source: trunk/sources/HeuristicLab.Problems.Instances.DataAnalysis/3.3/TableFileParser.cs @ 14285

#region License Information
/* HeuristicLab
 * Copyright (C) 2002-2016 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
 *
 * This file is part of HeuristicLab.
 *
 * HeuristicLab is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * HeuristicLab is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
 */
#endregion


using System;
using System.Collections;
using System.Collections.Generic;
using System.Diagnostics.Contracts;
using System.Globalization;
using System.IO;
using System.Linq;
using System.Runtime.Serialization;
using System.Text;

namespace HeuristicLab.Problems.Instances.DataAnalysis {
  public class TableFileParser : Progress<long> { // reports the number of bytes read
    private const int BUFFER_SIZE = 65536;
    // char used to symbolize whitespaces (no missing values can be handled with whitespaces)
    private const char WHITESPACECHAR = (char)0;
    private static readonly char[] POSSIBLE_SEPARATORS = new char[] { ',', ';', '\t', WHITESPACECHAR };
    private Tokenizer tokenizer;
    private int estimatedNumberOfLines = 200; // initial capacity for columns, will be set automatically when data is read from a file


    private Encoding encoding = Encoding.Default;

    public Encoding Encoding {
      get { return encoding; }
      set {
        if (value == null) throw new ArgumentNullException("Encoding");
        encoding = value;
      }
    }


    private int rows;
    public int Rows {
      get { return rows; }
      set { rows = value; }
    }

    private int columns;
    public int Columns {
      get { return columns; }
      set { columns = value; }
    }

    private List<IList> values;
    public List<IList> Values {
      get {
        return values;
      }
    }

    private List<string> variableNames;
    public IEnumerable<string> VariableNames {
      get {
        if (variableNames.Count > 0) return variableNames;
        else {
          string[] names = new string[columns];
          for (int i = 0; i < names.Length; i++) {
            names[i] = "X" + i.ToString("000");
          }
          return names;
        }
      }
    }

    public TableFileParser() {
      variableNames = new List<string>();
    }

    public bool AreColumnNamesInFirstLine(string fileName) {
      NumberFormatInfo numberFormat;
      DateTimeFormatInfo dateTimeFormatInfo;
      char separator;
      DetermineFileFormat(fileName, out numberFormat, out dateTimeFormatInfo, out separator);
      using (var stream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)) {
        return AreColumnNamesInFirstLine(stream, numberFormat, dateTimeFormatInfo, separator);
      }
    }

    public bool AreColumnNamesInFirstLine(Stream stream) {
      NumberFormatInfo numberFormat = NumberFormatInfo.InvariantInfo;
      DateTimeFormatInfo dateTimeFormatInfo = DateTimeFormatInfo.InvariantInfo;
      char separator = ',';
      return AreColumnNamesInFirstLine(stream, numberFormat, dateTimeFormatInfo, separator);
    }

    public bool AreColumnNamesInFirstLine(string fileName, NumberFormatInfo numberFormat,
                                         DateTimeFormatInfo dateTimeFormatInfo, char separator) {
      using (var stream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)) {
        return AreColumnNamesInFirstLine(stream, numberFormat, dateTimeFormatInfo, separator);
      }
    }

    public bool AreColumnNamesInFirstLine(Stream stream, NumberFormatInfo numberFormat,
                                          DateTimeFormatInfo dateTimeFormatInfo, char separator) {
      using (StreamReader reader = new StreamReader(stream, Encoding)) {
        tokenizer = new Tokenizer(reader, numberFormat, dateTimeFormatInfo, separator);
        return (tokenizer.PeekType() != TokenTypeEnum.Double);
      }
    }

    /// <summary>
    /// Parses a file and determines the format first
    /// </summary>
    /// <param name="fileName">file which is parsed</param>
    /// <param name="columnNamesInFirstLine"></param>
    public void Parse(string fileName, bool columnNamesInFirstLine, int lineLimit = -1) {
      NumberFormatInfo numberFormat;
      DateTimeFormatInfo dateTimeFormatInfo;
      char separator;
      DetermineFileFormat(fileName, out numberFormat, out dateTimeFormatInfo, out separator);
      EstimateNumberOfLines(fileName);
      Parse(new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite), numberFormat, dateTimeFormatInfo, separator, columnNamesInFirstLine, lineLimit);
    }

    /// <summary>
    /// Parses a file with the given formats
    /// </summary>
    /// <param name="fileName">file which is parsed</param>
    /// <param name="numberFormat">Format of numbers</param>
    /// <param name="dateTimeFormatInfo">Format of datetime</param>
    /// <param name="separator">defines the separator</param>
    /// <param name="columnNamesInFirstLine"></param>
    public void Parse(string fileName, NumberFormatInfo numberFormat, DateTimeFormatInfo dateTimeFormatInfo, char separator, bool columnNamesInFirstLine, int lineLimit = -1) {
      EstimateNumberOfLines(fileName);
      using (var stream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)) {
        Parse(stream, numberFormat, dateTimeFormatInfo, separator, columnNamesInFirstLine, lineLimit);
      }
    }

    // determines the number of newline characters in the first 64KB to guess the number of rows for a file
    private void EstimateNumberOfLines(string fileName) {
      var len = new System.IO.FileInfo(fileName).Length;
      var buf = new char[1024 * 1024];
      using (var reader = new StreamReader(fileName, Encoding)) {
        reader.ReadBlock(buf, 0, buf.Length);
      }
      int numNewLine = 0;
      int charsInCurrentLine = 0, charsInFirstLine = 0; // the first line (names) and the last line (incomplete) are not representative
      foreach (var ch in buf) {
        charsInCurrentLine++;
        if (ch == '\n') {
          if (numNewLine == 0) charsInFirstLine = charsInCurrentLine; // store the number of chars in the first line
          charsInCurrentLine = 0;
          numNewLine++;
        }
      }
      if (numNewLine <= 1) {
        // fail -> keep the default setting
        return;
      } else {
        double charsPerLineFactor = (buf.Length - charsInFirstLine - charsInCurrentLine) / ((double)numNewLine - 1);
        double estimatedLines = len / charsPerLineFactor;
        estimatedNumberOfLines = (int)Math.Round(estimatedLines * 1.1); // pessimistic allocation of 110% to make sure that the list is very likely large enough
      }
    }

    /// <summary>
    /// Takes a Stream and parses it with default format. NumberFormatInfo.InvariantInfo, DateTimeFormatInfo.InvariantInfo and separator = ','
    /// </summary>
    /// <param name="stream">stream which is parsed</param>
    /// <param name="columnNamesInFirstLine"></param>
    public void Parse(Stream stream, bool columnNamesInFirstLine, int lineLimit = -1) {
      NumberFormatInfo numberFormat = NumberFormatInfo.InvariantInfo;
      DateTimeFormatInfo dateTimeFormatInfo = DateTimeFormatInfo.InvariantInfo;
      char separator = ',';
      Parse(stream, numberFormat, dateTimeFormatInfo, separator, columnNamesInFirstLine, lineLimit);
    }

    /// <summary>
    /// Parses a stream with the given formats.
    /// </summary>
    /// <param name="stream">Stream which is parsed</param>    
    /// <param name="numberFormat">Format of numbers</param>
    /// <param name="dateTimeFormatInfo">Format of datetime</param>
    /// <param name="separator">defines the separator</param>
    /// <param name="columnNamesInFirstLine"></param>
    public void Parse(Stream stream, NumberFormatInfo numberFormat, DateTimeFormatInfo dateTimeFormatInfo, char separator, bool columnNamesInFirstLine, int lineLimit = -1) {
      using (StreamReader reader = new StreamReader(stream, Encoding)) {
        tokenizer = new Tokenizer(reader, numberFormat, dateTimeFormatInfo, separator);
        values = new List<IList>();
        if (lineLimit > 0) estimatedNumberOfLines = lineLimit;

        if (columnNamesInFirstLine) {
          ParseVariableNames();
          if (!tokenizer.HasNext())
            Error(
              "Couldn't parse data values. Probably because of incorrect number format (the parser expects english number format with a '.' as decimal separator).",
              "", tokenizer.CurrentLineNumber);
        }


        // read values... start in first row 
        int nLinesParsed = 0;
        int colIdx = 0;
        int numValuesInFirstRow = columnNamesInFirstLine ? variableNames.Count : -1; // number of variables or inizialize based on first row of values (-1)
        while (tokenizer.HasNext() && (lineLimit < 0 || nLinesParsed < lineLimit)) {
          if (tokenizer.PeekType() == TokenTypeEnum.NewLine) {
            tokenizer.Skip();

            // all rows have to have the same number of values
            // the first row defines how many samples are needed
            if (numValuesInFirstRow < 0) numValuesInFirstRow = values.Count; // set to number of colums in the first row
            else if (colIdx > 0 && numValuesInFirstRow != colIdx) { // read at least one value in the row (support for skipping empty lines)
              Error("The first row of the dataset has " + numValuesInFirstRow + " columns." + Environment.NewLine +
                    "Line " + tokenizer.CurrentLineNumber + " has " + colIdx + " columns.", "",
                    tokenizer.CurrentLineNumber);
            }
            OnReport(tokenizer.BytesRead);

            nLinesParsed++;
            colIdx = 0;
          } else {
            // read one value
            TokenTypeEnum type; string strVal; double dblVal; DateTime dateTimeVal;
            tokenizer.Next(out type, out strVal, out dblVal, out dateTimeVal);

            // initialize columns on the first row (fixing data types as presented in the first row...)
            if (nLinesParsed == 0) {
              values.Add(CreateList(type, estimatedNumberOfLines));
            } else if (colIdx == values.Count) {
              Error("The first row of the dataset has " + numValuesInFirstRow + " columns." + Environment.NewLine +
                    "Line " + tokenizer.CurrentLineNumber + " has more columns.", "",
                tokenizer.CurrentLineNumber);
            }
            if (!IsColumnTypeCompatible(values[colIdx], type)) {
              values[colIdx] = ConvertToStringColumn(values[colIdx]);
            }
            // add the value to the column
            AddValue(type, values[colIdx++], strVal, dblVal, dateTimeVal);
          }
        }

        if (!values.Any() || values.First().Count == 0)
          Error("Couldn't parse data values. Probably because of incorrect number format " +
                "(the parser expects english number format with a '.' as decimal separator).", "", tokenizer.CurrentLineNumber);
      }

      this.rows = values.First().Count;
      this.columns = values.Count;

      // after everything has been parsed make sure the lists are as compact as possible
      foreach (var l in values) {
        var dblList = l as List<double>;
        var byteList = l as List<byte>;
        var dateList = l as List<DateTime>;
        var stringList = l as List<string>;
        var objList = l as List<object>;
        if (dblList != null) dblList.TrimExcess();
        if (byteList != null) byteList.TrimExcess();
        if (dateList != null) dateList.TrimExcess();
        if (stringList != null) stringList.TrimExcess();
        if (objList != null) objList.TrimExcess();
      }

      // for large files we created a lot of memory pressure, cannot hurt to run GC.Collect here (TableFileParser is called seldomly on user interaction)
      GC.Collect(2, GCCollectionMode.Forced);
    }

    #region type-dependent dispatch
    private bool IsColumnTypeCompatible(IList list, TokenTypeEnum tokenType) {
      return (list is List<string>) || // all tokens can be added to a string list
             (tokenType == TokenTypeEnum.Missing) || // empty entries are allowed in all columns
             (tokenType == TokenTypeEnum.Double && list is List<double>) ||
             (tokenType == TokenTypeEnum.DateTime && list is List<DateTime>);
    }

    // all columns are converted to string columns when we find an non-empty value that has incorrect type
    private IList ConvertToStringColumn(IList list) {
      var dblL = list as List<double>;
      if (dblL != null) {
        var l = new List<string>(dblL.Capacity);
        l.AddRange(dblL.Select(dbl => dbl.ToString()));
        return l;
      }

      var dtL = list as List<DateTime>;
      if (dtL != null) {
        var l = new List<string>(dtL.Capacity);
        l.AddRange(dtL.Select(dbl => dbl.ToString()));
        return l;
      }

      if (list is List<string>) return list;

      throw new InvalidProgramException(string.Format("Cannot convert column of type {0} to string column", list.GetType()));
    }

    private void AddValue(TokenTypeEnum type, IList list, string strVal, double dblVal, DateTime dateTimeVal) {
      var dblList = list as List<double>;
      if (dblList != null) {
        AddValue(type, dblList, dblVal);
        return;
      }

      var strList = list as List<string>;
      if (strList != null) {
        AddValue(type, strList, strVal);
        return;
      }
      var dtList = list as List<DateTime>;
      if (dtList != null) {
        AddValue(type, dtList, dateTimeVal);
        return;
      }

      list.Add(strVal); // assumes List<object>
    }

    private void AddValue(TokenTypeEnum type, List<double> list, double dblVal) {
      Contract.Assert(type == TokenTypeEnum.Missing || type == TokenTypeEnum.Double);
      list.Add(type == TokenTypeEnum.Missing ? double.NaN : dblVal);
    }

    private void AddValue(TokenTypeEnum type, List<string> list, string strVal) {
      // assumes that strVal is always set to the original token read from the input file
      list.Add(type == TokenTypeEnum.Missing ? string.Empty : strVal);
    }

    private void AddValue(TokenTypeEnum type, List<DateTime> list, DateTime dtVal) {
      Contract.Assert(type == TokenTypeEnum.Missing || type == TokenTypeEnum.DateTime);
      list.Add(type == TokenTypeEnum.Missing ? DateTime.MinValue : dtVal);
    }

    private IList CreateList(TokenTypeEnum type, int estimatedNumberOfLines) {
      switch (type) {
        case TokenTypeEnum.String:
          return new List<string>(estimatedNumberOfLines);
        case TokenTypeEnum.Double:
        case TokenTypeEnum.Missing: // assume double columns
          return new List<double>(estimatedNumberOfLines);
        case TokenTypeEnum.DateTime:
          return new List<DateTime>(estimatedNumberOfLines);
        default:
          throw new InvalidOperationException();
      }
    }
    #endregion

    public static void DetermineFileFormat(string path, out NumberFormatInfo numberFormat, out DateTimeFormatInfo dateTimeFormatInfo, out char separator) {
      DetermineFileFormat(new FileStream(path, FileMode.Open, FileAccess.Read, FileShare.ReadWrite), out numberFormat, out dateTimeFormatInfo, out separator);
    }

    public static void DetermineFileFormat(Stream stream, out NumberFormatInfo numberFormat, out DateTimeFormatInfo dateTimeFormatInfo, out char separator) {
      using (StreamReader reader = new StreamReader(stream)) {
        // skip first line
        reader.ReadLine();
        // read a block
        char[] buffer = new char[BUFFER_SIZE];
        int charsRead = reader.ReadBlock(buffer, 0, BUFFER_SIZE);
        // count frequency of special characters
        Dictionary<char, int> charCounts = buffer.Take(charsRead)
          .GroupBy(c => c)
          .ToDictionary(g => g.Key, g => g.Count());

        // depending on the characters occuring in the block 
        // we distinghish a number of different cases based on the the following rules:
        // many points => it must be English number format, the other frequently occuring char is the separator
        // no points but many commas => this is the problematic case. Either German format (real numbers) or English format (only integer numbers) with ',' as separator
        //   => check the line in more detail:
        //            English: 0, 0, 0, 0
        //            German:  0,0 0,0 0,0 ...
        //            => if commas are followed by space => English format
        // no points no commas => English format (only integer numbers) use the other frequently occuring char as separator
        // in all cases only treat ' ' as separator if no other separator is possible (spaces can also occur additionally to separators)
        if (OccurrencesOf(charCounts, '.') > 10) {
          numberFormat = NumberFormatInfo.InvariantInfo;
          dateTimeFormatInfo = DateTimeFormatInfo.InvariantInfo;
          separator = POSSIBLE_SEPARATORS
            .Where(c => OccurrencesOf(charCounts, c) > 10)
            .OrderBy(c => -OccurrencesOf(charCounts, c))
            .DefaultIfEmpty(' ')
            .First();
        } else if (OccurrencesOf(charCounts, ',') > 10) {
          // no points and many commas
          // count the number of tokens (chains of only digits and commas) that contain multiple comma characters
          int tokensWithMultipleCommas = 0;
          for (int i = 0; i < charsRead; i++) {
            int nCommas = 0;
            while (i < charsRead && (buffer[i] == ',' || Char.IsDigit(buffer[i]))) {
              if (buffer[i] == ',') nCommas++;
              i++;
            }
            if (nCommas > 2) tokensWithMultipleCommas++;
          }
          if (tokensWithMultipleCommas > 1) {
            // English format (only integer values) with ',' as separator
            numberFormat = NumberFormatInfo.InvariantInfo;
            dateTimeFormatInfo = DateTimeFormatInfo.InvariantInfo;
            separator = ',';
          } else {
            char[] disallowedSeparators = new char[] { ',' }; // n. def. contains a space so ' ' should be disallowed to, however existing unit tests would fail
            // German format (real values)
            numberFormat = NumberFormatInfo.GetInstance(new CultureInfo("de-DE"));
            dateTimeFormatInfo = DateTimeFormatInfo.GetInstance(new CultureInfo("de-DE"));
            separator = POSSIBLE_SEPARATORS
              .Except(disallowedSeparators)
              .Where(c => OccurrencesOf(charCounts, c) > 10)
              .OrderBy(c => -OccurrencesOf(charCounts, c))
              .DefaultIfEmpty(' ')
              .First();
          }
        } else {
          // no points and no commas => English format
          numberFormat = NumberFormatInfo.InvariantInfo;
          dateTimeFormatInfo = DateTimeFormatInfo.InvariantInfo;
          separator = POSSIBLE_SEPARATORS
            .Where(c => OccurrencesOf(charCounts, c) > 10)
            .OrderBy(c => -OccurrencesOf(charCounts, c))
            .DefaultIfEmpty(' ')
            .First();
        }
      }
    }

    private static int OccurrencesOf(Dictionary<char, int> charCounts, char c) {
      return charCounts.ContainsKey(c) ? charCounts[c] : 0;
    }

    #region tokenizer
    // the tokenizer reads full lines and returns separated tokens in the line as well as a terminating end-of-line character
    internal enum TokenTypeEnum {
      NewLine, String, Double, DateTime, Missing
    }

    internal class Tokenizer {
      private StreamReader reader;
      // we assume that a buffer of 1024 tokens for a line is sufficient most of the time (the buffer is increased below if necessary)
      private TokenTypeEnum[] tokenTypes = new TokenTypeEnum[1024];
      private string[] stringVals = new string[1024];
      private double[] doubleVals = new double[1024];
      private DateTime[] dateTimeVals = new DateTime[1024];
      private int tokenPos;
      private int numTokens;
      private NumberFormatInfo numberFormatInfo;
      private DateTimeFormatInfo dateTimeFormatInfo;
      private char separator;

      // arrays for string.Split()
      private readonly char[] whiteSpaceSeparators = new char[0]; // string split uses separators as default
      private readonly char[] separators;

      private int currentLineNumber = 0;
      public int CurrentLineNumber {
        get { return currentLineNumber; }
        private set { currentLineNumber = value; }
      }
      private string currentLine;
      public string CurrentLine {
        get { return currentLine; }
        private set { currentLine = value; }
      }
      public long BytesRead {
        get;
        private set;
      }

      public Tokenizer(StreamReader reader, NumberFormatInfo numberFormatInfo, DateTimeFormatInfo dateTimeFormatInfo, char separator) {
        this.reader = reader;
        this.numberFormatInfo = numberFormatInfo;
        this.dateTimeFormatInfo = dateTimeFormatInfo;
        this.separator = separator;
        this.separators = new char[] { separator };
        ReadNextTokens();
      }

      public bool HasNext() {
        return numTokens > tokenPos || !reader.EndOfStream;
      }

      public TokenTypeEnum PeekType() {
        return tokenTypes[tokenPos];
      }

      public void Skip() {
        // simply skips one token without returning the result values
        tokenPos++;
        if (numTokens == tokenPos) {
          ReadNextTokens();
        }
      }

      public void Next(out TokenTypeEnum type, out string strVal, out double dblVal, out DateTime dateTimeVal) {
        type = tokenTypes[tokenPos];
        strVal = stringVals[tokenPos];
        dblVal = doubleVals[tokenPos];
        dateTimeVal = dateTimeVals[tokenPos];
        Skip();
      }

      private void ReadNextTokens() {
        if (!reader.EndOfStream) {
          CurrentLine = reader.ReadLine();
          CurrentLineNumber++;
          if (reader.BaseStream.CanSeek) {
            BytesRead = reader.BaseStream.Position;
          } else {
            BytesRead += CurrentLine.Length + 2; // guess
          }
          int i = 0;
          if (!string.IsNullOrWhiteSpace(CurrentLine)) {
            foreach (var tok in Split(CurrentLine)) {
              TokenTypeEnum type;
              double doubleVal;
              DateTime dateTimeValue;
              type = TokenTypeEnum.String; // default
              stringVals[i] = tok.Trim();
              if (double.TryParse(tok, NumberStyles.Float, numberFormatInfo, out doubleVal)) {
                type = TokenTypeEnum.Double;
                doubleVals[i] = doubleVal;
              } else if (DateTime.TryParse(tok, dateTimeFormatInfo, DateTimeStyles.None, out dateTimeValue)) {
                type = TokenTypeEnum.DateTime;
                dateTimeVals[i] = dateTimeValue;
              } else if (string.IsNullOrWhiteSpace(tok)) {
                type = TokenTypeEnum.Missing;
              }

              // couldn't parse the token as an int or float number or datetime value so return a string token

              tokenTypes[i] = type;
              i++;

              if (i >= tokenTypes.Length) {
                // increase buffer size if necessary
                IncreaseCapacity(ref tokenTypes);
                IncreaseCapacity(ref doubleVals);
                IncreaseCapacity(ref stringVals);
                IncreaseCapacity(ref dateTimeVals);
              }
            }
          }
          tokenTypes[i] = TokenTypeEnum.NewLine;
          numTokens = i + 1;
          tokenPos = 0;
        }
      }

      private IEnumerable<string> Split(string line) {
        return separator == WHITESPACECHAR ?
          line.Split(whiteSpaceSeparators, StringSplitOptions.RemoveEmptyEntries) :
          line.Split(separators);
      }

      private static void IncreaseCapacity<T>(ref T[] arr) {
        int n = (int)Math.Floor(arr.Length * 1.7); // guess
        T[] arr2 = new T[n];
        Array.Copy(arr, arr2, arr.Length);
        arr = arr2;
      }
    }
    #endregion

    #region parsing

    private void ParseVariableNames() {
      // the first line must contain variable names
      List<string> varNames = new List<string>();

      TokenTypeEnum type;
      string strVal;
      double dblVal;
      DateTime dateTimeVal;

      tokenizer.Next(out type, out strVal, out dblVal, out dateTimeVal);

      // the first token must be a variable name
      if (type != TokenTypeEnum.String)
        throw new ArgumentException("Error: Expected " + TokenTypeEnum.String + " got " + type);
      varNames.Add(strVal);

      while (tokenizer.HasNext() && tokenizer.PeekType() != TokenTypeEnum.NewLine) {
        tokenizer.Next(out type, out strVal, out dblVal, out dateTimeVal);
        varNames.Add(strVal);
      }
      ExpectType(TokenTypeEnum.NewLine);

      variableNames = varNames;
    }

    private void ExpectType(TokenTypeEnum expectedToken) {
      if (tokenizer.PeekType() != expectedToken)
        throw new ArgumentException("Error: Expected " + expectedToken + " got " + tokenizer.PeekType());
      tokenizer.Skip();
    }

    private void Error(string message, string token, int lineNumber) {
      throw new IOException(string.Format("Error while parsing. {0} (token: {1} lineNumber: {2}).", message, token, lineNumber));
    }
    #endregion
  }
}