index.rst

SeisTomo Tutorials

Note

From 2021/07/03, the tutorials are maintained on Seismology101, which are tutorials for absolute beginners in Seismology in Chinese.

Note

From 2021/07/03, the tutorials on this website and in BaiduDisk are not maintained any more.

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This website hosts a series of introductory tutorials about seimic tomography.

Note

The lecture resources and videos are also available in BaiduDisk with passwd 4vgu.

Schedule

Basics: 2020-12-07 14:00-16:00

Topic	Instructor	Lecture Resources
Seismology	Jiayuan YAO	pptx
File Management	Jiayuan YAO	pptx is included in the above pptx
Command Lines	Tianjue LI	command lines
Programming	Shijie HAO	pptx | programming

Data: 2020-12-14 14:00-16:00

Topic	Instructor	Lecture Resources
Data Fetching, Processing & Analysis	Jiayuan Yao	pptx | seismic-data

Seismic Tomography: 2020-12-21 14:00-16:00

Topic	Instructor	Lecture Resources
Seismic Tomography	Ping Tong	pptx

Requirements

In order to follow the toturials, you have to install the following terms in your computer.

1. Linux or macOS system
2. Install Anaconda: install on macOS, Linux, and Windows. The following is an example for Linux x86_64 system

• Download Anaconda installer for Linux: 64-Bit (x86) Installer (529 MB)

• Enter the following to install Anaconda: bash ~/Downloads/Anaconda3-2020.11-Linux-x86_64.sh

  • The default install path is ${HOME}/anaconda3. I usually install it in ${HOME}/.anaconda.
  • Other options can be referred to the official guide: https://docs.anaconda.com/anaconda/install/linux/

• Enter python, then you can see Python 3.8.6 | packaged by conda-forge

$ python
Python 3.8.6 | packaged by conda-forge | (default, Oct  7 2020, 19:08:05)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

• Add package sources

$ conda config --add channels conda-forge # this will reivse ~/.condarc

• Update anaconda and conda

$ conda update conda
$ conda update anaconda

• Create a new enviroment named seis

$ conda create --name seis       # creat a enviroment named seis
$ conda activate seis            # activate the environment

• Get familiar with conda environment

$ conda info --envs              # list all the enviroments
$ conda list                     # list all the packages in the current environment
$ conda deactivate               # deactivate an active environment
$ conda remove --name seis --all # remove an environment

• Install important python packages in the seis environment

$ conda activate seis                           # activate the environment
$ conda install numpy scipy matplotlib pandas   # install the packages
$ conda list | grep numpy                       # check numpy
$ conda list | grep scipy                       # check scipy
$ conda list | grep matplotlib                  # check matplotlib
$ conda list | grep pandas                      # check pandas

3. Install ObsPy in the seis environment

$ conda install obspy
$ conda install cartopy

4. Install SAC 101.6a: Install binary package is recommended. The installed directory is recommened to be /opt instead of /usr/local.
   • Linux: https://seisman.github.io/SAC_Docs_zh/introduction/linux-install/
   • maxOS: https://seisman.github.io/SAC_Docs_zh/introduction/macOS-install/
5. Install SOD

• Download SOD: http://www.seis.sc.edu/sod/download.html
• Extract SOD: tar -xvf sod-3.2.10.tgz
• Install SOD: sudo mv sod-3.2.10 /opt
• Update the enviroment variable $PATH

$ echo 'export PATH=${PATH}:/opt/sod-3.2.10/bin'>> ~/.bashrc

• Open a new terminal and run sod -h to test if SOD is installed.

6. Install TauP

• Java Runtime Environment has to be installed. Run java -version to check it. If it is not installed, please refer to seisman's blog
• Download TauP: https://www.seis.sc.edu/taup/
• Extract TauP: tar -xvf TauP-2.4.5.tgz
• Install TauP: sudo mv TauP-2.4.5 /opt
• Update the enviroment variable $PATH

$ echo 'export TAUPHOME=/opt/TauP-2.4.5' >> ~/.bashrc
$ echo 'export PATH=${TAUPHOME}/bin:${PATH}' >> ~/.bashrc
$ source ~/.bashrc

• Run taup to test if TauP is installed

7. Install GMT: https://docs.gmt-china.org/latest/install/ (I'd like to recommend installation via conda)
8. Install gcc, gfortran, make

• For Ubuntu, run the following command:

$ sudo apt install gcc
$ sudo apt install gfortran
$ sudo apt install make

.. toctree::
   :maxdepth: 3
   :hidden:
   :caption: Basics

   computer/index
   programming/index
   seismology/index

.. toctree::
   :maxdepth: 3
   :hidden:
   :caption: Data

   data-fetch/index
   data-process/index
   data-analysis/index

.. toctree::
   :maxdepth: 3
   :hidden:
   :caption: Tomography

   tomo-theory/index
   tomo-workflow/index

.. toctree::
   :maxdepth: 3
   :hidden:
   :caption: Exercises

   exercises/programming/index
   exercises/seismology/index
   exercises/data-fetch/index
   exercises/data-process/index
   exercises/data-analysis/index