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)