Add attribute for triangulated 3d pose #2066

justinvshen · 2024-12-18T06:58:35Z

Description

Added attribute for triangulated 3d pose

Types of changes

Does this address any currently open issues?

[list open issues here]

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Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
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coderabbitai · 2024-12-18T06:58:43Z

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roomrys

Make sure your branch is updated with the remote liezl/add-gui-elements-to-sessions
Rename the InstanceGroup.triangulated_3d_pose attribute to InstanceGroup._triangulation

Move the following lines from commands.py to InstanceGroup.update_points

sleap/sleap/gui/commands.py

Lines 3776 to 3784 in 9775fc2

    
           # Reproject onto all views 
        
           pts_reprojected = reproject( 
        
               points_3d, 
        
               calib=session.camera_cluster, 
        
               excluded_views=frame_group.excluded_views, 
        
           )  # M=include x F=1 x T x N x 2 
        
           # Sqeeze back to the original shape 
        
           points_reprojected = np.squeeze(pts_reprojected, axis=1)  # M=include x TxNx2

Pass points3d into FrameGroup.upsert_points

sleap/sleap/gui/commands.py

Lines 3786 to 3788 in 9775fc2

    
           # Update or create/insert ("upsert") instance points 
        
           frame_group.upsert_points( 
        
               points=points_reprojected,

Move the boundary finding code into InstanceGroup.update_points

sleap/sleap/io/cameras.py

Lines 2302 to 2316 in 9775fc2

    
           # Ensure we are working with a float array 
        
           points = points.astype(float) 
        
           # Get projection bounds (based on video height/width) 
        
           bounds = self.session.projection_bounds 
        
           bounds_expanded_x = bounds[:, None, None, 0] 
        
           bounds_expanded_y = bounds[:, None, None, 1] 
        
           # Create masks for out-of-bounds x and y coordinates 
        
           out_of_bounds_x = (points[..., 0] < 0) | (points[..., 0] > bounds_expanded_x) 
        
           out_of_bounds_y = (points[..., 1] < 0) | (points[..., 1] > bounds_expanded_y) 
        
           # Replace out-of-bounds x and y coordinates with nan 
        
           points[out_of_bounds_x, 0] = np.nan 
        
           points[out_of_bounds_y, 1] = np.nan

roomrys · 2025-01-08T17:08:44Z

sleap/io/cameras.py

+        # # Check that the correct shape was passed in
+        # n_views, n_instances, n_nodes, n_coords = points.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}."
+        # assert n_coords == 2, f"Expected 2 coordinates, got {n_coords}."



Let's move this check to InstanceGroup.update_points

roomrys · 2025-01-08T17:18:45Z

sleap/io/dataset.py

Do a git pull origin liezl/add-gui-elements-from-sessions, handle merge conflicts, make sure that there are no changes in dataset.py

roomrys · 2025-01-08T17:18:54Z

tests/io/test_dataset.py

Do a git pull origin liezl/add-gui-elements-from-sessions, handle merge conflicts, make sure that there are no changes in test_dataset.py

roomrys · 2025-01-08T17:23:13Z

sleap/io/cameras.py

@@ -449,6 +450,7 @@ class InstanceGroup:
    _dummy_instance: Optional[Instance] = field(default=None)
    camera_cluster: Optional[CameraCluster] = field(default=None)
    _score: Optional[float] = field(default=None)
+    triangulated_3d_pose: Optional[np.ndarray] = field(default=None)


Suggested change

triangulated_3d_pose: Optional[np.ndarray] = field(default=None)

_triangulation: Optional[np.ndarray] = field(default=None)

Let's make this a psuedo-private method by prefixing with "_". This prefixed underscore tells developers that this method either is only intended to be used (or only used) internally within the containing class. This also allows us to name this underlying attribute as _<name-of-referencing-property-method>.

roomrys · 2025-01-08T17:32:25Z

sleap/io/cameras.py

+        # Check if points are 3D
+        is_3d = points.shape[-1] == 3


THis would always evaluate to False at the moment since the points passed into InstanceGroup.update_points are:

points: Numpy array of shape (M, N, 2) where M is the number of views, N is the number of Nodes, and 2 is for x, y.

. We want the 3D points passed in here. That means we also want the 3D points passed into FrameGroup.upsert_points... which means we need to basically move code from both the following:

sleap/sleap/gui/commands.py

Lines 3769 to 3791 in 9775fc2

# Triangulate to one 3D pose per instance

points_3d = triangulate(

p2d=frame_group_tensor,

calib=session.camera_cluster,

excluded_views=frame_group.excluded_views,

) # F x T x N x 3

# Reproject onto all views

pts_reprojected = reproject(

points_3d,

calib=session.camera_cluster,

excluded_views=frame_group.excluded_views,

) # M=include x F=1 x T x N x 2

# Sqeeze back to the original shape

points_reprojected = np.squeeze(pts_reprojected, axis=1) # M=include x TxNx2

# Update or create/insert ("upsert") instance points

frame_group.upsert_points(

points=points_reprojected,

instance_groups=instance_groups,

exclude_complete=True,

)

and from FrameGroup.upsert_points to InstanceGroup.update_points

Jvshen added 3 commits November 19, 2024 16:01

Check if predicted instance is removed that it's not referenced

e4c542b

Add manual test for removing predicted instance

b59cfd4

Add attribute for triangulated 3d pose

1b8b0ea

roomrys requested changes Jan 8, 2025

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Add attribute for triangulated 3d pose #2066

Add attribute for triangulated 3d pose #2066

justinvshen commented Dec 18, 2024

coderabbitai bot commented Dec 18, 2024

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roomrys Jan 8, 2025

roomrys Jan 8, 2025

	# Reproject onto all views
	pts_reprojected = reproject(
	points_3d,
	calib=session.camera_cluster,
	excluded_views=frame_group.excluded_views,
	) # M=include x F=1 x T x N x 2

	# Sqeeze back to the original shape
	points_reprojected = np.squeeze(pts_reprojected, axis=1) # M=include x TxNx2

	# Update or create/insert ("upsert") instance points
	frame_group.upsert_points(
	points=points_reprojected,

	# Ensure we are working with a float array
	points = points.astype(float)

	# Get projection bounds (based on video height/width)
	bounds = self.session.projection_bounds
	bounds_expanded_x = bounds[:, None, None, 0]
	bounds_expanded_y = bounds[:, None, None, 1]

	# Create masks for out-of-bounds x and y coordinates
	out_of_bounds_x = (points[..., 0] < 0) \| (points[..., 0] > bounds_expanded_x)
	out_of_bounds_y = (points[..., 1] < 0) \| (points[..., 1] > bounds_expanded_y)

	# Replace out-of-bounds x and y coordinates with nan
	points[out_of_bounds_x, 0] = np.nan
	points[out_of_bounds_y, 1] = np.nan

	triangulated_3d_pose: Optional[np.ndarray] = field(default=None)
	_triangulation: Optional[np.ndarray] = field(default=None)

	# Triangulate to one 3D pose per instance
	points_3d = triangulate(
	p2d=frame_group_tensor,
	calib=session.camera_cluster,
	excluded_views=frame_group.excluded_views,
	) # F x T x N x 3

	# Reproject onto all views
	pts_reprojected = reproject(
	points_3d,
	calib=session.camera_cluster,
	excluded_views=frame_group.excluded_views,
	) # M=include x F=1 x T x N x 2

	# Sqeeze back to the original shape
	points_reprojected = np.squeeze(pts_reprojected, axis=1) # M=include x TxNx2

	# Update or create/insert ("upsert") instance points
	frame_group.upsert_points(
	points=points_reprojected,
	instance_groups=instance_groups,
	exclude_complete=True,
	)

Add attribute for triangulated 3d pose #2066

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justinvshen commented Dec 18, 2024

Description

Types of changes

Does this address any currently open issues?

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Thank you for contributing to SLEAP!

coderabbitai bot commented Dec 18, 2024

Review skipped

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