColors(curvesAndMembraneIndexes, curves[i], meshDisplayAdapter));
                curveRenderer.renderPropertyLineWidthMultiplier(curves[i], membrScale);
            }
            Graphics2D g = (Graphics2D) bufferedImage.getGraphics();
            curveRenderer.setAntialias(false);
            curveRenderer.draw(g);
        }
        return ((DataBufferInt) bufferedImage.getData().getDataBuffer()).getData();
    } else {
        throw new RuntimeException("unsupported VariableType " + getServerPDEDataContext().getDataIdentifier().getVariableType());
    }
}

Example 50 with Coordinate

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

the class PDEOffscreenRenderer method getPixelDelta.

private Coordinate getPixelDelta(Extent extent, CartesianMesh mesh, int meshMode, int imageScale) {
    ImagePaneModel imagePaneModel = new ImagePaneModel();
    imagePaneModel.setMode(meshMode);
    imagePaneModel.setZoom(imageScale);
    double pixelScaleX = extent.getX() / imagePaneModel.getScaledLength(mesh.getSizeX());
    double pixelScaleY = extent.getY() / imagePaneModel.getScaledLength(mesh.getSizeY());
    double pixelScaleZ = extent.getZ() / imagePaneModel.getScaledLength(mesh.getSizeZ());
    return new Coordinate(pixelScaleX, pixelScaleY, pixelScaleZ);
}