Update preprocessing

micro_sam/training/sam_trainer.py

@@ -118,13 +118,34 @@ def _compute_iou(self, pred, true, eps=1e-7):
         iou = overlap / (union + eps)
         return iou
 
+    def preprocess_one_hot_masks(self, y_one_hot):
+        """
+        """
+        # Convert the labels to "low_res_mask" shape
+        # First step is to use the logic from `ResizeLongestSide` to resize the longest side.
+        target_length = self.model.transform.target_length
+        target_shape = self.model.transform.get_preprocess_shape(y_one_hot.shape[2], y_one_hot.shape[3], target_length)
+        y_one_hot = F.interpolate(input=y_one_hot, size=target_shape)
+        # Next, we pad the remaining region to (1024, 1024)
+        h, w = y_one_hot.shape[-2:]
+        padh = self.model.sam.image_encoder.img_size - h
+        padw = self.model.sam.image_encoder.img_size - w
+        y_one_hot = F.pad(input=y_one_hot, pad=(0, padw, 0, padh))
+        # Finally, let's resize the labels to the desired shape (i.e. (256, 256))
+        y_one_hot = F.interpolate(input=y_one_hot, size=(256, 256))
+
+        return y_one_hot
+
     def _compute_loss(self, batched_outputs, y_one_hot):
         """Compute the loss for one iteration. The loss is made up of two components:
         - The mask loss: dice score between the predicted masks and targets.
         - The IOU loss: L2 loss between the predicted IOU and the actual IOU of prediction and target.
         """
         mask_loss, iou_regression_loss = 0.0, 0.0
 
+        # TODO
+        y_one_hot = self.preprocess_one_hot_masks(y_one_hot)
+
         # Loop over the batch.
         for batch_output, targets in zip(batched_outputs, y_one_hot):
             predicted_objects = torch.sigmoid(batch_output["low_res_masks"])
@@ -276,22 +297,6 @@ def _preprocess_batch(self, batched_inputs, y, sampled_ids):
         # number of objects across the batch.
         n_objects = min(len(ids) for ids in sampled_ids)
 
-        original_instance_ids = list(torch.unique(y))
-        # Convert the labels to "low_res_mask" shape
-        # First step is to use the logic from `ResizeLongestSide` to resize the longest side.
-        target_length = self.model.transform.target_length
-        target_shape = self.model.transform.get_preprocess_shape(y.shape[2], y.shape[3], target_length)
-        y = F.interpolate(input=y, size=target_shape)
-        # Next, we pad the remaining region to (1024, 1024)
-        h, w = y.shape[-2:]
-        padh = self.model.sam.image_encoder.img_size - h
-        padw = self.model.sam.image_encoder.img_size - w
-        y = F.pad(input=y, pad=(0, padw, 0, padh))
-        # Finally, let's resize the labels to the desired shape (i.e. (256, 256))
-        y = F.interpolate(input=y, size=(256, 256))
-
-        assert list(torch.unique(y)) == original_instance_ids
-
         y = y.to(self.device)
         # Compute the one hot targets for the seg-id.
         y_one_hot = torch.stack([