def test_register(tmpdir, test_config_path):
output_directory = os.path.join(str(tmpdir), "output")
amap_args = [
"amap",
data_dir,
output_directory,
"-x",
x_pix,
"-y",
y_pix,
"-z",
z_pix,
"--n-free-cpus",
"0",
"--registration-config",
test_config_path,
"-d",
data_dir,
]
sys.argv = amap_args
amap_run()
image_list = [
"annotations.nii",
"boundaries.nii",
"brain_filtered.nii",
"control_point_file.nii",
"downsampled.nii",
"hemispheres.nii",
"inverse_control_point_file.nii",
"registered_atlas.nii",
"registered_hemispheres.nii",
"downsampled_brain.nii",
]
for image in image_list:
are_images_equal(image, output_directory, test_output_dir)
assert get_text_lines(
os.path.join(output_directory, "affine_matrix.txt")
) == get_text_lines(os.path.join(test_output_dir, "affine_matrix.txt"))
assert get_text_lines(
os.path.join(output_directory, "invert_affine_matrix.txt")
) == get_text_lines(
os.path.join(test_output_dir, "invert_affine_matrix.txt")
)
assert (
(
pd.read_csv(os.path.join(output_directory, "volumes.csv"))
== pd.read_csv(os.path.join(test_output_dir, "volumes.csv"))
)
.all()
.all()
)
def get_sorted_file_paths(file_path, file_extension=None, encoding=None):
"""
Sorts file paths with numbers "naturally" (i.e. 1, 2, 10, a, b), not
lexiographically (i.e. 1, 10, 2, a, b).
:param str file_path: File containing file_paths in a text file,
or as a list.
:param str file_extension: Optional file extension (if a directory
is passed)
:param encoding: If opening a text file, what encoding it has.
Default: None (platform dependent)
:return: Sorted list of file paths
"""
if isinstance(file_path, list):
return natsorted(file_path)
# assume if not a list, is a file path
file_path = Path(file_path)
if file_path.suffix == ".txt":
return get_text_lines(file_path, sort=True, encoding=encoding)
elif file_path.is_dir():
if file_extension is None:
file_path = glob.glob(os.path.join(file_path, "*"))
else:
file_path = glob.glob(os.path.join(file_path,
"*" + file_extension))
return natsorted(file_path)
else:
message = (
"Input file path is not a recognised format. Please check it "
"is a list of file paths, a text file of these paths, or a "
"directory containing image files.")
raise NotImplementedError(message)
def test_get_sorted_file_paths():
# test list
shuffled = sorted_cubes_dir.copy()
shuffle(shuffled)
assert system.get_sorted_file_paths(shuffled) == sorted_cubes_dir
# test dir
assert system.get_sorted_file_paths(cubes_dir) == sorted_cubes_dir
assert (system.get_sorted_file_paths(
cubes_dir, file_extension=".tif") == sorted_cubes_dir)
# test text file
# specifying utf8, as written on linux
assert system.get_sorted_file_paths(
jabberwocky, encoding="utf8") == get_text_lines(jabberwocky_sorted,
encoding="utf8")
# test unsupported
with pytest.raises(NotImplementedError):
system.get_sorted_file_paths(shuffled[0])
def test_register(tmpdir, test_config_path):
output_directory = os.path.join(str(tmpdir), "output")
cellfinder_args = [
"cellfinder",
"-s",
data_dir,
"-b",
data_dir,
"-o",
output_directory,
"-x",
x_pix,
"-y",
y_pix,
"-z",
z_pix,
"--n-free-cpus",
"0",
"--registration-config",
test_config_path,
"--register",
"--no-detection",
"--no-classification",
]
sys.argv = cellfinder_args
cellfinder_run()
output_directory = os.path.join(output_directory, "registration")
# a hack because testing on linux on travis is 100% identical to local,
# but windows is not
if platform.system() == "Linux":
image_list = [
"annotations.nii",
"boundaries.nii",
"brain_filtered.nii",
"control_point_file.nii",
"downsampled.nii",
"hemispheres.nii",
"inverse_control_point_file.nii",
"registered_atlas.nii",
"registered_hemispheres.nii",
"downsampled_channel_0.nii",
]
else:
image_list = [
"annotations.nii",
# "boundaries.nii",
"brain_filtered.nii",
"control_point_file.nii",
"downsampled.nii",
"hemispheres.nii",
"inverse_control_point_file.nii",
# "registered_atlas.nii",
"registered_hemispheres.nii",
"downsampled_channel_0.nii",
]
for image in image_list:
are_images_equal(image, output_directory, test_output_dir)
assert get_text_lines(os.path.join(
output_directory, "affine_matrix.txt")) == get_text_lines(
os.path.join(test_output_dir, "affine_matrix.txt"))
assert get_text_lines(
os.path.join(output_directory,
"invert_affine_matrix.txt")) == get_text_lines(
os.path.join(test_output_dir,
"invert_affine_matrix.txt"))
pd.testing.assert_frame_equal(
pd.read_csv(os.path.join(output_directory, "volumes.csv")),
pd.read_csv(os.path.join(test_output_dir, "volumes.csv")),
check_exact=False,
check_less_precise=check_less_precise_pd,
)
def test_get_string_lines():
assert string.get_text_lines(jabberwocky) == jabberwocky_list
assert (string.get_text_lines(jabberwocky,
return_lines=8) == jabberwocky_list[8])
