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Merged
wyli merged 14 commits into from
Sep 11, 2023
Merged

Improve ckpt_export #6965

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bd918eb
fix #6953
KumoLiu Sep 8, 2023
2884928
minor fix
KumoLiu Sep 11, 2023
fc9cc21
Merge branch 'dev' of https://github.com/Project-MONAI/MONAI into ckp…
KumoLiu Sep 11, 2023
cf415b0
add unittests
KumoLiu Sep 11, 2023
0bf4acb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 11, 2023
abd83e1
update docstring
KumoLiu Sep 11, 2023
5eefa2c
update unittests
KumoLiu Sep 11, 2023
feecd1f
minor fix
KumoLiu Sep 11, 2023
f272778
fix flake8
KumoLiu Sep 11, 2023
1f5a26e
address comments
KumoLiu Sep 11, 2023
cb4e63e
address comments
KumoLiu Sep 11, 2023
39fd68d
Update monai/bundle/scripts.py
KumoLiu Sep 11, 2023
d821498
Update monai/bundle/scripts.py
KumoLiu Sep 11, 2023
4cccaa2
fix flake8
KumoLiu Sep 11, 2023
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35 changes: 25 additions & 10 deletions monai/bundle/scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1191,10 +1191,10 @@ def onnx_export(


def ckpt_export(
net_id: str | None = None,
filepath: PathLike | None = None,
ckpt_file: str | None = None,
meta_file: str | Sequence[str] | None = None,
net_id: str | None = "network_def",
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filepath: PathLike | None = "models/model.ts",
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ckpt_file: str | None = "models/model.pt",
meta_file: str | Sequence[str] | None = "configs/metadata.json",
config_file: str | Sequence[str] | None = None,
key_in_ckpt: str | None = None,
use_trace: bool | None = None,
Expand Down Expand Up @@ -1250,9 +1250,10 @@ def ckpt_export(
)
_log_input_summary(tag="ckpt_export", args=_args)
(
config_file_,
filepath_,
ckpt_file_,
config_file_,
bundle_root_,
net_id_,
meta_file_,
key_in_ckpt_,
Expand All @@ -1261,11 +1262,12 @@ def ckpt_export(
converter_kwargs_,
) = _pop_args(
_args,
"filepath",
"ckpt_file",
"config_file",
net_id="",
meta_file=None,
filepath="models/model.ts",
ckpt_file="models/model.pt",
bundle_root=os.getcwd(),
net_id="network_def",
meta_file="configs/metadata.json",
key_in_ckpt="",
use_trace=False,
input_shape=None,
Expand All @@ -1275,9 +1277,22 @@ def ckpt_export(
parser = ConfigParser()

parser.read_config(f=config_file_)
if meta_file_ is not None:
meta_file_ = (
os.path.join(bundle_root_, "configs/metadata.json") if meta_file_ == "configs/metadata.json" else meta_file_
)
filepath_ = os.path.join(bundle_root_, "models/model.ts") if filepath_ == "models/model.ts" else filepath_
ckpt_file_ = os.path.join(bundle_root_, "models/model.pt") if ckpt_file_ == "models/model.pt" else ckpt_file_
if not os.path.exists(ckpt_file_):
raise FileNotFoundError(f"ckpt_file in {ckpt_file_} does not exist, please specify it.")
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if os.path.exists(meta_file_):
parser.read_meta(f=meta_file_)

if net_id_ == "network_def":
try:
parser.get_parsed_content(net_id_)
except ValueError as e:
raise ValueError(f"Default net_id: network_def in {config_file_} does not exist.") from e

# the rest key-values in the _args are to override config content
for k, v in _args.items():
parser[k] = v
Expand Down
53 changes: 38 additions & 15 deletions tests/test_bundle_ckpt_export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,38 +43,61 @@ def tearDown(self):
else:
del os.environ["CUDA_VISIBLE_DEVICES"] # previously unset

# @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
# def test_export(self, key_in_ckpt, use_trace):
# 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.yaml")

# 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", f"['{config_file}','{def_args_file}']", "--ckpt_file"]
# cmd += [ckpt_file, "--key_in_ckpt", key_in_ckpt, "--args_file", def_args_file]
# if use_trace == "True":
# cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
# command_line_tests(cmd)
# self.assertTrue(os.path.exists(ts_file))

# _, metadata, extra_files = load_net_with_metadata(
# ts_file, more_extra_files=["inference.json", "def_args.json"]
# )
# self.assertTrue("schema" in metadata)
# self.assertTrue("meta_file" in json.loads(extra_files["def_args.json"]))
# self.assertTrue("network_def" in json.loads(extra_files["inference.json"]))

@parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
def test_export(self, key_in_ckpt, use_trace):
meta_file = os.path.join(os.path.dirname(__file__), "testing_data", "metadata.json")
def test_default_value(self, key_in_ckpt, use_trace):
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.yaml")

ckpt_file = os.path.join(tempdir, "model.pt")
ts_file = os.path.join(tempdir, "model.ts")
ckpt_file = os.path.join(tempdir, "models/model.pt")
ts_file = os.path.join(tempdir, "models/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", f"['{config_file}','{def_args_file}']", "--ckpt_file"]
cmd += [ckpt_file, "--key_in_ckpt", key_in_ckpt, "--args_file", def_args_file]
# check with default value
cmd = ["coverage", "run", "-m", "monai.bundle", "ckpt_export", "--key_in_ckpt", key_in_ckpt]
cmd += ["--config_file", config_file, "--bundle_root", tempdir]
if use_trace == "True":
cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
command_line_tests(cmd)
self.assertTrue(os.path.exists(ts_file))

_, metadata, extra_files = load_net_with_metadata(
ts_file, more_extra_files=["inference.json", "def_args.json"]
)
self.assertTrue("schema" in metadata)
self.assertTrue("meta_file" in json.loads(extra_files["def_args.json"]))
self.assertTrue("network_def" in json.loads(extra_files["inference.json"]))


if __name__ == "__main__":
unittest.main()