Fix vista3d transpose bug (#8059)

Fixes # .

### Description

A few sentences describing the changes proposed in this pull request.

### 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>
Signed-off-by: Yiheng Wang <vennw@nvidia.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>
Co-authored-by: Yiheng Wang <vennw@nvidia.com>
Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>

Author: 4 people

monai/apps/vista3d/inferer.py

@@ -100,7 +100,7 @@ def point_based_window_inferer(
                         point_labels=point_labels,
                         class_vector=class_vector,
                         prompt_class=prompt_class,
-                        patch_coords=unravel_slice,
+                        patch_coords=[unravel_slice],
                         prev_mask=prev_mask,
                         **kwargs,
                     )

monai/networks/nets/vista3d.py

@@ -336,7 +336,7 @@ 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,
+        patch_coords: list[Sequence[slice]] | None = None,
         point_coords: torch.Tensor | None = None,
         point_labels: torch.Tensor | None = None,
         class_vector: torch.Tensor | None = None,
@@ -364,8 +364,12 @@ def forward(
                 the points are for zero-shot or supported class. When class_vector and point_coords are both
                 provided, prompt_class is the same as class_vector. For prompt_class[b] > 512, point_coords[b]
                 will be considered novel class.
-            patch_coords: a sequence of the python slice objects representing the patch coordinates during sliding window inference.
-                This value is passed from sliding_window_inferer. This is an indicator for training phase or validation phase.
+            patch_coords: a list of sequence of the python slice objects representing the patch coordinates during sliding window
+                inference. This value is passed from sliding_window_inferer.
+                This is an indicator for training phase or validation phase.
+                Notice for sliding window batch size > 1 (only supported by automatic segmentation), patch_coords will inlcude
+                coordinates of multiple patches. If point prompts are included, the batch size can only be one and all the
+                functions using patch_coords will by default use patch_coords[0].
             labels: [1, 1, H, W, D], the groundtruth label tensor, only used for point-only evaluation
             label_set: the label index matching the indexes in labels. If labels are mapped to global index using RelabelID,
                 this label_set should be global mapped index. If labels are not mapped to global index, e.g. in zero-shot
@@ -395,14 +399,14 @@ def forward(
                 if val_point_sampler is None:
                     # TODO: think about how to refactor this part.
                     val_point_sampler = self.sample_points_patch_val
-                point_coords, point_labels, prompt_class = val_point_sampler(labels, patch_coords, label_set)
+                point_coords, point_labels, prompt_class = val_point_sampler(labels, patch_coords[0], label_set)
                 if prompt_class[0].item() == 0:  # type: ignore
                     point_labels[0] = -1  # type: ignore
                 labels, prev_mask = None, None
             elif point_coords is not None:
                 # If not performing patch-based point only validation, use user provided click points for inference.
                 # the point clicks is in original image space, convert it to current patch-coordinate space.
-                point_coords, point_labels = self.update_point_to_patch(patch_coords, point_coords, point_labels)  # type: ignore
+                point_coords, point_labels = self.update_point_to_patch(patch_coords[0], point_coords, point_labels)  # type: ignore
 
         if point_coords is not None and point_labels is not None:
             # remove points that used for padding purposes (point_label = -1)
@@ -455,7 +459,7 @@ def forward(
             logits[mapping_index] = self.point_head(out, point_coords, point_labels, class_vector=prompt_class)
             if prev_mask is not None and patch_coords is not None:
                 logits = self.connected_components_combine(
-                    prev_mask[patch_coords].transpose(1, 0).to(logits.device),
+                    prev_mask[patch_coords[0]].transpose(1, 0).to(logits.device),
                     logits[mapping_index],
                     point_coords,  # type: ignore
                     point_labels,  # type: ignore