### Install MNE-Connectivity with Pip Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/install.rst Installs MNE-Connectivity and all its dependencies using pip in a virtual environment. ```bash python -m venv .venv pip install -U mne-connectivity ``` -------------------------------- ### Install Documentation Dependencies Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Installs Python packages required for building the project documentation with Sphinx. ```bash pip install .[doc] ``` -------------------------------- ### Memory Profile Example Script Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Uses mprof to run a specific example script and profile its memory usage. ```bash mprof run examples/connectivity_classes.py ``` -------------------------------- ### Install Development MNE-Python Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Installs the latest development version of MNE-Python from its GitHub repository. ```bash pip install -U https://github.com/mne-tools/mne-python/archive/main.zip ``` -------------------------------- ### Clone and Install MNE-Connectivity in Editable Mode Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Clones the MNE-Connectivity repository and installs it in editable mode for development. ```bash git clone https://github.com//mne-connectivity pip install -e ./mne-connectivity ``` -------------------------------- ### Install Development Version with Pip Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/install.rst Installs the latest development version of MNE-Connectivity from GitHub using pip. ```bash pip install --user -U https://api.github.com/repos/mne-tools/mne-connectivity/zipball/main ``` -------------------------------- ### Verify MNE-Connectivity Installation Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/install.rst Checks if MNE-Connectivity has been installed correctly by attempting to import it. ```python python -c 'import mne_connectivity' ``` -------------------------------- ### Install Latest Development Version from GitHub Source: https://github.com/mne-tools/mne-connectivity/blob/main/README.rst Install the most recent development version of MNE-Connectivity directly from its GitHub repository using pip. ```bash pip install -U https://github.com/mne-tools/mne-connectivity/archive/main.zip ``` -------------------------------- ### Install Latest Stable MNE-Connectivity Source: https://github.com/mne-tools/mne-connectivity/blob/main/README.rst Use this command to install the latest stable version of MNE-Connectivity using pip. ```bash pip install -U mne-connectivity ``` -------------------------------- ### Install MNE-Connectivity with Conda Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/install.rst Installs MNE-Connectivity and its dependencies using conda in a new virtual environment. Requires Python 3.10 or higher. ```bash # with python>=3.10 at least conda create -n mne conda activate mne conda install -c conda-forge mne-connectivity ``` -------------------------------- ### Install Test Dependencies Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Installs Python packages required for running tests, including optional MNE-Connectivity dependencies. ```bash pip install .[test] ``` -------------------------------- ### Clone MNE-Connectivity Repository Source: https://github.com/mne-tools/mne-connectivity/blob/main/README.rst Clone the MNE-Connectivity source code from GitHub using git to get the latest development version. ```bash git clone https://github.com/mne-tools/mne-connectivity.git ``` -------------------------------- ### Build Documentation Locally Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Builds the project documentation locally using Sphinx. Use 'make html-noplot' to skip generating plots for a faster build. ```bash cd doc/ make html ``` ```bash make html-noplot ``` -------------------------------- ### Run Pytest Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Navigates to the MNE-Connectivity directory and executes the test suite using pytest. ```bash cd mne-connectivity pytest ``` -------------------------------- ### Generate Changelog with Towncrier Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Use this command to generate the changelog file for a new version. The current date is added by default, but can be specified with the --date parameter. ```bash towncrier --version X.Y.Z ``` -------------------------------- ### Update MNE-Python with Pip Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/install.rst Ensures MNE-Python is updated to the latest stable release. ```bash pip install --user -U mne ``` -------------------------------- ### Update Citation Information Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Run this script with the new version number to update theCITATION.cff file and package citation in doc/references.bib. This script uses the current date for the release date field. ```python tools/generate_citation.py 0.8.0 ``` -------------------------------- ### Dataset Functions Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions for generating connectivity datasets. ```APIDOC ## Dataset Functions ### Functions - **make_signals_in_freq_bands**: Generates signals in frequency bands. - **make_surrogate_data**: Generates surrogate data. ``` -------------------------------- ### Plot Memory Usage Source: https://github.com/mne-tools/mne-connectivity/blob/main/CONTRIBUTING.md Generates a plot of the memory usage profile collected by mprof. ```bash mprof plot ``` -------------------------------- ### Pre-processing on Connectivity Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions for pre-processing connectivity data. ```APIDOC ## Pre-processing on Connectivity ### Functions - **symmetric_orth**: Performs symmetric orthogonalization. ``` -------------------------------- ### Visualization Functions Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions for visualizing connectivity data. ```APIDOC ## Visualization Functions ### Functions - **plot_sensors_connectivity**: Plots connectivity on sensors. - **plot_connectivity_circle**: Plots connectivity as a circle. ``` -------------------------------- ### Connectivity Functions Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions to compute connectivity, returning one of the Connectivity data structure classes. ```APIDOC ## Connectivity Functions These functions compute connectivity and return one of the Connectivity data structure classes. They work with MNE-Python's ``Epochs`` class or numpy array inputs. ### Functions - **envelope_correlation**: Computes envelope correlation. - **phase_slope_index**: Computes the Phase Slope Index. - **phase_slope_index_time**: Computes the Phase Slope Index over time. - **vector_auto_regression**: Computes Vector Auto Regression. - **spectral_connectivity_epochs**: Computes spectral connectivity for epochs. - **spectral_connectivity_time**: Computes spectral connectivity over time. - **wsmi**: Computes Weighted Symbolic Mutual Information. ``` -------------------------------- ### Reading Functions Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions for reading connectivity data. ```APIDOC ## Reading Functions ### Functions - **read_connectivity**: Reads connectivity data from a file. ``` -------------------------------- ### Connectivity Data Structures Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Classes representing different types of connectivity data. ```APIDOC ## Connectivity Data Structures These classes contain different types of connectivity data. ### Classes - **Connectivity**: Base class for connectivity data. - **TemporalConnectivity**: Represents temporal connectivity data. - **SpectralConnectivity**: Represents spectral connectivity data. - **SpectroTemporalConnectivity**: Represents spectro-temporal connectivity data. - **EpochConnectivity**: Represents epoch-based connectivity data. - **EpochTemporalConnectivity**: Represents epoch-based temporal connectivity data. - **EpochSpectralConnectivity**: Represents epoch-based spectral connectivity data. - **EpochSpectroTemporalConnectivity**: Represents epoch-based spectro-temporal connectivity data. ``` -------------------------------- ### Post-processing on Connectivity Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Functions for post-processing connectivity data. ```APIDOC ## Post-processing on Connectivity ### Functions - **degree**: Computes the degree of connectivity. - **seed_target_indices**: Gets seed-target indices. - **seed_target_multivariate_indices**: Gets seed-target multivariate indices. - **check_indices**: Checks connectivity indices. - **select_order**: Selects the order of connectivity. ``` -------------------------------- ### Decoding Classes Source: https://github.com/mne-tools/mne-connectivity/blob/main/doc/api.rst Classes that fit filters to decompose data into discrete sources of connectivity. ```APIDOC ## Decoding Classes These classes fit filters which decompose data into discrete sources of connectivity, amplifying the signal-to-noise ratio of these interactions. ### Classes - **CoherencyDecomposition**: Decomposes data based on coherency. ``` === COMPLETE CONTENT === This response contains all available snippets from this library. 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