Examples with SubVolume cbit.vcell.geometry.SubVolume used on opensource projects

Example 31 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeChomboSpec.

private void writeChomboSpec() throws ExpressionException, SolverException, PropertyVetoException, ClassNotFoundException, IOException, GeometryException, ImageException {
    if (!bChomboSolver) {
        return;
    }
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    int dimension = geometrySpec.getDimension();
    if (dimension == 1) {
        throw new SolverException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " is only supported for simulations with 2D or 3D geometry.");
    }
    Simulation simulation = getSimulationTask().getSimulation();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    ChomboSolverSpec chomboSolverSpec = solverTaskDescription.getChomboSolverSpec();
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_BEGIN);
    printWriter.println(FVInputFileKeyword.DIMENSION + " " + geometrySpec.getDimension());
    Extent extent = geometrySpec.getExtent();
    Origin origin = geometrySpec.getOrigin();
    ISize isize = simulation.getMeshSpecification().getSamplingSize();
    switch(geometrySpec.getDimension()) {
        case 2:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY());
            break;
        case 3:
            printWriter.println(FVInputFileKeyword.MESH_SIZE + " " + isize.getX() + " " + isize.getY() + " " + isize.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_SIZE + " " + extent.getX() + " " + extent.getY() + " " + extent.getZ());
            printWriter.println(FVInputFileKeyword.DOMAIN_ORIGIN + " " + origin.getX() + " " + origin.getY() + " " + origin.getZ());
            break;
    }
    List<CompartmentSubDomain> featureList = new ArrayList<CompartmentSubDomain>();
    Enumeration<SubDomain> enum1 = simulation.getMathDescription().getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            featureList.add((CompartmentSubDomain) sd);
        }
    }
    int numFeatures = featureList.size();
    CompartmentSubDomain[] features = featureList.toArray(new CompartmentSubDomain[0]);
    int[] phases = new int[numFeatures];
    Arrays.fill(phases, -1);
    phases[numFeatures - 1] = 0;
    int[] numAssigned = new int[] { 1 };
    assignPhases(features, numFeatures - 1, phases, numAssigned);
    Map<String, Integer> subDomainPhaseMap = new HashMap<String, Integer>();
    for (int i = 0; i < phases.length; ++i) {
        if (phases[i] == -1) {
            throw new SolverException("Failed to assign a phase to CompartmentSubdomain '" + features[i].getName() + "'. It might be caused by too coarsh a mesh.");
        }
        subDomainPhaseMap.put(features[i].getName(), phases[i]);
    }
    SubVolume[] subVolumes = geometrySpec.getSubVolumes();
    if (geometrySpec.hasImage()) {
        Geometry geometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
        Geometry simGeometry = geometry;
        VCImage img = geometry.getGeometrySpec().getImage();
        int factor = Math.max(Math.max(img.getNumX(), img.getNumY()), img.getNumZ()) < 512 ? 2 : 1;
        ISize distanceMapMeshSize = new ISize(img.getNumX() * factor, img.getNumY() * factor, img.getNumZ() * factor);
        Vect3d deltaX = null;
        boolean bCellCentered = false;
        double dx = 0.5;
        double dy = 0.5;
        double dz = 0.5;
        int Nx = distanceMapMeshSize.getX();
        int Ny = distanceMapMeshSize.getY();
        int Nz = distanceMapMeshSize.getZ();
        if (dimension == 2) {
            // pad the 2D image with itself in order to obtain a 3D image used to compute the distance map
            // because the distance map algorithm is 3D only (using distance to triangles)
            byte[] oldPixels = img.getPixels();
            byte[] newPixels = new byte[oldPixels.length * 3];
            System.arraycopy(oldPixels, 0, newPixels, 0, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length, oldPixels.length);
            System.arraycopy(oldPixels, 0, newPixels, oldPixels.length * 2, oldPixels.length);
            double distX = geometry.getExtent().getX() / img.getNumX();
            double distY = geometry.getExtent().getY() / img.getNumY();
            // we set the distance on the z axis to something that makes sense
            double distZ = Math.max(distX, distY);
            Extent newExtent = new Extent(geometry.getExtent().getX(), geometry.getExtent().getY(), distZ * 3);
            VCImage newImage = new VCImageUncompressed(null, newPixels, newExtent, img.getNumX(), img.getNumY(), 3);
            // copy the pixel classes too
            ArrayList<VCPixelClass> newPixelClasses = new ArrayList<VCPixelClass>();
            for (VCPixelClass origPixelClass : geometry.getGeometrySpec().getImage().getPixelClasses()) {
                SubVolume origSubvolume = geometry.getGeometrySpec().getImageSubVolumeFromPixelValue(origPixelClass.getPixel());
                newPixelClasses.add(new VCPixelClass(null, origSubvolume.getName(), origPixelClass.getPixel()));
            }
            newImage.setPixelClasses(newPixelClasses.toArray(new VCPixelClass[newPixelClasses.size()]));
            simGeometry = new Geometry(geometry, newImage);
            Nz = 3;
        }
        GeometrySpec simGeometrySpec = simGeometry.getGeometrySpec();
        Extent simExtent = simGeometrySpec.getExtent();
        dx = simExtent.getX() / (Nx - 1);
        dy = simExtent.getY() / (Ny - 1);
        dz = simExtent.getZ() / (Nz - 1);
        if (Math.abs(dx - dy) > 0.1 * Math.max(dx, dy)) {
            dx = Math.min(dx, dy);
            dy = dx;
            Nx = (int) (simExtent.getX() / dx + 1);
            Ny = (int) (simExtent.getY() / dx + 1);
            if (dimension == 3) {
                dz = dx;
                Nz = (int) (simExtent.getZ() / dx + 1);
            }
        }
        deltaX = new Vect3d(dx, dy, dz);
        // one more point in each direction
        distanceMapMeshSize = new ISize(Nx + 1, Ny + 1, Nz + 1);
        Extent distanceMapExtent = new Extent(simExtent.getX() + dx, simExtent.getY() + dy, simExtent.getZ() + dz);
        simGeometrySpec.setExtent(distanceMapExtent);
        GeometrySurfaceDescription geoSurfaceDesc = simGeometry.getGeometrySurfaceDescription();
        geoSurfaceDesc.setVolumeSampleSize(distanceMapMeshSize);
        geoSurfaceDesc.updateAll();
        VCImage vcImage = RayCaster.sampleGeometry(simGeometry, distanceMapMeshSize, bCellCentered);
        SubvolumeSignedDistanceMap[] distanceMaps = DistanceMapGenerator.computeDistanceMaps(simGeometry, vcImage, bCellCentered);
        if (dimension == 2) {
            distanceMaps = DistanceMapGenerator.extractMiddleSlice(distanceMaps);
        }
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + simGeometrySpec.getNumSubVolumes() + " " + FVInputFileKeyword.DISTANCE_MAP);
        for (int i = 0; i < subVolumes.length; i++) {
            File distanceMapFile = new File(workingDirectory, getSimulationTask().getSimulationJobID() + "_" + subVolumes[i].getName() + DISTANCE_MAP_FILE_EXTENSION);
            writeDistanceMapFile(deltaX, distanceMaps[i], distanceMapFile);
            int phase = subDomainPhaseMap.get(subVolumes[i].getName());
            printWriter.println(subVolumes[i].getName() + " " + phase + " " + distanceMapFile.getAbsolutePath());
        }
    } else {
        printWriter.println(FVInputFileKeyword.SUBDOMAINS + " " + geometrySpec.getNumSubVolumes());
        Expression[] rvachevExps = convertAnalyticGeometryToRvachevFunction(geometrySpec);
        for (int i = 0; i < subVolumes.length; i++) {
            if (subVolumes[i] instanceof AnalyticSubVolume) {
                String name = subVolumes[i].getName();
                int phase = subDomainPhaseMap.get(name);
                printWriter.println(name + " " + phase + " ");
                printWriter.println(FVInputFileKeyword.IF + " " + rvachevExps[i].infix() + ";");
                printWriter.println(FVInputFileKeyword.USER + " " + ((AnalyticSubVolume) subVolumes[i]).getExpression().infix() + ";");
            }
        }
    }
    printWriter.println(FVInputFileKeyword.MAX_BOX_SIZE + " " + chomboSolverSpec.getMaxBoxSize());
    printWriter.println(FVInputFileKeyword.FILL_RATIO + " " + chomboSolverSpec.getFillRatio());
    printWriter.println(FVInputFileKeyword.RELATIVE_TOLERANCE + " " + simulation.getSolverTaskDescription().getErrorTolerance().getRelativeErrorTolerance());
    printWriter.println(FVInputFileKeyword.SAVE_VCELL_OUTPUT + " " + chomboSolverSpec.isSaveVCellOutput());
    printWriter.println(FVInputFileKeyword.SAVE_CHOMBO_OUTPUT + " " + chomboSolverSpec.isSaveChomboOutput());
    printWriter.println(FVInputFileKeyword.ACTIVATE_FEATURE_UNDER_DEVELOPMENT + " " + chomboSolverSpec.isActivateFeatureUnderDevelopment());
    printWriter.println(FVInputFileKeyword.SMALL_VOLFRAC_THRESHOLD + " " + chomboSolverSpec.getSmallVolfracThreshold());
    printWriter.println(FVInputFileKeyword.BLOCK_FACTOR + " " + chomboSolverSpec.getBlockFactor());
    printWriter.println(FVInputFileKeyword.TAGS_GROW + " " + chomboSolverSpec.getTagsGrow());
    // Refinement
    int numLevels = chomboSolverSpec.getNumRefinementLevels();
    // Refinements #Levels ratio 1, ratio 2, etc
    printWriter.print(FVInputFileKeyword.REFINEMENTS + " " + (numLevels + 1));
    List<Integer> ratios = chomboSolverSpec.getRefineRatioList();
    for (int i : ratios) {
        printWriter.print(" " + i);
    }
    // write last refinement ratio, fake
    printWriter.println(" 2");
    // membrane rois
    List<RefinementRoi> memRios = chomboSolverSpec.getMembraneRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Membrane + " " + memRios.size());
    for (RefinementRoi roi : memRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        // level tagsGrow ROIexpression
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    List<RefinementRoi> volRios = chomboSolverSpec.getVolumeRefinementRois();
    printWriter.println(FVInputFileKeyword.REFINEMENT_ROIS + " " + RoiType.Volume + " " + volRios.size());
    for (RefinementRoi roi : volRios) {
        if (roi.getRoiExpression() == null) {
            throw new SolverException("ROI expression cannot be null");
        }
        printWriter.println(roi.getLevel() + " " + roi.getRoiExpression().infix() + ";");
    }
    printWriter.println(FVInputFileKeyword.VIEW_LEVEL + " " + chomboSolverSpec.getViewLevel());
    printWriter.println(FVInputFileKeyword.CHOMBO_SPEC_END);
    printWriter.println();
}

Example 32 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class OutputFunctionContext method getAutoCompleteSymbolFilter.

public AutoCompleteSymbolFilter getAutoCompleteSymbolFilter(final Domain functionDomain) {
    AutoCompleteSymbolFilter stef = new AutoCompleteSymbolFilter() {

        public boolean accept(SymbolTableEntry ste) {
            if (simulationOwner.getGeometry().getDimension() > 0) {
                if (functionDomain == null) {
                    return true;
                }
                if (ste.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX) || ste.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    return false;
                }
                if (ste instanceof ReservedVariable) {
                    return true;
                }
                if (ste instanceof AnnotatedFunction) {
                    return functionDomain.compareEqual(((AnnotatedFunction) ste).getDomain());
                }
                if (ste instanceof Variable) {
                    Variable var = (Variable) ste;
                    if (var.getDomain() == null) {
                        return true;
                    }
                    GeometryClass gc = simulationOwner.getGeometry().getGeometryClass(functionDomain.getName());
                    GeometryClass vargc = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    if (gc instanceof SurfaceClass && vargc instanceof SubVolume) {
                        if (((SurfaceClass) gc).isAdjacentTo((SubVolume) vargc)) {
                            return true;
                        } else {
                            return false;
                        }
                    } else {
                        return var.getDomain().compareEqual(functionDomain);
                    }
                }
            }
            return true;
        }

        public boolean acceptFunction(String funcName) {
            return true;
        }
    };
    return stef;
}

Example 33 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class OutputFunctionContext method computeFunctionTypeWRTExpression.

// check if the new expression is valid for outputFunction of functionType
public VariableType computeFunctionTypeWRTExpression(AnnotatedFunction outputFunction, Expression exp) throws ExpressionException, InconsistentDomainException {
    MathDescription mathDescription = getSimulationOwner().getMathDescription();
    boolean bSpatial = getSimulationOwner().getGeometry().getDimension() > 0;
    if (!bSpatial) {
        return VariableType.NONSPATIAL;
    }
    Expression newexp = new Expression(exp);
    // making sure that output function is not direct function of constant.
    newexp.bindExpression(this);
    // here use math description as symbol table because we allow
    // new expression itself to be function of constant.
    newexp = MathUtilities.substituteFunctions(newexp, this).flatten();
    String[] symbols = newexp.getSymbols();
    VariableType functionType = outputFunction.getFunctionType();
    String funcName = outputFunction.getName();
    Domain funcDomain = outputFunction.getDomain();
    VariableType[] varTypes = null;
    if (symbols != null && symbols.length > 0) {
        // making sure that new expression is defined in the same domain
        varTypes = new VariableType[symbols.length];
        for (int i = 0; i < symbols.length; i++) {
            if (ReservedMathSymbolEntries.getReservedVariableEntry(symbols[i]) != null) {
                varTypes[i] = functionType;
            } else {
                Variable var = mathDescription.getVariable(symbols[i]);
                if (var == null) {
                    var = mathDescription.getPostProcessingBlock().getDataGenerator(symbols[i]);
                }
                varTypes[i] = VariableType.getVariableType(var);
                if (funcDomain != null) {
                    if (var.getDomain() == null) {
                        // OK
                        continue;
                    }
                    GeometryClass funcGeoClass = simulationOwner.getGeometry().getGeometryClass(funcDomain.getName());
                    GeometryClass varGeoClass = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    if (varGeoClass instanceof SubVolume && funcGeoClass instanceof SurfaceClass) {
                        // seems ok if membrane refereces volume
                        if (!((SurfaceClass) funcGeoClass).isAdjacentTo((SubVolume) varGeoClass)) {
                            // but has to be adjacent
                            String errMsg = "'" + funcName + "' defined on Membrane '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on Volume '" + var.getDomain().getName() + " which is not adjacent to Membrane '" + funcDomain.getName() + "'.";
                            throw new ExpressionException(errMsg);
                        }
                    } else if (!var.getDomain().compareEqual(funcDomain)) {
                        String errMsg = "'" + funcName + "' defined on '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on '" + var.getDomain().getName() + ".";
                        throw new ExpressionException(errMsg);
                    }
                }
            }
        }
    }
    // if there are no variables (like built in function, vcRegionArea), check with flattened expression to find out the variable type of the new expression
    VariableDomain functionVariableDomain = functionType.getVariableDomain();
    Function flattenedFunction = new Function(funcName, newexp, funcDomain);
    flattenedFunction.bind(this);
    VariableType newVarType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, bSpatial);
    if (!newVarType.getVariableDomain().equals(functionVariableDomain)) {
        String errMsg = "The expression for '" + funcName + "' includes at least one " + newVarType.getVariableDomain().getName() + " variable. Please make sure that only " + functionVariableDomain.getName() + " variables are " + "referenced in " + functionVariableDomain.getName() + " output functions.";
        throw new ExpressionException(errMsg);
    }
    return newVarType;
}

Example 34 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class GeometrySubVolumePanel method geometrySubVolumePanel_Initialize.

/**
 * Comment
 */
private void geometrySubVolumePanel_Initialize() {
    getScrollPaneTable().setDefaultRenderer(SubVolume.class, new GeometrySubVolumeTableCellRenderer());
    getScrollPaneTable().setDefaultEditor(SubVolume.class, new DefaultCellEditor(new JTextField()) {

        private int lastRow = -1;

        private int lastCol = -1;

        public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column) {
            lastRow = row;
            lastCol = column;
            delegate.setValue(((SubVolume) value).getName());
            return editorComponent;
        }

        public final boolean stopCellEditing() {
            // 
            try {
                String name = (String) delegate.getCellEditorValue();
                while (true) {
                    if (name.equals(TokenMangler.fixTokenStrict(name))) {
                        break;
                    }
                    name = DialogUtils.showInputDialog0(getComponent(), "Subdomain name " + name + " has illegal characters." + "\nProvide new value.", name);
                }
                // VALIDATE_OK, delegate gets New Good value
                delegate.setValue(name);
            } catch (UtilCancelException e) {
                // delegate gets Last Good value
                delegate.setValue(((SubVolume) getScrollPaneTable().getValueAt(lastRow, lastCol)).getName());
            } catch (Throwable e) {
            // Delegate keeps UNVALIDATED value
            }
            return super.stopCellEditing();
        }
    });
    getScrollPaneTable().setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
    refreshButtons();
}

Example 35 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class GeometrySubVolumeTableCellRenderer method getTableCellRendererComponent.

public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    if (value instanceof SubVolume) {
        SubVolume subVolume = (SubVolume) value;
        java.awt.Color handleColor = new java.awt.Color(colormap[subVolume.getHandle()]);
        setIcon(new ColorIcon(15, 15, handleColor));
        setText(subVolume.getName());
    }
    return this;
}