use of cbit.vcell.geometry.Curve 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());
}
}
use of cbit.vcell.geometry.Curve in project vcell by virtualcell.
the class Xmlproducer method getXML.
/**
* This method returns a XML Element from a Filament object.
* Creation date: (5/22/2001 4:03:13 PM)
* @return Element
* @param param cbit.vcell.geometry.Filament
*/
private Element getXML(Filament param) {
// --- create Element
Element filament = new Element(XMLTags.FilamentTag);
// Add atributes
filament.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
// add curves
Curve[] array = param.getCurves();
for (int i = 0; i < array.length; i++) {
filament.addContent(getXML((ControlPointCurve) array[i]));
}
return filament;
}
use of cbit.vcell.geometry.Curve 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);
}
}
}
}
use of cbit.vcell.geometry.Curve 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();
}
use of cbit.vcell.geometry.Curve 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;
}
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