Minor update to default rescaling params in resizerawtrafo (computati…

…onal-cell-analytics#635)
caroteu · Jun 12, 2024 · a75d581 · a75d581
1 parent e21006e
commit a75d581
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/finetuning/generalists/training/light_microscopy/obtain_lm_datasets.py b/finetuning/generalists/training/light_microscopy/obtain_lm_datasets.py
@@ -61,7 +61,8 @@ def get_ctc_datasets(
         datasets.get_tissuenet_dataset(
             path=os.path.join(input_path, "tissuenet"), split=split_choice, download=True, patch_shape=patch_shape,
             raw_channel="rgb", label_channel="cell", sampler=sampler, label_dtype=label_dtype,
-            raw_transform=ResizeRawTrafo(patch_shape), label_transform=ResizeLabelTrafo(patch_shape, min_size=0),
+            raw_transform=ResizeRawTrafo(patch_shape, do_rescaling=True),
+            label_transform=ResizeLabelTrafo(patch_shape, min_size=0),
             n_samples=1000 if split_choice == "train" else 100
         ),
         datasets.get_livecell_dataset(

diff --git a/finetuning/specialists/training/light_microscopy/tissuenet_finetuning.py b/finetuning/specialists/training/light_microscopy/tissuenet_finetuning.py
@@ -25,7 +25,7 @@ def get_dataloaders(patch_shape, data_path):
     I.e. a tensor of the same spatial shape as `x`, with each object mask having its own ID.
     Important: the ID 0 is reseved for background, and the IDs must be consecutive
     """
-    raw_transform = ResizeRawTrafo(patch_shape)
+    raw_transform = ResizeRawTrafo(patch_shape, do_rescaling=True)
     label_transform = ResizeLabelTrafo(patch_shape)
     sampler = MinInstanceSampler()
     label_dtype = torch.float32