feature: MIMIC-IV Replay Scenario Generator
This commit is contained in:
voltsrage
@@ -0,0 +1,191 @@
|
||||
public record MimicPatient(int SubjectId, string Gender, int AnchorAge, int AnchorYear, string? Dod);
|
||||
|
||||
public record MimicAdmission(
|
||||
int SubjectId, int HadmId,
|
||||
DateTime AdmitTime, DateTime DischTime, DateTime? DeathTime,
|
||||
string AdmissionType, string? AdmissionLocation, string? DischargeLocation,
|
||||
int HospitalExpireFlag);
|
||||
|
||||
public record MimicIcuStay(
|
||||
int SubjectId, int HadmId, int StayId,
|
||||
string FirstCareUnit, string LastCareUnit,
|
||||
DateTime InTime, DateTime OutTime, decimal Los);
|
||||
|
||||
public record MimicChartEvent(
|
||||
int StayId, DateTime ChartTime, int ItemId,
|
||||
string? TextValue, decimal? ValueNum);
|
||||
|
||||
public record MimicLabEvent(
|
||||
int HadmId, DateTime ChartTime, int ItemId,
|
||||
decimal? ValueNum, string? ValueUom);
|
||||
|
||||
public record MimicPrescription(
|
||||
int HadmId, DateTime StartTime,
|
||||
string Drug, string? DoseValRx, string? DoseUnitRx, string? Route);
|
||||
|
||||
public class MimicDataLoader
|
||||
{
|
||||
private readonly string _dataDir;
|
||||
|
||||
public MimicDataLoader(string dataDir)
|
||||
{
|
||||
if (!Directory.Exists(dataDir))
|
||||
throw new DirectoryNotFoundException($"MIMIC data directory not found: {dataDir}");
|
||||
_dataDir = dataDir;
|
||||
}
|
||||
|
||||
private string Path(string fileName) => System.IO.Path.Combine(_dataDir, fileName);
|
||||
|
||||
public List<MimicPatient> LoadPatients()
|
||||
{
|
||||
return MimicCsvReader.ReadAll(Path("patients.csv"), (f, h) =>
|
||||
{
|
||||
var id = MimicCsvReader.ColInt(f, h, "subject_id");
|
||||
var age = MimicCsvReader.ColInt(f, h, "anchor_age");
|
||||
var year = MimicCsvReader.ColInt(f, h, "anchor_year");
|
||||
if (id is null || age is null || year is null) return null;
|
||||
return new MimicPatient(
|
||||
id.Value,
|
||||
MimicCsvReader.Col(f, h, "gender"),
|
||||
age.Value,
|
||||
year.Value,
|
||||
MimicCsvReader.Col(f, h, "dod") is { Length: > 0 } dod ? dod : null);
|
||||
});
|
||||
}
|
||||
|
||||
public List<MimicAdmission> LoadAdmissions()
|
||||
{
|
||||
return MimicCsvReader.ReadAll(Path("admissions.csv"), (f, h) =>
|
||||
{
|
||||
var subjectId = MimicCsvReader.ColInt(f, h, "subject_id");
|
||||
var hadmId = MimicCsvReader.ColInt(f, h, "hadm_id");
|
||||
var admitTime = MimicCsvReader.ColDateTime(f, h, "admittime");
|
||||
var dischTime = MimicCsvReader.ColDateTime(f, h, "dischtime");
|
||||
if (subjectId is null || hadmId is null || admitTime is null || dischTime is null)
|
||||
return null;
|
||||
return new MimicAdmission(
|
||||
subjectId.Value, hadmId.Value,
|
||||
admitTime.Value, dischTime.Value,
|
||||
MimicCsvReader.ColDateTime(f, h, "deathtime"),
|
||||
MimicCsvReader.Col(f, h, "admission_type"),
|
||||
MimicCsvReader.Col(f, h, "admission_location") is { Length: > 0 } loc ? loc : null,
|
||||
MimicCsvReader.Col(f, h, "discharge_location") is { Length: > 0 } dloc ? dloc : null,
|
||||
MimicCsvReader.ColInt(f, h, "hospital_expire_flag") ?? 0);
|
||||
});
|
||||
}
|
||||
|
||||
public List<MimicIcuStay> LoadIcuStays()
|
||||
{
|
||||
return MimicCsvReader.ReadAll(Path("icustays.csv"), (f, h) =>
|
||||
{
|
||||
var subjectId = MimicCsvReader.ColInt(f, h, "subject_id");
|
||||
var hadmId = MimicCsvReader.ColInt(f, h, "hadm_id");
|
||||
var stayId = MimicCsvReader.ColInt(f, h, "stay_id");
|
||||
var inTime = MimicCsvReader.ColDateTime(f, h, "intime");
|
||||
var outTime = MimicCsvReader.ColDateTime(f, h, "outtime");
|
||||
if (subjectId is null || hadmId is null || stayId is null
|
||||
|| inTime is null || outTime is null)
|
||||
return null;
|
||||
return new MimicIcuStay(
|
||||
subjectId.Value, hadmId.Value, stayId.Value,
|
||||
MimicCsvReader.Col(f, h, "first_careunit"),
|
||||
MimicCsvReader.Col(f, h, "last_careunit"),
|
||||
inTime.Value, outTime.Value,
|
||||
MimicCsvReader.ColDecimal(f, h, "los") ?? 0m);
|
||||
});
|
||||
}
|
||||
|
||||
public IEnumerable<MimicChartEvent> StreamChartEvents(int stayId)
|
||||
{
|
||||
var stayIdStr = stayId.ToString();
|
||||
return MimicCsvReader.Read(
|
||||
Path("chartevents.csv"),
|
||||
parser: (f, h) =>
|
||||
{
|
||||
var itemId = MimicCsvReader.ColInt(f, h, "itemid");
|
||||
if (itemId is null || !MimicItemMap.AllChartItemIds.Contains(itemId.Value))
|
||||
return null;
|
||||
|
||||
var chartTime = MimicCsvReader.ColDateTime(f, h, "charttime");
|
||||
if (chartTime is null) return null;
|
||||
|
||||
var valueNum = MimicCsvReader.ColDecimal(f, h, "valuenum");
|
||||
var textValue = MimicCsvReader.Col(f, h, "value");
|
||||
|
||||
if (MimicItemMap.IsGcsItem(itemId.Value))
|
||||
{
|
||||
var gcsVal = MimicItemMap.ResolveGcsValue(itemId.Value, textValue, valueNum);
|
||||
if (gcsVal is null) return null;
|
||||
return new MimicChartEvent(stayId, chartTime.Value, itemId.Value, textValue, gcsVal);
|
||||
}
|
||||
|
||||
if (valueNum is null) return null;
|
||||
|
||||
return new MimicChartEvent(stayId, chartTime.Value, itemId.Value, textValue, valueNum);
|
||||
},
|
||||
filter: (f, h) =>
|
||||
{
|
||||
var sid = MimicCsvReader.Col(f, h, "stay_id");
|
||||
return sid == stayIdStr;
|
||||
});
|
||||
}
|
||||
|
||||
public IEnumerable<MimicLabEvent> StreamLabEvents(int hadmId, DateTime? after = null, DateTime? before = null)
|
||||
{
|
||||
var hadmIdStr = hadmId.ToString();
|
||||
return MimicCsvReader.Read(
|
||||
Path("labevents.csv"),
|
||||
parser: (f, h) =>
|
||||
{
|
||||
var itemId = MimicCsvReader.ColInt(f, h, "itemid");
|
||||
if (itemId is null || !MimicItemMap.AllLabItemIds.Contains(itemId.Value))
|
||||
return null;
|
||||
|
||||
var chartTime = MimicCsvReader.ColDateTime(f, h, "charttime");
|
||||
if (chartTime is null) return null;
|
||||
if (after.HasValue && chartTime.Value < after.Value) return null;
|
||||
if (before.HasValue && chartTime.Value > before.Value) return null;
|
||||
|
||||
var valueNum = MimicCsvReader.ColDecimal(f, h, "valuenum");
|
||||
if (valueNum is null) return null;
|
||||
|
||||
return new MimicLabEvent(
|
||||
hadmId, chartTime.Value, itemId.Value, valueNum,
|
||||
MimicCsvReader.Col(f, h, "valueuom") is { Length: > 0 } uom ? uom : null);
|
||||
},
|
||||
filter: (f, h) =>
|
||||
{
|
||||
var hid = MimicCsvReader.Col(f, h, "hadm_id");
|
||||
return hid == hadmIdStr;
|
||||
});
|
||||
}
|
||||
|
||||
public IEnumerable<MimicPrescription> StreamPrescriptions(
|
||||
int hadmId, DateTime? after = null, DateTime? before = null)
|
||||
{
|
||||
var hadmIdStr = hadmId.ToString();
|
||||
return MimicCsvReader.Read(
|
||||
Path("prescriptions.csv"),
|
||||
parser: (f, h) =>
|
||||
{
|
||||
var startTime = MimicCsvReader.ColDateTime(f, h, "starttime");
|
||||
if (startTime is null) return null;
|
||||
if (after.HasValue && startTime.Value < after.Value) return null;
|
||||
if (before.HasValue && startTime.Value > before.Value) return null;
|
||||
|
||||
var drug = MimicCsvReader.Col(f, h, "drug");
|
||||
if (string.IsNullOrWhiteSpace(drug)) return null;
|
||||
|
||||
return new MimicPrescription(
|
||||
hadmId, startTime.Value, drug,
|
||||
MimicCsvReader.Col(f, h, "dose_val_rx") is { Length: > 0 } d ? d : null,
|
||||
MimicCsvReader.Col(f, h, "dose_unit_rx") is { Length: > 0 } u ? u : null,
|
||||
MimicCsvReader.Col(f, h, "route") is { Length: > 0 } r ? r : null);
|
||||
},
|
||||
filter: (f, h) =>
|
||||
{
|
||||
var hid = MimicCsvReader.Col(f, h, "hadm_id");
|
||||
return hid == hadmIdStr;
|
||||
});
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user