Fix transpose and patch coords bug (#8047)

Fixes # .

### Description

Fix the bug that causes wrong results in model zoo finetuning. Patch
coords was not passed from sliding window to vista3d.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>

docs/requirements.txt

@@ -42,3 +42,4 @@ zarr
 huggingface_hub
 pyamg>=5.0.0
 packaging
+polygraphy

monai/apps/vista3d/sampler.py

@@ -20,8 +20,6 @@
 import torch
 from torch import Tensor
 
-__all__ = ["sample_prompt_pairs"]
-
 ENABLE_SPECIAL = True
 SPECIAL_INDEX = (23, 24, 25, 26, 27, 57, 128)
 MERGE_LIST = {
@@ -30,6 +28,8 @@
     132: [57],  # overlap with trachea merge into airway
 }
 
+__all__ = ["sample_prompt_pairs"]
+
 
 def _get_point_label(id: int) -> tuple[int, int]:
     if id in SPECIAL_INDEX and ENABLE_SPECIAL:
@@ -66,22 +66,29 @@ def sample_prompt_pairs(
         max_backprompt: int, max number of prompt from background.
         max_point: maximum number of points for each object.
         include_background: if include 0 into training prompt. If included, background 0 is treated
-            the same as foreground. Always be False for multi-partial-dataset training. If needed,
-            can be true for finetuning specific dataset, .
+            the same as foreground and points will be sampled. Can be true only if user want to segment
+            background 0 with point clicks, otherwise always be false.
         drop_label_prob: probability to drop label prompt.
         drop_point_prob: probability to drop point prompt.
         point_sampler: sampler to augment masks with supervoxel.
         point_sampler_kwargs: arguments for point_sampler.
 
     Returns:
-        label_prompt: [B, 1]. The classes used for training automatic segmentation.
-        point: [B, N, 3]. The corresponding points for each class.
-        Note that background label prompt requires matching point as well ([0,0,0] is used).
-        point_label: [B, N]. The corresponding point labels for each point (negative or positive).
-        -1 is used for padding the background label prompt and will be ignored.
-        prompt_class: [B, 1], exactly the same with label_prompt for label indexing for training loss.
-        label_prompt can be None, and prompt_class is used to identify point classes.
+        tuple:
+            - label_prompt (Tensor | None): Tensor of shape [B, 1] containing the classes used for
+              training automatic segmentation.
+            - point (Tensor | None): Tensor of shape [B, N, 3] representing the corresponding points
+              for each class. Note that background label prompts require matching points as well
+              (e.g., [0, 0, 0] is used).
+            - point_label (Tensor | None): Tensor of shape [B, N] representing the corresponding point
+              labels for each point (negative or positive). -1 is used for padding the background
+              label prompt and will be ignored.
+            - prompt_class (Tensor | None): Tensor of shape [B, 1], exactly the same as label_prompt
+              for label indexing during training. If label_prompt is None, prompt_class is used to
+              identify point classes.
+
     """
+
     # class label number
     if not labels.shape[0] == 1:
         raise ValueError("only support batch size 1")

monai/networks/nets/vista3d.py

@@ -336,11 +336,11 @@ def set_auto_grad(self, auto_freeze: bool = False, point_freeze: bool = False):
     def forward(
         self,
         input_images: torch.Tensor,
+        patch_coords: Sequence[slice] | None = None,
         point_coords: torch.Tensor | None = None,
         point_labels: torch.Tensor | None = None,
         class_vector: torch.Tensor | None = None,
         prompt_class: torch.Tensor | None = None,
-        patch_coords: Sequence[slice] | None = None,
         labels: torch.Tensor | None = None,
         label_set: Sequence[int] | None = None,
         prev_mask: torch.Tensor | None = None,
@@ -421,7 +421,10 @@ def forward(
                     point_coords, point_labels = None, None
 
         if point_coords is None and class_vector is None:
-            return self.NINF_VALUE + torch.zeros([bs, 1, *image_size], device=device)
+            logits = self.NINF_VALUE + torch.zeros([bs, 1, *image_size], device=device)
+            if transpose:
+                logits = logits.transpose(1, 0)
+            return logits
 
         if self.image_embeddings is not None and kwargs.get("keep_cache", False) and class_vector is None:
             out, out_auto = self.image_embeddings, None