import datetime import numpy 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').strpath 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').strpath 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').strpath expected_surface.write_triangular(output_path, creation_datetime=expected_surface.creation_datetime) resulted_surface = Surface.read_triangular(output_path) assert numpy.array_equal(expected_surface.vertices, resulted_surface.vertices) expected_surface.vertices = resulted_surface.vertices = [] 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').strpath 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', [ ((0, 0, 0), (2, 4, 0), (2, 4, 3)), ((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, 7), (1, 1, 1), (1, 1, 3), (3, 5, 9)), ]) def test_add_rectangle(vertices_coords): surface = Surface() for vertex_coords in vertices_coords: surface.add_vertex(Vertex(*(float(c) for c in vertex_coords))) surface.add_rectangle(range(len(vertices_coords))) assert len(surface.vertices) == 4 assert len(surface.triangles) == 2 assert surface.triangles[0].vertex_indices == (0, 1, 2) assert surface.triangles[1].vertex_indices == (2, 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_3(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) def test__get_vertex_label_index(): surface = Surface.read_triangular(SURFACE_FILE_PATH) surface.load_annotation_file(ANNOTATION_FILE_PATH) # pylint: disable=protected-access assert surface._get_vertex_label_index(64290) == 22 assert surface._get_vertex_label_index(72160) == 22 assert surface._get_vertex_label_index(84028) == 24 assert surface._get_vertex_label_index(97356) == 24 assert surface._get_vertex_label_index(123173) == 27 assert surface._get_vertex_label_index(140727) == 27 assert surface._get_vertex_label_index(93859) == 28 assert surface._get_vertex_label_index(78572) == 0 assert surface._get_vertex_label_index(120377) == 0 vertex_index = surface.add_vertex(Vertex(0.0, 21.0, 42.0)) assert surface._get_vertex_label_index(vertex_index) is None del surface.annotation.vertex_label_index[140727] assert surface._get_vertex_label_index(140727) is None 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_segments_incomplete_annotation(): 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 assert surface._find_label_border_segments(precentral_label) surface.triangles.append(Triangle([ surface.add_vertex(Vertex(0.0, 21.0 * factor, 42.0 * factor)) for factor in range(3) ])) border_segments = set( surface._find_label_border_segments(precentral_label)) assert len(border_segments) == 417 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]