Correct minor error in SSL using mae and inferring

BiaPyX · Feb 26, 2024 · 942b3ad · 942b3ad
1 parent da89c67
commit 942b3ad
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Showing 18 changed files with 36 additions and 19 deletions.
diff --git a/biapy/engine/self_supervised.py b/biapy/engine/self_supervised.py
@@ -194,7 +194,7 @@ def process_sample(self, norm):
                     if self.cfg.PROBLEM.SELF_SUPERVISED.PRETEXT_TASK == "masking":
                         loss, p, mask = p
                         p = self.apply_model_activations(p)
-                        p, m, pv = self.model.save_images(to_pytorch_format(self._X[k*self.cfg.TRAIN.BATCH_SIZE:top], self.axis_order, self.device), 
+                        p, m, pv = self.model_without_ddp.save_images(to_pytorch_format(self._X[k*self.cfg.TRAIN.BATCH_SIZE:top], self.axis_order, self.device), 
                             p, mask, self.dtype)
                     else:
                         p = self.apply_model_activations(p)

diff --git a/templates/classification/2d_classification.yaml b/templates/classification/2d_classification.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: CLASSIFICATION

diff --git a/templates/classification/2d_classification_rgb.yaml b/templates/classification/2d_classification_rgb.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: CLASSIFICATION

diff --git a/templates/classification/3d_classification.yaml b/templates/classification/3d_classification.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: CLASSIFICATION

diff --git a/templates/denoising/2d_denoising.yaml b/templates/denoising/2d_denoising.yaml
@@ -1,6 +1,7 @@
 # We try to mimic here N2Void project parameters 
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: DENOISING

diff --git a/templates/denoising/3d_denoising.yaml b/templates/denoising/3d_denoising.yaml
@@ -1,7 +1,8 @@
 # We try to mimic here N2Void project parameters 
 
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: DENOISING

diff --git a/templates/detection/2d_detection.yaml b/templates/detection/2d_detection.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: DETECTION

diff --git a/templates/detection/3d_detection.yaml b/templates/detection/3d_detection.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: DETECTION

diff --git a/templates/instance_segmentation/2d_instance_segmentation.yaml b/templates/instance_segmentation/2d_instance_segmentation.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: INSTANCE_SEG

diff --git a/templates/instance_segmentation/3d_instance_segmentation.yaml b/templates/instance_segmentation/3d_instance_segmentation.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: INSTANCE_SEG

diff --git a/templates/instance_segmentation/MitoEM_paper/mitoem.yaml b/templates/instance_segmentation/MitoEM_paper/mitoem.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: INSTANCE_SEG

diff --git a/templates/self-supervised/2d_self-supervised.yaml b/templates/self-supervised/2d_self-supervised.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SELF_SUPERVISED

diff --git a/templates/self-supervised/3d_self-supervised.yaml b/templates/self-supervised/3d_self-supervised.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SELF_SUPERVISED

diff --git a/templates/semantic_segmentation/2d_semantic_segmentation.yaml b/templates/semantic_segmentation/2d_semantic_segmentation.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SEMANTIC_SEG

diff --git a/templates/semantic_segmentation/3d_semantic_segmentation.yaml b/templates/semantic_segmentation/3d_semantic_segmentation.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SEMANTIC_SEG

diff --git a/templates/super-resolution/2d_super-resolution.yaml b/templates/super-resolution/2d_super-resolution.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SUPER_RESOLUTION

diff --git a/templates/super-resolution/2d_super-resolution_rgb.yaml b/templates/super-resolution/2d_super-resolution_rgb.yaml
@@ -1,5 +1,6 @@
 SYSTEM:
-    NUM_WORKERS: -1
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
 
 PROBLEM:
     TYPE: SUPER_RESOLUTION

diff --git a/templates/super-resolution/3d_super-resolution.yaml b/templates/super-resolution/3d_super-resolution.yaml
@@ -1,6 +1,7 @@
 SYSTEM:
-    NUM_WORKERS: -1
-
+    NUM_CPUS: -1
+    NUM_WORKERS: 5
+
 PROBLEM:
     TYPE: SUPER_RESOLUTION
     NDIM: 3D