From 2410d1adc7f5df6bdbc31203e115ac0f7735f0df Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 27 Sep 2024 14:52:41 +0800 Subject: [PATCH 1/4] update issue for IgniteInfo Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .../configs/metadata.json | 3 ++- .../scripts/ldm_trainer.py | 2 +- models/brats_mri_generative_diffusion/configs/metadata.json | 3 ++- models/brats_mri_generative_diffusion/scripts/ldm_trainer.py | 2 +- models/lung_nodule_ct_detection/configs/metadata.json | 3 ++- models/lung_nodule_ct_detection/scripts/detection_saver.py | 2 +- models/lung_nodule_ct_detection/scripts/evaluator.py | 2 +- models/lung_nodule_ct_detection/scripts/trainer.py | 2 +- models/maisi_ct_generative/configs/metadata.json | 3 ++- models/maisi_ct_generative/scripts/trainer.py | 2 +- models/pathology_nuclei_classification/configs/metadata.json | 3 ++- models/pathology_nuclei_classification/scripts/handlers.py | 2 +- models/pathology_nuclick_annotation/configs/metadata.json | 3 ++- models/pathology_nuclick_annotation/scripts/handlers.py | 2 +- 14 files changed, 20 insertions(+), 14 deletions(-) diff --git a/models/brats_mri_axial_slices_generative_diffusion/configs/metadata.json b/models/brats_mri_axial_slices_generative_diffusion/configs/metadata.json index 5be0baaf..fe5ce1c1 100644 --- a/models/brats_mri_axial_slices_generative_diffusion/configs/metadata.json +++ b/models/brats_mri_axial_slices_generative_diffusion/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20240725.json", - "version": "1.1.1", + "version": "1.1.2", "changelog": { + "1.1.2": "update issue for IgniteInfo", "1.1.1": "enable tensorrt", "1.1.0": "update to use monai 1.4, model ckpt not changed, rm GenerativeAI repo", "1.0.9": "update to use monai 1.3.1", diff --git a/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py b/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py index a298461e..998a2b93 100644 --- a/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py +++ b/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py @@ -14,7 +14,7 @@ from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence import torch -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch from monai.inferers import Inferer, SimpleInferer from monai.transforms import Transform diff --git a/models/brats_mri_generative_diffusion/configs/metadata.json b/models/brats_mri_generative_diffusion/configs/metadata.json index ec870a84..ce2305ea 100644 --- a/models/brats_mri_generative_diffusion/configs/metadata.json +++ b/models/brats_mri_generative_diffusion/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20240725.json", - "version": "1.1.1", + "version": "1.1.2", "changelog": { + "1.1.2": "update issue for IgniteInfo", "1.1.1": "enable tensorrt", "1.1.0": "update to use monai 1.4, model ckpt not changed, rm GenerativeAI repo", "1.0.9": "update to use monai 1.3.1", diff --git a/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py b/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py index c1a21bfa..fc91dc99 100644 --- a/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py +++ b/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py @@ -14,7 +14,7 @@ from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence import torch -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch from monai.inferers import Inferer, SimpleInferer from monai.transforms import Transform diff --git a/models/lung_nodule_ct_detection/configs/metadata.json b/models/lung_nodule_ct_detection/configs/metadata.json index 57cb3b51..4bc75d27 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": "0.6.7", + "version": "0.6.8", "changelog": { + "0.6.8": "update issue for IgniteInfo", "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", diff --git a/models/lung_nodule_ct_detection/scripts/detection_saver.py b/models/lung_nodule_ct_detection/scripts/detection_saver.py index 001b1cfb..712ae5b7 100644 --- a/models/lung_nodule_ct_detection/scripts/detection_saver.py +++ b/models/lung_nodule_ct_detection/scripts/detection_saver.py @@ -14,7 +14,7 @@ import warnings from typing import TYPE_CHECKING, Callable, Optional -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.handlers.classification_saver import ClassificationSaver from monai.utils import evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather diff --git a/models/lung_nodule_ct_detection/scripts/evaluator.py b/models/lung_nodule_ct_detection/scripts/evaluator.py index 501e75f1..461a8b83 100644 --- a/models/lung_nodule_ct_detection/scripts/evaluator.py +++ b/models/lung_nodule_ct_detection/scripts/evaluator.py @@ -15,7 +15,7 @@ import torch from monai.apps.detection.networks.retinanet_detector import RetinaNetDetector -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.engines.evaluator import SupervisedEvaluator from monai.engines.utils import IterationEvents, default_metric_cmp_fn from monai.transforms import Transform diff --git a/models/lung_nodule_ct_detection/scripts/trainer.py b/models/lung_nodule_ct_detection/scripts/trainer.py index 246910f1..6280ed3b 100644 --- a/models/lung_nodule_ct_detection/scripts/trainer.py +++ b/models/lung_nodule_ct_detection/scripts/trainer.py @@ -14,7 +14,7 @@ from typing import TYPE_CHECKING, Any, Callable, Dict, Iterable, List, Optional, Sequence, Tuple, Union import torch -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.engines.trainer import Trainer from monai.engines.utils import IterationEvents, default_metric_cmp_fn from monai.inferers import Inferer diff --git a/models/maisi_ct_generative/configs/metadata.json b/models/maisi_ct_generative/configs/metadata.json index a0d2c53e..ebe7cc43 100644 --- a/models/maisi_ct_generative/configs/metadata.json +++ b/models/maisi_ct_generative/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_generator_ldm_20240318.json", - "version": "0.4.3", + "version": "0.4.4", "changelog": { + "0.4.4": "update issue for IgniteInfo", "0.4.3": "remove download large files, add weights_only when loading weights and add label_dict to large files", "0.4.2": "update train.json to fix finetune ckpt bug", "0.4.1": "update large files", diff --git a/models/maisi_ct_generative/scripts/trainer.py b/models/maisi_ct_generative/scripts/trainer.py index 7b8eae9f..3621afc3 100644 --- a/models/maisi_ct_generative/scripts/trainer.py +++ b/models/maisi_ct_generative/scripts/trainer.py @@ -15,7 +15,7 @@ import torch import torch.nn.functional as F -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.engines.trainer import Trainer from monai.engines.utils import IterationEvents, PrepareBatchExtraInput, default_metric_cmp_fn from monai.inferers import Inferer diff --git a/models/pathology_nuclei_classification/configs/metadata.json b/models/pathology_nuclei_classification/configs/metadata.json index b5d8f780..6ca6d528 100644 --- a/models/pathology_nuclei_classification/configs/metadata.json +++ b/models/pathology_nuclei_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": "0.1.9", + "version": "0.2.0", "changelog": { + "0.2.0": "update issue for IgniteInfo", "0.1.9": "update tensorrt benchmark results", "0.1.8": "enable tensorrt", "0.1.7": "update to use monai 1.3.1", diff --git a/models/pathology_nuclei_classification/scripts/handlers.py b/models/pathology_nuclei_classification/scripts/handlers.py index 9d43ca76..1441fcb8 100644 --- a/models/pathology_nuclei_classification/scripts/handlers.py +++ b/models/pathology_nuclei_classification/scripts/handlers.py @@ -15,7 +15,7 @@ import numpy as np import torch import torch.distributed -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.utils import min_version, optional_import from sklearn.metrics import classification_report diff --git a/models/pathology_nuclick_annotation/configs/metadata.json b/models/pathology_nuclick_annotation/configs/metadata.json index feebbb98..51bc7244 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": "0.2.0", + "version": "0.2.1", "changelog": { + "0.2.1": "update issue for IgniteInfo", "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", diff --git a/models/pathology_nuclick_annotation/scripts/handlers.py b/models/pathology_nuclick_annotation/scripts/handlers.py index 55fd3e11..2683c620 100644 --- a/models/pathology_nuclick_annotation/scripts/handlers.py +++ b/models/pathology_nuclick_annotation/scripts/handlers.py @@ -15,7 +15,7 @@ import numpy as np import torch import torch.distributed -from monai.config import IgniteInfo +from monai.utils import IgniteInfo from monai.utils import min_version, optional_import Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events") From b17a8cdeaa6622f582c8498cb782d46ac59a8b07 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 27 Sep 2024 15:25:09 +0800 Subject: [PATCH 2/4] fix format Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .../scripts/ldm_trainer.py | 3 +-- models/brats_mri_generative_diffusion/scripts/ldm_trainer.py | 3 +-- models/lung_nodule_ct_detection/scripts/detection_saver.py | 3 +-- models/lung_nodule_ct_detection/scripts/evaluator.py | 3 +-- models/lung_nodule_ct_detection/scripts/trainer.py | 3 +-- models/maisi_ct_generative/scripts/trainer.py | 3 +-- models/pathology_nuclei_classification/scripts/handlers.py | 3 +-- models/pathology_nuclick_annotation/scripts/handlers.py | 3 +-- 8 files changed, 8 insertions(+), 16 deletions(-) diff --git a/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py b/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py index 998a2b93..c6a5ab89 100644 --- a/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py +++ b/models/brats_mri_axial_slices_generative_diffusion/scripts/ldm_trainer.py @@ -14,11 +14,10 @@ from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence import torch -from monai.utils import IgniteInfo from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch from monai.inferers import Inferer, SimpleInferer from monai.transforms import Transform -from monai.utils import min_version, optional_import +from monai.utils import IgniteInfo, min_version, optional_import from monai.utils.enums import CommonKeys, GanKeys from torch.optim.optimizer import Optimizer from torch.utils.data import DataLoader diff --git a/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py b/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py index fc91dc99..073607f7 100644 --- a/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py +++ b/models/brats_mri_generative_diffusion/scripts/ldm_trainer.py @@ -14,11 +14,10 @@ from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence import torch -from monai.utils import IgniteInfo from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch from monai.inferers import Inferer, SimpleInferer from monai.transforms import Transform -from monai.utils import min_version, optional_import +from monai.utils import IgniteInfo, min_version, optional_import from monai.utils.enums import CommonKeys, GanKeys from torch.optim.optimizer import Optimizer from torch.utils.data import DataLoader diff --git a/models/lung_nodule_ct_detection/scripts/detection_saver.py b/models/lung_nodule_ct_detection/scripts/detection_saver.py index 712ae5b7..805da7c3 100644 --- a/models/lung_nodule_ct_detection/scripts/detection_saver.py +++ b/models/lung_nodule_ct_detection/scripts/detection_saver.py @@ -14,9 +14,8 @@ import warnings from typing import TYPE_CHECKING, Callable, Optional -from monai.utils import IgniteInfo from monai.handlers.classification_saver import ClassificationSaver -from monai.utils import evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather +from monai.utils import IgniteInfo, evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather from .utils import detach_to_numpy diff --git a/models/lung_nodule_ct_detection/scripts/evaluator.py b/models/lung_nodule_ct_detection/scripts/evaluator.py index 461a8b83..2bd3e5c4 100644 --- a/models/lung_nodule_ct_detection/scripts/evaluator.py +++ b/models/lung_nodule_ct_detection/scripts/evaluator.py @@ -15,11 +15,10 @@ import torch from monai.apps.detection.networks.retinanet_detector import RetinaNetDetector -from monai.utils import IgniteInfo from monai.engines.evaluator import SupervisedEvaluator from monai.engines.utils import IterationEvents, default_metric_cmp_fn from monai.transforms import Transform -from monai.utils import ForwardMode, min_version, optional_import +from monai.utils import ForwardMode, IgniteInfo, min_version, optional_import from monai.utils.enums import CommonKeys as Keys from torch.utils.data import DataLoader diff --git a/models/lung_nodule_ct_detection/scripts/trainer.py b/models/lung_nodule_ct_detection/scripts/trainer.py index 6280ed3b..2b88ff41 100644 --- a/models/lung_nodule_ct_detection/scripts/trainer.py +++ b/models/lung_nodule_ct_detection/scripts/trainer.py @@ -14,12 +14,11 @@ from typing import TYPE_CHECKING, Any, Callable, Dict, Iterable, List, Optional, Sequence, Tuple, Union import torch -from monai.utils import IgniteInfo from monai.engines.trainer import Trainer from monai.engines.utils import IterationEvents, default_metric_cmp_fn from monai.inferers import Inferer from monai.transforms import Transform -from monai.utils import min_version, optional_import +from monai.utils import IgniteInfo, min_version, optional_import from monai.utils.enums import CommonKeys as Keys from torch.optim.optimizer import Optimizer from torch.utils.data import DataLoader diff --git a/models/maisi_ct_generative/scripts/trainer.py b/models/maisi_ct_generative/scripts/trainer.py index 3621afc3..7af78893 100644 --- a/models/maisi_ct_generative/scripts/trainer.py +++ b/models/maisi_ct_generative/scripts/trainer.py @@ -15,13 +15,12 @@ import torch import torch.nn.functional as F -from monai.utils import IgniteInfo from monai.engines.trainer import Trainer from monai.engines.utils import IterationEvents, PrepareBatchExtraInput, default_metric_cmp_fn from monai.inferers import Inferer from monai.networks.schedulers import Scheduler from monai.transforms import Transform -from monai.utils import RankFilter, min_version, optional_import +from monai.utils import IgniteInfo, RankFilter, min_version, optional_import from monai.utils.enums import CommonKeys as Keys from torch.optim.optimizer import Optimizer from torch.utils.data import DataLoader diff --git a/models/pathology_nuclei_classification/scripts/handlers.py b/models/pathology_nuclei_classification/scripts/handlers.py index 1441fcb8..b5f038e1 100644 --- a/models/pathology_nuclei_classification/scripts/handlers.py +++ b/models/pathology_nuclei_classification/scripts/handlers.py @@ -15,8 +15,7 @@ import numpy as np import torch import torch.distributed -from monai.utils import IgniteInfo -from monai.utils import min_version, optional_import +from monai.utils import IgniteInfo, min_version, optional_import from sklearn.metrics import classification_report Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events") diff --git a/models/pathology_nuclick_annotation/scripts/handlers.py b/models/pathology_nuclick_annotation/scripts/handlers.py index 2683c620..d76bd523 100644 --- a/models/pathology_nuclick_annotation/scripts/handlers.py +++ b/models/pathology_nuclick_annotation/scripts/handlers.py @@ -15,8 +15,7 @@ import numpy as np import torch import torch.distributed -from monai.utils import IgniteInfo -from monai.utils import min_version, optional_import +from monai.utils import IgniteInfo, min_version, optional_import Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events") make_grid, _ = optional_import("torchvision.utils", name="make_grid") From e410aef0c619035b87d8cdb2c0b7e8e063aa1393 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 27 Sep 2024 17:04:23 +0800 Subject: [PATCH 3/4] update location Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .../configs/inference.json | 2 +- .../configs/train.json | 12 ++++++------ .../pathology_nuclick_annotation/configs/train.json | 10 +++++----- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/models/pathology_nuclei_classification/configs/inference.json b/models/pathology_nuclei_classification/configs/inference.json index 3bbb3292..07cd012f 100644 --- a/models/pathology_nuclei_classification/configs/inference.json +++ b/models/pathology_nuclei_classification/configs/inference.json @@ -48,7 +48,7 @@ "b_max": 1.0 }, { - "_target_": "AddLabelAsGuidanced", + "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", "keys": "image", "source": "label" } diff --git a/models/pathology_nuclei_classification/configs/train.json b/models/pathology_nuclei_classification/configs/train.json index 517d7423..47776324 100644 --- a/models/pathology_nuclei_classification/configs/train.json +++ b/models/pathology_nuclei_classification/configs/train.json @@ -58,7 +58,7 @@ ] }, { - "_target_": "SplitLabeld", + "_target_": "monai.apps.nuclick.transforms.SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255, @@ -100,7 +100,7 @@ "b_max": 1.0 }, { - "_target_": "AddLabelAsGuidanced", + "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", "keys": "image", "source": "label" }, @@ -110,7 +110,7 @@ "offset": -1 }, { - "_target_": "SelectItemsd", + "_target_": "monai.apps.nuclick.transforms.SelectItemsd", "keys": [ "image", "label" @@ -244,7 +244,7 @@ ] }, { - "_target_": "SplitLabeld", + "_target_": "monai.apps.nuclick.transforms.SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255, @@ -259,12 +259,12 @@ "b_max": 1.0 }, { - "_target_": "AddLabelAsGuidanced", + "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", "keys": "image", "source": "label" }, { - "_target_": "SetLabelClassd", + "_target_": "monai.apps.nuclick.transforms.SetLabelClassd", "keys": "label", "offset": -1 }, diff --git a/models/pathology_nuclick_annotation/configs/train.json b/models/pathology_nuclick_annotation/configs/train.json index b1281626..aa02bae6 100644 --- a/models/pathology_nuclick_annotation/configs/train.json +++ b/models/pathology_nuclick_annotation/configs/train.json @@ -62,7 +62,7 @@ ] }, { - "_target_": "SplitLabeld", + "_target_": "monai.apps.nuclick.transforms.SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255 @@ -103,7 +103,7 @@ "b_max": 1.0 }, { - "_target_": "AddPointGuidanceSignald", + "_target_": "monai.apps.nuclick.transforms.AddPointGuidanceSignald", "image": "image", "label": "label", "others": "others", @@ -219,7 +219,7 @@ ] }, { - "_target_": "SplitLabeld", + "_target_": "monai.apps.nuclick.transforms.SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255 @@ -233,7 +233,7 @@ "b_max": 1.0 }, { - "_target_": "AddPointGuidanceSignald", + "_target_": "monai.apps.nuclick.transforms.AddPointGuidanceSignald", "image": "image", "label": "label", "others": "others", @@ -242,7 +242,7 @@ "drop_rate": 1.0 }, { - "_target_": "SelectItemsd", + "_target_": "monai.apps.nuclick.transforms.SelectItemsd", "keys": [ "image", "label", From 24f8e65bbf2c6fe3954cf23eec8549aacb413d9c Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 27 Sep 2024 19:45:24 +0800 Subject: [PATCH 4/4] Revert "update location" This reverts commit e410aef0c619035b87d8cdb2c0b7e8e063aa1393. --- .../configs/inference.json | 2 +- .../configs/train.json | 12 ++++++------ .../pathology_nuclick_annotation/configs/train.json | 10 +++++----- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/models/pathology_nuclei_classification/configs/inference.json b/models/pathology_nuclei_classification/configs/inference.json index 07cd012f..3bbb3292 100644 --- a/models/pathology_nuclei_classification/configs/inference.json +++ b/models/pathology_nuclei_classification/configs/inference.json @@ -48,7 +48,7 @@ "b_max": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", + "_target_": "AddLabelAsGuidanced", "keys": "image", "source": "label" } diff --git a/models/pathology_nuclei_classification/configs/train.json b/models/pathology_nuclei_classification/configs/train.json index 47776324..517d7423 100644 --- a/models/pathology_nuclei_classification/configs/train.json +++ b/models/pathology_nuclei_classification/configs/train.json @@ -58,7 +58,7 @@ ] }, { - "_target_": "monai.apps.nuclick.transforms.SplitLabeld", + "_target_": "SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255, @@ -100,7 +100,7 @@ "b_max": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", + "_target_": "AddLabelAsGuidanced", "keys": "image", "source": "label" }, @@ -110,7 +110,7 @@ "offset": -1 }, { - "_target_": "monai.apps.nuclick.transforms.SelectItemsd", + "_target_": "SelectItemsd", "keys": [ "image", "label" @@ -244,7 +244,7 @@ ] }, { - "_target_": "monai.apps.nuclick.transforms.SplitLabeld", + "_target_": "SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255, @@ -259,12 +259,12 @@ "b_max": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.AddLabelAsGuidanced", + "_target_": "AddLabelAsGuidanced", "keys": "image", "source": "label" }, { - "_target_": "monai.apps.nuclick.transforms.SetLabelClassd", + "_target_": "SetLabelClassd", "keys": "label", "offset": -1 }, diff --git a/models/pathology_nuclick_annotation/configs/train.json b/models/pathology_nuclick_annotation/configs/train.json index aa02bae6..b1281626 100644 --- a/models/pathology_nuclick_annotation/configs/train.json +++ b/models/pathology_nuclick_annotation/configs/train.json @@ -62,7 +62,7 @@ ] }, { - "_target_": "monai.apps.nuclick.transforms.SplitLabeld", + "_target_": "SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255 @@ -103,7 +103,7 @@ "b_max": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.AddPointGuidanceSignald", + "_target_": "AddPointGuidanceSignald", "image": "image", "label": "label", "others": "others", @@ -219,7 +219,7 @@ ] }, { - "_target_": "monai.apps.nuclick.transforms.SplitLabeld", + "_target_": "SplitLabeld", "keys": "label", "mask_value": "", "others_value": 255 @@ -233,7 +233,7 @@ "b_max": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.AddPointGuidanceSignald", + "_target_": "AddPointGuidanceSignald", "image": "image", "label": "label", "others": "others", @@ -242,7 +242,7 @@ "drop_rate": 1.0 }, { - "_target_": "monai.apps.nuclick.transforms.SelectItemsd", + "_target_": "SelectItemsd", "keys": [ "image", "label",