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

Example 36 with ExternalDataIdentifier

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

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}

Example 37 with ExternalDataIdentifier

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

the class MicroscopyXmlReader method getExternalDataIdentifier.

/**
 * Method getExternalDataIdentifier.
 * @param externalDataIDElement Element
 * @return ExternalDataIdentifier
 */
private static ExternalDataIdentifier getExternalDataIdentifier(Element externalDataIDElement) {
    String name = externalDataIDElement.getAttributeValue(XMLTags.NameAttrTag);
    String keyValueStr = externalDataIDElement.getAttributeValue(XMLTags.KeyValueAttrTag);
    String ownerName = externalDataIDElement.getAttributeValue(MicroscopyXMLTags.OwnerNameAttrTag);
    String ownerKey = externalDataIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag);
    return new ExternalDataIdentifier(new KeyValue(keyValueStr), new User(ownerName, new KeyValue(ownerKey)), name);
}

Example 38 with ExternalDataIdentifier

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

the class DataSetControllerImpl method getFieldDataIdentifierSpecs_private.

private FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs_private(FieldFunctionArguments[] fieldFuncArgumentsArr, User user, boolean bForceUpdate) throws DataAccessException {
    Vector<ExternalDataIdentifier> userExtDataIdentifiersV = userExtDataIDH.get(user);
    if (userExtDataIdentifiersV == null || userExtDataIdentifiersV.size() < fieldFuncArgumentsArr.length || bForceUpdate) {
        // must refresh
        ExternalDataIdentifierService extDataIDService = VCellServiceHelper.getInstance().loadService(ExternalDataIdentifierService.class);
        userExtDataIDH = extDataIDService.getAllExternalDataIdentifiers();
        userExtDataIdentifiersV = userExtDataIDH.get(user);
    }
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFuncArgumentsArr.length];
    Arrays.fill(fieldDataIdentifierSpecs, null);
    for (int i = 0; i < fieldFuncArgumentsArr.length; i++) {
        for (int j = 0; userExtDataIdentifiersV != null && j < userExtDataIdentifiersV.size(); j++) {
            if (fieldFuncArgumentsArr[i].getFieldName().equals(userExtDataIdentifiersV.elementAt(j).getName())) {
                fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFuncArgumentsArr[i], userExtDataIdentifiersV.elementAt(j));
                break;
            }
        }
        if (fieldDataIdentifierSpecs[i] == null) {
            throw new ObjectNotFoundException("The data locator for FieldData Function '" + fieldFuncArgumentsArr[i].getFieldName() + "' could not be found.");
        }
    }
    return fieldDataIdentifierSpecs;
}

Example 39 with ExternalDataIdentifier

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

the class DataProcessingInstructions method getSampleImageFieldData.

public FieldDataIdentifierSpec getSampleImageFieldData(User user) {
    if (scriptInput != null) {
        int index = scriptInput.indexOf("SampleImage");
        StringTokenizer st = new StringTokenizer(scriptInput.substring(index));
        // SampleImage
        st.nextToken();
        // numRegions
        st.nextToken();
        if (getScriptName().equals(VFRAP)) {
            // zSlice
            st.nextToken();
        }
        // key
        String key = st.nextToken();
        index = scriptInput.indexOf(FieldFunctionDefinition.FUNCTION_name);
        if (index >= 0) {
            st = new StringTokenizer(scriptInput.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;
}

Example 40 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;
}