Ejemplo n.º 1
0
  /**
   * Validate EIA template table
   *
   * @param eiaTemplate the EIA template table to be parsed
   * @return an array of Incompliances
   */
  public static ArrayList<Incompliance> parseEIATemplateTable(EDFTable eiaTemplate) {

    ArrayList<Incompliance> eiaIncompliances = new ArrayList<Incompliance>();

    final int errorSrcTypeIndex = Incompliance.index_incomp_src_eiatemplate;
    final String incomplianceType = Incompliance.typeOfErrorHeader[errorSrcTypeIndex];
    Incompliance incomp;
    String description;
    boolean bASCII;
    String fileName = eiaTemplate.getMasterFile().getPath();
    int row = 0, col;

    final int COL_INDEX_LOCAL_PATIENT_ID = 2;
    final int COL_INDEX_LOCAL_RECORDING_ID = 3;
    final int COL_INDEX_START_DATE = 4;

    /**
     * ********************************************************** 80 ascii : local patient
     * identification **********************************************************
     */
    col = 0;
    String partient_id =
        ((String) eiaTemplate.getModel().getValueAt(row, COL_INDEX_LOCAL_PATIENT_ID));
    if (partient_id == null || partient_id.equals("")) {
      // [Partient_id](B.2) can be empty field
    } else {
      // [Partient_id](B.1) check for ascii
      bASCII = checkAsciiF(partient_id);
      if (!bASCII) {
        description = Incompliance.error_eia_ascii;
        incomp =
            new Incompliance(incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
        eiaIncompliances.add(incomp);
      }
    }

    /**
     * ********************************************************** 80 ascii : local recording
     * identification **********************************************************
     */
    col = 1;
    String recording_id =
        ((String) eiaTemplate.getModel().getValueAt(row, COL_INDEX_LOCAL_RECORDING_ID));
    if (recording_id == null || recording_id.equals("")) {
      // [Recording_id](C.2) can be empty field
    } else {
      // [Recording_id](C.1) check for ascii
      bASCII = checkAsciiF(recording_id);
      if (!bASCII) {
        description = Incompliance.error_eia_ascii;
        incomp =
            new Incompliance(incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
        eiaIncompliances.add(incomp);
      }
    }

    /**
     * ********************************************************** 8 ascii : startdate of recording
     * (dd.mm.yy) **********************************************************
     */
    col = 2;
    String startdate =
        ((String) eiaTemplate.getModel().getValueAt(row, COL_INDEX_START_DATE)).trim();
    if (startdate == null || startdate.equals("")) {
      // [Startdate](D.2) cannot be empty field
      description = Incompliance.error_eia_empty;
      incomp =
          new Incompliance(incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
      eiaIncompliances.add(incomp);
    } else {
      // [Startdate](D.1) check for ascii
      bASCII = checkAsciiF(startdate);
      if (!bASCII) {
        description = Incompliance.error_eia_ascii;
        incomp =
            new Incompliance(incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
        eiaIncompliances.add(incomp);
      } else {
        // [Startdate](D.4) separator between digits should be only �period�
        String[] items = startdate.split("\\.");
        if (items.length != 3) {
          description = Incompliance.error_eia_dateformat;
          incomp =
              new Incompliance(
                  incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
          eiaIncompliances.add(incomp);
        } else {
          // [Startdate](D.3) dd:00-31, mm:00-12, yy:00-99
          try {
            int dd = Integer.parseInt(items[0]);
            int mm = Integer.parseInt(items[1]);
            int yy = Integer.parseInt(items[2]);
            if (dd >= 0 && dd <= 31 && mm >= 0 && mm <= 12 && yy >= 00 && yy <= 99) {
              // valid date format
            } else {
              description = Incompliance.error_eia_daterange;
              incomp =
                  new Incompliance(
                      incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
              eiaIncompliances.add(incomp);
            }
          } catch (NumberFormatException e) {
            description = Incompliance.error_eia_daterange;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, row, col, errorSrcTypeIndex);
            eiaIncompliances.add(incomp);
          }
        }
      }
    }

    if (eiaIncompliances.size() > 0) {
      eiaTemplate.setEdfValid(false);
    }

    return eiaIncompliances;
  }
Ejemplo n.º 2
0
  /**
   * Parses ESA table and records Incompliances
   *
   * @param esaTable the ESA table to be processed
   * @param edfFile the EDF file name
   * @return an array of Incompliances
   */
  public static ArrayList<Incompliance> parseESATable(EDFTable esaTable, String edfFile) {

    ArrayList<Incompliance> esaIncompliances = new ArrayList<Incompliance>();
    String incomplianceType;
    int errorSrcTypeIndex = -1;
    int nrow = esaTable.getRowCount();
    String fileName = edfFile;
    Incompliance incomp;
    String description;
    boolean bASCII;
    int col;

    /////
    int COL_INDEX_LABEL;
    int COL_INDEX_CORRECTED_LABEL = -1;
    int COL_INDEX_TRANSDUCER_TYPE;
    int COL_INDEX_PHYSICAL_DIMENSION;
    int COL_INDEX_PHYSICAL_MINIMUM;
    int COL_INDEX_PHYSICAL_MAXIMUM;
    int COL_INDEX_DIGITAL_MINIMUM;
    int COL_INDEX_DIGITAL_MAXIMUM;
    int COL_INDEX_PREFILTERING;
    int COL_INDEX_NR_OF_SAMPLES;
    int COL_INDEX_RESERVED;
    /////

    if (esaTable instanceof ESATable) {
      errorSrcTypeIndex = Incompliance.index_incomp_src_esa;
      incomplianceType = Incompliance.typeOfErrorHeader[errorSrcTypeIndex];

      // Check "ESA Table" fields
      COL_INDEX_LABEL = 0;
      COL_INDEX_TRANSDUCER_TYPE = 1;
      COL_INDEX_PHYSICAL_DIMENSION = 2;
      COL_INDEX_PHYSICAL_MINIMUM = 3;
      COL_INDEX_PHYSICAL_MAXIMUM = 4;
      COL_INDEX_DIGITAL_MINIMUM = 5;
      COL_INDEX_DIGITAL_MAXIMUM = 6;
      COL_INDEX_PREFILTERING = 7;
      COL_INDEX_NR_OF_SAMPLES = 8;
      COL_INDEX_RESERVED = 9;
    } else if (esaTable instanceof ESATemplateTable) {
      errorSrcTypeIndex = Incompliance.index_incomp_src_esatemplate;
      incomplianceType = Incompliance.typeOfErrorHeader[errorSrcTypeIndex];

      // Check "ESA Template" fields
      COL_INDEX_LABEL = 0;
      COL_INDEX_CORRECTED_LABEL = 1;
      COL_INDEX_TRANSDUCER_TYPE = 2;
      COL_INDEX_PHYSICAL_DIMENSION = 3;
      COL_INDEX_PHYSICAL_MINIMUM = 4;
      COL_INDEX_PHYSICAL_MAXIMUM = 5;
      COL_INDEX_DIGITAL_MINIMUM = 6;
      COL_INDEX_DIGITAL_MAXIMUM = 7;
      COL_INDEX_PREFILTERING = 8;
      COL_INDEX_NR_OF_SAMPLES = 9;
      COL_INDEX_RESERVED = 10;
    } else {
      return esaIncompliances; // at this time, esaIncompliances.size() = 0;
    }

    for (int i = 0; i < nrow; i++) {

      /**
       * ********************************************************** ns * 16 ascii : ns * label (e.g.
       * EEG Fpz-Cz or Body temp) **********************************************************
       */
      col = COL_INDEX_LABEL;
      String alabel = (String) esaTable.getModel().getValueAt(i, col);
      if (alabel == null || alabel.equals("")) {
        // [Label](K.3) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Label](K.1) check for ascii
        bASCII = checkAsciiF(alabel);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }

        // [Label](K.2) no duplicate signal labels
        boolean repeated = false;
        description = Incompliance.error_esa_label + (i + 1);
        for (int j = i + 1; j < nrow; j++) {
          String blabel = (String) esaTable.getModel().getValueAt(j, col);
          if (alabel.equalsIgnoreCase(blabel)) {
            repeated = true;
            description = description + ", " + (j + 1);
          }
        }
        if (repeated) {
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }

      if (esaTable instanceof ESATemplateTable && COL_INDEX_CORRECTED_LABEL != -1) {
        col = COL_INDEX_CORRECTED_LABEL;
        String alabel2 = (String) esaTable.getModel().getValueAt(i, col);
        if (alabel2 == null || alabel2.equals("")) {
          // [Label](K.3) cannot be empty field
          description = Incompliance.error_esa_empty;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Label](K.1) check for ascii
          bASCII = checkAsciiF(alabel2);
          if (!bASCII) {
            description = Incompliance.error_esa_ascii;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }

          // [Label](K.2) no duplicate signal labels
          boolean repeated = false;
          description = Incompliance.error_esa_label + (i + 1);
          for (int j = i + 1; j < nrow; j++) {
            String blabel = (String) esaTable.getModel().getValueAt(j, col);
            if (alabel2.equalsIgnoreCase(blabel)) {
              repeated = true;
              description = description + ", " + (j + 1);
            }
          }
          if (repeated) {
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      /**
       * ********************************************************** ns * 80 ascii : ns * transducer
       * type (e.g. AgAgCl electrode) **********************************************************
       */
      col = COL_INDEX_TRANSDUCER_TYPE;
      String transducer_type = (String) esaTable.getModel().getValueAt(i, col);
      if (transducer_type == null || transducer_type.equals("")) {
        // [Transducer_Type](L.2) can be empty field
      } else {
        // [Transducer_Type](L.1) check for ascii
        bASCII = checkAsciiF(transducer_type);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * physical
       * dimension (e.g. uV or degreeC) **********************************************************
       */
      col = COL_INDEX_PHYSICAL_DIMENSION;
      String physical_dimension = (String) esaTable.getModel().getValueAt(i, col);
      if (physical_dimension == null || physical_dimension.equals("")) {
        // [Physical_Dimension](M.2) can be empty field
      } else {
        // [Physical_Dimension](M.1) check for ascii
        bASCII = checkAsciiF(physical_dimension);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * physical
       * minimum (e.g. -500 or 34) **********************************************************
       */
      col = COL_INDEX_PHYSICAL_MINIMUM;
      String physical_minimum = (String) esaTable.getModel().getValueAt(i, col);
      boolean bGood_physical_minimum = false;
      if (physical_minimum == null || physical_minimum.equals("")) {
        // [Physical_Minimum](N.5) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Physical_Minimum](N.1) check for ascii
        bASCII = checkAsciiF(physical_minimum);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Physical_Minimum](N.2) is a floating point number
          try {
            Float.parseFloat(physical_minimum);
            bGood_physical_minimum = true;
          } catch (NumberFormatException e) {
            description = Incompliance.error_esa_phymin;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * physical
       * maximum (e.g. 500 or 40) **********************************************************
       */
      col = COL_INDEX_PHYSICAL_MAXIMUM;
      String physical_maximum = (String) esaTable.getModel().getValueAt(i, col);
      boolean bGood_physical_maximum = false;
      if (physical_maximum == null || physical_maximum.equals("")) {
        // [Physical_Maximum](O.4) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Physical_Maximum](O.1) check for ascii
        bASCII = checkAsciiF(physical_maximum);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Physical_Maximum](O.2) is a floating point number
          try {
            Float.parseFloat(physical_maximum);
            bGood_physical_maximum = true;
          } catch (NumberFormatException e) {
            description = Incompliance.error_esa_phymax;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      if (bGood_physical_minimum && bGood_physical_maximum) {
        float phy_minimum = Float.parseFloat(physical_minimum);
        float phy_maximum = Float.parseFloat(physical_maximum);

        // [Physical_Maximum](O.3) physical maximum NOT = physical minimum
        if (phy_minimum == phy_maximum) {
          description = Incompliance.error_esa_phy_equal;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }

        // [Physical_Maximum](O.5) physical minimum < physical maximum
        // ==============================
        // Shiqiang Tao
        // 12/9/2016
        // This is a false positive warning.
        // Physical maximum can be smaller than physical minimum due to negative amplifier
        // ==============================
        // else if (phy_minimum > phy_maximum) {
        // 	description = Incompliance.error_esa_phymaxmin;
        // 	incomp = new Incompliance(incomplianceType, description,
        // 			fileName, i, col, errorSrcTypeIndex);
        // 	esaIncompliances.add(incomp);
        // }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * digital
       * minimum (e.g. -2048) **********************************************************
       */
      col = COL_INDEX_DIGITAL_MINIMUM;
      String digital_minimum = (String) esaTable.getModel().getValueAt(i, col);
      boolean bGood_digital_minimum = false;
      if (digital_minimum == null || digital_minimum.equals("")) {
        // [Digital_Minimum](P.4) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Digital_Minimum](P.1) check for ascii
        bASCII = checkAsciiF(digital_minimum);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Digital_Minimum](P.2) is an integer
          try {
            int dig_minimum = Integer.parseInt(digital_minimum);
            bGood_digital_minimum = true;

            // [Digital_Minimum](P.3) since each date sample is a 2-byte integer, range check
            // [-32768,32767]
            boolean bRange = check_digital_range(dig_minimum);
            if (!bRange) {
              description = Incompliance.error_esa_digrange;
              incomp =
                  new Incompliance(
                      incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
              esaIncompliances.add(incomp);
            }
          } catch (NumberFormatException e) {
            description = Incompliance.error_esa_digmin;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * digital
       * maximum (e.g. 2047) **********************************************************
       */
      col = COL_INDEX_DIGITAL_MAXIMUM;
      String digital_maximum = (String) esaTable.getModel().getValueAt(i, col);
      boolean bGood_digital_maximum = false;
      if (digital_maximum == null || digital_maximum.equals("")) {
        // [Digital_Maximum](Q.4) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Digital_Maximum](Q.1) check for ascii
        bASCII = checkAsciiF(digital_maximum);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Digital_Maximum](Q.2) is an integer
          try {
            int dig_maximum = Integer.parseInt(digital_maximum);
            bGood_digital_maximum = true;

            // [Digital_Maximum](Q.3) since each date sample is a 2-byte integer, range check
            // [-32768,32767]
            boolean bRange = check_digital_range(dig_maximum);
            if (!bRange) {
              description = Incompliance.error_esa_digrange;
              incomp =
                  new Incompliance(
                      incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
              esaIncompliances.add(incomp);
            }
          } catch (NumberFormatException e) {
            description = Incompliance.error_esa_digmax;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      if (bGood_digital_minimum && bGood_digital_maximum) {
        int dig_minimum = Integer.parseInt(digital_minimum);
        int dig_maximum = Integer.parseInt(digital_maximum);

        // [Digital_Minimum](Q.6) digital minimum NOT = digital maximum (division-by-0 condition)
        if (dig_minimum == dig_maximum) {
          description = Incompliance.error_esa_dig_equal;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
        // [Digital_Minimum](Q.5) digital minimum < digital maximum
        else if (dig_minimum > dig_maximum) {
          description = Incompliance.error_esa_digmaxmin;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }

      /**
       * ********************************************************** ns * 80 ascii : ns *
       * prefiltering (e.g. HP:0.1Hz LP:75Hz)
       * **********************************************************
       */
      col = COL_INDEX_PREFILTERING;
      String prefiltering = (String) esaTable.getModel().getValueAt(i, col);
      if (prefiltering == null || prefiltering.equals("")) {
        // [Prefiltering](R.2) can be empty field
      } else {
        // [Prefiltering](R.1) check for ascii
        bASCII = checkAsciiF(prefiltering);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }

      /**
       * ********************************************************** ns * 8 ascii : ns * nr of
       * samples in each data record **********************************************************
       */
      col = COL_INDEX_NR_OF_SAMPLES;
      String num_signals = (String) esaTable.getModel().getValueAt(i, col);
      if (num_signals == null || num_signals.equals("")) {
        // [Num_signals](S.4) cannot be empty field
        description = Incompliance.error_esa_empty;
        incomp =
            new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
        esaIncompliances.add(incomp);
      } else {
        // [Num_signals](S.1) check for ascii
        bASCII = checkAsciiF(num_signals);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        } else {
          // [Num_signals](S.2) is an integer
          try {
            int n_signals = Integer.parseInt(num_signals);
            // [Num_signals](S.3) value is greater than 0
            if (n_signals <= 0) {
              description = Incompliance.error_esa_nrSig_range;
              incomp =
                  new Incompliance(
                      incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
              esaIncompliances.add(incomp);
            }
          } catch (NumberFormatException e) {
            description = Incompliance.error_esa_nrSig;
            incomp =
                new Incompliance(
                    incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
            esaIncompliances.add(incomp);
          }
        }
      }

      /**
       * ********************************************************** ns * 32 ascii : ns * reserved
       * **********************************************************
       */
      col = COL_INDEX_RESERVED;
      String reserved = (String) esaTable.getModel().getValueAt(i, col);
      if (reserved == null || reserved.equals("")) {
        // [Reserved](T.2) can be empty field
      } else {
        // [Reserved](T.1) check for ascii
        bASCII = checkAsciiF(reserved);
        if (!bASCII) {
          description = Incompliance.error_esa_ascii;
          incomp =
              new Incompliance(incomplianceType, description, fileName, i, col, errorSrcTypeIndex);
          esaIncompliances.add(incomp);
        }
      }
    } // for loop ends

    if (esaIncompliances.size() > 0) {
      esaTable.setEdfValid(false);
    }

    return esaIncompliances;
  }