OMERO.tables ============ OMERO.tables provide a way to efficiently store large, tabular results within OMERO. If you would like to find out more about the use of the OMERO.tables API, see :doc:`OMERO.analysis ` Requirements ------------ If you would like to help test the Tables API, you will need the following installed: - `HDF5 `_ - `NumPy `_ points to downloads at http://sourceforge.net/projects/numpy/ - `PyTables `_ (Some packages include HDF5) Unix ---- PyTables is likely available from the package repository of your Unix-flavor. This includes Mac OS X (homebrew), Debian and Ubuntu (apt-get), CentOS (yum), and SuSE (yast). Here we've shown manual instructions using virtualenv. Manually ~~~~~~~~ :: $ virtualenv $HOME/virtualenv $ uname -o -p unknown GNU/Linux $ gcc --version gcc-4.8.real (Debian 4.8.1-9) 4.8.1 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. $ wget "https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.11.tar.gz" $ tar xzf hdf5-1.8.11.tar.gz $ cd hdf5-1.8.11 $ ./configure --prefix=$HOME/virtualenv $ make $ make install $ export LD_LIBRARY_PATH=$HOME/virtualenv/lib $ . $HOME/virtualenv/bin/activate $ easy_install tables Checking that it works ~~~~~~~~~~~~~~~~~~~~~~ After that, the following should succeed: :: % python Python 2.7.5+ (default, Aug 4 2013, 10:07:17) [GCC 4.8.1] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import tables >>> tables.test() -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= PyTables version: 2.4.0 HDF5 version: 1.8.11 NumPy version: 1.7.1 Numexpr version: 2.0.1 (not using Intel's VML/MKL) Zlib version: 1.2.8 (in Python interpreter) LZO version: 2.06 (Aug 12 2011) BZIP2 version: 1.0.6 (6-Sept-2010) Blosc version: 1.1.3 (2010-11-16) Python version: 2.7.5+ (default, Aug 4 2013, 10:07:17) [GCC 4.8.1] Platform: linux2-x86_64 Byte-ordering: little Detected cores: 8 … .. note:: If the above test fails with:: ImportError: No module named mock then this is fixed by installing the corresponding Python module. Use your operating system's package installer if possible or if you must instead use PyPI_ directly:: pip install mock Once the required Python libraries are installed, starting OMERO will automatically start up the OMERO.tables service; there should be no need for further configuration or interaction.