Added model checkpoints, training logs and onnx-exported checkpoint

checkpoints/checkpoint_epoch_306.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:096a342aff5335b10764fe0d996ae6c554d5330cdc8647d767f98ba6df38b7cf
+size 191834693

config.toml

@@ -0,0 +1,44 @@
+experiment_name = "smp_unet++_july28"
+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 = 4
+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",]
+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",]
+dir_val_img = "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/images"
+dir_val_mask = "/exports/csce/eddie/eng/groups/DunnGroup/matthew/gel_data/neb_ladders/masks"
+split_training_dataset = false
+apply_augmentations = true
+padding = true
+
+[model]
+model_name = "smp_unetplusplus"
+classes = 2
+in_channels = 1
+encoder_name = "resnet18"
+
+[training]
+loss = "both"
+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 = "3qembm5h"
+
+[training.scheduler_specs]
+restart_period = 100

model_structure.txt

@@ -0,0 +1,226 @@
+======================================================================
+Layer (type:depth-idx)                        Param #
+======================================================================
+smp_UNetPlusPlus                              --
+├─ResNetEncoder: 1-1                          --
+│    └─Conv2d: 2-1                            3,136
+│    └─BatchNorm2d: 2-2                       128
+│    └─ReLU: 2-3                              --
+│    └─MaxPool2d: 2-4                         --
+│    └─Sequential: 2-5                        --
+│    │    └─BasicBlock: 3-1                   --
+│    │    │    └─Conv2d: 4-1                  36,864
+│    │    │    └─BatchNorm2d: 4-2             128
+│    │    │    └─ReLU: 4-3                    --
+│    │    │    └─Conv2d: 4-4                  36,864
+│    │    │    └─BatchNorm2d: 4-5             128
+│    │    └─BasicBlock: 3-2                   --
+│    │    │    └─Conv2d: 4-6                  36,864
+│    │    │    └─BatchNorm2d: 4-7             128
+│    │    │    └─ReLU: 4-8                    --
+│    │    │    └─Conv2d: 4-9                  36,864
+│    │    │    └─BatchNorm2d: 4-10            128
+│    └─Sequential: 2-6                        --
+│    │    └─BasicBlock: 3-3                   --
+│    │    │    └─Conv2d: 4-11                 73,728
+│    │    │    └─BatchNorm2d: 4-12            256
+│    │    │    └─ReLU: 4-13                   --
+│    │    │    └─Conv2d: 4-14                 147,456
+│    │    │    └─BatchNorm2d: 4-15            256
+│    │    │    └─Sequential: 4-16             --
+│    │    │    │    └─Conv2d: 5-1             8,192
+│    │    │    │    └─BatchNorm2d: 5-2        256
+│    │    └─BasicBlock: 3-4                   --
+│    │    │    └─Conv2d: 4-17                 147,456
+│    │    │    └─BatchNorm2d: 4-18            256
+│    │    │    └─ReLU: 4-19                   --
+│    │    │    └─Conv2d: 4-20                 147,456
+│    │    │    └─BatchNorm2d: 4-21            256
+│    └─Sequential: 2-7                        --
+│    │    └─BasicBlock: 3-5                   --
+│    │    │    └─Conv2d: 4-22                 294,912
+│    │    │    └─BatchNorm2d: 4-23            512
+│    │    │    └─ReLU: 4-24                   --
+│    │    │    └─Conv2d: 4-25                 589,824
+│    │    │    └─BatchNorm2d: 4-26            512
+│    │    │    └─Sequential: 4-27             --
+│    │    │    │    └─Conv2d: 5-3             32,768
+│    │    │    │    └─BatchNorm2d: 5-4        512
+│    │    └─BasicBlock: 3-6                   --
+│    │    │    └─Conv2d: 4-28                 589,824
+│    │    │    └─BatchNorm2d: 4-29            512
+│    │    │    └─ReLU: 4-30                   --
+│    │    │    └─Conv2d: 4-31                 589,824
+│    │    │    └─BatchNorm2d: 4-32            512
+│    └─Sequential: 2-8                        --
+│    │    └─BasicBlock: 3-7                   --
+│    │    │    └─Conv2d: 4-33                 1,179,648
+│    │    │    └─BatchNorm2d: 4-34            1,024
+│    │    │    └─ReLU: 4-35                   --
+│    │    │    └─Conv2d: 4-36                 2,359,296
+│    │    │    └─BatchNorm2d: 4-37            1,024
+│    │    │    └─Sequential: 4-38             --
+│    │    │    │    └─Conv2d: 5-5             131,072
+│    │    │    │    └─BatchNorm2d: 5-6        1,024
+│    │    └─BasicBlock: 3-8                   --
+│    │    │    └─Conv2d: 4-39                 2,359,296
+│    │    │    └─BatchNorm2d: 4-40            1,024
+│    │    │    └─ReLU: 4-41                   --
+│    │    │    └─Conv2d: 4-42                 2,359,296
+│    │    │    └─BatchNorm2d: 4-43            1,024
+├─UnetPlusPlusDecoder: 1-2                    --
+│    └─Identity: 2-9                          --
+│    └─ModuleDict: 2-10                       --
+│    │    └─DecoderBlock: 3-9                 --
+│    │    │    └─Conv2dReLU: 4-44             --
+│    │    │    │    └─Conv2d: 5-7             1,769,472
+│    │    │    │    └─BatchNorm2d: 5-8        512
+│    │    │    │    └─ReLU: 5-9               --
+│    │    │    └─Attention: 4-45              --
+│    │    │    │    └─Identity: 5-10          --
+│    │    │    └─Conv2dReLU: 4-46             --
+│    │    │    │    └─Conv2d: 5-11            589,824
+│    │    │    │    └─BatchNorm2d: 5-12       512
+│    │    ��    │    └─ReLU: 5-13              --
+│    │    │    └─Attention: 4-47              --
+│    │    │    │    └─Identity: 5-14          --
+│    │    └─DecoderBlock: 3-10                --
+│    │    │    └─Conv2dReLU: 4-48             --
+│    │    │    │    └─Conv2d: 5-15            589,824
+│    │    │    │    └─BatchNorm2d: 5-16       256
+│    │    │    │    └─ReLU: 5-17              --
+│    │    │    └─Attention: 4-49              --
+│    │    │    │    └─Identity: 5-18          --
+│    │    │    └─Conv2dReLU: 4-50             --
+│    │    │    │    └─Conv2d: 5-19            147,456
+│    │    │    │    └─BatchNorm2d: 5-20       256
+│    │    │    │    └─ReLU: 5-21              --
+│    │    │    └─Attention: 4-51              --
+│    │    │    │    └─Identity: 5-22          --
+│    │    └─DecoderBlock: 3-11                --
+│    │    │    └─Conv2dReLU: 4-52             --
+│    │    │    │    └─Conv2d: 5-23            442,368
+│    │    │    │    └─BatchNorm2d: 5-24       256
+│    │    │    │    └─ReLU: 5-25              --
+│    │    │    └─Attention: 4-53              --
+│    │    │    │    └─Identity: 5-26          --
+│    │    │    └─Conv2dReLU: 4-54             --
+│    │    │    │    └─Conv2d: 5-27            147,456
+│    │    │    │    └─BatchNorm2d: 5-28       256
+│    │    │    │    └─ReLU: 5-29              --
+│    │    │    └─Attention: 4-55              --
+│    │    │    │    └─Identity: 5-30          --
+│    │    └─DecoderBlock: 3-12                --
+│    │    │    └─Conv2dReLU: 4-56             --
+│    │    │    │    └─Conv2d: 5-31            184,320
+│    │    │    │    └─BatchNorm2d: 5-32       128
+│    │    │    │    └─ReLU: 5-33              --
+│    │    │    └─Attention: 4-57              --
+│    │    │    │    └─Identity: 5-34          --
+│    │    │    └─Conv2dReLU: 4-58             --
+│    │    │    │    └─Conv2d: 5-35            36,864
+│    │    │    │    └─BatchNorm2d: 5-36       128
+│    │    │    │    └─ReLU: 5-37              --
+│    │    │    └─Attention: 4-59              --
+│    │    │    │    └─Identity: 5-38          --
+│    │    └─DecoderBlock: 3-13                --
+│    │    │    └─Conv2dReLU: 4-60             --
+│    │    │    │    └─Conv2d: 5-39            147,456
+│    │    │    │    └─BatchNorm2d: 5-40       128
+│    │    │    │    └─ReLU: 5-41              --
+│    │    │    └─Attention: 4-61              --
+│    │    │    │    └─Identity: 5-42          --
+│    │    │    └─Conv2dReLU: 4-62             --
+│    │    │    │    └─Conv2d: 5-43            36,864
+│    │    │    │    └─BatchNorm2d: 5-44       128
+│    │    │    │    └─ReLU: 5-45              --
+│    │    │    └─Attention: 4-63              --
+│    │    │    │    └─Identity: 5-46          --
+│    │    └─DecoderBlock: 3-14                --
+│    │    │    └─Conv2dReLU: 4-64             --
+│    │    │    │    └─Conv2d: 5-47            110,592
+│    │    │    │    └─BatchNorm2d: 5-48       128
+│    │    │    │    └─ReLU: 5-49              --
+│    │    │    └─Attention: 4-65              --
+│    │    │    │    └─Identity: 5-50          --
+│    │    │    └─Conv2dReLU: 4-66             --
+│    │    │    │    └─Conv2d: 5-51            36,864
+│    │    │    │    └─BatchNorm2d: 5-52       128
+│    │    │    │    └─ReLU: 5-53              --
+│    │    │    └─Attention: 4-67              --
+│    │    │    │    └─Identity: 5-54          --
+│    │    └─DecoderBlock: 3-15                --
+│    │    │    └─Conv2dReLU: 4-68             --
+│    │    │    │    └─Conv2d: 5-55            92,160
+│    │    │    │    └─BatchNorm2d: 5-56       64
+│    │    │    │    └─ReLU: 5-57              --
+│    │    │    └─Attention: 4-69              --
+│    │    │    │    └─Identity: 5-58          --
+│    │    │    └─Conv2dReLU: 4-70             --
+│    │    │    │    └─Conv2d: 5-59            9,216
+│    │    │    │    └─BatchNorm2d: 5-60       64
+│    │    │    │    └─ReLU: 5-61              --
+│    │    │    └─Attention: 4-71              --
+│    │    │    │    └─Identity: 5-62          --
+│    │    └─DecoderBlock: 3-16                --
+│    │    │    └─Conv2dReLU: 4-72             --
+│    │    │    │    └─Conv2d: 5-63            147,456
+│    │    │    │    └─BatchNorm2d: 5-64       128
+│    │    │    │    └─ReLU: 5-65              --
+│    │    │    └─Attention: 4-73              --
+│    │    │    │    └─Identity: 5-66          --
+│    │    │    └─Conv2dReLU: 4-74             --
+│    │    │    │    └─Conv2d: 5-67            36,864
+│    │    │    │    └─BatchNorm2d: 5-68       128
+│    │    │    │    └─ReLU: 5-69              --
+│    │    │    └─Attention: 4-75              --
+│    │    │    │    └─Identity: 5-70          --
+│    │    └─DecoderBlock: 3-17                --
+│    │    │    └─Conv2dReLU: 4-76             --
+│    │    │    │    └─Conv2d: 5-71            110,592
+│    │    │    │    └─BatchNorm2d: 5-72       128
+│    │    │    │    └─ReLU: 5-73              --
+│    │    │    └─Attention: 4-77              --
+│    │    │    │    └─Identity: 5-74          --
+│    │    │    └─Conv2dReLU: 4-78             --
+│    │    │    │    └─Conv2d: 5-75            36,864
+│    │    │    │    └─BatchNorm2d: 5-76       128
+│    │    │    │    └─ReLU: 5-77              --
+│    │    │    └─Attention: 4-79              --
+│    │    │    │    └─Identity: 5-78          --
+│    │    └─DecoderBlock: 3-18                --
+│    │    │    └─Conv2dReLU: 4-80             --
+│    │    │    │    └─Conv2d: 5-79            73,728
+│    │    │    │    └─BatchNorm2d: 5-80       128
+│    │    │    │    └─ReLU: 5-81              --
+│    │    │    └─Attention: 4-81              --
+│    │    │    │    └─Identity: 5-82          --
+│    │    │    └─Conv2dReLU: 4-82             --
+│    │    │    │    └─Conv2d: 5-83            36,864
+│    │    │    │    └─BatchNorm2d: 5-84       128
+│    │    │    │    └─ReLU: 5-85              --
+│    │    │    └─Attention: 4-83              --
+│    │    │    │    └─Identity: 5-86          --
+│    │    └─DecoderBlock: 3-19                --
+│    │    │    └─Conv2dReLU: 4-84             --
+│    │    │    │    └─Conv2d: 5-87            4,608
+│    │    │    │    └─BatchNorm2d: 5-88       32
+│    │    │    │    └─ReLU: 5-89              --
+│    │    │    └─Attention: 4-85              --
+│    │    │    │    └─Identity: 5-90          --
+│    │    │    └─Conv2dReLU: 4-86             --
+│    │    │    │    └─Conv2d: 5-91            2,304
+│    │    │    │    └─BatchNorm2d: 5-92       32
+│    │    │    │    └─ReLU: 5-93              --
+│    │    │    └─Attention: 4-87              --
+│    │    │    │    └─Identity: 5-94          --
+├─SegmentationHead: 1-3                       --
+│    └─Conv2d: 2-11                           290
+│    └─Identity: 2-12                         --
+│    └─Activation: 2-13                       --
+│    │    └─Identity: 3-20                    --
+======================================================================
+Total params: 15,964,322
+Trainable params: 15,964,322
+Non-trainable params: 0
+======================================================================

model_summary.txt

@@ -0,0 +1,8 @@
+               Model Summary               
+┏━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┓
+┃      Parameter       ┃      Value       ┃
+┡━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━┩
+│       Network        │ smp_unetplusplus │
+│ Trainable Parameters │     15964322     │
+│   Output channels    │        2         │
+└──────────────────────┴──────────────────┘

onnx_format/exported_checkpoint.onnx

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:77a8d3d5e3d42a3a195b24e43ad6ea2b2f96f5d1b0e8fab8b5f783961bf1209a
+size 63853328

time_log.txt

@@ -0,0 +1 @@
+Time initiated first training run: 2023_07_29_11;25;21

training_logs/training_stats.csv

@@ -0,0 +1,601 @@
+Cross-Entropy Loss,Dice Loss,Training Loss,Learning Rate,Dice Score,Epoch
+0.6931996088136326,0.63664364408363,1.3298432501879605,0.0001,0.029339542508953147,1
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+0.0716631163588979,0.43193516677076166,0.5035982816056772,9.704699440926357e-05,0.37798380023903316,12
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+0.03341098773208531,0.29428849843415344,0.327699485827576,9.304406424884699e-05,0.47927411314513946,18
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+0.030463921520012347,0.24589050357991998,0.2763544256714257,8.951824286816573e-05,0.4273485235042042,22
+0.02932289274494079,0.24275320361961017,0.2720760960470546,8.853713647665068e-05,0.5161361551533142,23
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