class TestMorhologySetsRotations(unittest.TestCase):
"""
Test scaffold with cells associated to a certain rotated morphology
"""
@classmethod
def setUpClass(self):
import dbbs_models
test_setup.prep_morphologies()
test_setup.prep_rotations()
super().setUpClass()
config = JSONConfig(config_file)
self.scaffold = Scaffold(config)
self.scaffold.morphology_repository = MorphologyRepository(test_setup.mr_rot_path)
def test_morphology_map(self):
# Create and place a set of 10 Golgi cells and assign them to a morphology based on their rotation
cell_type = self.scaffold.get_cell_type("golgi_cell")
positions = np.random.rand(9, 3)
# Construct rotation matrix for cell_type
phi_values = np.linspace(0.0, 360.0, num=3)
theta_values = np.linspace(0.0, 360.0, num=3)
phi_values = np.repeat(
phi_values, 3
) # np.random.choice(len(phi_values), len(positions))
theta_values = np.repeat(
theta_values, 3
) # np.random.choice(len(theta_values), len(positions))
rotations = np.vstack((phi_values, theta_values)).T
# Place cells and generate hdf5 output
self.scaffold.place_cells(
cell_type, cell_type.placement.layer_instance, positions, rotations
)
self.scaffold.compile_output()
ps = PlacementSet(self.scaffold.output_formatter, cell_type)
ms = MorphologySet(self.scaffold, cell_type, ps)
self.assertEqual(
len(rotations),
len(ms._morphology_index),
"Not all cells assigned to a morphology!",
)
random_sel = np.random.choice(len(ms._morphology_index))
morpho_sel = ms._morphology_map[ms._morphology_index[random_sel]]
self.assertTrue(
morpho_sel.find(
"__"
+ str(int(rotations[random_sel, 0]))
+ "_"
+ str(int(rotations[random_sel, 1]))
)
!= -1,
"Wrong morphology map!",
)
class TestPlacementSets(unittest.TestCase):
"""
Check if the scaffold can create a single cell type.
"""
@classmethod
def setUpClass(self):
super(TestPlacementSets, self).setUpClass()
test_setup.prep_morphologies()
config = JSONConfig(file=double_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
def test_hdf5_structure(self):
with h5py.File(self.scaffold.output_formatter.file, "r") as h:
for key in ["from", "to"]:
group = h["cells/placement/" + key + "_cell"]
self.assertTrue(
"identifiers" in group,
"Identifiers dataset missing for the " + key + "_cell",
)
self.assertTrue(
"positions" in group,
"Positions dataset missing for the " + key + "_cell",
)
self.assertEqual(
group["positions"].shape,
(4, 3),
"Incorrect position dataset size for the " + key + "_cell",
)
self.assertTrue(
group["positions"].dtype == np.float64,
"Incorrect position dataset dtype ({}) for the ".format(
group["positions"].dtype) + key + "_cell",
)
self.assertEqual(
group["identifiers"].shape,
(2, ),
"Incorrect or noncontinuous identifiers dataset size for the "
+ key + "_cell",
)
self.assertTrue(
group["identifiers"].dtype == np.int32,
"Incorrect identifiers dataset dtype ({}) for the ".format(
group["identifiers"].dtype) + key + "_cell",
)
def test_placement_set_properties(self):
for key in ["from", "to"]:
cell_type = self.scaffold.get_cell_type(key + "_cell")
ps = PlacementSet(self.scaffold.output_formatter, cell_type)
self.assertEqual(
ps.identifiers.shape,
(4, ),
"Incorrect identifiers shape for " + key + "_cell",
)
self.assertEqual(
ps.positions.shape,
(4, 3),
"Incorrect positions shape for " + key + "_cell",
)
self.assertRaises(DatasetNotFoundError, lambda: ps.rotations)
self.assertEqual(type(ps.cells[0]), Cell,
"PlacementSet.cells did not return Cells")
self.assertEqual(
ps.cells[1].id,
1 if key == "from" else 5,
"PlacementSet.cells identifiers incorrect",
)
self.assertEqual(
ps.cells[1].position.shape,
(3, ),
"PlacementSet.cells positions wrong shape",
)