def test_close():
"""
check if close method works as intended
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
loader.close()
def test_set_data_structure_err2(self):
dir_paths = ["./data/test/nifti/paired/test"]
name = "error"
dir_path = os.path.join(dir_paths[0], name)
os.makedirs(dir_path, exist_ok=True)
with pytest.raises(ValueError) as err_info:
NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
assert "No data collected" in str(err_info.value)
os.removedirs(dir_path)
def test_set_data_structure():
"""
test set_data_structure in addition to tests above in test_init
"""
# test not existed directories
dir_paths = ["./data/test/nifti/paired/test"]
name = "images"
with pytest.raises(AssertionError) as err_info:
NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
assert "does not exist" in str(err_info.value)
def test_init_duplicated_dirs(self, name):
# duplicated dir_paths
loader = get_loader(name)
dir_paths = loader.dir_paths * 2
with pytest.raises(ValueError) as err_info:
NiftiFileLoader(dir_paths=dir_paths,
name=loader.name,
grouped=loader.grouped)
assert "dir_paths have repeated elements" in str(err_info.value)
loader.close()
def test_close():
"""
check if close method works as intended
close is the same code for all cases, so no need to test all cases
"""
# paired
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
loader.close()
def test_set_group_structure():
"""
test set_group_structure in addition to tests above in test_init
"""
# data is not grouped but try using group_struct
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
with pytest.raises(AttributeError) as err_info:
loader.group_struct
assert "object has no attribute" in str(err_info.value)
def test_init_sufficient_args():
"""
check if init method of loader returns any errors when all required
arguments given
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
loader.__init__(dir_path=dir_path, name=name, grouped=False)
loader.close()
def test_get_num_images():
"""
check if the get_num_images method works as expected
"""
# paired
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.get_num_images()
expected = 2
loader.close()
assert got == expected
# unpaired
dir_paths = ["./data/test/nifti/unpaired/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.get_num_images()
expected = 2
loader.close()
assert got == expected
# grouped
dir_paths = ["./data/test/nifti/grouped/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = loader.get_num_images()
expected = 2
loader.close()
assert got == expected
# multi dirs
dir_paths = [
"./data/test/nifti/grouped/train", "./data/test/nifti/grouped/test"
]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = loader.get_num_images()
expected = 9
loader.close()
assert got == expected
def test_get_data_out_of_range_sample_index():
"""
check if the get_data method works as expected and raises error when
incorrect group index is supplied
"""
dir_path = "./data/test/nifti/grouped/test"
name = "images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=True)
index = (0, 32)
with pytest.raises(AssertionError):
loader.get_data(index)
def test_get_num_images():
"""
check if the get_num_images method works as expected
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
got = int(loader.get_num_images())
expected = int(2)
loader.close()
assert got == expected
def test_get_data_ids():
"""
check if the get_data_ids method works as expected
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
got = loader.get_data_ids()
expected = ["/case000025.nii.gz", "/case000026.nii.gz"]
loader.close()
assert got == expected
def test_get_data_incompatible_args():
"""
check if the get_data method works as expected and raises an error when
data is ungrouped but index is not an int
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
index = (0, 1)
with pytest.raises(AssertionError):
loader.get_data(index)
def test_get_data_incorrect_args():
"""
check if the get_data method works as expected and raises an error when
an incorrect data type is fed in
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
index = "abc"
with pytest.raises(ValueError) as execinfo:
loader.get_data(index)
msg = " ".join(execinfo.value.args[0].split())
assert "must be int, or tuple" in msg
def test_set_group_structure_ungrouped():
"""
check if the set_group_structure method works as intended when data is
not grouped
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
loader.set_group_structure()
with pytest.raises(AttributeError) as execinfo:
loader.group_ids
msg = " ".join(execinfo.value.args[0].split())
assert "object has no attribute" in msg
def test_file_paths():
"""
check if the filepaths are the same as expected
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
got = loader.file_paths
expected = [
"./data/test/nifti/paired/test/fixed_images/case000025.nii.gz",
"./data/test/nifti/paired/test/fixed_images/case000026.nii.gz",
]
loader.close()
assert got == expected
def get_loader(loader_name):
if loader_name in [
"paired",
"unpaired",
"grouped",
]:
dir_paths = [f"./data/test/nifti/{loader_name}/test"]
name = "fixed_images" if loader_name == "paired" else "images"
grouped = loader_name == "grouped"
elif loader_name == "multi_dirs_grouped":
dir_paths = [
"./data/test/nifti/grouped/train",
"./data/test/nifti/grouped/test",
]
name = "images"
grouped = True
else:
raise ValueError
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=grouped)
return loader
def test_get_data():
"""
check if the get_data method works as expected and returns array
as expected
"""
dir_path = "./data/test/nifti/paired/test"
name = "fixed_images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=False)
index = 0
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array), np.amin(array), np.mean(array), np.std(array)],
]
expected = [(44, 59, 41), [255.0, 0.0, 68.359276, 65.84009]]
loader.close()
if got[0] == expected[0]:
assert check_equal(np.array(got[1]), np.array(expected[1])).all()
else:
raise AssertionError
def test_get_data_grouped():
"""
check if the get_data method works as expected and returns array
as expected
"""
dir_path = "./data/test/nifti/grouped/test"
name = "images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=True)
index = (0, 1)
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array), np.amin(array), np.mean(array), np.std(array)],
]
expected = [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]]
loader.close()
if got[0] == expected[0]:
assert check_equal(np.array(got[1]), np.array(expected[1])).all()
else:
raise AssertionError
def test_set_group_structure():
"""
check if the set_group_structure method works as intended when data is
grouped
"""
dir_path = "./data/test/nifti/grouped/test"
name = "images"
loader = NiftiFileLoader(dir_path=dir_path, name=name, grouped=True)
loader.set_group_structure()
got = [loader.group_ids, loader.group_sample_dict]
expected = [
["./data/test/nifti/grouped/test/images/group1"],
{
"./data/test/nifti/grouped/test/images/group1": [
"./data/test/nifti/grouped/test/images/group1/case000025.nii.gz",
"./data/test/nifti/grouped/test/images/group1/case000026.nii.gz",
]
},
]
loader.close()
assert got == expected
def test_get_data_ids():
"""
check if the get_data_ids method works as expected
"""
# paired
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.get_data_ids()
expected = [
("./data/test/nifti/paired/test", "case000025"),
("./data/test/nifti/paired/test", "case000026"),
]
loader.close()
assert got == expected
# unpaired
dir_paths = ["./data/test/nifti/unpaired/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.get_data_ids()
expected = [
("./data/test/nifti/unpaired/test", "case000025"),
("./data/test/nifti/unpaired/test", "case000026"),
]
loader.close()
assert got == expected
# grouped
dir_paths = ["./data/test/nifti/grouped/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = loader.get_data_ids()
expected = [
("./data/test/nifti/grouped/test", "group1", "case000025"),
("./data/test/nifti/grouped/test", "group1", "case000026"),
]
loader.close()
assert got == expected
# multi dirs
dir_paths = [
"./data/test/nifti/grouped/train", "./data/test/nifti/grouped/test"
]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = loader.get_data_ids()
expected = [
("./data/test/nifti/grouped/test", "group1", "case000025"),
("./data/test/nifti/grouped/test", "group1", "case000026"),
("./data/test/nifti/grouped/train", "group1", "case000000"),
("./data/test/nifti/grouped/train", "group1", "case000001"),
("./data/test/nifti/grouped/train", "group1", "case000003"),
("./data/test/nifti/grouped/train", "group1", "case000008"),
("./data/test/nifti/grouped/train", "group2", "case000009"),
("./data/test/nifti/grouped/train", "group2", "case000011"),
("./data/test/nifti/grouped/train", "group2", "case000012"),
]
loader.close()
assert got == expected
# wrong index for paired
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
with pytest.raises(AssertionError):
loader.get_data(index=(0, 1))
with pytest.raises(ValueError) as err_info:
loader.get_data(index=[0])
assert "must be int, or tuple" in str(err_info.value)
# wrong index for grouped
dir_paths = ["./data/test/nifti/grouped/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
with pytest.raises(AssertionError):
# negative group_index
loader.get_data(index=(-1, 1))
with pytest.raises(IndexError):
# out of range group_index
loader.get_data(index=(32, 1))
with pytest.raises(AssertionError):
# negative in_group_data_index
loader.get_data(index=(0, -1))
with pytest.raises(IndexError):
# out of range in_group_data_index
loader.get_data(index=(0, 32))
def test_set_data_structure_err1(self, name, err_msg):
dir_paths = ["./data/test/h5/paired/test"]
with pytest.raises(AssertionError) as err_info:
NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
assert err_msg in str(err_info.value)
def test_get_data():
"""
test get_data method by verifying returns' shape and value stats
"""
# paired
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
index = 0
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array),
np.amin(array),
np.mean(array),
np.std(array)],
]
expected = [(44, 59, 41), [255.0, 0.0, 68.359276, 65.84009]]
loader.close()
assert got[0] == expected[0]
assert is_equal_np(got[1], expected[1])
# unpaired
dir_paths = ["./data/test/nifti/unpaired/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
index = 0
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array),
np.amin(array),
np.mean(array),
np.std(array)],
]
expected = [(64, 64, 60), [255.0, 0.0, 60.073948, 47.27648]]
loader.close()
assert got[0] == expected[0]
assert is_equal_np(got[1], expected[1])
# grouped
dir_paths = ["./data/test/nifti/grouped/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
index = (0, 1)
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array),
np.amin(array),
np.mean(array),
np.std(array)],
]
expected = [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]]
loader.close()
assert got[0] == expected[0]
assert is_equal_np(got[1], expected[1])
# multi dirs
dir_paths = [
"./data/test/nifti/grouped/train", "./data/test/nifti/grouped/test"
]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
index = (0, 1)
array = loader.get_data(index)
got = [
np.shape(array),
[np.amax(array),
np.amin(array),
np.mean(array),
np.std(array)],
]
expected = [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]]
loader.close()
assert got[0] == expected[0]
assert is_equal_np(got[1], expected[1])
def test_init():
"""
check init of NiftiFileLoader
this includes some test on set_data_structure/set_group_structure
as these functions are called in init
"""
# paired
# test data_path_splits
dir_paths = ["./data/test/nifti/paired/test"]
name = "fixed_images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.data_path_splits
expected = [
("./data/test/nifti/paired/test", "case000025", "nii.gz"),
("./data/test/nifti/paired/test", "case000026", "nii.gz"),
]
loader.close()
assert got == expected
# unpaired
# test data_path_splits
dir_paths = ["./data/test/nifti/unpaired/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
got = loader.data_path_splits
expected = [
("./data/test/nifti/unpaired/test", "case000025", "nii.gz"),
("./data/test/nifti/unpaired/test", "case000026", "nii"),
]
loader.close()
assert got == expected
# grouped
# test data_path_splits and group_struct
dir_paths = ["./data/test/nifti/grouped/test"]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = [loader.data_path_splits, loader.group_struct]
expected = [
[
("./data/test/nifti/grouped/test", "group1", "case000025",
"nii.gz"),
("./data/test/nifti/grouped/test", "group1", "case000026",
"nii.gz"),
],
[[0, 1]],
]
loader.close()
assert got == expected
# multi dirs
# test data_path_splits and group_struct
dir_paths = [
"./data/test/nifti/grouped/train", "./data/test/nifti/grouped/test"
]
name = "images"
loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
got = [loader.data_path_splits, loader.group_struct]
expected = [
[
("./data/test/nifti/grouped/test", "group1", "case000025",
"nii.gz"),
("./data/test/nifti/grouped/test", "group1", "case000026",
"nii.gz"),
("./data/test/nifti/grouped/train", "group1", "case000000",
"nii.gz"),
("./data/test/nifti/grouped/train", "group1", "case000001",
"nii.gz"),
("./data/test/nifti/grouped/train", "group1", "case000003",
"nii.gz"),
("./data/test/nifti/grouped/train", "group1", "case000008",
"nii.gz"),
("./data/test/nifti/grouped/train", "group2", "case000009",
"nii.gz"),
("./data/test/nifti/grouped/train", "group2", "case000011",
"nii.gz"),
("./data/test/nifti/grouped/train", "group2", "case000012",
"nii.gz"),
],
[[0, 1], [2, 3, 4, 5], [6, 7, 8]],
]
loader.close()
assert got == expected
# duplicated dir_paths
dir_paths = [
"./data/test/nifti/grouped/test", "./data/test/nifti/grouped/test"
]
name = "images"
with pytest.raises(ValueError) as err_info:
NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
assert "dir_paths have repeated elements" in str(err_info.value)