Refactored to version 2.0.0

.github/workflows/test.yml

@@ -0,0 +1,20 @@
+# .github/workflows/run_mocha_tests.yml
+name: Test
+
+on: [push, workflow_dispatch]
+
+jobs:
+  build:
+    name: Test
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Use Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: '16.x'
+      - run: npm install
+      - run: npm run build --if-present
+      - run: npm test

.gitignore

@@ -1,5 +1,6 @@
 node_modules
+coverage
 dist
-examples/headlessComparativeStudyResults.json
-examples/headlessComparativeStudy.png
+examples/**.json
+examples/**.png
 package-lock.json

.mocharc.json

@@ -0,0 +1,11 @@
+{
+    "extension": ["ts", "js", "mjs"],
+    "spec": "test/**/*.test.*",
+    "node-option": [
+        "experimental-specifier-resolution=node",
+        "loader=ts-node/esm"
+      ],    
+    "package": "./package.json",
+    "bail": false,
+    "recursive": true
+}

.vscode/extensions.json

@@ -0,0 +1,6 @@
+{
+    "recommendations": [
+        "vue.vscode-typescript-vue-plugin",
+        "vue.volar"
+    ]
+}

.vscode/launch.json

@@ -0,0 +1,74 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Serve",
+            "command": "npm run serve",
+            "request": "launch",
+            "type": "node-terminal"
+        },
+        {
+            "name": "Build",
+            "command": "npm run build",
+            "request": "launch",
+            "type": "node-terminal"
+        },
+        {
+            "name": "Run unit tests",
+            "command": "npm run test",
+            "request": "launch",
+            "type": "node-terminal"
+        },
+        {
+            "name": "Launch Chrome (debug)",
+            "type": "chrome",
+            "request": "launch",
+            "url": "http://localhost:8080",
+            "webRoot": "${workspaceFolder}",
+            "sourceMaps": true
+        },
+        {
+            "name": "Launch Edge (debug)",
+            "type": "msedge",
+            "request": "launch",
+            "url": "http://localhost:8080",
+            "webRoot": "${workspaceFolder}",
+            "sourceMaps": true
+        },
+		{
+            "name": "Run minimal demo (JS)",
+            "command": "node --loader ts-node/esm ./MinimalDemoJS.js",
+            "request": "launch",
+            "cwd": "${workspaceRoot}/examples/MinimalDemo/",
+            "type": "node-terminal"
+        },
+        {
+            "name": "Run minimal demo (TS)",
+            "command": "node --loader ts-node/esm ./MinimalDemoTS.ts",
+            "request": "launch",
+            "cwd": "${workspaceRoot}/examples/MinimalDemo/",
+            "type": "node-terminal"
+        },
+		{
+            "name": "Run controller study demo",
+            "command": "node --loader ts-node/esm ./ControllerStudyDemo.ts",
+            "request": "launch",
+            "cwd": "${workspaceRoot}/examples/ControllerStudyDemo",
+            "type": "node-terminal"
+        },
+		{
+            "name": "Omnipod in silico study",
+            "command": "node --loader ts-node/esm ./OmnipodInSilicoStudy.ts",
+            "request": "launch",
+            "cwd": "${workspaceRoot}/examples/OmnipodStudy/",
+            "type": "node-terminal",
+        },
+        {
+            "name": "Exercise models comparison",
+            "command": "node --loader ts-node/esm ./ExerciseModelsComparison.ts",
+            "request": "launch",
+            "cwd": "${workspaceRoot}/examples/ExerciseModelsComparison/",
+            "type": "node-terminal",
+        },
+    ]
+}

@types/oref0.d.ts

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+declare module 'oref0/lib/determine-basal/determine-basal.js'
+declare module 'oref0/lib/basal-set-temp.js'
+declare module 'oref0/lib/iob/index.js'
+declare module 'oref0/lib/meal/total.js'
+declare module 'oref0/lib/glucose-get-last.js'

@types/shims-vue.d.ts

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+declare module '*.vue' {
+    import { DefineComponent } from 'vue'
+    const component: DefineComponent<{}, {}, any>
+    export default component
+}
+

@types/vue-i18n.d.ts

@@ -0,0 +1,2 @@
+
+declare module 'vue-i18n'

CONTRIBUTORS

@@ -0,0 +1,6 @@
+Heiko Peuscher
+Hariolf Betz
+Simone Hohm
+Isabell Seidler
+Lorenzo Sandini
+Tom Wetterich

LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Heiko Peuscher
+Copyright (c) 2021-present, Heiko Peuscher et al.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,13 +1,20 @@
-<p align="center">
+<p align="left">
   <a href="https://lt1.org/" target="_blank">
-    <img alt="LoopInsighT1" src="./src/assets/images/loopinsight1.png" width="240">
+    <img alt="LoopInsighT1" src="./src/frontend/assets/images/LT1_logo.png" width="200">
   </a>
 </p>
 
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![TypeScript](https://img.shields.io/badge/%3C%2F%3E-TypeScript-%230074c1.svg)](http://www.typescriptlang.org/)
+[![PR's welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](https://LT1.org/contribute)
+![test](https://github.com/hpeuscher/lt1-private/actions/workflows/test.yml/badge.svg)
+
+<hr/>
+
 This software is intended for closed-loop simulation of automatic insulin delivery systems for type 1 diabetic persons.
 
 # Demo and further information
-For a live demo, visit the [project website](https://lt1.org/simulator)
+For a live demo, visit the project website [https://LT1.org](https://lt1.org/simulator).
 
 # Installation / Quick start
 Follow these instructions to use the simulator locally and modify its source code.

examples/ControllerStudyDemo/ControllerStudyDemo.ts

@@ -0,0 +1,127 @@
+/** 
+ * This file is part of LoopInsighT1, an open source tool to
+ * simulate closed-loop glycemic control in type 1 diabetes.
+ * Distributed under the MIT software license.
+ * See https://lt1.org for further information.
+ */
+
+/**
+ * This file performs two simulations with identical scenarios but
+ * different controller algorithms. The results are stored to a
+ * JSON file, from which they can be imported and postprocessed
+ * in other tools like Matlab(R)
+ * 
+ * Usage:  cd ./examples/ControllerStudyDemo
+ *         node --loader ts-node/esm ./ControllerStudyDemo.ts
+ * 
+ * Or run the "Run controller study demo (JS)" configuration in VS Code 
+ *   (which will support debugging).
+ */
+
+import * as fs from 'fs'
+import Simulator from '../../src/core/Simulator.js'
+import VirtualPatientUvaPadova from '../../src/core/models/UvaPadova_T1DMS.js'
+import Controller from '../../src/types/Controller.js'
+import ControllerBasalBolus from '../../src/core/controllers/BasalBolus.js'
+import ControllerOref0 from '../../src/core/controllers/Oref0.js'
+import Meal from '../../src/types/Meal.js'
+import IdealCGM from '../../src/core/sensors/IdealCGM.js'
+import StaticInsulinPump from '../../src/core/actuators/StaticInsulinPump.js'
+import ControllerUnion from '../../src/core/ControllerUnion.js'
+import MealBolus from '../../src/core/controllers/MealBolus.js'
+
+
+// define a patient object
+const patient = new VirtualPatientUvaPadova()
+
+// define a set of meals
+const meals: Meal[] = [
+    {
+        start: new Date("2022-05-01T08:00:00Z"),
+        duration: 15,
+        carbs: 20,
+        announcement: {
+            start: new Date("2022-05-01T08:00:00Z"),
+            carbs: 20,
+            time: new Date("2022-05-01T07:00:00Z"),
+        },
+    },
+    {
+        start: new Date("2022-05-01T17:00:00Z"),
+        duration: 15,
+        carbs: 40,
+        announcement: {
+            start: new Date("2022-05-01T17:00:00Z"),
+            carbs: 40,
+            time: new Date("2022-05-01T16:00:00Z"),
+        },
+    },
+    {
+        start: new Date("2022-05-02T08:00:00Z"),
+        duration: 15,
+        carbs: 30,
+    },
+]
+
+// function for easy call of simulation
+function performSimulationWithController(id: string, controller: Controller) {
+    controller.autoConfigure?.(patient.getPatientProfile())
+    // prepare the simulator
+    const sim = new Simulator()
+    // prepare simulation
+    sim.setPatient(patient)
+    sim.setSensor(new IdealCGM())
+    sim.setActuator(new StaticInsulinPump())
+    sim.setController(controller)
+    sim.setMeals(meals)
+    sim.setOptions({
+        "t0": new Date("2022-05-01T00:00:00Z"),	// start at 0am
+        "tmax": new Date("2022-05-03T00:00:00Z"), 	// two days later 
+    })
+    // run simulation
+    sim.runSimulation()
+    const results = sim.getSimulationResults()
+    return { id, meals, results } // TODO: patient, controller, 
+}
+
+/** first controller */
+const controller1 = new ControllerBasalBolus({
+    premealTime: 30, carbFactor: 0.8	// meal bolus
+})
+
+/** second controller: oref0 with meal bolus */
+const controller2 = new ControllerUnion([
+    new ControllerOref0({
+        max_iob: 3.5,
+        dia: 6,
+        max_daily_basal: 1.3,
+        max_basal: 3.5,
+        max_bg: 100,
+        min_bg: 100,
+        sens: 40,
+        carb_ratio: 10 / 0.8,
+        maxCOB: 120,
+    }),
+    // meal bolus
+    new MealBolus({
+        premealTime: 30,
+        carbFactor: 0.8,
+    })
+])
+
+// run simulations
+const results = [
+    performSimulationWithController("Basal+Bolus", controller1),
+    performSimulationWithController("oref0", controller2),
+]
+
+// store simulation input and results to JSON file
+fs.writeFile("./ControllerStudyResults.json",
+    JSON.stringify(results),
+    function (err: NodeJS.ErrnoException | null) {
+        if (err) {
+            throw err
+        }
+        console.log("Done! Now run ControllerStudyPostprocess.m in Matlab(R)")
+    }
+)

examples/ControllerStudyDemo/ControllerStudyPostprocess.m

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+% This file is part of LoopInsighT1, an open source tool to
+% simulate closed-loop glycemic control in type 1 diabetes.
+% Distributed under the MIT software license.
+% See https://lt1.org for further information.
+
+clearvars;
+
+% add util path which contains importJsonData
+addpath('../util/')
+% import JSON file
+simDataJson = fileread('ControllerStudyResults.json');
+% decode JSON file
+simData = jsondecode(simDataJson);
+
+%% prepare figure
+clf(); set(gcf, 'Color', 'w', 'Position', [100 100 750 500]);
+tiledlayout(2,1);
+ax1 = nexttile(); set(ax1, 'NextPlot', 'add');
+ax2 = nexttile(); set(ax2, 'NextPlot', 'add');
+
+
+%% process data
+for i=1:length(simData)
+    data = simData(i);
+
+    % import data
+    [t, y, s, c, u, x] = importJsonData(data.results);
+
+    % hide zero boluses in diagram
+    c.ibolus(c.ibolus==0) = NaN;
+
+    % plot blood glucose and insulin infusion rate
+    h = plot(ax1, t, y.Gp, 'DisplayName', data.id);
+    stairs(ax2, t(~isnan(c.iir)), c.iir(~isnan(c.iir)), 'Color', h.Color);
+    plot(ax2, t, c.ibolus, '^',  ...
+        'MarkerEdgeColor', 'k', 'MarkerFaceColor', h.Color);
+end
+
+%% format graphs
+axes(ax1); 
+title('glucose concentration in mg/dl'); 
+hold on; box on; grid on;
+legend('show', 'Location', 'northwest')
+
+axes(ax2); 
+title('insulin infusion: basal rate in U/h and bolus in U'); 
+hold on; box on; grid on;
+
+%% store as file
+print('ControllerStudyDemo.png', '-dpng', '-r300');