INSTALL

Things that must installed at a system level:
 * gcc and gfortran (or another C and Fortran compiler)
 * Python 2.7
 * Python headers
 * virtualenv (could easily be installed manually though)

Recommended:
 * linear-algebra package including devel (in order of preference: MKL, ATLAS+LAPACK, OpenBLAS+LAPACK, any BLAS library)
 * devel packages for image formats you wish to read:
    * PNG: zlib (note: uncompressed always available)
    * TIFF: libtiff (note: uncompressed always available)
    * JPEG: libjpeg or libjpeg-turbo
    * JPEG2000: openjpeg
    * WebP: libwebp
    * tkinter bitmap/photos: tcl/tk
 * hdf5 devel package for reading and writing modern MATLAB files
 * fftw devel package for faster FFT calculations

So on CentOS-7 all of these can be installed with the following yum command.
The following command installs all of them (including recommended, but not all image formats):
    yum install gcc gcc-gfortran python python-devel python-virtualenv \
                atlas atlas-devel lapack lapack-devel lapack64 lapack64-devel \
                zlib zlib-devel libtiff libtiff-devel libjpeg-turbo libjpeg-turbo-devel \
                hdf5 hdf5-devel fftw fftw-devel

                
Now run these commands:

    cd ~               # or wherever
    mkdir imstack-env
    cd imstack-env
    virtualenv .
    source bin/activate
    git clone git@github.com:slash-segmentation/segtools.git
    pip install -e segtools[OPT,MATLAB,PIL]
    imstack --check

Where OPT forces cython and fftw to be installed (for optimum performance), PIL forces pillow to be
installed, and MATLAB forces h5py to be installed. Note that these cannot force the installation of
system devel packages, but may fail if those packages are not installed. One MAJOR exception is
that PIP will install just fine without support for PNGs, TIFFs, JPEGs, etc if those devel
libraries are not installed first!

## SDSC Installation Notes

On the SDSC Comet cluster I did the following to install (not all parts may be necessary though):

    module load python fftw hdf5 mkl atlas lapack eigen
    curl -O https://pypi.python.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz
    tar xvfz virtualenv-15.1.0.tar.gz
    cd virtualenv-15.1.0
    python virtualenv.py ../virtenv
    cd ../virtenv
    source bin/activate # must be done after module load
    pip install --no-binary :all: numpy cython scipy # numpy/scipy binary comes linked to a BLAS library that causes a seg-fault
    git clone git@github.com:slash-segmentation/segtools.git
    pip install -e segtools[OPT,MATLAB,PIL]
    imstack --check