{ "info": { "author": "", "author_email": "", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: BSD License", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4" ], "description": "klustakwik2\n-----------\n\n.. image:: https://travis-ci.org/kwikteam/klustakwik2.svg?branch=master\n :target: https://travis-ci.org/kwikteam/klustakwik2\n\n**NOTE: please follow the instructions for the klusta package https://github.com/kwikteam/klusta : the instructions below should not be used.**\n\nInstallation instructions\n=========================\n\nInstall Python using the `Anaconda distribution `_. You will\nneed to install the packages numpy, scipy, cython and nose. For Windows, Python 2.7 might be a better option than\n3.x.\n\nOn all platforms, KlustaKwik can be installed using ``pip install klustakwik2`` (from source) or ``conda install -c kwikteam klustakwik2`` (precompiled binary). The default installation options\nare as follows:\n\n* **Linux**: Multithreading on by default.\n* **Windows**: Multithreading on by default if MSVC installed, otherwise off. Note that under the Anaconda distribution,\n multithreading will be off by default, but this can be easily resolved if you have MSVC installed, see below.\n* **Mac**: Multithreading off by default.\n\nTo override these options, install from source (see below).\n\nMultithreading with Anaconda on Windows\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe Anaconda distribution installs its own compiler that doesn't support OpenMP for multithreading and uses this by\ndefault instead of the MSVC compiler, which does support OpenMP. To disable the Anaconda compiler, simply run the\nfollowing command before installing KlustaKwik.\n\n conda remove libpython\n\nInstalling from source\n~~~~~~~~~~~~~~~~~~~~~~\n\nDownload the source, either from one of the source distributions `on PyPI `_\nor get the latest version `from GitHub `_. Run one of the following commands\nfrom a command prompt in this directory. For default options:\n\n python setup.py install\n\nTo force multithreading to be on:\n\n python setup.py install --with-openmp\n\nTo force multithreading to be off:\n\n python setup.py install --no-openmp\n\nWindows\n~~~~~~~\n\nInstall a precompiled Windows binary with Anaconda in an anaconda package:\n conda install -c kwikteam klustakwik2\n\nIf you wish to compile from source, the instructions are a bit more complicated:\n\nUsing Python 2.7, you will need a copy of MS Visual Studio Express 2008 for Python, available for free\ndownload `here `_. Python 3.x might require a different\nversion of Visual Studio, we haven't tested this.\n\nDownload the source as above. Open a command prompt in the\ndirectory where you downloaded and extracted the files. If you installed Python for all users, then you will need\nadmin rights on this command prompt. To get this in Windows, press the Windows key, type \"cmd\", right click on\n\"cmd.exe\" and click \"Run as administrator\".\n\nNow run the commands as in the section on installing from source above.\n\nMac\n~~~\n\nIt is possible to install a version of ``gcc`` that allows for multithreading. TODO: details.\n\nUsage\n=====\n\nTo cluster a pair of files ``name.fet.n``, ``name.fmask.n`` run the command:\n\n kk2_legacy name n\n\nThis will generate a ``name.klg.n`` and ``name.clu.n`` file. Note that the first time you run it,\nit will generate a whole lot of warnings and compiler output: ignore this, it is normal.\n\nYou can specify additional options to this script. The major ones are explained below:\n\n* **max_iterations=1000**: the maximum number of full iterations to carry out before giving up.\n* **max_possible_clusters=1000**: the maximum number of clusters to output at the end. At the\n moment, this option limits RAM usage but in a future version there will be no such limit.\n* **drop_last_n_features=0**: don't use the last N features of the fet file for clustering.\n* **save_clu_every=None**: how often (in minutes) to save a temporary .clu file.\n* **num_starting_clusters=500**: how many initial clusters to use (should probably be higher than\n the number of final clusters you expect to find).\n* **start_from_clu=None**: if specified, start the clustering from a previously saved .clu file.\n* **use_mua_cluster=True**: whether or not to use \"black hole\" MUA cluster variant of the\n algorithm. This is designed to improve clustering on noisier data sets, but you can turn it off\n if you are having problems with it. 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