braintools 0.0.10__tar.gz

braintools-0.0.10/LICENSE

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braintools-0.0.10/PKG-INFO

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+Metadata-Version: 2.4
+Name: braintools
+Version: 0.0.10
+Summary: The Toolbox for Brain Modeling Ecosystem.
+Home-page: https://github.com/chaobrain/braintools
+Author: BrainTools Developers
+Author-email: BrainTools Developers <chao.brain@qq.com>
+License: Apache-2.0 license
+Project-URL: homepage, http://github.com/chaobrain/braintools
+Project-URL: repository, http://github.com/chaobrain/braintools
+Keywords: brain dynamics programming,brain simulation,brain-inspired computing
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: brainstate>=0.1.0
+Requires-Dist: brainunit>=0.0.8
+Requires-Dist: typing_extensions
+Provides-Extra: testing
+Requires-Dist: pytest; extra == "testing"
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# Tools/utilities for brain dynamics programming
+
+<p align="center">
+  	<img alt="Header image of braintools." src="https://raw.githubusercontent.com/chaobrain/braintools/main/docs/_static/braintools.jpg" width=50%>
+</p>
+
+
+<p align="center">
+	<a href="https://pypi.org/project/braintools/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/braintools"></a>
+	<a href="https://github.com/brainpy/braintools/blob/main/LICENSE"><img alt="LICENSE" src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"></a>
+    <a href='https://braintools.readthedocs.io/?badge=latest'>
+        <img src='https://readthedocs.org/projects/braintools/badge/?version=latest' alt='Documentation Status' />
+    </a>  	
+    <a href="https://badge.fury.io/py/braintools"><img alt="PyPI version" src="https://badge.fury.io/py/braintools.svg"></a>
+    <a href="https://github.com/brainpy/braintools/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/brainpy/braintools/actions/workflows/CI.yml/badge.svg"></a>
+</p>
+
+
+[``braintools``](https://github.com/brainpy/braintools) provides common toolboxes for brain dynamics programming (BDP). 
+
+
+## Installation
+
+You can install ``braintools`` via pip:
+
+```bash
+pip install braintools --upgrade
+```
+
+Alternatively, you can install `BrainX`, which bundles `braintools` with other compatible packages for a comprehensive brain modeling ecosystem:
+
+```bash
+pip install BrainX -U
+```
+
+
+## Documentation
+
+The official documentation is hosted on Read the Docs: [https://braintools.readthedocs.io](https://braintools.readthedocs.io)
+
+
+
+
+## See also the brain modeling ecosystem
+
+We are building the brain modeling ecosystem: https://brainmodeling.readthedocs.io/

braintools-0.0.10/README.md

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+# Tools/utilities for brain dynamics programming
+
+<p align="center">
+  	<img alt="Header image of braintools." src="https://raw.githubusercontent.com/chaobrain/braintools/main/docs/_static/braintools.jpg" width=50%>
+</p>
+
+
+<p align="center">
+	<a href="https://pypi.org/project/braintools/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/braintools"></a>
+	<a href="https://github.com/brainpy/braintools/blob/main/LICENSE"><img alt="LICENSE" src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"></a>
+    <a href='https://braintools.readthedocs.io/?badge=latest'>
+        <img src='https://readthedocs.org/projects/braintools/badge/?version=latest' alt='Documentation Status' />
+    </a>  	
+    <a href="https://badge.fury.io/py/braintools"><img alt="PyPI version" src="https://badge.fury.io/py/braintools.svg"></a>
+    <a href="https://github.com/brainpy/braintools/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/brainpy/braintools/actions/workflows/CI.yml/badge.svg"></a>
+</p>
+
+
+[``braintools``](https://github.com/brainpy/braintools) provides common toolboxes for brain dynamics programming (BDP). 
+
+
+## Installation
+
+You can install ``braintools`` via pip:
+
+```bash
+pip install braintools --upgrade
+```
+
+Alternatively, you can install `BrainX`, which bundles `braintools` with other compatible packages for a comprehensive brain modeling ecosystem:
+
+```bash
+pip install BrainX -U
+```
+
+
+## Documentation
+
+The official documentation is hosted on Read the Docs: [https://braintools.readthedocs.io](https://braintools.readthedocs.io)
+
+
+
+
+## See also the brain modeling ecosystem
+
+We are building the brain modeling ecosystem: https://brainmodeling.readthedocs.io/

braintools-0.0.10/braintools/__init__.py

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+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+
+__version__ = "0.0.10"
+
+from . import file
+from . import quad
+from . import input
+from . import metric
+from . import optim
+from . import tree
+from . import visualize
+from ._others import *
+from ._others import __all__ as _other_all
+
+__all__ = ['input', 'file', 'metric', 'visualize', 'optim', 'tree', 'quad'] + _other_all
+
+del _other_all

braintools-0.0.10/braintools/_others/__init__.py

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+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+
+from .spike_operation import *
+from .spike_operation import __all__ as operation_all
+from .spike_encoder import *
+from .spike_encoder import __all__ as encoder_all
+from .transform import *
+from .transform import __all__ as transform_all
+
+__all__ = encoder_all + transform_all + operation_all
+
+del encoder_all, transform_all, operation_all

braintools-0.0.10/braintools/_others/spike_encoder.py

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+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+
+from typing import Optional
+
+import brainstate
+import brainunit as u
+import jax
+import numpy as np
+
+__all__ = [
+    'LatencyEncoder',
+]
+
+
+class LatencyEncoder:
+    r"""Encode the rate input as the spike train using the latency encoding.
+
+    Use input features to determine time-to-first spike.
+
+    Expected inputs should be between 0 and 1. If not, the latency encoder will encode ``x``
+    (normalized into ``[0, 1]`` according to
+    :math:`x_{\text{normalize}} = \frac{x-\text{min_val}}{\text{max_val} - \text{min_val}}`)
+    to spikes whose firing time is :math:`0 \le t_f \le \text{num_period}-1`.
+    A larger ``x`` will cause the earlier firing time.
+
+
+    Example::
+
+      >>> import jax
+      >>> a = jax.numpy.array([0.02, 0.5, 1])
+      >>> encoder = LatencyEncoder(method='linear', normalize=True)
+      >>> encoder(a, n_time=5)
+      Array([[0., 0., 1.],
+             [0., 0., 0.],
+             [0., 1., 0.],
+             [0., 0., 0.],
+             [1., 0., 0.]])
+
+
+    Args:
+      min_val: float. The minimal value in the given data `x`, used to the data normalization.
+      max_val: float. The maximum value in the given data `x`, used to the data normalization.
+      method: str. How to convert intensity to firing time. Currently, we support `linear` or `log`.
+        - If ``method='linear'``, the firing rate is calculated as
+          :math:`t_f(x) = (\text{num_period} - 1)(1 - x)`.
+        - If ``method='log'``, the firing rate is calculated as
+          :math:`t_f(x) = (\text{num_period} - 1) - ln(\alpha * x + 1)`,
+          where :math:`\alpha` satisfies :math:`t_f(1) = \text{num_period} - 1`.
+      threshold: float. Input features below the threhold will fire at the
+        final time step unless ``clip=True`` in which case they will not
+        fire at all, defaults to ``0.01``.
+      clip: bool. Option to remove spikes from features that fall
+          below the threshold, defaults to ``False``.
+      tau: float. RC Time constant for LIF model used to calculate
+        firing time, defaults to ``1``.
+      normalize: bool. Option to normalize the latency code such that
+        the final spike(s) occur within num_steps, defaults to ``False``.
+      epsilon: float. A tiny positive value to avoid rounding errors when
+        using torch.arange, defaults to ``1e-7``.
+    """
+
+    def __init__(
+        self,
+        min_val: float = None,
+        max_val: float = None,
+        method: str = 'log',
+        threshold: float = 0.01,
+        clip: bool = False,
+        tau: float = 1. * u.ms,
+        normalize: bool = False,
+        first_spk_time: float = 0. * u.ms,
+        epsilon: float = 1e-7,
+    ):
+        super().__init__()
+
+        if method not in ['linear', 'log']:
+            raise ValueError('The conversion method can only be "linear" and "log".')
+        self.method = method
+        self.min_val = min_val
+        self.max_val = max_val
+        if threshold < 0 or threshold > 1:
+            raise ValueError(f"``threshold`` [{threshold}] must be between [0, 1]")
+        self.threshold = threshold
+        self.clip = clip
+        self.tau = tau
+        self.normalize = normalize
+        self.first_spk_time = first_spk_time
+        self.first_spk_step = int(first_spk_time / brainstate.environ.get_dt())
+        self.epsilon = epsilon
+
+    def __call__(self, data, n_time: Optional[brainstate.typing.ArrayLike] = None):
+        """Generate latency spikes according to the given input data.
+
+        Ensuring x in [0., 1.].
+
+        Args:
+          data: The rate-based input.
+          n_time: float. The total time to generate data. If None, use ``tau`` instead.
+
+        Returns:
+          out: array. The output spiking trains.
+        """
+        with jax.ensure_compile_time_eval():
+            if n_time is None:
+                n_time = self.tau
+            tau = n_time if self.normalize else self.tau
+            x = data
+            if self.min_val is not None and self.max_val is not None:
+                x = (x - self.min_val) / (self.max_val - self.min_val)
+
+            # Calculate the spike time
+            dt = brainstate.environ.get_dt()
+            if self.method == 'linear':
+                spike_time = (tau - self.first_spk_time - dt) * (1 - x) + self.first_spk_time
+
+            elif self.method == 'log':
+                x = u.math.maximum(x, self.threshold + self.epsilon)  # saturates all values below threshold.
+                spike_time = (tau - self.first_spk_time - dt) * u.math.log(
+                    x / (x - self.threshold)) + self.first_spk_time
+
+            else:
+                raise ValueError(f'Unsupported method: {self.method}. Only support "log" and "linear".')
+
+            # Clip the spike time
+            if self.clip:
+                spike_time = u.math.where(data < self.threshold, np.inf, spike_time)
+            spike_steps = u.math.round(spike_time / dt).astype(int)
+            return brainstate.functional.one_hot(spike_steps, num_classes=int(n_time / dt), axis=0, dtype=x.dtype)