Examples with Curve cbit.vcell.geometry.Curve used on opensource projects

Example 11 with Curve

use of cbit.vcell.geometry.Curve 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 12 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class PDEDataContextPanel method fireDataSamplers.

/**
 * Insert the method's description here.
 * Creation date: (7/6/2003 7:42:59 PM)
 * @param curve cbit.vcell.geometry.Curve
 */
private void fireDataSamplers() {
    // fire "dataSamplers" if there are any
    boolean bTimeDataSamplerVisible = false;
    boolean bSpatialDataSamplerVisible = false;
    CurveRenderer cr = getImagePlaneManagerPanel().getCurveRenderer();
    if (cr != null) {
        Curve[] curves = getImagePlaneManagerPanel().getCurveRenderer().getAllCurves();
        if (curves != null && curves.length > 0) {
            for (int i = 0; i < curves.length; i += 1) {
                if (membranesAndIndexes == null || !membranesAndIndexes.containsKey(curves[i])) {
                    boolean isCurveValidDataSampler = isValidDataSampler(curves[i]);
                    bTimeDataSamplerVisible = bTimeDataSamplerVisible || (isCurveValidDataSampler && curves[i] instanceof SinglePoint);
                    bSpatialDataSamplerVisible = bSpatialDataSamplerVisible || (isCurveValidDataSampler && !(curves[i] instanceof SinglePoint)) && cr.getSelection() != null && cr.getSelection().getCurve() == curves[i];
                }
            }
        }
    }
    // 
    firePropertyChange("timeDataSamplers", !bTimeDataSamplerVisible, bTimeDataSamplerVisible);
    firePropertyChange("spatialDataSamplers", !bSpatialDataSamplerVisible, bSpatialDataSamplerVisible);
}

Example 13 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class PDEDataContextPanel method isAddControlPointOK.

/**
 * Insert the method's description here.
 * Creation date: (7/4/2003 6:10:48 PM)
 */
public boolean isAddControlPointOK(int tool, Coordinate wc, Curve addedToThisCurve) {
    // 
    CurveRenderer curveR = getImagePlaneManagerPanel().getCurveRenderer();
    VariableType variableType = getPdeDataContext().getDataIdentifier().getVariableType();
    if (variableType.equals(VariableType.POSTPROCESSING) || variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION)) {
        return true;
    }
    if (variableType.equals(VariableType.MEMBRANE) || variableType.equals(VariableType.MEMBRANE_REGION)) {
        CurveSelectionInfo[] closeCSI = curveR.getCloseCurveSelectionInfos(wc);
        if (closeCSI != null && closeCSI.length > 0) {
            for (int i = 0; i < closeCSI.length; i += 1) {
                if (tool == CurveEditorTool.TOOL_POINT && addedToThisCurve instanceof SinglePoint && membranesAndIndexes != null && membranesAndIndexes.containsKey(closeCSI[i].getCurve())) {
                    return true;
                } else if (tool == CurveEditorTool.TOOL_LINE && addedToThisCurve instanceof CurveSelectionCurve) {
                    Curve sourceCurve = ((CurveSelectionCurve) (addedToThisCurve)).getSourceCurveSelectionInfo().getCurve();
                    if (sourceCurve == closeCSI[i].getCurve()) {
                        if (membranesAndIndexes != null && membranesAndIndexes.containsKey(sourceCurve)) {
                            return true;
                        }
                    }
                }
            }
        }
    }
    return false;
}

Example 14 with Curve

use of cbit.vcell.geometry.Curve 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 15 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class GeometryFilamentCurvePanel method setCurve2.

/**
 * Set the Curve2 to a new value.
 * @param newValue cbit.vcell.geometry.Curve
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setCurve2(cbit.vcell.geometry.Curve newValue) {
    if (ivjCurve2 != newValue) {
        try {
            cbit.vcell.geometry.Curve oldValue = getCurve2();
            ivjCurve2 = newValue;
            connPtoP6SetSource();
            firePropertyChange("curve", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}