def load_segmentation(filename: str) -> Segmentation:
"""Loads a segmentation from a FreeSurfer annot file.
Loads the a segmentation from a FreeSurfer annotation file. Because annot
files do not have a segmentation name, the file name is used instead.
Args:
filename: The name of the annot file that is loaded.
Returns:
segmentation: A segmentation whose name is `filename`.
"""
keys, ctab, names = nibfs.read_annot(filename)
segmentation = Segmentation(os.path.basename(filename), keys)
def rgbt2rgba(color):
return color[0], color[1], color[2], 255
# Add the label names.
for i, (color, name) in enumerate(zip(ctab, names)):
segmentation.add_label(i, Label(name.decode(), rgbt2rgba(color[:4])))
return segmentation
def test_segmentation_save_load(self):
"""Test saving a loading segmentations."""
segmentation = Segmentation('test', [0, 0, 1, 1, 2, 2, 3, 3])
segmentation.add_label(0, Label('unknown'))
segmentation.add_label(1, Label('red', (1, 0, 0, 1)))
segmentation.add_label(2, Label('green', (0, 1, 0, 1)))
segmentation.add_label(3, Label('blue', (0, 0, 1, 1)))
# Work in a temporary directory. This guarantees cleanup even on error.
with tempfile.TemporaryDirectory() as directory:
# Save the mesh and reload it.
filename = os.path.join(directory, 'segmentation.gii')
nimesh.io.gifti.save_segmentation(filename, segmentation)
loaded = nimesh.io.gifti.load_segmentation(filename)
# The loaded data should match the saved data.
np.testing.assert_array_almost_equal(segmentation.keys,
loaded.keys)
# Verify that the labels where loaded correctly.
self.assertEqual(len(loaded.labels), 4)
self.assertEqual(loaded.labels[0].name, 'unknown')
self.assertTupleEqual(loaded.labels[0].color, (0, 0, 0, 0))
self.assertEqual(loaded.labels[1].name, 'red')
self.assertTupleEqual(loaded.labels[1].color, (1, 0, 0, 1))
self.assertEqual(loaded.labels[2].name, 'green')
self.assertTupleEqual(loaded.labels[2].color, (0, 1, 0, 1))
self.assertEqual(loaded.labels[3].name, 'blue')
self.assertTupleEqual(loaded.labels[3].color, (0, 0, 1, 1))
def test_mesh_segmentation_save_load(self):
"""Test saving a mesh with a segmentation."""
mesh = minimal_mesh()
# Add a segmentation.
segmentation = Segmentation('seg', [0, 0, 1, 1])
mesh.add_segmentation(segmentation)
# Work in a temporary directory. This guarantees cleanup even on error.
with tempfile.TemporaryDirectory() as directory:
# Save the mesh and reload it.
filename = os.path.join(directory, 'mesh-segmentation.gii')
nimesh.io.save(filename, mesh)
loaded = nimesh.io.load(filename)
# The coordinate system should not have changed.
self.assertEqual(mesh.coordinate_system, loaded.coordinate_system)
# The loaded data should match the saved data. Because there is no
# data manipulation, this should be bit perfect.
np.testing.assert_array_equal(mesh.vertices, loaded.vertices)
np.testing.assert_array_equal(mesh.triangles, loaded.triangles)
# The segmentation should be present.
self.assertEqual(len(loaded.segmentations), 1)
loaded_segmentation = loaded.segmentations[0]
self.assertEqual(loaded_segmentation.name, segmentation.name)
np.testing.assert_array_almost_equal(loaded_segmentation.keys,
segmentation.keys)
def _get_segmentation_from_gii(gii) -> Segmentation:
"""Creates a segmentation from a nibabel GIfTI object.
Creates a new segmentation from the data array of a nibabel GIfTI
object. If none of the data arrays have an intent of NIFTI_INTENT_LABEL,
None is returned.
Args:
gii: The nibabel GIfTI object from which to create the segmentation.
Returns:
segmentation: The loaded segmentation or None.
"""
# Get the labels array. If there is more than one, warn the user and
# use the first one.
label_arrays = gii.get_arrays_from_intent('NIFTI_INTENT_LABEL')
if len(label_arrays) == 0:
return None
elif len(label_arrays) > 1:
warnings.warn(
'The file contains more than one label array. The '
'first one was used. Proceed with caution.', RuntimeWarning)
label_array = label_arrays[0]
labels = label_array.data
# If a segmentation name was not saved, tell the user and give it a name.
if 'name' in label_array.metadata:
name = label_array.metadata['name']
else:
warnings.warn('The name of the segmentation was not saved. Naming '
'it as "unknown".')
name = 'unknown'
segmentation = Segmentation(name, labels)
# Add the labels.
for label in gii.labeltable.labels:
# Convert the color back to integers.
color = np.round(np.array(label.rgba) * 255).astype(int)
segmentation.add_label(label.key, Label(label.label, color))
return segmentation
def test_segmentation_save_load(self):
"""Test saving and loading a segmentation."""
segmentation = Segmentation('test.annot', [1, 1, 2, 2])
segmentation.add_label(0, Label('no label', (0, 0, 0, 255)))
segmentation.add_label(1, Label('label 0', (255, 0, 0, 255)))
segmentation.add_label(2, Label('label 1', (0, 255, 0, 255)))
# Work in a temporary directory. This guarantees cleanup even on error.
with tempfile.TemporaryDirectory() as directory:
# Save and reload the test data.
filename = os.path.join(directory, segmentation.name)
nimesh.io.freesurfer.save_segmentation(filename, segmentation)
loaded = nimesh.io.freesurfer.load_segmentation(filename)
np.testing.assert_array_almost_equal(segmentation.keys,
loaded.keys)
self.assertEqual(segmentation.name, loaded.name)
# The labels should also match.
items = zip(segmentation.labels.items(), loaded.labels.items())
for (k1, l1), (k2, l2) in items:
self.assertEqual(k1, k2)
self.assertEqual(l1.color, l2.color)
def test_segmentation_fail_on_duplicate_color(self):
"""Test that meshes with duplicate colors cannot be saved."""
segmentation = Segmentation('test.annot', [1, 1, 2, 2])
segmentation.add_label(0, Label('no label', (0, 0, 0, 255)))
segmentation.add_label(1, Label('label 0', (255, 0, 0, 255)))
segmentation.add_label(2, Label('label 1', (0, 255, 0, 255)))
segmentation.add_label(3, Label('label 2', (0, 255, 0, 255)))
# Segmentation with identical colors cannot be saved.
with tempfile.TemporaryDirectory() as directory:
filename = os.path.join(directory, segmentation.name)
self.assertRaises(ValueError,
nimesh.io.freesurfer.save_segmentation, filename,
segmentation)
def test_repr(self):
"""Test the __repr__ method"""
segmentation = Segmentation('my-seg', [0, 0, 1, 2])
expected_str = 'Segmentation(name=my-seg, keys=[0 0 1 2])'
self.assertEqual(expected_str, repr(segmentation))
def test_str(self):
"""Test the __str__ method"""
segmentation = Segmentation('my-seg', [0, 0, 1, 2])
self.assertEqual('my-seg', str(segmentation))