nnUNet model weights

nnunet_model/nnUNetTrainer__nnUNetPlans__2d/dataset.json

@@ -0,0 +1,24 @@
+{
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+        "0": "OCT"
+    },
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+        "OS": "10",
+        "IDZ": "11",
+        "RPE": "12",
+        "choroid": "13",
+        "other": "14"
+    },
+    "numTraining": 407,
+    "file_ending": ".png"
+}

nnunet_model/nnUNetTrainer__nnUNetPlans__2d/dataset_fingerprint.json

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+    "configuration_name": "2d",
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+    "dataloader_train.num_processes": "12",
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+    "dataloader_val.num_processes": "6",
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+    "unpack_dataset": "True",
+    "was_initialized": "True",
+    "weight_decay": "3e-05"
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+    "local_rank": "0",
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+    "dataloader_val": "<nnunetv2.training.data_augmentation.custom_transforms.limited_length_multithreaded_augmenter.LimitedLenWrapper object at 0x1554a84c3280>",
+    "dataloader_val.generator": "<nnunetv2.training.dataloading.data_loader_2d.nnUNetDataLoader2D object at 0x1554a84c37c0>",
+    "dataloader_val.num_processes": "6",
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+    "disable_checkpointing": "False",
+    "fold": "3",
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+    "preprocessed_dataset_folder": "/trinity/home/kvangarderen/nnunet/preprocessed/Dataset506_layers_v2_correctedset/nnUNetPlans_2d",
+    "preprocessed_dataset_folder_base": "/trinity/home/kvangarderen/nnunet/preprocessed/Dataset506_layers_v2_correctedset",
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+    "torch_version": "2.0.0+cu118",
+    "unpack_dataset": "True",
+    "was_initialized": "True",
+    "weight_decay": "3e-05"
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+    "batch_size": "12",
+    "configuration_manager": "{'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 12, 'patch_size': [576, 448], 'median_image_size_in_voxels': [650.0, 512.0], 'spacing': [1.0, 1.0], 'normalization_schemes': ['ZScoreNormalization'], 'use_mask_for_norm': [False], 'UNet_class_name': 'PlainConvUNet', 'UNet_base_num_features': 32, 'n_conv_per_stage_encoder': [2, 2, 2, 2, 2, 2, 2], 'n_conv_per_stage_decoder': [2, 2, 2, 2, 2, 2], 'num_pool_per_axis': [6, 6], 'pool_op_kernel_sizes': [[1, 1], [2, 2], [2, 2], [2, 2], [2, 2], [2, 2], [2, 2]], 'conv_kernel_sizes': [[3, 3], [3, 3], [3, 3], [3, 3], [3, 3], [3, 3], [3, 3]], 'unet_max_num_features': 512, 'resampling_fn_data': 'resample_data_or_seg_to_shape', 'resampling_fn_seg': 'resample_data_or_seg_to_shape', 'resampling_fn_data_kwargs': {'is_seg': False, 'order': 3, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'batch_dice': True}",
+    "configuration_name": "2d",
+    "cudnn_version": 8700,
+    "current_epoch": "0",
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+    "dataloader_train.num_processes": "12",
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+    "dataloader_val.num_processes": "6",
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+    "device": "cuda:0",
+    "disable_checkpointing": "False",
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+    "folder_with_segs_from_previous_stage": "None",
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+    "hostname": "gpu005.cluster",
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+    "local_rank": "0",
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+    "loss": "DeepSupervisionWrapper(\n  (loss): DC_and_CE_loss(\n    (ce): RobustCrossEntropyLoss()\n    (dc): MemoryEfficientSoftDiceLoss()\n  )\n)",
+    "lr_scheduler": "<nnunetv2.training.lr_scheduler.polylr.PolyLRScheduler object at 0x15542b297af0>",
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+    "network": "PlainConvUNet",
+    "num_epochs": "1000",
+    "num_input_channels": "1",
+    "num_iterations_per_epoch": "250",
+    "num_val_iterations_per_epoch": "50",
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+    "output_folder_base": "/trinity/home/kvangarderen/nnunet/models/Dataset506_layers_v2_correctedset/nnUNetTrainer__nnUNetPlans__2d",
+    "oversample_foreground_percent": "0.33",
+    "plans_manager": "{'dataset_name': 'Dataset506_layers_v2_correctedset', 'plans_name': 'nnUNetPlans', 'original_median_spacing_after_transp': [999.0, 1.0, 1.0], 'original_median_shape_after_transp': [1, 650, 512], 'image_reader_writer': 'NaturalImage2DIO', 'transpose_forward': [0, 1, 2], 'transpose_backward': [0, 1, 2], 'configurations': {'2d': {'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 12, 'patch_size': [576, 448], 'median_image_size_in_voxels': [650.0, 512.0], 'spacing': [1.0, 1.0], 'normalization_schemes': ['ZScoreNormalization'], 'use_mask_for_norm': [False], 'UNet_class_name': 'PlainConvUNet', 'UNet_base_num_features': 32, 'n_conv_per_stage_encoder': [2, 2, 2, 2, 2, 2, 2], 'n_conv_per_stage_decoder': [2, 2, 2, 2, 2, 2], 'num_pool_per_axis': [6, 6], 'pool_op_kernel_sizes': [[1, 1], [2, 2], [2, 2], [2, 2], [2, 2], [2, 2], [2, 2]], 'conv_kernel_sizes': [[3, 3], [3, 3], [3, 3], [3, 3], [3, 3], [3, 3], [3, 3]], 'unet_max_num_features': 512, 'resampling_fn_data': 'resample_data_or_seg_to_shape', 'resampling_fn_seg': 'resample_data_or_seg_to_shape', 'resampling_fn_data_kwargs': {'is_seg': False, 'order': 3, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'batch_dice': True}}, 'experiment_planner_used': 'ExperimentPlanner', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 255.0, 'mean': 97.64109802246094, 'median': 92.0, 'min': 0.0, 'percentile_00_5': 13.0, 'percentile_99_5': 230.0, 'std': 40.59941101074219}}}",
+    "preprocessed_dataset_folder": "/trinity/home/kvangarderen/nnunet/preprocessed/Dataset506_layers_v2_correctedset/nnUNetPlans_2d",
+    "preprocessed_dataset_folder_base": "/trinity/home/kvangarderen/nnunet/preprocessed/Dataset506_layers_v2_correctedset",
+    "save_every": "50",
+    "torch_version": "2.0.0+cu118",
+    "unpack_dataset": "True",
+    "was_initialized": "True",
+    "weight_decay": "3e-05"
+}

nnunet_model/nnUNetTrainer__nnUNetPlans__2d/plans.json

@@ -0,0 +1,169 @@
+{
+    "dataset_name": "Dataset506_layers_v2_correctedset",
+    "plans_name": "nnUNetPlans",
+    "original_median_spacing_after_transp": [
+        999.0,
+        1.0,
+        1.0
+    ],
+    "original_median_shape_after_transp": [
+        1,
+        650,
+        512
+    ],
+    "image_reader_writer": "NaturalImage2DIO",
+    "transpose_forward": [
+        0,
+        1,
+        2
+    ],
+    "transpose_backward": [
+        0,
+        1,
+        2
+    ],
+    "configurations": {
+        "2d": {
+            "data_identifier": "nnUNetPlans_2d",
+            "preprocessor_name": "DefaultPreprocessor",
+            "batch_size": 12,
+            "patch_size": [
+                576,
+                448
+            ],
+            "median_image_size_in_voxels": [
+                650.0,
+                512.0
+            ],
+            "spacing": [
+                1.0,
+                1.0
+            ],
+            "normalization_schemes": [
+                "ZScoreNormalization"
+            ],
+            "use_mask_for_norm": [
+                false
+            ],
+            "UNet_class_name": "PlainConvUNet",
+            "UNet_base_num_features": 32,
+            "n_conv_per_stage_encoder": [
+                2,
+                2,
+                2,
+                2,
+                2,
+                2,
+                2
+            ],
+            "n_conv_per_stage_decoder": [
+                2,
+                2,
+                2,
+                2,
+                2,
+                2
+            ],
+            "num_pool_per_axis": [
+                6,
+                6
+            ],
+            "pool_op_kernel_sizes": [
+                [
+                    1,
+                    1
+                ],
+                [
+                    2,
+                    2
+                ],
+                [
+                    2,
+                    2
+                ],
+                [
+                    2,
+                    2
+                ],
+                [
+                    2,
+                    2
+                ],
+                [
+                    2,
+                    2
+                ],
+                [
+                    2,
+                    2
+                ]
+            ],
+            "conv_kernel_sizes": [
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ],
+                [
+                    3,
+                    3
+                ]
+            ],
+            "unet_max_num_features": 512,
+            "resampling_fn_data": "resample_data_or_seg_to_shape",
+            "resampling_fn_seg": "resample_data_or_seg_to_shape",
+            "resampling_fn_data_kwargs": {
+                "is_seg": false,
+                "order": 3,
+                "order_z": 0,
+                "force_separate_z": null
+            },
+            "resampling_fn_seg_kwargs": {
+                "is_seg": true,
+                "order": 1,
+                "order_z": 0,
+                "force_separate_z": null
+            },
+            "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
+            "resampling_fn_probabilities_kwargs": {
+                "is_seg": false,
+                "order": 1,
+                "order_z": 0,
+                "force_separate_z": null
+            },
+            "batch_dice": true
+        }
+    },
+    "experiment_planner_used": "ExperimentPlanner",
+    "label_manager": "LabelManager",
+    "foreground_intensity_properties_per_channel": {
+        "0": {
+            "max": 255.0,
+            "mean": 97.64109802246094,
+            "median": 92.0,
+            "min": 0.0,
+            "percentile_00_5": 13.0,
+            "percentile_99_5": 230.0,
+            "std": 40.59941101074219
+        }
+    }
+}