This information is out of date. To access the file for KlustaViewa, get the file here. Download 'klustaviewa-setup.exe' (for Windows; for Linux, continue to follow these instructions)
The KlustaSeries is and open-source software package that consists of three parts: SpikeDetekt, KlustaKwik, and KlustaViewa. The software can be found here. On this page you'll notice an "all-in-one" installer for Windows computers. It is recommended to NOT use this method and to use the method outlined below.
NOTE: KlustaSeries is now outdated and unmaintained.
This section will contain some background information for the KlustaSeries, such as the theory behind the algorithm and its intended use.
All operating systems require an isolated environment of Python 2.7. It is recommended to use either Anaconda or Miniconda for their built in module: conda. Conda is a cross-platform package manager and environment manager program that installs, runs, and updates packages and their dependencies, so you can easily set up and swich between environments on your local computer.
What's the difference between Acaconda and Miniconda?
Miniconda is a mini version of Anaconda that just includes conda, its dependencies, and Python. The Anaconda installation includes over 100 open source packages that are automatically installed, and over 200 packages that can be installed wiith the conda install command. Therefore, if you want a quick install just for the conda package, download Miniconda. If you have the disk space and want other Python packages installed at the same time, go with Anaconda. (You can always install the packages individually in Miniconda later.)
Should I install Python 2 or 3?
While Python 2.7 is required for KlustaViewa, you can still make an isolated environment with Python 2.7 while having downloaded Python 3 and vice versa. The only difference it makes, then, is which version your primary installation is associated with. To learn the differences between Python 2 and 3, visit this page listed on the Python wiki.
Anaconda: Install here.
Miniconda: Install here.
Directions to install Anaconda can be found here. This also walks you through setting up an environment, which is necessary for the next step below.
KlustaViewa needs and isolated environment for its dependencies on older python packages:
Python 2.7
NumPy 1.8.0
Pandas = 0.12.0
This may require NumPy 1.7.x instead of 1.8.0
PyTables = 3.0
matplotlib
PyOpenGL
PyQt4
Directions to install these packages in the new environment can be found here. Install each of the packages as directed, paying attention to the dependencies of each to make sure you don't overwrite a package you previously installed.
If you cannot find a package in Anaconda in the terminal, you may be able to use the package database to locate it. This will have a specific terminal command used to install the package from the website.
IMPORTANT NOTE: If installing on Windows 10, the latest release of PyQt4 is NOT compatible. Use PyQt 4.10 which can be istalled by inputting pyqt=4.10 in the below commands in place of pyqt.
Open a anaconda terminal or command prompt and enter the following commands to create the "klusta" environment.
conda create -n klusta python=2.7 --yes
conda install -n klusta scipy pandas=0.12 pytables=3.0 pyqt setuptools pip cython nose ipython-notebook matplotlib --yes
conda install -n klusta numpy=1.8 --yes
To activate the evironment in Linux of Mac OS X, enter the following code:
source activate klusta
For Windows, it is slightly different:
activate klusta
Once you've activated the environment, you'll see "(klusta)" appended to the beginning of your terminal/command prompt input line.
The last dependency needs to be installed from within the environment using pip. Enter the following command to install it.
pip install pyopengl
Now your environment is ready for the KlustaSeries to be installed.
Linux/Mac OS X
Download and extract the package klustaviewa-0.3.0.zip found here. Navigate to the extracted folder (while the klusta environment is activated) and enter the following command:
python setup.py install
This should install the KlustaViewa and SpikeDetekt packages in your klusta environment. To open KlustaViewa, activate your klusta environment and enter klustaviewa into your terminal.
To install KlustaKwik, dowload the source code for KlustaKwik found here. You can either clone the repository via GitHub or download and extract the ZIP file. Navigate to the extracted folder via a command terminal and enter the following:
make
This should create the executable KlustaKwik. Note that on some Mac versions, there is no OpenMP support in the default compiler, and so compilation will fail. In this case, build with the command:
make NOOPENMP=1
Add the location of KlustaKwik to your system path.
Windows
Download and extract the package klustaviewa-0.3.0.win-amd-py2.7.exe found here. Run the executable and follow the installation wizard. Install the package in the Scripts folder of your klusta environment. The executable will automatically check where your Python 2.7 installation exists. Once the package is installed, KlustaViewa will be ready to go.
What if the klusta environment doesn't show up as one of the installation paths?
If this is the case, then the folder of your klusta environment is not recognized by the registry. The fix for this will be added in the near future.
https://github.com/klusta-team/example
https://www.continuum.io/downloads
http://conda.pydata.org/docs/install/quick.html