UW-Madison dataset at S3 (#178)

InnopolisUni · May 18, 2023 · 1c9642c · 1c9642c
1 parent 2ce7ecc
commit 1c9642c
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diff --git a/config/datasets/semantic-segmentation/segmentation_uwmadison.yaml b/config/datasets/semantic-segmentation/segmentation_uwmadison.yaml
@@ -1,15 +1,15 @@
 _target_: innofw.core.datamodules.lightning_datamodules.segmentation_dir.DirSegmentationLightningDataModule
-channels_num: 1
-date_time: 30.09.2022
-description: stroke segmentation dataset
+date_time: 14.05.2022
+description: gastrointestinal organs segmentations dataset
 markup_info: segmentation masks
 name: UW-Madison dataset
 task:
   - multiclass-image-segmentation
 
 test:
-  source: ./data/organs/test
-  # target:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/uw_madison_organs/test.zip
+  target: ./data/organs/test
 train:
-  source: ./data/organs/train
-  # target:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/uw_madison_organs/train.zip
+  target: ./data/organs/train
+
diff --git a/..._150423_lsjdvnd8_segformer_uwmadison.yaml → ..._150423_lsjdvnd8_segformer_uwmadison.yaml b/..._150423_lsjdvnd8_segformer_uwmadison.yaml → ..._150423_lsjdvnd8_segformer_uwmadison.yaml
@@ -1,12 +1,12 @@
 # @package _global_
 defaults:
-  - override /models: segformer_for_segmentation.yaml
+  - override /models: semantic-segmentation/segformer_for_segmentation.yaml
   - override /datasets: semantic-segmentation/segmentation_uwmadison
   - override /optimizers: lion.yaml
   - override /augmentations_train: none
   - override /augmentations_val: none
   - override /augmentations_test: none
-#  - override /callbacks: multiclass_segmentation
+  - override /callbacks: multiclass_segmentation
   - override /losses: multiclass_segmentation_losses
   - override /loggers: wandb
 
@@ -23,6 +23,7 @@ task: "multiclass-image-segmentation"
 random_seed: 42
 weights_freq: 1
 batch_size: 16
+n_classes: 4
 epochs: 100
 accelerator: gpu
 override hydra/job_logging: stdout
@@ -32,11 +33,5 @@ wandb:
   project: uw_madison
   entity: "k-galliamov"
   group: none
-  tags:
-    - "SegFormer"
-    - "LION"
-    - "CrossEntropyLoss"
-    - "JaccardLoss"
-    - "DiceLoss"
   job_type: training
 
diff --git a/...ents/KG_260423_boqe16_unet_uwmadison.yaml → ...ison/KG_260423_boqe16_unet_uwmadison.yaml b/...ents/KG_260423_boqe16_unet_uwmadison.yaml → ...ison/KG_260423_boqe16_unet_uwmadison.yaml
@@ -1,14 +1,14 @@
 # @package _global_
 defaults:
-  - override /models: unet
+  - override /models: semantic-segmentation/unet
   - override /datasets: semantic-segmentation/segmentation_uwmadison
   - override /optimizers: adam.yaml
   - override /augmentations_train: none
   - override /augmentations_val: none
   - override /augmentations_test: none
   - override /callbacks: multiclass_segmentation
   - override /losses: multiclass_segmentation_losses
-#  - override /loggers: wandb
+  - override /loggers: wandb
 
 n_classes: 4
 
@@ -30,11 +30,9 @@ accelerator: gpu
 devices: 1
 override hydra/job_logging: stdout
 
-#wandb:
-#  enable: True
-#  tags:
-#    - "best_from_sweep"
-#  project: uw_madison
-#  entity: "k-galliamov"
-#  job_type: training
+wandb:
+ enable: True
+ project: uw_madison
+ entity: "k-galliamov"
+ job_type: training
 
diff --git a/...s/KG_260423_pgn135_deeplab_uwmadison.yaml → ...n/KG_260423_pgn135_deeplab_uwmadison.yaml b/...s/KG_260423_pgn135_deeplab_uwmadison.yaml → ...n/KG_260423_pgn135_deeplab_uwmadison.yaml
@@ -1,9 +1,9 @@
 # @package _global_
 defaults:
-  - override /models: deeplabv3plus.yaml
+  - override /models: semantic-segmentation/deeplabv3plus.yaml
   - override /datasets: semantic-segmentation/segmentation_uwmadison
   - override /optimizers: adam.yaml
-  - override /augmentations_train: position/random_horizontal_flip.yaml
+  - override /augmentations_train: ../augmentations/position/random_horizontal_flip.yaml
   - override /augmentations_val: none
   - override /augmentations_test: none
   - override /callbacks: multiclass_segmentation
@@ -18,14 +18,19 @@ models:
 optimizers:
   lr: 0.004313519324382217
 
+n_classes: 4
 project: "organs segmentation"
 task: "multiclass-image-segmentation"
 random_seed: 42
-# weights_freq: 1
+weights_freq: 1
+ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/segmentation/uw_madison_deeplabv3plus.pickle
+
+# When tuning from the checkpoint, the number of epochs has to be set to at least
+#  the № of epoch on which the checkpoint was created + 1 (in this case, 39 + 1 = 40 would be a lower bound)
+epochs: 50
 batch_size: 128
-epochs: 40
 accelerator: gpu
-devices: 2
+devices: 1
 override hydra/job_logging: stdout
 
 wandb:

diff --git a/innofw/core/models/torch_adapter.py b/innofw/core/models/torch_adapter.py
@@ -166,7 +166,7 @@ def predict(self, datamodule, ckpt_path=None):
         # )
 
     def train(self, data_module, ckpt_path=None):
-        self.trainer.fit(self.pl_module, data_module)
+        self.trainer.fit(self.pl_module, data_module, ckpt_path=ckpt_path)
 
     def test(self, data_module):
         outputs = self.trainer.test(self.pl_module, data_module)