use of cbit.vcell.data.FieldDataSymbol in project vcell by virtualcell.
the class DataSymbolsPanel method addAssociate.
private void addAssociate() {
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(this, DocumentWindow.class);
documentWindow.getTopLevelWindowManager().getRequestManager().showFieldDataWindow(new FieldDataWindowManager.DataSymbolCallBack() {
public void createDataSymbol(ExternalDataIdentifier dataSetID, String fieldDataVarName, VariableType fieldDataVarType, double fieldDataVarTime) {
System.out.println(dataSetID + " " + fieldDataVarName + " " + fieldDataVarType + " " + fieldDataVarTime);
// ex: incomplete 51780592 danv(26766043) fluor Volume_VariableType 23.680419921875
// max time interval we can display is about 11 days
DecimalFormat df = new DecimalFormat("###000.00");
String fluorName = fieldDataVarName + "_" + df.format(fieldDataVarTime).substring(0, df.format(fieldDataVarTime).indexOf(".")) + "s" + df.format(fieldDataVarTime).substring(1 + df.format(fieldDataVarTime).indexOf(".")) + "_" + dataSetID.getName();
// TODO: symbol names may not be unique, must check for unicity and prompt the user
FieldDataSymbol dataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.GENERIC_SYMBOL, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), dataSetID, fieldDataVarName, fieldDataVarType.getTypeName(), fieldDataVarTime);
simulationContext.getDataContext().addDataSymbol(dataSymbol);
}
});
}
use of cbit.vcell.data.FieldDataSymbol in project vcell by virtualcell.
the class DataSymbolsPanel method addVFrapOriginalImages.
private void addVFrapOriginalImages() {
// add dataset (normal images) from vFrap
AsynchClientTask[] taskArray = new AsynchClientTask[5];
// select the desired vfrap file
taskArray[0] = ChooseVFrapFile();
taskArray[1] = new AsynchClientTask("Import objects", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
File vFrapFile = (File) hashTable.get("vFrapFile");
Component requesterComponent = DataSymbolsPanel.this;
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (documentManager == null) {
throw new RuntimeException("Not connected to server.");
}
// ex ccc8.vfrap
String vFrapFileNameExtended = vFrapFile.getName();
{
// we want to make sure to reload these strings from the hash later on
String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
// we'll save here the "special" vFrap images (prebleach_avg, ...)
String mixedFieldDataName = initialFieldDataName + "Mx";
hashTable.put("initialFieldDataName", initialFieldDataName);
hashTable.put("mixedFieldDataName", mixedFieldDataName);
}
if (vFrapFileNameExtended.indexOf(".vfrap") <= -1) {
throw new RuntimeException("File extension must be .vfrap");
}
// normal images
checkNameAvailability(hashTable, false, documentManager, requesterComponent);
// ----- read needed info from Virtual FRAP xml file
System.out.println("Loading " + vFrapFileNameExtended + " ...");
String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
// loading frap images
AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
hashTable.put("annotatedImages", annotatedImages);
// loading ROIs for display purposes only (see next task)
ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
// Calendar cal = Calendar.getInstance();
// SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd_hhmmss");
// DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
// DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
// VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
// if(vFrapXmlHelper.isAlreadyImported(vFrapFileName, documentManager)) {
// throw new RuntimeException("FieldData name already in use.");
// }
// // bioModel.setName(vFrapFileName + "-" + sdf.format(cal.getTime()));
// bioModel.setName(vFrapFileName);
// BioModel feedbackModel = documentManager.save(bioModel, null);
// BioModelChildSummary childSummary = BioModelChildSummary.fromDatabaseSerialization(xmlString);
// BioModelInfo biomodelInfo = new BioModelInfo(feedbackModel.getVersion(), feedbackModel.getVersion().getVersionKey(), childSummary );
// documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(biomodelInfo, documentWindow.getTopLevelWindowManager(), true);
}
};
// show the images from the vfrap file in an OverlayEditorPanelJAI dialog
taskArray[2] = new AsynchClientTask("Display images", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
if (initialFieldDataName.equals("")) {
JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + initialFieldDataName + " already in use.");
// prevents the rest of tasks below from running
throw UserCancelException.CANCEL_GENERIC;
}
AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
BufferedImage[] displayROI = (BufferedImage[]) hashTable.get("displayROI");
if (annotatedImages == null || displayROI == null) {
return;
}
// display the images
OverlayEditorPanelJAI overlayPanel = new OverlayEditorPanelJAI();
overlayPanel.setAllowAddROI(false);
ImageDataset imageDataset = annotatedImages.getImageDataset();
overlayPanel.setImages(imageDataset, 1, 0, new OverlayEditorPanelJAI.AllPixelValuesRange(1, 200));
overlayPanel.setAllROICompositeImage(displayROI, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
int choice = DialogUtils.showComponentOKCancelDialog(DataSymbolsPanel.this, overlayPanel, "vFrap Field Data");
if (choice != JOptionPane.OK_OPTION) {
throw UserCancelException.CANCEL_GENERIC;
}
}
};
// save the timepoints from memory to the database as field data
taskArray[3] = new AsynchClientTask("Saving time series data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
DocumentManager dm = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
if (dm == null) {
throw new RuntimeException("Not connected to server.");
}
User owner = null;
Version version = simulationContext.getVersion();
if (version == null) {
// new document, so the owner is the user
owner = dm.getUser();
} else {
owner = simulationContext.getVersion().getOwner();
}
// mesh
ImageDataset imageDataset = annotatedImages.getImageDataset();
Extent extent = imageDataset.getExtent();
ISize isize = imageDataset.getISize();
Origin origin = new Origin(0, 0, 0);
CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
// save field data
int NumTimePoints = imageDataset.getImageTimeStamps().length;
int NumChannels = 1;
double[][][] pixData = new double[NumTimePoints][NumChannels][];
for (int i = 0; i < NumTimePoints; i++) {
// images according to zIndex at specific time points(tIndex)
short[] originalData = imageDataset.getPixelsZ(0, i);
double[] doubleData = new double[originalData.length];
for (int j = 0; j < originalData.length; j++) {
doubleData[j] = 0x0000ffff & originalData[j];
}
pixData[i][NumChannels - 1] = doubleData;
}
FieldDataFileOperationSpec timeSeriesFieldDataOpSpec = new FieldDataFileOperationSpec();
timeSeriesFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
timeSeriesFieldDataOpSpec.cartesianMesh = cartesianMesh;
timeSeriesFieldDataOpSpec.doubleSpecData = pixData;
timeSeriesFieldDataOpSpec.specEDI = null;
timeSeriesFieldDataOpSpec.varNames = new String[] { SimulationContext.FLUOR_DATA_NAME };
timeSeriesFieldDataOpSpec.owner = owner;
timeSeriesFieldDataOpSpec.times = imageDataset.getImageTimeStamps();
timeSeriesFieldDataOpSpec.variableTypes = new VariableType[] { VariableType.VOLUME };
timeSeriesFieldDataOpSpec.origin = origin;
timeSeriesFieldDataOpSpec.extent = extent;
timeSeriesFieldDataOpSpec.isize = isize;
// realignment for the case when first timepoint is not zero
if (timeSeriesFieldDataOpSpec.times[0] != 0) {
double shift = timeSeriesFieldDataOpSpec.times[0];
for (int i = 0; i < NumTimePoints; i++) {
timeSeriesFieldDataOpSpec.times[i] -= shift;
}
}
Calendar cal = Calendar.getInstance();
SimpleDateFormat sdf = new SimpleDateFormat("yyMMMdd_hhmmss");
String formattedDate = sdf.format(cal.getTime());
hashTable.put("formattedDate", formattedDate);
// ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec,
// initialFieldDataName + "_" + formattedDate);
ExternalDataIdentifier timeSeriesEDI = dm.saveFieldData(timeSeriesFieldDataOpSpec, initialFieldDataName);
hashTable.put("imageDataset", imageDataset);
hashTable.put("timeSeriesEDI", timeSeriesEDI);
}
};
// create the data symbols for the images saved above and display them in the tree/table
taskArray[4] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
// --- create the data symbols associated with the time series
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
ImageDataset imageDataset = (ImageDataset) hashTable.get("imageDataset");
ExternalDataIdentifier timeSeriesEDI = (ExternalDataIdentifier) hashTable.get("timeSeriesEDI");
for (double time : imageDataset.getImageTimeStamps()) {
// String fluorName = TokenMangler.fixTokenStrict("fluor_"+time+"_");
// while (simulationContext.getDataContext().getDataSymbol(fluorName)!=null){
// fluorName = TokenMangler.getNextEnumeratedToken(fluorName);
// }
// max time interval we can display is about 11 days
DecimalFormat df = new DecimalFormat("###000.00");
// String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
String fluorName = "fluor_" + df.format(time).substring(0, df.format(time).indexOf(".")) + "s" + df.format(time).substring(1 + df.format(time).indexOf(".")) + "_" + initialFieldDataName;
// FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
DataSymbol fluorDataSymbol = new FieldDataSymbol(fluorName, DataSymbolType.VFRAP_TIMEPOINT, simulationContext.getDataContext(), simulationContext.getModel().getUnitSystem().getInstance_TBD(), timeSeriesEDI, SimulationContext.FLUOR_DATA_NAME, VariableType.VOLUME.getTypeName(), time);
simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
}
}
};
Hashtable<String, Object> hash = new Hashtable<String, Object>();
ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
// String name = null;
// try {
// getNewDataSymbolPanel().setSymbolName("");
// getNewDataSymbolPanel().setSymbolExpression("vcField(dataset1,var1,0.0,Volume)");
// int newSettings = org.vcell.util.gui.DialogUtils.showComponentOKCancelDialog(this, getNewDataSymbolPanel(), "New DataSymbol");
// if (newSettings == JOptionPane.OK_OPTION) {
// name = getNewDataSymbolPanel().getSymbolName();
// String expression = getNewDataSymbolPanel().getSymbolExpression();
// Expression exp = new Expression(expression);
// FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
// // DataSymbol ds = new FieldDataSymbol(DataSymbolType.GENERIC_SYMBOL, name, "",
// // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
// // new FieldFunctionArguments(functionInvocations[0]));
// DataSymbol ds = new FieldDataSymbol(name, DataSymbolType.GENERIC_SYMBOL,
// simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD);
// simulationContext.getDataContext().addDataSymbol(ds);
// }
// } catch (java.lang.Throwable ivjExc) {
// DialogUtils.showErrorDialog(this, "Data symbol " + name + " already exists");
// }
}
use of cbit.vcell.data.FieldDataSymbol in project vcell by virtualcell.
the class DataSymbolTable method populateDataSymbols.
public void populateDataSymbols(Connection con, KeyValue simContextRef, DataContext dataContext, User simcontextOwner, VCUnitSystem unitSystem) throws SQLException, DataAccessException {
Statement stmt = null;
try {
HashMap<BigDecimal, ExternalDataIdentifier> extDataIDHashMap = new HashMap<BigDecimal, ExternalDataIdentifier>();
stmt = con.createStatement();
ResultSet rset = stmt.executeQuery("SELECT * FROM " + ExternalDataTable.table.getTableName() + " WHERE " + ExternalDataTable.table.ownerRef.getUnqualifiedColName() + " = " + simcontextOwner.getID().toString());
while (rset.next()) {
BigDecimal extdataIDBigDec = rset.getBigDecimal(ExternalDataTable.table.id.getUnqualifiedColName());
ExternalDataIdentifier extdataID = new ExternalDataIdentifier(new KeyValue(extdataIDBigDec), simcontextOwner, rset.getString(ExternalDataTable.table.externalDataName.getUnqualifiedColName()));
extDataIDHashMap.put(extdataIDBigDec, extdataID);
}
rset.close();
rset = stmt.executeQuery("SELECT * FROM " + DataSymbolTable.table.getTableName() + " WHERE " + DataSymbolTable.table.simContextRef.getUnqualifiedColName() + " = " + simContextRef.toString());
while (rset.next()) {
String nextDataSymbolName = rset.getString(DataSymbolTable.table.dataSymbolName.toString());
String nextDataSymbolTypeS = rset.getString(DataSymbolTable.table.dataSymbolType.toString());
DataSymbolType nextDataSymbolType = DataSymbolType.valueOf(nextDataSymbolTypeS);
String nextDataSymbolVCUnitDefS = rset.getString(DataSymbolTable.table.dataSymbolVCUnitDef.toString());
nextDataSymbolVCUnitDefS = TokenMangler.getSQLRestoredString(nextDataSymbolVCUnitDefS);
VCUnitDefinition nextVCUnitDefinition = unitSystem.getInstance(nextDataSymbolVCUnitDefS);
// FieldDataSymbol (ExternalDataIdentifier) - (only data symbol defined right now)
BigDecimal extDataBigDecimal = rset.getBigDecimal(DataSymbolTable.table.fieldDataRef.getUnqualifiedColName());
ExternalDataIdentifier nextExtDataID = null;
if (!rset.wasNull()) {
nextExtDataID = extDataIDHashMap.get(extDataBigDecimal);
if (nextExtDataID == null) {
throw new DataAccessException("PopulateDataSymbols extdataID " + extDataBigDecimal + " not found in database for user " + simcontextOwner.getName());
}
String nextFieldDataVarName = rset.getString(DataSymbolTable.table.fieldDataVarName.getUnqualifiedColName());
String nextFieldDataVarType = rset.getString(DataSymbolTable.table.fieldDataVarType.getUnqualifiedColName());
double nextFieldDataVarTime = rset.getDouble(DataSymbolTable.table.fieldDataVarTime.getUnqualifiedColName());
FieldDataSymbol fieldDataSymbol = new FieldDataSymbol(nextDataSymbolName, nextDataSymbolType, dataContext, nextVCUnitDefinition, nextExtDataID, nextFieldDataVarName, nextFieldDataVarType, nextFieldDataVarTime);
dataContext.addDataSymbol(fieldDataSymbol);
} else {
throw new DataAccessException("DataSymbol has no ExternalDataIdentifier");
}
}
} finally {
if (stmt != null) {
stmt.close();
}
}
}
use of cbit.vcell.data.FieldDataSymbol in project vcell by virtualcell.
the class DataSymbolTable method getSQLValueList.
public String getSQLValueList(DataSymbol dataSymbol, KeyValue simContextKey, KeyFactory keyFactory) throws DataAccessException {
FieldDataSymbol fieldDataSymbol = null;
if (dataSymbol instanceof FieldDataSymbol) {
fieldDataSymbol = (FieldDataSymbol) dataSymbol;
}
StringBuffer buffer = new StringBuffer();
buffer.append("(");
buffer.append(keyFactory.nextSEQ() + ",");
buffer.append("'" + dataSymbol.getName() + "',");
buffer.append("'" + dataSymbol.getDataSymbolType().toString() + "',");
buffer.append("'" + TokenMangler.getSQLEscapedString(dataSymbol.getUnitDefinition().getSymbol()) + "',");
buffer.append(simContextKey.toString() + ",");
buffer.append((fieldDataSymbol != null ? fieldDataSymbol.getExternalDataIdentifier().getKey().toString() : "null") + ",");
buffer.append((fieldDataSymbol != null ? "'" + fieldDataSymbol.getFieldDataVarName() + "'" : "null") + ",");
buffer.append((fieldDataSymbol != null ? "'" + fieldDataSymbol.getFieldDataVarType() + "'" : "null") + ",");
buffer.append((fieldDataSymbol != null ? fieldDataSymbol.getFieldDataVarTime() : "null"));
buffer.append(")");
return buffer.toString();
}
use of cbit.vcell.data.FieldDataSymbol in project vcell by virtualcell.
the class VFrapXmlHelper method CreateSaveVFrapDataSymbols.
public static void CreateSaveVFrapDataSymbols(Hashtable<String, Object> hashTable, BioModel bioModel, ExternalDataIdentifier vfrapMisc) {
String[] channelNames = (String[]) hashTable.get("channelNames");
DataSymbolType[] channelVFrapImageType = (DataSymbolType[]) hashTable.get("channelVFrapImageType");
String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
SimulationContext simContext = bioModel.getSimulationContexts()[0];
ModelUnitSystem modelUnitSystem = bioModel.getModel().getUnitSystem();
for (int i = 0; i < channelNames.length; i++) {
// TODO: construct dataSymbolName from vFrapConstants::nameFromToken()
// item name postfixed with field data name
String dataSymbolName = channelNames[i] + "_" + initialFieldDataName;
DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolName, channelVFrapImageType[i], simContext.getDataContext(), modelUnitSystem.getInstance_TBD(), vfrapMisc, channelNames[i], VariableType.VOLUME.getTypeName(), 0D);
simContext.getDataContext().addDataSymbol(dataSymbol);
}
}
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