AnimatLab
2
Test
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Firing rate neural module. More...
#include <FiringRateModule.h>
Public Member Functions | |
FiringRateModule () | |
Default constructor. More... | |
virtual | ~FiringRateModule () |
Destructor. More... | |
bool | ActiveArray () |
Gets the active array. More... | |
void | ActiveArray (bool bVal) |
Sets the active array. More... | |
virtual bool | AddItem (const std::string &strItemType, const std::string &strXml, bool bThrowError=true, bool bDoNotInit=false) |
Adds a new object to this parent. More... | |
virtual void | AddNeuron (std::string strXml, bool bDoNotInit=false) |
Adds a neuron to the module. More... | |
virtual long | CalculateSnapshotByteSize () |
Calculates the snapshot byte size. More... | |
virtual int | FindNeuronListPos (std::string strID, bool bThrowError=true) |
Searches for the neuron with the specified ID and returns its position in the list. More... | |
bool | InactiveArray () |
Gets the inactive array. More... | |
void | InactiveArray (bool bVal) |
Sets the inactive array. More... | |
virtual void | Initialize () |
Initializes this object. More... | |
virtual void | Kill (bool bState=true) |
Kills. More... | |
virtual void | Load (CStdXml &oXml) |
virtual void | LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex) |
Loads a key frame snapshot. More... | |
virtual std::string | ModuleName () |
Gets the module name. More... | |
virtual void | QueryProperties (CStdPtrArray< TypeProperty > &aryProperties) |
virtual bool | RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true) |
Removes a child item from this parent. More... | |
virtual void | RemoveNeuron (std::string strID, bool bThrowError=true) |
Removes the neuron with the specified ID. More... | |
virtual void | ResetSimulation () |
Resets the simulation back to time 0. More... | |
virtual void | SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex) |
Saves a key frame snapshot. More... | |
virtual bool | SetData (const std::string &strDataType, const std::string &strValue, bool bThrowError=true) |
Set a variable based on a string data type name. More... | |
virtual void | StepSimulation () |
Step the simulation for this object. More... | |
Public Member Functions inherited from AnimatSim::Behavior::NeuralModule | |
NeuralModule () | |
Default constructor. More... | |
virtual | ~NeuralModule () |
Destructor. More... | |
virtual void | AddExternalSynapse (AnimatSim::Link *lpSynapse) |
virtual void | AddExternalSynapse (std::string strXml, bool bDoNotInit) |
Adds a synapse using an xml packet. More... | |
virtual void | AttachSourceAdapter (Adapter *lpAdapter) |
Attaches a source adapter. More... | |
virtual void | AttachTargetAdapter (Adapter *lpAdapter) |
Attaches a target adapter. More... | |
virtual IStdClassFactory * | ClassFactory () |
Gets the class factory. More... | |
virtual void | ClassFactory (IStdClassFactory *lpFactory) |
virtual int | FindExternalSynapseListPos (std::string strID, bool bThrowError=true) |
Searches for a synapse with the specified ID and returns its position in the list. More... | |
virtual float * | GetDataPointer (const std::string &strDataType) |
Returns a float pointer to a data item of interest in this object. More... | |
Organism * | GetOrganism () |
Gets the organism. More... | |
Simulator * | GetSimulator () |
Gets the simulator. More... | |
virtual bool | NeedToStep (bool bIncrement) |
Tells whether this NeuralModule needs to call StepSimulation. More... | |
virtual void | RemoveExternalSynapse (std::string strID, bool bThrowError=true) |
Removes the synapse by the GUID ID. More... | |
virtual void | RemoveSourceAdapter (Adapter *lpAdapter) |
Removes a source adapter. More... | |
virtual void | RemoveTargetAdapter (Adapter *lpAdapter) |
Removes a target adapter. More... | |
virtual void | ResetStepCounter () |
virtual void | SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify) |
Sets the system pointers. More... | |
virtual void | StepAdapters () |
Step adapters. More... | |
virtual float | TimeStep () |
Gets the time step for this moudle in time units. More... | |
virtual void | TimeStep (float fltVal) |
Sets the Time step for this moudle in time units. More... | |
virtual short | TimeStepInterval () |
Gets the time step interval. More... | |
virtual void | TimeStepInterval (short iVal) |
Sets ime step interval. More... | |
virtual void | VerifySystemPointers () |
Verify that system pointers have been set correctly. More... | |
Public Member Functions inherited from AnimatSim::AnimatBase | |
AnimatBase () | |
Constructs an AnimatBase object. More... | |
virtual | ~AnimatBase () |
Destroys the AnimatBase object.. More... | |
virtual void | AfterResetSimulation () |
Called after a simulation reset for some objects. More... | |
virtual void | Copy (CStdSerialize *lpSource) |
virtual void | Enabled (bool bVal) |
Tells whether this item is enabled or not. This is not actually used for all objects, only specific ones. I am putting it in the base class though to prevent numerous duplications. More... | |
virtual bool | Enabled () |
Tells whether this item is enabled or not. This is not actually used for all objects, only specific ones. I am putting it in the base class though to prevent numerous duplications. More... | |
virtual NeuralModule * | GetNeuralModule () |
Gets the neural module. More... | |
virtual Node * | GetNode () |
Gets the node. More... | |
virtual Structure * | GetStructure () |
Gets the structure for this node. More... | |
virtual bool | HasProperty (const std::string &strName) |
Queries this object if it has a property with the given name. More... | |
virtual std::string | ID () |
Gets the unique GUID ID of this object. More... | |
virtual void | ID (std::string strValue) |
Sets the unique GUID ID of the object. More... | |
virtual void | Load (StdUtils::CStdXml &oXml) |
Loads the item using an XML data packet. More... | |
virtual std::string | Name () |
Gets the name of this object. More... | |
virtual void | Name (std::string strValue) |
Sets the name of the object. Blank is acceptable. More... | |
virtual AnimatPropertyType | PropertyType (const std::string &strName) |
virtual void | QueryProperties (CStdPtrArray< TypeProperty > &aryProperties) |
Queries this object for a list of properties that can be changed using SetData. More... | |
virtual void | ReInitialize () |
Re-initialize this object. More... | |
virtual void | Reset () |
Resets this object. More... | |
virtual void | RigidBodyAdded (std::string strID) |
virtual void | RigidBodyRemoved (std::string strID) |
virtual bool | Selected () |
Tells if this items is selected or not. More... | |
virtual void | Selected (bool bValue, bool bSelectMultiple) |
Selects this object. More... | |
virtual bool | SetData (const std::string &strDataType, const float fltValue, bool bThrowError=true) |
Set a variable based on a string data type name. More... | |
virtual bool | SetData (const std::string &strDataType, const long lValue, bool bThrowError=true) |
Set a variable based on a string data type name. More... | |
virtual void | SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify) |
Sets the system pointers. More... | |
virtual void | SimPausing () |
Called just before the simulation pauses. More... | |
virtual void | SimStarting () |
Called just before the simulation starts. More... | |
virtual void | SimStopping () |
Called just before the simulation stops. More... | |
virtual void | TimeStepModified () |
Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More... | |
virtual std::string | Type () |
returns the string type name of this object. More... | |
virtual void | Type (std::string strValue) |
Sets the class type for this object. More... | |
virtual void | VisualSelectionModeChanged (int iNewMode) |
Visual selection mode changed. More... | |
Protected Member Functions | |
void | LoadNetworkXml (CStdXml &oXml) |
Loads the network configuration. More... | |
Neuron * | LoadNeuron (CStdXml &oXml) |
Loads a neuron. More... | |
Protected Member Functions inherited from AnimatSim::Behavior::NeuralModule | |
virtual int | FindAdapterListIndex (CStdArray< Adapter * > aryAdapters, std::string strID, bool bThrowError=true) |
virtual AnimatSim::Link * | LoadExternalSynapse (CStdXml &oXml) |
Loads an external synapse. More... | |
virtual void | LoadExternalSynapses (CStdXml &oXml) |
Loads external synapses. More... | |
Protected Attributes | |
CStdPtrArray< Neuron > | m_aryNeurons |
The array of neurons in this module. | |
bool | m_bActiveArray |
CStdIPoint | m_oNetworkSize |
Size of the neural network. | |
Protected Attributes inherited from AnimatSim::Behavior::NeuralModule | |
CStdPtrArray< AnimatSim::Link > | m_aryExternalSynapses |
An array of external synapses connected to nodes within this module. | |
CStdArray< Adapter * > | m_arySourceAdapters |
An array of source adapters for this module. | |
CStdArray< Adapter * > | m_aryTargetAdapters |
An array of target adapters for this module. | |
float | m_fltTimeStep |
The DT time step for this neural module in seconds. | |
short | m_iTargetAdapterCount |
Number of target adapters. | |
short | m_iTimeStepCount |
Count variable that keeps track of how many slices have occured since the last StepSimulation. | |
short | m_iTimeStepInterval |
IStdClassFactory * | m_lpClassFactory |
The pointer to the class factory for this module. | |
Organism * | m_lpOrganism |
The pointer to the organism. | |
std::string | m_strNeuralNetworkFile |
The string neural network file name. | |
std::string | m_strProjectPath |
Full pathname of the string project file for this module. | |
Protected Attributes inherited from AnimatSim::AnimatBase | |
bool | m_bEnabled |
Tells if this item is enabled or not. If it is not enabled then it is not run. | |
bool | m_bSelected |
Tells whether the object is selected or not. | |
AnimatSim::Behavior::NeuralModule * | m_lpModule |
The pointer to this items parentNeuralModule. If this is not relevant for this object then this is NULL. | |
Node * | m_lpNode |
The pointer to this items parent Node. If this is not relevant for this object then this is NULL. | |
Simulator * | m_lpSim |
The pointer to a Simulation. | |
AnimatSim::Environment::Structure * | m_lpStructure |
The pointer to this items parent Structure. If this is not relevant for this object then this is NULL. | |
std::string | m_strID |
The unique Id for this object. | |
std::string | m_strName |
The name for this object. | |
std::string | m_strType |
The type for this object. Examples are Box, Plane, Neuron, etc.. | |
Additional Inherited Members | |
Static Public Member Functions inherited from AnimatSim::Behavior::NeuralModule | |
static NeuralModule * | CastToDerived (AnimatBase *lpBase) |
Firing rate neural module.
This neural module implements a firing rate neural model. The firing rate model is a more abstract representation of the neuron than an integrate and fire system. This type of model assumes that there is a linear relationship between cell depolarization and firing rate. After the neuron has depolarized beyond its threshold its firing rate increases linearly between 0 and 1 relative to the membrane potential and a gain value. Synapses inject current into post-synaptic neurons based on the firing rate. The synaptic weight is the amount of current to inject, and this is multiplied by the firing rate of the pre-synaptic neuron. this model also has modulatory and gated synapses.
Another feature of this model is that there are a few different types of neruons. These primarily differ based on how they implement intrinsic currents. Intrinsic currents are currents that are internal to the neuron. An exmample of this is the pacemaker neuron that generates currents internally to model bursting behavior.
Definition at line 30 of file FiringRateModule.h.
FiringRateSim::FiringRateModule::FiringRateModule | ( | ) |
Default constructor.
Definition at line 22 of file FiringRateModule.cpp.
References m_bActiveArray, and AnimatSim::Behavior::NeuralModule::m_lpClassFactory.
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Destructor.
Definition at line 34 of file FiringRateModule.cpp.
References m_aryNeurons, and StdUtils::Std_TraceMsg().
bool FiringRateSim::FiringRateModule::ActiveArray | ( | ) |
Gets the active array.
Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the active one.
Definition at line 58 of file FiringRateModule.cpp.
References m_bActiveArray.
Referenced by FiringRateSim::Neurons::Neuron::FiringFreq(), FiringRateSim::Neurons::PacemakerNeuron::StepSimulation(), and FiringRateSim::Neurons::Neuron::StepSimulation().
void FiringRateSim::FiringRateModule::ActiveArray | ( | bool | bVal | ) |
Sets the active array.
Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This sets which of these array elements is currently the active one.
bVal | true for array element 1, false for array element 0. |
Definition at line 72 of file FiringRateModule.cpp.
References m_bActiveArray.
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Adds a new object to this parent.
Generic method to add a new child item to this parent by specifying a string item type descriptor and an xml packet that can be used to load in the new object. The GUI uses this method to create new items that were added with the user interface. The item type lets the method determine what type of item is being created, like synapse, neuron, body part, etc.. It then gets the modulename, classname, and type from the xml and calls CreateObject to create the appropriate type of object. Then it passes in the xml packet to the new objects load method and does any needed initialization and adds it to the parent.
strItemType | String descriptor of the type of item that is being created. |
strXml | XML packet that is used to create and load the new item. |
bThrowError | If true then throw an error if there is a problem, otherwise return false. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 243 of file FiringRateModule.cpp.
References AddNeuron(), and StdUtils::Std_CheckString().
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Adds a neuron to the module.
strXml | The xml to use when loading the neuron. |
Definition at line 216 of file FiringRateModule.cpp.
References FiringRateSim::Neurons::Neuron::Initialize(), and LoadNeuron().
Referenced by AddItem().
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Calculates the snapshot byte size.
Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method calculates the number of bytes that will be required to store the entire object.
Reimplemented from AnimatSim::AnimatBase.
Definition at line 283 of file FiringRateModule.cpp.
References m_aryNeurons.
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Searches for the neuron with the specified ID and returns its position in the list.
strID | GUID ID of the neruon to find. |
bThrowError | true to throw error if nothing found. |
Definition at line 127 of file FiringRateModule.cpp.
References AnimatSim::AnimatBase::ID(), m_aryNeurons, StdUtils::Std_ToUpper(), and StdUtils::Std_Trim().
Referenced by RemoveNeuron().
bool FiringRateSim::FiringRateModule::InactiveArray | ( | ) |
Gets the inactive array.
Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the inactive one.
Definition at line 88 of file FiringRateModule.cpp.
References m_bActiveArray.
Referenced by FiringRateSim::Neurons::PacemakerNeuron::StepSimulation(), and FiringRateSim::Neurons::Neuron::StepSimulation().
void FiringRateSim::FiringRateModule::InactiveArray | ( | bool | bVal | ) |
Sets the inactive array.
Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This sets which of these array elements is currently the inactive one.
bVal | true for array element 1, false for array element 0. |
Definition at line 102 of file FiringRateModule.cpp.
References m_bActiveArray.
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Initializes this object.
After an object is loaded in it must be initialized before it can be used. This allows the object to retrieve any pointers or setup memory that it will need during execution. Each object is responsible for initializing any of its child objects, so you simply need to call this method on the containing class to init all child objects. It also calls VerifySystemPointers to make sure that the system pointers have been setup correctly.
Reimplemented from AnimatSim::Behavior::NeuralModule.
Definition at line 152 of file FiringRateModule.cpp.
References m_aryNeurons, and AnimatSim::AnimatBase::m_lpStructure.
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Kills.
Called to kill the organism, nervous system, neurons, and body parts. All neural items are disabled to prevent any further neural activity, and all joints are disabled to allow free rotation, and all biomechancical components are disabled so they can no longer produce forces. This method is only relevant to these types of objects, but I am putting the definition in the base class because a variety of different types of classes all need this method and I want it consolidated. Those classes that do not need it do not have to call it or do anything when it is called.
bState | true to state. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 108 of file FiringRateModule.cpp.
References m_aryNeurons.
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Loads a key frame snapshot.
Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method goes through each module and loads its data from the byte array.
[in,out] | aryBytes | The array of bytes where the data is being stored. |
[in,out] | lIndex | Current zero-based index of the read position in the array. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 302 of file FiringRateModule.cpp.
References m_aryNeurons.
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Loads the network configuration.
[in,out] | oXml | The xml to load. |
Definition at line 340 of file FiringRateModule.cpp.
References AnimatSim::Simulator::AddToObjectList(), AnimatSim::AnimatBase::ID(), AnimatSim::Behavior::NeuralModule::LoadExternalSynapses(), LoadNeuron(), m_aryNeurons, AnimatSim::Behavior::NeuralModule::m_fltTimeStep, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_strID, AnimatSim::AnimatBase::m_strName, AnimatSim::AnimatBase::m_strType, AnimatSim::AnimatBase::Name(), and AnimatSim::AnimatBase::Type().
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Loads a neuron.
[in,out] | oXml | The xml to load for the neuron. |
Definition at line 382 of file FiringRateModule.cpp.
References AnimatSim::Simulator::CreateObject(), m_aryNeurons, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and FiringRateSim::Neurons::Neuron::SetSystemPointers().
Referenced by AddNeuron(), and LoadNetworkXml().
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Gets the module name.
Implements AnimatSim::Behavior::NeuralModule.
Definition at line 45 of file FiringRateModule.cpp.
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Removes a child item from this parent.
This is a generic method that is used to delete a child object from this parent. The GUI uses this method to remove objects from the simulation that have been deleted in the UI. The item type lets the method determine what type of item is being deleted, like synapse, neuron, body part, etc.. The ID is then used to delete that specific item.
strItemType | String descriptor of the type of item that is being created. |
strID | Unique ID of the item that will be removed. |
bThrowError | If true then throw an error if there is a problem, otherwise return false. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 262 of file FiringRateModule.cpp.
References RemoveNeuron(), and StdUtils::Std_CheckString().
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Removes the neuron with the specified ID.
strID | GUID ID for the neuron. |
bThrowError | true to throw error if neuron found. |
Definition at line 237 of file FiringRateModule.cpp.
References FindNeuronListPos(), and m_aryNeurons.
Referenced by RemoveItem().
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Resets the simulation back to time 0.
This method calls the ResetSimulation method on all subitems in order to reset the simulation back to the beginning.
Reimplemented from AnimatSim::Behavior::NeuralModule.
Definition at line 142 of file FiringRateModule.cpp.
References m_aryNeurons.
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Saves a key frame snapshot.
Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method goes through each module and saves its data into the byte array.
[in,out] | aryBytes | The array of bytes where the data is being stored. |
[in,out] | lIndex | Current zero-based index of the write position in the array. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 294 of file FiringRateModule.cpp.
References m_aryNeurons.
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Set a variable based on a string data type name.
This is a generic method that can be used to set any variable in an AnimatBase object by specifying the name of the variable and a string representation of that data. The GUI uses this method to set data into variables in the simulation when the user changes them in the UI. The value string can be as simple as a float or int, or as complex as an xml packet. It is the developers responsibilty to know what type of data is needed and to process it accordingly.
strDataType | string name of the data type to set. |
strValue | The string value of the data. It is up to the developer to determine what this should be. For example, in most cases it is simply a float and you just have to convert it to a float and make the appropriate mutator method call. However, it can be any type of string, including an entire xml packet. It is the developers responsibility to know how to set and process the data as required. |
bThrowError | true to throw error if there is a problem. If false then it will not return an error, just return false. |
Reimplemented from AnimatSim::AnimatBase.
Definition at line 181 of file FiringRateModule.cpp.
References StdUtils::Std_CheckString(), and AnimatSim::Behavior::NeuralModule::TimeStep().
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Step the simulation for this object.
This is called on an object each time it is stepped in the simulation. this is where its simulation code is processed. However, StepSimulation is not necessarily called every single time that the simulation as a whole is stepped. A good example of this is that neural modules can have different integration time steps. So a firing rate module may have a DT of 0.5 ms, while an integrate and fire model may have one of 0.1 ms. So the firing rate module would only get its StepSimulation method called every 5th time that the other module was called. This is all handed in the StepSimulation method of the Simulator and NervousSystem.
Reimplemented from AnimatSim::Behavior::NeuralModule.
Definition at line 166 of file FiringRateModule.cpp.
References m_aryNeurons, and m_bActiveArray.
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Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the active one.
Definition at line 41 of file FiringRateModule.h.
Referenced by ActiveArray(), FiringRateModule(), InactiveArray(), and StepSimulation().