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123 lines (97 loc) · 4.49 KB
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"""Test conversion to Project files."""
import importlib
import os
import pathlib
import tempfile
import pytest
import ratapi
from ratapi.utils.convert import project_to_r1, r1_to_project
TEST_DIR_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)), "test_data")
@pytest.fixture
def dspc_bilayer():
"""The Project from the DSPC standard layers example,
with some changes to make it compatible with R1.
"""
project, _ = ratapi.examples.DSPC_standard_layers()
# change parameters to standardise arguments not in R1
for class_list in ratapi.project.parameter_class_lists:
params = getattr(project, class_list)
for param in params:
param.prior_type = "uniform"
param.mu = 0.0
param.sigma = float("inf")
for i in range(0, len(project.background_parameters)):
param = project.background_parameters[i]
for background in project.backgrounds:
if background.source == param.name:
background.source = f"Background parameter {i + 1}"
param.name = f"Background parameter {i + 1}"
for i in range(0, len(project.resolution_parameters)):
param = project.resolution_parameters[i]
for resolution in project.resolutions:
if resolution.source == param.name:
resolution.source = f"Resolution parameter {i + 1}"
param.name = f"Resolution parameter {i + 1}"
return project
@pytest.mark.parametrize(
["file", "project"],
[
["R1defaultProject.mat", "r1_default_project"],
["R1monolayerVolumeModel.mat", "r1_monolayer"],
["R1DSPCBilayer.mat", "dspc_bilayer"],
["R1Monolayer_8_contrasts.mat", "r1_monolayer_8_contrasts"],
["R1orsoPolymerExample.mat", "r1_orso_polymer"],
["R1motofitBenchMark.mat", "r1_motofit_bench_mark"],
],
)
@pytest.mark.parametrize("path_type", [os.path.join, pathlib.Path])
def test_r1_to_project(file, project, path_type, request):
"""Test that R1 to Project class conversion returns the expected Project."""
output_project = r1_to_project(path_type(TEST_DIR_PATH, file))
expected_project = request.getfixturevalue(project)
# assert statements have to be more careful due to R1 missing features
# e.g. R1 doesn't support background parameter names, mu, sigma...
for class_list in ratapi.project.class_lists:
assert getattr(output_project, class_list) == getattr(expected_project, class_list)
@pytest.mark.parametrize(
"project",
[
"r1_default_project",
"r1_monolayer",
"r1_monolayer_8_contrasts",
"r1_orso_polymer",
"r1_motofit_bench_mark",
"dspc_bilayer",
],
)
def test_r1_involution(project, request, monkeypatch):
"""Test that converting a Project to an R1 struct and back returns the same project."""
original_project = request.getfixturevalue(project)
r1_struct = project_to_r1(original_project, return_struct=True)
# rather than writing the struct to a file and reading the file, just directly
# hand the struct over
def mock_load(ignored_filename, **ignored_settings):
"""Load the generated R1 struct instead of reading a file."""
return {"problem": r1_struct}
monkeypatch.setattr("ratapi.utils.convert.loadmat", mock_load, raising=True)
converted_project = r1_to_project(project)
for class_list in ratapi.project.class_lists:
assert getattr(converted_project, class_list) == getattr(original_project, class_list)
def test_invalid_constraints():
"""Test that invalid constraints are fixed where necessary."""
with pytest.warns(
match=r"The parameter (.+) has invalid constraints,"
" these have been adjusted to satisfy the current value of the parameter."
):
output_project = r1_to_project(pathlib.Path(TEST_DIR_PATH, "R1DoubleBilayerVolumeModel.mat"))
assert output_project.background_parameters[0].min == output_project.background_parameters[0].value
@pytest.mark.skipif(importlib.util.find_spec("matlab") is None, reason="Matlab not installed")
@pytest.mark.parametrize("path_type", [os.path.join, pathlib.Path])
def test_matlab_save(path_type, request):
"""Test that MATLAB correctly saves the .mat file."""
project = request.getfixturevalue("r1_default_project")
with tempfile.TemporaryDirectory() as temp:
matfile = path_type(temp, "testfile.mat")
project_to_r1(project, filename=matfile)
converted_project = r1_to_project(matfile)
assert project == converted_project