Examples with ExternalDataIdentifier org.vcell.util.document.ExternalDataIdentifier used on opensource projects

Example 1 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier 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 ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class FRAPStudy method createNewExternalDataInfo.

public static ExternalDataInfo createNewExternalDataInfo(LocalWorkspace localWorkspace, String extDataIDName) {
    File targetDir = new File(localWorkspace.getDefaultSimDataDirectory());
    ExternalDataIdentifier newImageDataExtDataID = new ExternalDataIdentifier(LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), extDataIDName);
    ExternalDataInfo newImageDataExtDataInfo = new ExternalDataInfo(newImageDataExtDataID, new File(targetDir, newImageDataExtDataID.getID() + SimDataConstants.LOGFILE_EXTENSION).getAbsolutePath());
    return newImageDataExtDataInfo;
}

Example 3 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class FRAPStudy method getROIDataGenerator.

public ROIDataGenerator getROIDataGenerator(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] roiFieldData = null;
    ROI[] rois = getFrapData().getRois();
    if (rois.length > 0) {
        Extent extent = rois[0].getRoiImages()[0].getExtent();
        ISize isize = rois[0].getISize();
        int numROIX = rois[0].getISize().getX();
        int numROIY = rois[0].getISize().getY();
        roiFieldData = new short[numROIX * numROIY];
        short regionCounter = 1;
        for (int roiIdx = FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.ordinal(); roiIdx < rois.length; roiIdx++) {
            short[] roiImg = rois[roiIdx].getPixelsXYZ();
            for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
                if (roiImg[pixelIdx] > 0) {
                    roiFieldData[pixelIdx] = regionCounter;
                }
            }
            regionCounter++;
        }
        // create field data
        int NumTimePoints = 1;
        // 8 rois integrated into 1 image
        int NumChannels = 1;
        short[][][] pixData = new short[NumTimePoints][NumChannels][];
        pixData[0][0] = roiFieldData;
        // get extental data id
        ExternalDataIdentifier newROIExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_SUMDATA_NAME).getExternalDataIdentifier();
        CartesianMesh cartesianMesh;
        try {
            cartesianMesh = getCartesianMesh();
            Origin origin = new Origin(0, 0, 0);
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = cartesianMesh;
            fdos.shortSpecData = pixData;
            fdos.specEDI = newROIExtDataID;
            fdos.varNames = new String[] { "roiSumDataVar" };
            fdos.owner = LocalWorkspace.getDefaultOwner();
            fdos.times = new double[] { 0.0 };
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
        new int[] { 0 }, /* volumePoints*/
        new int[0], /* membranePoints*/
        regionCounter, /*numRegions*/
        0, /*zSlice*/
        newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
        new FieldFunctionArguments(FRAPStudy.ROI_SUMDATA_NAME, "roiSumDataVar", new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}

Example 4 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class MicroscopyXmlReader method getExternalDataInfo.

private static ExternalDataInfo getExternalDataInfo(Element extDataInfoElement) {
    String filename = extDataInfoElement.getAttributeValue(MicroscopyXMLTags.FilenameAttrTag);
    Element externalDataIDElement = extDataInfoElement.getChild(MicroscopyXMLTags.ExternalDataIdentifierTag);
    ExternalDataIdentifier externalDataID = getExternalDataIdentifier(externalDataIDElement);
    ExternalDataInfo externalDataInfo = new ExternalDataInfo(externalDataID, filename);
    return externalDataInfo;
}

Example 5 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class ROIDataGenerator method getSampleImageFieldData.

public FieldDataIdentifierSpec getSampleImageFieldData(User user) {
    // key
    String key = fieldDataKey.toString();
    String fieldInput = fieldFuncArguments.infix();
    StringTokenizer st = null;
    int index = fieldInput.indexOf(FieldFunctionDefinition.FUNCTION_name);
    if (index >= 0) {
        st = new StringTokenizer(fieldInput.substring(index), "\n");
        if (st.hasMoreTokens()) {
            String fieldFunction = st.nextToken();
            try {
                Expression exp = new Expression(fieldFunction);
                FieldFunctionArguments[] ffa = FieldUtilities.getFieldFunctionArguments(exp);
                return new FieldDataIdentifierSpec(ffa[0], new ExternalDataIdentifier(KeyValue.fromString(key), user, ffa[0].getFieldName()));
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException(e.getMessage());
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("Failed to load data processing script.");
            }
        }
    }
    return null;
}