Examples with ISize org.vcell.util.ISize used on opensource projects

Example 86 with ISize

use of org.vcell.util.ISize 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 87 with ISize

use of org.vcell.util.ISize 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 88 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class SimulationTask method getEstimatedMemorySizeMB.

public double getEstimatedMemorySizeMB() {
    // 
    // calculate number of PDE variables and total number of spatial variables
    // 
    SimulationSymbolTable simSymbolTable = getSimulationJob().getSimulationSymbolTable();
    Simulation simulation = simSymbolTable.getSimulation();
    MathDescription mathDescription = simulation.getMathDescription();
    int pdeVarCount = 0;
    int odeVarCount = 0;
    Variable[] variables = simSymbolTable.getVariables();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof VolVariable) {
            if (mathDescription.isPDE((VolVariable) variables[i])) {
                pdeVarCount++;
            } else {
                odeVarCount++;
            }
        } else if (variables[i] instanceof MemVariable) {
            if (mathDescription.isPDE((MemVariable) variables[i])) {
                pdeVarCount++;
            } else {
                odeVarCount++;
            }
        }
    }
    long numMeshPoints = 1;
    if (simulation.isSpatial()) {
        ISize samplingSize = simulation.getMeshSpecification().getSamplingSize();
        numMeshPoints = samplingSize.getX() * samplingSize.getY() * samplingSize.getZ();
    }
    // 180 bytes per pde variable plus ode per mesh point + 15M overhead
    // there is 70M PBS overhead which will be added when submitted to pbs
    double est = ((180 * pdeVarCount + 16 * odeVarCount) * numMeshPoints / 1e6 + 15);
    if (simulation.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
        est *= 2;
    }
    return est;
}

Example 89 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class DataSetControllerImpl method iterateHDF5.

private static void iterateHDF5(HObject hObject, String indent, DataProcessingHelper dataProcessingHelper) throws Exception {
    if (hObject instanceof Group) {
        Group group = ((Group) hObject);
        printInfo(group, indent);
        if (group.getName().equals("/") || group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_POSTPROCESSING)) {
            List<HObject> postProcessMembers = ((Group) hObject).getMemberList();
            for (HObject nextHObject : postProcessMembers) {
                iterateHDF5(nextHObject, indent + " ", dataProcessingHelper);
            }
        } else if (group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_VARIABLESTATISTICS) && dataProcessingHelper.isInfoOnly()) {
            populateStatNamesAndUnits(hObject, dataProcessingHelper);
            List<HObject> statDataAtEachTime = group.getMemberList();
            dataProcessingHelper.statValues = new double[dataProcessingHelper.statVarNames.length][statDataAtEachTime.size()];
            for (HObject nextStatData : statDataAtEachTime) {
                printInfo(nextStatData, indent + " ");
                // always get stats data when ask for info
                processDims(nextStatData, dataProcessingHelper, false);
                double[] stats = (double[]) dataProcessingHelper.tempData;
                int timeIndex = Integer.parseInt(nextStatData.getName().substring("time".length()));
                for (int j = 0; j < stats.length; j++) {
                    dataProcessingHelper.statValues[j][timeIndex] = stats[j];
                }
            }
        } else {
            // must be image data
            if (dataProcessingHelper.isInfoOnly()) {
                dataProcessingHelper.imageNames = new ArrayList<String>();
                dataProcessingHelper.imageISize = new ArrayList<ISize>();
                dataProcessingHelper.imageOrigin = new ArrayList<Origin>();
                dataProcessingHelper.imageExtent = new ArrayList<Extent>();
                Origin imgDataOrigin;
                Extent imgDataExtent;
                HashMap<String, String> attrHashMap = getHDF5Attributes(group);
                if (attrHashMap.size() == 2) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), 0, 0);
                    // this is 1D, however the extentY, Z cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), 1, 1);
                } else if (attrHashMap.size() == 4) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), 0);
                    // this is 2D, however the extentZ cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), 1);
                } else if (attrHashMap.size() == 6) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINZ)));
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTZ)));
                } else {
                    throw new Exception("Unexpected number of origin/extent values");
                }
                dataProcessingHelper.imageNames.add(hObject.getName());
                dataProcessingHelper.imageOrigin.add(imgDataOrigin);
                dataProcessingHelper.imageExtent.add(imgDataExtent);
                // get ISize
                processDims((H5ScalarDS) (((Group) hObject).getMemberList()).get(0), dataProcessingHelper, true);
                long[] dims = dataProcessingHelper.tempDims;
                ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                dataProcessingHelper.imageISize.add(isize);
            } else {
                int currentVarNameIndex = -1;
                for (int i = 0; i < dataProcessingHelper.specificVarNames.length; i++) {
                    if (group.getName().equals(dataProcessingHelper.specificVarNames[i])) {
                        currentVarNameIndex = i;
                        break;
                    }
                }
                if (currentVarNameIndex == -1) {
                    // skip this group
                    return;
                }
                dataProcessingHelper.specificDataValues[currentVarNameIndex] = new double[(dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? dataProcessingHelper.times.length : dataProcessingHelper.specificTimePointHelper.getTimePoints().length)][];
                List<HObject> imageDataAtEachTime = ((Group) hObject).getMemberList();
                int foundTimePointIndex = 0;
                for (HObject nextImageData : imageDataAtEachTime) {
                    // if(dataProcessingHelper.isInfoOnly()){
                    // printInfo(nextImageData,indent+" ");
                    // processDims(nextImageData, dataProcessingHelper,true);
                    // long[] dims = dataProcessingHelper.tempDims;
                    // ISize isize = new ISize((int)dims[0], (int)(dims.length>1?dims[1]:1), (int)(dims.length>2?dims[2]:1));
                    // dataProcessingHelper.imageISize.add(isize);
                    // break;//only need 1st one for info
                    // }else{
                    int hdf5GroupTimeIndex = Integer.parseInt(nextImageData.getName().substring(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMEPREFIX.length()));
                    if (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() || dataProcessingHelper.specificTimePointHelper.getTimePoints()[foundTimePointIndex] == dataProcessingHelper.times[hdf5GroupTimeIndex]) {
                        int timeIndex = (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? hdf5GroupTimeIndex : foundTimePointIndex);
                        processDims(nextImageData, dataProcessingHelper, false);
                        long[] dims = dataProcessingHelper.tempDims;
                        ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                        if (dataProcessingHelper.specificDataIndexHelper.isAllDataIndexes()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = (double[]) dataProcessingHelper.tempData;
                        } else if (dataProcessingHelper.specificDataIndexHelper.isSingleSlice()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[isize.getX() * isize.getY()];
                            System.arraycopy((double[]) dataProcessingHelper.tempData, dataProcessingHelper.specificDataIndexHelper.getSliceIndex() * (isize.getX() * isize.getY()), dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex], 0, isize.getX() * isize.getY());
                        } else {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length];
                            for (int i = 0; i < dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length; i++) {
                                dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex][i] = ((double[]) dataProcessingHelper.tempData)[dataProcessingHelper.specificDataIndexHelper.getDataIndexes()[i]];
                            }
                        }
                        foundTimePointIndex++;
                        if (!dataProcessingHelper.specificTimePointHelper.isAllTimePoints() && foundTimePointIndex == dataProcessingHelper.specificTimePointHelper.getTimePoints().length) {
                            // break out after we get our data
                            break;
                        }
                    }
                // }
                }
            }
        }
    } else if (hObject instanceof Dataset) {
        Dataset dataset = (Dataset) hObject;
        printInfo(dataset, indent);
        if (dataset.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMES)) {
            processDims(hObject, dataProcessingHelper, false);
            dataProcessingHelper.times = (double[]) dataProcessingHelper.tempData;
        }
    } else if (hObject instanceof Datatype) {
        printInfo(hObject, indent);
    } else {
        printInfo(hObject, indent);
    }
}

Example 90 with ISize

use of org.vcell.util.ISize 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());
    }
}