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

Example 1 with SampledCurve

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

the class PDEDataViewer method roiAction.

private void roiAction() {
    BeanUtils.setCursorThroughout(this, Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    try {
        final String[] ROI_COLUMN_NAMES = new String[] { "ROI source", "ROI source name", "ROI Description" };
        final Vector<Object> auxInfoV = new Vector<Object>();
        final DataIdentifier dataIdentifier = getPdeDataContext().getDataIdentifier();
        VariableType variableType = dataIdentifier.getVariableType();
        final boolean isVolume = variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION);
        DefaultTableModel tableModel = new DefaultTableModel() {

            public boolean isCellEditable(int row, int column) {
                return false;
            }
        };
        for (int i = 0; i < ROI_COLUMN_NAMES.length; i++) {
            tableModel.addColumn(ROI_COLUMN_NAMES[i]);
        }
        // Add Snapshot ROI
        if ((isVolume ? volumeSnapshotROI : membraneSnapshotROI) != null) {
            tableModel.addRow(new Object[] { (isVolume ? "Volume" : "Membrane") + " Variables and Functions", "Snapshot", (isVolume ? volumeSnapshotROIDescription : membraneSnapshotROIDescription) + ", (values = 1.0)" });
            auxInfoV.add((isVolume ? volumeSnapshotROI : membraneSnapshotROI));
        }
        // Add user ROIs
        SpatialSelection[] userROIArr = getPDEDataContextPanel1().fetchSpatialSelections(true, false);
        for (int i = 0; userROIArr != null && i < userROIArr.length; i += 1) {
            String descr = null;
            boolean bPoint = false;
            if (isVolume) {
                if (userROIArr[i] instanceof SpatialSelectionVolume) {
                    Curve curve = ((SpatialSelectionVolume) userROIArr[i]).getCurveSelectionInfo().getCurve();
                    descr = curve.getDescription();
                    if (curve instanceof SinglePoint) {
                        bPoint = true;
                    }
                }
            } else {
                if (userROIArr[i] instanceof SpatialSelectionMembrane) {
                    SampledCurve selectionSource = ((SpatialSelectionMembrane) userROIArr[i]).getSelectionSource();
                    descr = selectionSource.getDescription();
                    if (selectionSource instanceof SinglePoint) {
                        bPoint = true;
                    }
                }
            }
            // Add Area User ROI
            BitSet fillBitSet = null;
            if (userROIArr[i] instanceof SpatialSelectionVolume) {
                fillBitSet = getFillROI((SpatialSelectionVolume) userROIArr[i]);
                if (fillBitSet != null) {
                    tableModel.addRow(new Object[] { "User Defined", descr, "Area Enclosed Volume ROI" });
                    auxInfoV.add(fillBitSet);
                }
            }
            // Add Point and Line User ROI
            if (fillBitSet == null) {
                tableModel.addRow(new Object[] { "User Defined", descr, (bPoint ? "Point" : "Line") + (isVolume ? " Volume" : " Membrane") + " ROI " });
                auxInfoV.add(userROIArr[i]);
            }
        }
        // Add sorted Geometry ROI
        final CartesianMesh cartesianMesh = getPdeDataContext().getCartesianMesh();
        HashMap<Integer, ?> regionMapSubvolumesHashMap = (isVolume ? cartesianMesh.getVolumeRegionMapSubvolume() : cartesianMesh.getMembraneRegionMapSubvolumesInOut());
        Set<?> regionMapSubvolumesEntrySet = regionMapSubvolumesHashMap.entrySet();
        Iterator<?> regionMapSubvolumesEntryIter = regionMapSubvolumesEntrySet.iterator();
        TreeSet<Object[]> sortedGeomROITreeSet = new TreeSet<Object[]>(new Comparator<Object[]>() {

            public int compare(Object[] o1, Object[] o2) {
                int result = ((String) ((Object[]) o1[0])[1]).compareToIgnoreCase((String) ((Object[]) o2[0])[1]);
                if (result == 0) {
                    result = (((Entry<Integer, ?>) o1[1]).getKey()).compareTo(((Entry<Integer, ?>) o2[1]).getKey());
                }
                return result;
            }
        });
        while (regionMapSubvolumesEntryIter.hasNext()) {
            Entry<Integer, ?> regionMapSubvolumesEntry = (Entry<Integer, ?>) regionMapSubvolumesEntryIter.next();
            sortedGeomROITreeSet.add(new Object[] { new Object[] { "Geometry", (isVolume ? getSimulationModelInfo().getVolumeNamePhysiology(((Integer) regionMapSubvolumesEntry.getValue())) : getSimulationModelInfo().getMembraneName(((int[]) regionMapSubvolumesEntry.getValue())[0], ((int[]) regionMapSubvolumesEntry.getValue())[1], false)), (isVolume ? "(svID=" + regionMapSubvolumesEntry.getValue() + " " : "(") + "vrID=" + regionMapSubvolumesEntry.getKey() + ") Predefined " + (isVolume ? "volume" : "membrane") + " region" }, regionMapSubvolumesEntry });
        }
        Iterator<Object[]> sortedGeomROIIter = sortedGeomROITreeSet.iterator();
        while (sortedGeomROIIter.hasNext()) {
            Object[] sortedGeomROIObjArr = (Object[]) sortedGeomROIIter.next();
            tableModel.addRow((Object[]) sortedGeomROIObjArr[0]);
            auxInfoV.add(sortedGeomROIObjArr[1]);
        }
        final ScrollTable roiTable = new ScrollTable();
        roiTable.setModel(tableModel);
        roiTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        roiTable.setPreferredScrollableViewportSize(new Dimension(500, 200));
        final JPanel mainJPanel = new JPanel();
        BoxLayout mainBL = new BoxLayout(mainJPanel, BoxLayout.Y_AXIS);
        mainJPanel.setLayout(mainBL);
        MiniTimePanel timeJPanel = new MiniTimePanel();
        ActionListener okAction = new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                if (((Double) timeJPanel.jcb_time_begin.getSelectedItem()).compareTo((Double) timeJPanel.jcb_time_end.getSelectedItem()) > 0) {
                    PopupGenerator.showErrorDialog(PDEDataViewer.this, "Selected 'Begin Time' must be less than or equal to 'End Time'");
                    return;
                }
                int[] selectedRows = roiTable.getSelectedRows();
                if (selectedRows != null) {
                    try {
                        BitSet dataBitSet = new BitSet(getPdeDataContext().getDataValues().length);
                        for (int i = 0; i < selectedRows.length; i++) {
                            Object auxInfo = auxInfoV.elementAt(selectedRows[i]);
                            if (auxInfo instanceof BitSet) {
                                dataBitSet.or((BitSet) auxInfo);
                            } else if (auxInfo instanceof SpatialSelectionMembrane) {
                                int[] roiIndexes = ((SpatialSelectionMembrane) auxInfo).getIndexSamples().getSampledIndexes();
                                for (int j = 0; j < roiIndexes.length; j += 1) {
                                    dataBitSet.set(roiIndexes[j], true);
                                }
                            } else if (auxInfo instanceof SpatialSelectionVolume) {
                                int[] roiIndexes = ((SpatialSelectionVolume) auxInfo).getIndexSamples(0, 1).getSampledIndexes();
                                for (int j = 0; j < roiIndexes.length; j += 1) {
                                    dataBitSet.set(roiIndexes[j], true);
                                }
                            } else if (auxInfo instanceof Entry) {
                                Entry<Integer, Integer> entry = (Entry<Integer, Integer>) auxInfo;
                                if (isVolume) {
                                    int volumeRegionID = entry.getKey();
                                    dataBitSet.or(cartesianMesh.getVolumeROIFromVolumeRegionID(volumeRegionID));
                                } else {
                                    int membraneRegionID = entry.getKey();
                                    dataBitSet.or(cartesianMesh.getMembraneROIFromMembraneRegionID(membraneRegionID));
                                }
                            } else if (auxInfo instanceof BitSet) {
                                dataBitSet.or((BitSet) auxInfo);
                            } else {
                                throw new Exception("ROI table, Unknown data type: " + auxInfo.getClass().getName());
                            }
                        }
                        TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(new String[] { dataIdentifier.getName() }, new BitSet[] { dataBitSet }, ((Double) timeJPanel.jcb_time_begin.getSelectedItem()).doubleValue(), 1, ((Double) timeJPanel.jcb_time_end.getSelectedItem()).doubleValue(), true, false, VCDataJobID.createVCDataJobID(getDataViewerManager().getUser(), true));
                        Hashtable<String, Object> hash = new Hashtable<String, Object>();
                        hash.put(StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
                        AsynchClientTask task1 = new TimeSeriesDataRetrievalTask("Retrieve data for '" + dataIdentifier + "'", PDEDataViewer.this, getPdeDataContext());
                        AsynchClientTask task2 = new AsynchClientTask("Showing stat for '" + dataIdentifier + "'", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                            @Override
                            public void run(Hashtable<String, Object> hashTable) throws Exception {
                                TSJobResultsSpaceStats tsJobResultsSpaceStats = (TSJobResultsSpaceStats) hashTable.get(StringKey_timeSeriesJobResults);
                                plotSpaceStats(tsJobResultsSpaceStats);
                            }
                        };
                        ClientTaskDispatcher.dispatch(PDEDataViewer.this, hash, new AsynchClientTask[] { task1, task2 }, true, true, null);
                    } catch (Exception e1) {
                        e1.printStackTrace();
                        PopupGenerator.showErrorDialog(PDEDataViewer.this, "ROI Error.\n" + e1.getMessage(), e1);
                    }
                }
                BeanUtils.disposeParentWindow(mainJPanel);
            }
        };
        ActionListener cancelAction = new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                BeanUtils.disposeParentWindow(mainJPanel);
            }
        };
        OkCancelSubPanel okCancelJPanel = new OkCancelSubPanel(okAction, cancelAction);
        roiTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

            public void valueChanged(ListSelectionEvent e) {
                if (roiTable.getSelectedRows() != null && roiTable.getSelectedRows().length > 0) {
                    okCancelJPanel.okButton.setEnabled(true);
                } else {
                    okCancelJPanel.okButton.setEnabled(false);
                }
            }
        });
        mainJPanel.add(timeJPanel);
        mainJPanel.add(roiTable.getEnclosingScrollPane());
        mainJPanel.add(okCancelJPanel);
        // showComponentInFrame(mainJPanel,
        // "Calculate "+(isVolume?"volume":"membrane")+" statistics for '"+getPdeDataContext().getVariableName()+"'."+
        // "  Choose times and 1 or more ROI(s).");
        Frame dialogOwner = JOptionPane.getFrameForComponent(this);
        JOptionPane inputDialog = new JOptionPane(mainJPanel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[0]);
        final JDialog d = inputDialog.createDialog(dialogOwner, "Calculate " + (isVolume ? "volume" : "membrane") + " statistics for '" + getPdeDataContext().getVariableName() + "'." + "  Choose times and 1 or more ROI(s).");
        d.setResizable(true);
        try {
            DialogUtils.showModalJDialogOnTop(d, PDEDataViewer.this);
        } finally {
            d.dispose();
        }
    } finally {
        BeanUtils.setCursorThroughout(this, Cursor.getDefaultCursor());
    }
}

Example 2 with SampledCurve

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

the class XmlReader method getControlPointCurve.

/**
 * This method returns a ControlPointcurve object from a XML element.
 * Creation date: (5/22/2001 5:20:39 PM)
 * @return cbit.vcell.geometry.ControlPointCurve
 * @param param org.jdom.Element
 */
private ControlPointCurve getControlPointCurve(Element param) {
    ControlPointCurve curve = null;
    // get Attributes
    String type = param.getAttributeValue(XMLTags.TypeAttrTag);
    boolean closed = Boolean.valueOf(param.getAttributeValue(XMLTags.ClosedAttrTag)).booleanValue();
    List<Element> coordList = param.getChildren();
    // Upon de type, decide which Curve type to create
    if (type.equalsIgnoreCase(XMLTags.PolyLineTypeTag)) {
        if (coordList.size() == 2) {
            // I have a Line
            Coordinate begin = getCoordinate(coordList.get(0));
            Coordinate end = getCoordinate(coordList.get(1));
            // ****create new Line ****
            curve = new Line(begin, end);
        } else {
            // If it it is not a Line, then it is a SampledCurve
            Coordinate[] coords = new Coordinate[coordList.size()];
            for (int i = 0; i < coordList.size(); i++) {
                coords[i] = getCoordinate(coordList.get(i));
            }
            // ****create new SampledCurve ****
            curve = new SampledCurve(coords);
        }
    } else if (type.equalsIgnoreCase(XMLTags.SplineTypeTag)) {
        Coordinate[] coords = new Coordinate[coordList.size()];
        for (int i = 0; i < coordList.size(); i++) {
            coords[i] = getCoordinate(coordList.get(i));
        }
        // ****create new Spline ****
        curve = new Spline(coords);
    }
    // set Atributes
    curve.setClosed(closed);
    return curve;
}

Example 3 with SampledCurve

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

the class Xmlproducer method getXML.

/**
 * This method retruns a XML ELement from a ControlPointCurve object.
 * Creation date: (5/22/2001 4:11:37 PM)
 * @return Element
 * @param param cbit.vcell.geometry.ControlPointCurve
 */
private Element getXML(ControlPointCurve param) {
    Element curve = new Element(XMLTags.CurveTag);
    // Add attributes
    String type = null;
    if (param instanceof Spline) {
        type = XMLTags.SplineTypeTag;
    } else if (param instanceof Line || param instanceof SampledCurve) {
        type = XMLTags.PolyLineTypeTag;
    }
    curve.setAttribute(XMLTags.TypeAttrTag, type);
    curve.setAttribute(XMLTags.ClosedAttrTag, String.valueOf(param.isClosed()));
    // Add coordinates
    Vector<Coordinate> vector = param.getControlPointsVector();
    Iterator<Coordinate> iterator = vector.iterator();
    while (iterator.hasNext()) {
        curve.addContent(getXML(iterator.next()));
    }
    return curve;
}

Example 4 with SampledCurve

use of cbit.vcell.geometry.SampledCurve 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 5 with SampledCurve

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

the class PDEDataContextPanel method updateContours.

/**
 * Insert the method's description here.
 * Creation date: (11/9/2000 4:14:39 PM)
 */
private void updateContours() {
    // 
    if (getPdeDataContext() == null || getPdeDataContext().getDataIdentifier() == null) {
        return;
    }
    // Remove previous curves
    CurveRenderer curveRenderer = getImagePlaneManagerPanel().getCurveRenderer();
    if (contoursAndValues != null) {
        java.util.Enumeration<SampledCurve> keysEnum = contoursAndValues.keys();
        while (keysEnum.hasMoreElements()) {
            Curve curve = keysEnum.nextElement();
            curveRenderer.removeCurve(curve);
        }
    }
    // 
    contoursAndValues = null;
    boolean hasValues = false;
    if (meshDisplayAdapter != null) {
        VariableType variableType = getPdeDataContext().getDataIdentifier().getVariableType();
        if (variableType.equals(VariableType.VOLUME)) {
            // Get curves with no values for overlay on volume Data
            contoursAndValues = meshDisplayAdapter.getCurvesFromContours(null);
        } else if (variableType.equals(VariableType.CONTOUR)) {
            // get curves with values
            contoursAndValues = meshDisplayAdapter.getCurvesFromContours(getPdeDataContext().getDataValues());
            hasValues = true;
        }
    }
    // Add new curves to curveRenderer
    if (contoursAndValues != null) {
        java.util.Enumeration<SampledCurve> keysEnum = contoursAndValues.keys();
        while (keysEnum.hasMoreElements()) {
            Curve curve = (Curve) keysEnum.nextElement();
            // 
            curveRenderer.addCurve(curve);
            // 
            curveRenderer.renderPropertyEditable(curve, false);
            curveRenderer.renderPropertySelectable(curve, hasValues);
            if (hasValues) {
                curveRenderer.renderPropertySubSelectionType(curve, CurveRenderer.SUBSELECTION_SEGMENT);
            } else {
                curveRenderer.renderPropertyLineWidthMultiplier(curve, 3);
            }
        }
    }
}