def plot_3D_surfaces(inputfolder, outputfolder, points=True, gridsize=100):
"""
Plot 3D views of surfaces located in a given directory.
Parameters
----------
inputfolder : str
Input directory with surfaces.
outputfolder : str
Output directory to save the plots.
points : bool, optional
If True, surface points will be displayed.
Default is True.
gridsize : int, optional
Dimension of the square grid to interpolate the surface points.
Default is 100.
"""
files = filelib.list_subfolders(inputfolder, extensions=['csv'])
for fn in files:
s = Surface(filename=inputfolder + fn)
s.centrate()
s.to_spherical()
s.Rgrid = s.interpolate(grid_size=gridsize)
mesh = s.plot_surface(points=points)
mesh.magnification = 3
filelib.make_folders([os.path.dirname(outputfolder + fn[:-4])])
mesh.save(outputfolder + fn[:-4] + '.png', size=(200, 200))
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/')
def test_interpolate(self, grid_size):
img = ImageStack(filename='', load=False)
img.data = np.zeros([10, 100, 100])
img.data[2:7, 10:-10, 10:-10] = 1
voxel_size = [4, 0.3824, 0.3824]
img.extract_surfaces('data/test_data/surfaces/',
voxel_size=voxel_size,
reconstruct=False)
surf = Surface(filename='data/test_data/surfaces/_Cell00001.csv')
surf.centrate()
surf.to_spherical()
grid = surf.interpolate(grid_size=grid_size)
self.assertEqual(len(grid), grid_size)
shutil.rmtree('data/test_data/')
def test_spharm_transform(self):
img = ImageStack(filename='', load=False)
img.data = np.zeros([100, 100, 100])
img.data[48:52, 48:52, 48:52] = 1.
voxel_size = 0.3
img.extract_surfaces('data/test_data/surfaces/',
voxel_size=voxel_size,
reconstruct=True)
surf = Surface(filename='data/test_data/surfaces/_Cell00001.csv')
surf.centrate()
surf.to_spherical()
grid = surf.interpolate(grid_size=10)
surf.compute_spharm(grid_size=10)
ngrid = surf.inverse_spharm()
self.assertAlmostEqual(np.mean(np.abs(ngrid - grid)), 0, 1)
shutil.rmtree('data/test_data/')