%global _empty_manifest_terminate_build 0 Name: python-klusta Version: 3.0.16 Release: 1 Summary: Spike detection and automatic clustering for spike sorting License: BSD URL: https://klusta.cortexlab.net Source0: https://mirrors.nju.edu.cn/pypi/web/packages/46/d7/52ef7083c56d1bf1bf9d65c709f43c8802c45d7f5373182ddea367df2c4b/klusta-3.0.16.tar.gz BuildArch: noarch %description # Klusta: automatic spike sorting up to 64 channels [![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta) [![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master) [![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/) [![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta) [![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest) [**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. ## Overview **klusta** implements the following features: * **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. * **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. * **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. ## GUI You will need a GUI to visualize the spike sorting results. We have developed two GUI programs with the same features: * **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** * **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. Both GUIs work with the same **Kwik** format. ## Quick install guide The following instructions will install both **klusta** and the **phy KwikGUI**. 1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). 2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) 3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: ```bash conda env create -n klusta -f environment.yml ``` 4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: ```bash source activate klusta # omit the `source` on Windows klusta yourfile.prm # spikesort your data with a PRM file phy kwik-gui yourfile.kwik # open the GUI ``` See the documentation for more details. ### Updating the software To get the latest version of the software, open a terminal and type: ``` source activate klusta # omit the `source` on Windows pip install klusta phy phycontrib --upgrade ``` ## Technical details **klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). ## Links * [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) * [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) * [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) * [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) ## Credits **klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. %package -n python3-klusta Summary: Spike detection and automatic clustering for spike sorting Provides: python-klusta BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-klusta # Klusta: automatic spike sorting up to 64 channels [![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta) [![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master) [![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/) [![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta) [![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest) [**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. ## Overview **klusta** implements the following features: * **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. * **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. * **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. ## GUI You will need a GUI to visualize the spike sorting results. We have developed two GUI programs with the same features: * **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** * **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. Both GUIs work with the same **Kwik** format. ## Quick install guide The following instructions will install both **klusta** and the **phy KwikGUI**. 1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). 2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) 3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: ```bash conda env create -n klusta -f environment.yml ``` 4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: ```bash source activate klusta # omit the `source` on Windows klusta yourfile.prm # spikesort your data with a PRM file phy kwik-gui yourfile.kwik # open the GUI ``` See the documentation for more details. ### Updating the software To get the latest version of the software, open a terminal and type: ``` source activate klusta # omit the `source` on Windows pip install klusta phy phycontrib --upgrade ``` ## Technical details **klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). ## Links * [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) * [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) * [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) * [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) ## Credits **klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. %package help Summary: Development documents and examples for klusta Provides: python3-klusta-doc %description help # Klusta: automatic spike sorting up to 64 channels [![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta) [![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master) [![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/) [![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta) [![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest) [**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. ## Overview **klusta** implements the following features: * **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. * **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. * **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. ## GUI You will need a GUI to visualize the spike sorting results. We have developed two GUI programs with the same features: * **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** * **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. Both GUIs work with the same **Kwik** format. ## Quick install guide The following instructions will install both **klusta** and the **phy KwikGUI**. 1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). 2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) 3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: ```bash conda env create -n klusta -f environment.yml ``` 4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: ```bash source activate klusta # omit the `source` on Windows klusta yourfile.prm # spikesort your data with a PRM file phy kwik-gui yourfile.kwik # open the GUI ``` See the documentation for more details. ### Updating the software To get the latest version of the software, open a terminal and type: ``` source activate klusta # omit the `source` on Windows pip install klusta phy phycontrib --upgrade ``` ## Technical details **klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). ## Links * [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) * [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) * [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) * [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) ## Credits **klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. %prep %autosetup -n klusta-3.0.16 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-klusta -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Fri Apr 21 2023 Python_Bot - 3.0.16-1 - Package Spec generated