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_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_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, 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_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_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)
