Examples of org.aavso.tools.vstar.data.ValidObservation

org.aavso.tools.vstar.data.ValidObservation

This class corresponds to a single valid variable star observation. Depending upon the source, some fields may be null. Some are not permitted to be null however and these are documented below.

For reference, here are the fields in the order they appear in the AAVSO download format:

JD(0), MAGNITUDE(1), UNCERTAINTY(2), HQ_UNCERTAINTY(3), BAND(4), OBSERVER_CODE(5), COMMENT_CODE(6), COMP_STAR_1(7), COMP_STAR_2(8), CHARTS(9), COMMENTS(10), TRANSFORMED(11), AIRMASS(12), VALFLAG(13), CMAG(14), KMAG(15), HJD(16), NAME(17), AFFILIATION(18), MTYPE(19), GROUP(20)

The simple format file has these fields:

JD MAGNITUDE [UNCERTAINTY] [OBSERVER_CODE] [VALFLAG]

When VStar was first developed, observation source plugins were not anticipated, but should have been. The additional details members permit other string-based information to be stored for an observation.

  /**
   * @see javax.swing.table.TableModel#getValueAt(int, int)
   */
  public Object getValueAt(int rowIndex, int columnIndex) {
    assert columnIndex < columnCount;
    ValidObservation validOb = this.validObservations.get(rowIndex);
    return this.columnInfoSource.getTableColumnValue(columnIndex, validOb);
  }

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      // https://sourceforge.net/tracker/?func=detail&aid=2964224&group_id=263306&atid=1152052
      // for more detail.
      if (Mediator.getInstance().getAnalysisType() == AnalysisType.RAW_DATA) {


        // Toggle "is-discrepant" checkbox and value.
        ValidObservation ob = this.validObservations.get(rowIndex);
        boolean discrepant = ob.isDiscrepant();
        ob.setDiscrepant(!discrepant);
        // Tell anyone who's listening about the change.
        DiscrepantObservationMessage message = new DiscrepantObservationMessage(
            ob, this);
        Mediator.getInstance().getDiscrepantObservationNotifier()
            .notifyListeners(message);

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   * @throws ObservationValidationError
   */
  public ValidObservation validate(String line)
      throws IOException, ObservationValidationError, ObservationValidationWarning {


    ValidObservation observation = super.validate();
    
    // TODO: assert which fields should not be null


    return observation;
  }

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   *         created from the current record's fields.
   */
  public ValidObservation validate() throws IOException,
      ObservationValidationError, ObservationValidationWarning {


    ValidObservation observation = null;


    // Get an array of fields split on the expected delimiter.
    fields = fieldSplitter.getFields();


    if (fields.length != 0) {
      // Create a new valid observation, making the assumption
      // that validation will pass.
      observation = new ValidObservation();


      // Validate the fields.
      DateInfo dateInfo = julianDayValidator
          .validate(fields[fieldIndexMap.get("JD_FIELD")]);
      observation.setDateInfo(dateInfo);


      Magnitude magnitude = magnitudeFieldValidator
          .validate(fields[fieldIndexMap.get("MAGNITUDE_FIELD")]);


      Double uncertaintyMag = uncertaintyValueValidator
          .validate(fields[fieldIndexMap.get("UNCERTAINTY_FIELD")]);


      if (uncertaintyMag != null) {
        magnitude.setUncertainty(uncertaintyMag);
      }


      if (magnitude.isBrighterThan()) {
        throw new ObservationValidationError(
            "Was '>' intended (brighter than) or '<'?");
      }


      observation.setMagnitude(magnitude);


      if (observation.getBand() == null) {
        observation.setBand(SeriesType.Unspecified);
      }


      observation
          .setObsCode(observerCodeValidator
              .validate(fields[fieldIndexMap
                  .get("OBSERVER_CODE_FIELD")]));


      String valflag = fields[fieldIndexMap.get("VALFLAG_FIELD")];
      observation.setValidationType(valflagValidator.validate(valflag));
    }


    return observation;
  }

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   * @return The validated ValidObservation object.
   */
  public ValidObservation validate() throws IOException,
      ObservationValidationError, ObservationValidationWarning {


    ValidObservation observation = super.validate();


    // Validate the fields.


    Double hqUncertaintyMag = uncertaintyValueValidator
        .validate(fields[fieldIndexMap.get("HQ_UNCERTAINTY_FIELD")]);
    observation.setHqUncertainty(hqUncertaintyMag);


    // TODO: we should use a specific band validator that returns SeriesType
    String band = nonOptionalFieldValidator.validate(fields[fieldIndexMap
        .get("BAND_FIELD")]);
    observation.setBand(SeriesType.getSeriesFromShortName(band));


    String commentCode = commentCodeValidator.validate(fields[fieldIndexMap
        .get("COMMENT_CODE_FIELD")]);
    observation.setCommentCode(commentCode);


    String compStar1 = compStarValidator.validate(fields[fieldIndexMap
        .get("COMP_STAR_1_FIELD")]);
    observation.setCompStar1(compStar1);


    String compStar2 = compStarValidator.validate(fields[fieldIndexMap
        .get("COMP_STAR_2_FIELD")]);
    observation.setCompStar2(compStar2);


    String charts = optionalFieldValidator.validate(fields[fieldIndexMap
        .get("CHARTS_FIELD")]);
    observation.setCharts(charts);


    String comments = optionalFieldValidator.validate(fields[fieldIndexMap
        .get("COMMENTS_FIELD")]);
    observation.setComments(comments);


    boolean isTransformed = transformedValidator
        .validate(fields[fieldIndexMap.get("TRANSFORMED_FIELD")]);
    observation.setTransformed(isTransformed);


    String airmass = optionalFieldValidator.validate(fields[fieldIndexMap
        .get("AIRMASS_FIELD")]);
    observation.setAirmass(airmass);


    String cMag = cMagValidator.validate(fields[fieldIndexMap
        .get("CMAG_FIELD")]);
    observation.setCMag(cMag);


    String kMag = kMagValidator.validate(fields[fieldIndexMap
        .get("KMAG_FIELD")]);
    observation.setKMag(kMag);


    DateInfo hjdInfo = hjdValidator.validate(fields[fieldIndexMap
        .get("HJD_FIELD")]);
    observation.setHJD(hjdInfo);


    String name = nameFieldValidator.validate(fields[fieldIndexMap
        .get("NAME_FIELD")]);
    observation.setName(name);


    MTypeType mType = magTypeValidator.validate(fields[fieldIndexMap
        .get("MTYPE_FIELD")]);
    if (mType != null) {
      observation.setMType(mType);
    }


    // TODO: add group and affiliation fields and getters


    return observation;

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  private static final double DEFAULT_BIN_PHASE_INCREMENTS = 0.1;


  public static final PhaseTimeElementEntity instance = new PhaseTimeElementEntity();


  public double getTimeElement(List<ValidObservation> obs, int index) {
    ValidObservation ob = obs.get(index);
    Double phase = null;


    if (index < obs.size() / 2) {
      phase = ob.getPreviousCyclePhase();
    } else {
      phase = ob.getStandardPhase();
    }


    assert phase != null;


    return phase;

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    // TODO: fix wrt locale
    String comment = "From polynomial fit of degree " + degree;


    for (n = 1; n <= numred; n++) {
      // write(1,222)tfit(n)+dt0,xfit(n),ds9*sfit(n)
      ValidObservation fitOb = new ValidObservation();
      fitOb.setDateInfo(new DateInfo(tfit[n] + dt0));
      // double uncertainty = ds9*sfit[n]; // TODO: ask Matt about this;
      // uncertainty?
      fitOb.setMagnitude(new Magnitude(xfit[n], 0));
      fitOb.setComments(comment);
      fitOb.setBand(SeriesType.Model);
      fit.add(fitOb);
    }


    if (fit.isEmpty()) {
      throw new AlgorithmError("No observations in fit list.");
    }


    // Note: save residuals (to list)


    // 40 write(6,*) 'Residuals filename?'
    // read*,ftmp;
    // 41 open(unit=9,file=ftmp,status='unknown',err=42);
    // 42 write(6,*) 'Could not open file.'


    // Store the residuals resulting from the polynomial fit operation as
    // "residual observations".
    residuals = new ArrayList<ValidObservation>();


    for (n = nlolim; n <= nuplim; n++) {
      if (wvec[n] > 0.0) {
        dtime = tvec[n];
        dx = smooth(dtime);
        res = xvec[n] - dx;
        for (nb = 1; nb <= nbias; nb++) {
          if (obs[n] == obias[nb])
            res = res - dcoef[npoly + nb];
        }
        // write(9,240) tvec(n)+dt0,res
        ValidObservation residualOb = new ValidObservation();
        residualOb.setDateInfo(new DateInfo(tvec[n] + dt0));
        residualOb.setMagnitude(new Magnitude(res, 0));
        residualOb.setComments(comment);
        residualOb.setBand(SeriesType.Residuals);
        residuals.add(residualOb);
      }
    }


    // 211 format(7hTime0= ,f12.4)

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          String comment = "From WWZ, period "
              + NumericPrecisionPrefs.formatOther(period);


          // Create a fit observation from the average magnitude for
          // this time-frequency/period combination.
          ValidObservation fitOb = new ValidObservation();
          fitOb.setDateInfo(new DateInfo(stat.getTau()));
          fitOb.setMagnitude(new Magnitude(stat.getMave(), 0));
          fitOb.setBand(SeriesType.Model);
          fitOb.setComments(comment);
          fit.add(fitOb);


          // Create a residual observation for each observation since
          // the previous period. TODO: sanity check this approach,
          // i.e. does it actually make sense for a tau value to
          // represent a range of observation time values for the
          // purpose of residual creation?
          while (i < obs.size()
              && obs.get(i).getJD() <= stat.getTau()) {
            double residual = obs.get(i).getMag() - stat.getMave();
            ValidObservation residualOb = new ValidObservation();
            residualOb
                .setDateInfo(new DateInfo(obs.get(i).getJD()));
            residualOb.setMagnitude(new Magnitude(residual, 0));
            residualOb.setBand(SeriesType.Residuals);
            residualOb.setComments(comment);
            residuals.add(residualOb);
            i++;
          }
        }

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                  minMagErr = magErr;
                } else if (magErr > maxMagErr) {
                  maxMagErr = magErr;
                }


                ValidObservation ob = new ValidObservation();
                ob.setDateInfo(new DateInfo(hjd));
                ob.setMagnitude(new Magnitude(mag, magErr));
                ob.setBand(keplerSeries);
                ob.setRecordNumber(row);
                collectObservation(ob);
              }
            } catch (Exception e) {
              String input = tableHDU.getRow(row).toString();
              String error = e.getLocalizedMessage();
              InvalidObservation ob = new InvalidObservation(
                  input, error);
              ob.setRecordNumber(row);
              addInvalidObservation(ob);
            }
          }
        }
      }

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                  minMagErr = magErr;
                } else if (magErr > maxMagErr) {
                  maxMagErr = magErr;
                }


                ValidObservation ob = new ValidObservation();
                ob.setDateInfo(new DateInfo(hjd));
                ob.setMagnitude(new Magnitude(mag, magErr));
                ob.setBand(superWaspSeries);
                ob.setRecordNumber(row);
                ob.addDetail("IMAGE_ID", imageId, "Image ID");
                ob.addDetail("CCDX", ccdX + "", "CCD X");
                ob.addDetail("CCDY", ccdY + "", "CCD Y");
                ob.addDetail("FLUX", tamFlux + "", "Flux");
                ob.addDetail("FLUXERR", tamFluxErr + "",
                    "Flux Error");
//                ob.addDetail("FLAG", flag + "", "Flag");
                obs.add(ob);
              }
            } catch (Exception e) {
              String input = tableHDU.getRow(row).toString();
              String error = e.getLocalizedMessage();
              InvalidObservation ob = new InvalidObservation(
                  input, error);
              ob.setRecordNumber(row);
              addInvalidObservation(ob);
            }
          }
        }
      }

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