Merge pull request #253 from AllenNeuralDynamics/feat-add-patch-flanking

Implement patch flanking sites
AllenNeuralDynamics · Jun 4, 2024 · 6c3909b · 6c3909b
2 parents 2f76929 + a6a0544
commit 6c3909b
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Showing 9 changed files with 369 additions and 70 deletions.
diff --git a/src/DataSchemas/aind_behavior_vr_foraging/__init__.py b/src/DataSchemas/aind_behavior_vr_foraging/__init__.py
@@ -1 +1 @@
-__version__ = "0.4.2"
+__version__ = "0.4.0"
diff --git a/src/DataSchemas/aind_behavior_vr_foraging/rig.py b/src/DataSchemas/aind_behavior_vr_foraging/rig.py
@@ -10,7 +10,7 @@
 from aind_behavior_services.rig import AindBehaviorRigModel
 from pydantic import BaseModel, Field, RootModel
 
-__version__ = "0.3.1"
+__version__ = "0.3.0"
 
 TreadmillSettings = rig.Treadmill
 

diff --git a/src/DataSchemas/aind_behavior_vr_foraging/task_logic.py b/src/DataSchemas/aind_behavior_vr_foraging/task_logic.py
@@ -7,8 +7,7 @@
 from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters
 from pydantic import BaseModel, Field, RootModel
 
-
-__version__ = "0.4.1"
+__version__ = "0.4.0"
 
 
 def scalar_value(value: float) -> distributions.Scalar:
@@ -41,7 +40,7 @@ class Vector3(BaseModel):
 
 
 class Matrix2D(BaseModel):
-    data: List[List[float]] = Field([[1]], description="Defines a 2D matrix")
+    data: List[List[float]] = Field(default=[[1]], description="Defines a 2D matrix")
 
 
 # Updaters
@@ -66,7 +65,7 @@ class NumericalUpdater(BaseModel):
         default=NumericalUpdaterOperation.NONE, description="Operation to perform on the parameter"
     )
     parameters: NumericalUpdaterParameters = Field(
-        NumericalUpdaterParameters(), description="Parameters of the updater"
+        default=NumericalUpdaterParameters(), description="Parameters of the updater"
     )
 
 
@@ -149,7 +148,7 @@ class PatchRewardFunction(BaseModel):
 
 
 class RewardSpecification(BaseModel):
-    operant_logic: Optional[OperantLogic] = Field(None, description="The optional operant logic of the reward")
+    operant_logic: Optional[OperantLogic] = Field(default=None, description="The optional operant logic of the reward")
     delay: distributions.Distribution = Field(
         default=scalar_value(0),
         description="The optional distribution where the delay to reward will be drawn from",
@@ -163,6 +162,7 @@ class RewardSpecification(BaseModel):
 class VirtualSiteLabels(str, Enum):
     UNSPECIFIED = "Unspecified"
     INTERPATCH = "InterPatch"
+    POSTPATCH = "PostPatch"
     REWARDSITE = "RewardSite"
     INTERSITE = "InterSite"
 
@@ -183,29 +183,32 @@ class VirtualSiteGenerator(BaseModel):
 
 class VirtualSiteGeneration(BaseModel):
     inter_site: VirtualSiteGenerator = Field(
-        VirtualSiteGenerator(), description="Generator of the inter-site virtual sites"
+        default=VirtualSiteGenerator(), description="Generator of the inter-site virtual sites"
     )
     inter_patch: VirtualSiteGenerator = Field(
-        VirtualSiteGenerator(), description="Generator of the inter-patch virtual sites"
+        default=VirtualSiteGenerator(), description="Generator of the inter-patch virtual sites"
+    )
+    post_patch: VirtualSiteGenerator = Field(
+        default=VirtualSiteGenerator(), description="Generator of the post-inter-patch virtual sites"
     )
     reward_site: VirtualSiteGenerator = Field(
-        VirtualSiteGenerator(), description="Generator of the reward-site virtual sites"
+        default=VirtualSiteGenerator(), description="Generator of the reward-site virtual sites"
     )
 
 
 class VirtualSite(BaseModel):
     id: int = Field(default=0, ge=0, description="Id of the virtual site")
-    label: VirtualSiteLabels = Field(VirtualSiteLabels.UNSPECIFIED, description="Label of the virtual site")
-    length: float = Field(20, description="Length of the virtual site (cm)")
+    label: VirtualSiteLabels = Field(default=VirtualSiteLabels.UNSPECIFIED, description="Label of the virtual site")
+    length: float = Field(default=20, description="Length of the virtual site (cm)")
     start_position: float = Field(default=0, ge=0, description="Start position of the virtual site (cm)")
     odor_specification: Optional[OdorSpecification] = Field(
-        None, description="The optional odor specification of the virtual site"
+        default=None, description="The optional odor specification of the virtual site"
     )
     reward_specification: Optional[RewardSpecification] = Field(
-        None, description="The optional reward specification of the virtual site"
+        default=None, description="The optional reward specification of the virtual site"
     )
     render_specification: RenderSpecification = Field(
-        RenderSpecification(), description="The optional render specification of the virtual site"
+        default=RenderSpecification(), description="The optional render specification of the virtual site"
     )
 
 
@@ -219,7 +222,7 @@ class PatchStatistics(BaseModel):
         default=None, description="The optional reward specification of the patch"
     )
     virtual_site_generation: VirtualSiteGeneration = Field(
-        VirtualSiteGeneration(), description="Virtual site generation specification"
+        default=VirtualSiteGeneration(), description="Virtual site generation specification"
     )
 
 

diff --git a/src/DataSchemas/aind_vr_foraging_rig.json b/src/DataSchemas/aind_vr_foraging_rig.json
@@ -1326,8 +1326,8 @@
   },
   "properties": {
     "version": {
-      "const": "0.3.1",
-      "default": "0.3.1",
+      "const": "0.3.0",
+      "default": "0.3.0",
       "title": "Version",
       "type": "string"
     },

diff --git a/src/DataSchemas/aind_vr_foraging_task_logic.json b/src/DataSchemas/aind_vr_foraging_task_logic.json
@@ -1192,6 +1192,23 @@
                 "contrast": null
               }
             },
+            "post_patch": {
+              "label": "Unspecified",
+              "length_distribution": {
+                "distribution_parameters": {
+                  "family": "Scalar",
+                  "scaling_parameters": null,
+                  "truncation_parameters": null,
+                  "value": 20.0
+                },
+                "family": "Scalar",
+                "scaling_parameters": null,
+                "truncation_parameters": null
+              },
+              "render_specification": {
+                "contrast": null
+              }
+            },
             "reward_site": {
               "label": "Unspecified",
               "length_distribution": {
@@ -1923,6 +1940,31 @@
           },
           "description": "Generator of the inter-patch virtual sites"
         },
+        "post_patch": {
+          "allOf": [
+            {
+              "$ref": "#/definitions/VirtualSiteGenerator"
+            }
+          ],
+          "default": {
+            "render_specification": {
+              "contrast": null
+            },
+            "label": "Unspecified",
+            "length_distribution": {
+              "distribution_parameters": {
+                "family": "Scalar",
+                "scaling_parameters": null,
+                "truncation_parameters": null,
+                "value": 20.0
+              },
+              "family": "Scalar",
+              "scaling_parameters": null,
+              "truncation_parameters": null
+            }
+          },
+          "description": "Generator of the post-inter-patch virtual sites"
+        },
         "reward_site": {
           "allOf": [
             {
@@ -2001,6 +2043,7 @@
       "enum": [
         "Unspecified",
         "InterPatch",
+        "PostPatch",
         "RewardSite",
         "InterSite"
       ],
@@ -2117,8 +2160,8 @@
       "type": "string"
     },
     "version": {
-      "const": "0.4.1",
-      "default": "0.4.1",
+      "const": "0.4.0",
+      "default": "0.4.0",
       "title": "Version",
       "type": "string"
     },

diff --git a/src/Extensions/AddPostPatchSite.bonsai b/src/Extensions/AddPostPatchSite.bonsai
@@ -0,0 +1,159 @@
+<?xml version="1.0" encoding="utf-8"?>
+<WorkflowBuilder Version="2.8.2"
+                 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns:p1="clr-namespace:AindVrForagingDataSchema.TaskLogic;assembly=Extensions"
+                 xmlns:sys="clr-namespace:System;assembly=mscorlib"
+                 xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics"
+                 xmlns="https://bonsai-rx.org/2018/workflow">
+  <Workflow>
+    <Nodes>
+      <Expression xsi:type="WorkflowInput">
+        <Name>Source1</Name>
+      </Expression>
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="Contrast" />
+        <Property Name="Label" />
+        <Property Name="LengthDistribution" />
+      </Expression>
+      <Expression xsi:type="rx:SelectMany">
+        <Name>InterPatch</Name>
+        <Workflow>
+          <Nodes>
+            <Expression xsi:type="WorkflowInput">
+              <Name>Source1</Name>
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="rx:Take">
+                <rx:Count>1</rx:Count>
+              </Combinator>
+            </Expression>
+            <Expression xsi:type="rx:AsyncSubject">
+              <Name>PreviousSite</Name>
+            </Expression>
+            <Expression xsi:type="SubscribeSubject">
+              <Name>PreviousSite</Name>
+            </Expression>
+            <Expression xsi:type="MemberSelector">
+              <Selector>Length,StartPosition</Selector>
+            </Expression>
+            <Expression xsi:type="Add" />
+            <Expression xsi:type="SubscribeSubject">
+              <Name>SigmaZ</Name>
+            </Expression>
+            <Expression xsi:type="PropertyMapping">
+              <PropertyMappings>
+                <Property Name="Value" />
+              </PropertyMappings>
+            </Expression>
+            <Expression xsi:type="Add">
+              <Operand xsi:type="FloatProperty">
+                <Value>0</Value>
+              </Operand>
+            </Expression>
+            <Expression xsi:type="ExternalizedMapping">
+              <Property Name="Value" DisplayName="LengthDistribution" />
+            </Expression>
+            <Expression xsi:type="PropertySource" TypeArguments="p1:VirtualSiteGenerator,p1:Distribution">
+              <MemberName>LengthDistribution</MemberName>
+            </Expression>
+            <Expression xsi:type="SubscribeSubject">
+              <Name>RngSeed</Name>
+            </Expression>
+            <Expression xsi:type="PropertyMapping">
+              <PropertyMappings>
+                <Property Name="RandomSource" />
+              </PropertyMappings>
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="p1:SampleDistribution" />
+            </Expression>
+            <Expression xsi:type="InputMapping">
+              <PropertyMappings />
+              <TypeMapping xsi:type="TypeMapping" TypeArguments="sys:Double" />
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="num:Floor" />
+            </Expression>
+            <Expression xsi:type="InputMapping">
+              <PropertyMappings />
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="rx:Zip" />
+            </Expression>
+            <Expression xsi:type="InputMapping">
+              <PropertyMappings>
+                <Property Name="StartPosition" Selector="Item1" />
+                <Property Name="Length" Selector="Item2" />
+                <Property Name="Id" Selector="Item3" />
+              </PropertyMappings>
+            </Expression>
+            <Expression xsi:type="ExternalizedMapping">
+              <Property Name="Contrast" />
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="p1:RenderSpecification" />
+            </Expression>
+            <Expression xsi:type="PropertyMapping">
+              <PropertyMappings>
+                <Property Name="RenderSpecification" />
+              </PropertyMappings>
+            </Expression>
+            <Expression xsi:type="ExternalizedMapping">
+              <Property Name="Label" />
+            </Expression>
+            <Expression xsi:type="IncludeWorkflow" Path="Extensions\CreateSite.bonsai">
+              <Id>0</Id>
+              <Length>120</Length>
+              <StartPosition>0</StartPosition>
+            </Expression>
+            <Expression xsi:type="MulticastSubject">
+              <Name>SiteSpecs</Name>
+            </Expression>
+            <Expression xsi:type="Combinator">
+              <Combinator xsi:type="rx:Take">
+                <rx:Count>1</rx:Count>
+              </Combinator>
+            </Expression>
+            <Expression xsi:type="WorkflowOutput" />
+          </Nodes>
+          <Edges>
+            <Edge From="0" To="1" Label="Source1" />
+            <Edge From="1" To="2" Label="Source1" />
+            <Edge From="3" To="4" Label="Source1" />
+            <Edge From="4" To="5" Label="Source1" />
+            <Edge From="5" To="8" Label="Source1" />
+            <Edge From="6" To="7" Label="Source1" />
+            <Edge From="7" To="8" Label="Source2" />
+            <Edge From="8" To="10" Label="Source1" />
+            <Edge From="8" To="14" Label="Source1" />
+            <Edge From="8" To="17" Label="Source1" />
+            <Edge From="9" To="10" Label="Source2" />
+            <Edge From="10" To="13" Label="Source1" />
+            <Edge From="11" To="12" Label="Source1" />
+            <Edge From="12" To="13" Label="Source2" />
+            <Edge From="13" To="17" Label="Source3" />
+            <Edge From="14" To="15" Label="Source1" />
+            <Edge From="15" To="16" Label="Source1" />
+            <Edge From="16" To="17" Label="Source4" />
+            <Edge From="17" To="18" Label="Source1" />
+            <Edge From="18" To="23" Label="Source1" />
+            <Edge From="19" To="20" Label="Source1" />
+            <Edge From="20" To="21" Label="Source1" />
+            <Edge From="21" To="23" Label="Source2" />
+            <Edge From="22" To="23" Label="Source3" />
+            <Edge From="23" To="24" Label="Source1" />
+            <Edge From="24" To="25" Label="Source1" />
+            <Edge From="25" To="26" Label="Source1" />
+          </Edges>
+        </Workflow>
+      </Expression>
+      <Expression xsi:type="WorkflowOutput" />
+    </Nodes>
+    <Edges>
+      <Edge From="0" To="2" Label="Source1" />
+      <Edge From="1" To="2" Label="Source2" />
+      <Edge From="2" To="3" Label="Source1" />
+    </Edges>
+  </Workflow>
+</WorkflowBuilder>
diff --git a/src/Extensions/AindVrForagingRig.cs b/src/Extensions/AindVrForagingRig.cs
@@ -3620,7 +3620,7 @@ public override string ToString()
     public partial class AindVrForagingRig
     {
 
-        private string _version = "0.3.1";
+        private string _version = "0.3.0";
 
         private string _computerName;