Update inference schema and tutorials

Donglai Wei · Donglai Wei · commit 674de83566c6 · 2026-03-14T17:21:36.000-04:00
diff --git a/connectomics/config/schema/inference.py b/connectomics/config/schema/inference.py
@@ -201,4 +201,3 @@ class InferenceConfig:
     # Inference-specific runtime overrides (applied in test/tune modes)
     # `system` overrides selected keys on top-level cfg.system during stage resolution.
     system: SystemConfig = field(default_factory=lambda: SystemConfig(num_gpus=-1, num_workers=-1))
-    batch_size: int = -1  # Overrides data.dataloader.batch_size if >= 0
diff --git a/tutorials/fiber_linghu26.yaml b/tutorials/fiber_linghu26.yaml
@@ -164,7 +164,6 @@ test:
 inference:
   system:
     num_workers: 1
-  batch_size: 8
   sliding_window:
     window_size:
     - 32
diff --git a/tutorials/misc/hydra-lv-finetune.yaml b/tutorials/misc/hydra-lv-finetune.yaml
@@ -215,7 +215,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 1
-  batch_size: 1
   sliding_window:
     window_size: [32, 128, 128]
     sw_batch_size: 1
diff --git a/tutorials/misc/hydra-lv-finetune_v0.yaml b/tutorials/misc/hydra-lv-finetune_v0.yaml
@@ -218,7 +218,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 1
-  batch_size: 1
   sliding_window:
     window_size: [32, 128, 128]
     sw_batch_size: 1
diff --git a/tutorials/misc/hydra-lv.yaml b/tutorials/misc/hydra-lv.yaml
@@ -271,7 +271,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 1
-  batch_size: 1
   # MONAI SlidingWindowInferer parameters
   sliding_window:
     window_size: [32, 128, 128]        # Match training patch size (OPTION 3)
diff --git a/tutorials/misc/mito_2dsem_seg.yaml b/tutorials/misc/mito_2dsem_seg.yaml
@@ -152,7 +152,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 2
-  batch_size: 1
   # MONAI SlidingWindowInferer for 2D
   sliding_window:
     window_size: [1, 512, 512]     # 2D window
diff --git a/tutorials/misc/tsai_axon.yaml b/tutorials/misc/tsai_axon.yaml
@@ -147,7 +147,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 4
-  batch_size: 32
   data:
     test_image: /orcd/scratch/bcs/002/mansour/trailmap_data/testing/testing-original/volumes/*.tiff
     test_label: /orcd/scratch/bcs/002/mansour/trailmap_data/testing/testing-original/labels-original-backup/*.tiff
diff --git a/tutorials/misc/worm2d.yaml b/tutorials/misc/worm2d.yaml
@@ -147,7 +147,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 4
-  batch_size: 32
   data:
     test_image: /orcd/data/edboyden/002/shenb/wormbehavior/13/*.tif
     test_label:
diff --git a/tutorials/misc/zebrafish_neurons.yaml b/tutorials/misc/zebrafish_neurons.yaml
@@ -183,7 +183,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 4
-  batch_size: 64
   sliding_window:
     window_size: [256, 256]
     overlap: 0.5
diff --git a/tutorials/mito_betaseg.yaml b/tutorials/mito_betaseg.yaml
@@ -232,7 +232,6 @@ inference:
   system:
     num_gpus: 4
     num_workers: 8
-  batch_size: 1
   # MONAI SlidingWindowInferer parameters
   sliding_window:
     window_size: [128, 128, 128]         # Match training patch size
diff --git a/tutorials/mito_lucchi++.yaml b/tutorials/mito_lucchi++.yaml
@@ -23,7 +23,6 @@ default:
     augmentation:
       profile: aug_standard
   inference:
-    batch_size: 16
     sliding_window:
       window_size: [112, 112, 112]      
     test_time_augmentation:
diff --git a/tutorials/mito_mitoEM_H.yaml b/tutorials/mito_mitoEM_H.yaml
@@ -28,8 +28,5 @@ test:
       image: /projects/weilab/dataset/mito/mitoEM/EM30-H/im_test.h5
       label: /projects/weilab/dataset/mito/mitoEM/EM30-H/mito_test-v2.h5
 
-inference:
-  batch_size: 1
-
 train:
   system:
diff --git a/tutorials/mito_mitoEM_R.yaml b/tutorials/mito_mitoEM_R.yaml
@@ -28,8 +28,5 @@ test:
       image: /projects/weilab/dataset/mito/mitoEM/EM30-R/im_test.h5
       label: /projects/weilab/dataset/mito/mitoEM/EM30-R/mito_test-v2.h5
 
-inference:
-  batch_size: 1
-
 train:
   system:
diff --git a/tutorials/mito_mitoEM_common.yaml b/tutorials/mito_mitoEM_common.yaml
@@ -140,7 +140,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 2
-  batch_size: 6
   sliding_window:
     window_size:
     - 32
diff --git a/tutorials/mito_mitolab.yaml b/tutorials/mito_mitolab.yaml
@@ -121,7 +121,6 @@ test:
 inference:
   system:
     num_workers: 4
-  batch_size: 32
   test_time_augmentation:
     enabled: false
     channel_activations:
diff --git a/tutorials/neuron_nisb_9nm_base.yaml b/tutorials/neuron_nisb_9nm_base.yaml
@@ -172,7 +172,6 @@ inference:
   system:
     num_gpus: 1
     num_workers: 8
-  batch_size: 1
   sliding_window:
     window_size: [32, 256, 256]
     sw_batch_size: 1
diff --git a/tutorials/neuron_snemi.yaml b/tutorials/neuron_snemi.yaml
@@ -23,7 +23,6 @@ default:
     augmentation:
       profile: aug_em_neuron
   inference:
-    batch_size: 4    
     sliding_window:
       window_size: [16, 224, 224]
       sw_batch_size: 4
diff --git a/tutorials/nuc_nucmm-z.yaml b/tutorials/nuc_nucmm-z.yaml
@@ -117,7 +117,6 @@ test:
 inference:
   system:
     num_workers: 4
-  batch_size: 4
   sliding_window:
     window_size:
     - 64
diff --git a/tutorials/syn_cremi.yaml b/tutorials/syn_cremi.yaml
@@ -192,7 +192,6 @@ test:
     - cremi_distance
     - jaccard
 inference:
-  batch_size: 1
   sliding_window:
     window_size:
     - 18
diff --git a/tutorials/vesicle_xm.yaml b/tutorials/vesicle_xm.yaml
@@ -68,13 +68,11 @@ test:
   data:
     test:
       path: "/projects/weilab/dataset/xiaomeng/vesicle/"
-      #image: "im/Bouton_100_EM.tif"
-      #mask: "mask/Bouton_100_em_mask.tif"
-      image: "im/Bouton_*_EM.tif"
-      mask: "mask/Bouton_*_em_mask.tif"
-      #image: ["datasets/bouton-lv/train/vol0_im_bouton.h5", "datasets/hydra-lv/vol*_im.h5"]
-      #label: ["datasets/bouton-lv/train/vol0_lv_bouton.h5", "datasets/hydra-lv/vol*_vesicle_ins.h5"]
-      #mask: ["datasets/bouton-lv/train/vol0_mask_bouton.h5", "datasets/hydra-lv/vol*_mask.h5"]
+      # debugging 
+      image: "im/Bouton_228_EM.tif"
+      mask: "mask/Bouton_228_em_mask.tif"
+      #image: "im/Bouton_*_EM.tif"
+      #mask: "mask/Bouton_*_em_mask.tif"
       resolution: [30, 8, 8]
     # fix: the exported mask is 2x downsampled, so we need to upsample it to the original size
     mask_transform:
