def test_url_download_bundle(self, bundle_files, bundle_name, url,
hash_val):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {
"name": bundle_name,
"bundle_dir": tempdir,
"url": ""
}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args,
filepath=def_args_file)
cmd = [
"coverage", "run", "-m", "monai.bundle", "download",
"--args_file", def_args_file
]
cmd += ["--url", url]
subprocess.check_call(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
if file == "network.json":
self.assertTrue(
check_hash(filepath=file_path, val=hash_val))
def test_verify(self, meta_file, config_file):
with tempfile.TemporaryDirectory() as tempdir:
def_args = {
"meta_file": "will be replaced by `meta_file` arg",
"p": 2
}
def_args_file = os.path.join(tempdir, "def_args.json")
ConfigParser.export_config_file(config=def_args,
filepath=def_args_file)
cmd = [
"coverage", "run", "-m", "monai.bundle", "verify_net_in_out",
"network_def", "--meta_file"
]
cmd += [
meta_file, "--config_file", config_file, "-n", "4", "--any",
"16", "--args_file", def_args_file
]
cmd += [
"--_meta_#network_data_format#inputs#image#spatial_shape",
"[16,'*','2**p*n']"
]
test_env = os.environ.copy()
print(f"CUDA_VISIBLE_DEVICES in {__file__}",
test_env.get("CUDA_VISIBLE_DEVICES"))
subprocess.check_call(cmd, env=test_env)
def test_relative_id(self, config):
parser = ConfigParser(config=config)
for id in config:
item = parser.get_parsed_content(id=id)
if isinstance(item, int):
self.assertEqual(item, 1)
if isinstance(item, dict):
self.assertEqual(str(item), str({"key": 1, "value1": 2, "value2": 2, "value3": [3, 4, 4, 105]}))
def test_verify(self, meta_file, schema_file):
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"meta_file": "will be replaced by `meta_file` arg"}
def_args_file = os.path.join(tempdir, "def_args.json")
ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "verify_metadata", "--meta_file", meta_file]
cmd += ["--filepath", schema_file, "--hash_val", self.config["hash_val"], "--args_file", def_args_file]
subprocess.check_call(cmd)
def test_lambda_reference(self):
configs = {
"patch_size": [8, 8],
"transform": {"_target_": "Lambda", "func": "$lambda x: x.reshape((1, *@patch_size))"},
}
parser = ConfigParser(config=configs)
trans = parser.get_parsed_content(id="transform")
result = trans(np.ones(64))
self.assertTupleEqual(result.shape, (1, 8, 8))
def test_function(self, config):
parser = ConfigParser(config=config, globals={"TestClass": TestClass})
for id in config:
func = parser.get_parsed_content(id=id)
self.assertTrue(id in parser.ref_resolver.resolved_content)
if id == "error_func":
with self.assertRaises(TypeError):
func(1, 2)
continue
self.assertEqual(func(1, 2), 3)
def test_list_expressions(self):
config = {
"transform": {
"_target_": "Compose",
"transforms": [{"_target_": "RandScaleIntensity", "factors": 0.5, "prob": 1.0}],
},
"training": ["$monai.utils.set_determinism(seed=123)", "$@transform(np.asarray([1, 2]))"],
}
parser = ConfigParser(config=config)
parser.get_parsed_content("training", lazy=True, instantiate=True, eval_expr=True)
np.testing.assert_allclose(parser.get_parsed_content("training#1", lazy=True), [0.7942, 1.5885], atol=1e-4)
def test_shape(self, config_file, expected_shape):
test_image = np.random.rand(*expected_shape)
tempdir = self.data_dir
filename = os.path.join(tempdir, "image.nii")
nib.save(nib.Nifti1Image(test_image, np.eye(4)), filename)
# generate default args in a JSON file
logging_conf = os.path.join(os.path.dirname(__file__), "testing_data", "logging.conf")
def_args = {"config_file": "will be replaced by `config_file` arg", "logging_file": logging_conf}
def_args_file = os.path.join(tempdir, "def_args.json")
ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
meta = {"datalist": [{"image": filename}], "output_dir": tempdir, "window": (96, 96, 96)}
# test YAML file
meta_file = os.path.join(tempdir, "meta.yaml")
ConfigParser.export_config_file(config=meta, filepath=meta_file, fmt="yaml")
# test override with file, up case postfix
overridefile1 = os.path.join(tempdir, "override1.JSON")
with open(overridefile1, "w") as f:
# test override with part of the overriding file
json.dump({"move_net": "$@network_def.to(@device)"}, f)
os.makedirs(os.path.join(tempdir, "jsons"), exist_ok=True)
overridefile2 = os.path.join(tempdir, "jsons/override2.JSON")
with open(overridefile2, "w") as f:
# test override with the whole overriding file
json.dump("Dataset", f)
saver = LoadImage(image_only=True)
if sys.platform == "win32":
override = "--network $@network_def.to(@device) --dataset#_target_ Dataset"
else:
override = f"--network %{overridefile1}#move_net --dataset#_target_ %{overridefile2}"
# test with `monai.bundle` as CLI entry directly
cmd = f"-m monai.bundle run evaluator --postprocessing#transforms#2#output_postfix seg {override}"
la = ["coverage", "run"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
test_env = os.environ.copy()
print(f"CUDA_VISIBLE_DEVICES in {__file__}", test_env.get("CUDA_VISIBLE_DEVICES"))
subprocess.check_call(la + ["--args_file", def_args_file], env=test_env)
self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_seg.nii.gz")).shape, expected_shape)
# here test the script with `google fire` tool as CLI
cmd = "-m fire monai.bundle.scripts run --runner_id evaluator"
cmd += f" --evaluator#amp False {override}"
la = ["coverage", "run"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
subprocess.check_call(la, env=test_env)
self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_trans.nii.gz")).shape, expected_shape)
def test_export(self, key_in_ckpt):
meta_file = os.path.join(os.path.dirname(__file__), "testing_data",
"metadata.json")
config_file = os.path.join(os.path.dirname(__file__), "testing_data",
"inference.json")
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"meta_file": "will be replaced by `meta_file` arg"}
def_args_file = os.path.join(tempdir, "def_args.json")
ckpt_file = os.path.join(tempdir, "model.pt")
ts_file = os.path.join(tempdir, "model.ts")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
parser.read_config(config_file)
net = parser.get_parsed_content("network_def")
save_state(src=net if key_in_ckpt == "" else {key_in_ckpt: net},
path=ckpt_file)
cmd = [
"coverage", "run", "-m", "monai.bundle", "ckpt_export",
"network_def", "--filepath", ts_file
]
cmd += [
"--meta_file", meta_file, "--config_file", config_file,
"--ckpt_file", ckpt_file
]
cmd += ["--key_in_ckpt", key_in_ckpt, "--args_file", def_args_file]
subprocess.check_call(cmd)
self.assertTrue(os.path.exists(ts_file))
def test_macro_replace(self):
with tempfile.TemporaryDirectory() as tempdir:
another_file = os.path.join(tempdir, "another.json")
ConfigParser.export_config_file(config={"E": 4}, filepath=another_file)
# test macro with id, relative id, and macro in another file
config = {"A": {"B": 1, "C": 2}, "D": [3, "%A#B", "%#0", f"%{another_file}#E"]}
parser = ConfigParser(config=config)
parser.resolve_macro_and_relative_ids()
self.assertEqual(str(parser.get()), str({"A": {"B": 1, "C": 2}, "D": [3, 1, 3, 4]}))
def test_parse(self, config, expected_ids, output_types):
parser = ConfigParser(config=config, globals={"monai": "monai"})
# test lazy instantiation with original config content
parser["transform"]["transforms"][0]["keys"] = "label1"
trans = parser.get_parsed_content(id="transform#transforms#0")
self.assertEqual(trans.keys[0], "label1")
# test re-use the parsed content or not with the `lazy` option
self.assertEqual(trans, parser.get_parsed_content(id="transform#transforms#0"))
self.assertEqual(trans, parser.get_parsed_content(id="transform#transforms#0", lazy=True))
self.assertNotEqual(trans, parser.get_parsed_content(id="transform#transforms#0", lazy=False))
# test nested id
parser["transform#transforms#0#keys"] = "label2"
self.assertEqual(parser.get_parsed_content(id="transform#transforms#0").keys[0], "label2")
for id, cls in zip(expected_ids, output_types):
self.assertTrue(isinstance(parser.get_parsed_content(id), cls))
# test root content
root = parser.get_parsed_content(id="")
for v, cls in zip(root.values(), [Compose, Dataset, DataLoader]):
self.assertTrue(isinstance(v, cls))
# test default value
self.assertEqual(parser.get_parsed_content(id="abc", default=ConfigItem(12345, "abc")), 12345)
def test_config_content(self):
test_config = {"preprocessing": [{"_target_": "LoadImage"}], "dataset": {"_target_": "Dataset"}}
parser = ConfigParser(config=test_config)
# test `get`, `set`, `__getitem__`, `__setitem__`
self.assertEqual(str(parser.get()), str(test_config))
parser.set(config=test_config)
self.assertListEqual(parser["preprocessing"], test_config["preprocessing"])
parser["dataset"] = {"_target_": "CacheDataset"}
self.assertEqual(parser["dataset"]["_target_"], "CacheDataset")
# test nested ids
parser["dataset#_target_"] = "Dataset"
self.assertEqual(parser["dataset#_target_"], "Dataset")
parser.update({"dataset#_target_1": "Dataset1"})
self.assertEqual(parser["dataset#_target_1"], "Dataset1")
# test int id
parser.set(["test1", "test2", "test3"])
parser[1] = "test4"
self.assertEqual(parser[1], "test4")
def test_contains(self):
empty_parser = ConfigParser({})
empty_parser.parse()
parser = ConfigParser({"value": 1, "entry": "string content"})
parser.parse()
with self.subTest("Testing empty parser"):
self.assertFalse("something" in empty_parser)
with self.subTest("Testing with keys"):
self.assertTrue("value" in parser)
self.assertFalse("value1" in parser)
self.assertTrue("entry" in parser)
self.assertFalse("entr" in parser)
def test_allow_missing_reference(self, config):
default = ReferenceResolver.allow_missing_reference
ReferenceResolver.allow_missing_reference = True
parser = ConfigParser(config=config)
for id in config:
item = parser.get_parsed_content(id=id)
if id in ("A", "B"):
self.assertEqual(item, 1)
elif id == "C":
self.assertEqual(item, "@D")
elif id == "E":
self.assertEqual(item, "test@F")
# restore the default value
ReferenceResolver.allow_missing_reference = default
with self.assertRaises(ValueError):
parser.parse()
parser.get_parsed_content(id="E")
def test_transforms(self, case_id):
set_determinism(2022)
config = ConfigParser()
config.read_config(TEST_CASES)
config["input_keys"] = keys
test_case = config.get_parsed_content(id=case_id, instantiate=True) # transform instance
dataset = CacheDataset(self.files, transform=test_case)
loader = DataLoader(dataset, batch_size=3, shuffle=True)
for x in loader:
self.assertIsInstance(x[keys[0]], MetaTensor)
self.assertIsInstance(x[keys[1]], MetaTensor)
out = decollate_batch(x) # decollate every batch should work
# test forward patches
loaded = out[0]
self.assertEqual(len(loaded), len(keys))
img, seg = loaded[keys[0]], loaded[keys[1]]
expected = config.get_parsed_content(id=f"{case_id}_answer", instantiate=True) # expected results
self.assertEqual(expected["load_shape"], list(x[keys[0]].shape))
assert_allclose(expected["affine"], img.affine, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
assert_allclose(expected["affine"], seg.affine, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
test_cls = [type(x).__name__ for x in test_case.transforms]
tracked_cls = [x[TraceKeys.CLASS_NAME] for x in img.applied_operations]
self.assertTrue(len(tracked_cls) <= len(test_cls)) # tracked items should be no more than the compose items.
with tempfile.TemporaryDirectory() as tempdir: # test writer
SaveImageD(keys, resample=False, output_dir=tempdir, output_postfix=case_id)(loaded)
# test inverse
inv = InvertD(keys, orig_keys=keys, transform=test_case, nearest_interp=True)
out = inv(loaded)
img, seg = out[keys[0]], out[keys[1]]
assert_allclose(expected["inv_affine"], img.affine, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
assert_allclose(expected["inv_affine"], seg.affine, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
self.assertFalse(img.applied_operations)
self.assertFalse(seg.applied_operations)
assert_allclose(expected["inv_shape"], img.shape, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
assert_allclose(expected["inv_shape"], seg.shape, type_test=False, atol=TINY_DIFF, rtol=TINY_DIFF)
with tempfile.TemporaryDirectory() as tempdir: # test writer
SaveImageD(keys, resample=False, output_dir=tempdir, output_postfix=case_id)(out)
seg_file = os.path.join(tempdir, key_1, f"{key_1}_{case_id}.nii.gz")
segout = nib.load(seg_file).get_fdata()
segin = nib.load(FILE_PATH_1).get_fdata()
ndiff = np.sum(np.abs(segout - segin) > 0)
total = np.prod(segout.shape)
self.assertTrue(ndiff / total < 0.4, f"{ndiff / total}")
def test_parse(self, config, expected_ids, output_types):
parser = ConfigParser(config=config, globals={"monai": "monai"})
# test lazy instantiation with original config content
parser["transform"]["transforms"][0]["keys"] = "label1"
self.assertEqual(
parser.get_parsed_content(id="transform#transforms#0").keys[0],
"label1")
# test nested id
parser["transform#transforms#0#keys"] = "label2"
self.assertEqual(
parser.get_parsed_content(id="transform#transforms#0").keys[0],
"label2")
for id, cls in zip(expected_ids, output_types):
self.assertTrue(isinstance(parser.get_parsed_content(id), cls))
# test root content
root = parser.get_parsed_content(id="")
for v, cls in zip(root.values(), [Compose, Dataset, DataLoader]):
self.assertTrue(isinstance(v, cls))
def test_error_instance(self):
config = {"transform": {"_target_": "Compose", "transforms_wrong_key": []}}
parser = ConfigParser(config=config)
with self.assertRaises(RuntimeError):
parser.get_parsed_content("transform", instantiate=True, eval_expr=True)
