def test_h5_stack_via_star_file_glob_and_defined_inner_path(h5_stack_dir, empty_project_file: h5py.File):
h5_external_star_glob = os.path.join(h5_stack_dir, "*.h5")
internal_path = DatasetInfo.globInternalPaths(h5_external_star_glob, "*")[0]
total_path = os.path.join(h5_stack_dir, "*.h5", internal_path)
info = FilesystemDatasetInfo(filePath=total_path, sequence_axis="z", project_file=empty_project_file)
assert info.nickname == "2d_apoptotic_binary_-volume-data"
assert info.is_under_project_file()
def test_stack_via_colon_glob(png_colon_path_stack,
empty_project_file: h5py.File):
info = FilesystemDatasetInfo(filePath=png_colon_path_stack,
sequence_axis="t",
project_file=empty_project_file)
assert info.nickname == "c_cells_"
assert info.is_under_project_file()
def test_relative_paths(png_stack_dir: str, monkeypatch):
with h5py.File(os.path.join(png_stack_dir, "myproj.ilp"), "w") as project_file:
info = FilesystemDatasetInfo(
filePath=os.path.join(png_stack_dir, "*.png"), project_file=project_file, sequence_axis="z"
)
assert info.is_under_project_file()
assert info.get_relative_paths() == ["c_cells_0.png", "c_cells_1.png", "c_cells_2.png"]
def test_star_glob(png_colon_path_stack: str, empty_project_file: h5py.File):
info = FilesystemDatasetInfo(filePath=png_colon_path_stack,
sequence_axis="z",
project_file=empty_project_file)
assert info.nickname == "c_cells_"
assert info.laneDtype == numpy.uint8
assert info.laneShape == (3, 520, 697, 3)
assert info.is_under_project_file()
def test_stack_via_star_glob(png_star_stack: str, empty_project_file):
info = FilesystemDatasetInfo(filePath=png_star_stack,
sequence_axis="z",
project_file=empty_project_file)
assert info.nickname == "c_cells_"
# empty project lies in /tmp, so paths should be relative
assert info.is_under_project_file()
def test_create_using_paths_relative_to_project_file(png_stack_dir: str):
with h5py.File(os.path.join(png_stack_dir, "myproj.ilp"),
"w") as project_file:
info = FilesystemDatasetInfo(filePath="*.png",
project_file=project_file,
sequence_axis="z")
assert info.get_relative_paths() == [
"c_cells_0.png", "c_cells_1.png", "c_cells_2.png"
]
def test_no_relative_paths_when_project_file_not_in_same_tree_as_files(
png_stack_dir: str, monkeypatch):
with h5py.File(os.path.join(tempfile.mkdtemp(), "myproj.ilp"),
"w") as project_file:
info = FilesystemDatasetInfo(filePath=os.path.join(
png_stack_dir, "*.png"),
project_file=project_file,
sequence_axis="z")
assert not info.is_under_project_file()
def test_h5_stack_via_star_file_glob_and_stared_internal_path(h5_stack_dir, empty_project_file):
star_glob = h5_stack_dir / "*.h5/*"
info = FilesystemDatasetInfo(filePath=str(star_glob), sequence_axis="z", project_file=empty_project_file)
assert info.nickname == "2d_apoptotic_binary_-volume-data"
assert info.is_under_project_file()
expected_filepath = os.path.pathsep.join(
[
Path(h5_stack_dir).joinpath("2d_apoptotic_binary_0.h5/volume/data").as_posix(),
Path(h5_stack_dir).joinpath("2d_apoptotic_binary_1.h5/volume/data").as_posix(),
Path(h5_stack_dir).joinpath("2d_apoptotic_binary_2.h5/volume/data").as_posix(),
]
)
assert info.filePath == expected_filepath
def test_guess_tags_for_singleton_axes(h5_1_100_200_1_1, empty_project_file):
info = FilesystemDatasetInfo(
filePath=h5_1_100_200_1_1,
project_file=empty_project_file,
axistags=vigra.defaultAxistags("yx"),
guess_tags_for_singleton_axes=True,
sequence_axis="z",
)
assert info.axiskeys[1:3] == "yx"
def test_h5_stack_via_colon_glob(h5_colon_path_stack_with_inner_paths,
empty_project_file):
info = FilesystemDatasetInfo(filePath=h5_colon_path_stack_with_inner_paths,
sequence_axis="t",
project_file=empty_project_file)
assert info.nickname == "2d_apoptotic_binary_-volume-data"