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Add functionality to HMM package to load and save HMMs from pickle files #36

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Add functionality to HMM package to load and save HMMs from pickle files #36

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8a92e73
Fixed issue with loading and saving pickle object
ncguilbeault Oct 31, 2024
ee66f64
Added include workflow for loading from pkl
ncguilbeault Oct 31, 2024
4d86dd9
Update workflow to include quotes around string path
ncguilbeault Nov 1, 2024
5fa19f4
Add custom unpickler to fix issue with missing module
ncguilbeault Nov 1, 2024
2545e51
Added new include workflow to save HMM to pickle file
ncguilbeault Jan 10, 2025
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120 changes: 120 additions & 0 deletions src/Bonsai.ML.HiddenMarkovModels/LoadHMMFromPkl.bonsai
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<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.5"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns:p2="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" Category="ModelReference" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:CreateModelReference">
<p1:Name>hmm</p1:Name>
</Combinator>
</Expression>
<Expression xsi:type="rx:BehaviorSubject">
<Name>hmm</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Name</Selector>
</Expression>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="PathToPklFile" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="StringProperty">
<Value>model.pkl</Value>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="Format">
<Format>{0}=HiddenMarkovModel.load_model("{1}")</Format>
<Selector>Item1,Item2</Selector>
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="Script" Selector="it" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>HMMModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Exec">
<py:Script></py:Script>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="VariableName" Selector="Item2" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>HMMModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Get">
<py:VariableName>hmm</py:VariableName>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:ModelParameters">
<p2:NumStates>2</p2:NumStates>
<p2:Dimensions>2</p2:Dimensions>
<p2:ObservationsModelType>Gaussian</p2:ObservationsModelType>
<p2:TransitionsModelType>Stationary</p2:TransitionsModelType>
</Combinator>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="0" To="2" Label="Source2" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="7" Label="Source1" />
<Edge From="3" To="14" Label="Source2" />
<Edge From="4" To="6" Label="Source1" />
<Edge From="5" To="6" Label="Source2" />
<Edge From="6" To="7" Label="Source2" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="9" Label="Source1" />
<Edge From="9" To="10" Label="Source1" />
<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="14" Label="Source1" />
<Edge From="14" To="15" Label="Source1" />
<Edge From="15" To="18" Label="Source1" />
<Edge From="16" To="17" Label="Source1" />
<Edge From="17" To="18" Label="Source2" />
<Edge From="18" To="19" Label="Source1" />
<Edge From="19" To="20" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
81 changes: 81 additions & 0 deletions src/Bonsai.ML.HiddenMarkovModels/SaveHMMToPkl.bonsai
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<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.5"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" Category="ModelReference" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:CreateModelReference">
<p1:Name>hmm</p1:Name>
</Combinator>
</Expression>
<Expression xsi:type="rx:BehaviorSubject">
<Name>hmm</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Name</Selector>
</Expression>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="PathToPklFile" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="StringProperty">
<Value>model.pkl</Value>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="Format">
<Format>{0}.save_model("{1}")</Format>
<Selector>Item1,Item2</Selector>
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="Expression" Selector="it" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>HMMModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Eval" />
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="0" To="2" Label="Source2" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="7" Label="Source1" />
<Edge From="4" To="6" Label="Source1" />
<Edge From="5" To="6" Label="Source2" />
<Edge From="6" To="7" Label="Source2" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="9" Label="Source1" />
<Edge From="9" To="10" Label="Source1" />
<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="14" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
18 changes: 13 additions & 5 deletions src/Bonsai.ML.HiddenMarkovModels/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,11 @@

npr.seed(0)

class CustomUnpickler(pickle.Unpickler):
def find_class(self, module, name):
if module == 'main' and name == 'HiddenMarkovModel':
return HiddenMarkovModel
return super().find_class(module, name)

class HiddenMarkovModel(HMM):

Expand Down Expand Up @@ -151,11 +156,14 @@ def compute_log_alpha(self, obs, log_alpha=None):

return log_alpha - logsumexp(log_alpha)

def save_model_to_pickle(self, path: str):
pickle.save(self, path)

def load_model_from_pickle(self, path: str):
self = pickle.load(path)
def save_model(self, path: str):
with open(path, "wb") as f:
pickle.dump(self, f)

@classmethod
def load_model(cls, path: str):
with open(path, 'rb') as f:
return CustomUnpickler(f).load()

def fit_async(self,
observation: list[float],
Expand Down