bash_training.txt

Hello.

This is an introduction to Bash

Any line beginning with '$' is a bash command.

For example, try typing:


$ gedit bash_tutorial.txt &


This calls the program 'gedit' (a text editor) with the augment 'bash_tutorial.txt'

You should now be reading this inside gedit.

The commands you typed in at the start of this session was this:


$ wget https://someaddress.com/docs/bash_tutorial.txt
$ head bash_tutorial.txt


These commands do two things.;
-wget; gets a resource from the Internet. In this case, this document, but it can be anything: a program, a webpage, or a satellite image.
-head: Prints out the first 10 lines of a file; in this case, bash_tutorial.txt

The basic bash commands are these:

$ pwd

This stands for 'present working directory'. This tells you where you are in the filesystem.

$ ls

Short for 'list'. This tells you what files are where you are

$ cd some/path

Short for 'change directory'. This moves you to a different place.

$ cd ..

will move you up one directory.

$ mkdir my_directory

This creates a new directory, called (in this case) new_directory.


EXERCISE: 
You are in your home directory right now; the Linux shorthand for this is '~'.
Find out what ~ is short for (it might be different on every machine)

A Unix machine has a 'root'. This is the absolute bottom of the directory structure.
You can reach it with

$ cd /

Paths in Unix have two types:

Absolute:
Starts with a '/'
This is a path from the root of the directory structure; /home/john/pyeo/pyeo/core.py

Relative:
Does not start with a '/'
This is the path from your 'present working directory'; pyeo/pyeo/core.py


Now you know the basics, it's time to set up our environment for Pyeo.

We will need four programs for a full Pyeo installation:
-Git
-Pyeo itself
-Conda and the python environment
-Sen2Cor


***Installing Git and getting the Pyeo code***

This is easy.

$ sudo apt get install git

This command will download, install and set up Git on your machine.
It may ask for your password.

'sudo apt get install' is a command on Ubuntu for installing programs.
It is not the only way, but it often the easiest.


EXERCISE: Using apt, install the gis package 'qgis'

EXERCISE: Using what we covered in Friday's session, use Git to clone Pyeo to the machine you are using.


***Installing Conda and creating an environment***

Conda is not available on apt. Instead, you must get it using wget:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

After running the above commands, you will need to restart your terminal.

Now you have conda, you can create to environment used for Pyeo. 

$ cd 

to the folder you cloned Pyeo into.

Now, you can run this command:

$ conda env create --name pyeo_env --file environment.yml

This will download everything you need to run Pyeo, except Sen2Cor.

Once done, you can activate this environment with

$ conda actiavte pyeo_env

You will need to do this before working with Pyeo; you prompt should now say (pyeo_env)


***Installing Sen2Cor***

This is very similar to installing Conda:

$ wget http://step.esa.int/thirdparties/sen2cor/2.5.5/Sen2Cor-02.05.05-Linux64.run
$ bash Sen2Cor-02.05.05-Linux64.run

If you check your directory, you should see a folder called 'Sen2Cor-02.05.05'


***Final step***

You now have a system ready to download and preprocess images. To test this, try the following (with pyeo_env active):

$ cd pyeo/pyeo/apps/change_detection
$ python rolling_composite_s2_change_detection.py 

If you see something like this:

usage: rolling_composite_s2_change_detection.py [-h] [--start_date START_DATE]
                                                [--end_date END_DATE] [-b]
                                                [--chunks NUM_CHUNKS] [-d]
                                                [-p] [-m] [-a] [-s] [-c] [-u]
                                                [-r]
                                                config_path

...then you are ready.