package com.github.celldynamics.quimp.filesystem.converter;
   
   import java.io.IOException;
   import java.nio.file.Path;
   import java.nio.file.Paths;
   import java.util.ArrayList;
   import java.util.Arrays;
   import java.util.List;
   
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import com.github.celldynamics.quimp.CellStats;
  import com.github.celldynamics.quimp.FrameStatistics;
  import com.github.celldynamics.quimp.filesystem.FileExtensions;
  
  /**
   * Parse stQP files and convert it to StatsCollection.
   * 
   * @author p.baniukiewicz
   *
   */
  public class StatFileParser {
    static final int MAX_CELLS = 65535;
    /**
     * The Constant LOGGER.
     */
    static final Logger LOGGER = LoggerFactory.getLogger(StatFileParser.class.getName());
  
    private String name;
    private ArrayList<CellStats> stats;
  
    /**
     * CellStat getter.
     * 
     * @return the stats
     */
    public ArrayList<CellStats> getStats() {
      return stats;
    }
  
    /**
     * Construct object.
     * 
     * @param name corename of file with path. E.g path/to/file/test for files test_0.stQP.csv,...
     */
    public StatFileParser(String name) {
      stats = new ArrayList<>();
      this.name = name;
    }
  
    /**
     * Read all files along given path and prefix used for constructing the object and convert them to
     * CellStat objects.
     * 
     * @return Imported stats
     * 
     * @throws IOException on File read error
     */
    public ArrayList<CellStats> importStQp() throws IOException {
      List<Path> files = getAllFiles();
      for (Path p : files) {
        FrameStatistics[] fs = FrameStatistics.read(p.toFile());
        stats.add(new CellStats(new ArrayList<FrameStatistics>(Arrays.asList(fs))));
      }
      return getStats();
    }
  
    /**
     * Scan for stQP.csv files numbered consequently from _0.
     * 
     * @return List of full paths (related to path given in constructor) of stQP files or empty list.
     */
    List<Path> getAllFiles() {
      ArrayList<Path> ret = new ArrayList<>();
      Path pa = Paths.get(name);
      Path filename = pa.getFileName(); // file name without extension
      Path folder = pa.getParent();
      int i = 0;
      while (i < MAX_CELLS) {
        Path testFile;
        if (folder != null) {
          testFile = folder
                  .resolve(Paths.get(filename.toString() + "_" + i + FileExtensions.statsFileExt));
        } else {
          testFile = Paths.get(filename.toString() + "_" + i + FileExtensions.statsFileExt);
        }
        if (testFile.toFile().isFile()) { // check if _xx exists
          ret.add(testFile); // store
          i++; // go to next possible file
        } else {
          break;
        }
      }
      if (i >= MAX_CELLS) {
        LOGGER.warn("Reached maximal number of statistic files: " + MAX_CELLS);
      }
      return ret;
  
   }
 
 }