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

Example 46 with GeometryInfo

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

the class VCDatabaseScanner method scanGeometries.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void scanGeometries(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleGeometryKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning geometries......");
        logFilePrintStream.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            GeometryInfo[] geoInfos = dbServerImpl.getGeometryInfos(user, false);
            for (int j = 0; j < geoInfos.length; j++) {
                if (singleGeometryKey != null && !geoInfos[j].getVersion().getVersionKey().compareEqual(singleGeometryKey)) {
                    System.out.println("skipping geometry, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterGeometry(geoInfos[j])) {
                    continue;
                }
                try {
                    BigString geometryXML = dbServerImpl.getGeometryXML(user, geoInfos[j].getVersion().getVersionKey());
                    Geometry geometry = cbit.vcell.xml.XmlHelper.XMLToGeometry(new XMLSource(geometryXML.toString()));
                    geometry.refreshDependencies();
                    databaseVisitor.visitGeometry(geometry, logFilePrintStream);
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        System.err.println("error writing to log file.");
    }
}

Example 47 with GeometryInfo

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

the class GeometryTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con) throws SQLException, DataAccessException {
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    int dim = rset.getInt(GeometryTable.table.dimension.toString());
    double oX = rset.getBigDecimal(GeometryTable.table.originX.toString()).doubleValue();
    double oY = rset.getBigDecimal(GeometryTable.table.originY.toString()).doubleValue();
    double oZ = rset.getBigDecimal(GeometryTable.table.originZ.toString()).doubleValue();
    org.vcell.util.Origin origin = new org.vcell.util.Origin(oX, oY, oZ);
    double extentX = rset.getBigDecimal(ExtentTable.table.extentX.toString()).doubleValue();
    double extentY = rset.getBigDecimal(ExtentTable.table.extentY.toString()).doubleValue();
    double extentZ = rset.getBigDecimal(ExtentTable.table.extentZ.toString()).doubleValue();
    org.vcell.util.Extent extent = new org.vcell.util.Extent(extentX, extentY, extentZ);
    KeyValue imgRef = null;
    java.math.BigDecimal bigDecimal = rset.getBigDecimal(GeometryTable.table.imageRef.toString());
    if (!rset.wasNull()) {
        imgRef = new KeyValue(bigDecimal);
    }
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    GeometryInfo geomInfo = new GeometryInfo(version, dim, extent, origin, imgRef, VCellSoftwareVersion.fromString(softwareVersion));
    return geomInfo;
/*GeometryInfo geomInfo = new GeometryInfo();

	geomInfo.dimension = rset.getInt(GeometryTable.dimension.toString());
	geomInfo.originX = rset.getDouble(GeometryTable.originX.toString());
	geomInfo.originY = rset.getDouble(GeometryTable.originY.toString());
	geomInfo.originZ = rset.getDouble(GeometryTable.originZ.toString());
	geomInfo.extentRef = new KeyValue(rset.getBigDecimal(GeometryTable.extentRef.toString(), 0));
	geomInfo.imageRef = new KeyValue(rset.getBigDecimal(GeometryTable.imageRef.toString(), 0));

	geomInfo.version = getVersion(rset,log);
	
	return geomInfo;
	*/
}