Examples with DataSymbolType cbit.vcell.data.DataSymbol.DataSymbolType used on opensource projects

Example 1 with DataSymbolType

use of cbit.vcell.data.DataSymbol.DataSymbolType in project vcell by virtualcell.

the class XmlReader method getDataSymbols.

private ArrayList<DataSymbol> getDataSymbols(Element dataContextElement, DataContext dataContext, ModelUnitSystem modelUnitSystem) {
    ArrayList<DataSymbol> dataSymbolsList = new ArrayList<DataSymbol>();
    // iterate over fieldDatasymbols. When other dataSymbol types are implemented, repeat this loop.
    Iterator dataSymbolsElementIter = dataContextElement.getChildren(XMLTags.FieldDataSymbolTag, vcNamespace).iterator();
    while (dataSymbolsElementIter.hasNext()) {
        Element dataSymbolElement = (Element) dataSymbolsElementIter.next();
        String dataSymbolName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolNameTag));
        DataSymbolType dataSymbolType = DataSymbolType.fromDatabaseName(unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolTypeTag)));
        String symbol = dataSymbolElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
        VCUnitDefinition vcUnitDefinition = null;
        if (symbol != null) {
            vcUnitDefinition = modelUnitSystem.getInstance(symbol);
        }
        // ExternalDataIdentifier dataSetID in FieldDataSymbol
        Element dataSetIDElement = dataSymbolElement.getChild(XMLTags.ExternalDataIdentifierTag, vcNamespace);
        String name = unMangle(dataSetIDElement.getAttributeValue(XMLTags.NameAttrTag));
        String key = unMangle(dataSetIDElement.getAttributeValue(XMLTags.KeyValueAttrTag));
        String userID = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerNameAttrTag));
        String userKey = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag));
        User owner = new User(userID, new KeyValue(userKey));
        ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(key), owner, name);
        // ---
        String fieldItemName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemNameTag));
        String fieldItemType = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTypeTag));
        double fieldItemTime = Double.parseDouble(unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTimeTag)));
        FieldDataSymbol fds = new FieldDataSymbol(dataSymbolName, dataSymbolType, dataContext, vcUnitDefinition, edi, fieldItemName, fieldItemType, fieldItemTime);
        dataSymbolsList.add(fds);
    }
    return dataSymbolsList;
}

Example 2 with DataSymbolType

use of cbit.vcell.data.DataSymbol.DataSymbolType in project vcell by virtualcell.

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = 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));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}

Example 3 with DataSymbolType

use of cbit.vcell.data.DataSymbol.DataSymbolType 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 4 with DataSymbolType

use of cbit.vcell.data.DataSymbol.DataSymbolType in project vcell by virtualcell.

the class DataSymbolsSpecPanel method setDataSymbol.

// public void createDataSymbol() throws Exception, UserCancelException{
// final int VFRAP_DATASET = 0;
// final int VFRAP_SPECIALS = 1;
// final int ASSOCIATE_EXISTING_FD = 2;
// final int POINT_SPREAD_FUNCTION = 3;
// final int IMAGE_FILE = 4;
// final int COPY_FROM_BIOMODEL = 5;
// int[] dataSymbolSource = null;
// 
// String[][] choices = new String[][] {{ADD_VFRAP_DATASET_MENU},{ADD_VFRAP_SPECIALS_MENU},{ADD_ASSOCIATE_EXISTING_FD_MENU},
// {ADD_PSF_MENU},{ADD_IMAGE_FILE_MENU},{ADD_COPY_FROM_BIOMODEL_MENU} };
// 
// dataSymbolSource = DialogUtils.showComponentOKCancelTableList(
// getComponent(),
// "Choose a source for the data symbol.",
// new String[] {"Available Sources:"},
// choices, ListSelectionModel.SINGLE_SELECTION);
// 
// if(dataSymbolSource[0] == VFRAP_DATASET){
// getDataSymbolsPanel().addVFrapOriginalImages();
// }else if(dataSymbolSource[0] == VFRAP_SPECIALS){
// getDataSymbolsPanel().addVFrapDerivedImages();
// }else if(dataSymbolSource[0] == ASSOCIATE_EXISTING_FD){
// Component requesterComponent = DataSymbolsSpecPanel.this;
// DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(requesterComponent, 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
// 
// DecimalFormat df = new  DecimalFormat("###000.00");		// max time interval we can display is about 11 days
// 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,
// getSimulationContext().getDataContext(), VCUnitDefinition.UNIT_TBD,
// dataSetID,
// fieldDataVarName, fieldDataVarType.getTypeName(), fieldDataVarTime);
// getSimulationContext().getDataContext().addDataSymbol(dataSymbol);
// 
// }
// });
// }else if(dataSymbolSource[0] == POINT_SPREAD_FUNCTION){
// PointSpreadFunctionManagement psfManager = new PointSpreadFunctionManagement(DataSymbolsSpecPanel.this,
// getSimulationContext());
// psfManager.importPointSpreadFunction();
// }else if(dataSymbolSource[0] == IMAGE_FILE){
// throw new RuntimeException("Option not yet implemented.");
// }else if(dataSymbolSource[0] == COPY_FROM_BIOMODEL){
// throw new RuntimeException("Option not yet implemented.");
// }else{
// throw new IllegalArgumentException("Error selecting data symbol, Unknown Source type " + dataSymbolSource[0]);
// }
// }
public void setDataSymbol(Object object) {
    if (object == null) {
        // TODO: display empty image
        return;
    }
    if (((DataSymbol) object).equals(ivjCurrentSymbol)) {
        return;
    } else {
        ivjCurrentSymbol = (DataSymbol) object;
    }
    // manage checkbox status depending on type of current data symbol
    DataSymbolType dsType = ivjCurrentSymbol.getDataSymbolType();
    switch(dsType) {
        case GENERIC_SYMBOL:
            getChckbxPointSpreadFunction().setEnabled(true);
            getChckbxPointSpreadFunction().setSelected(false);
            break;
        case POINT_SPREAD_FUNCTION:
            getChckbxPointSpreadFunction().setEnabled(true);
            getChckbxPointSpreadFunction().setSelected(true);
            break;
        default:
            getChckbxPointSpreadFunction().setEnabled(false);
            getChckbxPointSpreadFunction().setSelected(false);
            break;
    }
    // displays iconized image for the current (field?) data symbol
    getImagePlaneManagerPanel().setMode(ImagePaneModel.MESH_MODE);
    int w = Integer.valueOf(30).intValue() + 5 * (countW % 5);
    int h = Integer.valueOf(20).intValue() + 3 * (countH % 7);
    String type = "double";
    System.out.println("  " + w + ", " + h);
    SourceDataInfo sdi = ImagePaneScrollerTest.getExampleSDI(type, w, h);
    getImagePlaneManagerPanel().setSourceDataInfo(sdi);
    countW++;
    countH++;
}

Example 5 with DataSymbolType

use of cbit.vcell.data.DataSymbol.DataSymbolType 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);
    }
}