Refactor Augmentation config (#67)

* Refactor Augmentation config * Modify ckpts * Refactor pipeline config (#68) * Refactor preprocessing config * Merge train and val data configs * Remove pipeline name * Modify backbone_config * Modify ckpts * Fix inference tests * Fix device for inference * Fix scale in inference * Fix Predictor * Modify `bottom_up` to `bottomup` * Fix bottomup inference * Fix scale in augmentation * Remove `image` key from TopDownConfmaps pipeline (#71) * Refactor preprocessing config * Merge train and val data configs * Remove pipeline name * Modify backbone_config * Modify ckpts * Fix inference tests * Fix device for inference * Fix scale in inference * Fix Predictor * Modify `bottom_up` to `bottomup` * Fix bottomup inference * Fix scale in augmentation * Test remove image * Fix instance cropping * Fix tests * Remove scale in pipelines
talmolab · Aug 14, 2024 · 2f44d2d · 2f44d2d
1 parent 08ac252
commit 2f44d2d
Show file tree

Hide file tree

Showing 34 changed files with 1,559 additions and 2,373 deletions.
diff --git a/docs/config.md b/docs/config.md
diff --git a/docs/config_bottomup.yaml b/docs/config_bottomup.yaml
@@ -1,118 +1,36 @@
 data_config:
   provider: LabelsReader
-  pipeline: BottomUp
-  train:
-    labels_path: minimal_instance.pkg.slp
+  train_labels_path: minimal_instance.pkg.slp
+  val_labels_path: minimal_instance.pkg.slp
+  preprocessing:
     max_width: null
     max_height: null
     scale: 1.0
     is_rgb: false
-    preprocessing:
-      crop_hw:
-      - 160
-      - 160
-    augmentation_config:
-      random_crop:
-        random_crop_p: 0
-        random_crop_hw:
-        - 160
-        - 160
-      use_augmentations: true
-      augmentations:
-        intensity:
-          uniform_noise:
-          - 0.0
-          - 0.04
-          uniform_noise_p: 0
-          gaussian_noise_mean: 0.02
-          gaussian_noise_std: 0.004
-          gaussian_noise_p: 0
-          contrast:
-          - 0.5
-          - 2.0
-          contrast_p: 0
-          brightness: 0.0
-          brightness_p: 0
-        geometric:
-          rotation: 180.0
-          scale: 0
-          translate:
-          - 0
-          - 0
-          affine_p: 0.5
-          erase_scale:
-          - 0.0001
-          - 0.01
-          erase_ratio:
-          - 1
-          - 1
-          erase_p: 0
-          mixup_lambda: null
-          mixup_p: 0
-  val:
-    labels_path: minimal_instance.pkg.slp
-    max_width: null
-    max_height: null
-    is_rgb: false
-    scale: 1.0
-    preprocessing:
-      crop_hw:
-      - 160
-      - 160
-    augmentation_config:
-      random_crop:
-        random_crop_p: 0
-        random_crop_hw:
-        - 160
-        - 160
-      use_augmentations: false
-      augmentations:
-        intensity:
-          uniform_noise:
-          - 0.0
-          - 0.04
-          uniform_noise_p: 0
-          gaussian_noise_mean: 0.02
-          gaussian_noise_std: 0.004
-          gaussian_noise_p: 0
-          contrast:
-          - 0.5
-          - 2.0
-          contrast_p: 0
-          brightness: 0.0
-          brightness_p: 0
-        geometric:
-          rotation: 180.0
-          scale: 0
-          translate:
-          - 0
-          - 0
-          affine_p: 0.5
-          erase_scale:
-          - 0.0001
-          - 0.01
-          erase_ratio:
-          - 1
-          - 1
-          erase_p: 0
-          mixup_lambda: null
-          mixup_p: 0
+  use_augmentations_train: true
+  augmentation_config:
+    geometric:
+      rotation: 180.0
+      scale: null
+      translate_width: 0
+      translate_height: 0
+      affine_p: 0.5
+
 model_config:
   init_weights: xavier
   pre_trained_weights: null
+  backbone_type: unet
   backbone_config:
-    backbone_type: unet
-    backbone_config:
-      in_channels: 1
-      kernel_size: 3
-      filters: 16
-      filters_rate: 2
-      max_stride: 16
-      convs_per_block: 2
-      stacks: 1
-      stem_stride: null
-      middle_block: true
-      up_interpolate: true
+    in_channels: 1
+    kernel_size: 3
+    filters: 16
+    filters_rate: 2
+    max_stride: 16
+    convs_per_block: 2
+    stacks: 1
+    stem_stride: null
+    middle_block: true
+    up_interpolate: true
 
 #   pre_trained_weights: ConvNeXt_Tiny_Weights
 #   backbone_config:
@@ -144,20 +62,20 @@ model_config:
 #     stem_patch_stride: 2
 
   head_configs:
-    confmaps:
-      head_type: MultiInstanceConfmapsHead
-      head_config:
-        part_names: None
-        sigma: 1.5
-        output_stride: 2
-        loss_weight: 1.0
-    pafs:
-      head_type: PartAffinityFieldsHead
-      head_config:
-        edges: None
-        sigma: 50
-        output_stride: 4
-        loss_weight: 1.0
+    single_instance: 
+    centered_instance:
+    centroid:
+    bottomup:
+      confmaps:
+          part_names: None
+          sigma: 1.5
+          output_stride: 2
+          loss_weight: 1.0
+      pafs:
+          edges: None
+          sigma: 50
+          output_stride: 4
+          loss_weight: 1.0
 trainer_config:
   train_data_loader:
     batch_size: 4
@@ -169,7 +87,6 @@ trainer_config:
   model_ckpt:
     save_top_k: 1
     save_last: true
-  device: cpu
   trainer_devices: 1
   trainer_accelerator: cpu
   enable_progress_bar: false
@@ -179,18 +96,6 @@ trainer_config:
   use_wandb: false
   save_ckpt: true
   save_ckpt_path: min_inst_bottomup1
-  wandb:
-    entity: team-ucsd
-    project: test_centroid_centered
-    name: fly_unet_centered
-    wandb_mode: ''
-    api_key: ''
-    log_params:
-    - trainer_config.optimizer_name
-    - trainer_config.optimizer.amsgrad
-    - trainer_config.optimizer.lr
-    - model_config.backbone_config.backbone_type
-    - model_config.init_weights
   optimizer_name: Adam
   optimizer:
     lr: 0.0001