642 (part 1) update large files for bundles [skip ci] (#646)

yiheng-wang-nv · ericspod · web-flow · commit ebdbeb6e1d37 · 2024-09-11T17:20:44.000+08:00
Fixes #642 . ### Description A few sentences describing the changes proposed in this pull request. ### Status **Ready/Work in progress/Hold** ### Please ensure all the checkboxes:  - [x] Codeformat tests passed locally by running `./runtests.sh --codeformat`. - [ ] In-line docstrings updated. - [ ] Update `version` and `changelog` in `metadata.json` if changing an existing bundle. - [ ] Please ensure the naming rules in config files meet our requirements (please refer to: `CONTRIBUTING.md`). - [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy` are correct in `metadata.json`. - [ ] Descriptions should be consistent with the content, such as `eval_metrics` of the provided weights and TorchScript modules. - [ ] Files larger than 25MB are excluded and replaced by providing download links in `large_file.yml`. - [ ] Avoid using path that contains personal information within config files (such as use `/home/your_name/` for `"bundle_root"`). --------- Signed-off-by: Yiheng Wang <vennw@nvidia.com> Signed-off-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
diff --git a/models/brats_mri_segmentation/configs/metadata.json b/models/brats_mri_segmentation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.5.1",
+    "version": "0.5.2",
     "changelog": {
+        "0.5.2": "use monai 1.4 and update large files",
         "0.5.1": "update to use monai 1.3.1",
         "0.5.0": "add load_pretrain flag for infer",
         "0.4.9": "add checkpoint loader for infer",
@@ -29,14 +30,14 @@
         "0.1.1": "update for MetaTensor",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "nibabel": "5.2.1",
         "pytorch-ignite": "0.4.11",
-        "scikit-learn": "1.2.0",
-        "tensorboard": "2.16.2"
+        "scikit-learn": "1.5.1",
+        "tensorboard": "2.17.0"
     },
     "name": "BraTS MRI segmentation",
     "task": "Multimodal Brain Tumor segmentation",
diff --git a/models/brats_mri_segmentation/large_files.yml b/models/brats_mri_segmentation/large_files.yml
@@ -1,9 +1,9 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/file/d/1UFERbDK-Q1hKHqH-shKFcEIE-WPvYMN_/view?usp=sharing"
-    hash_val: "870e677b782a5184cbc48db1456b78e8"
-    hash_type: "md5"
-  - path: "models/model.ts"
-    url: "https://drive.google.com/file/d/1s_sfFpCN7vkfNHdzH-ZvMlLpTE38Mx3o/view?usp=sharing"
-    hash_val: "c82f693c8f671e9899d21c2f241892f0"
-    hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_brats_mri_segmentation.pt"
+  hash_val: "870e677b782a5184cbc48db1456b78e8"
+  hash_type: "md5"
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_brats_mri_segmentation.ts"
+  hash_val: "c82f693c8f671e9899d21c2f241892f0"
+  hash_type: "md5"
diff --git a/models/endoscopic_inbody_classification/configs/metadata.json b/models/endoscopic_inbody_classification/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.4.8",
+    "version": "0.4.9",
     "changelog": {
+        "0.4.9": "use monai 1.4 and update large files",
         "0.4.8": "update to use monai 1.3.1",
         "0.4.7": "add load_pretrain flag for infer",
         "0.4.6": "add output for inference",
@@ -27,8 +28,8 @@
         "0.1.0": "complete the first version model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "nibabel": "5.2.1",
diff --git a/models/endoscopic_inbody_classification/large_files.yml b/models/endoscopic_inbody_classification/large_files.yml
@@ -1,9 +1,9 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/file/d/1zL74humdB89srDSZjcbYrOe-sqsEvmbw/view?usp=sharing"
-    hash_val: "e373019524bda213ccbce2251f057a5f"
-    hash_type: "md5"
-  - path: "models/model.ts"
-    url: "https://drive.google.com/file/d/1oW0B0moQEEcgn8suNI7g2d42ymHVNE6w/view?usp=sharing"
-    hash_val: "8596d8a288edc28a34384a1c3f464110"
-    hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_endoscopic_inbody_classification_v1.pt"
+  hash_val: "e373019524bda213ccbce2251f057a5f"
+  hash_type: "md5"
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_endoscopic_inbody_classification_v1.ts"
+  hash_val: "8596d8a288edc28a34384a1c3f464110"
+  hash_type: "md5"
diff --git a/models/endoscopic_tool_segmentation/configs/metadata.json b/models/endoscopic_tool_segmentation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.5.9",
+    "version": "0.6.0",
     "changelog": {
+        "0.6.0": "use monai 1.4 and update large files",
         "0.5.9": "update to use monai 1.3.1",
         "0.5.8": "add load_pretrain flag for infer",
         "0.5.7": "add checkpoint loader for infer",
@@ -30,8 +31,8 @@
         "0.1.0": "complete the first version model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "nibabel": "5.2.1",
diff --git a/models/endoscopic_tool_segmentation/large_files.yml b/models/endoscopic_tool_segmentation/large_files.yml
@@ -1,9 +1,9 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/file/d/1I7UtWDKDEcezMqYiA-i_hsRTCrvWwJ61/view?usp=sharing"
-    hash_val: "7ca94167f05ac9f62a16b1898155ff71"
-    hash_type: "md5"
-  - path: "models/model.ts"
-    url: "https://drive.google.com/file/d/1e_wYd1HjJQ0dz_HKdbthRcMOyUL02aLG/view?usp=sharing"
-    hash_val: "889a9659f5ab245bd5c4a0a36c80728f"
-    hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_endoscopic_tool_segmentation.pt"
+  hash_val: "7ca94167f05ac9f62a16b1898155ff71"
+  hash_type: "md5"
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_endoscopic_tool_segmentation.ts"
+  hash_val: "889a9659f5ab245bd5c4a0a36c80728f"
+  hash_type: "md5"
diff --git a/models/lung_nodule_ct_detection/configs/metadata.json b/models/lung_nodule_ct_detection/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.6.6",
+    "version": "0.6.7",
     "changelog": {
+        "0.6.7": "use monai 1.4 and update large files",
         "0.6.6": "update to use monai 1.3.1",
         "0.6.5": "remove notes for trt_export in readme",
         "0.6.4": "add notes for trt_export in readme",
@@ -30,13 +31,13 @@
         "0.1.1": "add reference for LIDC dataset",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "nibabel": "5.2.1",
         "pytorch-ignite": "0.4.11",
-        "torchvision": "0.17.2"
+        "torchvision": "0.19.0"
     },
     "name": "Lung nodule CT detection",
     "task": "CT lung nodule detection",
diff --git a/models/lung_nodule_ct_detection/large_files.yml b/models/lung_nodule_ct_detection/large_files.yml
@@ -1,9 +1,9 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/uc?id=14QUxVChL-BLFrWQRsiKn-4d1t6Qhx53S"
-    hash_val: "b2e732a7c2786e2f8398fa45293b1e73"
-    hash_type: "md5"
-  - path: "models/model.ts"
-    url: "https://drive.google.com/uc?id=1cywqiI9dLXX0_5z_MqvdXFgbXLbbZDjH"
-    hash_val: "f5567e1c74b41964b2a0b19ea855f3b0"
-    hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_lung_nodule_ct_detection.pt"
+  hash_val: "b2e732a7c2786e2f8398fa45293b1e73"
+  hash_type: "md5"
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_lung_nodule_ct_detection.ts"
+  hash_val: "f5567e1c74b41964b2a0b19ea855f3b0"
+  hash_type: "md5"
diff --git a/models/pancreas_ct_dints_segmentation/configs/metadata.json b/models/pancreas_ct_dints_segmentation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.4.9",
+    "version": "0.5.0",
     "changelog": {
+        "0.5.0": "use monai 1.4 and update large files",
         "0.4.9": "update to use monai 1.3.1",
         "0.4.8": "add load_pretrain flag for infer",
         "0.4.7": "add missing yaml lib requirement in metadata",
@@ -27,14 +28,14 @@
         "0.1.0": "complete the model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "fire": "0.6.0",
         "nibabel": "5.2.1",
         "pytorch-ignite": "0.4.11",
-        "PyYAML": "6.0"
+        "PyYAML": "6.0.1"
     },
     "name": "Pancreas CT DiNTS segmentation",
     "task": "Neural architecture search on pancreas CT segmentation",
diff --git a/models/pancreas_ct_dints_segmentation/large_files.yml b/models/pancreas_ct_dints_segmentation/large_files.yml
@@ -1,13 +1,13 @@
 large_files:
-  - path: "models/search_code_18590.pt"
-    url: "https://drive.google.com/uc?export=download&id=1ZRpQl6NGa6_tSATO7uULIBqxNtOvsy5j"
-    hash_val: "2ff53724aa9d80d9025034d36785cdb8"
-    hash_type: "md5"
-  - path: "models/model.pt"
-    url: "https://drive.google.com/uc?export=download&id=1p0GXjgUMLvOj3_6seBCtByMOdgWW0Wue"
-    hash_val: "ce8531b5143b417f65d5b481f72bc911"
-    hash_type: "md5"
-  - path: "models/model.ts"
-    url: "https://drive.google.com/uc?export=download&id=1nZHEM81FlAp5-vyk1vVwoBEjbDC9fKd4"
-    hash_val: "b42221639099a5548c1a0e27772252ec"
-    hash_type: "md5"
+- path: "models/search_code_18590.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pancreas_ct_dints_segmentation_search_code.pt"
+  hash_val: "2ff53724aa9d80d9025034d36785cdb8"
+  hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pancreas_ct_dints_segmentation.pt"
+  hash_val: "ce8531b5143b417f65d5b481f72bc911"
+  hash_type: "md5"
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pancreas_ct_dints_segmentation.ts"
+  hash_val: "b42221639099a5548c1a0e27772252ec"
+  hash_type: "md5"
diff --git a/models/pathology_nuclick_annotation/configs/metadata.json b/models/pathology_nuclick_annotation/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.1.9",
+    "version": "0.2.0",
     "changelog": {
+        "0.2.0": "use monai 1.4 and update large files",
         "0.1.9": "update to use monai 1.3.1",
         "0.1.8": "add load_pretrain flag for infer",
         "0.1.7": "add checkpoint loader for infer",
@@ -22,13 +23,13 @@
         "0.0.2": "Update The Torch Vision Transform",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
         "nibabel": "5.2.1",
         "pytorch-ignite": "0.4.11",
-        "torchvision": "0.17.2"
+        "torchvision": "0.19.0"
     },
     "name": "Pathology nuclick annotation",
     "task": "Pathology Nuclick annotation",
diff --git a/models/pathology_nuclick_annotation/large_files.yml b/models/pathology_nuclick_annotation/large_files.yml
@@ -1,9 +1,9 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/file/d/1J5xypdNvfohTsvHD__HWMoTCySJVu0tQ/view?usp=sharing"
-    hash_val: ""
-    hash_type: ""
-  - path: "models/model.ts"
-    url: "https://drive.google.com/file/d/1aoYevHZ48wnFzwXLosorxWvjs7y0bUth/view?usp=sharing"
-    hash_val: ""
-    hash_type: ""
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_nuclick_annotation.pt"
+  hash_val: ""
+  hash_type: ""
+- path: "models/model.ts"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_nuclick_annotation.ts"
+  hash_val: ""
+  hash_type: ""
diff --git a/models/pathology_tumor_detection/configs/metadata.json b/models/pathology_tumor_detection/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.5.9",
+    "version": "0.6.0",
     "changelog": {
+        "0.6.0": "use monai 1.4 and update large files",
         "0.5.9": "update to use monai 1.3.1",
         "0.5.8": "update readme to add memory warning",
         "0.5.7": "update channel_def in metadata",
@@ -30,13 +31,13 @@
         "0.1.1": "fix location variable name change",
         "0.1.0": "initialize release of the bundle"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
     "optional_packages_version": {
-        "cucim-cu12": "24.2.0",
-        "pandas": "1.5.3",
-        "torchvision": "0.17.2"
+        "cucim-cu12": "24.6.0",
+        "pandas": "2.2.1",
+        "torchvision": "0.19.0"
     },
     "name": "Pathology tumor detection",
     "task": "Pathology metastasis detection",
diff --git a/models/pathology_tumor_detection/large_files.yml b/models/pathology_tumor_detection/large_files.yml
@@ -1,17 +1,17 @@
 large_files:
-  - path: "models/model.pt"
-    url: "https://drive.google.com/uc?id=1k8CgZuqpQDlijfKikpNtxi0qSLG5ofNL"
-    hash_val: "56b78ef17fd5e693a818dd947f6f232a"
-    hash_type: "md5"
-  - path: "training.csv"
-    url: "https://drive.google.com/uc?id=1httIjgji6U6rMIb0P8pE0F-hXFAuvQEf"
-    hash_val: "6e6696a5fb3cb76f15ad0d64d867e457"
-    hash_type: "md5"
-  - path: "validation.csv"
-    url: "https://drive.google.com/uc?id=1tJulzl9m5LUm16IeFbOCoFnaSWoB6i5L"
-    hash_val: "dbfa883358fdd931cee5e887047dbb0a"
-    hash_type: "md5"
-  - path: "testing.csv"
-    url: "https://drive.google.com/uc?id=1IehEY2kfsbjNbccPd6tP4WrYv32miHnc"
-    hash_val: "b6f57855f6d7c38c6e4c859e8df60dd8"
-    hash_type: "md5"
+- path: "models/model.pt"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_tumor_detection_v1.pt"
+  hash_val: "56b78ef17fd5e693a818dd947f6f232a"
+  hash_type: "md5"
+- path: "training.csv"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_tumor_detection_training.csv"
+  hash_val: "6e6696a5fb3cb76f15ad0d64d867e457"
+  hash_type: "md5"
+- path: "validation.csv"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_tumor_detection_validation.csv"
+  hash_val: "dbfa883358fdd931cee5e887047dbb0a"
+  hash_type: "md5"
+- path: "testing.csv"
+  url: "https://developer.download.nvidia.com/assets/Clara/monai/tutorials/model_zoo/model_pathology_tumor_detection_test.csv"
+  hash_val: "b6f57855f6d7c38c6e4c859e8df60dd8"
+  hash_type: "md5"
diff --git a/models/prostate_mri_anatomy/configs/inference.json b/models/prostate_mri_anatomy/configs/inference.json
@@ -3,7 +3,7 @@
         "$import pandas as pd",
         "$import os"
     ],
-    "bundle_root": "/workspace/data/prostate_mri_anatomy",
+    "bundle_root": ".",
     "output_dir": "$@bundle_root + '/eval'",
     "dataset_dir": "/workspace/data/prostate158/prostate158_test/",
     "datalist": "$list(@dataset_dir + pd.read_csv(@dataset_dir + 'test.csv').t2)",
@@ -159,8 +159,10 @@
         "val_handlers": "@handlers",
         "amp": true
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@evaluator.run()"
     ]
 }
diff --git a/models/prostate_mri_anatomy/configs/metadata.json b/models/prostate_mri_anatomy/configs/metadata.json
@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.3",
+    "version": "0.3.4",
     "changelog": {
+        "0.3.4": "support monai 1.4",
         "0.3.3": "add invertd transformation",
         "0.3.2": "add name tag",
         "0.3.1": "fix license Copyright error",
@@ -10,14 +11,14 @@
         "0.1.1": "add torchscript model",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "0.9.1",
-    "pytorch_version": "1.11.0",
-    "numpy_version": "1.22.3",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
+    "numpy_version": "1.24.4",
     "optional_packages_version": {
-        "nibabel": "3.2.2",
-        "itk": "5.3",
-        "pytorch-ignite": "0.4.9",
-        "pandas": "1.4.2"
+        "nibabel": "5.2.1",
+        "itk": "5.4.0",
+        "pytorch-ignite": "0.4.11",
+        "pandas": "2.2.1"
     },
     "name": "Prostate MRI anatomy",
     "task": "Segmentation of peripheral zone and central gland in prostate MRI",
diff --git a/models/prostate_mri_anatomy/configs/train.json b/models/prostate_mri_anatomy/configs/train.json
diff --git a/models/spleen_ct_segmentation/configs/metadata.json b/models/spleen_ct_segmentation/configs/metadata.json
diff --git a/models/spleen_ct_segmentation/large_files.yml b/models/spleen_ct_segmentation/large_files.yml
diff --git a/models/spleen_deepedit_annotation/configs/metadata.json b/models/spleen_deepedit_annotation/configs/metadata.json
diff --git a/models/spleen_deepedit_annotation/large_files.yml b/models/spleen_deepedit_annotation/large_files.yml
diff --git a/models/wholeBody_ct_segmentation/configs/metadata.json b/models/wholeBody_ct_segmentation/configs/metadata.json
diff --git a/models/wholeBody_ct_segmentation/docs/README.md b/models/wholeBody_ct_segmentation/docs/README.md
diff --git a/models/wholeBody_ct_segmentation/large_files.yml b/models/wholeBody_ct_segmentation/large_files.yml
