AnimatLab
2
Test
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Firing rate synapse model. More...
#include <Synapse.h>
Public Member Functions | |
Synapse () | |
Default constructor. More... | |
virtual | ~Synapse () |
Destructor. 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 | AddSynapse (std::string strXml, bool bDoNotInit) |
Adds a compound synapse to this one. More... | |
virtual float | CalculateCurrent () |
Calculates the synaptic current for this synapse. More... | |
virtual float | CalculateModulation (FiringRateModule *lpModule) |
Calculates the synaptic modulation. More... | |
virtual void | DelayInterval (float fltVal) |
Sets the delay buffer interval. More... | |
virtual float | DelayInterval () |
Gets the delay buffer size in time. More... | |
virtual int | FindSynapseListPos (std::string strID, bool bThrowError=true) |
Searches for the first synapse list position. More... | |
Neuron * | FromNeuron () |
Gets the pre-synaptic neuron. More... | |
virtual Synapse * | GetCompoundSynapse (short iCompoundIndex) |
Gets a pointer to a compound synapse. More... | |
virtual float * | GetDataPointer (const std::string &strDataType) |
Returns a float pointer to a data item of interest in this object. More... | |
virtual bool | HasDelay () |
Gets whether this synapse has a delay associated with it. More... | |
virtual void | HasDelay (bool bVal) |
Sets whether this synapse has a delay associated with it. More... | |
virtual void | Initialize () |
Initializes this object. More... | |
virtual void | Load (CStdXml &oXml) |
float | Modulation () |
Gets the synaptic modulation. More... | |
float * | ModulationPointer () |
Gets a pointer to the synaptic modulation. More... | |
virtual void | Process (float &fltCurrent) |
Processes this synapse. 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 | RemoveSynapse (std::string strID, bool bThrowError=true) |
Removes the copmound synapse specified by ID. More... | |
virtual void | ResetSimulation () |
Resets the simulation back to time 0. 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 | SetDelayBufferSize () |
Recalculates the size of the delay buffer required. More... | |
virtual void | SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify) |
Sets the system pointers. More... | |
virtual void | TimeStepModified () |
If the time step is modified then we need to recalculate the length of the delay buffer. More... | |
virtual void | VerifySystemPointers () |
Verify that system pointers have been set correctly. More... | |
float | Weight () |
Gets the synaptic weight. More... | |
void | Weight (float fltVal) |
Sets the synaptic weight. More... | |
float * | WeightPointer () |
Gets a pointer to the synaptic weight. More... | |
Public Member Functions inherited from AnimatSim::Link | |
Link () | |
Default constructor. More... | |
virtual | ~Link () |
Destructor. More... | |
virtual bool | Enabled () |
Gets whether the link is enabled. More... | |
virtual void | Enabled (bool bValue) |
Sets whether the link is Enabled. More... | |
virtual void | QueryProperties (CStdPtrArray< TypeProperty > &aryProperties) |
Queries this object for a list of properties that can be changed using SetData. More... | |
virtual void | SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify) |
Sets the system pointers. 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 long | CalculateSnapshotByteSize () |
Calculates the snapshot byte size. More... | |
virtual void | Copy (CStdSerialize *lpSource) |
virtual NeuralModule * | GetNeuralModule () |
Gets the neural module. More... | |
virtual Node * | GetNode () |
Gets the node. More... | |
virtual Simulator * | GetSimulator () |
Gets the simulator pointer. 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 | Kill (bool bState=true) |
Kills. More... | |
virtual void | Load (StdUtils::CStdXml &oXml) |
Loads the item using an XML data packet. More... | |
virtual void | LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex) |
Loads a key frame snapshot. 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 | 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 void | SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex) |
Saves a key frame snapshot. More... | |
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 | 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 | StepSimulation () |
Step the simulation for this object. 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 | |
Synapse * | LoadSynapse (CStdXml &oXml) |
Loads a synapse. More... | |
Protected Member Functions inherited from AnimatSim::Link | |
virtual void | UpdateData () |
Called during the StepSimulation method to allow the link to update any internal data for reporting purposes. More... | |
Protected Attributes | |
CStdCircularArray< float > | m_aryDelayBuffer |
CStdPtrArray< Synapse > | m_arySynapses |
Array of moduled/gated child synapses. | |
bool | m_bHasDelay |
float | m_fltDelayInterval |
float | m_fltModulation |
The modulation value to use for this synapse. | |
float | m_fltWeight |
The weight of the synapse. This is a current value in nanoamps. | |
FiringRateModule * | m_lpFRModule |
Pointer to parent FiringRateModule. | |
Neuron * | m_lpFromNeuron |
The pointer to pre-synaptic neuron. | |
Neuron * | m_lpToNeuron |
The pointer to post-synaptic neuron. | |
std::string | m_strFromID |
GUID ID of the pre-synaptic neruon. | |
Protected Attributes inherited from AnimatSim::Link | |
float | m_fltEnabled |
This is for reporting purposes. | |
Organism * | m_lpOrganism |
The pointer to this link's organism. | |
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::Link | |
static Link * | CastToDerived (AnimatBase *lpBase) |
Firing rate synapse model.
This synapse type has a weight that is a current value. It injects a portion of that weight into the post-synaptic neuron based on the pre-synaptic neurons firing rate. I = W*F. (Where W is the weight, F is the firing rate, and I is the current.)
FiringRateSim::Synapses::Synapse::Synapse | ( | ) |
Default constructor.
Definition at line 24 of file Synapse.cpp.
References m_fltModulation, m_fltWeight, m_lpFRModule, m_lpFromNeuron, m_lpToNeuron, and AnimatSim::AnimatBase::m_strType.
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Destructor.
Definition at line 43 of file Synapse.cpp.
References m_arySynapses, and StdUtils::Std_TraceMsg().
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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 440 of file Synapse.cpp.
References AddSynapse(), and StdUtils::Std_CheckString().
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Adds a compound synapse to this one.
strXml | The xml packet to load. |
Definition at line 267 of file Synapse.cpp.
References Initialize(), and LoadSynapse().
Referenced by AddItem().
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Calculates the synaptic current for this synapse.
Definition at line 184 of file Synapse.cpp.
References CalculateModulation(), FiringRateSim::Neurons::Neuron::FiringFreq(), FromNeuron(), m_aryDelayBuffer, m_lpFRModule, and Weight().
Referenced by Process().
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Calculates the synaptic modulation.
[in,out] | m_lpFRModule | Pointer to a fast module. |
Reimplemented in FiringRateSim::Synapses::GatedSynapse, and FiringRateSim::Synapses::ModulatedSynapse.
Definition at line 331 of file Synapse.cpp.
References CalculateModulation(), m_arySynapses, and m_fltModulation.
Referenced by CalculateCurrent(), and CalculateModulation().
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Sets the delay buffer interval.
fltVal | The new value. |
Definition at line 118 of file Synapse.cpp.
References SetDelayBufferSize(), and StdUtils::Std_IsAboveMin().
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Gets the delay buffer size in time.
Definition at line 108 of file Synapse.cpp.
Referenced by SetData().
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Searches for the first synapse list position.
strID | Identifier for the std::string. |
bThrowError | true to throw error. |
Definition at line 306 of file Synapse.cpp.
References AnimatSim::AnimatBase::ID(), m_arySynapses, StdUtils::Std_ToUpper(), and StdUtils::Std_Trim().
Referenced by RemoveSynapse().
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Gets the pre-synaptic neuron.
Definition at line 77 of file Synapse.h.
Referenced by CalculateCurrent(), FiringRateSim::Neurons::Neuron::CalculateSynapticCurrent(), and FiringRateSim::Synapses::ModulateNeuronPropSynapse::Process().
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Gets a pointer to a compound synapse.
iCompoundIndex | Zero-based index of the synapse. |
Definition at line 251 of file Synapse.cpp.
References m_arySynapses.
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Returns a float pointer to a data item of interest in this object.
This is a generic method used to get a pointer to data variable of interest. It is used by a variety of systems in the simulation. The most prominent are the data charting and stimulus classes. Within this method we associate a variable with a string name. By passing in the name of the data type we are interested in we can recieve back a float pointer to that data type. We can use that to read or set the data item in other classes. For example, the data charting system gets the pointer and then each time it needs to log a data point it reads the value into an array.
strDataType | name of the data item for which we are looking. |
If | DataType is not found. |
Reimplemented from AnimatSim::AnimatBase.
Reimplemented in FiringRateSim::Synapses::GatedSynapse, and FiringRateSim::Synapses::ModulatedSynapse.
Definition at line 385 of file Synapse.cpp.
References m_fltModulation, m_fltWeight, and StdUtils::Std_CheckString().
Referenced by FiringRateSim::Synapses::ModulatedSynapse::GetDataPointer(), and FiringRateSim::Synapses::GatedSynapse::GetDataPointer().
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Gets whether this synapse has a delay associated with it.
Definition at line 84 of file Synapse.cpp.
Referenced by SetData().
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Sets whether this synapse has a delay associated with it.
fltVal | The new value. |
Definition at line 94 of file Synapse.cpp.
References SetDelayBufferSize().
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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::AnimatBase.
Reimplemented in FiringRateSim::Synapses::ModulateNeuronPropSynapse.
Definition at line 348 of file Synapse.cpp.
References AnimatSim::Simulator::FindByID(), m_arySynapses, m_lpFromNeuron, AnimatSim::AnimatBase::m_lpSim, m_strFromID, and SetDelayBufferSize().
Referenced by AddSynapse(), FiringRateSim::Neurons::Neuron::AddSynapse(), and FiringRateSim::Synapses::ModulateNeuronPropSynapse::Initialize().
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Loads a synapse.
[in,out] | oXml | The xml packet to load. |
Definition at line 539 of file Synapse.cpp.
References AnimatSim::Simulator::CreateObject(), m_arySynapses, m_lpFRModule, AnimatSim::AnimatBase::m_lpNode, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and SetSystemPointers().
Referenced by AddSynapse().
float FiringRateSim::Synapses::Synapse::Modulation | ( | ) |
Gets the synaptic modulation.
Definition at line 225 of file Synapse.cpp.
References m_fltModulation.
float * FiringRateSim::Synapses::Synapse::ModulationPointer | ( | ) |
Gets a pointer to the synaptic modulation.
This is so that other items can alter the synaptic modulation.
Definition at line 238 of file Synapse.cpp.
References m_fltModulation.
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Processes this synapse.
Reimplemented in FiringRateSim::Synapses::ModulateNeuronPropSynapse.
Definition at line 171 of file Synapse.cpp.
References CalculateCurrent().
Referenced by FiringRateSim::Neurons::Neuron::CalculateSynapticCurrent().
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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 458 of file Synapse.cpp.
References RemoveSynapse(), and StdUtils::Std_CheckString().
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Removes the copmound synapse specified by ID.
strID | GUID ID for the synaspe to remove. |
bThrowError | true to throw error if synapse is not found. |
Definition at line 289 of file Synapse.cpp.
References FindSynapseListPos(), and m_arySynapses.
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::AnimatBase.
Reimplemented in FiringRateSim::Synapses::ModulateNeuronPropSynapse.
Definition at line 477 of file Synapse.cpp.
References m_aryDelayBuffer, and m_arySynapses.
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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::Link.
Reimplemented in FiringRateSim::Synapses::ModulateNeuronPropSynapse, and FiringRateSim::Synapses::GatedSynapse.
Definition at line 397 of file Synapse.cpp.
References DelayInterval(), HasDelay(), StdUtils::Std_CheckString(), StdUtils::Std_ToBool(), and Weight().
Referenced by FiringRateSim::Synapses::GatedSynapse::SetData().
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Recalculates the size of the delay buffer required.
Definition at line 147 of file Synapse.cpp.
References m_aryDelayBuffer, m_lpFRModule, and AnimatSim::Behavior::NeuralModule::TimeStep().
Referenced by DelayInterval(), HasDelay(), Initialize(), and TimeStepModified().
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Sets the system pointers.
There are a number of system pointers that are needed for use in the objects. The primariy one being a pointer to the simulation object itself so that you can get global parameters like the scale units and so on. However, each object may need other types of pointers as well, for example neurons need to have a pointer to their parent structure/organism, and to the NeuralModule they reside within. So different types of objects will need different sets of system pointers. We call this method to set the pointers just after creation and before Load is called. We then call VerifySystemPointers here, during Load and during Initialize in order to ensure that the correct pointers have been set for each type of objects. These pointers can then be safely used throughout the rest of the system.
[in,out] | lpSim | The pointer to a simulation. |
[in,out] | lpStructure | The pointer to the parent structure. |
[in,out] | lpModule | The pointer to the parent module module. |
[in,out] | lpNode | The pointer to the parent node. |
bVerify | true to call VerifySystemPointers. |
Definition at line 363 of file Synapse.cpp.
References m_lpFRModule, and VerifySystemPointers().
Referenced by LoadSynapse(), and FiringRateSim::Neurons::Neuron::LoadSynapse().
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If the time step is modified then we need to recalculate the length of the delay buffer.
If a neural module has been assigned to this adapter then that is its target module and we need to use the time step associated with it to determine how big the delay buffer should be in length. If the module is NULL then the target for this adapter is the physics engine and we should use the physics time step instead.
Reimplemented from AnimatSim::AnimatBase.
Definition at line 135 of file Synapse.cpp.
References SetDelayBufferSize().
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Verify that system pointers have been set correctly.
The system pointers should be set just after an object is created. However, if for some reason it was not then this could cause read/write memory access errors later on because we would be using NULL pointers. This method is called during SetSystemPointers, Load, and Initialize to verify that the pointers for that type of object have been set correctly. We are calling three different places to ensure that it is checked before use. For example, if you are doing a Load call then you want to check it before attempting the load, but there may be an object that does not Load, but only does Initialize. So we need to check it there as well.
Reimplemented from AnimatSim::Link.
Definition at line 372 of file Synapse.cpp.
References AnimatSim::AnimatBase::ID(), m_lpFRModule, AnimatSim::Link::m_lpOrganism, and AnimatSim::AnimatBase::m_strID.
Referenced by SetSystemPointers().
float FiringRateSim::Synapses::Synapse::Weight | ( | ) |
Gets the synaptic weight.
Definition at line 62 of file Synapse.cpp.
References m_fltWeight.
Referenced by CalculateCurrent(), and SetData().
void FiringRateSim::Synapses::Synapse::Weight | ( | float | fltVal | ) |
Sets the synaptic weight.
fltVal | The new value. |
Definition at line 73 of file Synapse.cpp.
References m_fltWeight.
float * FiringRateSim::Synapses::Synapse::WeightPointer | ( | ) |
Gets a pointer to the synaptic weight.
This is so that other items can alter the synaptic weight.
Definition at line 214 of file Synapse.cpp.
References m_fltWeight.
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This buffer is used if the adapter has been setup to have delays between calcuating values and setting them in the target object.
Definition at line 61 of file Synapse.h.
Referenced by CalculateCurrent(), ResetSimulation(), and SetDelayBufferSize().