Examples with FieldDataSymbol cbit.vcell.data.FieldDataSymbol used on opensource projects

Example 6 with FieldDataSymbol

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);
        }
    });
}

Example 7 with FieldDataSymbol

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");
// }
}

Example 8 with FieldDataSymbol

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();
        }
    }
}

Example 9 with FieldDataSymbol

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();
}

Example 10 with FieldDataSymbol

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);
    }
}