def test_garbage_collection():
"""Test that recipe execution discards intermediate results that are no longer necessary."""
recipe_str = """
a = compute(Filter.SimpleFilterAlgorithm, file_inputs[0], multiplicand=0.5)
b = compute(Filter.SimpleFilterAlgorithm, a, multiplicand=0.3)
c = compute(Filter.SimpleFilterAlgorithm, b, multiplicand=4.)
d = compute(Filter.SimpleFilterAlgorithm, c, multiplicand=0.5)
file_outputs[0] = compute(Filter.SimpleFilterAlgorithm, d, multiplicand=0.5)
"""
with tempfile.TemporaryDirectory() as tempdir:
output_path = os.path.join(tempdir, "output.json")
recipe = Recipe(recipe_str, [URL], [output_path])
execution = recipe._execution()
execution._run_one_tick()
execution._run_one_tick()
assert len(execution._completed_results) == 1
execution.run_and_save()
result_stack = ImageStack.from_path_or_url(output_path)
assert np.allclose(BASE_EXPECTED * .15,
result_stack.xarray[2, 2, 0, 40:50, 40:50])
def test_simple_recipe():
"""Test that a simple recipe can execute correctly."""
recipe_str = """
file_outputs[0] = compute(Filter.SimpleFilterAlgorithm, file_inputs[0], multiplicand=0.5)
"""
with tempfile.TemporaryDirectory() as tempdir:
output_path = os.path.join(tempdir, "output.json")
recipe = Recipe(recipe_str, [URL], [output_path])
execution = recipe._execution()
execution.run_and_save()
result_stack = ImageStack.from_path_or_url(output_path)
assert np.allclose(BASE_EXPECTED * .5,
result_stack.xarray[2, 2, 0, 40:50, 40:50])
def test_recipe_constructor_extra_args():
"""Test that recipe construction detects missing arguments to the constructor."""
recipe_str = """
file_outputs[0] = compute(Filter.SimpleFilterAlgorithm, file_inputs[0], multiplicand=.5, x=1)
"""
with tempfile.TemporaryDirectory() as tempdir:
output_path = os.path.join(tempdir, "output.json")
with warnings.catch_warnings(record=True) as w:
recipe = Recipe(recipe_str, [URL], [output_path])
assert len(w) == 1
assert issubclass(w[-1].category, ConstructorExtraParameterWarning)
execution = recipe._execution()
execution.run_and_save()
result_stack = ImageStack.from_path_or_url(output_path)
assert np.allclose(BASE_EXPECTED * .5,
result_stack.xarray[2, 2, 0, 40:50, 40:50])
def test_chained_recipe():
"""Test that a recipe with a complex graph can execute correctly."""
recipe_str = """
a = compute(Filter.SimpleFilterAlgorithm, file_inputs[0], multiplicand=0.5)
b = compute(Filter.SimpleFilterAlgorithm, a, multiplicand=.3)
file_outputs[0] = compute(Filter.SimpleFilterAlgorithm, b, multiplicand=0.2)
c = compute(Filter.SimpleFilterAlgorithm, a, multiplicand=.2)
file_outputs[1] = compute(Filter.SimpleFilterAlgorithm, c, multiplicand=.3)
"""
with tempfile.TemporaryDirectory() as tempdir:
output_0_path = os.path.join(tempdir, "output_0.json")
output_1_path = os.path.join(tempdir, "output_1.json")
recipe = Recipe(recipe_str, [URL], [output_0_path, output_1_path])
execution = recipe._execution()
execution.run_and_save()
for path in (output_0_path, output_1_path):
result_stack = ImageStack.from_path_or_url(path)
assert np.allclose(BASE_EXPECTED * .03,
result_stack.xarray[2, 2, 0, 40:50, 40:50])
def _cli(ctx, imagestack):
ctx.obj["component"]._cli_run(
ctx,
FilterAlgorithmWithMissingConstructorTyping(
additive=ImageStack.from_path_or_url(imagestack)))
def _cli(ctx, imagestack):
ctx.obj["component"]._cli_run(
ctx,
AdditiveFilterAlgorithm(additive=ImageStack.from_path_or_url(imagestack)))
