From 53f4557733b304726040d4b6d0dd51b771427baa Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Thu, 27 Apr 2023 17:59:08 +0800 Subject: [PATCH 1/4] update train config Signed-off-by: KumoLiu --- .../configs/train.json | 222 +++++++++--------- 1 file changed, 109 insertions(+), 113 deletions(-) diff --git a/models/wholeBody_ct_segmentation/configs/train.json b/models/wholeBody_ct_segmentation/configs/train.json index 8caf7d2e..4c5fe0b5 100644 --- a/models/wholeBody_ct_segmentation/configs/train.json +++ b/models/wholeBody_ct_segmentation/configs/train.json @@ -21,6 +21,8 @@ "pixdim": "$[1.5, 1.5, 1.5] if @displayable_configs#highres else [3.0, 3.0, 3.0]", "modelname": "$'model.pt' if @displayable_configs#highres else 'model_lowres.pt'", "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", + "lazy": false, + "overrides": "${'mode': ('bilinear', 'nearest'), 'padding_mode': ('zeros', 'zeros'), 'dtype': torch.float32}", "network_def": { "_target_": "SegResNet", "spatial_dims": 3, @@ -96,9 +98,10 @@ ] }, { - "_target_": "NormalizeIntensityd", + "_target_": "ScaleIntensityd", "keys": "image", - "nonzero": true + "minv": 0.0, + "maxv": 1.0 }, { "_target_": "CropForegroundd", @@ -121,12 +124,6 @@ ], "sigma": 0.4 }, - { - "_target_": "ScaleIntensityd", - "keys": "image", - "minv": -1.0, - "maxv": 1.0 - }, { "_target_": "EnsureTyped", "keys": [ @@ -152,7 +149,10 @@ ], "preprocessing": { "_target_": "Compose", - "transforms": "$@train#deterministic_transforms + @train#random_transforms" + "transforms": "$@train#deterministic_transforms + @train#random_transforms", + "lazy_evaluation": "@lazy", + "override_keys": ["image", "label"], + "overrides": "@overrides" }, "dataset": { "_target_": "CacheDataset", @@ -213,9 +213,11 @@ } ], "key_metric": { - "train_accuracy": { - "_target_": "ignite.metrics.Accuracy", - "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" + "train_mean_dice": { + "_target_": "MeanDice", + "include_background": false, + "output_transform": "$monai.handlers.from_engine(['pred', 'label'])", + "num_classes": 105 } }, "trainer": { @@ -234,95 +236,98 @@ } }, "validate": { + "transforms": [ + { + "_target_": "LoadImaged", + "keys": [ + "image", + "label" + ] + }, + { + "_target_": "EnsureChannelFirstd", + "keys": [ + "image", + "label" + ] + }, + { + "_target_": "EnsureTyped", + "keys": [ + "image", + "label" + ] + }, + { + "_target_": "Orientationd", + "keys": [ + "image", + "label" + ], + "axcodes": "RAS" + }, + { + "_target_": "Spacingd", + "keys": [ + "image", + "label" + ], + "pixdim": "@pixdim", + "mode": [ + "bilinear", + "nearest" + ] + }, + { + "_target_": "Identityd", + "keys": "image" + }, + { + "_target_": "ScaleIntensityd", + "keys": "image", + "minv": 0.0, + "maxv": 1.0 + }, + { + "_target_": "CropForegroundd", + "keys": [ + "image", + "label" + ], + "source_key": "image", + "margin": 10, + "k_divisible": [ + 96, + 96, + 96 + ] + }, + { + "_target_": "GaussianSmoothd", + "keys": [ + "image" + ], + "sigma": 0.4 + }, + { + "_target_": "CenterSpatialCropd", + "keys": [ + "image", + "label" + ], + "roi_size": [ + 160, + 160, + 160 + ] + } + ], "preprocessing": { "_target_": "Compose", - "transforms": [ - { - "_target_": "LoadImaged", - "keys": [ - "image", - "label" - ] - }, - { - "_target_": "EnsureChannelFirstd", - "keys": [ - "image", - "label" - ] - }, - { - "_target_": "EnsureTyped", - "keys": [ - "image", - "label" - ] - }, - { - "_target_": "Orientationd", - "keys": [ - "image", - "label" - ], - "axcodes": "RAS" - }, - { - "_target_": "Spacingd", - "keys": [ - "image", - "label" - ], - "pixdim": "@pixdim", - "mode": [ - "bilinear", - "nearest" - ] - }, - { - "_target_": "NormalizeIntensityd", - "keys": "image", - "nonzero": true - }, - { - "_target_": "CropForegroundd", - "keys": [ - "image", - "label" - ], - "source_key": "image", - "margin": 10, - "k_divisible": [ - 96, - 96, - 96 - ] - }, - { - "_target_": "GaussianSmoothd", - "keys": [ - "image" - ], - "sigma": 0.4 - }, - { - "_target_": "ScaleIntensityd", - "keys": "image", - "minv": -1.0, - "maxv": 1.0 - }, - { - "_target_": "CenterSpatialCropd", - "keys": [ - "image", - "label" - ], - "roi_size": [ - 160, - 160, - 160 - ] - } - ] + "transforms": "@validate#transforms", + "lazy_evaluation": "@lazy", + "override_keys": ["image", "label"], + "overrides": "@overrides" }, "postprocessing": { "_target_": "Compose", @@ -335,14 +340,11 @@ { "_target_": "AsDiscreted", "keys": [ - "pred", - "label" + "pred" ], "argmax": [ - true, - false - ], - "to_onehot": 105 + true + ] } ] }, @@ -392,13 +394,8 @@ "val_mean_dice": { "_target_": "MeanDice", "include_background": false, - "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" - } - }, - "additional_metrics": { - "val_accuracy": { - "_target_": "ignite.metrics.Accuracy", - "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" + "output_transform": "$monai.handlers.from_engine(['pred', 'label'])", + "num_classes": 105 } }, "evaluator": { @@ -409,7 +406,6 @@ "inferer": "@validate#inferer", "postprocessing": "@validate#postprocessing", "key_val_metric": "@validate#key_metric", - "additional_metrics": "@validate#additional_metrics", "val_handlers": "@validate#handlers", "amp": true } From 2f09a8a903c516238fb3c369243061818d8fcd4d Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Thu, 27 Apr 2023 18:07:28 +0800 Subject: [PATCH 2/4] remove label change in evaluation Signed-off-by: KumoLiu --- .../configs/train.json | 51 +++++++------------ 1 file changed, 19 insertions(+), 32 deletions(-) diff --git a/models/wholeBody_ct_segmentation/configs/train.json b/models/wholeBody_ct_segmentation/configs/train.json index 4c5fe0b5..002cd65d 100644 --- a/models/wholeBody_ct_segmentation/configs/train.json +++ b/models/wholeBody_ct_segmentation/configs/train.json @@ -253,30 +253,18 @@ }, { "_target_": "EnsureTyped", - "keys": [ - "image", - "label" - ] + "keys": "image" }, { "_target_": "Orientationd", - "keys": [ - "image", - "label" - ], + "keys": "image", "axcodes": "RAS" }, { "_target_": "Spacingd", - "keys": [ - "image", - "label" - ], + "keys": "image", "pixdim": "@pixdim", - "mode": [ - "bilinear", - "nearest" - ] + "mode": "bilinear" }, { "_target_": "Identityd", @@ -290,10 +278,7 @@ }, { "_target_": "CropForegroundd", - "keys": [ - "image", - "label" - ], + "keys": "image", "source_key": "image", "margin": 10, "k_divisible": [ @@ -308,18 +293,6 @@ "image" ], "sigma": 0.4 - }, - { - "_target_": "CenterSpatialCropd", - "keys": [ - "image", - "label" - ], - "roi_size": [ - 160, - 160, - 160 - ] } ], "preprocessing": { @@ -329,6 +302,11 @@ "override_keys": ["image", "label"], "overrides": "@overrides" }, + "preprocessing_inverse": { + "_target_": "Compose", + "transforms": "@validate#transforms", + "lazy_evaluation": false + }, "postprocessing": { "_target_": "Compose", "transforms": [ @@ -345,6 +323,15 @@ "argmax": [ true ] + }, + { + "_target_": "Invertd", + "keys": "pred", + "transform": "@validate#preprocessing_inverse", + "orig_keys": "image", + "meta_key_postfix": "meta_dict", + "nearest_interp": true, + "to_tensor": true } ] }, From 0a97f2c115d7647a044f0051dd57ebc1d98aa662 Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Thu, 27 Apr 2023 18:09:15 +0800 Subject: [PATCH 3/4] update evaluate config Signed-off-by: KumoLiu --- .../configs/evaluate.json | 24 ++++--------------- 1 file changed, 5 insertions(+), 19 deletions(-) diff --git a/models/wholeBody_ct_segmentation/configs/evaluate.json b/models/wholeBody_ct_segmentation/configs/evaluate.json index 0c6cc91c..147046fd 100644 --- a/models/wholeBody_ct_segmentation/configs/evaluate.json +++ b/models/wholeBody_ct_segmentation/configs/evaluate.json @@ -9,30 +9,17 @@ }, { "_target_": "Invertd", - "keys": [ - "pred", - "label" - ], + "keys": "pred", "transform": "@validate#preprocessing", "orig_keys": "image", "meta_key_postfix": "meta_dict", - "nearest_interp": [ - true, - true - ], + "nearest_interp": true, "to_tensor": true }, { "_target_": "AsDiscreted", - "keys": [ - "pred", - "label" - ], - "argmax": [ - true, - false - ], - "to_onehot": 105 + "keys": "pred", + "argmax": true }, { "_target_": "SaveImaged", @@ -61,8 +48,7 @@ "_target_": "MetricsSaver", "save_dir": "@output_dir", "metrics": [ - "val_mean_dice", - "val_acc" + "val_mean_dice" ], "metric_details": [ "val_mean_dice" From 5de57e35a79c72e0e78a68392a71394430f0e863 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 27 Apr 2023 10:23:23 +0000 Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- models/wholeBody_ct_segmentation/configs/train.json | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/models/wholeBody_ct_segmentation/configs/train.json b/models/wholeBody_ct_segmentation/configs/train.json index 002cd65d..977b1b99 100644 --- a/models/wholeBody_ct_segmentation/configs/train.json +++ b/models/wholeBody_ct_segmentation/configs/train.json @@ -151,7 +151,10 @@ "_target_": "Compose", "transforms": "$@train#deterministic_transforms + @train#random_transforms", "lazy_evaluation": "@lazy", - "override_keys": ["image", "label"], + "override_keys": [ + "image", + "label" + ], "overrides": "@overrides" }, "dataset": { @@ -299,7 +302,10 @@ "_target_": "Compose", "transforms": "@validate#transforms", "lazy_evaluation": "@lazy", - "override_keys": ["image", "label"], + "override_keys": [ + "image", + "label" + ], "overrides": "@overrides" }, "preprocessing_inverse": {