diff --git a/talks/introduction/example_project/myscript.py b/talks/introduction/example_project/myscript.py
old mode 100644
new mode 100755
index 3b768e3f0f9e01019ec53b555ddbcacb3fa1174f..02f2bc91fa5bcad1b387512986fc75f6f0b499b9
--- a/talks/introduction/example_project/myscript.py
+++ b/talks/introduction/example_project/myscript.py
@@ -6,42 +6,23 @@
# Python script, you should use this line
# instead: #!/usr/bin/env python
-
# In Python, we need to "import" libraries
# (called modules) before we can use them.
import sys
import nibabel as nib
-# Python uses indentation instead of braces
-# for all of its control structures - if
-# while, and for statements, functions and
-# classes, and so on and so forth.
-#
-# The standard convention for indentation
-# is four spaces. Please don't use tab
-# characters!
-def main():
-
- # We can get to our command
- # line arguments via sys.argv
- fpath = sys.argv[1]
-
- # We can use nibabel to load
- # NIFTI images (and other
- # neuroimaging data formats)
- img = nib.load(fpath)
- data = img.get_data()
-
- # Now we're working with a
- # numpy array.
- nzmean = data[data != 0].mean()
-
- print('mean:', nzmean)
+# We can get to our command
+# line arguments via sys.argv
+fpath = sys.argv[1]
- sys.exit(0)
+# We can use nibabel to load
+# NIFTI images (and other
+# neuroimaging data formats)
+img = nib.load(fpath)
+data = img.get_data()
+# Now we're working with a
+# numpy array.
+nzmean = data[data != 0].mean()
-# This bit is the Python equivalent of
-# "int main()" in a C or C++ program.
-if __name__ == '__main__':
- main()
+print('mean:', nzmean)
diff --git a/talks/introduction/pytreat_intro.ipynb b/talks/introduction/pytreat_intro.ipynb
index 270b2b264db137fb6bb4101c1dd00a3bd2b0eb42..5eed1ef09bb1faa4a040c571a360f16df964364f 100644
--- a/talks/introduction/pytreat_intro.ipynb
+++ b/talks/introduction/pytreat_intro.ipynb
@@ -10,13 +10,15 @@
"Program: https://docs.google.com/document/d/10CwLEhUi-YiwfC2F40QCVm6eEVwKiaXkfTKz67xWAfM/edit?usp=sharing\n",
"\n",
"\n",
- "__Get your laptop ready!__\n",
+ "__We need to do some setting up, so get your laptop ready!__\n",
"\n",
"__Make sure you have FSL 5.0.10 installed and working!__\n",
"\n",
+ "__End all sentences with an exclamation mark!__\n",
+ "\n",
"__Open this page in your web browser!__\n",
"\n",
- "https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.ipynb\n",
+ "https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.md\n",
"\n",
"\n",
"## Overview\n",
@@ -120,7 +122,7 @@
"## Running Python scripts\n",
"\n",
"\n",
- "Here's a basic Python script:\n",
+ "Here's a basic Python script - a _Hello world_ for neuroimaging:\n",
"\n",
"\n",
"> ```\n",
@@ -132,56 +134,37 @@
"> # Python script, you should use this line\n",
"> # instead: #!/usr/bin/env python\n",
">\n",
- ">\n",
"> # In Python, we need to \"import\" libraries\n",
"> # (called modules) before we can use them.\n",
"> import sys\n",
"> import nibabel as nib\n",
">\n",
- "> # Python uses indentation instead of braces\n",
- "> # for all of its control structures - if\n",
- "> # while, and for statements, functions and\n",
- "> # classes, and so on and so forth.\n",
- "> #\n",
- "> # The standard convention for indentation\n",
- "> # is four spaces. Please don't use tab\n",
- "> # characters!\n",
- "> def main():\n",
- ">\n",
- "> # We can get to our command\n",
- "> # line arguments via sys.argv\n",
- "> fpath = sys.argv[1]\n",
- ">\n",
- "> # We can use nibabel to load\n",
- "> # NIFTI images (and other\n",
- "> # neuroimaging data formats)\n",
- "> img = nib.load(fpath)\n",
- "> data = img.get_data()\n",
+ "> # We can get to our command\n",
+ "> # line arguments via sys.argv\n",
+ "> fpath = sys.argv[1]\n",
">\n",
- "> # Now we're working with a\n",
- "> # numpy array.\n",
- "> nzmean = data[data != 0].mean()\n",
+ "> # We can use nibabel to load\n",
+ "> # NIFTI images (and other\n",
+ "> # neuroimaging data formats)\n",
+ "> img = nib.load(fpath)\n",
+ "> data = img.get_data()\n",
">\n",
- "> print('mean:', nzmean)\n",
+ "> # Now we're working with a\n",
+ "> # numpy array.\n",
+ "> nzmean = data[data != 0].mean()\n",
">\n",
- "> sys.exit(0)\n",
- ">\n",
- ">\n",
- "> # This bit is the Python equivalent of\n",
- "> # \"int main()\" in a C or C++ program.\n",
- "> if __name__ == '__main__':\n",
- "> main()\n",
+ "> print('mean:', nzmean)\n",
"> ```\n",
"\n",
"\n",
"__Exercise__ Save the above code to a file called `script.py`, then run this\n",
- "in a terminal (replace `/path/to/some/image.nii.gz` with a path to some image\n",
- "on your computer):\n",
+ "in a terminal (replace `/path/to/some/image/on/your/computer.nii.gz` with a\n",
+ "path to some image on your computer):\n",
"\n",
"\n",
"> ```\n",
"> chmod a+x script.py\n",
- "> ./script.py /path/to/some/image.nii.gz\n",
+ "> ./script.py /path/to/some/image/on/your/computer.nii.gz\n",
"> ```\n",
"\n",
"\n",
@@ -205,12 +188,10 @@
"link to it - do this now in a terminal:\n",
"\n",
"\n",
- "> ```\n",
- "> # You might need to \"sudo\" this\n",
- "> # if your version of FSL needs\n",
- "> # admin privileges to modify.\n",
- "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/ipython $FSLDIR/bin/fslipython\n",
- "> ```\n",
+ "> You might need to \"sudo\" this if your version of FSL needs admin privileges\n",
+ "> to modify.\n",
+ ">\n",
+ "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/ipython $FSLDIR/bin/fslipython\n",
"\n",
"\n",
"Now if you want to do some interactive work, you can use `fslipython` in a\n",
@@ -287,6 +268,20 @@
"rather than experimenting, then go with PyCharm.\n",
"\n",
"\n",
+ "Importantly, both PyCharm and Spyder will correctly indent your Python code!\n",
+ "\n",
+ "\n",
+ "> If you are going to stick with Emacs for your Python development, then it\n",
+ "> should correctly indent Python code by default. But if it isn't, add\n",
+ "> the following to your `~/.emacs` file:\n",
+ ">\n",
+ "> (defun my-python-mode-hook ()\n",
+ "> (setq indent-tabs-mode nil)\n",
+ "> (setq python-indent 4) ; for versions prior to 24.3\n",
+ "> (setq python-indent-offset 4)) ; for versions 24.3 or newer\n",
+ "> (add-hook 'python-mode-hook 'my-python-mode-hook)\n",
+ "\n",
+ "\n",
"### Spyder\n",
"\n",
"\n",
@@ -302,15 +297,16 @@
"Spyder can be installed directly into `fslpython`:\n",
"\n",
"\n",
- "> ```\n",
- "> # If your FSL installation requires\n",
- "> # administrative privileges to modify,\n",
- "> # you will need to prefix these\n",
- "> # commands with sudo.\n",
- "> $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder\n",
- "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder\n",
- "> ```\n",
+ "> If your FSL installation requires administrative privileges to modify, you\n",
+ "> will need to prefix these commands with sudo.\n",
+ ">\n",
+ "> Install Spyder:\n",
+ ">\n",
+ "> $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder\n",
"\n",
+ "> Create a link so you can call it easily:\n",
+ ">\n",
+ "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder\n",
"\n",
"Now to run Spyder, you can just type:\n",
"\n",
@@ -350,10 +346,10 @@
"### PyCharm\n",
"\n",
"\n",
- "PyCharm is a general-purpose Python development environment. Unlike Spyder, it\n",
- "does not have an integrated console or variable explorer. But it has more\n",
- "tools to help you write code, and better file management/version control\n",
- "integration.\n",
+ "PyCharm is a general-purpose Python development environment. When compared to\n",
+ "Spyder, it is less geared towards interactive analysis, but has better code\n",
+ "editing tools (e.g. autocomplete and refactoring), and better file\n",
+ "management/version control integration.\n",
"\n",
"\n",
"And it is also easy to install - simply download the Community edition from\n",
@@ -426,12 +422,14 @@
"terminal:\n",
"\n",
"\n",
- "> ```\n",
- "> # Remember to prefix with sudo if your\n",
- "> # FSL install needs admin to modify.\n",
- "> $FSLDIR/fslpython/bin/conda install -n fslpython -y jupyter\n",
- "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter\n",
- "> ```\n",
+ "\n",
+ "> Remember to prefix with sudo if your FSL install needs admin to modify.\n",
+ ">\n",
+ "> $FSLDIR/fslpython/bin/conda install -n fslpython -y jupyter\n",
+ "\n",
+ "> And add a link so you can call it easily:\n",
+ ">\n",
+ "> ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter\n",
"\n",
"\n",
"<a class=\"anchor\" id=\"git\"></a>\n",
@@ -439,7 +437,8 @@
"\n",
"\n",
"All the cool kids these days use [git](https://git-scm.com/) to\n",
- "collaboratively work on their Python code.\n",
+ "collaboratively work on their Python code. The PyTreat is a great opportunity\n",
+ "to start learning and using it for your own work!\n",
"\n",
"\n",
"Git is different from CVS and SVN in that it is _distributed_. In CVS and SVN,\n",
@@ -498,66 +497,53 @@
"1. Add new files to your local repository, or make changes to existing files.\n",
"2. Run `git add` on the new/changed files to _stage_ them.\n",
"3. Run `git commit` to commit all staged changes to your local repository.\n",
- "4. Run `git push` to push those changes to your gitlab repository.\n",
+ "4. Run `git push` to push those commits to your gitlab repository.\n",
"\n",
"\n",
"When you start working on a new project (or if you have an existing project\n",
"that you want to put into git):\n",
"\n",
"\n",
- "__1. Create a project directory__\n",
+ "__1. Organise all of your project files into their own folder__\n",
"\n",
- "Or navigate to your existing project directory.\n",
"\n",
+ "This sounds obvious, but just to be sure.\n",
"\n",
- "__2. Turn the directory into a git repository__\n",
- "\n",
- "> ```\n",
- "> cd path/to/super/cool/project\n",
- "> git init\n",
- "> ```\n",
- "\n",
- "\n",
- "__3. Add your files to git__\n",
- "\n",
- "If you want to add all of the files in your project directory into git, type\n",
- "this:\n",
- "\n",
- "> ```\n",
- "> git add .\n",
- "> ```\n",
"\n",
+ "__2. Create a repository for your project on gitlab__\n",
"\n",
- "Otherwise, if you only want certain files in git, then `git add` them one by\n",
- "one (or with standard bash file patterns).\n",
- "\n",
- "You should avoid putting large binary files or data files into git - it works\n",
- "best with source code. Talk to the FMRIB IT people if you really need to store\n",
- "large files in git, as they can help you with this.\n",
"\n",
+ "Log in to gitlab (https://git.fmrib.ox.ac.uk/), then click on the _+_ button\n",
+ "towards the top right, and select _New project_. Give the project a name and\n",
+ "choose its visiblity (note that _Public_ means your project will be visible to\n",
+ "the world).\n",
"\n",
- "__4. Commit your changes__\n",
"\n",
+ "__3. Turn your project folder into a git repository__\n",
"\n",
- "> ```\n",
- "> git commit -m \"A useful message describing the changes you are committing.\"\n",
- "> ```\n",
"\n",
+ "Now, follow the instructions that are listd on your gitlab project home page,\n",
+ "under __Existing folder__ (repeated here):\n",
"\n",
- "__5. Create a repository for your project on gitlab__\n",
"\n",
+ "> cd existing_folder\n",
+ "> git init\n",
+ "> git remote add origin git@git.fmrib.ox.ac.uk:username/project.git\n",
+ "> git add .\n",
+ "> git commit -m \"Initial commit\"\n",
+ "> git push -u origin master\n",
"\n",
- "Log in to gitlab (https://git.fmrib.ox.ac.uk/), then click on the _+_ button\n",
- "towards the top right, and select _New project_. Give the project a name and\n",
- "choose its visiblity (note that _Public_ means your project will be visible to\n",
- "the world).\n",
"\n",
+ "The `git add .` line will add _all_ of the files in your project directory\n",
+ "into git. If you only want certain files in git, then `git add` them one by\n",
+ "one (or use standard bash file patterns, e.g. `git add *.py`).\n",
"\n",
- "Now, follow the instructions under __Existing Git repository__ to \"link\" your\n",
- "local project repository to the one on gitlab.\n",
+ "You should avoid putting large binary files or data files into git - it works\n",
+ "best with plain text. Talk to the FMRIB IT people if you really need to store\n",
+ "large files in git, as they can help you with this.\n",
"\n",
"\n",
- "__6. Develop your super cool project!__\n",
+ "__4. Develop your super cool project!__\n",
"\n",
"\n",
"Now you can get to work! Whenever you make changes to your code that you want\n",
diff --git a/talks/introduction/pytreat_intro.md b/talks/introduction/pytreat_intro.md
index e663f009f7ebb47ec661d6e3cc5aadcf5d60e80e..6600f479dc3ebd3bf48e853945c5387bb99ce100 100644
--- a/talks/introduction/pytreat_intro.md
+++ b/talks/introduction/pytreat_intro.md
@@ -4,13 +4,15 @@
Program: https://docs.google.com/document/d/10CwLEhUi-YiwfC2F40QCVm6eEVwKiaXkfTKz67xWAfM/edit?usp=sharing
-__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!__
+__End all sentences with an exclamation mark!__
+
__Open this page in your web browser!__
-https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.ipynb
+https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals/tree/master/talks/introduction/pytreat_intro.md
## Overview
@@ -98,7 +100,7 @@ will work in FSL!
## Running Python scripts
-Here's a basic Python script:
+Here's a basic Python script - a _Hello world_ for neuroimaging:
> ```
@@ -110,56 +112,37 @@ Here's a basic Python script:
> # Python script, you should use this line
> # instead: #!/usr/bin/env python
>
->
> # In Python, we need to "import" libraries
> # (called modules) before we can use them.
> import sys
> import nibabel as nib
>
-> # Python uses indentation instead of braces
-> # for all of its control structures - if
-> # while, and for statements, functions and
-> # classes, and so on and so forth.
-> #
-> # The standard convention for indentation
-> # is four spaces. Please don't use tab
-> # characters!
-> def main():
->
-> # We can get to our command
-> # line arguments via sys.argv
-> fpath = sys.argv[1]
->
-> # We can use nibabel to load
-> # NIFTI images (and other
-> # neuroimaging data formats)
-> img = nib.load(fpath)
-> data = img.get_data()
+> # We can get to our command
+> # line arguments via sys.argv
+> fpath = sys.argv[1]
>
-> # Now we're working with a
-> # numpy array.
-> nzmean = data[data != 0].mean()
+> # We can use nibabel to load
+> # NIFTI images (and other
+> # neuroimaging data formats)
+> img = nib.load(fpath)
+> data = img.get_data()
>
-> print('mean:', nzmean)
+> # Now we're working with a
+> # numpy array.
+> nzmean = data[data != 0].mean()
>
-> sys.exit(0)
->
->
-> # This bit is the Python equivalent of
-> # "int main()" in a C or C++ program.
-> if __name__ == '__main__':
-> main()
+> print('mean:', nzmean)
> ```
__Exercise__ Save the above code to a file called `script.py`, then run this
-in a terminal (replace `/path/to/some/image.nii.gz` with a path to some image
-on your computer):
+in a terminal (replace `/path/to/some/image/on/your/computer.nii.gz` with a
+path to some image on your computer):
> ```
> chmod a+x script.py
-> ./script.py /path/to/some/image.nii.gz
+> ./script.py /path/to/some/image/on/your/computer.nii.gz
> ```
@@ -183,12 +166,10 @@ instead! It is already installed in `fslpython`, but we just need to create a
link to it - do this now 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
-> ```
+> 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
@@ -265,6 +246,20 @@ work, then you might like Spyder. If you spend most of your time writing code
rather than experimenting, then go with PyCharm.
+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
+> should correctly indent Python code by default. But if it isn't, add
+> the following to your `~/.emacs` file:
+>
+> (defun my-python-mode-hook ()
+> (setq indent-tabs-mode nil)
+> (setq python-indent 4) ; for versions prior to 24.3
+> (setq python-indent-offset 4)) ; for versions 24.3 or newer
+> (add-hook 'python-mode-hook 'my-python-mode-hook)
+
+
### Spyder
@@ -280,15 +275,16 @@ project management tools, or integration with version control (i.e. `git`).
Spyder can be installed directly into `fslpython`:
-> ```
-> # If your FSL installation requires
-> # administrative privileges to modify,
-> # you will need to prefix these
-> # commands with sudo.
-> $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder
-> ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder
-> ```
+> If your FSL installation requires administrative privileges to modify, you
+> will need to prefix these commands with sudo.
+>
+> Install Spyder:
+>
+> $FSLDIR/fslpython/bin/conda install -n fslpython -y spyder
+> Create a link so you can call it easily:
+>
+> ln -s $FSLDIR/fslpython/envs/fslpython/bin/spyder $FSLDIR/bin/fslspyder
Now to run Spyder, you can just type:
@@ -320,10 +316,10 @@ plt.plot([1, 2, 3], [4, 5, 6])
### PyCharm
-PyCharm is a general-purpose Python development environment. Unlike Spyder, it
-does not have an integrated console or variable explorer. But it has more
-tools to help you write code, and better file management/version control
-integration.
+PyCharm is a general-purpose Python development environment. When compared to
+Spyder, it is less geared towards interactive analysis, but has better code
+editing tools (e.g. autocomplete and refactoring), and better file
+management/version control integration.
And it is also easy to install - simply download the Community edition from
@@ -396,12 +392,14 @@ __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
-> ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
-> ```
+
+> 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>
@@ -409,7 +407,8 @@ terminal:
All the cool kids these days use [git](https://git-scm.com/) to
-collaboratively work on their Python code.
+collaboratively work on their Python code. The PyTreat is a great opportunity
+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,
@@ -475,59 +474,46 @@ When you start working on a new project (or if you have an existing project
that you want to put into git):
-__1. Create a project directory__
+__1. Organise all of your project files into their own folder__
-Or navigate to your existing project directory.
+This sounds obvious, but just to be sure.
-__2. Turn the directory into a git repository__
-
-> ```
-> cd path/to/super/cool/project
-> git init
-> ```
-
-
-__3. Add your files to git__
-
-If you want to add all of the files in your project directory into git, type
-this:
-
-> ```
-> git add .
-> ```
+__2. Create a repository for your project on gitlab__
-Otherwise, if you only want certain files in git, then `git add` them one by
-one (or with standard bash file patterns).
-
-You should avoid putting large binary files or data files into git - it works
-best with source code. Talk to the FMRIB IT people if you really need to store
-large files in git, as they can help you with this.
+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
+choose its visiblity (note that _Public_ means your project will be visible to
+the world).
-__4. Commit your changes__
+__3. Turn your project folder into a git repository__
-> ```
-> git commit -m "A useful message describing the changes you are committing."
-> ```
+Now, follow the instructions that are listd on your gitlab project home page,
+under __Existing folder__ (repeated here):
-__5. Create a repository for your project on gitlab__
+> cd existing_folder
+> git init
+> git remote add origin git@git.fmrib.ox.ac.uk:username/project.git
+> git add .
+> git commit -m "Initial commit"
+> git push -u origin master
-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
-choose its visiblity (note that _Public_ means your project will be visible to
-the world).
+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
+one (or use standard bash file patterns, e.g. `git add *.py`).
-Now, follow the instructions under __Existing Git repository__ to "link" your
-local project repository to the one on gitlab.
+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
+large files in git, as they can help you with this.
-__6. 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