PyBispectra

https://pybispectra.readthedocs.io/1.3/
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PyBispectra is a Python signal processing package for computing spectral- and time-domain...
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### Import modules and set up example

Source: https://pybispectra.readthedocs.io/1.3/auto_examples/plot_compute_time_resolved.html

Imports required libraries and PyBispectra modules for the example. The RandomState is used for reproducibility.

```python
# Author(s):
#   Thomas S. Binns | github.com/tsbinns

# sphinx_gallery_multi_image = "single"

```

```python
import numpy as np
from matplotlib import pyplot as plt
from numpy.random import RandomState

from pybispectra import WaveShape, compute_tfr, get_example_data_paths

```

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

### Create uv environment and install PyBispectra

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Creates a virtual environment named 'pybispectra_env' using uv, then installs PyBispectra with uv pip. Activate the environment first.

```bash
uv venv pybispectra_env
```

```bash
uv pip install pybispectra
```

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

### Install pre-commit for PyBispectra

Source: https://pybispectra.readthedocs.io/1.3/development.html

Install pre-commit in the base directory to have style and spelling checks run automatically on each commit.

```bash
pre-commit install

```

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

### Install PyBispectra in editable mode with development requirements

Source: https://pybispectra.readthedocs.io/1.3/_sources/development.rst.txt

Install the package in editable mode and install development dependencies using pip. Run these commands in the cloned repository directory.

```bash
pip install -e .
pip install .[dev]
```

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

### get_example_data_paths

Source: https://pybispectra.readthedocs.io/1.3/_sources/utils.rst.txt

Returns the file paths to example data included with the package.

```APIDOC
## get_example_data_paths

### Description
Returns the file paths to example data included with the package.

### Method
Function

### Signature
get_example_data_paths(...)

### Returns
- **paths** (list of str) - List of file paths to example data.

### Notes
Refer to the pybispectra documentation for full parameter details.
```

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

### Install pre-commit hooks

Source: https://pybispectra.readthedocs.io/1.3/_sources/development.rst.txt

Install pre-commit hooks to automatically run style and spelling checks on each commit. Run in the base directory.

```bash
pre-commit install
```

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

### Load example data and compute Fourier coefficients

Source: https://pybispectra.readthedocs.io/1.3/_downloads/df175fc7c2712b645c381aa0f368a5cb/plot_compute_waveshape.ipynb

Loads example data (sawtooth waves and peak/trough dominant waves) and computes Fourier coefficients using compute_fft.

```python
# Load example data
# (code not shown in source)
```

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

### Example script header with author and Sphinx-Gallery directive

Source: https://pybispectra.readthedocs.io/1.3/auto_examples/plot_compute_tde_fbands.html

Header comment block for the example script, including the author and a Sphinx-Gallery directive for rendering a single image.

```python
# Author(s):
#   Thomas S. Binns | github.com/tsbinns

# sphinx_gallery_multi_image = "single"

```

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

### Install PyBispectra with uv

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Installs the PyBispectra package using uv's pip interface.

```bash
uv pip install pybispectra
```

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

### Create conda environment and install PyBispectra

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Creates a conda environment named 'pybispectra_env', activates it, and installs PyBispectra from conda-forge.

```bash
conda create -n pybispectra_env
```

```bash
conda activate pybispectra_env
```

```bash
conda install -c conda-forge pybispectra
```

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

### Create venv environment and install PyBispectra

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Creates a virtual environment named 'pybispectra_env' using venv, then installs PyBispectra with pip. Activate the environment first.

```bash
python -m venv pybispectra_env
```

```bash
pip install pybispectra
```

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

### Install PyBispectra with pip

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Installs the PyBispectra package using pip. Requires Python ≥ 3.10.

```bash
pip install pybispectra
```

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

### Import modules for waveshape computation

Source: https://pybispectra.readthedocs.io/1.3/_downloads/df175fc7c2712b645c381aa0f368a5cb/plot_compute_waveshape.ipynb

Imports numpy, matplotlib, RandomState, and PyBispectra functions (WaveShape, compute_fft, get_example_data_paths) needed for the example.

```python
import numpy as np
from matplotlib import pyplot as plt
from numpy.random import RandomState

from pybispectra import WaveShape, compute_fft, get_example_data_paths
```

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

### get_example_data_paths

Source: https://pybispectra.readthedocs.io/1.3/_sources/generated/pybispectra.utils.get_example_data_paths.rst.txt

Returns the file paths to example data files bundled with the pybispectra package. This function is part of the pybispectra.utils module and is used to locate example datasets for testing and demonstration purposes.

```APIDOC
## get_example_data_paths

### Description
Returns the file paths to example data files bundled with the pybispectra package. This function is part of the pybispectra.utils module and is used to locate example datasets for testing and demonstration purposes.

### Function Signature
`get_example_data_paths()`

### Parameters
None

### Returns
- **paths** (list of str) - List of file paths to the example data files.

### Example
```python
from pybispectra.utils import get_example_data_paths

paths = get_example_data_paths()
print(paths)
```
```

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

### Import PyBispectra modules

Source: https://pybispectra.readthedocs.io/1.3/_downloads/9bc501133a13404e9f275d38327de709/plot_compute_pac.ipynb

Imports required for the example: numpy and the PyBispectra functions compute_fft and get_example_data_paths, as well as the PAC class.

```python
import numpy as np

from pybispectra import PAC, compute_fft, get_example_data_paths
```

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

### Import required libraries

Source: https://pybispectra.readthedocs.io/1.3/_downloads/df378e14326b24e9d8dcce7efdebff44/plot_compute_time_resolved.ipynb

Imports numpy, matplotlib, RandomState, and PyBispectra functions for the example.

```python
import numpy as np
from matplotlib import pyplot as plt
from numpy.random import RandomState

from pybispectra import WaveShape, compute_tfr, get_example_data_paths
```

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

### Install PyBispectra with pixi

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Adds PyBispectra as a dependency to a pixi project.

```bash
pixi add pybispectra
```

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

### Import NumPy and PyBispectra modules

Source: https://pybispectra.readthedocs.io/1.3/auto_examples/plot_compute_tde_fbands.html

Imports required for the example: NumPy and the PyBispectra functions/classes TDE, compute_fft, and get_example_data_paths.

```python
import numpy as np

from pybispectra import TDE, compute_fft, get_example_data_paths

```

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

### Import PyBispectra modules for TDE computation

Source: https://pybispectra.readthedocs.io/1.3/_downloads/193d002eb10af492d167a98732c9e4d0/plot_compute_tde.ipynb

Imports numpy and the TDE, compute_fft, and get_example_data_paths functions from pybispectra. This is the initial setup for computing time delay estimates.

```python
import numpy as np

from pybispectra import TDE, compute_fft, get_example_data_paths
```

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

### Install PyBispectra with conda

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Installs the PyBispectra package from conda-forge using conda.

```bash
conda install -c conda-forge pybispectra
```

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

### Build documentation with Sphinx

Source: https://pybispectra.readthedocs.io/1.3/_sources/development.rst.txt

Build the documentation locally using Sphinx. Run in the /docs directory; outputs are placed in /docs/build/html.

```bash
make html
```

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

### Initialize pixi project and add PyBispectra

Source: https://pybispectra.readthedocs.io/1.3/_sources/installation.rst.txt

Initializes a pixi project, runs the shell hook, and adds PyBispectra as a dependency.

```bash
pixi init
```

```bash
pixi shell-hook
```

```bash
pixi add pybispectra
```

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

### Build PyBispectra documentation with Sphinx

Source: https://pybispectra.readthedocs.io/1.3/development.html

Build the documentation locally from the /docs directory. Outputs are placed in /docs/build/html.

```bash
make html

```

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

### Load example data and perform HPMax spatio-spectral filtering

Source: https://pybispectra.readthedocs.io/1.3/_sources/auto_examples/plot_compute_waveshape_noisy_data.rst.txt

Loads example data and applies HPMax filtering to improve the signal-to-noise ratio. The signal band is 18-22 Hz, noise bands are 15-18 Hz and 22-25 Hz, and harmonics at 36-44 Hz and 54-66 Hz are included. Only the first component is kept.

```Python
# Load the example data

data = np.load(get_example_data_paths()["sim_data"])["data"]
sfreq = 200

# Compute the FFT of the data
fft = compute_fft(data, sfreq=sfreq)

# Compute the rank of the data
rank = compute_rank(data)

# Initialise the SpatioSpectralFilter object
ssf = SpatioSpectralFilter(data, sfreq=sfreq)

# Compute HPMax filters
ssf.fit_transform_hpmax(
    signal_freqs=[18, 22],
    noise_freqs=[[15, 18], [22, 25]],
    harmonics=[2, 3],
    rank=rank,
)

# Transform the data using the filters
filtered_data = ssf.transform(data, n_components=1)
```

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

### Author comment

Source: https://pybispectra.readthedocs.io/1.3/_downloads/9bc501133a13404e9f275d38327de709/plot_compute_pac.ipynb

A comment line indicating the author of the example. This is not executable code but is part of the source code cell.

```python
# Author(s):
#   Thomas S. Binns | github.com/tsbinns
```
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