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AnimatLab
2
Test
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AnimatLab
2
Test
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Firing rate synapse model. More...
#include <CsSpikingCurrentSynapse.h>
Inheritance diagram for AnimatCarlSim::CsSpikingCurrentSynapse: Collaboration diagram for AnimatCarlSim::CsSpikingCurrentSynapse:Public Member Functions | |
| CsSpikingCurrentSynapse () | |
| Default constructor. More... | |
| virtual | ~CsSpikingCurrentSynapse () |
| Destructor. More... | |
| virtual void | Cells (std::string strXml) |
| virtual void | Coverage (std::string strType) |
| CsNeuronGroup * | FromNeuron () |
| Gets the pre-synaptic neuron. More... | |
| virtual float * | GetDataPointer (const std::string &strDataType) |
| Returns a float pointer to a data item of interest in this object. More... | |
| virtual void | Initialize () |
| Initializes this object. More... | |
| virtual void | Load (CStdXml &oXml) |
| virtual void | PulseCurrent (float fltVal) |
| virtual float | PulseCurrent () |
| virtual void | PulseDecay (float fltVal) |
| virtual float | PulseDecay () |
| virtual void | QueryProperties (CStdPtrArray< TypeProperty > &aryProperties) |
| 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 | StepSimulation () |
| Step the simulation for this object. More... | |
| virtual void | TimeStepModified () |
| Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More... | |
| virtual void | VerifySystemPointers () |
| Verify that system pointers have been set correctly. More... | |
| virtual bool | WholePopulation () |
| virtual void | WholePopulation (bool bVal) |
| 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 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 | 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 bool | RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true) |
| Removes a child item from this parent. 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 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... | |
Static Public Member Functions | |
| static CsSpikingCurrentSynapse * | CastToDerived (AnimatBase *lpBase) |
| Static Public Member Functions inherited from AnimatSim::Link | |
| static Link * | CastToDerived (AnimatBase *lpBase) |
Protected Member Functions | |
| virtual void | CalculateStepsPerTest () |
| virtual void | LoadCells (CStdXml &oXml) |
| virtual void | MonitorSpikeEventFired (int iGroupID, int iNeuronID, long lTimeIdx) |
| virtual void | ProcessSpikes () |
| 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 | |
| boost::interprocess::interprocess_mutex | m_AccessSpikes |
| mutex used to try and access matches variable. | |
| CStdMap< int, int > | m_aryCells |
| An array of neuron indices for individual neurons we want to stimulate. | |
| CStdArray< long > | m_arySpikeTimes |
| bool | m_bWholePopulation |
| Tells whether this entire population is monitored or just individual cells. | |
| float | m_fltAppliedCurrent |
| The actual applied current with sign. | |
| float | m_fltCurrentMagnitude |
| The magnitude of the current applied to the target neuron. | |
| float | m_fltDecrementCurrent |
| The amount by which the current is decremented each step. | |
| float | m_fltPulseDecay |
| The decay rate for which a current pulse. | |
| float | m_fltPulseMagnitude |
| The magnitude amount of the current to apply for a single pulse. | |
| float | m_fltPulseSign |
| The sign of the current to apply for a single pulse. | |
| float | m_fltPulseTC |
| The exponential decay constant calculated from the time step and decay rate. | |
| int | m_iStepsPerTest |
| Keeps track of the number of steps till we need to test for spikes to process. | |
| int | m_iStepsPerTestCount |
| Keeps track of how my steps we have take tiil we are ready to test again. | |
| CsNeuronGroup * | m_lpFromNeuron |
| The pointer to pre-synaptic neuron. | |
| AnimatSim::Node * | m_lpToNeuron |
| The pointer to post-synaptic neuron. | |
| long | m_lTotalSpikesAdded |
| boost::signals2::connection | m_MonitoredSpikeEvent |
| std::string | m_strFromID |
| GUID ID of the pre-synaptic neruon. | |
| std::string | m_strToID |
| GUID ID of the pre-synaptic neruon. | |
| unsigned long | m_ulSpikeTestTime |
| 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.. | |
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.)
Definition at line 22 of file CsSpikingCurrentSynapse.h.
| AnimatCarlSim::CsSpikingCurrentSynapse::CsSpikingCurrentSynapse | ( | ) |
Default constructor.
Definition at line 22 of file CsSpikingCurrentSynapse.cpp.
References m_bWholePopulation, m_fltAppliedCurrent, m_fltCurrentMagnitude, m_fltDecrementCurrent, m_fltPulseDecay, m_fltPulseMagnitude, m_fltPulseSign, m_fltPulseTC, m_iStepsPerTest, m_iStepsPerTestCount, m_lpFromNeuron, and m_lpToNeuron.
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Destructor.
Definition at line 46 of file CsSpikingCurrentSynapse.cpp.
References StdUtils::Std_TraceMsg().
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Gets the pre-synaptic neuron.
Definition at line 119 of file CsSpikingCurrentSynapse.h.
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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.
Definition at line 177 of file CsSpikingCurrentSynapse.cpp.
References m_fltAppliedCurrent, m_fltDecrementCurrent, and StdUtils::Std_CheckString().
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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.
Definition at line 149 of file CsSpikingCurrentSynapse.cpp.
References AnimatSim::Simulator::FindByID(), m_bWholePopulation, m_lpFromNeuron, AnimatSim::AnimatBase::m_lpSim, m_lpToNeuron, m_strFromID, and m_strToID.
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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.
Definition at line 256 of file CsSpikingCurrentSynapse.cpp.
References m_fltAppliedCurrent, m_fltCurrentMagnitude, m_fltDecrementCurrent, and m_iStepsPerTestCount.
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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.
Definition at line 205 of file CsSpikingCurrentSynapse.cpp.
References StdUtils::Std_CheckString().
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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::AnimatBase.
Definition at line 312 of file CsSpikingCurrentSynapse.cpp.
References AnimatSim::Node::AddExternalNodeInput(), AnimatSim::AnimatBase::m_bEnabled, m_fltAppliedCurrent, m_fltCurrentMagnitude, m_fltDecrementCurrent, m_fltPulseSign, m_fltPulseTC, m_lpFromNeuron, and m_lpToNeuron.
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Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed.
Reimplemented from AnimatSim::AnimatBase.
Definition at line 125 of file CsSpikingCurrentSynapse.cpp.
References m_fltPulseDecay.
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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 191 of file CsSpikingCurrentSynapse.cpp.
References AnimatSim::AnimatBase::m_lpModule, AnimatSim::Link::m_lpOrganism, AnimatSim::AnimatBase::m_lpStructure, and AnimatSim::AnimatBase::m_strID.
1.8.10 
