Examples with CartesianMesh cbit.vcell.solvers.CartesianMesh used on opensource projects

Example 31 with CartesianMesh

use of cbit.vcell.solvers.CartesianMesh in project vcell by virtualcell.

the class FunctionRangeGenerator method main.

public static void main(String[] args) {
    try {
        Expression exp = new Expression("a+log(b)+c");
        VarStatistics[] varStats = new VarStatistics[3];
        varStats[0] = new VarStatistics("a", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[1] = new VarStatistics("b", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[2] = new VarStatistics("c", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        double[] times = new double[] { 0.0, 1.0, 2.0 };
        Extent extent = new Extent(5, 5, 5);
        Origin origin = new Origin(0, 0, 0);
        // int numSamplesPerDim = 10;
        byte[] pixels = new byte[3 * 3 * 3];
        BitSet indomain = new BitSet(pixels.length);
        for (int i = 0; i < pixels.length; i++) {
            indomain.set(i);
        }
        VCImageUncompressed vcImage = new VCImageUncompressed(null, pixels, extent, 3, 3, 3);
        RegionImage regionImage = new RegionImage(vcImage, 3, extent, origin, RegionImage.NO_SMOOTHING);
        CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, new ISize(regionImage.getNumX(), regionImage.getNumY(), regionImage.getNumZ()), regionImage, true);
        FunctionStatistics results = FunctionRangeGenerator.getFunctionStatistics(exp, varStats, times, mesh, indomain, VariableType.VOLUME);
        System.out.println(results.getDefaultDatasetRange().toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 32 with CartesianMesh

use of cbit.vcell.solvers.CartesianMesh 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 33 with CartesianMesh

use of cbit.vcell.solvers.CartesianMesh in project vcell by virtualcell.

the class FRAPStudy method getCartesianMesh.

public CartesianMesh getCartesianMesh() throws Exception {
    CartesianMesh cartesianMesh = null;
    ImageDataset imgDataSet = getFrapData().getImageDataset();
    Extent extent = imgDataSet.getExtent();
    ISize isize = imgDataSet.getISize();
    Origin origin = new Origin(0, 0, 0);
    if (getBioModel() == null) {
        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));
    } else {
        RegionImage regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        if (regionImage == null) {
            getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().updateAll();
            regionImage = getBioModel().getSimulationContexts()[0].getGeometry().getGeometrySurfaceDescription().getRegionImage();
        }
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    }
    return cartesianMesh;
}

Example 34 with CartesianMesh

use of cbit.vcell.solvers.CartesianMesh 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();
}

Example 35 with CartesianMesh

use of cbit.vcell.solvers.CartesianMesh in project vcell by virtualcell.

the class DataSetControllerImpl method getMesh.

/**
 * This method was created in VisualAge.
 * @return CartesianMesh
 */
public CartesianMesh getMesh(VCDataIdentifier vcdID) throws DataAccessException, IOException, MathException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getMesh(" + vcdID.getID() + ")  <<EXIT>>");
    if (lg.isTraceEnabled())
        lg.trace("DataSetControllerImpl.getMesh(" + vcdID.getOwner().getName() + "," + vcdID.getID() + ")");
    VCData simData = null;
    try {
        simData = getVCData(vcdID);
    } catch (DataAccessException e) {
    }
    if (simData == null) {
        throw new DataAccessException("no simResults for user " + vcdID.getOwner().getName() + " with simID=" + vcdID.getID());
    }
    CartesianMesh mesh = simData.getMesh();
    if (mesh == null) {
        if (lg.isWarnEnabled())
            lg.warn("DataSetControllerImpl.getMesh(): creating dummy CartesianMesh");
        try {
            int[] size = simData.getVolumeSize();
            if (size == null) {
                VCMongoMessage.sendTrace("DataSetControllerImpl.getMesh(" + vcdID.getID() + ")  <<EXIT size==null>>");
                return null;
            }
            VCMongoMessage.sendTrace("DataSetControllerImpl.getMesh(" + vcdID.getID() + ")  <<EXIT size not null but can't read>>");
            throw new RuntimeException("DataSetControllerImpl.getMesh(): size not null but couldn't read Mesh");
        } catch (Throwable e2) {
            lg.error(e2.getMessage(), e2);
            if (lg.isWarnEnabled())
                lg.warn("DataSetControllerImpl.getMesh(): error creating dummy mesh: " + e2.getMessage());
            VCMongoMessage.sendTrace("DataSetControllerImpl.getMesh(" + vcdID.getID() + ")  <<EXIT null>>");
            return null;
        }
    } else {
        VCMongoMessage.sendTrace("DataSetControllerImpl.getMesh(" + vcdID.getID() + ")  <<EXIT non-null>>");
        return mesh;
    }
}