import csv import io import subprocess import typing import unittest.mock import numpy from conftest import ANNOTATION_FILE_PATH, SURFACE_FILE_PATH from freesurfer_surface import Surface, Triangle, Vertex from freesurfer_surface.__main__ import annotation_labels, unite_surfaces def check_rows(csv_rows: typing.List[str]): assert len(csv_rows) == 36 + 1 assert csv_rows[0] == ['index', 'color', 'name'] assert csv_rows[1] == ['0', '#190519', 'unknown'] assert csv_rows[23] == ['22', '#dc1414', 'postcentral'] assert csv_rows[25] == ['24', '#3c14dc', 'precentral'] def test_annotation_labels_function(capsys): with unittest.mock.patch('sys.argv', ['', ANNOTATION_FILE_PATH]): annotation_labels() out, err = capsys.readouterr() assert not err check_rows(list(csv.reader(io.StringIO(out), delimiter='\t'))) def test_annotation_labels_function_delimiter(capsys): with unittest.mock.patch('sys.argv', ['', '--delimiter', ',', ANNOTATION_FILE_PATH]): annotation_labels() out, err = capsys.readouterr() assert not err check_rows(list(csv.reader(io.StringIO(out), delimiter=','))) def test_annotation_labels_script(): proc_info = subprocess.run(['freesurfer-annotation-labels', ANNOTATION_FILE_PATH], check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) assert not proc_info.stderr check_rows(list(csv.reader(io.StringIO(proc_info.stdout.decode()), delimiter='\t'))) def test_unite_surfaces_function(tmpdir, capsys): surface_b = Surface.read_triangular(SURFACE_FILE_PATH) surface_b.vertices = [] for i in range(5): surface_b.add_vertex(Vertex(i, i, i)) surface_b.triangles = [Triangle((0, 1, 3)), Triangle((1, 3, 4))] surface_b_path = tmpdir.join('b').strpath surface_b.write_triangular(surface_b_path) output_path = tmpdir.join('output_path').strpath with unittest.mock.patch('sys.argv', ['', '--output', output_path, SURFACE_FILE_PATH, surface_b_path]): unite_surfaces() out, err = capsys.readouterr() assert not out assert not err union = Surface.read_triangular(output_path) assert len(union.vertices) == 155627 assert len(union.triangles) == 311242 assert numpy.allclose(union.vertices[-5:], surface_b.vertices) def test_unite_surfaces_script(tmpdir): surface_b = Surface.read_triangular(SURFACE_FILE_PATH) surface_b.vertices = [] for i in range(5): surface_b.add_vertex(Vertex(i, i, i)) surface_b.triangles = [Triangle((0, 1, 3)), Triangle((1, 3, 4))] surface_b_path = tmpdir.join('b').strpath surface_b.write_triangular(surface_b_path) output_path = tmpdir.join('output_path').strpath proc_info = subprocess.run(['unite-freesurfer-surfaces', '--output', output_path, SURFACE_FILE_PATH, surface_b_path, surface_b_path], check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) assert not proc_info.stdout assert not proc_info.stderr union = Surface.read_triangular(output_path) assert len(union.vertices) == 155622 + (5 * 2) assert len(union.triangles) == 311240 + (2 * 2)