feature: MIMIC-IV Replay Scenario Generator

2026-06-25 13:35:09 +08:00
parent 069881991a
commit a8964381a2
29 changed files with 916019 additions and 8 deletions
@@ -0,0 +1,75 @@
+using System.CommandLine;
+using Spectre.Console;
+
+public static class MimicListCommand
+{
+    public static Command Create()
+    {
+        var dataDirArg = new Argument<DirectoryInfo>("mimic-dir",
+            "Path to directory containing MIMIC-IV CSV files");
+        var subjectIdOpt = new Option<int?>("--subject-id", "Filter to a specific patient");
+        var stayIdOpt = new Option<int?>("--stay-id", "Filter to a specific ICU stay");
+
+        var command = new Command("mimic-list",
+            "List available MIMIC-IV patients and ICU stays")
+        {
+            dataDirArg, subjectIdOpt, stayIdOpt
+        };
+
+        command.SetHandler(context =>
+        {
+            var dataDir = context.ParseResult.GetValueForArgument(dataDirArg);
+            var subjectId = context.ParseResult.GetValueForOption(subjectIdOpt);
+            var stayId = context.ParseResult.GetValueForOption(stayIdOpt);
+
+            var loader = new MimicDataLoader(dataDir.FullName);
+            var patients = loader.LoadPatients().ToDictionary(p => p.SubjectId);
+            var admissions = loader.LoadAdmissions().ToDictionary(a => a.HadmId);
+            var stays = loader.LoadIcuStays();
+
+            if (subjectId.HasValue)
+                stays = stays.Where(s => s.SubjectId == subjectId.Value).ToList();
+            if (stayId.HasValue)
+                stays = stays.Where(s => s.StayId == stayId.Value).ToList();
+
+            var table = new Table()
+                .Border(TableBorder.Rounded)
+                .Title("[bold]MIMIC-IV ICU Stays[/]");
+
+            table.AddColumn("StayId");
+            table.AddColumn("SubjectId");
+            table.AddColumn("HadmId");
+            table.AddColumn("Gender");
+            table.AddColumn("Age");
+            table.AddColumn("Care Unit");
+            table.AddColumn("Admission");
+            table.AddColumn("LOS (d)");
+            table.AddColumn("Expired");
+
+            foreach (var stay in stays.OrderBy(s => s.SubjectId).ThenBy(s => s.InTime))
+            {
+                var pt = patients.GetValueOrDefault(stay.SubjectId);
+                var adm = admissions.GetValueOrDefault(stay.HadmId);
+
+                table.AddRow(
+                    stay.StayId.ToString(),
+                    stay.SubjectId.ToString(),
+                    stay.HadmId.ToString(),
+                    pt?.Gender ?? "?",
+                    pt?.AnchorAge.ToString() ?? "?",
+                    Markup.Escape(stay.FirstCareUnit),
+                    adm?.AdmissionType ?? "?",
+                    stay.Los.ToString("F1"),
+                    adm?.HospitalExpireFlag == 1 ? "[red]Yes[/]" : "No");
+            }
+
+            AnsiConsole.Write(table);
+
+            var patientCount = stays.Select(s => s.SubjectId).Distinct().Count();
+            AnsiConsole.MarkupLine(
+                $"\nFound [bold]{stays.Count}[/] ICU stays across [bold]{patientCount}[/] patients.");
+        });
+
+        return command;
+    }
+}