pytreat_intro.md

a = 'Great, I am _so_ sick of writing "char *a;"!'
print(a)

a = 12345
print('a is now an number!', a)
a = [1, 2, 3, 4, 5]

for elem in a:
    print(elem)
#!/usr/bin/env fslpython

# That first line up there ensures that your
# script will be executed in the fslpython
# environment. If you are writing a general
# 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)

    sys.exit(0)


# This bit is the Python equivalent of
# "int main()" in a C or C++ program.
if __name__ == '__main__':
    main()
chmod a+x script.py
./script.py /path/to/some/image.nii.gz
# 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
# this line is not python - it is
# specific to ipython/jupyter notebook
%matplotlib

import numpy as np

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))))

import matplotlib.pyplot as plt

fig = plt.figure()
ax  = fig.add_subplot(111)

ax.scatter(x, y)
# 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
fslspyder &
import matplotlib.pyplot as plt
plt.plot([1, 2, 3], [4, 5, 6])
# 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
git config --global user.name "Your name"
git config --global user.email "Your email address"
cd path/to/super/cool/project
git init
git add .
git commit -m "A useful message describing the changes you are committing."
git add cool_module.py
git commit -m "Added cool module. It's super cool"
git push origin master
git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
cd pytreat-2018-practicals
fsljupyter notebook