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

Example 6 with SinglePoint

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

the class PDEDataContextPanel method findChomboSinglePointSelectionInfoForPoint.

public CurveSelectionInfo findChomboSinglePointSelectionInfoForPoint(Coordinate wc) {
    if (getPdeDataContext().getCartesianMesh().isChomboMesh()) {
        CartesianMeshChombo chomboMesh = (CartesianMeshChombo) getPdeDataContext().getCartesianMesh();
        int memIndex = chomboMesh.findMembraneIndexFromVolumeCoordinate(wc);
        if (memIndex >= 0) {
            Coordinate coord = chomboMesh.getMembraneElements()[memIndex].getCentroid();
            return new CurveSelectionInfo(new SinglePoint(coord));
        }
    }
    return null;
}

Example 7 with SinglePoint

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

the class PDEDataContextPanel method fetchSpatialSelections0.

/**
 * Insert the method's description here.
 * Creation date: (6/28/2003 4:57:18 PM)
 * @return cbit.vcell.simdata.gui.SpatialSelection[]
 */
private SpatialSelection[] fetchSpatialSelections0(Curve curveOfInterest, boolean bFetchOnlyVisible, VariableType vt) {
    // 
    java.util.Vector<SpatialSelection> spatialSelection = new java.util.Vector<SpatialSelection>();
    // 
    if (getPdeDataContext() != null && getPdeDataContext().getCartesianMesh() != null && getImagePlaneManagerPanel() != null && getImagePlaneManagerPanel().getCurveRenderer() != null) {
        // 
        CartesianMesh cm = getPdeDataContext().getCartesianMesh();
        Curve[] curves = getImagePlaneManagerPanel().getCurveRenderer().getAllCurves();
        // 
        if (curves != null && curves.length > 0) {
            for (int i = 0; i < curves.length; i += 1) {
                boolean bIsVisible = getImagePlaneManagerPanel().getCurveRenderer().getRenderPropertyVisible(curves[i]);
                if ((bFetchOnlyVisible && !bIsVisible) || (curveOfInterest != null && curves[i] != curveOfInterest)) {
                    continue;
                }
                // 
                if ((vt.equals(VariableType.POSTPROCESSING) || vt.equals(VariableType.VOLUME) || vt.equals(VariableType.VOLUME_REGION)) && curves[i] instanceof ControlPointCurve && !(curves[i] instanceof CurveSelectionCurve) && (curves[i].getDescription() == null || curves[i].getDescription().startsWith(CurveValueProvider.DESCRIPTION_VOLUME)) && (membranesAndIndexes == null || !membranesAndIndexes.containsKey(curves[i]))) {
                    // Volume
                    // 
                    Curve samplerCurve = null;
                    // if(isSpatial2D){
                    samplerCurve = projectCurveOntoSlice(curves[i].getSampledCurve());
                    // }
                    if (samplerCurve != null) {
                        samplerCurve.setDescription(curves[i].getDescription());
                        spatialSelection.add(new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), vt, cm));
                    }
                } else if ((vt.equals(VariableType.MEMBRANE) || vt.equals(VariableType.MEMBRANE_REGION)) && membranesAndIndexes != null) {
                    // 
                    if (curves[i] instanceof CurveSelectionCurve) {
                        CurveSelectionCurve csCurve = (CurveSelectionCurve) curves[i];
                        if (csCurve.getSourceCurveSelectionInfo().getCurve() instanceof ControlPointCurve) {
                            int[] csisegsel = csCurve.getSourceCurveSelectionInfo().getSegmentsInSelectionOrder();
                            if (csisegsel != null) {
                                ControlPointCurve cscpcCurve = (ControlPointCurve) (csCurve.getSourceCurveSelectionInfo().getCurve());
                                Curve[] membraneCurves = (Curve[]) (membranesAndIndexes.keySet().toArray(new Curve[membranesAndIndexes.size()]));
                                // See if CurveSelectionCurve matches controlpoints in space of a membrane we have
                                for (int j = 0; j < membraneCurves.length; j += 1) {
                                    if (membraneCurves[j] instanceof ControlPointCurve) {
                                        // They should all be
                                        ControlPointCurve cpc = (ControlPointCurve) membraneCurves[j];
                                        boolean bSame = true;
                                        for (int k = 0; k < csisegsel.length; k += 1) {
                                            if (csisegsel[k] >= cpc.getControlPointCount() || csisegsel[k] >= cscpcCurve.getControlPointCount() || !Coordinate.get2DProjection(cpc.getControlPoint(csisegsel[k]), getNormalAxis()).equals(Coordinate.get2DProjection(cscpcCurve.getControlPoint(csisegsel[k]), getNormalAxis()))) {
                                                // 
                                                bSame = false;
                                                break;
                                            }
                                        }
                                        if (bSame) {
                                            int[] mi = (int[]) membranesAndIndexes.get(membraneCurves[j]);
                                            spatialSelection.add(new SpatialSelectionMembrane(new CurveSelectionInfo(membraneCurves[j], csisegsel[0], csisegsel[csisegsel.length - 1], csCurve.getSourceCurveSelectionInfo().getDirectionNegative()), vt, cm, mi, csCurve));
                                        }
                                    }
                                }
                            }
                        }
                    } else if (curves[i] instanceof SinglePoint && (curves[i].getDescription() == null || curves[i].getDescription().startsWith(CurveValueProvider.DESCRIPTION_MEMBRANE))) {
                        CurveSelectionInfo[] csiArr = getImagePlaneManagerPanel().getCurveRenderer().getCloseCurveSelectionInfos(curves[i].getBeginningCoordinate());
                        if (csiArr != null && csiArr.length > 0) {
                            for (int j = 0; j < csiArr.length; j += 1) {
                                if (membranesAndIndexes.containsKey(csiArr[j].getCurve())) {
                                    CurveSelectionInfo closestCSI = getImagePlaneManagerPanel().getCurveRenderer().getClosestSegmentSelectionInfo(curves[i].getBeginningCoordinate(), csiArr[j].getCurve());
                                    int[] mi = (int[]) membranesAndIndexes.get(csiArr[j].getCurve());
                                    spatialSelection.add(new SpatialSelectionMembrane(closestCSI, vt, cm, mi, (SinglePoint) curves[i]));
                                    break;
                                }
                            }
                        }
                    }
                }
            }
        }
    }
    // 
    if (spatialSelection.size() > 0) {
        SpatialSelection[] ss = new SpatialSelection[spatialSelection.size()];
        spatialSelection.copyInto(ss);
        return ss;
    }
    return null;
}

Example 8 with SinglePoint

use of cbit.vcell.geometry.SinglePoint 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 SinglePoint

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

the class ASCIIExporter method getallSampleIndexes.

private int[] getallSampleIndexes(GeometrySpecs geometrySpecs, CartesianMesh mesh) throws DataAccessException {
    ArrayList<Integer> sampleIndexes = new ArrayList<>();
    SpatialSelection[] spatialSelections = geometrySpecs.getSelections();
    for (int i = 0; i < spatialSelections.length; i++) {
        spatialSelections[i].setMesh(mesh);
    }
    // Add points
    if (geometrySpecs.getPointIndexes().length > 0) {
        for (int i = 0; i < geometrySpecs.getPointIndexes().length; i++) {
            sampleIndexes.add(geometrySpecs.getPointIndexes()[i]);
        }
    }
    // Add curves
    if (geometrySpecs.getCurves().length != 0) {
        for (int i = 0; i < geometrySpecs.getCurves().length; i++) {
            SpatialSelection curve = geometrySpecs.getCurves()[i];
            curve.setMesh(mesh);
            if (curve instanceof SpatialSelectionVolume) {
                SpatialSelection.SSHelper ssh = ((SpatialSelectionVolume) curve).getIndexSamples(0.0, 1.0);
                for (int j = 0; j < ssh.getSampledIndexes().length; j++) {
                    sampleIndexes.add(ssh.getSampledIndexes()[j]);
                }
            // numSamplePoints+= ssh.getSampledIndexes().length;
            // pointIndexes = ssh.getSampledIndexes();
            // distances = ssh.getWorldCoordinateLengths();
            // crossingMembraneIndexes = ssh.getMembraneIndexesInOut();
            } else if (curve instanceof SpatialSelectionMembrane) {
                SpatialSelection.SSHelper ssh = ((SpatialSelectionMembrane) curve).getIndexSamples();
                if (((SpatialSelectionMembrane) curve).getSelectionSource() instanceof SinglePoint) {
                    sampleIndexes.add(ssh.getSampledIndexes()[0]);
                // numSamplePoints++;
                // pointIndexes = new int[] {ssh.getSampledIndexes()[0]};
                // distances = new double[] {0};
                } else {
                    for (int j = 0; j < ssh.getSampledIndexes().length; j++) {
                        sampleIndexes.add(ssh.getSampledIndexes()[j]);
                    }
                // numSamplePoints+= ssh.getSampledIndexes().length;
                // pointIndexes = ssh.getSampledIndexes();
                // distances = ssh.getWorldCoordinateLengths();
                }
            }
        }
    }
    if (sampleIndexes.size() > 0) {
        int[] allSampleIndexes = new int[sampleIndexes.size()];
        for (int i = 0; i < allSampleIndexes.length; i++) {
            allSampleIndexes[i] = sampleIndexes.get(i);
        }
        return allSampleIndexes;
    }
    return null;
}

Example 10 with SinglePoint

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

the class ASCIIExporter method getCurveTimeSeries.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @throws IOException
 */
private FileDataContainerID getCurveTimeSeries(int hdf5GroupVarID, PointsCurvesSlices pointsCurvesSlices, OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variableName, SpatialSelection curve, double[] allTimes, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    int[] pointIndexes = null;
    double[] distances = null;
    int[] crossingMembraneIndexes = null;
    if (curve instanceof SpatialSelectionVolume) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionVolume) curve).getIndexSamples(0.0, 1.0);
        pointIndexes = ssh.getSampledIndexes();
        distances = ssh.getWorldCoordinateLengths();
        crossingMembraneIndexes = ssh.getMembraneIndexesInOut();
    } else if (curve instanceof SpatialSelectionMembrane) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionMembrane) curve).getIndexSamples();
        if (((SpatialSelectionMembrane) curve).getSelectionSource() instanceof SinglePoint) {
            pointIndexes = new int[] { ssh.getSampledIndexes()[0] };
            distances = new double[] { 0 };
        } else {
            pointIndexes = ssh.getSampledIndexes();
            distances = ssh.getWorldCoordinateLengths();
        }
    }
    pointsCurvesSlices.data.put(PCS.TIMES, new ArrayList<Double>());
    pointsCurvesSlices.data.put(PCS.TIMEBOUNDS, new int[] { beginIndex, endIndex });
    final TreeMap<PCS, Object> treePCS = new TreeMap<PCS, Object>();
    ((TreeMap<String, TreeMap<PCS, Object>>) pointsCurvesSlices.data.get(PCS.CURVES)).put(getSpatialSelectionDescription(curve), treePCS);
    treePCS.put(PCS.CURVEINDEXES, pointIndexes);
    treePCS.put(PCS.CURVEDISTANCES, distances);
    if (crossingMembraneIndexes != null) {
        treePCS.put(PCS.CURVECROSSMEMBRINDEX, crossingMembraneIndexes);
    }
    treePCS.put(PCS.CURVEVALS, new ArrayList<Double>());
    org.vcell.util.document.TimeSeriesJobSpec timeSeriesJobSpec = new org.vcell.util.document.TimeSeriesJobSpec(new String[] { variableName }, new int[][] { pointIndexes }, new int[][] { crossingMembraneIndexes }, allTimes[beginIndex], 1, allTimes[endIndex], VCDataJobID.createVCDataJobID(user, false));
    org.vcell.util.document.TSJobResultsNoStats timeSeriesJobResults = (org.vcell.util.document.TSJobResultsNoStats) dataServerImpl.getTimeSeriesValues(outputContext, user, vcdID, timeSeriesJobSpec);
    // variableValues[0] is time array
    // variableValues[1] is values for 1st spatial point.
    // variableValues[2] is values for 2nd spatial point.
    // variableValues[n] (n>=1) is values for nth spatial point.
    // the length of variableValues should always be 1 + pointIndexes.length
    // the length of variableValues[n] is allTimes.length
    final double[][] variableValues = timeSeriesJobResults.getTimesAndValuesForVariable(variableName);
    // 
    // put data in csv format
    // 
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    fileDataContainerManager.append(fileDataContainerID, "\"variable ('" + variableName + "') times (" + allTimes[beginIndex] + " " + allTimes[endIndex] + ") " + getSpatialSelectionDescription(curve) + "\"\n");
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Distances\n");
        fileDataContainerManager.append(fileDataContainerID, "Times,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            ((ArrayList<Double>) pointsCurvesSlices.data.get(PCS.TIMES)).add(allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int j = 0; j < distances.length; j++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[j]);
            for (int i = beginIndex; i <= endIndex; i++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
                ((ArrayList<Double>) treePCS.get(PCS.CURVEVALS)).add(variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        fileDataContainerManager.append(fileDataContainerID, ",Times\n");
        fileDataContainerManager.append(fileDataContainerID, "Distances,");
        for (int i = 0; i < distances.length; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            ((ArrayList<Double>) pointsCurvesSlices.data.get(PCS.TIMES)).add(allTimes[i]);
            for (int j = 0; j < distances.length; j++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
                ((ArrayList<Double>) treePCS.get(PCS.CURVEVALS)).add(variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    if (curve instanceof SpatialSelectionMembrane) {
        fileDataContainerManager.append(fileDataContainerID, "\n");
        fileDataContainerManager.append(fileDataContainerID, "\"Centroid(XYZ):Times:Values[Times,Centroid]\",X,Y,Z,distance");
        for (int i = 0; i < variableValues[0].length; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + variableValues[0][i]);
            ((ArrayList<Double>) pointsCurvesSlices.data.get(PCS.TIMES)).add(variableValues[0][i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        double distance = 0;
        for (int i = 0; i < pointIndexes.length; i++) {
            if (pointIndexes.length > 1 && (i == (pointIndexes.length - 1)) && pointIndexes[i] == pointIndexes[i - 1]) {
                continue;
            }
            Coordinate coord = curve.getMesh().getCoordinateFromMembraneIndex(pointIndexes[i]);
            // double value = variableValues[i+1][0];
            fileDataContainerManager.append(fileDataContainerID, "," + coord.getX() + "," + coord.getY() + "," + coord.getZ());
            if (i > 0) {
                Coordinate prevCoord = curve.getMesh().getCoordinateFromMembraneIndex(pointIndexes[i - 1]);
                distance += coord.distanceTo(prevCoord);
            }
            fileDataContainerManager.append(fileDataContainerID, "," + distance);
            for (int t = 0; t < variableValues[t].length; t++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[i + 1][t]);
                ((ArrayList<Double>) treePCS.get(PCS.CURVEVALS)).add(variableValues[i + 1][t]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    if (hdf5GroupVarID != -1) {
        try {
            int hdf5GroupCurveID = H5.H5Gcreate(hdf5GroupVarID, getSpatialSelectionDescription(curve), HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            // Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[] {((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (int[])treePCS.get(PCS.CURVEINDEXES),false);
            Hdf5Utils.insertInts(hdf5GroupCurveID, PCS.CURVEINDEXES.name(), new long[] { ((int[]) treePCS.get(PCS.CURVEINDEXES)).length }, (int[]) treePCS.get(PCS.CURVEINDEXES));
            // Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[] {((double[])treePCS.get(PCS.CURVEDISTANCES)).length}, (double[])treePCS.get(PCS.CURVEDISTANCES),false);
            Hdf5Utils.insertDoubles(hdf5GroupCurveID, PCS.CURVEDISTANCES.name(), new long[] { ((double[]) treePCS.get(PCS.CURVEDISTANCES)).length }, (double[]) treePCS.get(PCS.CURVEDISTANCES));
            if (treePCS.get(PCS.CURVECROSSMEMBRINDEX) != null) {
                // Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[] {((int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length}, (int[])treePCS.get(PCS.CURVECROSSMEMBRINDEX),false);
                Hdf5Utils.insertInts(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name(), new long[] { ((int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX)).length }, (int[]) treePCS.get(PCS.CURVECROSSMEMBRINDEX));
                ArrayList<Integer> crossPoints = new ArrayList<Integer>();
                for (int i = 0; i < crossingMembraneIndexes.length; i++) {
                    if (crossingMembraneIndexes[i] != -1) {
                        crossPoints.add(i);
                    }
                }
                String attrText = PCS.CURVEVALS.name() + " columns " + crossPoints.get(0) + " and " + crossPoints.get(1) + " are added points of interpolation near membrane";
                // Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name()+" Info", null, attrText,true);
                Hdf5Utils.insertAttribute(hdf5GroupCurveID, PCS.CURVECROSSMEMBRINDEX.name() + " Info", attrText);
            }
            // Hdf5Utils.writeHDF5Dataset(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[] {endIndex-beginIndex+1,((int[])treePCS.get(PCS.CURVEINDEXES)).length}, (ArrayList<Double>)treePCS.get(PCS.CURVEVALS),false);
            Hdf5Utils.insertDoubles(hdf5GroupCurveID, PCS.CURVEVALS.name(), new long[] { endIndex - beginIndex + 1, ((int[]) treePCS.get(PCS.CURVEINDEXES)).length }, (ArrayList<Double>) treePCS.get(PCS.CURVEVALS));
            H5.H5Gclose(hdf5GroupCurveID);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage(), e);
        }
    }
    return fileDataContainerID;
}