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create_pdf.py
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import pyvista as pv
import os
import matplotlib.pyplot as plt
import numpy as np
def extract_surfaces(file_path):
# set file names
lh_pial_fn = os.path.join(file_path, 'lh.pial.vtk')
rh_pial_fn = os.path.join(file_path, 'rh.pial.vtk')
lh_white_fn = os.path.join(file_path, 'lh.white.vtk')
rh_white_fn = os.path.join(file_path, 'rh.white.vtk')
# read surface files
lh_pial = pv.read(lh_pial_fn)
rh_pial = pv.read(rh_pial_fn)
lh_white = pv.read(lh_white_fn)
rh_white = pv.read(rh_white_fn)
return lh_pial, rh_pial, lh_white, rh_white
def plot_lh_pial(lh_pial, file_path=None):
# plot left hemisphere pial surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_pial,
scalars=lh_pial['thickness'],
clim=[0, 5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
lhpr = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_pial_r.png')
# plotter.show(screenshot=save_fn)
# plotter.close()
# plot left hemisphere pial surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_pial,
scalars=lh_pial['thickness'],
clim=[0, 5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 180
lhpl = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_pial_l.png')
# plotter.show(screenshot=save_fn)
# plotter.close()
return (
lhpr, lhpl,
np.percentile(lh_pial['thickness'], 5),
np.percentile(lh_pial['thickness'], 95),
)
def plot_rh_pial(rh_pial, file_path=None):
# plot right hemisphere pial surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_pial,
scalars=rh_pial['thickness'],
clim=[0, 5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
rhpr = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_pial_r.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot right hemisphere pial surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_pial,
scalars=rh_pial['thickness'],
clim=[0, 5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 180
rhpl = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_pial_l.png')
# plotter.show(screenshot=save_fn)
plotter.close()
return (
rhpr, rhpl,
np.percentile(rh_pial['thickness'], 5),
np.percentile(rh_pial['thickness'], 95),
)
def plot_lh_white(lh_white, file_path):
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_white,
scalars=lh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
lhwr = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_white_r.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_white,
scalars=lh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 180
lhwl = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_white_l.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_white,
scalars=lh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 225
lhwlb = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_white_lb.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
lh_white,
scalars=lh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 135
lhwlf = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'lh_white_lf.png')
# plotter.show(screenshot=save_fn)
plotter.close()
return (
lhwr, lhwl, lhwlb, lhwlf,
np.percentile(lh_white['curv'], 5),
np.percentile(lh_white['curv'], 95),
)
def plot_rh_white(rh_white, file_path):
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_white,
scalars=rh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
rhwr = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_white_r.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_white,
scalars=rh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 180
rhwl = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_white_l.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_white,
scalars=rh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = 45
rhwrf = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_white_rf.png')
# plotter.show(screenshot=save_fn)
plotter.close()
# plot left hemisphere white surface
plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(
rh_white,
scalars=rh_white['curv'],
clim=[-0.5, 0.5],
cmap='jet',
show_scalar_bar=False,
)
plotter.camera_position = 'yz'
plotter.camera.zoom(1.6)
plotter.camera.azimuth = -45
rhwrb = plotter.screenshot(return_img=True)
# plotter.show(auto_close=False)
# save_fn = os.path.join(file_path, 'rh_white_rb.png')
# plotter.show(screenshot=save_fn)
plotter.close()
return (
rhwr, rhwl, rhwrf, rhwrb,
np.percentile(rh_white['curv'], 5),
np.percentile(rh_white['curv'], 95),
)
def plot_all(file_path, output_path, index, group_num):
lh_pial, rh_pial, lh_white, rh_white = extract_surfaces(file_path)
lhpr, lhpl, lhp5, lhp95 = plot_lh_pial(lh_pial, file_path)
rhpr, rhpl, rhp5, rhp95 = plot_rh_pial(rh_pial, file_path)
lhwr, lhwl, lhwlb, lhwlf, lhw5, lhw95 = plot_lh_white(lh_white, file_path)
rhwr, rhwl, rhwrf, rhwrb, rhw5, rhw95 = plot_rh_white(rh_white, file_path)
ses_name = file_path.split('/')[-1]
sub_name = file_path.split('/')[-2]
output_fn = os.path.join(output_path, f'{index:02d}_{sub_name}_{ses_name}.pdf')
fig = plt.figure(figsize=(16, 9), layout='constrained')
subfigs = fig.subfigures(1, 2)
ax = subfigs[0].subplots(3, 2)
subfigs[0].suptitle(
f'LH Thickness @ 5%: {lhp5:.2f}, 95%: {lhp95:.2f}\n'
f'LH Curvature @ 5%: {lhw5:.2f}, 95%: {lhw95:.2f}',
fontsize='x-large',
)
ax[0, 0].imshow(lhpl)
ax[0, 0].axis('off')
ax[0, 1].imshow(lhpr)
ax[0, 1].axis('off')
ax[1, 0].imshow(lhwl)
ax[1, 0].axis('off')
ax[1, 1].imshow(lhwr)
ax[1, 1].axis('off')
ax[2, 0].imshow(lhwlf)
ax[2, 0].axis('off')
ax[2, 1].imshow(lhwlb)
ax[2, 1].axis('off')
ax = subfigs[1].subplots(3, 2)
subfigs[1].suptitle(
f'RH Thickness @ 5%: {rhp5:.2f}, 95%: {rhp95:.2f}\n'
f'RH Curvature @ 5%: {rhw5:.2f}, 95%: {rhw95:.2f}',
fontsize='x-large',
)
ax[0, 0].imshow(rhpl)
ax[0, 0].axis('off')
ax[0, 1].imshow(rhpr)
ax[0, 1].axis('off')
ax[1, 0].imshow(rhwl)
ax[1, 0].axis('off')
ax[1, 1].imshow(rhwr)
ax[1, 1].axis('off')
ax[2, 0].imshow(rhwrf)
ax[2, 0].axis('off')
ax[2, 1].imshow(rhwrb)
ax[2, 1].axis('off')
fig.suptitle(
f'Group {group_num:03d} #{index:02d} Subject {sub_name} Session {ses_name}',
fontsize='x-large',
)
fig.savefig(
output_fn,
dpi=160,
metadata={
'Author': 'Kaibo Tang',
'Creator': __file__
},
)
plt.close(fig)
return (
f'{index:02d}_{sub_name}_{ses_name}.pdf',
(lhp5 + rhp5) / 2,
(lhp95 + rhp95) / 2,
(lhw5 + rhw5) / 2,
(lhw95 + rhw95) / 2,
)