Add triangulated 3d pose attribute #2082

justinvshen · 2025-01-09T22:43:19Z

Description

Added triangulated 3d pose attribute

Types of changes

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

Review the guidelines for contributing to this repository
Read and sign the CLA and add yourself to the authors list
Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
Add tests that prove your fix is effective or that your feature works
Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

❤️

coderabbitai · 2025-01-09T22:43:27Z

Important

Review skipped

Draft detected.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

Review comments: Directly reply to a review comment made by CodeRabbit. Example:
- I pushed a fix in commit <commit_id>, please review it.
- Generate unit testing code for this file.
- Open a follow-up GitHub issue for this discussion.
Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
- @coderabbitai generate unit testing code for this file.
- @coderabbitai modularize this function.
PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
- @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
- @coderabbitai read src/utils.ts and generate unit testing code.
- @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
- @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

@coderabbitai pause to pause the reviews on a PR.
@coderabbitai resume to resume the paused reviews.
@coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
@coderabbitai full review to do a full review from scratch and review all the files again.
@coderabbitai summary to regenerate the summary of the PR.
@coderabbitai generate docstrings to generate docstrings for this PR. (Beta)
@coderabbitai resolve resolve all the CodeRabbit review comments.
@coderabbitai configuration to show the current CodeRabbit configuration for the repository.
@coderabbitai help to get help.

Other keywords and placeholders

Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (`.coderabbit.yaml`)

You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
Please see the configuration documentation for more information.
If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

Visit our Documentation for detailed information on how to use CodeRabbit.
Join our Discord Community to get help, request features, and share feedback.
Follow us on X/Twitter for updates and announcements.

roomrys · 2025-01-13T22:12:57Z

sleap/io/cameras.py

@@ -837,7 +847,8 @@ def get_cam(self, instance: Instance) -> Optional[Camcorder]:

    def update_points(
        self,
-        points: np.ndarray,
+        points_3d: np.ndarray,
+        instance_groups: List['InstanceGroup'],


We don't need to take in a list of InstanceGroups here.

Suggested change

instance_groups: List['InstanceGroup'],

roomrys · 2025-01-13T22:13:52Z

sleap/io/cameras.py

+        # Check if points are 3D
+        is_3d = points_3d.shape[-1] == 3
+        if not is_3d:
+            raise ValueError("Expected 3D points with shape (M, T, N, 3).")


This is redundant since we have a n_coords == 3 check below.

Suggested change

# Check if points are 3D

is_3d = points_3d.shape[-1] == 3

if not is_3d:

raise ValueError("Expected 3D points with shape (M, T, N, 3).")

roomrys · 2025-01-13T22:16:56Z

sleap/io/cameras.py

+        # Check that the correct shape was passed in
+        n_views, n_instances, n_nodes, n_coords = points_3d.shape
+        assert n_views == len(
+            self.cams_to_include
+        ), f"Expected {len(self.cams_to_include)} views, got {n_views}."
+        assert n_instances == len(
+            instance_groups
+        ), f"Expected {len(instance_groups)} instances, got {n_instances}."


We expect the 3D shape to be n_nodes, n_coords only

Suggested change

# Check that the correct shape was passed in

n_views, n_instances, n_nodes, n_coords = points_3d.shape

assert n_views == len(

self.cams_to_include

), f"Expected {len(self.cams_to_include)} views, got {n_views}."

assert n_instances == len(

instance_groups

), f"Expected {len(instance_groups)} instances, got {n_instances}."

# Check that the correct shape was passed in

n_nodes, n_coords = points_3d.shape

roomrys · 2025-01-13T22:19:45Z

sleap/io/cameras.py

+        # Reproject 3D points into 2D points for each camera view
+        pts_reprojected = reproject(
+            points_3d,
+            calib=self.session.camera_cluster,


We don't have a InstanceGroup.session attribute, so we'll need to find another way to get the camera_cluster -> see InstanceGroup.camera_cluster

roomrys · 2025-01-13T22:24:34Z

sleap/io/cameras.py

+        pts_reprojected = reproject(
+            points_3d,
+            calib=self.session.camera_cluster,
+            excluded_views=self.excluded_views,


Similarly, there is no InstanceGroup.excluded_views. I think we should either add this as an input into InstanceGroup.update_points (and get rid of the cams_to_include input) or derive it from the existing cams_to_include input and InstanceGroup.camera_cluster attribute.

roomrys · 2025-01-13T22:36:40Z

sleap/io/cameras.py

+        # Update points for each `InstanceGroup`
+        for ig_idx, instance_group in enumerate(instance_groups):
+            # Ensure that `InstanceGroup`s is in this `FrameGroup`
+            self._raise_if_instance_group_not_in_frame_group(
+                instance_group=instance_group
+            )
+            # Update points for the instance group
+            instance_group.points = points_reprojected[ig_idx]


We will just be passing in points for a single InstanceGroup, so we won't be needing this here (but, this will still be similar to how we call InstanceGroup.update_points from FrameGroup.upsert_points).

Suggested change

# Update points for each `InstanceGroup`

for ig_idx, instance_group in enumerate(instance_groups):

# Ensure that `InstanceGroup`s is in this `FrameGroup`

self._raise_if_instance_group_not_in_frame_group(

instance_group=instance_group

)

# Update points for the instance group

instance_group.points = points_reprojected[ig_idx]

roomrys · 2025-01-13T22:51:34Z

sleap/io/cameras.py

        # Check that correct shape was passed in
-        n_views, n_nodes, _ = points.shape
+        n_views, n_nodes, _ = points_3d.shape


points_3d will have only n_nodes, 3 shape. But, we can do this check on points_reprojected

Suggested change

# Check that correct shape was passed in

n_views, n_nodes, _ = points.shape

n_views, n_nodes, _ = points_3d.shape

# Check that correct shape was passed in

n_views, n_nodes, _ = points_reprojected.shape

roomrys · 2025-01-13T22:52:27Z

sleap/io/cameras.py

@@ -883,13 +943,13 @@ def update_points(
            if not isinstance(instance, PredictedInstance):
                instance_oks = compute_oks(
                    gt_points[cam_idx, :, :],
-                    points[cam_idx, :, :],
+                    points_3d[cam_idx, :, :],


Here we want to use points_reprojected

Suggested change

points_3d[cam_idx, :, :],

points_reprojected[cam_idx, :, :],

roomrys · 2025-01-13T22:52:40Z

sleap/io/cameras.py

                )
                oks_scores[cam_idx] = instance_oks

            # Update the points for the instance
            instance.update_points(
-                points=points[cam_idx, :, :], exclude_complete=exclude_complete
+                points=points_3d[cam_idx, :, :], exclude_complete=exclude_complete


Here we want to use points_reprojected

Suggested change

points=points_3d[cam_idx, :, :], exclude_complete=exclude_complete

points=points_reprojected[cam_idx, :, :], exclude_complete=exclude_complete

roomrys · 2025-01-13T22:53:57Z

sleap/io/cameras.py

@@ -2331,6 +2381,7 @@ def upsert_points(
                points=instance_points,
                cams_to_include=self.cams_to_include,
                exclude_complete=exclude_complete,
+                bounds=bounds,


Make sure this input name matches the name you decided on for projection bounds in the definition for InstanceGroup.update_points

…d updated doc string

n_coords, cams_to_include, excluded_views, len(self.camera_cluster)

Add attribute for 3d triangulation

31ac7b6

roomrys requested changes Jan 13, 2025

View reviewed changes

Jvshen added 5 commits January 13, 2025 16:59

Added projection bounds and excluded views inputs to update_points an…

ba04209

…d updated doc string

Verify inputs

a32dbaa

n_coords, cams_to_include, excluded_views, len(self.camera_cluster)

Fix shapes

3715a59

Rename points_3d to points_reprojected

68e5746

Change tests to match changes

f3bce0d

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add triangulated 3d pose attribute #2082

Add triangulated 3d pose attribute #2082

justinvshen commented Jan 9, 2025

coderabbitai bot commented Jan 9, 2025

Review skipped

Chat

CodeRabbit Commands (Invoked using PR comments)

Other keywords and placeholders

CodeRabbit Configuration File (`.coderabbit.yaml`)

Documentation and Community

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

roomrys Jan 13, 2025

	points=points_3d[cam_idx, :, :], exclude_complete=exclude_complete
	points=points_reprojected[cam_idx, :, :], exclude_complete=exclude_complete

Add triangulated 3d pose attribute #2082

Are you sure you want to change the base?

Add triangulated 3d pose attribute #2082

Conversation

justinvshen commented Jan 9, 2025

Description

Types of changes

Does this address any currently open issues?

Outside contributors checklist

Thank you for contributing to SLEAP!

coderabbitai bot commented Jan 9, 2025

Review skipped

Chat

CodeRabbit Commands (Invoked using PR comments)

Other keywords and placeholders

CodeRabbit Configuration File (.coderabbit.yaml)

Documentation and Community

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

CodeRabbit Configuration File (`.coderabbit.yaml`)