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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);
        }
    });
}
Also used : DocumentWindow(cbit.vcell.client.desktop.DocumentWindow) VariableType(cbit.vcell.math.VariableType) DecimalFormat(java.text.DecimalFormat) FieldDataWindowManager(cbit.vcell.client.FieldDataWindowManager) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

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");
// }
}
Also used : Origin(org.vcell.util.Origin) AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) User(org.vcell.util.document.User) AnnotatedImageDataset(cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset) ImageDataset(cbit.vcell.VirtualMicroscopy.ImageDataset) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) Element(org.jdom.Element) DecimalFormat(java.text.DecimalFormat) BufferedImage(java.awt.image.BufferedImage) Version(org.vcell.util.document.Version) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) Component(java.awt.Component) AnnotatedImageDataset(cbit.vcell.VirtualMicroscopy.importer.AnnotatedImageDataset) VariableType(cbit.vcell.math.VariableType) Hashtable(java.util.Hashtable) Calendar(java.util.Calendar) DocumentManager(cbit.vcell.clientdb.DocumentManager) VCImageUncompressed(cbit.image.VCImageUncompressed) UserCancelException(org.vcell.util.UserCancelException) DocumentWindow(cbit.vcell.client.desktop.DocumentWindow) MicroscopyXmlReader(cbit.vcell.VirtualMicroscopy.importer.MicroscopyXmlReader) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol) DataSymbol(cbit.vcell.data.DataSymbol) CartesianMesh(cbit.vcell.solvers.CartesianMesh) RegionImage(cbit.vcell.geometry.RegionImage) File(java.io.File) OverlayEditorPanelJAI(cbit.vcell.geometry.gui.OverlayEditorPanelJAI) SimpleDateFormat(java.text.SimpleDateFormat) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

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();
        }
    }
}
Also used : KeyValue(org.vcell.util.document.KeyValue) HashMap(java.util.HashMap) Statement(java.sql.Statement) BigDecimal(java.math.BigDecimal) VCUnitDefinition(cbit.vcell.units.VCUnitDefinition) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) ResultSet(java.sql.ResultSet) DataSymbolType(cbit.vcell.data.DataSymbol.DataSymbolType) DataAccessException(org.vcell.util.DataAccessException) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

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();
}
Also used : FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

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);
    }
}
Also used : FieldDataSymbol(cbit.vcell.data.FieldDataSymbol) DataSymbol(cbit.vcell.data.DataSymbol) DataSymbolType(cbit.vcell.data.DataSymbol.DataSymbolType) SimulationContext(cbit.vcell.mapping.SimulationContext) ModelUnitSystem(cbit.vcell.model.ModelUnitSystem) FieldDataSymbol(cbit.vcell.data.FieldDataSymbol)

Aggregations

FieldDataSymbol (cbit.vcell.data.FieldDataSymbol)10 DataSymbol (cbit.vcell.data.DataSymbol)7 ExternalDataIdentifier (org.vcell.util.document.ExternalDataIdentifier)5 DocumentWindow (cbit.vcell.client.desktop.DocumentWindow)3 DataSymbolType (cbit.vcell.data.DataSymbol.DataSymbolType)3 VariableType (cbit.vcell.math.VariableType)3 VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)3 Element (org.jdom.Element)3 VCImageUncompressed (cbit.image.VCImageUncompressed)2 ImageDataset (cbit.vcell.VirtualMicroscopy.ImageDataset)2 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)2 DocumentManager (cbit.vcell.clientdb.DocumentManager)2 FieldFunctionArguments (cbit.vcell.field.FieldFunctionArguments)2 FieldDataFileOperationSpec (cbit.vcell.field.io.FieldDataFileOperationSpec)2 RegionImage (cbit.vcell.geometry.RegionImage)2 Expression (cbit.vcell.parser.Expression)2 CartesianMesh (cbit.vcell.solvers.CartesianMesh)2 Component (java.awt.Component)2 File (java.io.File)2 DecimalFormat (java.text.DecimalFormat)2