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4001 update mmars #4002

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Merged
wyli merged 4 commits into from
Mar 25, 2022
Merged

4001 update mmars #4002

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97f3a89
update mmars, fixes https://github.com/Project-MONAI/MONAI/issues/4003
wyli Mar 25, 2022
398f4d5
adds typing
wyli Mar 25, 2022
3c864bf
update based on comments
wyli Mar 25, 2022
4baf495
workaround cucim
wyli Mar 25, 2022
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7 changes: 5 additions & 2 deletions monai/apps/mmars/mmars.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import monai.networks.nets as monai_nets
from monai.apps.utils import download_and_extract, logger
from monai.config.type_definitions import PathLike
from monai.networks.utils import copy_model_state
from monai.utils.module import optional_import

from .model_desc import MODEL_DESC
Expand Down Expand Up @@ -243,7 +244,7 @@ def load_from_mmar(

# 1. search `model_dict['train_config]` for model config spec.
model_config = _get_val(dict(model_dict).get("train_conf", {}), key=model_key, default={})
if not model_config:
if not model_config or not isinstance(model_config, Mapping):
# 2. search json CONFIG_FILE for model config spec.
json_path = model_dir / item.get(Keys.CONFIG_FILE, os.path.join("config", "config_train.json"))
with open(json_path) as f:
Expand Down Expand Up @@ -285,7 +286,9 @@ def load_from_mmar(
else:
model_inst = model_cls()
if pretrained:
model_inst.load_state_dict(model_dict.get(model_key, model_dict))
_, changed, unchanged = copy_model_state(model_inst, model_dict.get(model_key, model_dict), inplace=True)
if not (changed and not unchanged): # not all model_inst varaibles are changed
logger.warning(f"*** Loading model state -- unchanged: {len(unchanged)}, changed: {len(changed)}.")
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logger.info("\n---")
doc_url = item.get(Keys.DOC) or _get_ngc_doc_url(item[Keys.NAME], model_prefix="nvidia:med:")
logger.info(f"For more information, please visit {doc_url}\n")
Expand Down
33 changes: 32 additions & 1 deletion monai/apps/mmars/model_desc.py
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Expand Up @@ -17,6 +17,7 @@
"""

import os
from typing import Any, Dict, Tuple

__all__ = ["MODEL_DESC", "RemoteMMARKeys"]

Expand All @@ -39,7 +40,7 @@ class RemoteMMARKeys:
VERSION = "version" # version of the MMAR


MODEL_DESC = (
MODEL_DESC: Tuple[Dict[Any, Any], ...] = (
{
RemoteMMARKeys.ID: "clara_pt_spleen_ct_segmentation_1",
RemoteMMARKeys.NAME: "clara_pt_spleen_ct_segmentation",
Expand Down Expand Up @@ -194,4 +195,34 @@ class RemoteMMARKeys:
RemoteMMARKeys.CONFIG_FILE: os.path.join("config", "config_train.json"),
RemoteMMARKeys.VERSION: 1,
},
{
RemoteMMARKeys.ID: "clara_pt_unetr_ct_btcv_segmentation",
RemoteMMARKeys.NAME: "clara_pt_unetr_ct_btcv_segmentation",
RemoteMMARKeys.FILE_TYPE: "zip",
RemoteMMARKeys.HASH_TYPE: "md5",
RemoteMMARKeys.HASH_VAL: None,
RemoteMMARKeys.MODEL_FILE: os.path.join("models", "model.pt"),
RemoteMMARKeys.CONFIG_FILE: os.path.join("config", "config_train.json"),
RemoteMMARKeys.VERSION: 4.1,
},
{
RemoteMMARKeys.ID: "clara_pt_chest_xray_classification",
RemoteMMARKeys.NAME: "clara_pt_chest_xray_classification",
RemoteMMARKeys.FILE_TYPE: "zip",
RemoteMMARKeys.HASH_TYPE: "md5",
RemoteMMARKeys.HASH_VAL: None,
RemoteMMARKeys.MODEL_FILE: os.path.join("models", "model.pt"),
RemoteMMARKeys.CONFIG_FILE: os.path.join("config", "config_train.json"),
RemoteMMARKeys.VERSION: 4.1,
},
{
RemoteMMARKeys.ID: "clara_pt_self_supervised_learning_segmentation",
RemoteMMARKeys.NAME: "clara_pt_self_supervised_learning_segmentation",
RemoteMMARKeys.FILE_TYPE: "zip",
RemoteMMARKeys.HASH_TYPE: "md5",
RemoteMMARKeys.HASH_VAL: None,
RemoteMMARKeys.MODEL_FILE: os.path.join("models_2gpu", "best_metric_model.pt"),
RemoteMMARKeys.CONFIG_FILE: os.path.join("config", "config_train.json"),
RemoteMMARKeys.VERSION: 4.1,
},
)
4 changes: 2 additions & 2 deletions requirements-dev.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ flake8-bugbear
flake8-comprehensions
flake8-executable
flake8-pyi
pylint
pylint!=2.13 # https://github.com/PyCQA/pylint/issues/5969
mccabe
pep8-naming
pycodestyle
Expand All @@ -32,7 +32,7 @@ Sphinx==3.5.3
recommonmark==0.6.0
sphinx-autodoc-typehints==1.11.1
sphinx-rtd-theme==0.5.2
cucim>=21.8.2; platform_system == "Linux"
cucim==22.2.0; platform_system == "Linux"
openslide-python==1.1.2
imagecodecs; platform_system == "Linux"
tifffile; platform_system == "Linux"
Expand Down
2 changes: 2 additions & 0 deletions tests/ngc_mmar_loading.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@ def setUp(self):
def test_loading_mmar(self, item):
if item["name"] == "clara_pt_fed_learning_brain_tumor_mri_segmentation":
default_model_file = os.path.join("models", "server", "best_FL_global_model.pt")
elif item["name"] == "clara_pt_self_supervised_learning_segmentation":
default_model_file = os.path.join("models_2gpu", "best_metric_model.pt")
else:
default_model_file = None
pretrained_model = load_from_mmar(
Expand Down
36 changes: 24 additions & 12 deletions tests/test_mmar_download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,19 +45,19 @@
np.array(
[
[
[-0.21147135, 0.10815059, -0.04733997],
[-0.3425553, 0.03304602, 0.113512],
[0.1278807, 0.26298857, -0.0583012],
[0.01671106, 0.08502351, -0.1766469],
[-0.13039736, -0.06137804, 0.03924942],
[0.02268324, 0.159056, -0.03485069],
],
[
[-0.3658006, -0.14725913, 0.01149207],
[-0.5453718, -0.12894264, -0.05492746],
[0.16887102, 0.17586298, 0.03977356],
[0.04788467, -0.09365353, -0.05802464],
[-0.19500689, -0.13514304, -0.08191573],
[0.0238207, 0.08029253, 0.10818923],
],
[
[-0.12767333, -0.07876065, 0.03136465],
[0.26057404, -0.03538669, 0.07552322],
[0.23879515, 0.04919613, 0.01725162],
[-0.11541673, -0.10622888, 0.039689],
[0.18462701, -0.0499289, 0.14309818],
[0.00528282, 0.02152331, 0.1698219],
],
]
),
Expand All @@ -71,9 +71,21 @@
"SegResNet",
np.array(
[
[[-0.0839, 0.0715, -0.0760], [0.0645, 0.1186, 0.0218], [0.0303, 0.0631, -0.0648]],
[[0.0128, 0.1440, 0.0213], [0.1658, 0.1813, 0.0541], [-0.0627, 0.0839, 0.0660]],
[[-0.1207, 0.0138, -0.0808], [0.0277, 0.0416, 0.0597], [0.0455, -0.0134, -0.0949]],
[
[0.01874463, 0.12237817, 0.09269974],
[0.07691482, 0.00621202, -0.06682577],
[-0.07718472, 0.08637864, -0.03222707],
],
[
[0.05117761, 0.07428649, -0.03053505],
[0.11045473, 0.07083791, 0.06547518],
[0.09555705, -0.03950734, -0.00819483],
],
[
[0.03704128, 0.062543, 0.0380853],
[-0.02814676, -0.03078287, -0.01383446],
[-0.08137762, 0.01385882, 0.01229484],
],
]
),
),
Expand Down