Commit ff333602 authored by Sean Fitzgibbon's avatar Sean Fitzgibbon
Browse files

Merge branch 'last_minute_mods' into 'master'

Some last minute mods

See merge request !21
parents 5b574d14 5c9e8e18
# ------------------------------
# Run in terminal with command: bokeh serve --show ./
# ------------------------------
import os
import os.path as op
from subprocess import check_output as run
from tempfile import TemporaryDirectory
import nibabel as nb
from bokeh.layouts import column
from bokeh.models import Button
from bokeh.plotting import figure, curdoc
# load MNI152
FSLDIR = os.environ['FSLDIR']
fname = f'{FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz'
d = nb.load(fname).get_fdata()
d0 = d[:, :, d.shape[2] // 2].squeeze()
# plot center axial slice
p = figure(x_range=(0, 100), y_range=(0, 100), tooltips=[("x", "$x"), ("y", "$y"), ("value", "@image")])
p.image(image=[d0.T], x=0, y=0, dw=100, dh=100, palette="Greys256", level="image")
# create a callback to run BET and show result
def callback():
with TemporaryDirectory() as tmp:
bet_name = op.join(tmp, 'betted_img.nii.gz')
print('running bet')
out = run(f'bet {fname} {bet_name}'.split())
d = nb.load(bet_name).get_fdata()
d0 = d[:, :, d.shape[2] // 2].squeeze()
p.image(image=[d0.T], x=0, y=0, dw=100, dh=100, palette="Greys256", level="image")
# add a button widget and configure with the call back
button = Button(label="BET Me")
# put the button and plot in a layout and add to the document
curdoc().add_root(column(button, p))
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