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

Example 56 with Extent

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

the class SimulationSummaryPanel method displayOther.

/**
 * Comment
 */
private void displayOther() {
    boolean isSpatial = getSimulation().isSpatial();
    try {
        getJLabel8().setVisible(isSpatial);
        getJLabelGeometrySize().setVisible(isSpatial);
        Extent extent = getSimulation().getMathDescription().getGeometry().getExtent();
        String labelText = "";
        switch(getSimulation().getMathDescription().getGeometry().getDimension()) {
            case 0:
                {
                    break;
                }
            case 1:
                {
                    labelText = extent.getX() + " microns";
                    break;
                }
            case 2:
                {
                    labelText = "(" + extent.getX() + "," + extent.getY() + ") microns";
                    break;
                }
            case 3:
                {
                    labelText = "(" + extent.getX() + "," + extent.getY() + "," + extent.getZ() + ") microns";
                    break;
                }
        }
        getJLabelGeometrySize().setText(labelText);
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelGeometrySize().setText("");
    }
}

Example 57 with Extent

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

the class CartesianMeshChombo method readMeshFile.

public static CartesianMeshChombo readMeshFile(File chomboMeshFile) throws Exception {
    CartesianMeshChombo chomboMesh = new CartesianMeshChombo();
    if (H5.H5open() < 0) {
        throw new Exception("H5.H5open() failed");
    }
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        throw new Exception("FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5) failed, returned null.");
    }
    FileFormat meshFile = null;
    try {
        meshFile = fileFormat.createInstance(chomboMeshFile.getAbsolutePath(), FileFormat.READ);
        meshFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group meshGroup = (Group) rootGroup.getMemberList().get(0);
        List<Attribute> meshAttrList = meshGroup.getMetadata();
        for (Attribute attr : meshAttrList) {
            String attrName = attr.getName();
            MeshAttribute mattr = null;
            try {
                mattr = MeshAttribute.valueOf(attrName);
            } catch (IllegalArgumentException ex) {
            }
            if (mattr == null) {
                // if not found, then we don't care about this attribute
                logger.debug("mesh attribute " + attrName + " is not defined in Java");
                continue;
            }
            Object value = attr.getValue();
            switch(mattr) {
                case dimension:
                    chomboMesh.dimension = ((int[]) value)[0];
                    break;
                case numLevels:
                    chomboMesh.numLevels = ((int[]) value)[0];
                    break;
                case viewLevel:
                    chomboMesh.viewLevel = ((int[]) value)[0];
                    break;
                case refineRatios:
                    chomboMesh.refineRatios = (int[]) value;
                    break;
                case Dx:
                case extent:
                case Nx:
                case origin:
                    // these 4 has format of {};
                    String[] valueStrArray = (String[]) value;
                    String value0 = valueStrArray[0];
                    StringTokenizer st = new StringTokenizer(value0, "{,} ");
                    int numTokens = st.countTokens();
                    // we need 3 for 3d
                    double[] values = new double[Math.max(3, numTokens)];
                    for (int i = 0; i < Math.min(3, numTokens); ++i) {
                        String token = st.nextToken();
                        values[i] = Double.parseDouble(token);
                    }
                    switch(mattr) {
                        case Dx:
                            chomboMesh.dx = new double[3];
                            System.arraycopy(values, 0, chomboMesh.dx, 0, values.length);
                            break;
                        case extent:
                            chomboMesh.extent = new Extent(values[0], values[1], values[2] == 0 ? 1 : values[2]);
                            break;
                        case Nx:
                            chomboMesh.size = new ISize((int) values[0], (int) values[1], values[2] == 0 ? 1 : (int) values[2]);
                            break;
                        case origin:
                            chomboMesh.origin = new Origin(values[0], values[1], values[2]);
                            break;
                    }
                    break;
            }
        }
        List<HObject> memberList = meshGroup.getMemberList();
        for (HObject member : memberList) {
            if (!(member instanceof Dataset)) {
                continue;
            }
            Dataset dataset = (Dataset) member;
            Vector vectValues = (Vector) dataset.read();
            String name = dataset.getName();
            MeshDataSet mdataset = null;
            try {
                mdataset = MeshDataSet.valueOfName(name);
            } catch (IllegalArgumentException ex) {
                logger.debug("mesh dataset " + name + " is not defined in Java");
            }
            if (mdataset == null) {
                // if not found, then we don't care about this dataset
                continue;
            }
            switch(mdataset) {
                case vertices:
                    collectVertices(chomboMesh, vectValues);
                    break;
                case segments:
                    collect2dSegments(chomboMesh, vectValues);
                    break;
                case structures:
                    collectStructures(chomboMesh, vectValues);
                    break;
                case featurephasevols:
                    collectFeaturePhaseVols(chomboMesh, vectValues);
                    break;
                case membraneids:
                    collectMembraneIds(chomboMesh, vectValues);
                    break;
                case membrane_elements:
                case membrane_elements_old:
                    collectMembraneElements(chomboMesh, vectValues);
                    break;
                case surface_triangles:
                    collect3dSurfaceTriangles(chomboMesh, vectValues);
                    break;
                case slice_view:
                    collect3dSliceView(chomboMesh, vectValues);
                    break;
            }
        }
    } finally {
        if (meshFile != null) {
            meshFile.close();
        }
    }
    // set neighbors to membrane elements
    if (chomboMesh.dimension == 2 && chomboMesh.membraneElements != null) {
        for (int i = 0; i < chomboMesh.membraneElements.length; ++i) {
            MembraneElement me = chomboMesh.membraneElements[i];
            me.setConnectivity(chomboMesh.segments[i].prevNeigbhor, chomboMesh.segments[i].nextNeigbhor, -1, -1);
        }
    }
    return chomboMesh;
}

Example 58 with Extent

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

the class ChomboMeshARGenerator method main.

public static void main(String[] args) {
    ChomboMeshARGenerator generator = new ChomboMeshARGenerator();
    Extent extent = new Extent(1.175, 7.333, 2);
    generator.findMyAR(2, extent);
}

Example 59 with Extent

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

the class RefinementRoi method getDx.

public double getDx(Simulation simulation) {
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    ISize levelSize = simulation.getSolverTaskDescription().getChomboSolverSpec().getLevelSamplingSize(simulation.getMeshSpecification().getSamplingSize(), level);
    return extent.getX() / levelSize.getX();
}

Example 60 with Extent

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

the class FieldDataGUIPanel method copyMethod.

private void copyMethod(int copyMode) {
    String delimiter = "";
    if (copyMode == COPY_NL) {
        delimiter = "\n";
    } else if (copyMode == COPY_CRNL) {
        delimiter = "\r\n";
    } else if (copyMode == COPY_CSV) {
        delimiter = ",";
    } else if (copyMode == COPY_SPACE) {
        delimiter = " ";
    }
    String copyString = "";
    javax.swing.tree.TreePath selPath = getJTree1().getSelectionPath();
    if (selPath != null) {
        javax.swing.tree.DefaultMutableTreeNode lastPathComponent = (javax.swing.tree.DefaultMutableTreeNode) selPath.getLastPathComponent();
        if (lastPathComponent.equals(getJTree1().getModel().getRoot())) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataMainList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).externalDataIdentifier.getName();
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataOriginList) {
            Origin origin = ((FieldDataOriginList) lastPathComponent.getUserObject()).origin;
            copyString = origin.getX() + delimiter + origin.getY() + delimiter + origin.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataExtentList) {
            Extent extent = ((FieldDataExtentList) lastPathComponent.getUserObject()).extent;
            copyString = extent.getX() + delimiter + extent.getY() + delimiter + extent.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataISizeList) {
            ISize isize = ((FieldDataISizeList) lastPathComponent.getUserObject()).isize;
            copyString = isize.getX() + delimiter + isize.getY() + delimiter + isize.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataTimeList) {
            double[] times = ((FieldDataTimeList) lastPathComponent.getUserObject()).times;
            for (int i = 0; i < times.length; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += times[i] + "";
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataMainList) {
            ExternalDataIdentifier extDataID = ((FieldDataMainList) lastPathComponent.getUserObject()).externalDataIdentifier;
            copyString = extDataID.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarList) {
            DataIdentifier dataIdentifier = ((FieldDataVarList) lastPathComponent.getUserObject()).dataIdentifier;
            copyString = dataIdentifier.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarMainList) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataVarList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).dataIdentifier.getName();
            }
        }
        if (copyString.length() > 0) {
            VCellTransferable.sendToClipboard(copyString);
        }
    }
}