Add first example

_topics/_08_reproducible_research_practices/src/bonsai/Extensions/Experiment.cs

@@ -0,0 +1,353 @@
+//----------------------
+// <auto-generated>
+//     Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org)
+// </auto-generated>
+//----------------------
+
+
+namespace Experiment
+{
+    #pragma warning disable // Disable all warnings
+
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [Bonsai.CombinatorAttribute()]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+    public partial class Trial
+    {
+
+        private double _interTrialInterval = 1D;
+
+        private int _rewardAmount = 1;
+
+        public Trial()
+        {
+        }
+
+        protected Trial(Trial other)
+        {
+            _interTrialInterval = other._interTrialInterval;
+            _rewardAmount = other._rewardAmount;
+        }
+
+        /// <summary>
+        /// Interval between trials in seconds
+        /// </summary>
+        [Newtonsoft.Json.JsonPropertyAttribute("inter_trial_interval")]
+        [YamlDotNet.Serialization.YamlMemberAttribute(Alias="inter_trial_interval")]
+        [System.ComponentModel.DescriptionAttribute("Interval between trials in seconds")]
+        public double InterTrialInterval
+        {
+            get
+            {
+                return _interTrialInterval;
+            }
+            set
+            {
+                _interTrialInterval = value;
+            }
+        }
+
+        /// <summary>
+        /// Amount of reward given to the animal
+        /// </summary>
+        [Newtonsoft.Json.JsonPropertyAttribute("reward_amount")]
+        [YamlDotNet.Serialization.YamlMemberAttribute(Alias="reward_amount")]
+        [System.ComponentModel.DescriptionAttribute("Amount of reward given to the animal")]
+        public int RewardAmount
+        {
+            get
+            {
+                return _rewardAmount;
+            }
+            set
+            {
+                _rewardAmount = value;
+            }
+        }
+
+        public System.IObservable<Trial> Process()
+        {
+            return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Trial(this)));
+        }
+
+        public System.IObservable<Trial> Process<TSource>(System.IObservable<TSource> source)
+        {
+            return System.Reactive.Linq.Observable.Select(source, _ => new Trial(this));
+        }
+
+        protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+        {
+            stringBuilder.Append("inter_trial_interval = " + _interTrialInterval + ", ");
+            stringBuilder.Append("reward_amount = " + _rewardAmount);
+            return true;
+        }
+
+        public override string ToString()
+        {
+            System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
+            stringBuilder.Append(GetType().Name);
+            stringBuilder.Append(" { ");
+            if (PrintMembers(stringBuilder))
+            {
+                stringBuilder.Append(" ");
+            }
+            stringBuilder.Append("}");
+            return stringBuilder.ToString();
+        }
+    }
+
+
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [Bonsai.CombinatorAttribute()]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+    public partial class Experiment
+    {
+
+        private string _animalId;
+
+        private System.Collections.Generic.List<Trial> _trials = new System.Collections.Generic.List<Trial>();
+
+        private int? _rngSeed;
+
+        public Experiment()
+        {
+        }
+
+        protected Experiment(Experiment other)
+        {
+            _animalId = other._animalId;
+            _trials = other._trials;
+            _rngSeed = other._rngSeed;
+        }
+
+        /// <summary>
+        /// ID of the animal
+        /// </summary>
+        [Newtonsoft.Json.JsonPropertyAttribute("animal_id", Required=Newtonsoft.Json.Required.Always)]
+        [YamlDotNet.Serialization.YamlMemberAttribute(Alias="animal_id")]
+        [System.ComponentModel.DescriptionAttribute("ID of the animal")]
+        public string AnimalId
+        {
+            get
+            {
+                return _animalId;
+            }
+            set
+            {
+                _animalId = value;
+            }
+        }
+
+        /// <summary>
+        /// List of trials in the experiment
+        /// </summary>
+        [System.Xml.Serialization.XmlIgnoreAttribute()]
+        [Newtonsoft.Json.JsonPropertyAttribute("trials", Required=Newtonsoft.Json.Required.Always)]
+        [YamlDotNet.Serialization.YamlMemberAttribute(Alias="trials")]
+        [System.ComponentModel.DescriptionAttribute("List of trials in the experiment")]
+        public System.Collections.Generic.List<Trial> Trials
+        {
+            get
+            {
+                return _trials;
+            }
+            set
+            {
+                _trials = value;
+            }
+        }
+
+        /// <summary>
+        /// Seed for the random number generator
+        /// </summary>
+        [System.Xml.Serialization.XmlIgnoreAttribute()]
+        [Newtonsoft.Json.JsonPropertyAttribute("rng_seed")]
+        [YamlDotNet.Serialization.YamlMemberAttribute(Alias="rng_seed")]
+        [System.ComponentModel.DescriptionAttribute("Seed for the random number generator")]
+        public int? RngSeed
+        {
+            get
+            {
+                return _rngSeed;
+            }
+            set
+            {
+                _rngSeed = value;
+            }
+        }
+
+        public System.IObservable<Experiment> Process()
+        {
+            return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Experiment(this)));
+        }
+
+        public System.IObservable<Experiment> Process<TSource>(System.IObservable<TSource> source)
+        {
+            return System.Reactive.Linq.Observable.Select(source, _ => new Experiment(this));
+        }
+
+        protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+        {
+            stringBuilder.Append("animal_id = " + _animalId + ", ");
+            stringBuilder.Append("trials = " + _trials + ", ");
+            stringBuilder.Append("rng_seed = " + _rngSeed);
+            return true;
+        }
+
+        public override string ToString()
+        {
+            System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
+            stringBuilder.Append(GetType().Name);
+            stringBuilder.Append(" { ");
+            if (PrintMembers(stringBuilder))
+            {
+                stringBuilder.Append(" ");
+            }
+            stringBuilder.Append("}");
+            return stringBuilder.ToString();
+        }
+    }
+
+
+    /// <summary>
+    /// Serializes a sequence of data model objects into JSON strings.
+    /// </summary>
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")]
+    [Bonsai.CombinatorAttribute()]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)]
+    public partial class SerializeToJson
+    {
+
+        private System.IObservable<string> Process<T>(System.IObservable<T> source)
+        {
+            return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value));
+        }
+
+        public System.IObservable<string> Process(System.IObservable<Trial> source)
+        {
+            return Process<Trial>(source);
+        }
+
+        public System.IObservable<string> Process(System.IObservable<Experiment> source)
+        {
+            return Process<Experiment>(source);
+        }
+    }
+
+
+    /// <summary>
+    /// Deserializes a sequence of JSON strings into data model objects.
+    /// </summary>
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")]
+    [System.ComponentModel.DefaultPropertyAttribute("Type")]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)]
+    [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Trial>))]
+    [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Experiment>))]
+    public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder
+    {
+
+        public DeserializeFromJson()
+        {
+            Type = new Bonsai.Expressions.TypeMapping<Experiment>();
+        }
+
+        public Bonsai.Expressions.TypeMapping Type { get; set; }
+
+        public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable<System.Linq.Expressions.Expression> arguments)
+        {
+            var typeMapping = (Bonsai.Expressions.TypeMapping)Type;
+            var returnType = typeMapping.GetType().GetGenericArguments()[0];
+            return System.Linq.Expressions.Expression.Call(
+                typeof(DeserializeFromJson),
+                "Process",
+                new System.Type[] { returnType },
+                System.Linq.Enumerable.Single(arguments));
+        }
+
+        private static System.IObservable<T> Process<T>(System.IObservable<string> source)
+        {
+            return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject<T>(value));
+        }
+    }
+
+
+    /// <summary>
+    /// Serializes a sequence of data model objects into YAML strings.
+    /// </summary>
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into YAML strings.")]
+    [Bonsai.CombinatorAttribute()]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)]
+    public partial class SerializeToYaml
+    {
+
+        private System.IObservable<string> Process<T>(System.IObservable<T> source)
+        {
+            return System.Reactive.Linq.Observable.Defer(() =>
+            {
+                var serializer = new YamlDotNet.Serialization.SerializerBuilder()
+                    .Build();
+                return System.Reactive.Linq.Observable.Select(source, value => serializer.Serialize(value)); 
+            });
+        }
+
+        public System.IObservable<string> Process(System.IObservable<Trial> source)
+        {
+            return Process<Trial>(source);
+        }
+
+        public System.IObservable<string> Process(System.IObservable<Experiment> source)
+        {
+            return Process<Experiment>(source);
+        }
+    }
+
+
+    /// <summary>
+    /// Deserializes a sequence of YAML strings into data model objects.
+    /// </summary>
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0, YamlDotNet v13.0.0.0)")]
+    [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of YAML strings into data model objects.")]
+    [System.ComponentModel.DefaultPropertyAttribute("Type")]
+    [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)]
+    [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Trial>))]
+    [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Experiment>))]
+    public partial class DeserializeFromYaml : Bonsai.Expressions.SingleArgumentExpressionBuilder
+    {
+
+        public DeserializeFromYaml()
+        {
+            Type = new Bonsai.Expressions.TypeMapping<Experiment>();
+        }
+
+        public Bonsai.Expressions.TypeMapping Type { get; set; }
+
+        public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable<System.Linq.Expressions.Expression> arguments)
+        {
+            var typeMapping = (Bonsai.Expressions.TypeMapping)Type;
+            var returnType = typeMapping.GetType().GetGenericArguments()[0];
+            return System.Linq.Expressions.Expression.Call(
+                typeof(DeserializeFromYaml),
+                "Process",
+                new System.Type[] { returnType },
+                System.Linq.Enumerable.Single(arguments));
+        }
+
+        private static System.IObservable<T> Process<T>(System.IObservable<string> source)
+        {
+            return System.Reactive.Linq.Observable.Defer(() =>
+            {
+                var serializer = new YamlDotNet.Serialization.DeserializerBuilder()
+                    .Build();
+                return System.Reactive.Linq.Observable.Select(source, value =>
+                {
+                    var reader = new System.IO.StringReader(value);
+                    var parser = new YamlDotNet.Core.MergingParser(new YamlDotNet.Core.Parser(reader));
+                    return serializer.Deserialize<T>(parser);
+                });
+            });
+        }
+    }
+}

_topics/_08_reproducible_research_practices/src/json/experiment-example.json

@@ -0,0 +1,14 @@
+{
+  "animal_id": "my_mouse",
+  "trials": [
+    {
+      "inter_trial_interval": 1.0,
+      "reward_amount": 1
+    },
+    {
+      "inter_trial_interval": 0.5,
+      "reward_amount": 0
+    }
+  ],
+  "rng_seed": null
+}