GeoTessModelGA.java

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package gov.sandia.geotess.examples.customdata;
 
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
 
import gov.sandia.geotess.GeoTessException;
import gov.sandia.geotess.GeoTessGrid;
import gov.sandia.geotess.GeoTessMetaData;
import gov.sandia.geotess.GeoTessModel;
import gov.sandia.geotess.GeoTessUtils;
 
public class GeoTessModelGA extends GeoTessModel {
 
 /**
  * A list of all the station names supported by this model
  */
 protected String[] stationNames;
 
 /**
  * A list of all the phase names supported by this model.
  */
 private SeismicPhase[] phaseNames;
 
 /**
  * A list of all the attributes supported by this model.
  * All of these attributes will have values in each PhaseData map and will
  * be read from, and written to the output files.
  */
 private GeoAttributes[] attributes;
 
 /**
  * Map from index -> [Station Name, Phase Name, Attribute Name]
  * Includes every combination of station - phase - attribute.
  * Size equals nStations * nPhases * nAttributes.
  */
 private List<Triple> indexList;
 
 /**
  * Map from station -> phase -> attribute -> attribute index
  * Includes every combination of station - phase - attribute.
  * Maximum index equals nStations * nPhases * nAttributes -1.
  */
 private Map<String, Map<SeismicPhase,Map<GeoAttributes, Integer>>> indexMap;
 
 /**
  * Construct a new GeoTessModel object and populate it with information from
  * the specified file.
  * 
  * @param modelInputFile
  *            name of file containing the model.
  * @param relativeGridPath
  *            the relative path from the directory where the model is stored
  *            to the directory where the grid is stored. Often, the model
  *            and grid are stored together in the same file in which case
  *            this parameter is ignored. Sometimes, however, the grid is
  *            stored in a separate file and only the name of the grid file
  *            (without path information) is stored in the model file. In
  *            this case, the code needs to know which directory to search
  *            for the grid file. The default is "" (empty string), which
  *            will cause the code to search for the grid file in the same
  *            directory in which the model file resides. Bottom line is that
  *            the default value is appropriate when the grid is stored in
  *            the same file as the model, or the model file is in the same
  *            directory as the model file.
  * @throws IOException
  */
 public GeoTessModelGA(File modelInputFile, String relativeGridPath) throws IOException
 { 
  super(); 
  loadModel(modelInputFile, relativeGridPath);
 }
 
 /**
  * Construct a new GeoTessModel object and populate it with information from
  * the specified file.
  * 
  * <p>relativeGridPath is assumed to be "" (empty string), which is appropriate
  * when the grid information is stored in the same file as the model or when
  * the grid is stored in a separate file located in the same directory as the
  * model file.
  * 
  * @param modelInputFile
  *            name of file containing the model.
  * @throws IOException
  */
 public GeoTessModelGA(File modelInputFile) throws IOException
 { 
  super(); 
  loadModel(modelInputFile, "");
 }
 
 /**
  * Construct a new GeoTessModel object and populate it with information from
  * the specified file.
  * 
  * @param modelInputFile
  *            name of file containing the model.
  * @param relativeGridPath
  *            the relative path from the directory where the model is stored
  *            to the directory where the grid is stored. Often, the model
  *            and grid are stored together in the same file in which case
  *            this parameter is ignored. Sometimes, however, the grid is
  *            stored in a separate file and only the name of the grid file
  *            (without path information) is stored in the model file. In
  *            this case, the code needs to know which directory to search
  *            for the grid file. The default is "" (empty string), which
  *            will cause the code to search for the grid file in the same
  *            directory in which the model file resides. Bottom line is that
  *            the default value is appropriate when the grid is stored in
  *            the same file as the model, or the model file is in the same
  *            directory as the model file.
  * @throws IOException
  */
 public GeoTessModelGA(String modelInputFile, String relativeGridPath) throws IOException
 { 
  super(); 
  loadModel(modelInputFile, relativeGridPath);
 }
 
 /**
  * Construct a new GeoTessModel object and populate it with information from
  * the specified file.
  * 
  * <p>relativeGridPath is assumed to be "" (empty string), which is appropriate
  * when the grid information is stored in the same file as the model or when
  * the grid is stored in a separate file located in the same directory as the
  * model file.
  * 
  * @param modelInputFile
  *            name of file containing the model.
  * @throws IOException
  */
 public GeoTessModelGA(String modelInputFile) throws IOException
 { 
  super(); 
  loadModel(modelInputFile, "");
 }
 
 /**
  * Parameterized constructor, specifying the grid and metadata for the
  * model. The grid is constructed and the data structures are initialized
  * based on information supplied in metadata. The data structures are not
  * populated with any information however (all Profiles are null). The
  * application should populate the new model's Profiles after this
  * constructor completes.
  * 
  * <p>
  * Before calling this constructor, the supplied MetaData object must be
  * populated with required information by calling the following MetaData
  * methods:
  * <ul>
  * <li>setDescription()
  * <li>setLayerNames()
  * <li>setAttributes()
  * <li>setDataType()
  * <li>setLayerTessIds() (only required if grid has more than one
  * multi-level tessellation)
  * </ul>
  * 
  * @param gridFileName
  *            name of file from which to load the grid.
  * @param metaData
  *            MetaData the new GeoTessModel instantiates a reference to the
  *            supplied metaData. No copy is made.
  * @throws IOException
  */
 public GeoTessModelGA(String gridFileName, GeoTessMetaData metaData) throws IOException
 { 
  super(gridFileName, metaData); 
 }
 
 /**
  * Parameterized constructor, specifying the grid and metadata for the
  * model. The grid is constructed and the data structures are initialized
  * based on information supplied in metadata. The data structures are not
  * populated with any information however (all Profiles are null). The
  * application should populate the new model's Profiles after this
  * constructor completes.
  * 
  * <p>
  * Before calling this constructor, the supplied MetaData object must be
  * populated with required information by calling the following MetaData
  * methods:
  * <ul>
  * <li>setDescription()
  * <li>setLayerNames()
  * <li>setAttributes()
  * <li>setDataType()
  * <li>setLayerTessIds() (only required if grid has more than one
  * multi-level tessellation)
  * <li>setSoftwareVersion()
  * <li>setGenerationDate()
  * </ul>
  * 
  * @param grid
  *            a reference to the GeoTessGrid that will support this
  *            GeoTessModel.
  * @param metaData
  *            MetaData the new GeoTessModel instantiates a reference to the
  *            supplied metaData. No copy is made.
  * @throws GeoTessException
  *             if metadata is incomplete.
  */
 public GeoTessModelGA(GeoTessGrid grid, GeoTessMetaData metaData) throws GeoTessException, IOException
 { 
  super(grid, metaData); 
 }
 
 /**
  * Construct a new GAModel with all the structures from the supplied
  * baseModel.  The new GAModel will be built with references to the 
  * GeoTessMetaData, GeoTessGrid and all the Profiles in the baseModel.  
  * No copies are made. Changes to one will be reflected in the other.  
  * All of the extraData will be set to default values.
  * @param baseModel
  * @throws GeoTessException
  */
 public GeoTessModelGA(GeoTessModel baseModel) throws GeoTessException
 {
  super(baseModel.getGrid(), baseModel.getMetaData());
  for (int i = 0; i < baseModel.getNVertices(); ++i)
   for (int j=0; j<baseModel.getNLayers(); ++j)
    setProfile(i,j,baseModel.getProfile(i, j));
 }
 
 public String[] getStationNames() {
  return stationNames;
 }
 
 public SeismicPhase[] getPhaseNames() {
  return phaseNames;
 }
 
 public GeoAttributes[] getAttributes() {
  return attributes;
 }
 
 public List<Triple> getIndexList() {
  return indexList;
 }
 
 public int getAttributeIndex(String station, SeismicPhase phase, GeoAttributes attribute)
 { return indexMap.get(station).get(phase).get(attribute); }
 
 /**
  * Overridden IO method.
  */
 @Override
 protected void loadModelBinary(DataInputStream input,
   String inputDirectory, String relGridFilePath)
   throws GeoTessException, IOException
 {
  // call super class to load model data from binary file.
  super.loadModelBinary(input, inputDirectory, relGridFilePath);
  
  // it is good practice, but not required, to store the class
  // name as the first thing added by the extending class.
  String className = GeoTessUtils.readString(input);
  if (!className.equals(this.getClass().getSimpleName()))
   throw new IOException("Found class name "+className
     +" but expecting "
  +this.getClass().getSimpleName());
  
  // it is good practice, but not required, to store a format 
  // version number as the second thing added by the extending class.
  // With this information, if the format changes in a future release
  // it may be possible to make the class backward compatible.
  int formatVersion = input.readInt();
  
  if (formatVersion != 1)
   throw new IOException("GAModel Format version "+formatVersion+" is not supported.");
  
  // Read in list of station names supported by this model
  int nStations = input.readInt();
  String[] stations = new String[nStations];
  for (int i=0; i<nStations; ++i)
   stations[i] = GeoTessUtils.readString(input);
 
  // Read in list of phase names supported by this model
  int nPhases = input.readInt();
  SeismicPhase[] phases = new SeismicPhase[nPhases];
  for (int i=0; i<nPhases; ++i)
   phases[i] = SeismicPhase.valueOf(GeoTessUtils.readString(input));
 
  // Read in list of GeoAttributes supported by this model.
  int nAttributes = input.readInt();
  GeoAttributes[] attributes = new GeoAttributes[nAttributes];
  for (int i=0; i<nAttributes; ++i)
   attributes[i] = GeoAttributes.valueOf(GeoTessUtils.readString(input));
  
  setStationsPhasesAttributes(stations, phases, attributes);
 }
 
 /**
  * Overridden IO method.
  */
 @Override
 protected void writeModelBinary(DataOutputStream output, String gridFileName)
   throws IOException
 {
  // call super class to write standard model information to binary file.
  super.writeModelBinary(output, gridFileName);
 
  // it is good practice, but not required, to store the class
  // name as the first thing added by the extending class.
  GeoTessUtils.writeString(output, this.getClass().getSimpleName());
  
  // it is good practice, but not required, to store a format 
  // version number as the second thing added by the extending class.
  // With this information, if the format changes in a future release
  // it may be possible to make the class backward compatible.
  output.writeInt(1);
  
  // now output the extraData
  output.writeInt(stationNames.length);
  for (String station : stationNames)
   GeoTessUtils.writeString(output, station);
  
  output.writeInt(phaseNames.length);
  for (SeismicPhase phase : phaseNames)
   GeoTessUtils.writeString(output, phase.toString());
  
  output.writeInt(attributes.length);
  for (GeoAttributes a : attributes)
   GeoTessUtils.writeString(output, a.toString());
 }
 
 /**
  * Overridden IO method.
  */
 @Override
 protected void loadModelAscii(Scanner input, String inputDirectory,
   String relGridFilePath) throws GeoTessException, IOException
 {
  super.loadModelAscii(input, inputDirectory, relGridFilePath);
  
  // it is good practice, but not required, to store the class
  // name as the first thing added by the extending class.
  String className = input.nextLine();
  if (!className.equals(this.getClass().getSimpleName()))
   throw new IOException("Found class name "+className
     +" but expecting "
  +this.getClass().getSimpleName());
  
  // it is good practice, but not required, to store a format 
  // version number as the second thing added by the extending class.
  // With this information, if the format changes in a future release
  // it may be possible to make the class backward compatible.
  int formatVersion = input.nextInt();
  input.nextLine();
  
  if (formatVersion != 1)
   throw new IOException("GAModel Format version "+formatVersion+" is not supported.");
  
  // Read in list of station names supported by this model
  int nStations = input.nextInt();
  String[] stations = new String[nStations];
  for (int i=0; i<nStations; ++i)
   stations[i] = input.next();
 
  // Read in list of phase names supported by this model
  int nPhases = input.nextInt();
  SeismicPhase[] phases = new SeismicPhase[nPhases];
  for (int i=0; i<nPhases; ++i)
   phases[i] = SeismicPhase.valueOf(input.next());
 
  // Read in list of GeoAttribute names supported by this model
  int nAttributes = input.nextInt();
  GeoAttributes[] attributes = new GeoAttributes[nAttributes];
  for (int i=0; i<nAttributes; ++i)
   attributes[i] = GeoAttributes.valueOf(input.next());
  
  setStationsPhasesAttributes(stations, phases, attributes);
 }
 
 public void setStationsPhasesAttributes(
   String[] stations, SeismicPhase[] phases, GeoAttributes[] attributes)
 {
  this.stationNames = stations;
  this.phaseNames = phases;
  this.attributes = attributes;
  
  indexList = new ArrayList<>(stationNames.length*phaseNames.length*attributes.length);
  indexMap = new HashMap<String, Map<SeismicPhase,Map<GeoAttributes,Integer>>>(stations.length);
  
  for (String s : stationNames)
  {
   Map<SeismicPhase, Map<GeoAttributes, Integer>> m2 = 
     new HashMap<SeismicPhase, Map<GeoAttributes,Integer>>(phases.length);
   indexMap.put(s, m2);
   for (SeismicPhase p : phaseNames)
   {
    Map<GeoAttributes, Integer> m3 = new HashMap<GeoAttributes, Integer>(attributes.length);
    m2.put(p, m3);
    for (GeoAttributes a : attributes)
    {
     m3.put(a, indexList.size());
     indexList.add(new Triple(s, p, a));
    }
   }
  }
 }
 
 /**
  * Overridden IO method.
  */
 @Override
 protected void writeModelAscii(Writer output, String gridFileName)
   throws IOException
 {
  // call super class to write standard model information to ascii file.
  super.writeModelAscii(output, gridFileName);
 
  // it is good practice, but not required, to store the class
  // name and a format version number as the first things added 
  // by the extending class.
  // With this information, if the format changes in a future release
  // it may be possible to make the class backward compatible.
  output.write(String.format("%s%n%d%n", this.getClass().getSimpleName(), 1));
  
  // now output the extraData
  output.write(stationNames.length);
  for (String station : stationNames)
   output.write(' '+station);
  output.write("\n");
  
  output.write(phaseNames.length);
  for (SeismicPhase phase : phaseNames)
   output.write(' '+phase.toString());
  output.write("\n");
  
  output.write(attributes.length);
  for (GeoAttributes a : attributes)
   output.write(' '+a.toString());
  output.write("\n");
 }
 
}