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Examples of BrainPy

Home Page: https://brainpy.tech/examples/

License: GNU General Public License v3.0

Makefile 0.01% Jupyter Notebook 99.06% Python 0.94% Batchfile 0.01%

biological-simulations brain-simulations brainpy neural-modeling

examples's Introduction

BrainPy is a flexible, efficient, and extensible framework for computational neuroscience and brain-inspired computation based on the Just-In-Time (JIT) compilation (built on top of JAX, Taichi, Numba, and others). It provides an integrative ecosystem for brain dynamics programming, including brain dynamics building, simulation, training, analysis, etc.

Website (documentation and APIs): https://brainpy.readthedocs.io/en/latest
Source: https://github.com/brainpy/BrainPy
Bug reports: https://github.com/brainpy/BrainPy/issues
Source on OpenI: https://git.openi.org.cn/OpenI/BrainPy

Installation

BrainPy is based on Python (>=3.8) and can be installed on Linux (Ubuntu 16.04 or later), macOS (10.12 or later), and Windows platforms.

For detailed installation instructions, please refer to the documentation: Quickstart/Installation

Using BrainPy with docker

We provide a docker image for BrainPy. You can use the following command to pull the image:

$ docker pull brainpy/brainpy:latest

Then, you can run the image with the following command:

$ docker run -it --platform linux/amd64 brainpy/brainpy:latest

Using BrainPy with Binder

We provide a Binder environment for BrainPy. You can use the following button to launch the environment:

Ecosystem

BrainPy: The solution for the general-purpose brain dynamics programming.
brainpy-examples: Comprehensive examples of BrainPy computation.
brainpy-datasets: Neuromorphic and Cognitive Datasets for Brain Dynamics Modeling.
《神经计算建模实战》 (Neural Modeling in Action)
第一届神经计算建模与编程培训班 (First Training Course on Neural Modeling and Programming)
第二届神经计算建模与编程培训班 (Second Training Course on Neural Modeling and Programming)

Citing

BrainPy is developed by a team in Neural Information Processing Lab at Peking University, China. Our team is committed to the long-term maintenance and development of the project.

If you are using brainpy, please consider citing the corresponding papers.

Ongoing development plans

We highlight the key features and functionalities that are currently under active development.

We also welcome your contributions (see Contributing to BrainPy).

model and data parallelization on multiple devices for dense connection models
model parallelization on multiple devices for sparse spiking network models
data parallelization on multiple devices for sparse spiking network models
pipeline parallelization on multiple devices for sparse spiking network models
multi-compartment modeling
measurements, analysis, and visualization methods for large-scale spiking data
Online learning methods for large-scale spiking network models
Classical plasticity rules for large-scale spiking network models

examples's People

Contributors

Stargazers

Watchers

Forkers

ppl91 chaoming0625 congcongdu 00mjk jowisdom hhoku123 pikapei

examples's Issues

Errors in Import brainpy

I can pip the packages brainpy, braipylib, jax, jaxlib successfully according to the documentation guide, but when I import brainpy in my script the error occurs: "AttributeError: module 'jax' has no attribute 'version' ", I have no idea why this appears, and found no solutions. Any help is appreciated. Thank you.

TypeError in mnist_lif_readout.py

Came from #9. Thanks for solving that problem!
There's another error in the same example:

Namespace(T=100, platform='cpu', batch=64, epochs=15, out_dir='./logs', lr=0.001, tau=2.0)
Traceback (most recent call last):
  File "/Users/pei/project/computational-neuroscience/mnist_lif_readout.py", line 103, in <module>
    l, correct_num = train(X, Y)
                     ^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/jit.py", line 208, in __call__
    rets = self._get_transform(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/jit.py", line 155, in _get_transform
    self._dyn_vars, rets = evaluate_dyn_vars(
                           ^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/tools.py", line 101, in evaluate_dyn_vars
    rets = jax.eval_shape(f2, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/project/computational-neuroscience/mnist_lif_readout.py", line 86, in train
    grads, l, n = grad_fun(xs, ys)
                  ^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/autograd.py", line 209, in __call__
    rets = self._transform(
           ^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/autograd.py", line 133, in _f_grad_with_aux_to_transform
    outputs = self.target(*args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/project/computational-neuroscience/mnist_lif_readout.py", line 69, in loss_fun
    out_fr = jnp.mean(outs, axis=0)
             ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/jax/_src/numpy/reductions.py", line 319, in mean
    return _mean(a, _ensure_optional_axes(axis), dtype, out, keepdims,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/jax/_src/numpy/reductions.py", line 351, in _mean
    sum(a, axis, dtype=computation_dtype, keepdims=keepdims, where=where),
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/jax/_src/numpy/reductions.py", line 222, in sum
    return _reduce_sum(a, axis=_ensure_optional_axes(axis), dtype=dtype, out=out,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/jax/_src/numpy/reductions.py", line 212, in _reduce_sum
    return _reduction(a, "sum", np.sum, lax.add, 0, preproc=_cast_to_numeric,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/jax/_src/numpy/reductions.py", line 94, in _reduction
    a = a if isinstance(a, Array) else lax_internal.asarray(a)
                                       ^^^^^^^^^^^^^^^^^^^^^^^
TypeError: asarray: expected ArrayLike, got Traced<ShapedArray(float32[100,64,10])>with<DynamicJaxprTrace(level=5/0)> of type <class 'brainpy._src.math.ndarray.Array'>.

I found a subtle bug in CANN tutorial

Hi! I found a bug in CANN tutorial that module bp is miswritten as op both in .py (line 75) and .ipynb (line 64) files. i.e.

self.integral = op.odeint(self.derivative)

should be

self.integral = bp.odeint(self.derivative)

'PoissonEncoder' object is not callable

Hello,

When I ran this example https://github.com/brainpy/examples/blob/main/brain_inspired_computing/mnist_lif_readout.py, the error showed:

Namespace(T=100, platform='cpu', batch=64, epochs=15, out_dir='./logs', lr=0.001, tau=2.0)
Traceback (most recent call last):
  File "/Users/pei/Downloads/mnist_lif_readout.py", line 103, in <module>
    l, correct_num = train(X, Y)
                     ^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/jit.py", line 208, in __call__
    rets = self._get_transform(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/jit.py", line 155, in _get_transform
    self._dyn_vars, rets = evaluate_dyn_vars(
                           ^^^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/tools.py", line 101, in evaluate_dyn_vars
    rets = jax.eval_shape(f2, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/Downloads/mnist_lif_readout.py", line 86, in train
    grads, l, n = grad_fun(xs, ys)
                  ^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/autograd.py", line 209, in __call__
    rets = self._transform(
           ^^^^^^^^^^^^^^^^
  File "/Users/pei/.pyenv/versions/mambaforge-22.9.0-2/envs/brainpy-env/lib/python3.11/site-packages/brainpy/_src/math/object_transform/autograd.py", line 133, in _f_grad_with_aux_to_transform
    outputs = self.target(*args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pei/Downloads/mnist_lif_readout.py", line 65, in loss_fun
    xs = encoder(xs, num_step=args.T)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'PoissonEncoder' object is not callable

Any help would be appreciated. Thank you!

error on numpy_ops.py

I try the https://brainpy-examples.readthedocs.io/en/latest/neurons/JR_1995_jansen_rit_model.html

python jansen_rit_model_001.py
Traceback (most recent call last):
  File "C:\PythonProjects\test_brainmodels\jansen_rit_model_001.py", line 1, in <module>
    import brainpy as bp
  File "C:\Python312\Lib\site-packages\brainpy\__init__.py", line 28, in <module>
    from . import math
  File "C:\Python312\Lib\site-packages\brainpy\math\__init__.py", line 35, in <module>
    from .delayvars import *
  File "C:\Python312\Lib\site-packages\brainpy\math\delayvars.py", line 12, in <module>
    from brainpy.math import numpy_ops as bm
  File "C:\Python312\Lib\site-packages\brainpy\math\numpy_ops.py", line 354, in <module>
    @wraps(jnp.in1d)
           ^^^^^^^^
  File "C:\Python312\Lib\site-packages\jax\_src\deprecations.py", line 54, in getattr
    raise AttributeError(f"module {module!r} has no attribute {name!r}")
AttributeError: module 'jax.numpy' has no attribute 'in1d'. Did you mean: 'int16'?