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 +1,136 @@
+using System.CommandLine;
+using System.Text.Json;
+using Spectre.Console;
+
+public static class MimicGenerateCommand
+{
+    public static Command Create()
+    {
+        var dataDirArg = new Argument<DirectoryInfo>("mimic-dir",
+            "Path to directory containing MIMIC-IV CSV files");
+        var stayIdOpt = new Option<int>("--stay-id", "ICU stay ID to generate scenario for")
+        { IsRequired = true };
+        var maxHoursOpt = new Option<int?>("--max-hours", "Limit scenario duration in hours");
+        var noMedsOpt = new Option<bool>("--no-medications", () => false,
+            "Exclude medication events");
+        var noLabsOpt = new Option<bool>("--no-labs", () => false,
+            "Exclude lab observations");
+        var outputOpt = new Option<string?>("--output", "Output file path (default: auto-named)");
+        var validateOpt = new Option<bool>("--validate", () => false,
+            "Run scenario validation after generation");
+
+        var command = new Command("mimic-generate",
+            "Generate a VigilCare scenario JSON from a MIMIC-IV ICU stay")
+        {
+            dataDirArg, stayIdOpt, maxHoursOpt, noMedsOpt, noLabsOpt, outputOpt, validateOpt
+        };
+
+        command.SetHandler(context =>
+        {
+            var dataDir = context.ParseResult.GetValueForArgument(dataDirArg);
+            var stayId = context.ParseResult.GetValueForOption(stayIdOpt);
+            var maxHours = context.ParseResult.GetValueForOption(maxHoursOpt);
+            var noMeds = context.ParseResult.GetValueForOption(noMedsOpt);
+            var noLabs = context.ParseResult.GetValueForOption(noLabsOpt);
+            var outputPath = context.ParseResult.GetValueForOption(outputOpt);
+            var validate = context.ParseResult.GetValueForOption(validateOpt);
+
+            var loader = new MimicDataLoader(dataDir.FullName);
+
+            AnsiConsole.MarkupLine($"[bold]Loading MIMIC-IV data for stay {stayId}...[/]");
+
+            var stays = loader.LoadIcuStays();
+            var stay = stays.FirstOrDefault(s => s.StayId == stayId);
+            if (stay is null)
+            {
+                AnsiConsole.MarkupLine($"[red]ICU stay {stayId} not found.[/]");
+                var available = stays.Select(s => s.StayId).OrderBy(x => x).ToList();
+                AnsiConsole.MarkupLine($"Available stay IDs: {string.Join(", ", available.Take(20))}...");
+                return;
+            }
+
+            var admissions = loader.LoadAdmissions();
+            var admission = admissions.FirstOrDefault(a => a.HadmId == stay.HadmId);
+            if (admission is null)
+            {
+                AnsiConsole.MarkupLine($"[red]Admission {stay.HadmId} not found.[/]");
+                return;
+            }
+
+            var patients = loader.LoadPatients();
+            var patient = patients.FirstOrDefault(p => p.SubjectId == stay.SubjectId);
+            if (patient is null)
+            {
+                AnsiConsole.MarkupLine($"[red]Patient {stay.SubjectId} not found.[/]");
+                return;
+            }
+
+            AnsiConsole.MarkupLine(
+                $"  Patient: [cyan]{patient.SubjectId}[/] ({patient.Gender}, ~{patient.AnchorAge}y)");
+            AnsiConsole.MarkupLine(
+                $"  Stay:    [cyan]{stay.StayId}[/] in {stay.FirstCareUnit}");
+            AnsiConsole.MarkupLine(
+                $"  LOS:     {stay.Los:F1} days ({stay.InTime:g} → {stay.OutTime:g})");
+            AnsiConsole.MarkupLine(
+                $"  Outcome: {(admission.HospitalExpireFlag == 1 ? "[red]Expired[/]" : "Survived")}");
+
+            var options = new MimicGenerateOptions(
+                MaxHours: maxHours,
+                IncludeMedications: !noMeds,
+                IncludeLabs: !noLabs);
+
+            AnsiConsole.MarkupLine("\n[bold]Generating scenario...[/]");
+
+            var builder = new MimicScenarioBuilder(loader);
+            var (scenario, warnings) = builder.Build(stay, admission, patient, options);
+
+            foreach (var warning in warnings)
+                AnsiConsole.MarkupLine($"  [yellow]WARNING:[/] {Markup.Escape(warning)}");
+
+            var obsCount = scenario.Events.Count(e => e.Type == "observation");
+            var medCount = scenario.Events.Count(e => e.Type == "medication");
+            AnsiConsole.MarkupLine(
+                $"  Events: [green]{obsCount}[/] observations, [green]{medCount}[/] medications");
+            AnsiConsole.MarkupLine(
+                $"  Duration: {scenario.Scenario.DurationMinutes} minutes " +
+                $"({scenario.Scenario.DurationMinutes / 60.0:F1} hours)");
+
+            if (validate)
+            {
+                var errors = ScenarioValidator.Validate(scenario);
+                if (errors.Count == 0)
+                {
+                    AnsiConsole.MarkupLine("  [green]Validation: PASSED[/]");
+                }
+                else
+                {
+                    AnsiConsole.MarkupLine($"  [red]Validation: {errors.Count} error(s)[/]");
+                    foreach (var err in errors)
+                        AnsiConsole.MarkupLine($"    [red]• {Markup.Escape(err)}[/]");
+                }
+            }
+
+            var jsonOptions = new JsonSerializerOptions
+            {
+                PropertyNamingPolicy = JsonNamingPolicy.CamelCase,
+                WriteIndented = true,
+                Encoder = System.Text.Encodings.Web.JavaScriptEncoder.UnsafeRelaxedJsonEscaping
+            };
+
+            var json = JsonSerializer.Serialize(scenario, jsonOptions);
+
+            var filePath = outputPath
+                ?? Path.Combine("Scenarios", "List", $"mimic-s{stayId}.json");
+
+            var dir = Path.GetDirectoryName(filePath);
+            if (!string.IsNullOrEmpty(dir) && !Directory.Exists(dir))
+                Directory.CreateDirectory(dir);
+
+            File.WriteAllText(filePath, json);
+            AnsiConsole.MarkupLine($"\n[bold green]Scenario written to:[/] {filePath}");
+            AnsiConsole.MarkupLine($"  Replay with: [dim]dotnet run -- replay {filePath}[/]");
+        });
+
+        return command;
+    }
+}