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|
%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
[](https://travis-ci.org/kwikteam/klusta)
[](http://codecov.io/github/kwikteam/klusta?branch=master)
[](http://klusta.readthedocs.org/en/latest/)
[](https://pypi.python.org/pypi/klusta)
[](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
[](https://travis-ci.org/kwikteam/klusta)
[](http://codecov.io/github/kwikteam/klusta?branch=master)
[](http://klusta.readthedocs.org/en/latest/)
[](https://pypi.python.org/pypi/klusta)
[](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
[](https://travis-ci.org/kwikteam/klusta)
[](http://codecov.io/github/kwikteam/klusta?branch=master)
[](http://klusta.readthedocs.org/en/latest/)
[](https://pypi.python.org/pypi/klusta)
[](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
* Thu Mar 09 2023 Python_Bot <Python_Bot@openeuler.org> - 3.0.16-1
- Package Spec generated
|
