update sample configs with shift/scale augmentation

wolny · Jan 6, 2025 · 9551cef · 9551cef
1 parent c3f18ed
commit 9551cef
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Showing 4 changed files with 25 additions and 9 deletions.
diff --git a/resources/3DUnet_confocal_boundary/train_config.yml b/resources/3DUnet_confocal_boundary/train_config.yml
@@ -65,11 +65,15 @@ trainer:
 # Configure training and validation loaders
 loaders:
   # how many subprocesses to use for data loading
-  num_workers: 8
+  num_workers: 32
   # path to the raw data within the H5
-  raw_internal_path: /raw
-  # path to the the label data withtin the H5
-  label_internal_path: /label
+  raw_internal_path: raw
+  # path to  the label data within the H5
+  label_internal_path: label
+  # apply random shifting and scaling of the patches; value of 20 mean that patches may shrink/stretch by 20px in each dimension
+  random_scale: 20
+  # random scale execution probability; since random scale is quite slow for 3D data, we set it to 0.1
+  random_scale_probability: 0.1
   # configuration of the train loader
   train:
     # path to the training datasets

diff --git a/resources/3DUnet_lightsheet_boundary/train_config.yml b/resources/3DUnet_lightsheet_boundary/train_config.yml
@@ -66,11 +66,15 @@ trainer:
 # Configure training and validation loaders
 loaders:
   # how many subprocesses to use for data loading
-  num_workers: 8
+  num_workers: 32
   # path to the raw data within the H5
-  raw_internal_path: /raw
-  # path to the the label data withtin the H5
-  label_internal_path: /label
+  raw_internal_path: raw
+  # path to  the label data within the H5
+  label_internal_path: label
+  # apply random shifting and scaling of the patches; value of 20 mean that patches may shrink/stretch by 20px in each dimension
+  random_scale: 20
+  # random scale execution probability; since random scale is quite slow for 3D data, we set it to 0.1
+  random_scale_probability: 0.1
   # configuration of the train loader
   train:
     # path to the training datasets

diff --git a/resources/3DUnet_lightsheet_nuclei/train_config.yaml b/resources/3DUnet_lightsheet_nuclei/train_config.yaml
@@ -83,8 +83,12 @@ loaders:
   num_workers: 8
   # path to the raw data within the H5
   raw_internal_path: raw
-  # path to the the label data within the H5
+  # path to the label data within the H5
   label_internal_path: label
+  # apply random shifting and scaling of the patches; value of 20 mean that patches may shrink/stretch by 20px in each dimension
+  random_scale: 20
+  # random scale execution probability; since random scale is quite slow for 3D data, we set it to 0.1
+  random_scale_probability: 0.1
   # path to the pixel-wise weight map withing the H5 if present
   weight_internal_path: null
   # configuration of the train loader

diff --git a/resources/3DUnet_multiclass/train_config.yaml b/resources/3DUnet_multiclass/train_config.yaml
@@ -74,6 +74,10 @@ loaders:
   raw_internal_path: raw
   # path to the label data within the H5
   label_internal_path: label
+  # apply random shifting and scaling of the patches; value of 20 mean that patches may shrink/stretch by 20px in each dimension
+  random_scale: 20
+  # random scale execution probability; since random scale is quite slow for 3D data, we set it to 0.1
+  random_scale_probability: 0.1
   # path to the pixel-wise weight map withing the H5 if present
   weight_internal_path: null
   # configuration of the train loader