Examples with FieldDataIdentifierSpec cbit.vcell.field.FieldDataIdentifierSpec used on opensource projects

Example 21 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec 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 22 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class DataSetControllerImpl method writeFieldFunctionData.

/**
 * Insert the method's description here.
 * Creation date: (9/21/2006 1:28:12 PM)
 * @throws FileNotFoundException
 * @throws DataAccessException
 */
public void writeFieldFunctionData(OutputContext outputContext, FieldDataIdentifierSpec[] argFieldDataIDSpecs, boolean[] bResampleFlags, CartesianMesh newMesh, SimResampleInfoProvider simResampleInfoProvider, int simResampleMembraneDataLength, int handleExistingResampleMode) throws FileNotFoundException, DataAccessException, IOException {
    if (handleExistingResampleMode != FVSolverStandalone.HESM_KEEP_AND_CONTINUE && handleExistingResampleMode != FVSolverStandalone.HESM_OVERWRITE_AND_CONTINUE && handleExistingResampleMode != FVSolverStandalone.HESM_THROW_EXCEPTION) {
        throw new IllegalArgumentException("Unknown mode " + handleExistingResampleMode);
    }
    if (argFieldDataIDSpecs == null || argFieldDataIDSpecs.length == 0) {
        return;
    }
    HashMap<FieldDataIdentifierSpec, File> uniqueFieldDataIDSpecAndFileH = new HashMap<FieldDataIdentifierSpec, File>();
    HashMap<FieldDataIdentifierSpec, Boolean> bFieldDataResample = new HashMap<FieldDataIdentifierSpec, Boolean>();
    for (int i = 0; i < argFieldDataIDSpecs.length; i++) {
        if (!uniqueFieldDataIDSpecAndFileH.containsKey(argFieldDataIDSpecs[i])) {
            File newResampledFieldDataFile = null;
            try {
                newResampledFieldDataFile = ((SimulationData) getVCData(simResampleInfoProvider)).getFieldDataFile(simResampleInfoProvider, argFieldDataIDSpecs[i].getFieldFuncArgs());
            } catch (FileNotFoundException e) {
                e.printStackTrace();
                // use the original way
                newResampledFieldDataFile = new File(getPrimaryUserDir(simResampleInfoProvider.getOwner(), true), SimulationData.createCanonicalResampleFileName(simResampleInfoProvider, argFieldDataIDSpecs[i].getFieldFuncArgs()));
            }
            if (handleExistingResampleMode == FVSolverStandalone.HESM_THROW_EXCEPTION && newResampledFieldDataFile.exists()) {
                throw new RuntimeException("Resample Error: mode not allow overwrite or ignore of " + "existing file\n" + newResampledFieldDataFile.getAbsolutePath());
            }
            uniqueFieldDataIDSpecAndFileH.put(argFieldDataIDSpecs[i], newResampledFieldDataFile);
            bFieldDataResample.put(argFieldDataIDSpecs[i], bResampleFlags[i]);
        }
    }
    try {
        Set<Entry<FieldDataIdentifierSpec, File>> resampleSet = uniqueFieldDataIDSpecAndFileH.entrySet();
        Iterator<Entry<FieldDataIdentifierSpec, File>> resampleSetIter = resampleSet.iterator();
        while (resampleSetIter.hasNext()) {
            Entry<FieldDataIdentifierSpec, File> resampleEntry = resampleSetIter.next();
            if (handleExistingResampleMode == FVSolverStandalone.HESM_KEEP_AND_CONTINUE && resampleEntry.getValue().exists()) {
                continue;
            }
            FieldDataIdentifierSpec fieldDataIdSpec = resampleEntry.getKey();
            boolean bResample = bFieldDataResample.get(fieldDataIdSpec);
            CartesianMesh origMesh = getMesh(fieldDataIdSpec.getExternalDataIdentifier());
            SimDataBlock simDataBlock = getSimDataBlock(outputContext, fieldDataIdSpec.getExternalDataIdentifier(), fieldDataIdSpec.getFieldFuncArgs().getVariableName(), fieldDataIdSpec.getFieldFuncArgs().getTime().evaluateConstant());
            VariableType varType = fieldDataIdSpec.getFieldFuncArgs().getVariableType();
            VariableType dataVarType = simDataBlock.getVariableType();
            if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
                throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
            }
            double[] origData = simDataBlock.getData();
            double[] newData = null;
            CartesianMesh resampleMesh = newMesh;
            if (!bResample) {
                if (resampleMesh.getGeometryDimension() != origMesh.getGeometryDimension()) {
                    throw new DataAccessException("Field data " + fieldDataIdSpec.getFieldFuncArgs().getFieldName() + " (" + origMesh.getGeometryDimension() + "D) should have same dimension as simulation mesh (" + resampleMesh.getGeometryDimension() + "D) because it is not resampled to simulation mesh (e.g. Point Spread Function)");
                }
                newData = origData;
                resampleMesh = origMesh;
            } else {
                if (CartesianMesh.isSpatialDomainSame(origMesh, resampleMesh)) {
                    newData = origData;
                    if (simDataBlock.getVariableType().equals(VariableType.MEMBRANE)) {
                        if (origData.length != simResampleMembraneDataLength) {
                            throw new Exception("FieldData variable \"" + fieldDataIdSpec.getFieldFuncArgs().getVariableName() + "\" (" + simDataBlock.getVariableType().getTypeName() + ") " + "resampling failed: Membrane Data lengths must be equal");
                        }
                    } else if (!simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                        throw new Exception("FieldData variable \"" + fieldDataIdSpec.getFieldFuncArgs().getVariableName() + "\" (" + simDataBlock.getVariableType().getTypeName() + ") " + "resampling failed: Only Volume and Membrane variable types are supported");
                    }
                } else {
                    if (!simDataBlock.getVariableType().compareEqual(VariableType.VOLUME)) {
                        throw new Exception("FieldData variable \"" + fieldDataIdSpec.getFieldFuncArgs().getVariableName() + "\" (" + simDataBlock.getVariableType().getTypeName() + ") " + "resampling failed: Only VOLUME FieldData variable type allowed when\n" + "FieldData spatial domain does not match Simulation spatial domain.\n" + "Check dimension, xsize, ysize, zsize, origin and extent are equal.");
                    }
                    if (origMesh.getSizeY() == 1 && origMesh.getSizeZ() == 1) {
                        newData = MathTestingUtilities.resample1DSpatialSimple(origData, origMesh, resampleMesh);
                    } else if (origMesh.getSizeZ() == 1) {
                        newData = MathTestingUtilities.resample2DSpatialSimple(origData, origMesh, resampleMesh);
                    } else {
                        newData = MathTestingUtilities.resample3DSpatialSimple(origData, origMesh, resampleMesh);
                    }
                }
            }
            DataSet.writeNew(resampleEntry.getValue(), new String[] { fieldDataIdSpec.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(resampleMesh.getSizeX(), resampleMesh.getSizeY(), resampleMesh.getSizeZ()), new double[][] { newData });
        }
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        throw new DataAccessException(ex.getMessage());
    }
}

Example 23 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec 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 24 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec 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;
}

Example 25 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class ROIDataGenerator method getROIDataGeneratorDescription.

public String getROIDataGeneratorDescription(File userDirectory, SimulationJob simulationJob) throws Exception {
    // DataAccessException, FileNotFoundException, MathException, IOException, DivideByZeroException, ExpressionException
    Simulation simulation = simulationJob.getSimulation();
    StringBuffer sb = new StringBuffer();
    sb.append(ROI_GENERATOR_BEGIN + " " + name + "\n");
    sb.append("VolumePoints " + volumePoints.length + "\n");
    for (int i = 0; i < volumePoints.length; i++) {
        sb.append(volumePoints[i] + " ");
        if ((i + 1) % 20 == 0) {
            sb.append("\n");
        }
    }
    sb.append("\n");
    if (membranePoints != null && membranePoints.length > 0) {
        sb.append("MembranePoints " + membranePoints.length + "\n");
        for (int i = 0; i < membranePoints.length; i++) {
            sb.append(membranePoints[i] + " ");
            if ((i + 1) % 20 == 0) {
                sb.append("\n");
            }
        }
        sb.append("\n");
    }
    sb.append("SampleImage " + numImgRegions + " " + zSlice + " " + fieldDataKey + " " + fieldFuncArguments.infix() + "\n");
    sb.append("StoreEnabled " + bStoreEnabled + "\n");
    // sample image field data file
    FieldDataIdentifierSpec fdis = getSampleImageFieldData(simulation.getVersion().getOwner());
    if (fdis == null) {
        throw new DataAccessException("Can't find sample image in ROI data generator.");
    }
    String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
    DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
    CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
    SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
    VariableType varType = fdis.getFieldFuncArgs().getVariableType();
    VariableType dataVarType = simDataBlock.getVariableType();
    if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
        throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
    }
    double[] origData = simDataBlock.getData();
    String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simulationJob.getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
    File fdatFile = new File(userDirectory, filename);
    DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
    sb.append("SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile + "\n");
    sb.append(ROI_GENERATOR_END);
    return sb.toString();
}