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

Example 6 with Coordinate

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

the class PdeTimePlotMultipleVariablesPanel method initialize.

private void initialize() {
    VariableType varType = multiTimePlotHelper.getPdeDatacontext().getDataIdentifier().getVariableType();
    String varName = multiTimePlotHelper.getPdeDatacontext().getVariableName();
    String[] plotNames = new String[pointVector.size()];
    final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotNames.length];
    DefaultListModel<String> pointListModel = new DefaultListModel<String>();
    for (int i = 0; i < pointVector.size(); i++) {
        Coordinate tp = null;
        if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
            SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
            tp = ssv.getCurveSelectionInfo().getCurve().getBeginningCoordinate();
        } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
            SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
            double midU = ssm.getCurveSelectionInfo().getCurveUfromSelectionU(.5);
            tp = ((SampledCurve) ssm.getCurveSelectionInfo().getCurve()).coordinateFromNormalizedU(midU);
        }
        plotNames[i] = varName + " at P[" + i + "]";
        String point = "P[" + i + "]  (" + niceCoordinateString(tp) + ")";
        pointListModel.addElement(point);
        if (multiTimePlotHelper.getsimulation() != null) {
            symbolTableEntries[0] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
        } else {
            System.out.println("PdeTimePlotMultipleVariablesPanel.initialize() adding artificial symbol table entries for field data");
            SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { varName });
            symbolTableEntries[0] = simpleSymbolTable.getEntry(varName);
        }
    }
    pointJList.setModel(pointListModel);
    pointJList.setForeground(variableJList.getForeground());
    pointJList.setVisibleRowCount(3);
    pointJList.setBackground(getBackground());
    pointJList.setSelectionBackground(getBackground());
    pointJList.setSelectionForeground(Color.black);
    plotPane = new PlotPane();
    double[][] plotDatas = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
    Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
    plotPane.setPlot2D(plot2D);
    DataIdentifier[] dis = (multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() != null ? multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() : DataIdentifier.collectSortedSimilarDataTypes(multiTimePlotHelper.getVariableType(), multiTimePlotHelper.getPdeDatacontext().getDataIdentifiers()));
    Arrays.sort(dis, new Comparator<DataIdentifier>() {

        public int compare(DataIdentifier o1, DataIdentifier o2) {
            int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
            if (bEqualIgnoreCase == 0) {
                return o1.getDisplayName().compareTo(o2.getDisplayName());
            }
            return bEqualIgnoreCase;
        }
    });
    variableJList.setListData(dis);
    initVariableListSelected(variableJList, multiTimePlotHelper.getPdeDatacontext().getDataIdentifier());
    variableJList.setCellRenderer(multiTimePlotHelper.getListCellRenderer());
    setLayout(new GridBagLayout());
    JLabel label = new JLabel("Selected Points");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(15, 10, 4, 4);
    add(label, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.gridheight = 4;
    gbc.weightx = 1;
    gbc.weighty = 1;
    gbc.fill = GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(0, 4, 0, 0);
    add(plotPane, gbc);
    JScrollPane sp = new JScrollPane(pointJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weighty = 0.5;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(sp, gbc);
    label = new JLabel("Y Axis");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 2;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(label, gbc);
    sp = new JScrollPane(variableJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 3;
    gbc.weightx = 0.2;
    gbc.weighty = 1;
    gbc.insets = new java.awt.Insets(4, 10, 50, 4);
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    add(sp, gbc);
    variableJList.addListSelectionListener(eventHandler);
    multiTimePlotHelper.addPropertyChangeListener(eventHandler);
}

Example 7 with Coordinate

use of org.vcell.util.Coordinate 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 8 with Coordinate

use of org.vcell.util.Coordinate 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 9 with Coordinate

use of org.vcell.util.Coordinate 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 10 with Coordinate

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

the class ASCIIExporter method exportParticleData.

/**
 * Insert the method's description here.
 * Creation date: (1/12/00 5:00:28 PM)
 * @return cbit.vcell.export.server.ExportOutput[]
 * @param dsc cbit.vcell.server.DataSetController
 * @param timeSpecs cbit.vcell.export.server.TimeSpecs
 * @throws IOException
 */
private List<ExportOutput> exportParticleData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, ASCIISpecs asciiSpecs, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    String simID = vcdID.getID();
    String dataType = ".csv";
    // in switched format, how many rows for each particle
    final int N_PARTICLE_PIECES = 1;
    // get parameters
    boolean switchRowsColumns = asciiSpecs.getSwitchRowsColumns();
    double[] allTimes = timeSpecs.getAllTimes();
    int beginIndex = timeSpecs.getBeginTimeIndex();
    int endIndex = timeSpecs.getEndTimeIndex();
    ParticleDataBlock particleDataBlk = dataServerImpl.getParticleDataBlock(user, vcdID, allTimes[beginIndex]);
    VariableSpecs vs = exportSpecs.getVariableSpecs();
    VCAssert.assertValid(vs);
    String[] vnames = vs.getVariableNames();
    if (vnames.length == 0) {
        throw new IllegalArgumentException("No variables selected");
    }
    // need array for SimulationDescription, later
    final String[] currentVariableName = new String[1];
    ArrayList<ExportOutput> rval = new ArrayList<>(vnames.length);
    Set<String> species = particleDataBlk.getSpecies();
    ParticleProgress particleProgress = null;
    for (String vcellName : vnames) {
        String smoldynSpecies = null;
        for (int i = 0; smoldynSpecies == null && i < SMOLDYN_KEYWORDS_USED.length; i++) {
            SmoldynKeyword kw = SMOLDYN_KEYWORDS_USED[i];
            String smoldynName = SmoldynVCellMapper.vcellToSmoldyn(vcellName, kw);
            if (species.contains(smoldynName)) {
                smoldynSpecies = smoldynName;
            }
        }
        if (smoldynSpecies == null) {
            throw new DataAccessException("Unable to find match for variable name " + vcellName + " in " + StringUtils.join(species, ", "));
        }
        List<Coordinate> particles = particleDataBlk.getCoordinates(smoldynSpecies);
        int numberOfParticles = particles.size();
        int numberOfTimes = endIndex - beginIndex + 1;
        if (particleProgress != null) {
            particleProgress.nextName();
        } else {
            particleProgress = new ParticleProgress(jobID, vcdID, vnames.length, numberOfTimes, numberOfParticles);
        }
        // now make csv formatted data
        StringBuilder header = new StringBuilder();
        StringBuilder[] dataLines = null;
        final int NUMBER_HEADING_LINES = SwitchedRowsHeading.DATA.ordinal();
        if (switchRowsColumns) {
            dataLines = stringBuilderArray(numberOfParticles * N_PARTICLE_PIECES + NUMBER_HEADING_LINES);
            dataLines[SwitchedRowsHeading.TIME.ordinal()].append("Time,");
            final String particleLine = "Particle" + StringUtils.repeat(",x,y,z", numberOfTimes);
            dataLines[SwitchedRowsHeading.PARTICLE.ordinal()].append(particleLine);
            dataLines[SwitchedRowsHeading.XYZ.ordinal()].append("#,");
            // "first data line"
            final int FDL = SwitchedRowsHeading.DATA.ordinal();
            for (int i = 0; i < numberOfParticles; i++) {
                dataLines[FDL + N_PARTICLE_PIECES * i].append(i);
                dataLines[FDL + N_PARTICLE_PIECES * i].append(',');
            }
        } else {
            dataLines = stringBuilderArray(numberOfTimes);
        }
        currentVariableName[0] = vcellName;
        SimulationDescription simulationDescription = new SimulationDescription(outputContext, user, dataServerImpl, vcdID, false, currentVariableName);
        header.append(simulationDescription.getHeader(dataType));
        if (switchRowsColumns) {
        // implemented using first few data lines
        } else {
            header.append(",Time\n");
            header.append("Particle #,,");
            for (int k = 0; k < numberOfParticles; k++) {
                header.append(k + StringUtils.repeat(',', N_PARTICLE_PIECES));
            }
            header.append("\n,,");
            for (int k = 0; k < numberOfParticles; k++) {
                header.append("x,y,z,");
            }
        }
        final char COMMA = ',';
        int nextTimeIndex = particleProgress.nextTimeIndex(0, false);
        for (int i = beginIndex; i <= endIndex; i++) {
            particleDataBlk = dataServerImpl.getParticleDataBlock(user, vcdID, allTimes[i]);
            particles = particleDataBlk.getCoordinates(smoldynSpecies);
            if (i >= nextTimeIndex) {
                nextTimeIndex = particleProgress.nextTimeIndex(i, true);
            }
            if (switchRowsColumns) {
                // "first data line"
                final int FDL = SwitchedRowsHeading.DATA.ordinal();
                StringBuilder timeSb = dataLines[SwitchedRowsHeading.TIME.ordinal()];
                timeSb.append(allTimes[i]);
                timeSb.append(",,,");
                for (int j = 0; j < numberOfParticles; j++) {
                    StringBuilder sb = dataLines[FDL + N_PARTICLE_PIECES * j];
                    Coordinate coordinate = particles.get(j);
                    sb.append(coordinate.getX());
                    sb.append(COMMA);
                    sb.append(coordinate.getY());
                    sb.append(COMMA);
                    sb.append(coordinate.getZ());
                    sb.append(COMMA);
                }
            } else {
                StringBuilder particleSb = dataLines[i - beginIndex];
                particleSb.append(COMMA);
                particleSb.append(allTimes[i]);
                particleSb.append(COMMA);
                for (int j = 0; j < numberOfParticles; j++) {
                    Coordinate coordinate = particles.get(j);
                    particleSb.append(coordinate.getX());
                    particleSb.append(COMMA);
                    particleSb.append(coordinate.getY());
                    particleSb.append(COMMA);
                    particleSb.append(coordinate.getZ());
                }
            }
        }
        particleProgress.endOfTimes();
        final String dataID = vcellName + "_Particles";
        ExportOutput exportOutputCSV = new ExportOutput(true, dataType, simID, dataID, fileDataContainerManager);
        fileDataContainerManager.append(exportOutputCSV.getFileDataContainerID(), header.toString());
        int nextDataIndex = particleProgress.nextDataIndex(0, false);
        StringBuilder all = new StringBuilder();
        for (int i = 0; i < dataLines.length; i++) {
            final char NEWLINE = '\n';
            all.append(dataLines[i]);
            // kill reference to allow garbage collection
            dataLines[i] = null;
            all.append(NEWLINE);
            if (i >= nextDataIndex) {
                nextDataIndex = particleProgress.nextDataIndex(i, true);
            }
        }
        fileDataContainerManager.append(exportOutputCSV.getFileDataContainerID(), all.toString());
        rval.add(exportOutputCSV);
    }
    return rval;
}