def test_save_maxproj(self):
fn = 'data/test_data/test_stack.tif'
img = ImageStack(filename=fn, load=False)
img.data = np.zeros([10, 100, 100])
img.data[2:7, 10:-10, 10:-10] = 50
img.save_max_projection(filename=fn)
self.assertEqual(os.path.exists(fn), True)
shutil.rmtree('data/test_data/')
def test_load_and_save(self):
fn = 'data/test_data/test_stack.tif'
img = ImageStack(filename=fn, load=False)
img.data = np.ones([10, 100, 100])
img.save(filename=fn)
self.assertEqual(os.path.exists(fn), True)
img = ImageStack(filename=fn)
self.assertIsInstance(img.data, np.ndarray)
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_transforms(self):
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.to_spherical()
x, y, z = tr.spherical_to_cart(surf.R, surf.theta, surf.phi)
self.assertAlmostEqual(np.sum(np.abs(surf.x - x)), 0, 7)
self.assertAlmostEqual(np.sum(np.abs(surf.y - y)), 0, 7)
self.assertAlmostEqual(np.sum(np.abs(surf.z - z)), 0, 7)
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/')
def test_read_surface_and_save_as_stack(self):
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')
for coord in ['x', 'y', 'z']:
self.assertIsNotNone(surf.__dict__[coord])
surf.save_as_stack(filename='data/test_data/stack.tif', voxel_size=0.5)
self.assertEqual(os.path.exists('data/test_data/stack.tif'), True)
self.assertEqual(os.path.exists('data/test_data/stack.txt'), True)
shutil.rmtree('data/test_data/')
def test_extract_surfaces(self):
fn = 'data/test_data/test_stack.tif'
img = ImageStack(filename=fn, load=False)
img.data = np.zeros([10, 100, 100])
img.data[2:7, 10:-10, 10:-10] = 50
voxel_size = [4, 0.3824, 0.3824]
img.extract_surfaces('data/test_data/surfaces/',
voxel_size=voxel_size,
reconstruct=False)
img.extract_surfaces('data/test_data/surfaces_reconstructed/',
voxel_size=voxel_size,
reconstruct=True)
files = os.listdir('data/test_data/surfaces_reconstructed/')
self.assertEqual(len(files), 1)
files = os.listdir('data/test_data/surfaces/')
self.assertEqual(len(files), 1)
shutil.rmtree('data/test_data/')