"""
vb = Brain(source_obj=s_obj, connect_obj=c_obj)
vb.brain_control(alpha=0.1, hemisphere='both')
rotation = 'axial_0'
vb.rotate('axial_0') # top
#vb.rotate('axial_1') #bottom
#vb.rotate('sagittal_0') # left
#vb.rotate('sagittal_1') # right
#vb.rotate('coronal_0') # front
#vb.rotate('coronal_1') # back
# Save the brain
vb.screenshot('main2.png',
canvas='main',
print_size=(10, 20),
dpi=300,
autocrop=True)
# What is left to do here is to take different shot of the brain to create a figure of the overal connectivity
# through time
#vb.show()
'''
Bottom line: We can't set the width of our edges to be bigger or smaller
We can modify the colormap thought.
we can use a combination of vmin,under, vmax,over and cmap to highlight
different connection stength
to rotate the view in the image we need to do:
n_connections = 150
rnd_selection = np.random.randint(0, N**2, n_connections)
connect = np.random.randint(0, 20, (N, N))
mask = np.ones(N**2, dtype=bool)
mask[rnd_selection] = False
mask = mask.reshape(N, N)
connect = np.ma.masked_array(connect, mask=mask)
kwargs['c_connect'] = connect
kwargs['ui_bgcolor'] = 'white'
vb = Brain(**kwargs)
# ============= Sources =============
# # Screenshot of the default view :
vb.screenshot('default.png', autocrop=True)
# Hide sources that are not in the brain :
vb.sources_display('inside')
vb.screenshot('inside.png', autocrop=True)
# ============= Connectivity =============
# Colorby network density :
vb.sources_display('none')
vb.connect_control(show=True,
cmap='magma',
colorby='density',
clim=(0., 35.),
vmin=10.,
vmax=30.,
under='gray',
idx_4_6[1]: 'green'}
roi_obj.select_roi(idx_4_6, unique_color=True, roi_to_color=roi_color,
smooth=7)
"""Create a brain object
"""
b_obj = BrainObj('B1', hemisphere='both', translucent=True)
"""Pass the brain, source and ROI object to the GUI
"""
vb = Brain(brain_obj=b_obj, source_obj=s_obj, roi_obj=roi_obj)
"""Render the scene and save the jpg picture with a 300dpi
"""
save_as = os.path.join(save_pic_path, '0_main_brain.jpg')
vb.screenshot(save_as, dpi=300, print_size=(10, 10), autocrop=True)
"""Project source's activity onto the surface
"""
vb.cortical_projection(clim=(0, 50), cmap='Spectral_r', vmin=10.1,
under='black', vmax=41.2, over='green')
vb.sources_control('Sobj', visible=False) # Hide sources
vb.rotate(custom=(-160., 10.)) # Rotate the brain
vb.brain_control(translucent=False) # Make the brain opaque
"""Now, we take a screenthot of the scene but this time, we used the
autocrop argument to crop the image as close as possible to the brain.
Then, we used the print_size, dpi and unit inputs to get higher resolution
image.
Taken together, this mean that the image should have a sufficient size to be
rnd_selection = np.random.randint(0, N ** 2, n_connections)
connect = np.random.randint(0, 20, (N, N))
mask = np.ones(N ** 2, dtype=bool)
mask[rnd_selection] = False
mask = mask.reshape(N, N)
connect = np.ma.masked_array(connect, mask=mask)
kwargs['c_connect'] = connect
kwargs['ui_bgcolor'] = 'white'
vb = Brain(**kwargs)
# ============= Sources =============
# # Screenshot of the default view :
vb.screenshot('default.png', autocrop=True)
# Hide sources that are not in the brain :
vb.sources_display('inside')
vb.screenshot('inside.png', autocrop=True)
# ============= Connectivity =============
# Colorby network density :
vb.sources_display('none')
vb.connect_control(show=True, cmap='magma', colorby='density', clim=(0., 35.),
vmin=10., vmax=30., under='gray', over='darkred',
dynamic=(.7, 1.))
vb.screenshot('density.png', autocrop=True)
# Color by number of connections per node :
vb.connect_control(show=True, cmap='viridis', colorby='count', clim=(1., 5.),
vmin=0., vmax=10., dynamic=(.1, 1.))
idx_4_6[1]: 'green'
}
roi_obj.select_roi(idx_4_6,
unique_color=True,
roi_to_color=roi_color,
smooth=7)
"""Create a brain object
"""
b_obj = BrainObj('B1', hemisphere='both', translucent=True)
"""Pass the brain, source and ROI object to the GUI
"""
vb = Brain(brain_obj=b_obj, source_obj=s_obj, roi_obj=roi_obj)
"""Render the scene and save the jpg picture with a 300dpi
"""
save_as = os.path.join(save_pic_path, '0_main_brain.jpg')
vb.screenshot(save_as, dpi=300, print_size=(10, 10), autocrop=True)
"""Project source's activity onto the surface
"""
vb.cortical_projection(clim=(0, 50),
cmap='Spectral_r',
vmin=10.1,
under='black',
vmax=41.2,
over='green')
vb.sources_control('Sobj', visible=False) # Hide sources
vb.rotate(custom=(-160., 10.)) # Rotate the brain
vb.brain_control(translucent=False) # Make the brain opaque
"""Now, we take a screenthot of the scene but this time, we used the
autocrop argument to crop the image as close as possible to the brain.
Then, we used the print_size, dpi and unit inputs to get higher resolution
