def main():
import os,sys
import glob
import json
import numpy as np
import matplotlib
matplotlib.use('Agg')
import os
import json
import numpy as np
import nibabel as nib
os.environ['ETS_TOOLKIT'] = 'qt4'
os.environ['QT_API'] = 'pyqt5'
import pyvista
from pyvista.utilities import xvfb
pyvista.OFF_SCREEN=True
xvfb.start_xvfb()
from mne.viz import set_3d_backend
set_3d_backend('pyvista')
# grab config
with open('config.json','r') as config_f:
config = json.load(config_f)
# set up paths and variables
freesurfer='./output'
cortexmap='./cortexmap'
colormap = config['colormap']
min_percentile = config['min_percentile']
max_percentile = config['max_percentile']
threshold = np.float(config['threshold'])
measureFiles = np.unique([ f.split('h.')[1] for f in os.listdir('./'+cortexmap+'/func') if f.split('h.')[1] != 'goodvertex.func.gii' ])
surface = config['surface']
hemi=["lh","rh"]
#### set up other inputs ####
# set outdir
outdir = 'images'
# generate output directory if not already there
if os.path.isdir(outdir):
print("directory exits")
else:
print("making output directory")
os.mkdir(outdir)
for h in hemi:
for i in measureFiles:
print('generating image for %s.%s' %(h,i))
if surface == 'midthickness':
generateMeasureOverlayImage(freesurfer,h,'midthickness.very_inflated',i,colormap,min_percentile,max_percentile,threshold,outdir,'cortexmap')
else:
generateMeasureOverlayImage(freesurfer,h,surface,i,colormap,min_percentile,max_percentile,threshold,outdir,'cortexmap')
def test_viz():
Lx = 1.0
Ly = 0.1
_nel = 30
gmsh_model, tdim = mesh_bar_gmshapi("bar", Lx, Ly, 1/_nel, 2)
mesh, mts = gmsh_model_to_mesh(
gmsh_model, cell_data=False, facet_data=True, gdim=2)
element_u = ufl.VectorElement("Lagrange", mesh.ufl_cell(), degree=1, dim=2)
V_u = dolfinx.fem.FunctionSpace(mesh, element_u)
element_alpha = ufl.FiniteElement("Lagrange", mesh.ufl_cell(), degree=1)
V_alpha = dolfinx.fem.FunctionSpace(mesh, element_alpha)
def scal_2D(x):
return np.sin(np.pi * x[0] * 3.0)
def vect_2D(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = np.sin(x[1])
vals[1] = 0.1 * x[0]
return vals
# Define the state
u = Function(V_u, name="Displacement")
u.interpolate(vect_2D)
alpha = Function(V_alpha, name="Damage")
alpha.interpolate(scal_2D)
xvfb.start_xvfb(wait=0.05)
pyvista.OFF_SCREEN = True
plotter = pyvista.Plotter(
title="Test Viz",
window_size=[1600, 600],
shape=(1, 2),
)
_plt = plot_scalar(alpha, plotter, subplot=(0, 0))
logging.critical('plotted scalar')
_plt = plot_vector(u, plotter, subplot=(0, 1))
logging.critical('plotted vector')
_plt.screenshot(f"./output/test_viz/test_viz_MPI{comm.size}-.png")
if not pyvista.OFF_SCREEN:
plotter.show()
from pathlib import Path
import dolfinx.plot
gmsh_model, tdim = mesh_bar_gmshapi("bar",
1,
0.1,
0.01,
2,
msh_file="output/bar.msh")
mesh, mts = gmsh_to_dolfin(gmsh_model, tdim, prune_z=True)
Path("output").mkdir(parents=True, exist_ok=True)
with XDMFFile(MPI.COMM_WORLD, "output/bar.xdmf", "w") as ofile:
ofile.write_mesh_meshtags(mesh, mts)
import pyvista
from pyvista.utilities import xvfb
xvfb.start_xvfb(wait=0.05)
pyvista.OFF_SCREEN = True
plotter = pyvista.Plotter(title="Bar mesh")
topology, cell_types = dolfinx.plot.create_vtk_topology(
mesh, mesh.topology.dim)
grid = pyvista.UnstructuredGrid(topology, cell_types, mesh.geometry.x)
# plotter.subplot(0, 0)
actor_1 = plotter.add_mesh(grid, show_edges=True)
plotter.view_xy()
if not pyvista.OFF_SCREEN:
plotter.show()
figure = plotter.screenshot("output/bar.png")
import dolfinx.plot
import numpy as np
import ufl
from mpi4py import MPI
try:
import pyvista
except ModuleNotFoundError:
print("pyvista is required for this demo")
exit(0)
# If environment variable PYVISTA_OFF_SCREEN is set to true save a png
# otherwise create interactive plot
if pyvista.OFF_SCREEN:
from pyvista.utilities.xvfb import start_xvfb
start_xvfb(wait=0.1)
# Set some global options for all plots
transparent = False
figsize = 800
pyvista.rcParams["background"] = [0.5, 0.5, 0.5]
# Plotting a 3D dolfinx.Function with pyvista
# ===========================================
# Interpolate a simple scalar function in 3D
def int_u(x):
return x[0] + 3 * x[1] + 5 * x[2]
# Save solution in XDMF format
with XDMFFile(MPI.COMM_WORLD, "poisson.xdmf", "w") as file:
file.write_mesh(mesh)
file.write_function(uh)
# Update ghost entries and plot
uh.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT,
mode=PETSc.ScatterMode.FORWARD)
try:
import pyvista
topology, cell_types = plot.create_vtk_topology(mesh, mesh.topology.dim)
grid = pyvista.UnstructuredGrid(topology, cell_types, mesh.geometry.x)
grid.point_arrays["u"] = uh.compute_point_values().real
grid.set_active_scalars("u")
plotter = pyvista.Plotter()
plotter.add_mesh(grid, show_edges=True)
warped = grid.warp_by_scalar()
plotter.add_mesh(warped)
# If pyvista environment variable is set to off-screen (static) plotting save png
if pyvista.OFF_SCREEN:
from pyvista.utilities.xvfb import start_xvfb
start_xvfb(wait=0)
plotter.screenshot("uh.png")
else:
plotter.show()
except ModuleNotFoundError:
print("pyvista is required to visualise the solution")