freesurfer-surface/tests/test_main.py

# freesurfer-surface - Read and Write Surface Files in Freesurfer’s TriangularSurface Format
#
# Copyright (C) 2020 Fabian Peter Hammerle <fabian@hammerle.me>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.

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)