diff --git a/models/brats_mri_segmentation/configs/inference.json b/models/brats_mri_segmentation/configs/inference.json index 04e673b4..a6d5f887 100644 --- a/models/brats_mri_segmentation/configs/inference.json +++ b/models/brats_mri_segmentation/configs/inference.json @@ -12,6 +12,7 @@ "output_dtype": "uint8", "output_postfix": "seg", "separate_folder": true, + "load_pretrain": true, "data_list_file_path": "$@bundle_root + '/configs/datalist.json'", "dataset_dir": "/workspace/data/medical/brats2018challenge", "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='testing', base_dir=@dataset_dir)", @@ -140,7 +141,7 @@ }, "initialize": [ "$setattr(torch.backends.cudnn, 'benchmark', True)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/brats_mri_segmentation/configs/metadata.json b/models/brats_mri_segmentation/configs/metadata.json index 9679fa09..8b206ffb 100644 --- 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": "0.4.9", + "version": "0.5.0", "changelog": { + "0.5.0": "add load_pretrain flag for infer", "0.4.9": "add checkpoint loader for infer", "0.4.8": "fix the wrong GPU index issue of multi-node", "0.4.7": "enhance prepare datalist file", diff --git a/models/endoscopic_inbody_classification/configs/inference.json b/models/endoscopic_inbody_classification/configs/inference.json index 4c0a4279..fe955f5e 100644 --- a/models/endoscopic_inbody_classification/configs/inference.json +++ b/models/endoscopic_inbody_classification/configs/inference.json @@ -7,6 +7,7 @@ ], "bundle_root": ".", "image_key": "image", + "load_pretrain": true, "output_dir": "$@bundle_root + '/eval'", "output_filename": "predictions.csv", "dataset_dir": "/workspace/data/endoscopic_inbody_classification", @@ -119,7 +120,7 @@ }, "initialize": [ "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/endoscopic_inbody_classification/configs/metadata.json b/models/endoscopic_inbody_classification/configs/metadata.json index a409a130..3601e141 100644 --- a/models/endoscopic_inbody_classification/configs/metadata.json +++ b/models/endoscopic_inbody_classification/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.4.6", + "version": "0.4.7", "changelog": { + "0.4.7": "add load_pretrain flag for infer", "0.4.6": "add output for inference", "0.4.5": "update with EnsureChannelFirstd and remove meta dict usage", "0.4.4": "fix the wrong GPU index issue of multi-node", diff --git a/models/endoscopic_tool_segmentation/configs/inference.json b/models/endoscopic_tool_segmentation/configs/inference.json index aec38d88..2aa5e79b 100644 --- a/models/endoscopic_tool_segmentation/configs/inference.json +++ b/models/endoscopic_tool_segmentation/configs/inference.json @@ -11,6 +11,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "/workspace/data/endoscopic_tool_dataset", "datalist": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'test', '*', '*[!seg].jpg'))))", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", @@ -140,7 +141,7 @@ }, "initialize": [ "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/endoscopic_tool_segmentation/configs/metadata.json b/models/endoscopic_tool_segmentation/configs/metadata.json index 612e253b..edfd0a94 100644 --- 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": "0.5.7", + "version": "0.5.8", "changelog": { + "0.5.8": "add load_pretrain flag for infer", "0.5.7": "add checkpoint loader for infer", "0.5.6": "update to use monai 1.3.0", "0.5.5": "update AddChanneld with EnsureChannelFirstd and set image_only to False", diff --git a/models/lung_nodule_ct_detection/configs/inference.json b/models/lung_nodule_ct_detection/configs/inference.json index 1a1682e1..2fc82727 100644 --- a/models/lung_nodule_ct_detection/configs/inference.json +++ b/models/lung_nodule_ct_detection/configs/inference.json @@ -16,6 +16,7 @@ "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, is_segmentation=True, data_list_key='validation', base_dir=@dataset_dir)", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", "amp": true, + "load_pretrain": true, "spatial_dims": 3, "num_classes": 1, "force_sliding_window": false, @@ -212,7 +213,7 @@ }, "initialize": [ "$setattr(torch.backends.cudnn, 'benchmark', True)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/lung_nodule_ct_detection/configs/metadata.json b/models/lung_nodule_ct_detection/configs/metadata.json index fdf52609..437422c2 100644 --- 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": "0.6.2", + "version": "0.6.3", "changelog": { + "0.6.3": "add load_pretrain flag for infer", "0.6.2": "add checkpoint loader for infer", "0.6.1": "fix format error", "0.6.0": "remove meta_dict usage", diff --git a/models/pancreas_ct_dints_segmentation/configs/inference.yaml b/models/pancreas_ct_dints_segmentation/configs/inference.yaml index ef81e4cf..319af066 100644 --- a/models/pancreas_ct_dints_segmentation/configs/inference.yaml +++ b/models/pancreas_ct_dints_segmentation/configs/inference.yaml @@ -14,6 +14,7 @@ output_ext: ".nii.gz" output_dtype: "$numpy.float32" output_postfix: "trans" separate_folder: true +load_pretrain: true dataset_dir: "/workspace/data/msd/Task07_Pancreas" data_list_file_path: "$@bundle_root + '/configs/dataset_0.json'" datalist: "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='testing', @@ -124,6 +125,6 @@ checkpointloader: model: "@network" initialize: - "$setattr(torch.backends.cudnn, 'benchmark', True)" -- "$@checkpointloader(@evaluator)" +- "$@checkpointloader(@evaluator) if @load_pretrain else None" run: - "$@evaluator.run()" diff --git a/models/pancreas_ct_dints_segmentation/configs/metadata.json b/models/pancreas_ct_dints_segmentation/configs/metadata.json index 0bed3dbb..cd3966af 100644 --- a/models/pancreas_ct_dints_segmentation/configs/metadata.json +++ b/models/pancreas_ct_dints_segmentation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.4.7", + "version": "0.4.8", "changelog": { + "0.4.8": "add load_pretrain flag for infer", "0.4.7": "add missing yaml lib requirement in metadata", "0.4.6": "add checkpoint loader for infer", "0.4.5": "set image_only to False", diff --git a/models/pathology_nuclick_annotation/configs/inference.json b/models/pathology_nuclick_annotation/configs/inference.json index bb3e4661..9ce3127f 100644 --- a/models/pathology_nuclick_annotation/configs/inference.json +++ b/models/pathology_nuclick_annotation/configs/inference.json @@ -13,6 +13,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "/workspace/data/CoNSePNuclei", "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]", "centroids": "$list(sorted(glob.glob(@dataset_dir + '/Test/Centroids/*.txt')))[:1]", @@ -137,7 +138,7 @@ "$import sys", "$sys.path.append(@bundle_root)", "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/pathology_nuclick_annotation/configs/metadata.json b/models/pathology_nuclick_annotation/configs/metadata.json index 1dfafe62..f9875252 100644 --- 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": "0.1.7", + "version": "0.1.8", "changelog": { + "0.1.8": "add load_pretrain flag for infer", "0.1.7": "add checkpoint loader for infer", "0.1.6": "set image_only to False", "0.1.5": "add support for TensorRT conversion and inference", diff --git a/models/spleen_ct_segmentation/configs/inference.json b/models/spleen_ct_segmentation/configs/inference.json index 4ee2705f..f843dcf9 100644 --- a/models/spleen_ct_segmentation/configs/inference.json +++ b/models/spleen_ct_segmentation/configs/inference.json @@ -11,6 +11,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "/workspace/data/Task09_Spleen", "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", @@ -156,7 +157,7 @@ }, "initialize": [ "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/spleen_ct_segmentation/configs/metadata.json b/models/spleen_ct_segmentation/configs/metadata.json index 50cb819b..a8ecaab7 100644 --- a/models/spleen_ct_segmentation/configs/metadata.json +++ b/models/spleen_ct_segmentation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.5.5", + "version": "0.5.6", "changelog": { + "0.5.6": "add load_pretrain flag for infer", "0.5.5": "add checkpoint loader for infer", "0.5.4": "update to use monai 1.3.0", "0.5.3": "fix the wrong GPU index issue of multi-node", diff --git a/models/spleen_deepedit_annotation/configs/inference.json b/models/spleen_deepedit_annotation/configs/inference.json index beec2b49..560194ab 100644 --- a/models/spleen_deepedit_annotation/configs/inference.json +++ b/models/spleen_deepedit_annotation/configs/inference.json @@ -12,6 +12,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "/workspace/Datasets/MSD_datasets/Task09_Spleen", "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", "label_names": { @@ -207,7 +208,7 @@ }, "initialize": [ "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/spleen_deepedit_annotation/configs/metadata.json b/models/spleen_deepedit_annotation/configs/metadata.json index 3afadb0d..c5dcbaac 100644 --- a/models/spleen_deepedit_annotation/configs/metadata.json +++ b/models/spleen_deepedit_annotation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.5.3", + "version": "0.5.4", "changelog": { + "0.5.4": "add load_pretrain flag for infer", "0.5.3": "update to use monai 1.3.0", "0.5.2": "update the checkpoint loader logic for inference", "0.5.1": "add option to validate at training start, and I/O param entries", diff --git a/models/swin_unetr_btcv_segmentation/configs/inference.json b/models/swin_unetr_btcv_segmentation/configs/inference.json index be9bb859..a7488e07 100644 --- a/models/swin_unetr_btcv_segmentation/configs/inference.json +++ b/models/swin_unetr_btcv_segmentation/configs/inference.json @@ -11,6 +11,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "/workspace/data/RawData/", "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", @@ -145,7 +146,7 @@ }, "initialize": [ "$monai.utils.set_determinism(seed=123)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/swin_unetr_btcv_segmentation/configs/metadata.json b/models/swin_unetr_btcv_segmentation/configs/metadata.json index 96a75990..3e8c5b1f 100644 --- a/models/swin_unetr_btcv_segmentation/configs/metadata.json +++ b/models/swin_unetr_btcv_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": "0.5.2", + "version": "0.5.3", "changelog": { + "0.5.3": "add load_pretrain flag for infer", "0.5.2": "add checkpoint loader for infer", "0.5.1": "remove meta_dict usage", "0.5.0": "fix the wrong GPU index issue of multi-node", diff --git a/models/wholeBody_ct_segmentation/configs/inference.json b/models/wholeBody_ct_segmentation/configs/inference.json index 8fcf0e2b..1252c48d 100644 --- a/models/wholeBody_ct_segmentation/configs/inference.json +++ b/models/wholeBody_ct_segmentation/configs/inference.json @@ -16,6 +16,7 @@ "output_dtype": "$numpy.float32", "output_postfix": "trans", "separate_folder": true, + "load_pretrain": true, "dataset_dir": "sampledata", "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", @@ -162,7 +163,7 @@ }, "initialize": [ "$setattr(torch.backends.cudnn, 'benchmark', True)", - "$@checkpointloader(@evaluator)" + "$@checkpointloader(@evaluator) if @load_pretrain else None" ], "run": [ "$@evaluator.run()" diff --git a/models/wholeBody_ct_segmentation/configs/metadata.json b/models/wholeBody_ct_segmentation/configs/metadata.json index 9bb779b1..5a25c67e 100644 --- a/models/wholeBody_ct_segmentation/configs/metadata.json +++ b/models/wholeBody_ct_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": "0.2.2", + "version": "0.2.3", "changelog": { + "0.2.3": "add load_pretrain flag for infer", "0.2.2": "add checkpoint loader for infer", "0.2.1": "remove meta_dict usage", "0.2.0": "add support for TensorRT conversion and inference",