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.gitattributes

@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+onnx_checkpoints/visual_comparison_attunet_nov_4_class_weighting_epoch_338.png filter=lfs diff=lfs merge=lfs -text

checkpoints/checkpoint_epoch_338.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:769e808f32d33cad957d990781f9246742e35dcf9d96dc6b18da1ba9868679b2
+size 24044797

config.toml

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+experiment_name = "attunet_nov_4_class_weighting"
+base_dir = "/exports/csce/eddie/eng/groups/DunnGroup/matthew/models_gelgenie"
+
+[processing]
+base_hardware = "EDDIE"
+device = "GPU"
+pe = 1
+memory = 64
+
+[data]
+n_channels = 1
+batch_size = 1
+num_workers = 1
+val_percent = 10
+dir_train_mask = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/masks",]
+dir_train_img = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/images",]
+dir_val_img = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/val_images", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/val_images",]
+dir_val_mask = [ "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/nathan_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/lsdb_gels/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/matthew_gels_2/val_masks", "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/val_masks",]
+split_training_dataset = false
+apply_augmentations = true
+padding = false
+individual_padding = true
+weak_augmentations = false
+
+[model]
+model_name = "monai_attunet"
+classes = 2
+in_channels = 1
+
+[training]
+loss = [ "dice", "crossentropy",]
+loss_component_weighting = [ 1, 1,]
+class_loss_weighting = true
+class_loss_weight_damper = [ 1.0, 1.0,]
+lr = 0.0001
+epochs = 600
+grad_scaler = true
+load_checkpoint = false
+optimizer_type = "adam"
+scheduler_type = "CosineAnnealingWarmRestarts"
+save_checkpoint = true
+checkpoint_frequency = 1
+wandb_track = true
+model_cleanup_frequency = 20
+wandb_id = "1hxhgztf"
+
+[training.scheduler_specs]
+restart_period = 100

model_structure.txt

@@ -0,0 +1,51 @@
+==============================================================================================================
+Layer (type:depth-idx)                                                                Param #
+==============================================================================================================
+monai_attunet                                                                         --
+├─Sequential: 1-1                                                                     --
+│    └─ConvBlock: 2-1                                                                 --
+│    │    └─Sequential: 3-1                                                           --
+│    │    │    └─Convolution: 4-1                                                     --
+│    │    │    │    └─Conv2d: 5-1                                                     160
+│    │    │    │    └─ADN: 5-2                                                        32
+│    │    │    └─Convolution: 4-2                                                     --
+│    │    │    │    └─Conv2d: 5-3                                                     2,320
+│    │    │    │    └─ADN: 5-4                                                        32
+│    └─AttentionLayer: 2-2                                                            --
+│    │    └─AttentionBlock: 3-2                                                       --
+│    │    │    └─Sequential: 4-3                                                      --
+│    │    │    │    └─Convolution: 5-5                                                136
+│    │    │    │    └─BatchNorm2d: 5-6                                                16
+│    │    │    └─Sequential: 4-4                                                      --
+│    │    │    │    └─Convolution: 5-7                                                136
+│    │    │    │    └─BatchNorm2d: 5-8                                                16
+│    │    │    └─Sequential: 4-5                                                      --
+│    │    │    │    └─Convolution: 5-9                                                9
+│    │    │    │    └─BatchNorm2d: 5-10                                               2
+│    │    │    │    └─Sigmoid: 5-11                                                   --
+│    │    │    └─ReLU: 4-6                                                            --
+│    │    └─UpConv: 3-3                                                               --
+│    │    │    └─Convolution: 4-7                                                     --
+│    │    │    │    └─ConvTranspose2d: 5-12                                           4,624
+│    │    │    │    └─ADN: 5-13                                                       32
+│    │    └─Convolution: 3-4                                                          --
+│    │    │    └─Conv2d: 4-8                                                          4,624
+│    │    │    └─ADN: 4-9                                                             --
+│    │    │    │    └─InstanceNorm2d: 5-14                                            --
+│    │    │    │    └─Dropout: 5-15                                                   --
+│    │    │    │    └─PReLU: 5-16                                                     1
+│    │    └─Sequential: 3-5                                                           --
+│    │    │    └─ConvBlock: 4-10                                                      --
+│    │    │    │    └─Sequential: 5-17                                                14,016
+│    │    │    └─AttentionLayer: 4-11                                                 --
+│    │    │    │    └─AttentionBlock: 5-18                                            1,139
+│    │    │    │    └─UpConv: 5-19                                                    18,528
+│    │    │    │    └─Convolution: 5-20                                               18,465
+│    │    │    │    └─Sequential: 5-21                                                1,923,112
+│    └─Convolution: 2-3                                                               --
+│    │    └─Conv2d: 3-6                                                               34
+==============================================================================================================
+Total params: 1,987,434
+Trainable params: 1,987,434
+Non-trainable params: 0
+==============================================================================================================

model_summary.txt

@@ -0,0 +1,8 @@
+             Model Summary              
+┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
+┃      Parameter       ┃     Value     ┃
+┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
+│       Network        │ monai_attunet │
+│ Trainable Parameters │    1987434    │
+│   Output channels    │       2       │
+└──────────────────────┴───────────────┘

onnx_checkpoints/attunet_nov_4_class_weighting_epoch_338.onnx

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onnx_checkpoints/temp_checkpoint.onnx

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time_log.txt

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+Time initiated first training run: 2023_11_04_22;26;18

torchscript_checkpoints/attunet_nov_4_class_weighting_epoch_338.pt

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training_logs/training_stats.csv

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