import datetime
import pytest
from freesurfer_surface import setlocale, Vertex, Triangle, _LineSegment, \
Annotation, Surface
from conftest import ANNOTATION_FILE_PATH, SURFACE_FILE_PATH
def test_read_triangular():
surface = Surface.read_triangular(SURFACE_FILE_PATH)
assert surface.creator == b'fabianpeter'
assert surface.creation_datetime \
== datetime.datetime(2019, 5, 9, 22, 37, 41)
assert len(surface.vertices) == 155622
assert len(surface.triangles) == 311240
assert not surface.using_old_real_ras
assert surface.volume_geometry_info == (
b'valid = 1 # volume info valid\n',
b'filename = ../mri/filled-pretess255.mgz\n',
b'volume = 256 256 256\n',
b'voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00\n',
b'xras = -1.000000000000000e+00 0.000000000000000e+00 1.862645149230957e-09\n',
b'yras = 0.000000000000000e+00 -6.655682227574289e-09 -1.000000000000000e+00\n',
b'zras = 0.000000000000000e+00 1.000000000000000e+00 -8.300048648379743e-09\n',
b'cras = -2.773597717285156e+00 1.566547393798828e+01 -7.504364013671875e+00\n')
assert surface.command_lines == [
b'mris_remove_intersection ../surf/lh.orig ../surf/lh.orig'
b' ProgramVersion: $Name: stable6 $'
b' TimeStamp: 2019/05/09-17:42:36-GMT'
b' BuildTimeStamp: Jan 18 2017 16:38:58'
b' CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $'
b' User: fabianpeter'
b' Machine: host12345'
b' Platform: Linux'
b' PlatformVersion: 4.15.0-46-generic'
b' CompilerName: GCC'
b' CompilerVersion: 40400'
b' ',
b'mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc'
b' -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs'
b' fabian20190509 lh ProgramVersion: $Name: $'
b' TimeStamp: 2019/05/09-20:27:28-GMT'
b' BuildTimeStamp: Jan 18 2017 16:38:58'
b' CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $'
b' User: fabianpeter'
b' Machine: host12345'
b' Platform: Linux'
b' PlatformVersion: 4.15.0-46-generic'
b' CompilerName: GCC'
b' CompilerVersion: 40400'
b' ']
def test_read_triangular_locale():
with setlocale('de_AT.utf8'):
surface = Surface.read_triangular(SURFACE_FILE_PATH)
assert surface.creation_datetime \
== datetime.datetime(2019, 5, 9, 22, 37, 41)
@pytest.mark.parametrize(('creation_datetime', 'expected_str'), [
(datetime.datetime(2019, 5, 9, 22, 37, 41), b'Thu May 9 22:37:41 2019'),
(datetime.datetime(2019, 4, 24, 23, 29, 22), b'Wed Apr 24 23:29:22 2019'),
])
def test_triangular_strftime(creation_datetime, expected_str):
# pylint: disable=protected-access
assert expected_str == Surface._triangular_strftime(creation_datetime)
def test_read_write_triangular_same(tmpdir):
surface = Surface.read_triangular(SURFACE_FILE_PATH)
output_path = tmpdir.join('surface')
surface.write_triangular(output_path,
creation_datetime=surface.creation_datetime)
with open(output_path, 'rb') as output_file:
with open(SURFACE_FILE_PATH, 'rb') as expected_file:
assert expected_file.read() == output_file.read()
def test_read_write_datetime(tmpdir):
surface = Surface.read_triangular(SURFACE_FILE_PATH)
original_creation_datetime = surface.creation_datetime
output_path = tmpdir.join('surface')
surface.write_triangular(output_path)
assert original_creation_datetime == surface.creation_datetime
new_surface = Surface.read_triangular(output_path)
assert new_surface.creation_datetime > original_creation_datetime
assert datetime.datetime.now() > new_surface.creation_datetime
assert (datetime.datetime.now() - new_surface.creation_datetime) \
< datetime.timedelta(seconds=20)
def test_write_read_triangular_same(tmpdir):
expected_surface = Surface()
expected_surface.creator = b'pytest'
expected_surface.creation_datetime = datetime.datetime.now().replace(microsecond=0)
expected_surface.vertices = [Vertex(0.0, 0.0, 0.0),
Vertex(1.0, 2.0, 3.0),
Vertex(2.0, 4.0, 6.0),
Vertex(3.0, 5.0, 7.0)]
expected_surface.triangles = [Triangle((0, 1, 2)),
Triangle((0, 1, 3)),
Triangle((3, 2, 1))]
expected_surface.using_old_real_ras = False
expected_surface.volume_geometry_info = tuple(b'?\n' for _ in range(8))
expected_surface.command_lines = [b'?', b'!']
output_path = tmpdir.join('surface')
expected_surface.write_triangular(output_path,
creation_datetime=expected_surface.creation_datetime)
resulted_surface = Surface.read_triangular(output_path)
assert vars(expected_surface) == vars(resulted_surface)
def test_write_triangular_same_locale(tmpdir):
surface = Surface()
surface.creator = b'pytest'
surface.volume_geometry_info = tuple(b'?' for _ in range(8))
creation_datetime = datetime.datetime(2018, 12, 31, 21, 42)
output_path = tmpdir.join('surface')
with setlocale('de_AT.utf8'):
surface.write_triangular(output_path,
creation_datetime=creation_datetime)
resulted_surface = Surface.read_triangular(output_path)
assert resulted_surface.creation_datetime == creation_datetime
with open(output_path, 'rb') as output_file:
assert output_file.read().split(b' on ')[1] \
.startswith(b'Mon Dec 31 21:42:00 2018\n')
def test_load_annotation():
surface = Surface.read_triangular(SURFACE_FILE_PATH)
assert not surface.annotation
surface.load_annotation_file(ANNOTATION_FILE_PATH)
assert isinstance(surface.annotation, Annotation)
assert len(surface.annotation.vertex_label_index) == 155622
assert surface.annotation.vertex_label_index[0] == 5
def test_add_vertex():
surface = Surface()
assert not surface.vertices
assert surface.add_vertex(Vertex(1.0, 1.5, 2.0)) == 0
assert len(surface.vertices) == 1
assert surface.vertices[0].anterior == pytest.approx(1.5)
assert surface.add_vertex(Vertex(-3.0, 0.0, 4.0)) == 1
assert len(surface.vertices) == 2
assert surface.vertices[1].right == pytest.approx(-3.0)
@pytest.mark.parametrize(('vertices_coords', 'expected_extra_vertex_coords'), [
(((0, 0, 0), (2, 4, 0), (2, 4, 3)), (0, 0, 3)),
(((1, 1, 0), (3, 5, 0), (3, 5, 3)), (1, 1, 3)),
(((1, 1, 7), (3, 5, 7), (3, 5, 3)), (1, 1, 3)),
(((1, 1, 1), (3, 5, 7), (3, 5, 9)), (1, 1, 3)),
(((3, 5, 7), (1, 1, 1), (1, 1, 3)), (3, 5, 9)),
])
def test_add_rectangle(vertices_coords, expected_extra_vertex_coords):
surface = Surface()
for vertex_coords in vertices_coords:
surface.add_vertex(Vertex(*(float(c) for c in vertex_coords)))
surface.add_rectangle(range(3))
assert tuple(surface.vertices[3]) \
== pytest.approx(expected_extra_vertex_coords)
assert len(surface.triangles) == 2
assert surface.triangles[0].vertex_indices == (0, 1, 2)
assert surface.triangles[1].vertex_indices == (2, 3, 0)
def test__find_label_border_segments():
surface = Surface.read_triangular(SURFACE_FILE_PATH)
surface.load_annotation_file(ANNOTATION_FILE_PATH)
precentral_label, = filter(lambda l: l.name == 'precentral',
surface.annotation.labels.values())
# pylint: disable=protected-access
border_segments = set(
surface._find_label_border_segments(precentral_label))
assert len(border_segments) == 417
assert _LineSegment((33450, 32065)) in border_segments
assert _LineSegment((33454, 33450)) in border_segments
for border_vertex_index in [33450, 33454, 32065]:
assert surface.annotation.vertex_label_index[border_vertex_index] == precentral_label.index
for other_vertex_index in [32064, 33449, 33455, 33449, 33455]:
assert _LineSegment((other_vertex_index, border_vertex_index)) \
not in border_segments
assert _LineSegment((border_vertex_index, other_vertex_index)) \
not in border_segments
def test_find_label_border_polygonal_chains():
surface = Surface.read_triangular(SURFACE_FILE_PATH)
surface.load_annotation_file(ANNOTATION_FILE_PATH)
precentral_label, = filter(lambda l: l.name == 'precentral',
surface.annotation.labels.values())
border_chain, = surface.find_label_border_polygonal_chains(precentral_label)
vertex_indices = list(border_chain.vertex_indices)
assert len(vertex_indices) == 418
min_index = vertex_indices.index(min(vertex_indices))
vertex_indices_normalized = vertex_indices[min_index:] + vertex_indices[:min_index]
assert vertex_indices_normalized[:4] == [32065, 32072, 32073, 32080]
assert vertex_indices_normalized[-4:] == [36281, 34870, 33454, 33450]