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@@ -5,68 +5,78 @@ import numpy
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import pytest
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from conftest import ANNOTATION_FILE_PATH, SURFACE_FILE_PATH
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-from freesurfer_surface import (Annotation, LineSegment, PolygonalCircuit,
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- Surface, Triangle, Vertex, setlocale)
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+from freesurfer_surface import (
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+ Annotation,
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+ LineSegment,
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+ PolygonalCircuit,
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+ Surface,
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+ Triangle,
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+ Vertex,
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+ setlocale,
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+)
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def test_read_triangular():
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surface = Surface.read_triangular(SURFACE_FILE_PATH)
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- assert surface.creator == b'fabianpeter'
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- assert surface.creation_datetime \
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- == datetime.datetime(2019, 5, 9, 22, 37, 41)
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+ assert surface.creator == b"fabianpeter"
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+ assert surface.creation_datetime == datetime.datetime(2019, 5, 9, 22, 37, 41)
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assert len(surface.vertices) == 155622
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assert len(surface.triangles) == 311240
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assert not surface.using_old_real_ras
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assert surface.volume_geometry_info == (
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- b'valid = 1 # volume info valid\n',
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- b'filename = ../mri/filled-pretess255.mgz\n',
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- b'volume = 256 256 256\n',
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- b'voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00\n',
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- b'xras = -1.000000000000000e+00 0.000000000000000e+00 1.862645149230957e-09\n',
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- b'yras = 0.000000000000000e+00 -6.655682227574289e-09 -1.000000000000000e+00\n',
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- b'zras = 0.000000000000000e+00 1.000000000000000e+00 -8.300048648379743e-09\n',
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- b'cras = -2.773597717285156e+00 1.566547393798828e+01 -7.504364013671875e+00\n')
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+ b"valid = 1 # volume info valid\n",
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+ b"filename = ../mri/filled-pretess255.mgz\n",
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+ b"volume = 256 256 256\n",
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+ b"voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00\n",
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+ b"xras = -1.000000000000000e+00 0.000000000000000e+00 1.862645149230957e-09\n",
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+ b"yras = 0.000000000000000e+00 -6.655682227574289e-09 -1.000000000000000e+00\n",
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+ b"zras = 0.000000000000000e+00 1.000000000000000e+00 -8.300048648379743e-09\n",
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+ b"cras = -2.773597717285156e+00 1.566547393798828e+01 -7.504364013671875e+00\n",
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+ )
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assert surface.command_lines == [
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- b'mris_remove_intersection ../surf/lh.orig ../surf/lh.orig'
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- b' ProgramVersion: $Name: stable6 $'
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- b' TimeStamp: 2019/05/09-17:42:36-GMT'
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- b' BuildTimeStamp: Jan 18 2017 16:38:58'
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- b' CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $'
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- b' User: fabianpeter'
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- b' Machine: host12345'
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- b' Platform: Linux'
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- b' PlatformVersion: 4.15.0-46-generic'
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- b' CompilerName: GCC'
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- b' CompilerVersion: 40400'
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- b' ',
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- b'mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc'
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- b' -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs'
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- b' fabian20190509 lh ProgramVersion: $Name: $'
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- b' TimeStamp: 2019/05/09-20:27:28-GMT'
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- b' BuildTimeStamp: Jan 18 2017 16:38:58'
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- b' CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $'
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- b' User: fabianpeter'
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- b' Machine: host12345'
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- b' Platform: Linux'
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- b' PlatformVersion: 4.15.0-46-generic'
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- b' CompilerName: GCC'
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- b' CompilerVersion: 40400'
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- b' ']
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+ b"mris_remove_intersection ../surf/lh.orig ../surf/lh.orig"
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+ b" ProgramVersion: $Name: stable6 $"
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+ b" TimeStamp: 2019/05/09-17:42:36-GMT"
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+ b" BuildTimeStamp: Jan 18 2017 16:38:58"
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+ b" CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $"
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+ b" User: fabianpeter"
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+ b" Machine: host12345"
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+ b" Platform: Linux"
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+ b" PlatformVersion: 4.15.0-46-generic"
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+ b" CompilerName: GCC"
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+ b" CompilerVersion: 40400"
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+ b" ",
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+ b"mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc"
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+ b" -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs"
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+ b" fabian20190509 lh ProgramVersion: $Name: $"
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+ b" TimeStamp: 2019/05/09-20:27:28-GMT"
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+ b" BuildTimeStamp: Jan 18 2017 16:38:58"
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+ b" CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $"
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+ b" User: fabianpeter"
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+ b" Machine: host12345"
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+ b" Platform: Linux"
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+ b" PlatformVersion: 4.15.0-46-generic"
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+ b" CompilerName: GCC"
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+ b" CompilerVersion: 40400"
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+ b" ",
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+ ]
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def test_read_triangular_locale():
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- with setlocale('de_AT.utf8'):
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+ with setlocale("de_AT.utf8"):
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surface = Surface.read_triangular(SURFACE_FILE_PATH)
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- assert surface.creation_datetime \
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- == datetime.datetime(2019, 5, 9, 22, 37, 41)
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+ assert surface.creation_datetime == datetime.datetime(2019, 5, 9, 22, 37, 41)
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-@pytest.mark.parametrize(('creation_datetime', 'expected_str'), [
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- (datetime.datetime(2019, 5, 9, 22, 37, 41), b'Thu May 9 22:37:41 2019'),
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- (datetime.datetime(2019, 4, 24, 23, 29, 22), b'Wed Apr 24 23:29:22 2019'),
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-])
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+@pytest.mark.parametrize(
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+ ("creation_datetime", "expected_str"),
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+ [
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+ (datetime.datetime(2019, 5, 9, 22, 37, 41), b"Thu May 9 22:37:41 2019"),
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+ (datetime.datetime(2019, 4, 24, 23, 29, 22), b"Wed Apr 24 23:29:22 2019"),
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+ ],
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+)
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def test_triangular_strftime(creation_datetime, expected_str):
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assert expected_str == Surface._triangular_strftime(creation_datetime)
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@@ -74,65 +84,71 @@ def test_triangular_strftime(creation_datetime, expected_str):
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def test_read_write_triangular_same(tmpdir):
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surface = Surface.read_triangular(SURFACE_FILE_PATH)
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- output_path = tmpdir.join('surface').strpath
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- surface.write_triangular(output_path,
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- creation_datetime=surface.creation_datetime)
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- with open(output_path, 'rb') as output_file:
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- with open(SURFACE_FILE_PATH, 'rb') as expected_file:
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+ output_path = tmpdir.join("surface").strpath
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+ surface.write_triangular(output_path, creation_datetime=surface.creation_datetime)
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+ with open(output_path, "rb") as output_file:
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+ with open(SURFACE_FILE_PATH, "rb") as expected_file:
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assert expected_file.read() == output_file.read()
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def test_read_write_datetime(tmpdir):
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surface = Surface.read_triangular(SURFACE_FILE_PATH)
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original_creation_datetime = surface.creation_datetime
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- output_path = tmpdir.join('surface').strpath
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+ output_path = tmpdir.join("surface").strpath
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surface.write_triangular(output_path)
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assert original_creation_datetime == surface.creation_datetime
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new_surface = Surface.read_triangular(output_path)
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assert new_surface.creation_datetime > original_creation_datetime
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assert datetime.datetime.now() > new_surface.creation_datetime
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- assert (datetime.datetime.now() - new_surface.creation_datetime) \
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- < datetime.timedelta(seconds=20)
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+ assert (
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+ datetime.datetime.now() - new_surface.creation_datetime
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+ ) < datetime.timedelta(seconds=20)
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def test_write_read_triangular_same(tmpdir):
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expected_surface = Surface()
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- expected_surface.creator = b'pytest'
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+ expected_surface.creator = b"pytest"
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expected_surface.creation_datetime = datetime.datetime.now().replace(microsecond=0)
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- expected_surface.vertices = [Vertex(0.0, 0.0, 0.0),
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- Vertex(1.0, 2.0, 3.0),
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- Vertex(2.0, 4.0, 6.0),
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- Vertex(3.0, 5.0, 7.0)]
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- expected_surface.triangles = [Triangle((0, 1, 2)),
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- Triangle((0, 1, 3)),
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- Triangle((3, 2, 1))]
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+ expected_surface.vertices = [
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+ Vertex(0.0, 0.0, 0.0),
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+ Vertex(1.0, 2.0, 3.0),
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+ Vertex(2.0, 4.0, 6.0),
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+ Vertex(3.0, 5.0, 7.0),
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+ ]
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+ expected_surface.triangles = [
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+ Triangle((0, 1, 2)),
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+ Triangle((0, 1, 3)),
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+ Triangle((3, 2, 1)),
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+ ]
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expected_surface.using_old_real_ras = False
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- expected_surface.volume_geometry_info = tuple(b'?\n' for _ in range(8))
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- expected_surface.command_lines = [b'?', b'!']
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- output_path = tmpdir.join('surface').strpath
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- expected_surface.write_triangular(output_path,
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- creation_datetime=expected_surface.creation_datetime)
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+ expected_surface.volume_geometry_info = tuple(b"?\n" for _ in range(8))
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+ expected_surface.command_lines = [b"?", b"!"]
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+ output_path = tmpdir.join("surface").strpath
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+ expected_surface.write_triangular(
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+ output_path, creation_datetime=expected_surface.creation_datetime
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+ )
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resulted_surface = Surface.read_triangular(output_path)
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- assert numpy.array_equal(expected_surface.vertices,
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- resulted_surface.vertices)
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+ assert numpy.array_equal(expected_surface.vertices, resulted_surface.vertices)
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expected_surface.vertices = resulted_surface.vertices = []
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assert vars(expected_surface) == vars(resulted_surface)
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def test_write_triangular_same_locale(tmpdir):
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surface = Surface()
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- surface.creator = b'pytest'
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- surface.volume_geometry_info = tuple(b'?' for _ in range(8))
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+ surface.creator = b"pytest"
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+ surface.volume_geometry_info = tuple(b"?" for _ in range(8))
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creation_datetime = datetime.datetime(2018, 12, 31, 21, 42)
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- output_path = tmpdir.join('surface').strpath
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- with setlocale('de_AT.utf8'):
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- surface.write_triangular(output_path,
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- creation_datetime=creation_datetime)
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+ output_path = tmpdir.join("surface").strpath
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+ with setlocale("de_AT.utf8"):
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+ surface.write_triangular(output_path, creation_datetime=creation_datetime)
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resulted_surface = Surface.read_triangular(output_path)
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assert resulted_surface.creation_datetime == creation_datetime
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- with open(output_path, 'rb') as output_file:
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- assert output_file.read().split(b' on ')[1] \
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- .startswith(b'Mon Dec 31 21:42:00 2018\n')
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+ with open(output_path, "rb") as output_file:
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+ assert (
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+ output_file.read()
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+ .split(b" on ")[1]
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+ .startswith(b"Mon Dec 31 21:42:00 2018\n")
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+ )
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def test_load_annotation():
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@@ -155,15 +171,18 @@ def test_add_vertex():
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assert surface.vertices[1].right == pytest.approx(-3.0)
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-@pytest.mark.parametrize('vertices_coords', [
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- ((0, 0, 0), (2, 4, 0), (2, 4, 3)),
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- ((0, 0, 0), (2, 4, 0), (2, 4, 3), (0, 0, 3)),
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- ((1, 1, 0), (3, 5, 0), (3, 5, 3), (1, 1, 3)),
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- ((1, 1, 7), (3, 5, 7), (3, 5, 3), (1, 1, 3)),
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- ((1, 1, 1), (3, 5, 7), (3, 5, 9), (1, 1, 3)),
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- ((3, 5, 7), (1, 1, 1), (1, 1, 3)),
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- ((3, 5, 7), (1, 1, 1), (1, 1, 3), (3, 5, 9)),
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-])
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+@pytest.mark.parametrize(
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+ "vertices_coords",
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+ [
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+ ((0, 0, 0), (2, 4, 0), (2, 4, 3)),
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+ ((0, 0, 0), (2, 4, 0), (2, 4, 3), (0, 0, 3)),
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+ ((1, 1, 0), (3, 5, 0), (3, 5, 3), (1, 1, 3)),
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+ ((1, 1, 7), (3, 5, 7), (3, 5, 3), (1, 1, 3)),
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+ ((1, 1, 1), (3, 5, 7), (3, 5, 9), (1, 1, 3)),
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+ ((3, 5, 7), (1, 1, 1), (1, 1, 3)),
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+ ((3, 5, 7), (1, 1, 1), (1, 1, 3), (3, 5, 9)),
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+ ],
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+)
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def test_add_rectangle(vertices_coords):
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surface = Surface()
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for vertex_coords in vertices_coords:
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@@ -175,20 +194,22 @@ def test_add_rectangle(vertices_coords):
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assert surface.triangles[1].vertex_indices == (2, 3, 0)
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-@pytest.mark.parametrize(('vertices_coords', 'expected_extra_vertex_coords'), [
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- (((0, 0, 0), (2, 4, 0), (2, 4, 3)), (0, 0, 3)),
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- (((1, 1, 0), (3, 5, 0), (3, 5, 3)), (1, 1, 3)),
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- (((1, 1, 7), (3, 5, 7), (3, 5, 3)), (1, 1, 3)),
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- (((1, 1, 1), (3, 5, 7), (3, 5, 9)), (1, 1, 3)),
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- (((3, 5, 7), (1, 1, 1), (1, 1, 3)), (3, 5, 9)),
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-])
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+@pytest.mark.parametrize(
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+ ("vertices_coords", "expected_extra_vertex_coords"),
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+ [
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+ (((0, 0, 0), (2, 4, 0), (2, 4, 3)), (0, 0, 3)),
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+ (((1, 1, 0), (3, 5, 0), (3, 5, 3)), (1, 1, 3)),
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+ (((1, 1, 7), (3, 5, 7), (3, 5, 3)), (1, 1, 3)),
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+ (((1, 1, 1), (3, 5, 7), (3, 5, 9)), (1, 1, 3)),
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+ (((3, 5, 7), (1, 1, 1), (1, 1, 3)), (3, 5, 9)),
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+ ],
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+)
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def test_add_rectangle_3(vertices_coords, expected_extra_vertex_coords):
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surface = Surface()
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for vertex_coords in vertices_coords:
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surface.add_vertex(Vertex(*(float(c) for c in vertex_coords)))
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surface.add_rectangle(range(3))
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- assert tuple(surface.vertices[3]) \
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- == pytest.approx(expected_extra_vertex_coords)
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+ assert tuple(surface.vertices[3]) == pytest.approx(expected_extra_vertex_coords)
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def test__triangle_count_by_adjacent_vertex_indices_empty():
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@@ -201,18 +222,19 @@ def test__triangle_count_by_adjacent_vertex_indices_none():
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surface.vertices.append(Vertex(1, 0, 0))
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surface.vertices.append(Vertex(2, 0, 0))
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surface.vertices.append(Vertex(3, 0, 0))
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- assert surface._triangle_count_by_adjacent_vertex_indices() \
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- == {0: {}, 1: {}, 2: {}}
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+ assert surface._triangle_count_by_adjacent_vertex_indices() == {0: {}, 1: {}, 2: {}}
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def test__triangle_count_by_adjacent_vertex_indices_single():
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surface = Surface()
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- surface.triangles.append(Triangle([surface.add_vertex(Vertex(i, 0, 0))
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- for i in range(3)]))
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- assert surface._triangle_count_by_adjacent_vertex_indices() \
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- == {0: {1: 1, 2: 1},
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- 1: {0: 1, 2: 1},
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- 2: {0: 1, 1: 1}}
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+ surface.triangles.append(
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+ Triangle([surface.add_vertex(Vertex(i, 0, 0)) for i in range(3)])
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+ )
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+ assert surface._triangle_count_by_adjacent_vertex_indices() == {
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+ 0: {1: 1, 2: 1},
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+ 1: {0: 1, 2: 1},
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+ 2: {0: 1, 1: 1},
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+ }
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def test__triangle_count_by_adjacent_vertex_indices_multiple():
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@@ -221,26 +243,29 @@ def test__triangle_count_by_adjacent_vertex_indices_multiple():
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surface.add_vertex(Vertex(i, 0, 0))
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surface.triangles.append(Triangle((0, 1, 2)))
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surface.triangles.append(Triangle((3, 1, 2)))
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- assert surface._triangle_count_by_adjacent_vertex_indices() \
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- == {0: {1: 1, 2: 1},
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- 1: {0: 1, 2: 2, 3: 1},
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- 2: {0: 1, 1: 2, 3: 1},
|
|
|
- 3: {1: 1, 2: 1},
|
|
|
- 4: {}}
|
|
|
+ assert surface._triangle_count_by_adjacent_vertex_indices() == {
|
|
|
+ 0: {1: 1, 2: 1},
|
|
|
+ 1: {0: 1, 2: 2, 3: 1},
|
|
|
+ 2: {0: 1, 1: 2, 3: 1},
|
|
|
+ 3: {1: 1, 2: 1},
|
|
|
+ 4: {},
|
|
|
+ }
|
|
|
surface.triangles.append(Triangle((3, 4, 2)))
|
|
|
- assert surface._triangle_count_by_adjacent_vertex_indices() \
|
|
|
- == {0: {1: 1, 2: 1},
|
|
|
- 1: {0: 1, 2: 2, 3: 1},
|
|
|
- 2: {0: 1, 1: 2, 3: 2, 4: 1},
|
|
|
- 3: {1: 1, 2: 2, 4: 1},
|
|
|
- 4: {2: 1, 3: 1}}
|
|
|
+ assert surface._triangle_count_by_adjacent_vertex_indices() == {
|
|
|
+ 0: {1: 1, 2: 1},
|
|
|
+ 1: {0: 1, 2: 2, 3: 1},
|
|
|
+ 2: {0: 1, 1: 2, 3: 2, 4: 1},
|
|
|
+ 3: {1: 1, 2: 2, 4: 1},
|
|
|
+ 4: {2: 1, 3: 1},
|
|
|
+ }
|
|
|
surface.triangles.append(Triangle((3, 0, 2)))
|
|
|
- assert surface._triangle_count_by_adjacent_vertex_indices() \
|
|
|
- == {0: {1: 1, 2: 2, 3: 1},
|
|
|
- 1: {0: 1, 2: 2, 3: 1},
|
|
|
- 2: {0: 2, 1: 2, 3: 3, 4: 1},
|
|
|
- 3: {0: 1, 1: 1, 2: 3, 4: 1},
|
|
|
- 4: {2: 1, 3: 1}}
|
|
|
+ assert surface._triangle_count_by_adjacent_vertex_indices() == {
|
|
|
+ 0: {1: 1, 2: 2, 3: 1},
|
|
|
+ 1: {0: 1, 2: 2, 3: 1},
|
|
|
+ 2: {0: 2, 1: 2, 3: 3, 4: 1},
|
|
|
+ 3: {0: 1, 1: 1, 2: 3, 4: 1},
|
|
|
+ 4: {2: 1, 3: 1},
|
|
|
+ }
|
|
|
|
|
|
|
|
|
def test__triangle_count_by_adjacent_vertex_indices_real():
|
|
|
@@ -248,12 +273,19 @@ def test__triangle_count_by_adjacent_vertex_indices_real():
|
|
|
counts = surface._triangle_count_by_adjacent_vertex_indices()
|
|
|
assert len(counts) == len(surface.vertices)
|
|
|
assert all(counts.values())
|
|
|
- assert all(count == 2
|
|
|
- for vertex_counts in counts.values()
|
|
|
- for count in vertex_counts.values())
|
|
|
- assert sum(count for vertex_counts in counts.values()
|
|
|
- for count in vertex_counts.values()) \
|
|
|
+ assert all(
|
|
|
+ count == 2
|
|
|
+ for vertex_counts in counts.values()
|
|
|
+ for count in vertex_counts.values()
|
|
|
+ )
|
|
|
+ assert (
|
|
|
+ sum(
|
|
|
+ count
|
|
|
+ for vertex_counts in counts.values()
|
|
|
+ for count in vertex_counts.values()
|
|
|
+ )
|
|
|
== len(surface.triangles) * 6
|
|
|
+ )
|
|
|
|
|
|
|
|
|
def test_find_borders_none():
|
|
|
@@ -271,8 +303,7 @@ def test_find_borders_single():
|
|
|
|
|
|
def test_find_borders_singles():
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
- single_indices = [surface.add_vertex(Vertex(i, 21, 42))
|
|
|
- for i in range(3)]
|
|
|
+ single_indices = [surface.add_vertex(Vertex(i, 21, 42)) for i in range(3)]
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 3
|
|
|
assert PolygonalCircuit((single_indices[0],)) in borders
|
|
|
@@ -282,8 +313,7 @@ def test_find_borders_singles():
|
|
|
|
|
|
def test_find_borders_single_triangle_simple():
|
|
|
surface = Surface()
|
|
|
- vertex_indices = [surface.add_vertex(Vertex(i, 21, 42))
|
|
|
- for i in range(3)]
|
|
|
+ vertex_indices = [surface.add_vertex(Vertex(i, 21, 42)) for i in range(3)]
|
|
|
surface.triangles.append(Triangle(vertex_indices))
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 1
|
|
|
@@ -292,8 +322,7 @@ def test_find_borders_single_triangle_simple():
|
|
|
|
|
|
def test_find_borders_single_triangle_real():
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
- vertex_indices = [surface.add_vertex(Vertex(i, 21, 42))
|
|
|
- for i in range(3)]
|
|
|
+ vertex_indices = [surface.add_vertex(Vertex(i, 21, 42)) for i in range(3)]
|
|
|
surface.triangles.append(Triangle(vertex_indices))
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 1
|
|
|
@@ -310,8 +339,7 @@ def test_find_borders_remove_triangle():
|
|
|
|
|
|
def test_find_borders_remove_non_adjacent_triangles():
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
- triangles = [surface.triangles.pop(),
|
|
|
- surface.triangles.pop()]
|
|
|
+ triangles = [surface.triangles.pop(), surface.triangles.pop()]
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 2
|
|
|
assert triangles[0] in borders
|
|
|
@@ -320,8 +348,7 @@ def test_find_borders_remove_non_adjacent_triangles():
|
|
|
|
|
|
def test_find_borders_remove_adjacent_triangles():
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
- triangles = [surface.triangles.pop(),
|
|
|
- surface.triangles.pop()]
|
|
|
+ triangles = [surface.triangles.pop(), surface.triangles.pop()]
|
|
|
triangles.append(surface.triangles.pop(270682))
|
|
|
assert triangles[1] == Triangle((136141, 136142, 137076))
|
|
|
assert triangles[2] == Triangle((136141, 136142, 135263))
|
|
|
@@ -333,45 +360,52 @@ def test_find_borders_remove_adjacent_triangles():
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 2
|
|
|
assert triangles[0] in borders
|
|
|
- assert PolygonalCircuit((137076, 136141, 135263,
|
|
|
- 135264, 136142)) in borders
|
|
|
+ assert PolygonalCircuit((137076, 136141, 135263, 135264, 136142)) in borders
|
|
|
surface.triangles.pop(274320)
|
|
|
borders = set(surface.find_borders())
|
|
|
assert len(borders) == 2
|
|
|
assert PolygonalCircuit((136143, 138007, 138008, 137078)) in borders
|
|
|
- assert PolygonalCircuit((137076, 136141, 135263,
|
|
|
- 135264, 136142)) in borders
|
|
|
-
|
|
|
-
|
|
|
-@pytest.mark.parametrize(('label_name', 'expected_border_lens'), [
|
|
|
- ('precentral', [416]),
|
|
|
- ('postcentral', [395]),
|
|
|
- ('medialorbitofrontal', [6, 246]),
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
- ('posteriorcingulate', [4, 190]),
|
|
|
- ('unknown', [3, 390]),
|
|
|
-])
|
|
|
+ assert PolygonalCircuit((137076, 136141, 135263, 135264, 136142)) in borders
|
|
|
+
|
|
|
+
|
|
|
+@pytest.mark.parametrize(
|
|
|
+ ("label_name", "expected_border_lens"),
|
|
|
+ [
|
|
|
+ ("precentral", [416]),
|
|
|
+ ("postcentral", [395]),
|
|
|
+ ("medialorbitofrontal", [6, 246]),
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ ("posteriorcingulate", [4, 190]),
|
|
|
+ ("unknown", [3, 390]),
|
|
|
+ ],
|
|
|
+)
|
|
|
def test_find_borders_real(label_name, expected_border_lens):
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
surface.load_annotation_file(ANNOTATION_FILE_PATH)
|
|
|
- label, = filter(lambda l: l.name == label_name,
|
|
|
- surface.annotation.labels.values())
|
|
|
- surface.triangles = list(filter(
|
|
|
- lambda t: all(surface.annotation.vertex_label_index[vertex_idx]
|
|
|
- == label.index for vertex_idx in t.vertex_indices),
|
|
|
- surface.triangles,
|
|
|
- ))
|
|
|
+ (label,) = filter(
|
|
|
+ lambda l: l.name == label_name, surface.annotation.labels.values()
|
|
|
+ )
|
|
|
+ surface.triangles = list(
|
|
|
+ filter(
|
|
|
+ lambda t: all(
|
|
|
+ surface.annotation.vertex_label_index[vertex_idx] == label.index
|
|
|
+ for vertex_idx in t.vertex_indices
|
|
|
+ ),
|
|
|
+ surface.triangles,
|
|
|
+ )
|
|
|
+ )
|
|
|
surface.remove_unused_vertices()
|
|
|
borders = list(surface.find_borders())
|
|
|
border_lens = [len(b.vertex_indices) for b in borders]
|
|
|
|
|
|
|
|
|
- assert sorted(border_lens) == expected_border_lens \
|
|
|
- or sum(border_lens) == sum(expected_border_lens)
|
|
|
+ assert sorted(border_lens) == expected_border_lens or sum(border_lens) == sum(
|
|
|
+ expected_border_lens
|
|
|
+ )
|
|
|
|
|
|
|
|
|
def test__get_vertex_label_index():
|
|
|
@@ -396,46 +430,57 @@ def test__get_vertex_label_index():
|
|
|
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())
|
|
|
+ (precentral_label,) = filter(
|
|
|
+ lambda l: l.name == "precentral", surface.annotation.labels.values()
|
|
|
+ )
|
|
|
|
|
|
- border_segments = set(
|
|
|
- surface._find_label_border_segments(precentral_label))
|
|
|
+ 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
|
|
|
+ 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)) \
|
|
|
+ assert (
|
|
|
+ LineSegment((other_vertex_index, border_vertex_index))
|
|
|
not in border_segments
|
|
|
- assert LineSegment((border_vertex_index, other_vertex_index)) \
|
|
|
+ )
|
|
|
+ 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())
|
|
|
+ (precentral_label,) = filter(
|
|
|
+ lambda l: l.name == "precentral", surface.annotation.labels.values()
|
|
|
+ )
|
|
|
|
|
|
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))
|
|
|
+ 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)
|
|
|
+ (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))
|
|
|
@@ -461,8 +506,9 @@ def test__unused_vertices():
|
|
|
def test__unused_vertices_real():
|
|
|
surface = Surface.read_triangular(SURFACE_FILE_PATH)
|
|
|
assert not surface._unused_vertices()
|
|
|
- surface.triangles = list(filter(lambda t: 42 not in t.vertex_indices,
|
|
|
- surface.triangles))
|
|
|
+ surface.triangles = list(
|
|
|
+ filter(lambda t: 42 not in t.vertex_indices, surface.triangles)
|
|
|
+ )
|
|
|
assert surface._unused_vertices() == {42}
|
|
|
|
|
|
|
|
|
@@ -534,31 +580,36 @@ def test_remove_unused_vertices_single():
|
|
|
assert len(surface.vertices) == 155622
|
|
|
assert len(surface.triangles) == 311240
|
|
|
assert surface.triangles[-1] == Triangle((136143, 138007, 137078))
|
|
|
- surface.triangles = list(filter(lambda t: 42 not in t.vertex_indices,
|
|
|
- surface.triangles))
|
|
|
+ surface.triangles = list(
|
|
|
+ filter(lambda t: 42 not in t.vertex_indices, surface.triangles)
|
|
|
+ )
|
|
|
assert surface._unused_vertices() == {42}
|
|
|
surface.remove_unused_vertices()
|
|
|
assert len(surface.vertices) == 155622 - 1
|
|
|
assert len(surface.triangles) == 311240 - 7
|
|
|
assert surface.triangles[-1] == Triangle((136142, 138006, 137077))
|
|
|
- assert all(vertex_index < len(surface.vertices)
|
|
|
- for triangle in surface.triangles
|
|
|
- for vertex_index in triangle.vertex_indices)
|
|
|
+ assert all(
|
|
|
+ vertex_index < len(surface.vertices)
|
|
|
+ for triangle in surface.triangles
|
|
|
+ for vertex_index in triangle.vertex_indices
|
|
|
+ )
|
|
|
|
|
|
|
|
|
def test_select_vertices():
|
|
|
surface = Surface()
|
|
|
for i in range(4):
|
|
|
surface.add_vertex(Vertex(i, i, i))
|
|
|
- assert numpy.allclose(surface.select_vertices([2, 1]),
|
|
|
- [surface.vertices[2], surface.vertices[1]])
|
|
|
- assert numpy.allclose(surface.select_vertices([3, 2]),
|
|
|
- [surface.vertices[3], surface.vertices[2]])
|
|
|
- assert numpy.allclose(surface.select_vertices((3, 2)),
|
|
|
- [[3, 3, 3], [2, 2, 2]])
|
|
|
- assert numpy.allclose(surface.select_vertices(filter(lambda i: i % 2 == 1,
|
|
|
- range(4))),
|
|
|
- [[1, 1, 1], [3, 3, 3]])
|
|
|
+ assert numpy.allclose(
|
|
|
+ surface.select_vertices([2, 1]), [surface.vertices[2], surface.vertices[1]]
|
|
|
+ )
|
|
|
+ assert numpy.allclose(
|
|
|
+ surface.select_vertices([3, 2]), [surface.vertices[3], surface.vertices[2]]
|
|
|
+ )
|
|
|
+ assert numpy.allclose(surface.select_vertices((3, 2)), [[3, 3, 3], [2, 2, 2]])
|
|
|
+ assert numpy.allclose(
|
|
|
+ surface.select_vertices(filter(lambda i: i % 2 == 1, range(4))),
|
|
|
+ [[1, 1, 1], [3, 3, 3]],
|
|
|
+ )
|
|
|
|
|
|
|
|
|
def test_unite_2():
|
|
|
@@ -621,7 +672,8 @@ def test_unite_real():
|
|
|
assert union.triangles[:-2] == surface_a.triangles
|
|
|
assert union.triangles[-2:] == [
|
|
|
Triangle((155622, 155623, 155625)),
|
|
|
- Triangle((155623, 155625, 155626))]
|
|
|
+ Triangle((155623, 155625, 155626)),
|
|
|
+ ]
|
|
|
assert union.creator == surface_a.creator
|
|
|
assert union.creation_datetime == surface_a.creation_datetime
|
|
|
assert union.using_old_real_ras == surface_a.using_old_real_ras
|
