### Instantiate BCMSynapse

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/hebbian/BCMSynapse.html

Demonstrates how to instantiate the BCMSynapse component within a simulation context. This example shows basic parameter setup for a synapse.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = BCMSynapse("Wab", (2, 3), 0.0004, 1, 1)
    print(Wab)
```

--------------------------------

### Install ngc-learn from Source

Source: https://ngc-learn.readthedocs.io/en/latest/installation.html

Install the ngc-learn package after cloning the repository. Use the editable install option for development purposes.

```bash
$ pip install .

```

```bash
$ pip install -e .

```

--------------------------------

### Install NGC-Learn Package from Source

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/installation.md.txt

Install the NGC-Learn package after cloning the repository. Use this command for a standard installation from source.

```bash
$ pip install .
```

--------------------------------

### QuadLIFCell Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/quadLIFCell.html

Demonstrates how to initialize a QuadLIFCell within a simulation context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = QuadLIFCell("X", 9, 0.0004, 3)
    print(X)
```

--------------------------------

### ExpSTDPSynapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/hebbian/expSTDPSynapse.html

Demonstrates how to instantiate an ExpSTDPSynapse object with specified parameters within a ngcsimlib Context. This is a basic usage example.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = ExpSTDPSynapse("Wab", (2, 3), 1, 1, 1, 0.0004, 1)
    print(Wab)
```

--------------------------------

### sLIFCell Example Initialization

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/sLIFCell.html

Demonstrates how to initialize an sLIFCell with specified parameters within a simulation context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = SLIFCell("X", 9, 0.0004, 3, 0.3)
    print(X)
```

--------------------------------

### Install CPU Version of NGC-Learn

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/installation.md.txt

Use this command to install the CPU-only version of NGC-Learn. This is the default if no JAX is pre-installed or only the CPU version of JAX is installed.

```bash
$ pip install ngclearn
```

--------------------------------

### LIFCell Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/LIFCell.html

Demonstrates how to initialize a LIFCell with specified parameters and print its representation. Requires the ngcsimlib.context module.

```python
from ngcsimlib.context import Context
with Context("Bar") as bar:
    X = LIFCell("X", 9, 0.0004, 3)
print(X)
```

--------------------------------

### AdExCell Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/adExCell.html

Demonstrates how to initialize an AdExCell component within a Context. This example shows the creation of an AdExCell instance with specified parameters.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = AdExCell("X", 9)
    print(X)

```

--------------------------------

### Example Logging Configuration (Write to File)

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/tutorials/model_basics/configuration.md.txt

An example configuration that directs all logging messages to a specified file and hides console output. It also sets the logging level to INFO.

```json
{
  "logging": {
    "logging_file": "path/to/log/file.txt",
    "logging_level": "INFO",
    "hide_console": true
  }
}
```

--------------------------------

### ART2ASynapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/competitive/ART2ASynapse.html

Demonstrates how to initialize an ART2ASynapse object. This requires setting up a context and providing parameters for the synapse.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = ART2ASynapse("Wab", (2, 3), 4, 4, 1.)
    print(Wab)
```

--------------------------------

### REINFORCE Synapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/modulated/REINFORCESynapse.html

Demonstrates how to initialize and use the REINFORCE Synapse component within the NGC Learn framework. This example shows setting up the synapse with a specified shape and accessing its weights.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        syn = REINFORCESynapse(
            name="reinforce_syn",
            shape=(3, 2)
        )
        # Wab = syn.weights.get()
    print(syn)
```

--------------------------------

### Adam Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/optim/adam.html

Demonstrates the usage of Adam initialization and step update with sample weights and updates.

```python
import numpy as np
from jax import jit, numpy as jnp, random, nn, lax
from functools import partial




[docs]
def step_update(param, update, g1, g2, eta, beta1, beta2, time_step, eps):
    """
    Runs one step of Adam over a set of parameters given updates.
    The dynamics for any set of parameters is as follows:

    | g1 = beta1 * g1 + (1 - beta1) * update
    | g2 = beta2 * g2 + (1 - beta2) * (update)^2
    | g1_unbiased = g1 / (1 - beta1**time)
    | g2_unbiased = g2 / (1 - beta2**time)
    | param = param - lr * g1_unbiased / (sqrt(g2_unbiased) + epsilon)

    Args:
        param: parameter tensor to change/adjust

        update: update tensor to be applied to parameter tensor (must be same
            shape as "param")

        g1: first moment factor/correction factor to use in parameter update
            (must be same shape as "update")

        g2: second moment factor/correction factor to use in parameter update
            (must be same shape as "update")

        eta: global step size value to be applied to updates to parameters

        beta1: 1st moment control factor

        beta2: 2nd moment control factor

        time_step: current time t or iteration step/call to this Adam update

        eps: numberical stability coefficient (for calculating final update)

    Returns:
        adjusted parameter tensor (same shape as "param"), adjusted g1, adjusted g2
    """
    _g1 = beta1 * g1 + (1. - beta1) * update
    _g2 = beta2 * g2 + (1. - beta2) * jnp.square(update)
    g1_unb = _g1 / (1. - jnp.power(beta1, time_step))
    g2_unb = _g2 / (1. - jnp.power(beta2, time_step))
    _param = param - eta * g1_unb/(jnp.sqrt(g2_unb) + eps)
    return _param, _g1, _g2




[docs]
@jit
def adam_step(opt_params, theta, updates, eta=0.001, beta1=0.9, beta2=0.999, eps=1e-8):  ## apply adjustment to theta
    """Implements the adaptive moment estimation (Adam) algorithm as a decoupled
        update rule given adjustments produced by a credit assignment algorithm/process.

    Args:
        opt_params: (ArrayLike) parameters of the optimization algorithm

        theta: (ArrayLike) the weights of neural network

        updates: (ArrayLike) the updates of neural network

        eta: (float, optional) step size coefficient for Adam update (Default: 0.001)

        beta1: (float, optional) 1st moment control factor. (Default: 0.9)

        beta2: (float, optional) 2nd moment control factor. (Default: 0.999)

        eps: (float, optional) numberical stability coefficient (for calculating
            final update). (Default: 1e-8)

    Returns:
        ArrayLike: opt_params. New opt params, ArrayLike: theta. The updated weights
    """
    g1, g2, time_step = opt_params
    time_step = time_step + 1
    new_theta = []
    new_g1 = []
    new_g2 = []
    for i in range(len(theta)):
        px_i, g1_i, g2_i = step_update(theta[i], updates[i], g1[i], g2[i], eta, beta1, beta2, time_step, eps)
        new_theta.append(px_i)
        new_g1.append(g1_i)
        new_g2.append(g2_i)
    return (new_g1, new_g2, time_step), new_theta




[docs]
@jit
def adam_init(theta):
    time_step = jnp.asarray(0.0)
    g1 = [jnp.zeros(theta[i].shape) for i in range(len(theta))]
    g2 = [jnp.zeros(theta[i].shape) for i in range(len(theta))]
    return g1, g2, time_step



if __name__ == '__main__':
    weights = [jnp.asarray([3.0, 3.0]), jnp.asarray([3.0, 3.0])]
    updates = [jnp.asarray([3.0, 3.0]), jnp.asarray([3.0, 3.0])]
    opt_params = adam_init(weights)
    opt_params, theta = adam_step(opt_params, weights, updates)
    print(f"opt_params: {opt_params}, theta: {theta}")

```

--------------------------------

### MPS Synapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/mpsSynapse.html

Example of initializing an MPSSynapse component within a ngcsimlib Context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("MPS_Test") as ctx:
        Wab = MPSSynapse("Wab", (10, 5), bond_dim=4)
    print(Wab)
```

--------------------------------

### EventSTDPSynapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/hebbian/eventSTDPSynapse.html

Demonstrates how to instantiate an EventSTDPSynapse component with a specified name, shape, and initial weight bound. This example is useful for setting up a new synapse in a simulation context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = EventSTDPSynapse("Wab", (2, 3), 1.)
    print(Wab)
```

--------------------------------

### Install NGC-Learn as Editable Install

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/installation.md.txt

Install the NGC-Learn package in editable mode from source. This is useful for development purposes, allowing changes to be reflected immediately.

```bash
$ pip install -e .
```

--------------------------------

### ExpKernel Class Definition and Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/other/expKernel.html

Shows the definition of the ExpKernel class and a basic example of its instantiation and usage within a Context manager.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = ExpKernel("X", 1, 1.)
    print(X)
```

--------------------------------

### DenseSynapse Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/denseSynapse.html

Demonstrates how to instantiate a DenseSynapse component with specified dimensions and context. This is useful for setting up dense synaptic layers in a simulation.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = DenseSynapse("Wab", (2, 3))
    print(Wab)
```

--------------------------------

### Verify NGC-Learn Installation

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/installation.md.txt

Verify that NGC-Learn has been installed successfully by importing it in a Python interpreter and checking its version. A successful import and version display indicate a correct installation.

```python
Python 3.11.4 (main, MONTH  DAY YEAR, TIME) [GCC XX.X.X] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ngclearn
>>> ngclearn.__version__
'3.0.1'
```

--------------------------------

### PatchedSynapse Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/patched/patchedSynapse.html

Demonstrates the instantiation and basic usage of the PatchedSynapse component, including visualization of its weights.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = PatchedSynapse("Wab", (9, 30), 3)
    print(Wab)
    plt.imshow(Wab.weights.get(), cmap='gray')
    plt.show()
```

--------------------------------

### NAG Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/optim/nag.html

Demonstrates the usage of the `nag_init` and `nag_step` functions with sample weights and updates. It shows how the parameters evolve over two steps of the NAG algorithm.

```python
if __name__ == '__main__':
    weights = [jnp.asarray([3.0, 3.0]), jnp.asarray([3.0, 3.0])]
    updates = [jnp.asarray([3.0, 3.0]), jnp.asarray([3.0, 3.0])]
    opt_params = nag_init(weights)
    opt_params, theta = nag_step(opt_params, weights, updates)
    print(f"opt_params: {opt_params}, theta: {theta}")
    weights = theta
    print("##################")
    opt_params, theta = nag_step(opt_params, weights, updates)
    print(f"opt_params: {opt_params}, theta: {theta}")
```

--------------------------------

### SGD Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/optim/sgd.html

Demonstrates the usage of the sgd_step function with sample parameters, weights, updates, and step size.

```python
if __name__ == '__main__':
    opt_params, theta = sgd_step((2.0), [1.0, 1.0], [3.0, 4.0], 3e-2)
    print(f"opt_params: {opt_params}, theta: {theta}")
```

--------------------------------

### Clone NGC-Learn Repository

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/installation.md.txt

Clone the NGC-Learn repository from GitHub and navigate into the project directory. This is the first step for installing from source.

```bash
$ git clone https://github.com/NACLab/ngc-learn.git
$ cd ngc-learn
```

--------------------------------

### BernoulliCell Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/input_encoders/bernoulliCell.html

Demonstrates basic usage of the BernoulliCell by creating an instance and setting its batch size within a Context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = BernoulliCell("X", 9)

    X.batch_size.set(10)

```

--------------------------------

### TraceSTDPSynapse Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/hebbian/traceSTDPSynapse.html

Demonstrates how to instantiate and print a TraceSTDPSynapse component within a ngcsimlib Context. This shows basic usage and initialization.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = TraceSTDPSynapse("Wab", (2, 3), 1, 1, 0.0004)
    print(Wab)
```

--------------------------------

### Hodgkin-Huxley Cell Initialization Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/hodgkinHuxleyCell.html

This snippet demonstrates how to instantiate and initialize a HodgkinHuxleyCell component within the NGC Learn simulation context. It shows the basic setup for creating a cell layer.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = HodgkinHuxleyCell("X", 1, 1.)
    print(X)
```

--------------------------------

### LeakyNoiseCell Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/graded/leakyNoiseCell.html

Demonstrates a basic example of how to instantiate and use the LeakyNoiseCell within an ngcsimlib Context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = LeakyNoiseCell("X", 9, 0.03)
    print(X)
```

--------------------------------

### IFCell Compartment Setup

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/IFCell.html

Initializes the compartments for the IFCell, including current, voltage, spikes, refractory period, and time-of-last-spike. This setup is crucial before the cell can be simulated.

```python
## Compartment setup
        restVals = jnp.zeros((self.batch_size, self.n_units))
        self.j = Compartment(restVals, display_name="Current", units="mA")
        self.v = Compartment(restVals + self.v_rest,
                             display_name="Voltage", units="mV")
        self.s = Compartment(restVals, display_name="Spikes")
        self.rfr = Compartment(restVals + self.refract_T,
                               display_name="Refractory Time Period", units="ms")
        self.tols = Compartment(restVals, display_name="Time-of-Last-Spike",
                                units="ms") ## time-of-last-spike
        #self.surrogate = Compartment(restVals + 1., display_name="Surrogate State Value")
```

--------------------------------

### Import Dynamic Synapse Models and Setup

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/tutorials/neurocog/dynamic_synapses.md.txt

Imports necessary components from ngc-learn and JAX for dynamic synapse modeling. Sets up meta-parameters for simulation duration and time constant.

```python
from jax import numpy as jnp, random, jit
from ngclearn import Context, MethodProcess
from ngclearn.components import ExponentialSynapse, AlphaSynapse, DoubleExpSynapse
from ngclearn.utils.distribution_generator import DistributionGenerator


dkey = random.PRNGKey(1234) ## creating seeding keys for synapses
dkey, *subkeys = random.split(dkey, 6)
dt = 0.1 # ms ## integration time constant
T = 8. # ms ## total duration time

```

--------------------------------

### Initialize and Print SOMSynapse

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/competitive/SOMSynapse.html

Demonstrates how to initialize a SOMSynapse object and print its representation. Requires ngcsimlib.context.Context for proper initialization.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = SOMSynapse("Wab", (2, 3), 4, 4, 1.)
    print(Wab)
```

--------------------------------

### KNNProbe Initialization and Usage Example

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/analysis/knn_probe.html

Demonstrates how to initialize a KNNProbe, update it with data, and process inputs to observe the output. This is useful for verifying the probe's functionality and understanding its behavior with sample data.

```python
seed = 42
D = 7
C = 5
dkey = random.PRNGKey(seed)
dkey, *subkeys = random.split(dkey, 3)
knn = KNNProbe(
    subkeys[0], 1, input_dim=D, out_dim=C, K=1, dist_function="euclidean"
)
X = random.uniform(subkeys[1], shape=(10, D))
Y = jnp.concat(
    [
        jnp.ones((2, C)) * jnp.array([[1., 0., 0., 0., 0.]]),
        jnp.ones((2, C)) * jnp.array([[0., 1., 0., 0., 0.]]),
        jnp.ones((2, C)) * jnp.array([[0., 0., 1., 0., 0.]]),
        jnp.ones((2, C)) * jnp.array([[0., 0., 0., 1., 0.]]),
        jnp.ones((2, C)) * jnp.array([[0., 0., 0., 0., 1.]])
     ],
    axis=0
)
knn.update(X, Y) ## fit KNN to data
print(knn.process(X)) ## should construct the (smeared) identity matrix, exactly same as Y
```

--------------------------------

### RetinalGanglionCell Example Usage

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/input_encoders/ganglionCell.html

Demonstrates how to instantiate and use the RetinalGanglionCell component within a simulation context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = RetinalGanglionCell(
                "RGC", 
                filter_type="gaussian",
                sigma=2.3,
                area_shape=(16, 26),
                n_cells = 3,
                patch_shape=(16, 16),
                step_shape=(0, 5)
        )
    print(X)
```

--------------------------------

### Setting up a Trace-Based STDP Model

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/tutorials/neurocog/stdp.md.txt

This code initializes a system with two VarTrace components and a TraceSTDPSynapse. It demonstrates how to wire these components and define methods for evolving the synapse and advancing the state of the traces.

```python
from jax import numpy as jnp, random, jit

from ngclearn import Context, MethodProcess
## import model-specific mechanisms
from ngclearn.components.other.varTrace import VarTrace
from ngclearn.components.synapses.hebbian.traceSTDPSynapse import TraceSTDPSynapse
from ngclearn.utils.distribution_generator import DistributionGenerator

## create seeding keys (JAX-style)
dkey = random.PRNGKey(231)
dkey, *subkeys = random.split(dkey, 2)

dt = 1.  # ms # integration time constant
T_max = 100  ## number time steps to simulate

with Context("Model") as model:
    tr0 = VarTrace("tr0", n_units=1, tau_tr=8., a_delta=1.)
    tr1 = VarTrace("tr1", n_units=1, tau_tr=8., a_delta=1.)
    W = TraceSTDPSynapse(
        "W1", shape=(1, 1), eta=0., A_plus=1., A_minus=0.8, 
        weight_init=DistributionGenerator.uniform(low=0.0, high=0.3), key=subkeys[0]
    )

    # wire only relevant compartments to synaptic cable W for demo purposes
    tr0.trace >> W.preTrace 
    # self.z0.outputs >> self.W1.preSpike ## we disable this as we will manually
    ##                                       insert a binary value (for a spike) in this tutorial
    tr1.trace >> W.postTrace 
    # self.z1e.s >> self.W1.postSpike ## we disable this as we will manually
    ##                                   insert a binary value (for a spike) in this tutorial

    evolve_synapse = (MethodProcess("evolve")
                      >> W.evolve)

    advance_traces = (MethodProcess("advance")
                      >> tr0.advance_state
                      >> tr1.advance_state
                      >> W.advance_state)

    reset = (MethodProcess("reset")
             >> tr0.reset
             >> tr1.reset
             >> W.reset)

## set up some utility functions for the model context
def clamp_synapse(pre_spk, post_spk):
    W.preSpike.set(pre_spk)
    W.postSpike.set(post_spk)

def clamp_traces(pre_spk, post_spk):
    tr0.inputs.set(pre_spk)
    tr1.inputs.set(post_spk)

```

--------------------------------

### Example Usage (Fitzhugh-Nagumo Cell)

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/spiking/fitzhughNagumoCell.html

Demonstrates how to instantiate and use the FitzhughNagumoCell component within a ngcsimlib Context.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = FitzhughNagumoCell("X", 9)
    print(X)
```

--------------------------------

### RewardErrorCell Initialization and Print

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/neurons/graded/rewardErrorCell.html

Demonstrates how to initialize a RewardErrorCell and print its representation. This is useful for verifying component setup.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        X = RewardErrorCell("X", 9, 0.03)
    print(X)
```

--------------------------------

### Initialize and Print VectorQuantizeSynapse

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/competitive/vectorQuantizeSynapse.html

Demonstrates how to initialize a VectorQuantizeSynapse and print its representation. This is useful for verifying the synapse's creation and initial state.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = VectorQuantizeSynapse("Wab", (2, 3), 4, 4, 1.)
    print(Wab)
```

--------------------------------

### Make Video

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/viz/synapse_plot.html

Placeholder function for creating a video from a start and end frame. The implementation is not provided in the source.

```python
def make_video(
        f_start,
        f_end,
        path,
        prefix,

```

--------------------------------

### Instantiate HopfieldSynapse

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/components/synapses/competitive/hopfieldSynapse.html

Demonstrates how to instantiate the HopfieldSynapse class within a context. Requires importing Context and HopfieldSynapse.

```python
if __name__ == '__main__':
    from ngcsimlib.context import Context
    with Context("Bar") as bar:
        Wab = HopfieldSynapse("Wab", (2, 3), 4, 4, 1.)
    print(Wab)
```

--------------------------------

### PatchGenerator Iterator Implementation

Source: https://ngc-learn.readthedocs.io/en/latest/_modules/ngclearn/utils/patch.html

Implements the iterator protocol for PatchGenerator. It checks if an image has been provided before starting the iteration.

```python
    def __iter__(self):
        if self._current_img is None:
            error("Attempting to generate patches but no image has been provided")

        self._current_idx = 0
        return self
```

--------------------------------

### Instantiate FitzhughNagumoCell

Source: https://ngc-learn.readthedocs.io/en/latest/_sources/tutorials/neurocog/fitzhugh_nagumo_cell.md.txt

Sets up the controller and constructs a single Fitzhugh-Nagumo cell component with specified hyperparameters. Includes compilation of core simulation commands.

```python
from jax import numpy as jnp, random, jit
import numpy as np

from ngclearn import Context, MethodProcess
## import model-specific mechanisms
from ngclearn.components.neurons.spiking.fitzhughNagumoCell import FitzhughNagumoCell

## create seeding keys (JAX-style)
dkey = random.PRNGKey(1234)
dkey, *subkeys = random.split(dkey, 6)

## F-N cell hyperparameters
alpha = 0.3  ## recovery variable shift factor
beta = 1.4  ## recovery variable scale factor
gamma = 1.  ## membrane potential power term denominator
tau_w = 20.  ## recovery variable time constant
v0 = -0.63605838  ## initial membrane potential (for reset condition)
w0 = -0.16983366  ## initial recovery value (for reset condition)

## create simple system with only one F-N cell
with Context("Model") as model:
    cell = FitzhughNagumoCell(
        "z0", n_units=1, tau_w=tau_w, alpha=alpha, beta=beta, gamma=gamma, v0=v0, w0=w0, integration_type="euler"
    )

    ## create and compile core simulation commands
    advance_process = (MethodProcess("advance")
                       >> cell.advance_state)

    reset_process = (MethodProcess("reset")
                     >> cell.reset)

## set up non-compiled utility commands
def clamp(x):
    cell.j.set(x)
```

--------------------------------

### ngclearn.utils.io_utils.makedir

Source: https://ngc-learn.readthedocs.io/en/latest/source/ngclearn.utils.html

Creates a folder/directory on disk.

```APIDOC
## ngclearn.utils.io_utils.makedir

### Description
Creates a folder/directory on disk.

### Parameters
* **directory** (string) - string name of directory/folder to create on disk
```