def test05_plot(self):
path = site.getsitepackages()[0] + '/SPHARM/tests/'
fn = path + 'data/synthetic_cell.txt'
surf = Surface(filename=fn)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mesh = surf.plot_points()
os.makedirs('data/test_data')
mesh.save('data/test_data/points_3D.png', size=(200, 200))
surf.centrate()
surf.to_spherical()
surf.Rgrid = surf.interpolate(grid_size=100)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mesh = surf.plot_surface(points=False)
mesh.save('data/test_data/surface_3D.png', size=(200, 200))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mesh = surf.plot_surface(points=True)
mesh.save('data/test_data/surface_with_points_3D.png',
size=(200, 200))
self.assertEqual(os.path.exists('data/test_data/surface_3D.png'), True)
self.assertEqual(os.path.exists('data/test_data/points_3D.png'), True)
self.assertEqual(
os.path.exists('data/test_data/surface_with_points_3D.png'), True)
shutil.rmtree('data/test_data/')
path += '/'
path += 'output/'
track_stat = pd.DataFrame()
summary_stat = pd.DataFrame()
groups = os.listdir(path + 'surfaces/')
for gr in groups:
print(gr)
files = os.listdir(path + 'surfaces/' + gr + '/')
for fn in files:
stat = pd.read_csv(path + 'surfaces/' + gr + '/' + fn, sep='\t', index_col=0)
t1 = stat['Time'].unique()[0]
stat = stat[stat['Time'] == t1]
print(fn, len(stat))
surface = Surface(data=stat)
mesh = surface.plot_points(scale_factor=0.2)
filelib.make_folders([os.path.dirname(path + 'surface_plots/' + gr + '_' + fn[:-4])])
mesh.save(path + 'surface_plots/' + gr + '_' + fn[:-4] + '_init.png', size=(100, 100))
mlab.clf()
surface.centrate()
surface.to_spherical()
surface.compute_spharm(grid_size=120, normalize=True)
mesh = surface.plot_surface(points=False)
filelib.make_folders([os.path.dirname(path + 'surface_plots/' + gr + '_' + fn[:-4])])
mesh.save(path + 'surface_plots/' + gr + '_' + fn[:-4] + '_grid.png', size=(100, 100))
mlab.clf()
surface.inverse_spharm(lmax=10)
mesh = surface.plot_surface(points=False)
filelib.make_folders([os.path.dirname(path + 'surface_plots/' + gr + '_' + fn[:-4])])