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

Example 6 with SampledCurve

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

the class PDEDataContextPanel method updateMembraneCurves.

/**
 * Insert the method's description here.
 * Creation date: (10/22/00 3:15:49 PM)
 */
private void updateMembraneCurves() {
    // 
    if (getPdeDataContext() == null || getPdeDataContext().getDataIdentifier() == null) {
        return;
    }
    int normalAxis = getImagePlaneManagerPanel().getImagePlaneManager().getNormalAxis();
    int slice = getImagePlaneManagerPanel().getImagePlaneManager().getSlice();
    // Remove previous curves
    CurveRenderer curveRenderer = getImagePlaneManagerPanel().getCurveRenderer();
    if (membranesAndIndexes != null) {
        java.util.Enumeration<SampledCurve> keysEnum = membranesAndIndexes.keys();
        while (keysEnum.hasMoreElements()) {
            Curve curve = keysEnum.nextElement();
            curveRenderer.removeCurve(curve);
        }
    }
    // 
    membranesAndIndexes = null;
    boolean hasValues = false;
    if (meshDisplayAdapter != null) {
        // Get new curves for slice and normalAxis
        VariableType variableType = getPdeDataContext().getDataIdentifier().getVariableType();
        if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION)) {
            // Turn off showing Membrane values over mouse
            // getImagePlaneManagerPanel().setCurveValueProvider(null);
            // 
            // GET CURVES WITH NO VALUES FOR OVERLAY ON VOLUME DATA
            membranesAndIndexes = meshDisplayAdapter.getCurvesAndMembraneIndexes(normalAxis, slice);
        } else if (variableType.equals(VariableType.MEMBRANE)) {
            // Turn on showing Membrane values over mouse
            // getImagePlaneManagerPanel().setCurveValueProvider(this);
            // 
            // GET CURVES WITH VALUES
            membranesAndIndexes = meshDisplayAdapter.getCurvesAndMembraneIndexes(normalAxis, slice);
            hasValues = true;
        } else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
            // Turn on showing Membrane values over mouse
            // getImagePlaneManagerPanel().setCurveValueProvider(this);
            // 
            // GET CURVES WITH REGIONIDS
            membranesAndIndexes = meshDisplayAdapter.getCurvesAndMembraneIndexes(normalAxis, slice);
            /*
			//RegionID values
			double[] regionValues = getPdeDataContext().getDataValues();
			java.util.Iterator regionIDCurveValues = membranesAndValues.values().iterator();
			//convert RegionID to value
			while(regionIDCurveValues.hasNext()){
				java.util.Vector regionIDValues = (java.util.Vector)regionIDCurveValues.next();
				for(int i = 0;i < regionIDValues.size();i+= 1){
					int regionID = (int)(((Double)(regionIDValues.elementAt(i))).doubleValue());
					Double decodedRegionValue = new Double(regionValues[regionID]);
					regionIDValues.setElementAt(decodedRegionValue,i);
				}
			}
			*/
            hasValues = true;
        }
    }
    // Add new curves to curveRenderer
    if (membranesAndIndexes != null) {
        java.util.Enumeration<SampledCurve> keysEnum = membranesAndIndexes.keys();
        while (keysEnum.hasMoreElements()) {
            Curve curve = keysEnum.nextElement();
            // 
            curveRenderer.addCurve(curve);
            // 
            curveRenderer.renderPropertyEditable(curve, false);
            curveRenderer.renderPropertySelectable(curve, false);
            if (!hasValues) {
                curveRenderer.renderPropertyLineWidthMultiplier(curve, 3);
            }
        // getImagePlaneManagerPanel().getCurveRenderer().renderPropertySelectable(curve, hasValues);
        // if (hasValues) {
        // getImagePlaneManagerPanel().getCurveRenderer().renderPropertySubSelectionType(curve, cbit.vcell.geometry.gui.CurveRenderer.SUBSELECTION_SEGMENT);
        // }else{
        // getImagePlaneManagerPanel().getCurveRenderer().renderPropertyLineWidthMultiplier(curve,3);
        // }
        }
    }
    // 
    refreshColorCurves();
    // 
    // Set visibility of curve samplers
    Curve[] curves = curveRenderer.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]);
                curveRenderer.renderPropertyVisible(curves[i], isCurveValidDataSampler);
                curveRenderer.renderPropertyEditable(curves[i], (membraneSamplerCurves != null && membraneSamplerCurves.contains(curves[i]) ? false : true));
            }
        }
    }
    // See if we should keep selection
    if (curveRenderer.getSelection() != null) {
        CurveSelectionInfo csi = curveRenderer.getSelection();
        curveRenderer.selectNothing();
        if (isValidDataSampler(csi.getCurve())) {
            curveRenderer.setSelection(csi);
        }
    }
    // 
    // 
    fireDataSamplers();
}

Example 7 with SampledCurve

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

the class PDEDataContextPanel method projectCurveOntoSlice.

/**
 * Insert the method's description here.
 * Creation date: (7/16/2003 1:05:56 PM)
 * @return cbit.vcell.geometry.ControlPointCurve
 * @param curve cbit.vcell.geometry.ControlPointCurve
 */
private ControlPointCurve projectCurveOntoSlice(ControlPointCurve curve) {
    // for SinglePoint(timepoint) and PolyLine(spatial) samplers(always stored in world coordinates),
    // convert the curve coordinates into view coordinates from the sliceviewer
    ControlPointCurve cpCurve = null;
    java.util.Vector<Coordinate> cpV = new java.util.Vector<Coordinate>();
    int normalAxis = getimagePlaneManager1().getNormalAxis();
    for (int i = 0; i < curve.getControlPointCount(); i += 1) {
        // convert curves that are always stored in world coordinates into coordinates that
        // represent how user sees them in the slice viewer
        double xCoord = Coordinate.convertAxisFromStandardXYZToNormal(curve.getControlPoint(i), Coordinate.X_AXIS, normalAxis);
        double yCoord = Coordinate.convertAxisFromStandardXYZToNormal(curve.getControlPoint(i), Coordinate.Y_AXIS, normalAxis);
        // Get z from slice
        double zCoord = Coordinate.convertAxisFromStandardXYZToNormal(getimagePlaneManager1().getWorldCoordinateFromUnitized2D(0, 0), Coordinate.Z_AXIS, normalAxis);
        // These are now the real coordinates as they are viewed in the slice viewer
        // Coordinate newCoord = new Coordinate(xCoord,yCoord,zCoord);
        Coordinate newCoord = Coordinate.convertCoordinateFromNormalToStandardXYZ(xCoord, yCoord, zCoord, normalAxis);
        cpV.add(newCoord);
    }
    if (cpV.size() > 0) {
        Coordinate[] cpArr = new Coordinate[cpV.size()];
        cpV.copyInto(cpArr);
        // Determine if curve has been projected down to a single point
        boolean bSinglePoint = true;
        for (int i = 0; i < cpArr.length; i += 1) {
            if (i > 0 && !cpArr[i].equals(cpArr[i - 1])) {
                bSinglePoint = false;
                break;
            }
        }
        // if(curve instanceof SinglePoint){
        if (bSinglePoint) {
            cpCurve = new SinglePoint(cpArr[0]);
        } else if (curve instanceof SampledCurve) {
            cpCurve = new PolyLine(cpArr);
        }
    }
    return cpCurve;
}

Example 8 with SampledCurve

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

the class PDEDataContextPanel method getInitalCurveSelection.

/**
 * Insert the method's description here.
 * Creation date: (7/4/2003 6:10:48 PM)
 */
public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
    // 
    CurveSelectionInfo newCurveSelection = null;
    VariableType variableType = getPdeDataContext().getDataIdentifier().getVariableType();
    if (variableType.equals(VariableType.MEMBRANE) || variableType.equals(VariableType.MEMBRANE_REGION)) {
        if (getPdeDataContext().getCartesianMesh().isChomboMesh() && tool == CurveEditorTool.TOOL_POINT) {
            newCurveSelection = findChomboSinglePointSelectionInfoForPoint(wc);
        } else {
            CurveSelectionInfo[] closeCSI = getImagePlaneManagerPanel().getCurveRenderer().getCloseCurveSelectionInfos(wc);
            if (closeCSI != null) {
                for (int i = 0; i < closeCSI.length; i += 1) {
                    if (membranesAndIndexes != null && membranesAndIndexes.containsKey(closeCSI[i].getCurve())) {
                        if (tool == CurveEditorTool.TOOL_LINE) {
                            newCurveSelection = new CurveSelectionInfo(new CurveSelectionCurve((SampledCurve) (closeCSI[i].getCurve())));
                        } else if (tool == CurveEditorTool.TOOL_POINT) {
                            newCurveSelection = new CurveSelectionInfo(new CurveSelectionCurve((SampledCurve) (closeCSI[i].getCurve())));
                            double dist = closeCSI[i].getCurve().getDistanceTo(wc);
                            int segmentIndex = closeCSI[i].getCurve().pickSegment(wc, dist * 1.1);
                            Coordinate[] coordArr = closeCSI[i].getCurve().getSampledCurve().getControlPointsForSegment(segmentIndex);
                            Coordinate middleCoord = new Coordinate((coordArr[0].getX() + coordArr[1].getX()) / 2, (coordArr[0].getY() + coordArr[1].getY()) / 2, (coordArr[0].getZ() + coordArr[1].getZ()) / 2);
                            newCurveSelection = new CurveSelectionInfo(new SinglePoint(middleCoord));
                        }
                        break;
                    }
                }
            }
        }
    }
    if (newCurveSelection != null) {
        if (membraneSamplerCurves == null) {
            membraneSamplerCurves = new java.util.Vector<Curve>();
        }
        membraneSamplerCurves.add(newCurveSelection.getCurve());
    }
    return newCurveSelection;
}

Example 9 with SampledCurve

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

the class PDEDataContextPanel method colorMembraneCurvesPrivate.

/**
 * Insert the method's description here.
 * Creation date: (10/26/00 4:49:39 PM)
 */
private void colorMembraneCurvesPrivate(java.util.Hashtable<SampledCurve, int[]> curvesAndMembraneIndexes, MeshDisplayAdapter meshDisplayAdapter) {
    DisplayAdapterService das = getdisplayAdapterService1();
    if (curvesAndMembraneIndexes != null) {
        java.util.Enumeration<SampledCurve> keysEnum = curvesAndMembraneIndexes.keys();
        while (keysEnum.hasMoreElements()) {
            SampledCurve curve = keysEnum.nextElement();
            int[] membraneIndexes = curvesAndMembraneIndexes.get(curve);
            double[] membraneValues = null;
            if (membraneIndexes != null && getPdeDataContext().getDataValues() != null && getPdeDataContext().getDataIdentifier() != null) {
                membraneValues = meshDisplayAdapter.getDataValuesForMembraneIndexes(membraneIndexes, (recodeDataForDomainInfo.isRecoded ? recodeDataForDomainInfo.getRecodedDataForDomain() : getPdeDataContext().getDataValues()), getPdeDataContext().getDataIdentifier().getVariableType());
            }
            if (membraneValues != null) {
                int[] valueColors = new int[membraneValues.length];
                for (int i = 0; i < membraneValues.length; i += 1) {
                    valueColors[i] = das.getColorFromValue(membraneValues[i]);
                }
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentColors(curve, valueColors);
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentIndexes(curve, membraneIndexes);
            } else {
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentColors(curve, null);
                getImagePlaneManagerPanel().getCurveRenderer().renderPropertySegmentIndexes(curve, null);
            }
        }
    }
}

Example 10 with SampledCurve

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

the class MeshDisplayAdapter method constructChomboCurves.

private Hashtable<SampledCurve, int[]> constructChomboCurves(int normalAxis, int slice) {
    Hashtable<SampledCurve, int[]> curvesAndValues = null;
    if (mesh.isChomboMesh() && mesh.getMembraneElements() != null) {
        CartesianMeshChombo chomboMesh = (CartesianMeshChombo) mesh;
        curvesAndValues = new Hashtable<SampledCurve, int[]>();
        if (chomboMesh.getDimension() == 2) {
            MembraneElement[] membraneElements = mesh.getMembraneElements();
            List<MembraneElement> melist = new ArrayList<MembraneElement>();
            Segment2D[] segments = chomboMesh.get2DSegments();
            List<MembraneElement> openCurveStartingPointList = new ArrayList<MembraneElement>();
            for (MembraneElement me : membraneElements) {
                melist.add(me);
                Segment2D segment = segments[me.getMembraneIndex()];
                if (segment.prevNeigbhor < 0) {
                    openCurveStartingPointList.add(me);
                }
            }
            MembraneElement me = null;
            Coordinate[] vertices = chomboMesh.getVertices();
            SampledCurve curve = null;
            List<Integer> indexList = new ArrayList<Integer>();
            int startingIndex = -1;
            boolean bOpen = false;
            while (melist.size() > 0) {
                if (me == null) {
                    if (openCurveStartingPointList.size() > 0) {
                        me = openCurveStartingPointList.remove(0);
                        bOpen = true;
                    } else {
                        me = melist.get(0);
                        bOpen = false;
                    }
                    startingIndex = me.getMembraneIndex();
                    curve = new SampledCurve();
                    indexList.clear();
                }
                melist.remove(me);
                Segment2D segment = segments[me.getMembraneIndex()];
                indexList.add(me.getMembraneIndex());
                int pcnt = curve.getControlPointCount();
                if (pcnt == 0 && segment.prevVertex >= 0) {
                    Coordinate p1 = vertices[segment.prevVertex];
                    curve.appendControlPoint(p1);
                }
                if (segment.nextVertex >= 0 && segment.nextNeigbhor != startingIndex) {
                    Coordinate p2 = vertices[segment.nextVertex];
                    curve.appendControlPoint(p2);
                }
                int nextIndex = segment.nextNeigbhor;
                if (nextIndex == startingIndex || nextIndex < 0) {
                    // curve complete
                    int[] rmi = new int[indexList.size()];
                    for (int i = 0; i < indexList.size(); ++i) {
                        rmi[i] = indexList.get(i);
                    }
                    curve.setClosed(!bOpen);
                    curvesAndValues.put(curve, rmi);
                    // start a new curve
                    me = null;
                } else {
                    me = membraneElements[nextIndex];
                }
            }
        } else {
        // 3D
        }
    }
    return curvesAndValues;
}