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fix test io
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@Henley13
Henley13 committed May 5, 2020
1 parent 85d9275 commit e564089
Showing 1 changed file with 79 additions and 91 deletions.
170 changes: 79 additions & 91 deletions tests/stack/test_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,134 +17,122 @@
from numpy.testing import assert_array_equal


def test_io():

# build different arrays to write and read
shapes = [(64, 64), (20, 64, 64), (5, 20, 64, 64), (10, 5, 20, 64, 64)]
dtypes = [np.uint8, np.uint16, np.uint32,
np.int8, np.int16, np.int32,
np.float32, np.float64, bool]
extensions = ["png", "jpg", "jpeg", "tif", "tiff"]

@pytest.mark.parametrize("shape", [
(8, 8), (8, 8, 8), (8, 8, 8, 8), (8, 8, 8, 8, 8)])
@pytest.mark.parametrize("dtype", [
np.uint8, np.uint16, np.uint32,
np.int8, np.int16, np.int32,
np.float32, np.float64, bool])
@pytest.mark.parametrize("extension", [
"png", "jpg", "jpeg", "tif", "tiff"])
def test_io(shape, dtype, extension):
# build a temporary directory and save tensors inside
with tempfile.TemporaryDirectory() as tmp_dir:
test = np.zeros(shape, dtype=dtype)
path = os.path.join(tmp_dir, "test." + extension)

# error: boolean multidimensional image
if (extension in ["png", "jpg", "jpeg", "tif", "tiff"]
and len(test.shape) > 2
and test.dtype == bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# error: non-boolean multidimensional image with 'png', 'jpg' or 'jpeg'
elif (extension in ["png", "jpg", "jpeg"]
and len(test.shape) > 2
and test.dtype != bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# error: boolean 2-d image with 'tig' and 'tiff'
elif (extension in ["tif", "tiff"]
and len(test.shape) == 2
and test.dtype == bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# warning: 2-d image with 'png', 'jpg' or 'jpeg'
elif (extension in ["png", "jpg", "jpeg"]
and len(test.shape) == 2):
with pytest.warns(UserWarning):
stack.save_image(test, path)
tensor = stack.read_image(path, sanity_check=True)
assert_array_equal(test, tensor)

for shape in shapes:
for dtype in dtypes:
for extension in extensions:
test = np.zeros(shape, dtype=dtype)
path = os.path.join(tmp_dir, "test." + extension)

# multidimensional image
if (extension in ["png", "jpg", "jpeg"]
and len(test.shape) > 2
and test.dtype != bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# 2-d image
elif (extension in ["png", "jpg", "jpeg"]
and len(test.shape) == 2):
with pytest.warns(UserWarning):
stack.save_image(test, path)
tensor = stack.read_image(path, sanity_check=True)
assert_array_equal(test, tensor)

# boolean image
elif (extension in ["tif", "tiff"]
and len(test.shape) == 2
and test.dtype == bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# multidimensional boolean image
elif (extension in ["png", "jpg", "jpeg", "tif", "tiff"]
and len(test.shape) > 2
and test.dtype == bool):
with pytest.raises(ValueError):
stack.save_image(test, path)

# others valid images
else:
stack.save_image(test, path)
tensor = stack.read_image(path, sanity_check=True)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype
# others valid images
else:
stack.save_image(test, path)
tensor = stack.read_image(path, sanity_check=True)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype


def test_io_specific():
# build a temporary directory and save tensors inside
with tempfile.TemporaryDirectory() as tmp_dir:
# non-supported image (1 dimension)
test = np.array([1, 2, 3], dtype=np.float32)
path = os.path.join(tmp_dir, "test")
with pytest.raises(ValueError):
stack.save_image(test, path)

# non-supported image (6 dimensions)
test = np.zeros((1, 10, 5, 20, 64, 64), dtype=np.float32)
test = np.zeros((8, 8, 8, 8, 8, 8), dtype=np.float32)
path = os.path.join(tmp_dir, "test")
with pytest.raises(ValueError):
stack.save_image(test, path)

# non-supported image (np.int64)
test = np.zeros((64, 64), dtype=np.int64)
test = np.zeros((8, 8), dtype=np.int64)
path = os.path.join(tmp_dir, "test")
with pytest.raises(TypeError):
stack.save_image(test, path)

# non-supported image (missing values)
test = np.zeros((64, 64), dtype=np.float32)
test = np.zeros((8, 8), dtype=np.float32)
test[0, 0] = np.nan
path = os.path.join(tmp_dir, "test")
with pytest.raises(ValueError):
stack.save_image(test, path)

# non-supported extensions
test = np.zeros((64, 64), dtype=np.float32)
test = np.zeros((8, 8), dtype=np.float32)
path = os.path.join(tmp_dir, "test.foo")
with pytest.raises(ValueError):
stack.save_image(test, path)
path = os.path.join(tmp_dir, "test")
with pytest.raises(ValueError):
stack.save_image(test, path, extension="bar")

return


def test_dv():
# build different arrays to write and read
dtypes = [np.uint16, np.int16, np.int32, np.float32]

@pytest.mark.parametrize("dtype", [np.uint16, np.int16, np.int32, np.float32])
def test_dv(dtype):
# build a temporary directory and save a dv file inside
with tempfile.TemporaryDirectory() as tmp_dir:
for dtype in dtypes:
test = np.zeros((20, 5, 256, 256), dtype=dtype)
path = os.path.join(tmp_dir, "test")
mrc.imsave(path, test)

# read and test the dv file
path = os.path.join(tmp_dir, "test")
tensor = stack.read_dv(path, sanity_check=True)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype

return


def test_npy():
# build different arrays to write and read
shapes = [(64, 64), (20, 64, 64), (5, 20, 64, 64), (10, 5, 20, 64, 64)]
dtypes = [np.uint8, np.uint16, np.uint32,
np.int8, np.int16, np.int32, np.int64,
np.float32, np.float64, bool]
test = np.zeros((8, 8, 8, 8), dtype=dtype)
path = os.path.join(tmp_dir, "test")
mrc.imsave(path, test)

# read and test the dv file
path = os.path.join(tmp_dir, "test")
tensor = stack.read_dv(path, sanity_check=True)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype


@pytest.mark.parametrize("shape", [
(8, 8), (8, 8, 8), (8, 8, 8, 8), (8, 8, 8, 8, 8)])
@pytest.mark.parametrize("dtype", [
np.uint8, np.uint16, np.uint32,
np.int8, np.int16, np.int32, np.int64,
np.float32, np.float64, bool])
def test_npy(shape, dtype):
# build a temporary directory and save tensors inside
with tempfile.TemporaryDirectory() as tmp_dir:

for shape in shapes:
for dtype in dtypes:
test = np.zeros(shape, dtype=dtype)
path = os.path.join(tmp_dir, "test.npy")
stack.save_array(test, path)
tensor = stack.read_array(path)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype

return
test = np.zeros(shape, dtype=dtype)
path = os.path.join(tmp_dir, "test.npy")
stack.save_array(test, path)
tensor = stack.read_array(path)
assert_array_equal(test, tensor)
assert test.dtype == tensor.dtype

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