// Pregnancy episode start marker types: LMP: Last menstrual period date, GEST: Gestational age record, FERT: Assisted
// conception procedure date, ULS: Nuchal ultrasound date, AFP: Alpha feto protein test date, AMEN: Amenorrhea record date,
// URINE: Urine pregnancy test date
private static IEnumerable <KeyValuePair <Event, Event> > FindPregnancEpisodes(
Dictionary <string, List <Event> > validOutcomes, RawEvents raw,
Dictionary <string, TermDurations> termDurations, Dictionary <string, GestEst> gestEst, string[] markers, bool hasDefault, bool desc)
{
var outcomes = new List <Event>();
foreach (var outcomeCategory in validOutcomes.Keys)
{
outcomes.AddRange(validOutcomes[outcomeCategory]);
}
foreach (var outcome in outcomes)
{
var duration = termDurations[outcome.Category];
var ge = gestEst[outcome.Category];
var priorOutcomeDate = DateTime.MinValue;
var priorOutcomes = outcomes.Where(o => o.Date < outcome.Date).ToArray();
TermDurations durationPrior = null;
if (priorOutcomes.Any())
{
var po = priorOutcomes.OrderByDescending(o => o.Date).First();
priorOutcomeDate = po.Date;
durationPrior = termDurations[po.Category];
}
foreach (var startEpisodeOutcome in FindPregnancyStartEvent(raw, duration, durationPrior, outcome, priorOutcomeDate,
ge, markers, hasDefault, desc))
{
yield return(new KeyValuePair <Event, Event>(outcome, startEpisodeOutcome));
}
}
}
private static IEnumerable <Event> FindPregnancyStartEvent(RawEvents raw, TermDurations duration,
TermDurations durationPrior, Event outcome, DateTime priorOutcomeDate, GestEst g, string[] markers,
bool hasDefault, bool desc)
{
List <Event> starts = new List <Event>();
foreach (var startMarker in markers)
{
if (!raw.PregnancyEvents.ContainsKey(startMarker))
{
continue;
}
foreach (var pe in raw.PregnancyEvents[startMarker]
.OrderBy(e => e.Date))
{
var e = FindStart(outcome, pe, duration, priorOutcomeDate);
if (e == null)
{
continue;
}
e.OriginalDate = pe.Date;
starts.Add(e);
}
}
if (starts.Any())
{
foreach (var group in starts.GroupBy(s => s.Category))
{
if (desc)
{
var maxDate = group.Max(e => e.OriginalDate);
yield return(group.Where(e => e.OriginalDate == maxDate).OrderBy(e => e.EventId).First());
}
else
{
var minDate = group.Min(e => e.OriginalDate);
yield return(group.Where(e => e.OriginalDate == minDate).OrderBy(e => e.EventId).First());
}
}
}
if (hasDefault)
{
var wStart = outcome.Date.Date.AddDays(-1 * duration.MaxTerm);
var wEnd = outcome.Date.AddDays(30);
if (outcome.Date.Between(priorOutcomeDate > wStart ? priorOutcomeDate : wStart,
wEnd))
{
var episodeStartDate = outcome.Date;
var category = "DEFAULT";
if (raw.PregnancyEvents.ContainsKey("PREM") && raw.PregnancyEvents["PREM"].Count(e =>
e.Date.Between(priorOutcomeDate > wStart ? priorOutcomeDate : wStart,
wEnd)) > 0)
{
episodeStartDate = episodeStartDate.Date.AddDays(-1 * g.PreTerm);
category = "PREM";
}
else if (raw.PregnancyEvents.ContainsKey("FT") && raw.PregnancyEvents["FT"].Count(e =>
e.Date.Between(priorOutcomeDate > wStart ? priorOutcomeDate : wStart,
wEnd)) > 0)
{
episodeStartDate = episodeStartDate.Date.AddDays(-1 * g.FullTerm);
}
else
{
episodeStartDate = episodeStartDate.Date.AddDays(-1 * g.NoData);
}
if (durationPrior != null && priorOutcomeDate.AddDays(durationPrior.Retry) > episodeStartDate)
{
episodeStartDate = priorOutcomeDate.AddDays(durationPrior.Retry);
}
yield return(new Event {
EventId = outcome.EventId, Category = category, Date = episodeStartDate
});
}
}
}
public IEnumerable <ConditionEra> GetPregnancyEpisodes(IVocabulary vocab, Person person, ObservationPeriod[] observationPeriods,
ConditionOccurrence[] conditionOccurrences,
ProcedureOccurrence[] procedureOccurrences, Observation[] observations, Measurement[] measurements,
DrugExposure[] drugExposures)
{
if (person.GenderConceptId != 8532)
{
yield break;
}
var raw = new RawEvents();
raw.Fill(vocab, conditionOccurrences, procedureOccurrences, observations, measurements, drugExposures);
if (raw.PregnancyEvents.Count == 0)
{
yield break;
}
var outcomeLimits = new Dictionary <string, Dictionary <string, OutcomeLimit> >();
foreach (var ol in _outcomeLimits)
{
if (!outcomeLimits.ContainsKey(ol.FirstPregCategory))
{
outcomeLimits.Add(ol.FirstPregCategory, new Dictionary <string, OutcomeLimit>());
}
outcomeLimits[ol.FirstPregCategory].Add(ol.OutcomePregCategory, ol);
}
var termDurations = _termDurations.ToDictionary(termDuration => termDuration.Category);
var gestEsts = _gestEsts.ToDictionary(ge => ge.Category);
var validOutcomes = new Dictionary <string, List <Event> >();
foreach (var outcomeType in _outcomeTypes)
{
if (!raw.PregnancyEvents.ContainsKey(outcomeType))
{
continue;
}
foreach (var g in raw.PregnancyEvents[outcomeType].OrderBy(pe => pe.Date).GroupBy(pe => pe.Date))
{
var e = g.First();
if (outcomeType == "AB" || outcomeType == "SA")
{
// Reassign abortion outcome date to last abortion date within 2 weeks after
var revisedDates = new List <DateTime>(2)
{
GetRevisedDate("SA", 14, e, raw.PregnancyEvents),
GetRevisedDate("AB", 14, e, raw.PregnancyEvents)
};
var revisedDate = revisedDates.Max();
if (revisedDate != DateTime.MinValue)
{
e.Date = revisedDate;
}
}
else if (outcomeType == "ECT")
{
// Reassign ectopic pregnancy outcome date to last treatment date within 2 weeks after
var revisedDates = new List <DateTime>(2)
{
GetRevisedDate("ECT_SURG1", 14, e, raw.PregnancyEvents),
GetRevisedDate("MTX", 14, e, raw.PregnancyEvents)
};
var revisedDate = revisedDates.Max();
if (revisedDate != DateTime.MinValue)
{
e.Date = revisedDate;
}
}
if (!HasInvalidWindow(e, outcomeLimits, validOutcomes) && IsValid(e, raw.PregnancyEvents))
{
if (!validOutcomes.ContainsKey(e.Category))
{
validOutcomes.Add(e.Category, new List <Event>());
}
validOutcomes[e.Category].Add(e);
}
}
}
if (validOutcomes.Count > 0)
{
var allEpisodes = FindPregnancEpisodes(validOutcomes, raw, termDurations, gestEsts,
new[] { "OVUL", "OVUL2", "NULS", "AFP", "AMEN", "UP" }, true, false).ToList();
allEpisodes.AddRange(FindPregnancEpisodes(validOutcomes, raw, termDurations, gestEsts,
new[] { "LMP", "GEST" }, false, true));
var pconf = FindPregnancEpisodes(validOutcomes, raw, termDurations, gestEsts,
new[] { "PCONF", "AGP", "PCOMP", "TA" }, false, false).ToArray();
var pconfEpisodes = new List <KeyValuePair <Event, Event> >();
if (pconf.Any())
{
pconfEpisodes.AddRange(pconf.GroupBy(p => p.Key.Guid)
.Select(g => g.OrderBy(e => e.Value.Date).First()));
}
var contraEpisodes = FindPregnancEpisodes(validOutcomes, raw, termDurations, gestEsts,
new[] { "CONTRA" }, false, true).ToArray();
var all = GetEpisodesAllStarts(person, allEpisodes, pconfEpisodes, contraEpisodes).ToArray();
foreach (var episodes in all.GroupBy(e => e.EndDate))
{
var pe = episodes.OrderBy(e => e.TypeConceptId).ThenBy(e => e.StartDate).First();
var startDate = pe.StartDate;
var endDate = pe.EndDate.Value;
if (startDate.Year - person.YearOfBirth >= 12 && startDate.Year - person.YearOfBirth <= 55 &&
observationPeriods.Any(op =>
startDate >= op.StartDate && endDate.Between(op.StartDate, op.EndDate.Value)))
{
int cnt = 0;
foreach (var c in raw.PregnancyEvents.Keys)
{
foreach (var e in raw.PregnancyEvents[c])
{
if (e.Date.Between(
endDate.AddDays(-1 * termDurations[pe.SourceValue].MaxTerm + 1), endDate))
{
cnt++;
}
}
}
if (cnt >= 2)
{
pe.ConceptId = GetConceptId(pe);
yield return(pe);
}
}
}
}
}
