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%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# Welcome to the WIN PyTreat 2018! # Welcome to the WIN PyTreat 2020!
Program: https://docs.google.com/document/d/10CwLEhUi-YiwfC2F40QCVm6eEVwKiaXkfTKz67xWAfM/edit?usp=sharing Program: https://docs.google.com/document/d/11LQgxC-LZPG_TXS3MP9tYXNWABAQdTI00iavk-tKttU/edit
__We need to do some setting up, so get your laptop ready!__ __We need to do some setting up, so get your laptop ready!__
__Make sure you have FSL 5.0.10 installed and working!__ __Make sure you have FSL 6.0.3 installed and working!__
__End all sentences with an exclamation mark!__ __End all sentences with an exclamation mark!__
__Open this page in your web browser!__ __Open this page in your web browser!__
https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.md https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020/tree/master/talks/introduction/pytreat_intro.md
## Overview ## Overview
* [Python in a nutshell](#python-in-a-nutshell) * [Python in a nutshell](#python-in-a-nutshell)
* [`fslpython`](#fslpython) * [`fslpython`](#fslpython)
* [Running Python scripts](#running-python-scripts) * [Running Python scripts](#running-python-scripts)
* [Interactive Python: IPython](#interactive-python-ipython) * [Interactive Python: IPython](#interactive-python-ipython)
* [Python editors](#python-editors) * [Python editors](#python-editors)
* [Python in your browser: Jupyter Notebook](#python-in-your-browser-jupyter-notebook) * [Python in your browser: Jupyter Notebook](#python-in-your-browser-jupyter-notebook)
* [Git](#git) * [Git](#git)
* [The PyTreat practicals](#the-pytreat-practicals) * [The PyTreat practicals](#the-pytreat-practicals)
<a class="anchor" id="python-in-a-nutshell"></a> <a class="anchor" id="python-in-a-nutshell"></a>
## Python in a nutshell ## Python in a nutshell
### Pros ### Pros
* _Flexible_ Feel free to use functions, classes, objects, modules and * _Flexible_ Feel free to use functions, classes, objects, modules and
packages. Or don't - it's up to you! packages. Or don't - it's up to you!
* _Fast_ If you do things right (in other words, if you use `numpy`) * _Fast_ If you do things right (in other words, if you use `numpy`)
* _Dynamically typed_ No need to declare your variables, or specify their * _Dynamically typed_ No need to declare your variables, or specify their
types. types.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
a = 'Great, I am _so_ sick of writing "char *a;"!' a = 'Great, I am _so_ sick of writing "char *a;"!'
print(a) print(a)
a = 12345 a = 12345
print('a is now an number!', a) print('a is now an number!', a)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
* _Intuitive syntax_ How do I run some code for each of the elements in my * _Intuitive syntax_ How do I run some code for each of the elements in my
list? list?
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
a = [1, 2, 3, 4, 5] a = [1, 2, 3, 4, 5]
for elem in a: for elem in a:
print(elem) print(elem)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Cons ### Cons
* _Dynamically typed_ Easier to make mistakes, harder to catch them * _Dynamically typed_ Easier to make mistakes, harder to catch them
* _No compiler_ See above * _No compiler_ See above
* _Slow_ if you don't do things the right way * _Slow_ if you don't do things the right way
* _Python 2 is not the same as Python 3_ But there's an easy solution: Forget * _Python 2 is not the same as Python 3_ But there's an easy solution: Forget
that Python 2 exists. that Python 2 exists.
* _Hard to manage different versions of python_ But we have a solution for * _Hard to manage different versions of python_ But we have a solution for
you: `fslpython`. you: `fslpython`.
<a class="anchor" id="fslpython"></a> <a class="anchor" id="fslpython"></a>
## `fslpython` ## `fslpython`
FSL 5.0.10 and newer comes with its own version of Python, bundled with nearly FSL 5.0.10 and newer comes with its own version of Python, bundled with nearly
all of the scientific libraries that you are likely to need. all of the scientific libraries that you are likely to need.
So if you use `fslpython` for all of your development, you can be sure that it So if you use `fslpython` for all of your development, you can be sure that it
will work in FSL! will work in FSL!
> `fslpython` is based on _conda_ and, in FSL 5.0.10, is Python version > `fslpython` is based on _conda_ and, in FSL 6.0.3, is Python version
> 3.5.2. You can read more about conda [here](https://conda.io/docs/). > 3.7.3. You can read more about conda [here](https://conda.io/docs/).
<a class="anchor" id="running-python-scripts"></a> <a class="anchor" id="running-python-scripts"></a>
## Running Python scripts ## Running Python scripts
Here's a basic Python script - a _Hello world_ for neuroimaging: Here's a basic Python script - a _Hello world_ for neuroimaging:
> ``` > ```
> #!/usr/bin/env fslpython > #!/usr/bin/env fslpython
> >
> # That first line up there ensures that your > # That first line up there ensures that your
> # script will be executed in the fslpython > # script will be executed in the fslpython
> # environment. If you are writing a general > # environment. If you are writing a general
> # Python script, you should use this line > # Python script, you should use this line
> # instead: #!/usr/bin/env python > # instead: #!/usr/bin/env python
> >
> # In Python, we need to "import" libraries > # In Python, we need to "import" libraries
> # (called modules) before we can use them. > # (called modules) before we can use them.
> import sys > import sys
> import nibabel as nib > import nibabel as nib
> >
> # We can get to our command > # We can get to our command
> # line arguments via sys.argv > # line arguments via sys.argv
> fpath = sys.argv[1] > fpath = sys.argv[1]
> >
> # We can use nibabel to load > # We can use nibabel to load
> # NIFTI images (and other > # NIFTI images (and other
> # neuroimaging data formats) > # neuroimaging data formats)
> img = nib.load(fpath) > img = nib.load(fpath)
> data = img.get_data() > data = img.get_data()
> >
> # Now we're working with a > # Now we're working with a
> # numpy array. > # numpy array.
> nzmean = data[data != 0].mean() > nzmean = data[data != 0].mean()
> >
> print('mean:', nzmean) > print('mean:', nzmean)
> ``` > ```
__Exercise__ Save the above code to a file called `script.py`, then run this __Exercise__ Save the above code to a file called `script.py`, then run this
in a terminal (replace `/path/to/some/image/on/your/computer.nii.gz` with a in a terminal (replace `/path/to/some/image/on/your/computer.nii.gz` with a
path to some image on your computer): path to some image on your computer):
> ``` > ```
> chmod a+x script.py > chmod a+x script.py
> ./script.py /path/to/some/image/on/your/computer.nii.gz > ./script.py /path/to/some/image/on/your/computer.nii.gz
> ``` > ```
<a class="anchor" id="interactive-python-ipython"></a> <a class="anchor" id="interactive-python-ipython"></a>
## Interactive Python: IPython ## Interactive Python: IPython
Python is an [_interpreted Python is an [_interpreted
language_](https://en.wikipedia.org/wiki/Interpreted_language), like MATLAB. So language_](https://en.wikipedia.org/wiki/Interpreted_language), like MATLAB. So
you can either write your code into a file, and then run that file, or you can you can either write your code into a file, and then run that file, or you can
type code directly into a Python interpreter. type code directly into a Python interpreter.
Python has a standard interpreter built-in - run `fslpython` in a terminal, Python has a standard interpreter built-in - run `fslpython` in a terminal,
and see what happens (use CTRL+D to exit). and see what happens (use CTRL+D to exit).
__But__ there is another interpreter called [`ipython`](https://ipython.org/) __But__ there is another interpreter called [IPython](https://ipython.org/)
which is vastly superior to the standard Python interpreter. Use `ipython` which is vastly superior to the standard Python interpreter. Use IPython
instead! It is already installed in `fslpython`, but we just need to create a instead! It is already installed in `fslpython`, so if you want to do some
link to it - do this now in a terminal: interactive work, you can use `fslipython` in a terminal.
> You might need to "sudo" this if your version of FSL needs admin privileges
> to modify.
>
> ln -s $FSLDIR/fslpython/envs/fslpython/bin/ipython $FSLDIR/bin/fslipython
Now if you want to do some interactive work, you can use `fslipython` in a
terminal.
__Exercise__ Do it now! Start `fslipython`, then copy/paste this code into the __Exercise__ Do it now! Start `fslipython`, then copy/paste this code into the
prompt! prompt!
> ``` > ```
> # this line is not python - it is > # this line is not python - it is
> # specific to ipython/jupyter notebook > # specific to ipython/jupyter notebook
> %matplotlib > %matplotlib
> >
> import numpy as np > import numpy as np
> >
> x = np.concatenate(([0.25, 0.75], np.arange(0.1, 1.0, 0.1))) > x = np.concatenate(([0.25, 0.75], np.arange(0.1, 1.0, 0.1)))
> y = np.concatenate(([0.75, 0.75], -np.sin(np.linspace(np.pi / 4, 3 * np.pi / 4, 9)))) > y = np.concatenate(([0.75, 0.75], -np.sin(np.linspace(np.pi / 4, 3 * np.pi / 4, 9))))
> >
> import matplotlib.pyplot as plt > import matplotlib.pyplot as plt
> >
> fig = plt.figure() > fig = plt.figure()
> ax = fig.add_subplot(111) > ax = fig.add_subplot(111)
> >
> ax.scatter(x, y) > ax.scatter(x, y)
> ``` > ```
<a class="anchor" id="python-editors"></a> <a class="anchor" id="python-editors"></a>
## Python editors ## Python editors
> Summary: > Summary:
> - Make your tab key insert four spaces. Don't use tab characters in Python > - Make your tab key insert four spaces. Don't use tab characters in Python
> code. > code.
> >
> - Use [Spyder](https://pythonhosted.org/spyder/) if you want a MATLAB-like > - Use [Spyder](https://pythonhosted.org/spyder/) if you want a MATLAB-like
> envionment (focus on analysis, rather than coding). > envionment (focus on analysis, rather than coding).
> >
> - Use [PyCharm](https://www.jetbrains.com/pycharm/) if you want an IDE-like > - Use [PyCharm](https://www.jetbrains.com/pycharm/) if you want an IDE-like
> environment (focus on coding, rather than analysis). > environment (focus on coding, rather than analysis).
> >
> - Use [Atom](https://atom.io/) or [VS Code](https://code.visualstudio.com/) > - Use [Atom](https://atom.io/) or [VS Code](https://code.visualstudio.com/)
> if you like using the latest and greatest. > if you like using the latest and greatest.
> >
> - If you like your existing editor, use it. But you will be better off if > - If you like your existing editor, use it. But you will be better off if
> you can integrate it with `fslpython`, [pylint](https://www.pylint.org/) > you can integrate it with `fslpython`, [pylint](https://www.pylint.org/)
> and [pyflakes](https://github.com/PyCQA/pyflakes). > and [pyflakes](https://github.com/PyCQA/pyflakes).
You can use any text editor that you want to edit Python files. But the one You can use any text editor that you want to edit Python files. But the one
golden rule that you must follow, no matter what editor you use: golden rule that you must follow, no matter what editor you use:
__Configure your tab key to insert four spaces. Don't use tab characters in __Configure your tab key to insert four spaces. Don't use tab characters in
Python code!__ Python code!__
This is the [standard This is the [standard
convention](https://www.python.org/dev/peps/pep-0008/#indentation) for Python convention](https://www.python.org/dev/peps/pep-0008/#indentation) for Python
code. If you deviate from this convention, and somebody else needs to work code. If you deviate from this convention, and somebody else needs to work
with your code, they will be angry at you! with your code, they will be angry at you!
Now, with that out of the way, there are several good Python editors available Now, with that out of the way, there are several good Python editors available
to you. If you are getting started with Python, we recommend to you. If you are getting started with Python, we recommend
[PyCharm](https://www.jetbrains.com/pycharm/) or [PyCharm](https://www.jetbrains.com/pycharm/) or
[Spyder](https://pythonhosted.org/spyder/). [Spyder](https://pythonhosted.org/spyder/).
If you are used to MATLAB, and you do a lot of experimenting or interactive If you are used to MATLAB, and you do a lot of experimenting or interactive
work, then you might like Spyder. If you spend most of your time writing code work, then you might like Spyder. If you spend most of your time writing code
rather than experimenting, then go with PyCharm. rather than experimenting, then go with PyCharm.
Importantly, both PyCharm and Spyder will correctly indent your Python code! Importantly, both PyCharm and Spyder will correctly indent your Python code!
> If you are going to stick with Emacs for your Python development, then it > If you are going to stick with Emacs for your Python development, then it
> should correctly indent Python code by default. But if it isn't, add > should correctly indent Python code by default. But if it isn't, add
> the following to your `~/.emacs` file: > the following to your `~/.emacs` file:
> >
> (defun my-python-mode-hook () > (defun my-python-mode-hook ()
> (setq indent-tabs-mode nil) > (setq indent-tabs-mode nil)
> (setq python-indent 4) ; for versions prior to 24.3 > (setq python-indent 4) ; for versions prior to 24.3
> (setq python-indent-offset 4)) ; for versions 24.3 or newer > (setq python-indent-offset 4)) ; for versions 24.3 or newer
> (add-hook 'python-mode-hook 'my-python-mode-hook) > (add-hook 'python-mode-hook 'my-python-mode-hook)
### Spyder ### Spyder
Spyder is a MATLAB-like environment for Python. It has a code editor and an Spyder is a MATLAB-like environment for Python. It has a code editor and an
interactive IPython prompt. You can inspect variables that are in your interactive IPython prompt. You can inspect variables that are in your
workspace, plot data, and so on and so forth. workspace, plot data, and so on and so forth.
Beyond that, Spyder is fairly simple - it does not have much in the way of Beyond that, Spyder is fairly simple - it does not have much in the way of
project management tools, or integration with version control (i.e. `git`). project management tools, or integration with version control (i.e. `git`).
Spyder can be installed directly into `fslpython`: Spyder can be installed directly into `fslpython`:
> If your FSL installation requires administrative privileges to modify, you > If your FSL installation requires administrative privileges to modify, you
> will need to prefix these commands with sudo. > will need to prefix these commands with sudo.
> >
> Install Spyder: > Install Spyder:
> >
> $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder > $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder
> Create a link so you can call it easily: > Create a link so you can call it easily:
> >
> ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder > ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder
Now to run Spyder, you can just type: Now to run Spyder, you can just type:
> ``` > ```
> fslspyder & > fslspyder &
> ``` > ```
Now you need to make sure that Spyder is using the `fslpython` environment to Now you need to make sure that Spyder is using the `fslpython` environment to
run your code. run your code.
1. Go to _python_ (the menu) > _Preferences_ > Python Interpreter 1. Go to _python_ (the menu) > _Preferences_ > Python Interpreter
2. Make sure that _Use the following Python interpreter_ is selected 2. Make sure that _Use the following Python interpreter_ is selected
3. Make sure that the path is `$FSLDIR/fslpython/envs/fslpython/bin/python` 3. Make sure that the path is `$FSLDIR/fslpython/envs/fslpython/bin/python`
(for your specific value of `$FSLDIR`). (for your specific value of `$FSLDIR`).
Type the following into the console to test that everything is working: Type the following into the console to test that everything is working:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
plt.plot([1, 2, 3], [4, 5, 6]) plt.plot([1, 2, 3], [4, 5, 6])
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### PyCharm ### PyCharm
PyCharm is a general-purpose Python development environment. When compared to PyCharm is a general-purpose Python development environment. When compared to
Spyder, it is less geared towards interactive analysis, but has better code Spyder, it is less geared towards interactive analysis, but has better code
editing tools (e.g. autocomplete and refactoring), and better file editing tools (e.g. autocomplete and refactoring), and better file
management/version control integration. management/version control integration.
And it is also easy to install - simply download the Community edition from And it is also easy to install - simply download the Community edition from
the [home page](https://www.jetbrains.com/pycharm/). Then, if you are on a the [home page](https://www.jetbrains.com/pycharm/). Then, if you are on a
mac, double-click the `.dmg` file, and drag PyCharm into your `/Applications/` mac, double-click the `.dmg` file, and drag PyCharm into your `/Applications/`
folder. Then double-click on PyCharm to start it. folder. Then double-click on PyCharm to start it.
Once you have chosen a theme, you will be asked if you would like to create a Once you have chosen a theme, you will be asked if you would like to create a
_Launcher script_ - do this, because you will then be able to open files from _Launcher script_ - do this, because you will then be able to open files from
the terminal by typing `charm [filename]`. the terminal by typing `charm [filename]`.
Now you will be presented with a _Welcome to PyCharm_ window. __Before doing Now you will be presented with a _Welcome to PyCharm_ window. __Before doing
anything else__, click on the _Configure_ button down in the bottom right, and anything else__, click on the _Configure_ button down in the bottom right, and
choose _Preferences_. Then in the _Project Interpreter_ section: choose _Preferences_. Then in the _Project Interpreter_ section:
1. Click on the gear button and choose _Add local..._ 1. Click on the gear button and choose _Add local..._
2. Choose _Existing environment_ 2. Choose _Existing environment_
3. Click on the _..._ button, and navigate to 3. Click on the _..._ button, and navigate to
`$FSLDIR/fslpython/envs/fslpython/bin/python`. `$FSLDIR/fslpython/envs/fslpython/bin/python`.
### Other options ### Other options
Emacs is capable of being used as a fully-fledged Python IDE, if you have the Emacs is capable of being used as a fully-fledged Python IDE, if you have the
time and patience to configure it. time and patience to configure it.
If you are the fashionable sort, try one of these: If you are the fashionable sort, try one of these:
- [Visual Studio Code](https://code.visualstudio.com/) - [Visual Studio Code](https://code.visualstudio.com/)
- [Atom](https://atom.io/) - [Atom](https://atom.io/)
<a class="anchor" id="python-in-your-browser-jupyter-notebook"></a> <a class="anchor" id="python-in-your-browser-jupyter-notebook"></a>
## Python in your browser: Jupyter Notebook ## Python in your browser: Jupyter Notebook
It is possible to do your Python-based development and experimentation inside It is possible to do your Python-based development and experimentation inside
your web browser, thanks to the [Jupyter project](https://jupyter.org/). your web browser, thanks to the [Jupyter project](https://jupyter.org/).
Jupyter works in the following way: Jupyter works in the following way:
1. You start a Juptyer web server on your computer. This web server provides 1. You start a Juptyer web server on your computer. This web server provides
the environment in which your Python code is executed. the environment in which your Python code is executed.
2. You open https://localhost:8888 (or similar) in a web browser - this opens 2. You open https://localhost:8888 (or similar) in a web browser - this opens
a connection to the (locally running) web server. a connection to the (locally running) web server.
3. You start a "Notebook" (Jupyter's version of a file), and start typing. 3. You start a "Notebook" (Jupyter's version of a file), and start typing.
You can put text, LaTeX, and of course Python code into a notebook. You can put text, LaTeX, and of course Python code into a notebook.
4. All of the code that you write gets sent to the web server and 4. All of the code that you write gets sent to the web server and
executed. Then the results get sent back to the web browser, and displayed executed. Then the results get sent back to the web browser, and displayed
in your notebook - magic! in your notebook - magic!
All of the PyTreat practicals are written in a Jupyter notebook. Some of the All of the PyTreat practicals are written in a Jupyter notebook. Some of the
talks are too - you're looking at a Jupyter Notebook right now! talks are too - you're looking at a Jupyter Notebook right now!
So you're going to need to install Jupyter to get the most out of the
practicals that we have prepared for you.
__Exercise__ Install Jupyter into `fslpython` - run these commands in a
terminal:
> Remember to prefix with sudo if your FSL install needs admin to modify.
>
> $FSLDIR/fslpython/bin/conda install -n fslpython -y jupyter
> And add a link so you can call it easily:
>
> ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
<a class="anchor" id="git"></a> <a class="anchor" id="git"></a>
## Git ## Git
All the cool kids these days use [git](https://git-scm.com/) to All the cool kids these days use [git](https://git-scm.com/) to
collaboratively work on their Python code. The PyTreat is a great opportunity collaboratively work on their Python code. The PyTreat is a great opportunity
to start learning and using it for your own work! to start learning and using it for your own work!
Git is different from CVS and SVN in that it is _distributed_. In CVS and SVN, Git is different from CVS and SVN in that it is _distributed_. In CVS and SVN,
there is only one central repository. You check out a copy of the source from there is only one central repository. You check out a copy of the source from
the repository, make some changes, and then commit those changes back to the the repository, make some changes, and then commit those changes back to the
central repository. central repository.
In git, there are multiple repositories. There is usually one repository which In git, there are multiple repositories. There is usually one repository which
acts as the central one, but you will _clone_ (or _fork_) that central acts as the central one, but you will _clone_ (or _fork_) that central
repository to create your own full copy of the repository. repository to create your own full copy of the repository.
Then, you can make changes and commit them in your own repository. And at any Then, you can make changes and commit them in your own repository. And at any
point, you can push your changes back to the central repository. point, you can push your changes back to the central repository.
### WIN's gitlab server ### WIN's gitlab server
https://git.fmrib.ox.ac.uk/ https://git.fmrib.ox.ac.uk/
If you have a FMRIB account, then you also have a Gitlab account. Gitlab is a If you have a FMRIB account, then you also have a Gitlab account. Gitlab is a
git server that you can use to store your "central" git repository. Gitlab is git server that you can use to store your "central" git repository. Gitlab is
very similar to https://www.github.com, but it is managed by WIN, and your very similar to https://www.github.com, but it is managed by WIN, and your
code is not publicly visible (although it can be if you want). Gitlab backs code is not publicly visible (although it can be if you want). Gitlab backs
up your code automatically, and has a nice web interface. up your code automatically, and has a nice web interface.
You can have up to 10 projects on your gitlab account - talk to the FMRIB IT You can have up to 10 projects on your gitlab account - talk to the FMRIB IT
people if you need more. people if you need more.
### Using git and gitlab ### Using git and gitlab
> We need to go through a couple of intiial configuration steps before > We need to go through a couple of intiial configuration steps before
> proceeding. You only need to do this once (for each computer that you use). > proceeding. You only need to do this once (for each computer that you use).
> >
> First, run these commands to configure git on your system. > First, run these commands to configure git on your system.
> >
> ``` > ```
> git config --global user.name "Your name" > git config --global user.name "Your name"
> git config --global user.email "Your email address" > git config --global user.email "Your email address"
> ``` > ```
> >
> Now you need to create a SSH key pair, so your computer can talk to the > Now you need to create a SSH key pair, so your computer can talk to the
> gitlab server without you having to log in. Don't be scared - there are > gitlab server without you having to log in. Don't be scared - there are
> detailed instructions on doing this at > detailed instructions on doing this at
> https://git.fmrib.ox.ac.uk/help/ssh/README.md - follow the instructions > https://git.fmrib.ox.ac.uk/help/ssh/README.md - follow the instructions
> under the section entitled __Generating a new SSH key pair__. > under the section entitled __Generating a new SSH key pair__.
Working with git and gitlab generally involves these steps: Working with git and gitlab generally involves these steps:
1. Add new files to your local repository, or make changes to existing files. 1. Add new files to your local repository, or make changes to existing files.
2. Run `git add` on the new/changed files to _stage_ them. 2. Run `git add` on the new/changed files to _stage_ them.
3. Run `git commit` to commit all staged changes to your local repository. 3. Run `git commit` to commit all staged changes to your local repository.
4. Run `git push` to push those commits to your gitlab repository. 4. Run `git push` to push those commits to your gitlab repository.
When you start working on a new project (or if you have an existing project When you start working on a new project (or if you have an existing project
that you want to put into git): that you want to put into git):
__1. Organise all of your project files into their own folder__ __1. Organise all of your project files into their own folder__
This sounds obvious, but just to be sure. This sounds obvious, but just to be sure.
__2. Create a repository for your project on gitlab__ __2. Create a repository for your project on gitlab__
Log in to gitlab (https://git.fmrib.ox.ac.uk/), then click on the _+_ button Log in to gitlab (https://git.fmrib.ox.ac.uk/), then click on the _+_ button
towards the top right, and select _New project_. Give the project a name and towards the top right, and select _New project_. Give the project a name and
choose its visiblity (note that _Public_ means your project will be visible to choose its visiblity (note that _Public_ means your project will be visible to
the world). the world).
__3. Turn your project folder into a git repository__ __3. Turn your project folder into a git repository__
Now, follow the instructions that are listd on your gitlab project home page, Now, follow the instructions that are listd on your gitlab project home page,
under __Existing folder__ (repeated here): under __Existing folder__ (repeated here):
> cd existing_folder > cd existing_folder
> git init > git init
> git remote add origin git@git.fmrib.ox.ac.uk:username/project.git > git remote add origin git@git.fmrib.ox.ac.uk:username/project.git
> git add . > git add .
> git commit -m "Initial commit" > git commit -m "Initial commit"
> git push -u origin master > git push -u origin master
The `git add .` line will add _all_ of the files in your project directory The `git add .` line will add _all_ of the files in your project directory
into git. If you only want certain files in git, then `git add` them one by into git. If you only want certain files in git, then `git add` them one by
one (or use standard bash file patterns, e.g. `git add *.py`). one (or use standard bash file patterns, e.g. `git add *.py`).
You should avoid putting large binary files or data files into git - it works You should avoid putting large binary files or data files into git - it works
best with plain text. Talk to the FMRIB IT people if you really need to store best with plain text. Talk to the FMRIB IT people if you really need to store
large files in git, as they can help you with this. large files in git, as they can help you with this.
__4. Develop your super cool project!__ __4. Develop your super cool project!__
Now you can get to work! Whenever you make changes to your code that you want Now you can get to work! Whenever you make changes to your code that you want
saved, follow the `git add`, `git commit`, `git push` steps described above. saved, follow the `git add`, `git commit`, `git push` steps described above.
For example, let's say we have added a new file called `cool_module.py`. To For example, let's say we have added a new file called `cool_module.py`. To
get this into git, we would do the following: get this into git, we would do the following:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
git add cool_module.py git add cool_module.py
git commit -m "Added cool module. It's super cool" git commit -m "Added cool module. It's super cool"
git push origin master git push origin master
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="the-pytreat-practicals"></a> <a class="anchor" id="the-pytreat-practicals"></a>
## The PyTreat practicals ## The PyTreat practicals
All of the practicals for PyTreat are hosted in a git repository at: All of the practicals for PyTreat are hosted in a git repository at:
https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020
So let's go get them! So let's go get them!
> ``` > ```
> git clone https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals.git > git clone https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020.git
> cd pytreat-2018-practicals > cd pytreat-practicals-2020
> fsljupyter notebook > fslpython -m notebook
> ``` > ```
......
talks/introduction/pytreat_intro.md
+ 14
− 42
View file @ 9a900bc1
# Welcome to the WIN PyTreat 2018! # Welcome to the WIN PyTreat 2020!
Program: https://docs.google.com/document/d/10CwLEhUi-YiwfC2F40QCVm6eEVwKiaXkfTKz67xWAfM/edit?usp=sharing Program: https://docs.google.com/document/d/11LQgxC-LZPG_TXS3MP9tYXNWABAQdTI00iavk-tKttU/edit
__We need to do some setting up, so get your laptop ready!__ __We need to do some setting up, so get your laptop ready!__
__Make sure you have FSL 5.0.10 installed and working!__ __Make sure you have FSL 6.0.3 installed and working!__
__End all sentences with an exclamation mark!__ __End all sentences with an exclamation mark!__
__Open this page in your web browser!__ __Open this page in your web browser!__
https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.md https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020/tree/master/talks/introduction/pytreat_intro.md
## Overview ## Overview
...@@ -92,8 +92,8 @@ So if you use `fslpython` for all of your development, you can be sure that it ...@@ -92,8 +92,8 @@ So if you use `fslpython` for all of your development, you can be sure that it
will work in FSL! will work in FSL!
> `fslpython` is based on _conda_ and, in FSL 5.0.10, is Python version > `fslpython` is based on _conda_ and, in FSL 6.0.3, is Python version
> 3.5.2. You can read more about conda [here](https://conda.io/docs/). > 3.7.3. You can read more about conda [here](https://conda.io/docs/).
<a class="anchor" id="running-python-scripts"></a> <a class="anchor" id="running-python-scripts"></a>
...@@ -160,20 +160,10 @@ Python has a standard interpreter built-in - run `fslpython` in a terminal, ...@@ -160,20 +160,10 @@ Python has a standard interpreter built-in - run `fslpython` in a terminal,
and see what happens (use CTRL+D to exit). and see what happens (use CTRL+D to exit).
__But__ there is another interpreter called [`ipython`](https://ipython.org/) __But__ there is another interpreter called [IPython](https://ipython.org/)
which is vastly superior to the standard Python interpreter. Use `ipython` which is vastly superior to the standard Python interpreter. Use IPython
instead! It is already installed in `fslpython`, but we just need to create a instead! It is already installed in `fslpython`, so if you want to do some
link to it - do this now in a terminal: interactive work, you can use `fslipython` in a terminal.
> You might need to "sudo" this if your version of FSL needs admin privileges
> to modify.
>
> ln -s $FSLDIR/fslpython/envs/fslpython/bin/ipython $FSLDIR/bin/fslipython
Now if you want to do some interactive work, you can use `fslipython` in a
terminal.
__Exercise__ Do it now! Start `fslipython`, then copy/paste this code into the __Exercise__ Do it now! Start `fslipython`, then copy/paste this code into the
...@@ -384,24 +374,6 @@ All of the PyTreat practicals are written in a Jupyter notebook. Some of the ...@@ -384,24 +374,6 @@ All of the PyTreat practicals are written in a Jupyter notebook. Some of the
talks are too - you're looking at a Jupyter Notebook right now! talks are too - you're looking at a Jupyter Notebook right now!
So you're going to need to install Jupyter to get the most out of the
practicals that we have prepared for you.
__Exercise__ Install Jupyter into `fslpython` - run these commands in a
terminal:
> Remember to prefix with sudo if your FSL install needs admin to modify.
>
> $FSLDIR/fslpython/bin/conda install -n fslpython -y jupyter
> And add a link so you can call it easily:
>
> ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
<a class="anchor" id="git"></a> <a class="anchor" id="git"></a>
## Git ## Git
...@@ -538,14 +510,14 @@ git push origin master ...@@ -538,14 +510,14 @@ git push origin master
All of the practicals for PyTreat are hosted in a git repository at: All of the practicals for PyTreat are hosted in a git repository at:
https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020
So let's go get them! So let's go get them!
> ``` > ```
> git clone https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals.git > git clone https://git.fmrib.ox.ac.uk/fsl/pytreat-practicals-2020.git
> cd pytreat-2018-practicals > cd pytreat-practicals-2020
> fsljupyter notebook > fslpython -m notebook
> ``` > ```
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