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Installing python dependencies

Pytomo3d has dependancies on the following packages:

  1. obspy
  2. pyflex devel branch
  3. pyadjoint dev branch
  4. spaceweight

Manual installation

Wenjie: If you are new to python, anaconda is recommmended. Please download the newest version( >= Anaconda2 - 2.5.0) since it already contains a lot of useful python packages, like pip, numpy and scipy. Older versions is not recommended since it usually has compliers inside, like gfortran and gcc. It is always better to use comiplers coming from your system rather than the very old ones embeded in anaconda. If you are expert in python, please choose the way you like.

  1. downwnload Anaconda for Python 2.7 and 64 bit Linux and install it (http://continuum.io/downloads) (optional) or you get download the install binary using:
wget https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda2-2.5.0-Linux-x86_64.sh

And then install anaconda using:

bash Anaconda2-2.5.0-Linux-x86_64.sh
  1. install obspy using anaconda.
conda install -c obspy obspy=1.0.3

Recently, obspy group has a big upgrade for obspy, which boost the version number from 0.10.x to 1.0.0. A lot of kernel functions has changed its module path. The recent version of pytomo3d also now no longer supports older version of obspy. Please upgrade your obspy version to at least 1.0.0.

Or install from source code:

git clone https://github.com/obspy/obspy.git
cd obspy
pip install -v -e . (--user)
cd ..

If you pip tool is from system module, please add --user at installation to make sure it is installed at your home directory. If you install conda yourself, then you don't need to do this.

  1. install pyflex.
git clone --branch devel https://github.com/wjlei1990/pyflex 
cd pyflex
pip install -v -e . (--user)
cd ..

pyflex is used for seismic window selection.

  1. Install pyadjoint
git clone --branch dev https://github.com/chukren/pyadjoint 
cd pyadjoint
pip install -v -e . (--user)
cd ..

pyadjoint is used for calculating adjoint sources.

  1. Install spaceweight
git clone https://github.com/wjlei1990/spaceweight
cd spaceweight
pip install -v -e . (--user)
cd ..
  1. Install pytomo3d.
git clone https://github.com/wjlei1990/pytomo3d
cd pytomo3d
pip install -v -e . (--user)
cd ..

Script installation

Wenjie: recommended for experienced user.

  1. install obspy and pip yourself.

  2. get the pytomo3d code using:

git clone https://github.com/wjlei1990/pytomo3d
cd pytomo3d
  1. install pyflex and pyadjoint by:
pip install -r requirements.txt

After installation, you can run py.test in pytomo3d directory to see if you installed all the things correctly.

Notes

  1. If you already have some of the packages, please make sure to update them(not including anaconda)